@article {1063, title = {Synthesis, Characterization and Simulation of Four-Armed Megamolecules}, journal = {Biomacromolecules}, volume = {22}, year = {2021}, month = {06/2021}, pages = {2363{\textendash}2372}, doi = {10.1021/acs.biomac.1c00118}, author = {S. Zhou and P. He and S. Dhindwal and V. L. Grum-Tokars and Y. Li, K. Parker and J. A. Modica and R. Bleher and R. dos Reis and J. Zuchniarz and V. P. Dravid and G. A. Voth and B. Roux and M. Mrksich} } @article {1005, title = {Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability}, journal = {J. Phys. Chem. Lett.}, volume = {10}, year = {2019}, month = {08/2019}, pages = {4549{\textendash}4557}, doi = {10.1021/acs.jpclett.9b01228}, author = {J. Jin and A. J. Pak and G. A. Voth} } @article {946, title = {Coarse-Grained Directed Simulation}, journal = {J. Chem. Theory Comput.}, year = {2017}, doi = {10.1021/acs.jctc.7b00690}, author = {G. M. Hocky and T. Dannenhoffer-Lafage and G. A. Voth} } @article {923, title = {Competition Between Tropomyosin, Fimbrin, and ADF/Cofilin Drive Their Sorting to Distinct Actin Filament Networks}, journal = {eLife}, volume = {6}, year = {2017}, doi = {https://doi.org/10.7554/eLife.23152}, author = {J. R. Christensen and G. M. Hocky and A. N. Morganthaler and K. E. Homa and S. E. Hitchcock-DeGregori and G. A. Voth and D. R. Kovar} } @article {943, title = {Delocalization and Stretch-Bend Mixing of the HOH Bend in Liquid Water}, journal = {J. Chem. Phys.}, volume = {147}, year = {2017}, chapter = {1}, abstract = {


}, author = {W. B. Carpenter and J. A. Fournier and R. Biswas and G. A. Voth} } @article {942, title = {Development of Reactive Force Fields Using Ab Initio Molecular Dynamics Simulation Minimally Biased to Experimental Data}, journal = {J. Chem. Phys.}, year = {2017}, doi = {10.1063/1.4985903}, author = {C. Chen and C. Arntsen and G. A. Voth} } @article {944, title = {Extending the Range and Physical Accuracy of Coarse-grained Models: Order Parameter Dependent Interactions}, journal = {J. Chem. Phys.}, year = {2017}, doi = {https://doi.org/10.1063/1.4995946}, author = {J. W. Wagner and T. Dannenhoffer-Lafage and J. Jin and G. A. Voth} } @article {919, title = {Friction Mediates Scission of Tubular Membranes Scaffolded by BAR Proteins}, journal = {Cell}, volume = {170}, year = {2017}, chapter = {172}, doi = {http://dx.doi.org/10.1016/j.cell.2017.05.047}, author = {M. Simunovic and J.-B. Manneville and H.-F. Renard and E. Evergren and K. Raghunathan and A. K. Kenworthy and G. A. Voth and J. Prost and H. T. McMahon and L. Johannes and P. Bassereau and A. Callan-Jones} } @article {932, title = {Highly Coarse-grained Representations of Transmembrane Proteins}, journal = {J. Chem. Theory Comput.}, volume = {13}, year = {2017}, chapter = {935}, doi = {10.1021/acs.jctc.6b01076}, author = {J. J. Madsen and A. V. Sinitskiy and J. Li and G. A. Voth} } @article {913, title = {Improved Ab Initio Molecular Dynamics by Minimally Biasing with Experimental Data}, journal = {J. Chem. Phys.}, volume = {146}, year = {2017}, chapter = {041102}, doi = {10.1063/1.4974837}, author = {A. D. White and C. Knight and G. M. Hocky and G. A. Voth} } @article {933, title = {IR Spectral Assignments for the Hydrated Excess Proton in Liquid Water}, journal = {J. Chem. Phys.}, volume = {146}, year = {2017}, doi = {http://dx.doi.org/10.1063/1.4980121}, author = {R. Biswas and W. Carpenter and J. A. Fournier and G. A. Voth and A. Tokmakoff} } @article {899, title = {Lipid Membrane Mediates Long-Range Interactions Between Linear Filaments of Membrane-Curving Proteins}, journal = {ACS Cen. Sci.}, volume = {3}, year = {2017}, pages = {1246-1253 }, author = {M Simunovic and A {\v S}ari{\'c} and J. M. Henderson and K-Y C Lee and G. A. Voth} } @article {918, title = {Mechanosensitive Inhibition of Formin Facilitates Contractile Actomyosin Ring Assembly}, journal = {Nat. Comm.}, volume = {8 }, year = {2017}, chapter = {2017}, author = {D. Zimmerman and K. E. Homa and G. M. Hocky and L. W. Pollard and E. M. De La Cruz and G. A. Voth and K. M. Trybus and D. R. Kovar} } @article {924, title = {A Multiscale Description of Biological Active Matter: The Chemistry Underlying Many Life Processes}, journal = {Acc. Chem. Res.}, volume = {50}, year = {2017}, chapter = {594}, doi = {10.1021/acs.accounts.6b00572}, author = {G. A. Voth} } @article {952, title = {Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments}, journal = {J. Biol. Chem.}, volume = {292}, year = {2017}, pages = {19565-19579 }, author = {W. A. Elam and W. Cao and H. Kang and A. Huehn and G. M. Hocky and E. Prochniewicz and A. C. Schramm and K. Negr{\'o}n and J. Garcia and T. T. Bonello and P. W. Gunning and D. D. Thomas and G. A. Voth and C. V. Sindelar and E. M. De La Cruz} } @article {934, title = {Reactive Molecular Dynamics Models from Ab Initio Molecular Dynamics Data Using Relative Entropy Minimization}, journal = {Chem. Phys. Lett.}, volume = {683}, year = {2017}, chapter = {573}, doi = {https://doi.org/10.1016/j.cplett.2017.04.064}, author = {C. Arntsen and C. Chen and G. A. Voth} } @article {936, title = {Role of Solvation Structure in the Shuttling of the Hydrated Excess Proton}, journal = {J. Chem. Sci.}, volume = {129}, year = {2017}, doi = {10.1007/s12039-017-1283-5}, author = {R. Biswas and G. A. Voth} } @article {935, title = {Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics}, journal = {J. Chem. Theory Comput.}, volume = {13}, year = {2017}, chapter = {2332}, doi = {10.1021/acs.jctc.7b00077}, author = {R. Sun and O. Sode and J. F. Dama and G. A. Voth} } @article {922, title = {The Theory of Ultra-Coarse-Graining. 3. Coarse-grained Sites with Rapid Local Equilibrium of Internal States}, journal = {J. Chem. Theory Comput.}, volume = {13}, year = {2017}, chapter = {1010}, doi = {10.1021/acs.jctc.6b01081}, author = {J. F. Dama and J. Jin and G. A. Voth} } @article {916, title = {Acid Activation Mechanism of the Influenza A M2 Proton Channel}, journal = {Proc. Nat. Acad. Sci. USA}, year = {2016}, doi = {10.1073/pnas.1615471113}, author = {R. Liang and J. M. J. Swanson and J. J. Madsen and M. Hong and W. F. DeGrado and G. A. Voth} } @article {889, title = {Can Quantum Transition State Theory be Defined as a t = 0+ Limit?}, journal = {J. Chem. Phys.}, volume = {144}, year = {2016}, pages = {1-12}, doi = {10.1063/1.4942482}, author = {S. Jang and G. A. Voth} } @article {903, title = {Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits}, journal = {J. Phys. Chem. B}, volume = {120}, year = {2016}, doi = {10.1021/acs.jpcb.6b02741}, author = {G. M. Hocky and J. L. Baker and M. J. Bradley and A. V. Sinitskiy and E. M. De La Cruz and G. A. Voth} } @article {892, title = {Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins}, journal = {J. Chem. Theory Comp. }, volume = {12}, year = {2016}, pages = {879-891}, doi = {10.1021/acs.jctc.5b01109}, author = {S. Lee and R. Liang and G. A. Voth and J. M. J. Swason} } @article {902, title = {Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II}, journal = {J. Phys. Chem. B}, year = {2016}, pages = {8389-8404 }, doi = {10.1021/acs.jpcb.6b02166}, author = {S. Taraphder and C. M. Maupin and J. M. J. Swanson and G. A. Voth} } @article {898, title = {A Direct Method for Incorporating Experimental Data into Multiscale Coarse-grained Models}, journal = {J Chem Theory Comp}, volume = {12}, year = {2016}, pages = {2144-2153}, doi = {10.1021/acs.jctc.6b00043}, author = {T. Dannenhoffer-Lafage and A. D. White and G. A. Voth} } @article {917, title = {Dynamic Force Matching: Construction of Dynamic Coarse-Grained Models with Realistic Short Time Dynamics and Accurate Long Time Dynamics}, journal = {J Chem Phys}, volume = {145}, year = {2016}, pages = {224107}, doi = { 10.1063/1.4971430}, author = {A. Davtyan and G. A. Voth and H. C. Andersen} } @article {897, title = {The F-Actin Bundler α-Actinin Ain1 is Tailored for Ring Assembly and Constriction during Cytokinesis in Fission Yeast}, journal = {Mol Biol Cell}, volume = {27}, year = {2016}, pages = {1821-1833}, doi = {10.1091/mbc.E16-01-0010}, author = {Y. Li and J. R. Christensen and K. E. Homa and G. M. Hocky and A. Fok and J. A. Sees and G. A. Voth and D. R. Kovar} } @article {909, title = {How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes}, journal = {Proc. Nat. Acad. Sci. USA}, year = {2016}, doi = {10.1073/pnas.1606943113}, author = {M. Simunovic and E. Evergren and I. Golushko and C. Pr{\'e}vost and H. -F. Renard and L. Johannes and H. McMahon and V. Lorman and G. A. Voth and P. Bassereau} } @article {891, title = {Hydroxide Solvation and Transport in Anion Exchange Membranes}, journal = {J. Am. Chem. Soc.}, volume = {138}, year = {2016}, pages = {991-1000}, doi = {10.1021/jacs.5b11951}, author = {C. Chen and Y.-L. S. Tse and G. E. Lindberg and C. Knight and G. A. Voth} } @article {914, title = {Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water}, journal = {J. Chem. Phys. }, year = {2016}, doi = {10.1063/1.4964723}, author = {R. Biswas and W. Carpenter and G. A. Voth and A. Tokmakoff} } @article {908, title = {Multiscale Simulations of Protein Facilitated Membrane Remodeling}, journal = {J. Struct. Biol.}, year = {2016}, doi = {10.1016/j.jsb.2016.06.012}, author = {A. Davtyan and M. Simunovic and G. A. Voth} } @article {912, title = {The Origin of Coupled Chloride and Proton Transport in a Cl{\textendash}/H+ Antiporter}, journal = {J. Am. Chem. Soc. }, year = {2016}, doi = {10.1021/jacs.6b06683}, author = {S. Lee and H. B. Mayes and J. M. J. Swanson and G. A. Voth} } @article {890, title = {Proton Solvation and Transport in Realistic Proton Exchange Membrane Morphologies}, journal = {J. Phys. Chem. C}, volume = {120}, year = {2016}, pages = {3176{\textendash}3186}, doi = {10.1021/acs.jpcc.5b11168}, author = {J. Savage and G. A. Voth} } @article {910, title = {On the Representability Problem and the Physical Meaning of Coarse-Grained Models}, journal = {J. Chem. Phys.}, volume = {145}, year = {2016}, pages = {1-12}, doi = {10.1063/1.4959168}, author = {J. W. Wagner and J. F. Dama and A. E. P. Durumeric and G. A. Voth} } @article {900, title = {Simulation of Proton Transport in Proton Exchange Membranes with Reactive Molecular Dynamics}, journal = {Fuel Cells}, volume = {0000}, year = {2016}, pages = {1-9}, doi = {10.1002/fuce.201600024 }, author = {C. Arntsen and J. Savage and Y.-L. S. Tse and G. A. Voth} } @article {901, title = {Transition-Tempered Metadynamics is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes}, journal = {J. Chem. Theory Comp. }, year = {2016}, doi = {10.1021/acs.jctc.6b00206}, author = {R. Sun and J. F. Dama and J. S. Tan and J. P. Rose and G. A. Voth} } @article {861, title = {An Analysis of Hydrated Proton Diffusion in Ab Initio Molecular Dynamics}, journal = {J. Chem. Phys.}, volume = {142}, year = {2015}, pages = {1-13}, doi = {10.1063/1.4905077}, author = {Y.-L. S. Tse and C. Knight and G. A. Voth} } @article {862, title = {Ion Transport through Ultra-Thin Electrolyte under Applied Voltages}, journal = {J. Phys. Chem. B}, volume = {119}, year = {2015}, pages = {7516-7521}, doi = {10.1021/jp511260v}, author = {Z. Cao and Y. Peng and G. A. Voth} } @article {879, title = {Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface}, journal = {J. Am. Chem. Soc.}, volume = {137}, year = {2015}, pages = {12610-12616}, doi = {10.1021/jacs.5b07232}, author = {Y.-L. S. Tse and C. Chen and G. E. Lindberg and R. Kumar and G. A. Voth} } @article {878, title = {A Reductionist Perspective on Quantum Statistical Mechanics: Coarse-Graining of Path Integrals}, journal = {J. Chem. Phys.}, volume = {143}, year = {2015}, pages = {1-10}, doi = {10.1063/1.4929790}, author = {A. V. Sinitskiy and G. A. Voth} } @article {807, title = {Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel}, journal = { J. Chem. Theor. Comp.}, volume = {10}, year = {2014}, pages = {451{\textendash}462}, doi = {10.1021/ct400832r}, author = {R. Liang and Swanson, J. M. J. and G. A. Voth} } @article {831, title = {Can the Ring Polymer Molecular Dynamics Method be Interpreted as Real Time Quantum Dynamics?}, journal = {J. Chem. Phys.}, volume = {140}, year = {2014}, pages = {1-11}, chapter = {154103}, doi = {10.1063/1.4870717}, author = {S. Jang and Sinitskiy, A. V. and G. A. Voth} } @article {805, title = {Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems}, journal = {J. Phys. Chem. C}, volume = {118}, year = {2014}, pages = {845-853}, doi = {10.1021/jp409728a}, author = {Y.-L. S. Tse and G. E. Lindberg and H. N. Sarode and T. A. Witten and Y. Yang and A. M. Herring and G. A. Voth} } @article {808, title = {An Electrochemically and Thermally Switchable Donor-Acceptor [c2]Daisy Chain Rotaxane}, journal = {Angewandte Chemie}, volume = {53}, year = {2014}, pages = {1953-1958}, edition = {Int. Ed.}, doi = {10.1002/anie.201308498}, author = {Bruns, C. J. and Li, J. and Frasconi, S. T. and Schneebeli, J. and Iehl, J. and Jacquot de Rouville, H.-P. and Stupp, S. I. and G. A. Voth and Stoddart, J. F.} } @article {791, title = {Highly Scalable and Memory Efficient Ultra-coarse-grained Molecular Dynamics Simulations}, journal = {J. Chem. Theor. Comp.}, volume = {10}, year = {2014}, pages = {423-431}, doi = {10.1021/ct400727q}, author = {Grime, J. M. A. and G. A. Voth} } @article {806, title = {Insights into the Transport of Aqueous Quaternary Ammonium Cations: A Combined Experimental and Computational Study}, journal = {J. Phys. Chem. B}, volume = {118}, year = {2014}, pages = {1363-1372}, doi = {10.1021/jp4085662}, author = {H. N. Sarode* and G. E. Lindberg* and Y. Yang and L. E. Felberg and G. A. Voth and A. M. Herring} } @article {833, title = {Multiscale Simulation Reveals a Multifaceted Mechanism of Proton Permeation through the Influenza A M2 Proton Channel}, journal = {Proc. Nat. Acad. Sci. USA}, volume = {111}, year = {2014}, pages = {9396-9401}, doi = {10.1073/pnas.1401997111}, author = {R. Liang and Li, H. and Swanson, J. M. J. and G. A. Voth} } @article {830, title = {Nucleotide Regulation of the Structure and Dynamics of G-actin}, journal = {Biophys. J.}, volume = {106}, year = {2014}, pages = {1710-1720}, doi = {10.1016/j.bpj.2014.03.012}, author = {Saunders, M. G. and J. Tempkin and Weare, J. and Dinner, A. R. and B. Roux and G. A. Voth} } @article {836, title = {The Proton Transport Mechanism of Perfluorosulfonic Acid Membranes}, journal = {J. Phys. Chem. C}, volume = {118}, year = {2014}, pages = {17436{\textendash}17445}, doi = {10.1021/jp504714d}, author = {Savage, J. and Y.-L. S. Tse and G. A. Voth} } @article {832, title = {Proton Transport Under External Applied Voltage}, journal = {J. Phys. Chem. B}, year = {2014}, doi = {10.1021/jp501130m}, author = {Cao, Z. and Kumar, R. and Peng, Y. and G. A. Voth} } @article {809, title = {Single Molecule Studies Reveal A Hidden Key Step in the Activation Mechanism of Membrane-Bound Protein Kinase C alpha}, journal = {Biochemistry}, volume = {53}, year = {2014}, pages = {1697-1713}, doi = {10.1021/bi4016082}, author = {Ziemba, B. P. and Li, J. and Landgraf, K. E. and Knight, J. D. and G. A. Voth and Falke, J. J.} } @article {858, title = {The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation}, journal = {J. Chem. Theory Comp. }, volume = {10}, year = {2014}, pages = {5265-5275}, doi = {10.1021/ct500834t}, author = {A. Davtyan and J. F. Dama and A. V. Sinitskiy and G. A. Voth} } @article {834, title = {Well-tempered Metadynamics Converges Asymptotically}, journal = {Phys. Rev. Lett.}, volume = {112}, year = {2014}, pages = {1-6}, chapter = {240602}, doi = {10.1103/PhysRevLett.112.240602}, author = {J. F. Dama and M. Parrinello and G. A. Voth} } @article {795, title = {Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions}, journal = {J. Phys. Chem. B }, volume = {117}, year = {2013}, pages = {5165-5179}, doi = {10.1021/jp400953a}, author = {T. H. Choi and R. Liang and Maupin, C. M. and G. A. Voth} } @article {765, title = {Atomistic Modeling of the Electrode-Electrolyte Interface in Li-ion Energy Storage Systems: Electrolyte Structuring}, journal = {J. Phys. Chem. C}, volume = {17}, year = {2013}, note = {*contributed equally}, chapter = {3747-3761}, doi = {10.1021/jp3102282}, author = {Jorn*, R. and Kumar*, R. and Abraham, D. P. and G. A. Voth} } @article {670, title = {Autoinhibition of Endophilin in Solution via Inter-domain Interactions}, journal = {Biophys. J.}, volume = {104}, year = {2013}, pages = {396-403}, doi = {10.1016/j.bpj.2012.12.009}, author = {V{\'a}zquez, F. X. and Unger, V. M. and G. A. Voth} } @article {777, title = {Coarse-graining Methods for Computational Biology}, journal = {Annu. Rev. Biophysics}, volume = {42}, year = {2013}, pages = {73-93}, doi = {10.1146/annurev-biophys-083012-130348}, author = {Saunders, M. G. and G. A. Voth} } @article {772, title = {Coarse-Graining of Proteins Based on Elastic Network Models}, journal = {Chem. Phys.}, volume = {422}, year = {2013}, pages = {165-174}, doi = {10.1016/j.chemphys.2013.01.024}, author = {Sinitskiy, A. V. and G. A. Voth} } @article {794, title = {Diffusion Mechanisms in Smectic Ionic Liquid Crystals: Insights from Coarse-grained MD Simulations}, journal = {Soft Matter}, volume = {9}, year = {2013}, pages = {5716-5725}, doi = {10.1039/C3SM50375E}, author = {G. Saielli and G. A. Voth and Wang, Y.} } @article {788, title = {Discovering Crystals Using Shape Matching and Machine Learning}, journal = {Soft Matter}, volume = {9}, year = {2013}, pages = {8552}, doi = {10.1039/C3SM51449H}, author = {C. L. Phillips and G. A. Voth} } @article {783, title = {Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain}, journal = {Biophys. J.}, volume = {105}, year = {2013}, pages = {1624-1634}, doi = {10.1016/j.bpj.2013.08.023}, author = {Baker, J. L. and G. A. Voth} } @article {786, title = {Exploring the Behavior of the Hydrated Excess Proton at Hydrophobic Interfaces}, journal = {Faraday Discussions}, year = {2013}, doi = {10.1039/C3FD00087G}, author = {Kumar, R. and Knight, C. and G. A. Voth} } @article {784, title = {Fitting coarse-grained distribution functions through an iterative force-matching method}, journal = {J. Chem. Phys.}, volume = {139}, year = {2013}, pages = {1-10}, doi = {10.1063/1.4811667}, author = {Lanyuan Lu and J. F. Dama and G. A. Voth} } @article {778, title = {A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models}, journal = {J. Chem. Theor. Comp.}, volume = {9}, year = {2013}, pages = {750-765}, doi = {10.1021/ct300751h}, author = {Srivastava, A. and G. A. Voth} } @article {769, title = {Ligand-Dependent Activation and Deactivation of a G Protein-Coupled Receptor}, journal = {J. Am. Chem. Soc.}, volume = {135}, year = {2013}, pages = {8749-8759}, doi = {10.1021/ja404391q}, author = {Li, J. and Jonsson, A. L. and Shelley, J. C. and Beuming, T. and G. A. Voth} } @article {771, title = {Linear Aggregation of Proteins on the Membrane as a Prelude to Membrane Remodeling}, journal = {Proc. Natl. Acad. Sci.}, volume = {110}, year = {2013}, doi = {10.1073/pnas.1309819110}, author = {Simunovic, M. and Srivastava, A. and G. A. Voth} } @article {799, title = {Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling}, journal = {Blood}, volume = {122}, year = {2013}, pages = {1695-1706}, doi = {10.1182/blood-2013-03-484550}, author = {Y. Chen and J. Aardema and S. Kale and Z. L. Whichard and A. Awomolo and E. Blanchard and B. Chang and D. R. Myers and L. Ju and R. Tran and D. Reece and H. Christensen and S. Boukour and N. Debili and T. S. Strom and D. Rawlings and V{\'a}zquez, F. X. and G. A. Voth and C. Zhu and W. H. A. Kahr and W. A. Lam and S. J. Corey} } @article {764, title = {Minimizing Memory as an Objective for Coarse-Graining}, journal = {J. Chem. Phys.}, volume = {138}, year = {2013}, chapter = {094111}, doi = {10.1063/1.4793313}, author = {Guttenberg, N. and J. F. Dama and Saunders, M. G. and G. A. Voth and Weare, J. and Dinner, A. R.} } @article {780, title = {Molecular Dynamics Simulations of Proton Transport in 3M and Nafion Perfluorosulfonic Acid Membranes}, journal = {J. Phys. Chem. C}, year = {2013}, doi = {10.1021/jp400693g}, author = {Y.-L. S. Tse and A. M. Herring and G. A. Voth} } @article {782, title = {Molecular Mechanism of Membrane Binding of the GRP1 PH Domain}, journal = {J. Mol. Biol.}, volume = {425}, year = {2013}, pages = {3073-3090}, doi = {10.1016/j.jmb.2013.05.026}, author = {Lai, C-L. and Srivastava, A. and Pilling, C. and Falke, J. J. and G. A. Voth} } @article {762, title = {Molecular Origins of Cofilin-linked Changes in Actin Filament Mechanics}, journal = {J. Mol. Biol.}, volume = {425}, year = {2013}, chapter = {1225{\textendash}1240}, doi = {10.1016/j.jmb.2013.01.020}, author = {Fan, J. and Saunders, M. G. and Haddadian, E. J. and Freed, K. F. and Cruz, E. M. De La and G. A. Voth} } @article {789, title = {A Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations}, journal = {J. Chem. Theor. Comp.}, volume = {9}, year = {2013}, pages = {4018{\textendash}4025}, doi = {10.1021/ct400516x}, author = {A. W. Lange and G. A. Voth} } @article {793, title = {New and Notable: Key New Insights into Membrane Targeting by Proteins}, journal = {Biophys. J.}, volume = {104}, year = {2013}, pages = {517-519}, doi = {10.1016/j.bpj.2012.12.029}, author = {G. A. Voth} } @article {779, title = {Nucleotide-dependent Lateral and Longitudinal Interactions in Microtubules}, journal = {J. Mol. Biol.}, year = {2013}, doi = {10.1016/j.jmb.2013.03.029}, author = {A. Grafmuller and E. G. Noya and G. A. Voth} } @article {787, title = {On the Origin of Proton Mobility Suppression in Aqueous Solutions of Amphiphiles}, journal = {J. Phys. Chem. B }, volume = {117}, year = {2013}, pages = {15426-15435}, doi = {10.1021/jp4051726}, author = {Xu, J. and Yamashita, T. and Agmon, N. and G. A. Voth} } @article {785, title = {Protein-Mediated Transformation of Lipid Vesicles into Tubular Networks}, journal = {Biophys. J.}, volume = {105}, year = {2013}, pages = {711-719}, doi = {10.1016/j.bpj.2013.06.039}, author = {Simunovic, M. and Mim, C. and T. Marlovits and G. Resch and G. Unger and G. A. Voth} } @article {759, title = {The Role of Amino Acid Sequence in the Self-Association of Therapeutic Monoclonal Antibodies: Insights from Coarse Grained Modeling}, journal = {J. Chem. Phys. B.}, year = {2013}, doi = {10.1021/jp3108396}, author = {Chaudhri, A. and Zarraga, I. E. and Yadav, S. and Patapoff, T. W. and Shire, S. J. and G. A. Voth} } @article {800, title = {A Solid-Solid Phase Transition in Carbon Dioxide at High Pressures and Intermediate Temperatures}, journal = {Nat. Commun.}, volume = {4}, year = {2013}, doi = {10.1038/ncomms3647}, author = {Li, J. and O. Sode and G. A. Voth and S. Hirata} } @article {775, title = {Solvent Free Ionic Solution Models from Multiscale Coarse-Graining}, journal = {J Chem Theory Comput}, volume = {9}, year = {2013}, pages = {172-178}, doi = {10.1021/ct3007277}, author = {Cao, Z. and J. F. Dama and Lu, L. and G. A. Voth} } @article {761, title = {Theory of Ultra Coarse-Graining. I. General Principles}, journal = {J. Chem. Theor. Comp.}, volume = {9}, year = {2013}, pages = {2466-2480}, doi = {10.1021/ct4000444}, author = {J. F. Dama and Sinitskiy, A. V. and McCullagh, M. and Weare, J. and Roux, B. and Dinner, A. R. and G. A. Voth} } @article {436, title = {Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling}, journal = {Biophys. J.}, volume = {104}, year = {2013}, pages = {404-411}, doi = {10.1016/j.bpj.2012.12.006}, author = {Cui, H. and Mim, C. and Lyman, E. and Unger, V. M. and G. A. Voth} } @article {770, title = {Unraveling the Role of the Protein Environment for [FeFe]-Hydrogenase Charge Transfer: A New Application of Coarse-Graining}, journal = {J. Phys. Chem. B}, volume = {17}, year = {2013}, pages = {4062-4071}, doi = {10.1021/jp402441s}, author = {McCullagh, M. and G. A. Voth} } @article {420, title = {Coarse-Grained Modeling of the Self-Association of Therapeutic Monoclonal Antibodies}, journal = {J. Phys. Chem. B}, volume = {116}, year = {2012}, pages = {8045-8057}, doi = {10.1021/jp301140u}, author = {Chaudhri, A. and Zarraga, I. E. and Kamerzell, T. J. and Brandt, J. P. and Patapoff, T. W. and Shire, S. J. and G. A. Voth} } @article {514, title = {Coarse-graining Away Electronic Structure: A Rigorous Route to Accurate Condensed Phase Interaction Potentials}, journal = {Mol. Phys.}, volume = {110}, year = {2012}, pages = {935-944}, doi = {10.1080/00268976.2012.668621}, author = {Knight, C. and G. A. Voth} } @article {630, title = {Coarse-graining of Multi-Protein Assemblies}, journal = {Curr. Opin. Struct. Biol.}, volume = {22}, year = {2012}, pages = {144-150}, doi = {10.1016/j.sbi.2012.01.003}, author = {Saunders, M. G. and G. A. Voth} } @article {756, title = {Coarse-Graining Provides Insight on the Essential Nature of Heterogeneity in Actin Filaments}, journal = {Biophys. J.}, volume = {103}, year = {2012}, pages = {1334-1342}, doi = {10.1016/j.bpj.2012.08.029}, author = {Fan, J. and Saunders, M. G. and G. A. Voth} } @article {629, title = {Comparison Between Actin Filament Models: Coarse-Graining Reveals Essential Differences}, journal = {Structure}, volume = {20}, year = {2012}, pages = {641-653}, doi = {10.1016/j.str.2012.02.008}, author = {Saunders, M. G. and G. A. Voth} } @article {748, title = {Computationally Efficient Multiconfigurational Reactive Molecular Dynamics}, journal = {J. Chem. Theory Comput.}, volume = {8}, year = {2012}, pages = {4863-4875}, doi = {10.1021/ct3006437}, author = {Yamashita, T. and Peng, Y. and Knight, C. and G. A. Voth} } @article {608, title = {A Computationally Efficient Treatment of Polarizable Electrochemical Cells Held at a Constant Potential}, journal = {J. Phys. Chem. C}, volume = {116}, year = {2012}, pages = {4903-4912}, doi = {10.1021/jp210252g}, author = {Petersen, M. K. and Kumar, R. and White, H. S. and G. A. Voth} } @article {766, title = {The Curious Case of the Hydrated Proton}, journal = {Acc. Chem. Res.}, volume = {45}, year = {2012}, pages = {101-109}, doi = {10.1021/ar200140h}, author = {Knight, C. and G. A. Voth} } @article {776, title = {Early Stages of the HIV-1 Capsid Protein Lattice Formation}, journal = {Biophys. J.}, volume = {103}, year = {2012}, pages = {1774-1783}, doi = {10.1016/j.bpj.2012.09.007}, author = {Grime, J. M. A. and G. A. Voth} } @article {763, title = {Effect of Polymer Morphology on Proton Solvation and Transport in Proton Exchange Membranes}, journal = {J. Phys. Chem C}, volume = {116}, year = {2012}, pages = {19104-19116}, doi = {10.1021/jp304783z}, author = {Feng, S. and Savage, J. and G. A. Voth} } @article {605, title = {Expanding the View of Proton Pumping in Cytochrome c Oxidase through Computer Simulation}, journal = {Biochim. et Biophys. Acta-Bioenergetics}, volume = {1817}, year = {2012}, pages = {518-525}, doi = {10.1016/j.bbabio.2011.11.017}, author = {Peng, Y. and G. A. Voth} } @article {718, title = {Insights into the Mechanism of Proton Transport in Cytochrome c Oxidase}, journal = {J. Am. Chem. Soc.}, volume = {134}, year = {2012}, pages = {1147-1152}, doi = {10.1021/ja209176e}, author = {Yamashita, T. and G. A. Voth} } @article {615, title = {Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation}, journal = {J. Mol. Biol.}, volume = {416}, year = {2012}, pages = {148{\textendash}161}, doi = {10.1016/j.jmb.2011.12.025}, author = {Pfaendtner, J. and Volkmann, N. and Hanein, D. and Dalhaimer, P. and Pollard, T. D. and G. A. Voth} } @article {757, title = {Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain}, journal = {J. Mol. Biol.}, volume = {423}, number = {5}, year = {2012}, pages = {800-817}, doi = {10.1016/j.jmb.2012.08.010}, author = {Lai, C-L. and Jao, C. C. and Lyman, E. and Gallop, J. L. and Peter, B. J. and McMahon, H. T. and Langen, R. and G. A. Voth} } @article {506, title = {Mesoscale Simulation of Proton Transport in Proton Exchange Membranes}, journal = {J. Phys. Chem. C}, volume = {116}, year = {2012}, pages = {935-944}, doi = {10.1021/jp300040w}, author = {Jorn, R. and G. A. Voth} } @article {747, title = {Molecular and Thermodynamic Insights into the Conformational Transitions of Hsp90}, journal = {Biophys. J.}, volume = {103}, year = {2012}, pages = {284-292}, doi = {10.1016/j.bpj.2012.06.018}, author = {Simunovic, M. and G. A. Voth} } @article {439, title = {The Multiscale Coarse-Graining Method. X. Improved Algorithms for Constructing Coarse-Grained Potentials for Molecular Systems}, journal = {J. Chem. Phys.}, volume = {136}, year = {2012}, pages = {194115}, doi = {10.1063/1.4705420}, author = {Das, A. and Lu, L. and Andersen, H. C. and G. A. Voth} } @article {745, title = {Multiscale Reactive Molecular Dynamics}, journal = {J. Chem. Phys.}, volume = {137}, year = {2012}, pages = {22A525}, doi = {10.1063/1.4743958}, author = {Knight, C. and Lindberg, G. and G. A. Voth} } @article {383, title = {Nanostructural Organization in Acetonitrile/Ionic Liquid Mixtures: Molecular Dynamics Simulations and Optical Kerr Effect Spectroscopy}, journal = {ChemPhysChem}, volume = {13}, year = {2012}, pages = {1687-1700}, doi = {10.1002/cphc.201200026}, author = {Bardak, F. and Xiao, D. and Jr., L. G. Hines and Son, P. and Bartsch, R. A. and Quitevis, E. L. and Yang, P. and G. A. Voth} } @inbook {781, title = {OKE Spectroscopy and Molecular Dynamics Simulations of Polar and Nonpolar Molecules in Ionic Liquids}, booktitle = {Ionic Liquids: Science and Applications}, year = {2012}, pages = {271-287}, publisher = {American Chemical Society}, organization = {American Chemical Society}, edition = {ACS Symposium Series 1117}, chapter = {13}, address = {Washington, DC}, doi = {10.1021/bk-2012-1117.ch013}, author = {Quitevis, E. L. and Bardak, F. and Xiao, D. and L. G. Hines, Jr. and Son, P. and Bartsch, R. A. and Yang, P. and G. A. Voth} } @article {735, title = {Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes}, journal = {J. Phys. Chem. B}, volume = {116}, year = {2012}, pages = {8363-8374}, doi = {10.1021/jp2108895}, author = {Sinitskiy, A. V. and Saunders, M. G. and G. A. Voth} } @article {505, title = {Proton Conduction in Exchange Membranes Across Multiple Length Scales}, journal = {Acc. Chem. Res.}, volume = {45}, year = {2012}, pages = {2002-2010}, doi = {10.1021/ar200323q}, author = {Jorn, R. and Savage, J. and G. A. Voth} } @article {654, title = {Proton Transport Pathways in [NiFe]-Hydrogenase}, journal = {J. Phys. Chem. B}, volume = {116}, year = {2012}, pages = {2917{\textendash}2926}, doi = {10.1021/jp208512y}, author = {Sumner, I. and G. A. Voth} } @article {576, title = {Structural Basis of Membrane Bending by the N-BAR Protein Endophilin}, journal = {Cell}, volume = {149}, number = {137-145}, year = {2012}, doi = {10.1016/j.cell.2012.01.048}, author = {Mim, C. and Cui, H. and Gawronski-Salerno, J. A. and Frost, A. and Lyman, E. and G. A. Voth and Unger, V. M.} } @article {567, title = {Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II}, journal = {J. Am. Chem. Soc.}, volume = {133}, year = {2011}, pages = {6223{\textendash}6234}, doi = {10.1021/ja1097594}, author = {Maupin, C. M. and Castillo, N. and Taraphder, S. and C. Tu, R. McKenna and Silverman, D. N. and G. A. Voth} } @article {723, title = {A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles}, journal = {J. Chem. Theor. Comp}, volume = {7}, year = {2011}, pages = {2277-2283}, doi = {10.1021/ct200100e}, author = {Zhang, Y. and G. A. Voth} } @article {773, title = {The Coupled Proton Transport in the ClC-ec1 Cl-/H+ Antiporter}, journal = {Biophys. J.}, volume = {101}, year = {2011}, pages = {L47-L49}, doi = {10.1016/j.bpj.2011.10.021}, author = {Zhang, Y. and G. A. Voth} } @article {539, title = {Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1}, journal = {J. Mol. Biol.}, volume = {407}, year = {2011}, pages = {607{\textendash}620}, doi = {10.1016/j.jmb.2011.01.036}, author = {Li, H. and Chen, H. and Zeuthen, T. and Conrad, C. and Wu, B. and Beitz, E. and G. A. Voth} } @article {663, title = {An Exploration of Transferability in Multiscale Coarse-grained Peptide Models}, journal = {J. Phys. Chem. B}, volume = {115}, year = {2011}, pages = {11911-11926}, doi = {10.1021/jp204455g}, author = {Thorpe, I. F. and Goldenberg, D. P. and G. A. Voth} } @article {716, title = {Infrared Spectrum of the Hydrated Proton in Water}, journal = {J. Phys. Chem. Lett.}, volume = {2}, year = {2011}, pages = {81-86}, doi = {10.1021/jz101536b}, author = {Xu, J. and Zhang, Y. and G. A. Voth} } @article {453, title = {Intrinsic Bending of Microtubule Protofilaments}, journal = {Structure}, volume = {19}, year = {2011}, pages = {409{\textendash}417}, doi = {10.1016/j.str.2010.12.020}, author = {Grafm{\"u}ller, A. and G. A. Voth} } @article {726, title = {Key Inter-molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis}, journal = {J. Am. Chem. Soc.}, volume = {133}, year = {2011}, pages = {16828-16838}, doi = {10.1021/ja2028487}, author = {Zhang, Z. and Sanbonmatsu, K. Y. and G. A. Voth} } @article {435, title = {Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins}, journal = {Biophys. J.}, volume = {100}, year = {2011}, pages = {1271-1279}, doi = {10.1016/j.bpj.2011.01.036}, author = {Cui, H. and Lyman, E. and G. A. Voth} } @article {555, title = {The Multiscale Coarse-Graining Method. VII. Free Energy Decomposition of Coarse-Grained Effective Potentials}, journal = {J. Chem. Phys.}, volume = {134}, year = {2011}, pages = {224107}, doi = {10.1063/1.3599049}, author = {Lu, L. and G. A. Voth} } @article {721, title = {Nanostructural Organization in Carbon Disulfide/Ionic Liquid Mixtures: Optical Kerr Effect Spectroscopy and Molecular Dynamics Simulations}, journal = {J. Chem. Phys.}, volume = {135}, year = {2011}, pages = {034502}, doi = {10.1063/1.3601752}, author = {Yang, P. and G. A. Voth and Xiao, D. and L. G. Hines, Jr. and Bartsch, R. A. and Quitevis, E. L.} } @article {445, title = {Proton Solvation and Transport in Hydrated Nafion}, journal = {J. Phys. Chem. B}, volume = {115}, year = {2011}, pages = {5903-5912}, doi = {10.1021/jp2002194}, author = {Feng, S. and G. A. Voth} } @article {557, title = {Reconstructing Protein Remodeled Membranes in Molecular Detail From Mesoscopic Models}, journal = {Phys. Chem. Chem. Phys.}, number = {13}, year = {2011}, pages = {10430{\textendash}10436}, doi = {10.1039/C0CP02978E}, author = {Lyman, E. and Cui, H. and G. A. Voth} } @article {628, title = {Water Molecules in the Nucleotide Binding Cleft of Actin: Effects on Subunit Conformation and Implications for ATP Hydrolysis}, journal = {J. Mol. Biol.}, volume = {413}, year = {2011}, pages = {279-291}, doi = {10.1016/j.jmb.2011.07.068}, author = {Saunders, M. G. and G. A. Voth} } @article {613, title = {Actin Filament Remodeling by Actin Depolymerization Factor/Cofilin}, journal = {Proc. Natl. Acad. Sci. USA}, volume = {107}, year = {2010}, pages = {7299{\textendash}7304}, doi = {10.1073/pnas.0911675107}, author = {Pfaendtner, J. and Cruz, E. M. De La and G. A. Voth} } @article {727, title = {Coarse-Grained Representations of Large Biomolecular Complexes from Low Resolution Structural Data}, journal = {J. Chem. Theor. Comp.}, volume = {6}, year = {2010}, pages = {2990{\textendash}3002}, doi = {10.1021/ct100374a}, author = {Zhang, Z. and G. A. Voth} } @article {382, title = {Conformational Switching Between Protein Substates Studied with 2D IR Vibrational Echo Spectroscopy and Molecular Dynamics Simulations}, journal = {J. Phys. Chem. B}, volume = {114}, year = {2010}, pages = {17187{\textendash}17193}, doi = {10.1021/jp109203b}, author = {Bagchi, S. and Thorpe, D. G. and Thorpe, I. F. and G. A. Voth and Fayer, M. D.} } @article {513, title = {Defining Condensed Phase Reactive Force Fields From Ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton}, journal = {J. Chem. Theor. Comp.}, volume = {6}, year = {2010}, pages = {3223{\textendash}3232}, doi = {10.1021/ct1004438}, author = {Knight, C. and Maupin, C. M. and Izvekov, S. and G. A. Voth} } @article {423, title = {An Efficient Multi-State Reactive Molecular Dynamics Approach Based on Short-Ranged Effective Potentials}, journal = {J. Chem. Theor. Comp.}, volume = {6}, year = {2010}, pages = {3039{\textendash}3047}, doi = {10.1021/ct100318f}, author = {Chen, H. and Liu, P. and G. A. Voth} } @article {553, title = {Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining}, journal = {J. Chem. Theor. Comp.}, volume = {6}, year = {2010}, pages = {954-965}, doi = {10.1021/ct900643r}, author = {Lu, L. and Izvekov, S. and Das, A. and Andersen, H. C. and G. A. Voth} } @article {530, title = {The Intricate Role of Water in Proton Transport through Cytochrome c Oxidase}, journal = {J. Am. Chem. Soc.}, volume = {132}, year = {2010}, pages = {16225{\textendash}16239}, doi = {10.1021/ja107244g}, author = {Lee, H. J. and Svahn, E. and Swanson, J. M. J. and Lepp, H. and G. A. Voth and Brzezinski, P. and Gennis, R. B.} } @article {424, title = {The Kinetics of Proton Migration in Liquid Water}, journal = {J. Phys. Chem. B}, volume = {114}, year = {2010}, pages = {333{\textendash}339}, doi = {10.1021/jp908126a}, author = {Chen, H. and G. A. Voth} } @article {417, title = {Mechanism of Fast Proton Transport along One-Dimensional Water Chains Confined in Carbon Nanotubes}, journal = {J. Am. Chem. Soc.}, volume = {132}, year = {2010}, pages = {11395{\textendash}11397}, doi = {10.1021/ja1046704}, author = {Cao, Z. and Peng, Y. and T. Yan and Li, S. and Li, A. and G. A. Voth} } @article {768, title = {Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKCα C2 Domain: A Combined Molecular Dynamics and Experimental Study}, journal = {J. Mol. Biol.}, volume = {402}, year = {2010}, pages = {301{\textendash}310}, doi = {10.1016/j.jmb.2010.07.037}, author = {Lai, C-L. and Landgraf, K. E. and G. A. Voth and Falke, J. J.} } @article {444, title = {Molecular Dynamics Simulations of Imidazolium-based Ionic Liquid/Water Mixtures: Alkyl Side Chain Length and Anion Effects}, journal = {Fluid Phase Equilibria (Special Issue)}, volume = {294}, year = {2010}, pages = {148{\textendash}156}, doi = {10.1016/j.fluid.2010.02.034}, author = {Feng, S. and G. A. Voth} } @article {702, title = {Molecular Dynamics Simulations of Polyglutamine Aggregation using Solvent-Free Multiscale Coarse-Grained Models}, journal = {J. Phys. Chem. B}, volume = {114}, year = {2010}, pages = {8735{\textendash}8743}, doi = {10.1021/jp1007768}, author = {Wang, Y. and G. A. Voth} } @article {527, title = {The Multiscale Coarse-Graining Method. VI. Implementation of Three-Body Coarse-Grained Potentials}, journal = {J. Chem. Phys.}, volume = {132}, year = {2010}, pages = {164107}, doi = {10.1063/1.3394863}, author = {Larini, L. and Lu, L. and G. A. Voth} } @article {507, title = {Multiscale Coarse-Graining of the Protein Energy Landscape}, journal = {PLoS Comp. Bio.}, volume = {6}, year = {2010}, pages = {e1000827}, doi = {10.1371/journal.pcbi.1000827}, author = {Jr., R. D. Hills and Lu, L. and G. A. Voth} } @article {380, title = {Multiscale Computer Simulation of the Immature HIV-1 Virion}, journal = {Biophys. J.}, volume = {99}, year = {2010}, pages = {2757{\textendash}2765}, doi = {10.1016/j.bpj.2010.08.018}, author = {Ayton, G. S. and G. A. Voth} } @article {381, title = {Multiscale Simulation of Protein Mediated Membrane Remodeling}, journal = {Seminars in Cell and Developmental Biology}, volume = {21}, year = {2010}, pages = {357-362}, doi = {10.1016/j.semcdb.2009.11.011}, author = {Ayton, G. S. and G. A. Voth} } @article {516, title = {Probing Selected Morphological Models of Hydrated Nafion Using Large Scale Molecular Dynamics Simulations}, journal = {J. Phys. Chem. B.}, volume = {114}, year = {2010}, pages = {3205{\textendash}3218}, doi = {10.1021/jp9112409}, author = {Knox, C. K. and G. A. Voth} } @article {717, title = {Properties of Hydrated Excess Protons Near Phospholipid Bilayers}, journal = {J. Phys. Chem. B}, volume = {114}, year = {2010}, pages = {592{\textendash}603}, doi = {10.1021/jp908768c}, author = {Yamashita, T. and G. A. Voth} } @article {703, title = {Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology}, journal = {J. Chem. Theor. Comp.}, volume = {6}, year = {2010}, pages = {2566{\textendash}2580}, doi = {10.1021/ct900579k}, author = {Wong, K. F. and Sonnenberg, J. L. and Paesani, F. and Yamamoto, T. and Van{\'\i}{\v c}ek, J. and Zhang, W. and H. B. Schlegel and Case, D. A. and T. E. Cheatham, III and W. H. Miller and G. A. Voth} } @article {591, title = {A Quantitative Assessment of the Accuracy of Centroid Molecular Dynamics for the Calculation of the Infrared Spectrum of Liquid Water}, journal = {J. Chem. Phys.}, volume = {132}, year = {2010}, pages = {014105}, doi = {10.1063/1.3291212}, author = {Paesani, F. and G. A. Voth} } @article {520, title = {Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-grained Analysis}, journal = {Biophys. J.}, volume = {98}, year = {2010}, pages = {18-26}, doi = {10.1016/j.bpj.2009.09.049}, author = {Krishna, V. and Ayton, G. S. and G. A. Voth} } @article {566, title = {The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations}, journal = {J. Phys. Chem. B}, volume = {114}, year = {2010}, pages = {6922-6931}, doi = {10.1021/jp1010555}, author = {Maupin, C. M. and Aradi, B. and G. A. Voth} } @article {711, title = {Structure and Dynamics of Concentrated Hydrochloric Acid Solutions}, journal = {J. Phys. Chem. B}, volume = {114}, year = {2010}, pages = {9555{\textendash}9562}, doi = {10.1021/jp102516h}, author = {Xu, J. and Izvekov, S. and G. A. Voth} } @article {614, title = {Structure and Dynamics of the Actin Filament}, journal = {J. Mol. Biol.}, volume = {396}, year = {2010}, pages = {252{\textendash}263}, doi = {10.1016/j.jmb.2009.11.034}, author = {Pfaendtner, J. and Lyman, E. and Pollard, T. D. and G. A. Voth} } @article {556, title = {Water Under the BAR}, journal = {Biophys. J.}, volume = {99}, year = {2010}, pages = {1783{\textendash}1790}, doi = {10.1016/j.bpj.2010.06.074}, author = {Lyman, E. and Cui, H. and G. A. Voth} } @article {710, title = {Aqueous Solutions and their Interfaces}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {3997}, doi = {10.1021/jp900202a}, author = {Xantheas, S. S. and G. A. Voth} } @article {428, title = {A Computer Simulation Model for Proton Transport in Liquid Imidazole}, journal = {J. Phys. Chem. A}, volume = {113}, year = {2009}, pages = {4507-4517}, doi = {10.1021/jp811156r}, author = {Chen, H. and T. Yan and G. A. Voth} } @article {725, title = {Defining Coarse-grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models}, journal = {Biophys. J.}, volume = {97}, year = {2009}, pages = {2327-2337}, doi = {10.1016/j.bpj.2009.08.007}, author = {Zhang, Z. and Pfaendtner, J. and Grafm{\"u}ller, A. and G. A. Voth} } @article {649, title = {A Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations}, journal = {J. Chem. Theory. Comp.}, volume = {5}, year = {2009}, pages = {949-961}, doi = {10.1021/ct800477y}, author = {Sonnenberg, J. L. and Wong, K. F. and G. A. Voth and H. B. Schlegel} } @article {573, title = {Effect of Active-site Mutations at Asn67 on the Proton Transfer Mechanism of Human Carbonic Anhydrase II}, journal = {Biochem.}, volume = {48}, year = {2009}, pages = {7996-8005}, doi = {10.1021/bi901037u}, author = {Maupin, C. M. and Zheng, J. and Tu, C. and McKenna, R. and Silverman, D. N. and G. A. Voth} } @article {699, title = {Effective Force Coarse-Graining}, journal = {Phys. Chem. Chem. Phys.}, volume = {11}, year = {2009}, pages = {2002-2015}, doi = {10.1039/B819182D}, author = {Wang, Y. and Noid, W. G. and Liu, P. and G. A. Voth} } @article {569, title = {Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II}, journal = {J. Am. Chem. Soc.}, volume = {131}, year = {2009}, pages = {7598-7608}, doi = {10.1021/ja8091938}, author = {Maupin, C. M. and McKenna, R. and Silverman, D. N. and G. A. Voth} } @article {379, title = {A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {4413-4424}, doi = {10.1021/jp8087868}, author = {Ayton, G. S. and G. A. Voth} } @article {467, title = {The Hydrated Excess Proton at Water-Hydrophobic Interfaces}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {4017-4030}, doi = {10.1021/jp805304j}, author = {Iuchi, S. and Chen, H. and Paesani, F. and G. A. Voth} } @article {592, title = {Infrared Spectroscopy and Hydrogen-Bond Dynamics in Liquid Water from Quantum Simulations}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {13118{\textendash}13130}, doi = {10.1021/jp907648y}, author = {Paesani, F. and Xantheas, S. S. and G. A. Voth} } @article {434, title = {Membrane Binding by the Endophilin N-BAR Domain}, journal = {Biophys. J.}, volume = {97}, year = {2009}, pages = {2746-2753}, doi = {10.1016/j.bpj.2009.08.043}, author = {Cui, H. and Ayton, G. S. and G. A. Voth} } @article {486, title = {Mixed Resolution Modeling of Interactions in Condensed Phase Systems}, journal = {J. Chem. Theor. Comp.}, volume = {5}, year = {2009}, pages = {3232{\textendash}3244}, doi = {10.1021/ct900414p}, author = {Izvekov, S. and G. A. Voth} } @article {521, title = {The Multiscale Coarse-graining Method. IV. Transferring Coarse-grained Potentials Between Temperatures}, journal = {J. Chem. Phys.}, volume = {131}, year = {2009}, pages = {024103}, doi = {10.1063/1.3167797}, author = {Krishna, V. and Noid, W. G. and G. A. Voth} } @article {369, title = {New Insights into BAR Domain Induced Membrane Remodeling}, journal = {Biophys. J.}, volume = {97}, year = {2009}, pages = {1616{\textendash}1625}, doi = {10.1016/j.bpj.2009.06.036}, author = {Ayton, G. S. and Lyman, E. and Krishna, V. and Swenson, R. D. and Mim, C. and Unger, V. and G. A. Voth} } @article {612, title = {Nucleotide-Dependent Conformational States of Actin}, journal = {Proc. Natl. Acad. Sci. USA}, volume = {106}, year = {2009}, pages = {12723{\textendash}12728}, doi = {10.1073/pnas.0902092106}, author = {Pfaendtner, J. and Branduardi, D. and Pollard, T. D. and M. Parrinello and G. A. Voth} } @article {590, title = {The Properties of Water: Insights from Quantum Simulations}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {5702{\textendash}5719}, doi = {10.1021/jp810590c}, author = {Paesani, F. and G. A. Voth} } @article {693, title = {Proton Transport Pathway in the ClC Cl{\textendash}/H+ Antiporter}, journal = {Biophys. J.}, volume = {97}, year = {2009}, pages = {121-131}, doi = {10.1016/j.bpj.2009.04.038}, author = {Wang, D. and G. A. Voth} } @article {558, title = {A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor}, journal = {Structure}, volume = {17}, year = {2009}, pages = {1660{\textendash}1668}, doi = {10.1016/j.str.2009.10.010}, author = {Lyman, E. and Higgs, C. and Kim, B. and Lupyan, D. and Shelley, J. C. and Farid, R. and G. A. Voth} } @article {487, title = {A Solvent Free Lipid Bilayer Model Using Multiscale Coarse-graining}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {4443-4455}, doi = {10.1021/jp810440c}, author = {Izvekov, S. and G. A. Voth} } @article {554, title = {Systematic Coarse-graining of a Multi-component Lipid Bilayer}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {1501-1510}, doi = {10.1021/jp809604k}, author = {Lu, L. and G. A. Voth} } @article {378, title = {Systematic Multiscale Simulation of Membrane Protein Systems}, journal = {Curr. Opin. Struct. Biol.}, volume = {19}, year = {2009}, pages = {138-144}, doi = {10.1016/j.sbi.2009.03.001}, author = {Ayton, G. S. and G. A. Voth} } @article {696, title = {Transferable Coarse-Grained Models for Ionic Liquids}, journal = {J. Chem. Theor. Comp.}, volume = {5}, year = {2009}, pages = {1091-1098}, doi = {10.1021/ct800548t}, author = {Wang, Y. and Feng, S. and G. A. Voth} } @article {427, title = {Unusual Hydrophobic Interactions in Acidic Aqueous Solutions}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {7291-7297}, doi = {10.1021/jp9025909}, author = {Chen, H. and Xu, J. and G. A. Voth} } @article {418, title = {Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems}, journal = {J. Chem. Theor. Comp.}, volume = {4}, year = {2008}, pages = {560-568}, doi = {10.1021/ct7003275}, author = {Ceotto, M. and Ayton, G. S. and G. A. Voth} } @article {542, title = {A Bayesian Statistics Approach to Multiscale Coarse-graining}, journal = {J. Chem. Phys.}, volume = {129}, year = {2008}, pages = {214114}, doi = {10.1063/1.3033218}, author = {Liu, P. and III, H. Daum{\'e} and G. A. Voth} } @article {488, title = {Coarse-graining in Interaction Space: A Systematic Approach for Replacing Long-ranged Electrostatics by Short-ranged Effective Potentials}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, note = {*Contributed equally to this work}, pages = {4711-4724}, doi = {10.1021/jp710339n}, author = {Izvekov*, S. and Swanson*, J. M. J. and G. A. Voth} } @article {643, title = {Coarse-Graining in Interaction Space: An Analytical Approximation for the Effective Short-Ranged Electrostatics}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, pages = {16230{\textendash}16237}, doi = {10.1021/jp807205q}, author = {Shi, Q. and Liu, P. and G. A. Voth} } @article {388, title = {Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations}, journal = {Biophys. J.}, volume = {95}, year = {2008}, pages = {1866-1876}, doi = {10.1529/biophysj.107.121160}, author = {Blood, P. D. and Swenson, R. D. and G. A. Voth} } @article {500, title = {Gating of the Mechanosensitive Channel Protein MscL: The Interplay of Membrane and Protein}, journal = {Biophys. J.}, volume = {94}, year = {2008}, pages = {3497-3511}, doi = {10.1529/biophysj.107.109850}, author = {J. Jeon and G. A. Voth} } @article {704, title = {An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, pages = {467-482}, doi = {10.1021/jp076658h}, author = {Y. Wu and Chen, H. and Wang, F. and Paesani, F. and G. A. Voth} } @article {451, title = {Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-grained Analysis}, journal = {Biophys. J.}, volume = {95}, year = {2008}, pages = {2487-2499}, doi = {10.1529/biophysj.108.129072}, author = {Gebremichael, Y. and Chu, J.-W. and G. A. Voth} } @article {616, title = {Molecular Dynamics Simulation and Coarse-grained Analysis of the Arp2/3 Complex}, journal = {Biophys. J.}, volume = {95}, year = {2008}, pages = {5324-5333}, doi = {10.1529/biophysj.108.143313}, author = {Pfaendtner, J. and G. A. Voth} } @article {503, title = {Molecular Dynamics Simulation of the Energetic Room Temperature Ionic Liquid 1-Hydroxyethyl-4Amino-1, 2, 4-Triazolium Nitrate (HEATN)}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, pages = {3121-3131}, doi = {10.1021/jp710653g}, author = {Jiang, W. and T. Yan and Wang, Y. and G. A. Voth} } @article {583, title = {The Multiscale Coarse-graining Method I: A Rigorous Bridge between Atomistic and Coarse-grained Models}, journal = {J. Chem. Phys.}, volume = {128}, year = {2008}, pages = {244114}, doi = {10.1063/1.2938860}, author = {Noid, W. G. and Chu, J.-W. and Ayton, G. S. and Krishna, V. and Izvekov, S. and G. A. Voth and Das, A. and Andersen, H. C.} } @article {585, title = {The Multiscale Coarse-graining Method. II. Numerical Implementation for Coarse-grained Molecular Models}, journal = {J. Chem. Phys.}, volume = {128}, year = {2008}, pages = {244115}, doi = {10.1063/1.2938857}, author = {Noid, W. G. and Liu, P. and Wang, Y. and Chu, J.-W. and Ayton, G. S. and Izvekov, S. and Andersen, H. C. and G. A. Voth} } @article {502, title = {A Multiscale Coarse-Graining Study of Liquid/Vacuum Interface of Room-Temperature Ionic Liquids with Alkyl Substituents of Different Lengths}, journal = {J. Phys. Chem. C}, volume = {112}, year = {2008}, pages = {1132-1139}, doi = {10.1021/jp077643m}, author = {Jiang, W. and Wang, Y. and T. Yan and G. A. Voth} } @article {367, title = {Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior}, journal = {Current Topics in Membranes}, volume = {60}, year = {2008}, pages = {181-225}, doi = {10.1016/S1063-5823(08)00007-0}, author = {Ayton, G. S. and Izvekov, S. and Noid, W. G. and G. A. Voth} } @article {588, title = {Nonlinear Quantum Time Correlation Functions from Centroid Molecular Dynamics and the Maximum Entropy Method}, journal = {J. Chem. Phys.}, volume = {129}, year = {2008}, pages = {194113}, doi = {10.1063/1.3013365}, author = {Paesani, F. and G. A. Voth} } @article {606, title = {Orientational Dynamics of Water in the Nafion Polymer Electrolyte Membrane and Its Relationship to Proton Transport}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, pages = {7754{\textendash}7761}, doi = {10.1021/jp800221x}, author = {Petersen, M. K. and Hatt, A. J. and G. A. Voth} } @article {570, title = {Origins of Enhanced Proton Transport in the Y7F Mutant of Human Carbonic Anhydrase II}, journal = {J. Am. Chem. Soc.}, volume = {130}, year = {2008}, pages = {11399{\textendash}11408}, doi = {10.1021/ja802264j}, author = {Maupin, C. M. and Saunders, M. G. and Thorpe, I. F. and McKenna, R. and Silverman, D. N. and G. A. Voth} } @article {664, title = {Peptide Folding Using Multiscale Coarse-grained Models}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, pages = {13079{\textendash}13090}, doi = {10.1021/jp8015968}, author = {Thorpe, I. F. and Zhou, J. and G. A. Voth} } @article {589, title = {Quantum Effects Strongly Influence the Surface Premelting of Ice}, journal = {J. Phys. Chem. C}, volume = {112}, year = {2008}, pages = {324-327}, doi = {10.1021/jp710640e}, author = {Paesani, F. and G. A. Voth} } @article {544, title = {Reconstructing Atomistic Detail from Coarse-grained Models with Resolution Exchange}, journal = {J. Chem. Phys.}, volume = {129}, year = {2008}, pages = {114103}, doi = {10.1063/1.2976663}, author = {Liu, P. and Shi, Q. and Lyman, E. and G. A. Voth} } @article {715, title = {Redox-Coupled Proton Pumping in Cytochrome c Oxidase: Further Insights from Computer Simulation}, journal = {Biochim. et Biophys. Acta-Bioenergetics}, volume = {1777}, year = {2008}, pages = {196-201}, doi = {10.1063/1.2976663}, author = {Xu, J. and G. A. Voth} } @article {560, title = {Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, pages = {9456-9466}, doi = {10.1021/jp804018y}, author = {Markovitch, O. and Chen, H. and Izvekov, S. and Paesani, F. and G. A. Voth and Agmon, N.} } @article {724, title = {A Systematic Methodology for Defining Coarse-grained Sites in Large Biomolecules}, journal = {Biophys. J.}, volume = {95}, year = {2008}, pages = {5073-5083}, doi = {10.1529/biophysj.108.139626}, author = {Zhang, Z. and Lu, L. and Noid, W. G. and Krishna, V. and Pfaendtner, J. and G. A. Voth} } @article {559, title = {Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins}, journal = {Biophys. J.}, volume = {95}, year = {2008}, pages = {4183{\textendash}4192}, doi = {10.1529/biophysj.108.139733}, author = {Lyman, E. and Pfaendtner, J. and G. A. Voth} } @article {580, title = {Unique Elastic Properties of the Spectrin Tetramer as Revealed by Multiscale Coarse-Grained Modeling}, journal = {Proc. Natl. Acad. Sci. USA}, volume = {105}, year = {2008}, pages = {1204-1208}, doi = {10.1073/pnas.0707500105}, author = {D. T. Mirijanian and G. A. Voth} } @article {694, title = {Unusual {\textquoteleft}Amphiphilic{\textquoteright} Association of Hydrated Protons in Strong Acid Solution}, journal = {J. Am. Chem. Soc.}, volume = {130}, year = {2008}, pages = {3120-3126}, doi = {10.1021/ja078106i}, author = {Wang, F. and Izvekov, S. and G. A. Voth} } @article {468, title = {Are Many-body Electronic Polarization Effects Important in Liquid Water?}, journal = {J Chem Phys}, volume = {126}, number = {12}, year = {2007}, note = {Iuchi, Satoru Izvekov, Sergei Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2007 Mar 28;126(12):124505.}, pages = {124505}, abstract = {

Many-body electronic polarization effects may be important for an accurate description of aqueous environments. As a result, numerous polarizable water models have been developed to include explicit polarization effects in intermolecular potential functions. In this paper, it is shown for liquid water at ambient conditions that such many-body polarization interactions can be decomposed into effective pairwise contributions using the force-matching (FM) method [Izvekov et al., J. Chem. Phys. 120, 10896 (2004)]. It is found that an effective pairwise water model obtained by the FM method can accurately reproduce various bulk structural and thermodynamic properties obtained from an accurate fully polarizable water model. In addition, the effective pairwise water model also provides a reasonable description of the water liquid-vapor interface, thus exhibiting a degree of transferability to heterogeneous environments. These results suggest that the role and importance of many-body electronic polarization effects in aqueous systems might be fruitfully explored relative to the best possible pairwise decomposable bulk phase model as the reference state.

}, keywords = {Chemical Phase Transition Water/*chemistry, Computer Simulation *Models}, doi = {10.1063/1.2710252}, author = {Iuchi, S. and Izvekov, S. and G. A. Voth} } @article {446, title = {Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism}, journal = {Biochemistry}, volume = {46}, number = {11}, year = {2007}, note = {Fisher, S Zoe Maupin, C Mark Budayova-Spano, Monika Govindasamy, Lakshmanan Tu, Chingkuang Agbandje-McKenna, Mavis Silverman, David N Voth, Gregory A McKenna, Robert GM25154/GM/NIGMS NIH HHS/United States GM53148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t United States Biochemistry Biochemistry. 2007 Mar 20;46(11):2930-7. Epub 2007 Feb 24.}, pages = {2930-7}, abstract = {

Human carbonic anhydrase II (HCA II) is a zinc-metalloenzyme that catalyzes the reversible interconversion of CO2 and HCO3-. The rate-limiting step of this catalysis is the transfer of a proton between the Zn-bound solvent molecule and residue His64. In order to fully characterize the active site structural features implicated in the proton transfer mechanism, the refined X-ray crystal structure of uncomplexed wild type HCA II to 1.05 A resolution with an Rcryst value of 12.0\% and an Rfree value of 15.1\% has been elucidated. This structure provides strong clues as to the pathway of the intramolecular proton transfer between the Zn-bound solvent and His64. The structure emphasizes the role of the solvent network, the unique positioning of solvent molecule W2, and the significance of the dual conformation of His64 in the active site. The structure is compared with molecular dynamics (MD) simulation calculations of the Zn-bound hydroxyl/His64+ (charged) and the Zn-bound water/His64 (uncharged) HCA II states. A comparison of the crystallographic anisotropic atomic thermal parameters and MD simulation root-mean-square fluctuation values show excellent agreement in the atomic motion observed between the two methods. It is also interesting that the observed active site solvent positions in the crystal structure are also the most probable positions of the solvent during the MD simulations. On the basis of the comparative study of the MD simulation results, the HCA II crystal structure observed is most likely in the Zn-bound water/His64 state. This conclusion is based on the following observations: His64 is mainly (80\%) orientated in an inward conformation; electron density omit maps infer that His64 is not charged in an either inward or outward conformation; and the Zn-bound solvent is most likely a water molecule.

}, keywords = {Amino Acid Sequence Carbonic Anhydrase II/*chemistry Computational Biology Computer Simulation Crystallization Crystallography, Molecular *Protons, X-Ray Histidine/chemistry Humans Models}, doi = {10.1021/bi062066y}, author = {Fisher, S. Z. and Maupin, C. M. and Budayova-Spano, M. and Govindasamy, L. and Tu, C. and Agbandje-McKenna, M. and Silverman, D. N. and G. A. Voth and McKenna, R.} } @article {579, title = {Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: the Molecular Origins of Flexibility}, journal = {J Mol Biol}, volume = {365}, number = {2}, year = {2007}, note = {Mirijanian, Dina T Chu, Jhih-Wei Ayton, Gary S Voth, Gregory A 1S10 RR17214-01/RR/NCRR NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. England Journal of molecular biology J Mol Biol. 2007 Jan 12;365(2):523-34. Epub 2006 Oct 6.}, pages = {523-34}, abstract = {

Spectrin is an ubiquitous protein in metazoan cells, and its flexibility is one of the keys to maintaining cellular structure and organization. Both alpha-spectrin and beta-spectrin polypeptides consist primarily of triple coiled-coil modular repeat units, and two important factors that determine spectrin flexibility are the bending flexibility between two consecutive repeat units and the conformational flexibility of individual repeat units. Atomistic molecular dynamics (MD) simulations are used here to study double spectrin repeat units (DSRUs) from the human erythrocyte beta-spectrin (HEbeta89) and the chicken brain alpha-spectrin (CBalpha1617). From the results of MD simulations, a highly conserved Trp residue in the A-helix of most repeat units that has been suggested to be important in conferring stability to the coiled-coil structures is found not to have a significant effect on the conformational flexibility of individual repeat units. Characterization of the bending flexibility for two consecutive repeats of spectrin via atomistic simulations and coarse-grained (CG) modeling indicate that the bending flexibility is governed by the interactions between the AB-loop of the first repeat unit, the BC-loop of the second repeat unit and the linker region. Specifically, interactions between residues in these regions can lead to a strong directionality in the bending behavior of two repeat units. The biological implications of these finding are discussed.

}, keywords = {Amino Acid Sequence Humans Models, Amino Acid Spectrin/*chemistry, Molecular Protein Conformation *Repetitive Sequences}, doi = {10.1016/j.jmb.2006.10.003}, author = {D. T. Mirijanian and Chu, J. W. and Ayton, G. S. and G. A. Voth} } @article {422, title = {Charge Delocalization in Proton Channels, I: the Aquaporin Channels and Proton Blockage}, journal = {Biophys J}, volume = {92}, number = {1}, year = {2007}, note = {Chen, Hanning Ilan, Boaz Wu, Yujie Zhu, Fangqiang Schulten, Klaus Voth, Gregory A 2 P41 RR05969/RR/NCRR NIH HHS/United States R01 GM067887/GM/NIGMS NIH HHS/United States R01-GM53148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2007 Jan 1;92(1):46-60. Epub 2006 Oct 20.}, pages = {46-60}, abstract = {

The explicit contribution to the free energy barrier and proton conductance from the delocalized nature of the excess proton is examined in aquaporin channels using an accurate all-atom molecular dynamics computer simulation model. In particular, the channel permeation free energy profiles are calculated and compared for both a delocalized (fully Grotthuss shuttling) proton and a classical (nonshuttling) hydronium ion along two aquaporin channels, Aqp1 and GlpF. To elucidate the effects of the bipolar field thought to arise from two alpha-helical macrodipoles on proton blockage, free energy profiles were also calculated for computational mutants of the two channels where the bipolar field was eliminated by artificially discharging the backbone atoms. Comparison of the free energy profiles between the proton and hydronium cases indicates that the magnitude of the free energy barrier and position of the barrier peak for the fully delocalized and shuttling proton are somewhat different from the case of the (localized) classical hydronium. The proton conductance through the two aquaporin channels is also estimated using Poisson-Nernst-Planck theory for both the Grotthuss shuttling excess proton and the classical hydronium cation.

}, keywords = {Aquaporin 1/*chemistry Aquaporins/*chemistry Biological Transport Biophysics/*methods Escherichia coli Proteins/*chemistry Ions Models, Chemical Models, Molecular Models, Secondary Protons Thermodynamics, Statistical Mutation Oxygen/chemistry Protein Structure}, doi = {10.1529/biophysj.106.091934}, author = {Chen, H. and B. Ilan and Y. Wu and Zhu, F. and K. Schulten and G. A. Voth} } @article {705, title = {Charge Delocalization in Proton Channels, II: The Synthetic LS2 Channel and Proton Selectivity}, journal = {Biophys J}, volume = {92}, number = {1}, year = {2007}, note = {Wu, Yujie Ilan, Boaz Voth, Gregory A R01-GM53148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2007 Jan 1;92(1):61-9. Epub 2006 Oct 20.}, pages = {61-9}, abstract = {

In this study, the minimalist synthetic LS2 channel is used as a prototype to examine the selectivity of protons over other cations. The free-energy profiles along the transport pathway of LS2 are calculated for three cation species: a realistic delocalized proton (including Grotthuss shuttling){\textendash}H(+), a classical (nonshuttling) hydronium{\textendash}H(3)O(+), and a potassium cation{\textendash}K(+). The overall barrier for K(+) is approximately twice as large as that for H(+), explaining the \>100 times larger maximal ion conductance for the latter, in qualitative agreement with the experimental result. The profile for the classical hydronium is quantitatively intermediate between those of H(+) and K(+) and qualitatively more similar to that of H(+), for which the locations of the peaks are well correlated with the troughs of the pore radius profile. There is a strong correlation between the free-energy profiles and the very different characteristic hydration structures of the three cation species. This work suggests that the passage of various cations through ion channels cannot always be explained by simple electrostatic desolvation considerations.

}, keywords = {Biophysics/*methods Cations Electric Conductivity Electrons Hydrogen/chemistry Ion Channel Gating Ion Channels/*chemistry Models, Molecular Molecular Conformation Potassium/chemistry Protein Conformation Protons Reproducibility of Results Thermodynamics Water/chemistry}, doi = {10.1529/biophysj.106.091942}, author = {Y. Wu and B. Ilan and G. A. Voth} } @article {433, title = {Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model}, journal = {Biophys. J.}, volume = {93}, year = {2007}, pages = {3860-3871}, doi = {10.1529/biophysj.107.112060}, author = {Chu, J. W. and G. A. Voth} } @article {728, title = {Coarse-Grained Peptide Modeling Using a Systematic Multiscale Approach}, journal = {Biophys J}, volume = {92}, number = {12}, year = {2007}, note = {Zhou, Jian Thorpe, Ian F Izvekov, Sergey Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2007 Jun 15;92(12):4289-303. Epub 2007 Mar 30.}, pages = {4289-303}, abstract = {

A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically detailed simulations to derive CG forces and associated effective potentials. In this work, the MS-CG methodology is extended to study two peptides representing distinct structural motifs, alpha-helical polyalanine and the beta-hairpin V(5)PGV(5). These studies represent the first known application of this approach to peptide systems. Good agreement between the MS-CG and atomistic models is achieved for several structural properties including radial distribution functions, root mean-square deviation, and radius of gyration. The new MS-CG models are able to preserve the native states of these peptides within approximately 1 A backbone root mean-square deviation during CG simulations. The MS-CG approach, as with most coarse-grained models, has the potential to increase the length and timescales accessible to molecular simulations. However, it is also able to maintain a clear connection to the underlying atomistic-scale interactions.

}, keywords = {*Algorithms Computer Simulation *Models, Chemical *Models, Molecular Peptides/*chemistry Protein Conformation}, doi = {10.1529/biophysj.106.094425}, author = {Zhou, J. and Thorpe, I. F. and Izvekov, S. and G. A. Voth} } @article {618, title = {Effect of Membrane Environment on Proton Permeation through Gramicidin A Channels}, journal = {J. Phys. Chem. B}, volume = {111}, year = {2007}, pages = {9931-9939}, doi = {10.1021/jp0708998}, author = {Qin, Z. and H. L. Tepper and G. A. Voth} } @article {429, title = {Emerging Methods for Multiscale Simulation of Biomolecular Systems}, journal = {Mol. Phys.}, volume = {105}, year = {2007}, pages = {167-175}, doi = {10.1080/00268970701256696}, author = {Chu, J. W. and Izvekov, S. and Ayton, G. S. and G. A. Voth} } @article {598, title = {Extending the Fluctuation Theorem to Describe Reaction Coordinates}, journal = {J Chem Phys}, volume = {126}, number = {5}, year = {2007}, note = {Paramore, Sterling Ayton, Gary S Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2007 Feb 7;126(5):051102.}, pages = {051102}, abstract = {

The fluctuation theorem describes the distribution of work done on small systems which have been pushed out of equilibrium in response to an external field. The theorem has recently been a subject of much interest for describing single-molecule experiments and simulations. In this communication, it is shown how the fluctuation theorem can be extended to describe fluctuations not only in the work done on a system, but also in a reaction coordinate. The extension explored in this work allows for a generalized derivation of Hummer and Szabo{\textquoteright}s expression (G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. 98, 3658 (2001)) for reconstructing the potential of mean force from nonequilibrium trajectories. The derivation demonstrates how implementation of this expression can be more easily facilitated. Atomistic simulations of a biomolecular system are presented which support these results.

}, keywords = {*Algorithms *Computational Biology *Computer Simulation Diffusion *Energy Transfer Models, Molecular Statistical Distributions Thermodynamics}, doi = {10.1063/1.2463306}, author = {S. Paramore and Ayton, G. S. and G. A. Voth} } @article {366, title = {Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation}, journal = {Biophys J}, volume = {92}, number = {10}, year = {2007}, note = {Ayton, Gary S Blood, Philip D Voth, Gregory A 5 R01 GM063796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States Biophysical journal Biophys J. 2007 May 15;92(10):3595-602. Epub 2007 Feb 26.}, pages = {3595-602}, abstract = {

Liposome remodeling processes (e.g., vesiculation and tubulation) due to N-BAR domain interactions with the lipid bilayer are explored with a multi-scale simulation approach. Results from atomistic-level molecular dynamics simulations of membrane binding to the concave face of N-BAR domains are used along with discretized mesoscopic field-theoretic simulations to examine how the spontaneous curvature fields generated by N-BAR domains result in membrane remodeling. It is found that tubulation can be generated by anisotropic N-BAR spontaneous curvature fields, whereas vesiculation is only observed with isotropic N-BAR spontaneous curvature fields at high density. The results of the multi-scale simulations provide insight into recent experimental observations.

}, keywords = {Binding Sites Computer Simulation Lipid Bilayers/*chemistry Liposomes/*chemistry *Membrane Fluidity *Models, Chemical *Models, Molecular Molecular Conformation Nerve Tissue Proteins/*chemistry/*ultrastructure Protein Binding Protein Structure, Tertiary}, doi = {10.1529/biophysj.106.101709}, author = {Ayton, G. S. and Blood, P. D. and G. A. Voth} } @article {501, title = {Molecular Dynamics Simulation of Nanostructural Organization in Ionic Liquid/Water Mixtures}, journal = {J Phys Chem B}, volume = {111}, number = {18}, year = {2007}, note = {Jiang, Wei Wang, Yanting Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2007 May 10;111(18):4812-8. Epub 2007 Feb 27.}, pages = {4812-8}, abstract = {

Molecular dynamics simulations have been carried out to investigate nanostructural organization in mixtures of 1-octyl-3-methylimidazolium nitrate ionic liquid and water at multiple water concentrations. Evolution of the polar network, water network, and micelle structures is visualized and analyzed via partial radial distribution functions. The calculated static partial structure factors show that within the range of water contents examined, polar networks, water networks, and micelles possess an approximately invariant characteristic length at around 20 A. Furthermore, the above calculations point out that, as the amount of water increases, the polar network is continuously broken up (screened) by the intruding water, while the structural organization of the water network and the micelle exhibits a turnover. At the turnover point, the most ordered micelle (cation-cation) structure and water (water-anion-water) network are formed. Thereafter, the structural organization abates drastically, and only loose micelle structure exists due to the dominant water-water interactions. The simulated turnover of structural organization agrees with the sharpest peak in the experimentally obtained structure factor in aqueous solutions of similar ionic liquids; the simulated water structure reveals that water can form liquidlike associated aggregates due to the planar symmetry and strong basicity of NO(3)-, in agreement with experiment. The turnover of structural organization of micelles results from the persistent competition between the hydrophobic interactions of the nonpolar groups and the breakup of the charged polar network with increasing water content, whereas the turnover of the water network results from the competition between the water-water and water-anion interactions.

}, keywords = {*Computer Simulation Imidazoles/*chemistry Ionic Liquids/*chemistry Micelles *Models, Chemical Models, Molecular Molecular Structure Nanostructures/*chemistry Water/chemistry}, doi = {10.1021/jp067142l}, author = {Jiang, W. and Wang, Y. and G. A. Voth} } @article {584, title = {Multiscale Coarse-graining and Structural Correlations: Connections to Liquid State Theory}, journal = {J Phys Chem B}, volume = {111}, number = {16}, year = {2007}, note = {Noid, W G Chu, Jhih-Wei Ayton, Gary S Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States 5F32GM076839-02/GM/NIGMS NIH HHS/United States F32 GM076839-02/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2007 Apr 26;111(16):4116-27. Epub 2007 Mar 30.}, pages = {4116-27}, abstract = {

A statistical mechanical framework elucidates the significance of structural correlations between coarse-grained (CG) sites in the multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105). If no approximations are made, then the MS-CG method yields a many-body multidimensional potential of mean force describing the interactions between CG sites. However, numerical applications of the MS-CG method typically employ a set of pair potentials to describe nonbonded interactions. The analogy between coarse-graining and the inverse problem of liquid-state theory clarifies the general significance of three-particle correlations for the development of such CG pair potentials. It is demonstrated that the MS-CG methodology incorporates critical three-body correlation effects and that, for isotropic homogeneous systems evolving under a central pair potential, the MS-CG equations are a discretized representation of the well-known Yvon-Born-Green equation. Numerical calculations validate the theory and illustrate the role of these structural correlations in the MS-CG method.

}, keywords = {*Models, Theoretical}, doi = {10.1021/jp068549t}, author = {Noid, W. G. and Chu, J. W. and Ayton, G. S. and G. A. Voth} } @article {543, title = {Multiscale Coarse-Graining of Monosaccharides}, journal = {J. Phys. Chem. B}, volume = {111}, year = {2007}, pages = {11566-11575}, doi = {10.1021/jp0721494}, author = {Liu, P. and Izvekov, S. and G. A. Voth} } @article {373, title = {Multiscale Modeling of Biomolecular Systems: in Serial and in Parallel}, journal = {Curr Opin Struct Biol}, volume = {17}, number = {2}, year = {2007}, note = {Ayton, Gary S Noid, Will G Voth, Gregory A 5 F32 GM076839-02/GM/NIGMS NIH HHS/United States GM063796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Review England Current opinion in structural biology Curr Opin Struct Biol. 2007 Apr;17(2):192-8. Epub 2007 Mar 23.}, pages = {192-8}, abstract = {

Considerable progress has been recently achieved in the multiscale modeling of complex biological processes. Multiscale models have now investigated the structure and dynamics of lipid membranes, proteins, peptides and DNA over length and time scales ranging from the atomic to the macroscopic. Serial multiscale methods that parameterize low-resolution coarse-grained models with data from high-resolution models have studied long time or length scale phenomena that cannot be investigated with atomically detailed models. Parallel multiscale methods that directly couple high- and low-resolution models have efficiently explored slow structural transitions and the importance of long-wavelength fluctuations for biological molecules. The success of such models relies upon new theories and methods for constructing accurate multiscale bridges that transfer information between models with different resolutions.

}, keywords = {Computer Simulation DNA/chemistry Membrane Lipids/chemistry *Models, Molecular Peptides/chemistry Proteins/chemistry *Systems Biology}, doi = {10.1016/j.sbi.2007.03.004}, author = {Ayton, G. S. and Noid, W. G. and G. A. Voth} } @article {377, title = {Multiscale Simulation of Transmembrane Proteins}, journal = {J Struct Biol}, volume = {157}, number = {3}, year = {2007}, note = {Ayton, Gary S Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t United States Journal of structural biology J Struct Biol. 2007 Mar;157(3):570-8. Epub 2006 Oct 27.}, pages = {570-8}, abstract = {

Multiscale simulation is employed to examine changes in atomistic-level protein structure due to long wavelength membrane undulations and plane stress fields. An ensemble of atomistic-level simulations of a model of a transmembrane influenza A virus M2 proton channel in a dimyristoylphosphatidylcholine (DMPC) bilayer is coupled to a corresponding mesoscopic model of a DMPC bilayer in an explicit mesoscopic solvent. Structural variations in the key proton gating His37 residues of the M2 channel are examined. Small, but distinct variations in the structure of the His37 residues are observed in both the open and closed states of the channel as a result of the coupling to mesoscopic-level membrane motions.

}, keywords = {Dimyristoylphosphatidylcholine/chemistry Histidine/chemistry Lipid Bilayers/chemistry Membrane Proteins/*chemistry Protein Conformation Solvents/chemistry Viral Matrix Proteins/*chemistry}, doi = {10.1016/j.jsb.2006.10.020}, author = {Ayton, G. S. and G. A. Voth} } @article {571, title = {Preferred Orientations of His-64 in Human Carbonic Anhydrase II}, journal = {Biochemistry}, volume = {46}, number = {11}, year = {2007}, note = {Maupin, C Mark Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States GM53148/GM/NIGMS NIH HHS/United States R01 GM053148-13/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States Biochemistry Biochemistry. 2007 Mar 20;46(11):2938-47. Epub 2007 Feb 24.}, pages = {2938-47}, abstract = {

Histidine at position 64 (His64) in human carbonic anhydrase II (HCA II) is believed to be the proton acceptor in the hydration direction and the proton donor in the dehydration direction for the rate-limiting proton transfer (PT) event. Although the biochemical effect of histidine at position 64 has been thoroughly investigated, the role of its orientation in the PT event is a topic of considerable debate. X-ray data of HCA II suggests that His64 can adopt either an "in" or "out" orientation. The "in" orientation is believed to be favored for the hydration direction PT event because the Ndelta of His64 is closer to the catalytic zinc. This orientation allows for smaller water bridges, which are postulated to be more conducive to PT. In the present work, classical molecular dynamics simulations have been conducted to elucidate the role that the His64 orientation may play in its ability to act as a proton donor/acceptor in HCA II. The free energy profile for the orientation of His64 suggests that the histidine will adopt an "in" orientation in the hydration direction, which brings Ndelta in close proximity to the catalytic zinc. When the histidine becomes protonated, it then rotates to an "out" orientation, creating a more favorable solvation environment for the protonated His64. In this "out" orientation, the imidazole ring releases the delta nitrogen{\textquoteright}s excess proton into the bulk environment. After the second PT event and when the zinc-bound water is regenerated, the His64 is again favored to reorient to the "in" orientation, completing the catalytic cycle.

}, keywords = {Amino Acid Sequence Binding Sites Carbonic Anhydrase II/*chemistry Computational Biology Computer Simulation Histidine/*chemistry Humans Models, Molecular *Molecular Conformation Thermodynamics}, doi = {10.1021/bi062170f}, author = {Maupin, C. M. and G. A. Voth} } @article {659, title = {Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations}, journal = {J Phys Chem B}, volume = {111}, number = {17}, year = {2007}, note = {Swanson, Jessica M J Maupin, C Mark Chen, Hanning Petersen, Matt K Xu, Jiancong Wu, Yujie Voth, Gregory A R01 GM053148-12/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Review United States The journal of physical chemistry. B J Phys Chem B. 2007 May 3;111(17):4300-14. Epub 2007 Apr 13.}, pages = {4300-14}, abstract = {

The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article, various efforts to address this problem through computer modeling and simulation will be described. Applications of computer simulations to a number of important and interesting systems will be presented, highlighting the roles of charge delocalization and Grotthuss shuttling, a phenomenon unique in many ways to the excess proton in water.

}, keywords = {Biological Transport *Computer Simulation *Protons Solubility Solvents/*chemistry Water/chemistry}, doi = {10.1021/jp070104x}, author = {Swanson, J. M. and Maupin, C. M. and Chen, H. and Petersen, M. K. and Xu, J. and Y. Wu and G. A. Voth} } @article {426, title = {Proton Transport Behavior Through the Influenza A M2 Channel: Insights from Molecular Simulation}, journal = {Biophys. J.}, volume = {93}, year = {2007}, pages = {3470-3479}, doi = {10.1529/biophysj.107.105742}, author = {Chen, H. and Y. Wu and G. A. Voth} } @article {587, title = {Quantum Effects in Liquid Water from an Ab Initio-Based Polarizable Force Field}, journal = {J. Chem. Phys.}, volume = {127}, year = {2007}, pages = {074506}, doi = {10.1063/1.2759484}, author = {Paesani, F. and Iuchi, S. and G. A. Voth} } @article {545, title = {Smart Resolution Replica Exchange: an Efficient Algorithm for Exploring Complex Energy Landscapes}, journal = {J Chem Phys}, volume = {126}, number = {4}, year = {2007}, note = {Liu, Pu Voth, Gregory A GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2007 Jan 28;126(4):045106.}, pages = {045106}, abstract = {

A coarse-grained representation of a condensed phase system can significantly reduce the number of system degrees of freedom, making coarse-grained simulations very computationally efficient. Moreover, coarse graining can smoothen the free energy landscape of the system. Thus coarse-grained dynamics is usually faster than its fully atomistic counterpart. In this work, the smart resolution replica exchange method is introduced that incorporates the information from coarse-grained simulations into atomistic simulations in order to accelerate the sampling of rough, complex atomistic energy landscapes. Within this methodology, interactions between particles are defined by a potential energy that interpolates between a fully atomistic potential and a fully coarse-grained effective potential according to a parameter lambda. Instead of exchanging the configurations from neighboring resolutions directly, as has been done in the resolution replica exchange methods [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006); M. Christen and W. F. v. Gunsteren, J. Chem. Phys. 124, 154106 (2006)], the configuration described at the coarser resolution is first relaxed before an exchange is attempted, similar to the smart walking method [R. Zhou and B. J. Berne, J. Chem. Phys. 107, 9185 (1997)]. This approach greatly increases the acceptance ratio of exchange and only two replicas, one at the atomistic level and one at the coarse-grained level, are usually required (although more can be implemented if desired). This new method can approximately obtain the correct canonical sampling if the exchange interval is sufficiently large to allow the system to explore the local energy landscape. The method is demonstrated for a two-dimensional model system, where the ideal population distribution can be recovered, and also for an alanine polypeptide (Ala(15)) model with explicit water, where its native structure, an alpha helix, is obtained from the extended structure within 1 ns.

}, keywords = {*Algorithms Biopolymers/*chemistry Computer Simulation *Energy Transfer *Models, Chemical *Models, Molecular}, doi = {10.1063/1.2408415}, author = {Liu, P. and G. A. Voth} } @inbook {743, title = {Spatial Heterogeneity in Ionic Liquids}, booktitle = {Ionic Liquids IV. Not Just Solvents Anymore}, year = {2007}, pages = {272-307}, publisher = {American Chemical Society}, organization = {American Chemical Society}, address = {Washington DC}, doi = {10.1021/bk-2007-0975.ch020}, author = {Wang, Y. and Jiang, W. and G. A. Voth}, editor = {Brennecke, J. F. and Rogers, R. D. and Seddon, K. R.} } @article {712, title = {Storage of an Excess Proton in the Hydrogen-bonded Network of the D-pathway of Cytochrome c Oxidase: Identification of a Protonated Water Cluster}, journal = {J Am Chem Soc}, volume = {129}, number = {10}, year = {2007}, note = {Xu, Jiancong Sharpe, Martyn A Qin, Ling Ferguson-Miller, Shelagh Voth, Gregory A GM053148/GM/NIGMS NIH HHS/United States GM26916/GM/NIGMS NIH HHS/United States R01 GM053148-05/GM/NIGMS NIH HHS/United States R01 GM053148-13/GM/NIGMS NIH HHS/United States R37 GM026916-29/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States Journal of the American Chemical Society J Am Chem Soc. 2007 Mar 14;129(10):2910-3. Epub 2007 Feb 20.}, pages = {2910-3}, abstract = {

The mechanism of proton transport in the D-pathway of cytochrome c oxidase (CcO) is further elucidated through examining a protonated water/hydroxyl cluster inside the channel. The second generation multi-state empirical valence bond (MS-EVB2) model was employed in a molecular dynamics study based on a high-resolution X-ray structure to simulate the interaction of the excess proton with the channel environment. Our results indicate that a hydrogen-bonded network consisting of about 5 water molecules surrounded by three side chains and two backbone groups (S197, S200, S201, F108) is involved in storage and translocation of an excess proton to the extracellular side of CcO.

}, keywords = {Computer Simulation Electron Transport Complex IV/*chemistry/metabolism Hydrogen Bonding Models, Molecular Molecular Structure *Protons Rhodobacter sphaeroides/enzymology Water/*chemistry}, doi = {10.1021/ja067360s}, url = { }, author = {Xu, J. and Sharpe, M. A. and Qin, L. and Ferguson-Miller, S. and G. A. Voth} } @article {372, title = {Systematic Coarse-graining of Biomolecular and Soft Matter Systems}, journal = {MRS Bulletin}, volume = {32}, year = {2007}, pages = {929-934}, doi = {10.1557/mrs2007.190}, author = {Ayton, G. S. and Noid, W. G. and G. A. Voth} } @article {597, title = {Transient Violations of the Second Law of Thermodynamics in Protein Unfolding Examined using Synthetic Atomic Force Microscopy and the Fluctuation Theorem}, journal = {J. Chem. Phys.}, volume = {127}, year = {2007}, pages = {105105}, doi = {10.1063/1.2764487}, author = {S. Paramore and Ayton, G. S. and G. A. Voth} } @article {698, title = {Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations}, journal = {Acc Chem Res}, volume = {40}, number = {11}, year = {2007}, note = {Wang, Yanting Jiang, Wei Yan, Tianying Voth, Gregory A Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Review United States Accounts of chemical research Acc Chem Res. 2007 Nov;40(11):1193-9. Epub 2007 Oct 13.}, pages = {1193-9}, abstract = {

Understanding the physical properties of ionic liquids (ILs) via computer simulation is important for their potential technological applications. The goal of our IL research is to obtain a unified understanding of the properties of ILs with respect to their underlying molecular structure. From atomistic molecular dynamics simulations, the many-body electronic polarization effect was found to be important for modeling ILs, especially their dynamics. The multiscale coarse-graining methodology has also been employed to increase the simulation speed by a factor of 100 or more, thereby making it possible to study the mesoscopic behavior of ILs by computer simulations. With these simulation techniques, ILs with an amphiphilic cation were found to exhibit a spatial heterogeneity due to the aggregation of their nonpolar alkyl tails. This spatial heterogeneity is a key feature in interpreting many physical phenomena of ILs, such as their heterogeneous self-diffusion and surface layering, as well as their surfactant-like micelles formed in IL/water mixtures.

}, keywords = {Chemical Models, Chemistry, Molecular Physicochemical Phenomena Surface Properties, Physical *Computer Simulation Ionic Liquids/*chemistry *Models}, doi = {10.1021/ar700160p}, author = {Wang, Y. and Jiang, W. and T. Yan and G. A. Voth} } @article {593, title = {An Accurate and Simple Quantum Model for Liquid Water}, journal = {J Chem Phys}, volume = {125}, number = {18}, year = {2006}, note = {Paesani, Francesco Zhang, Wei Case, David A Cheatham, Thomas E 3rd Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2006 Nov 14;125(18):184507.}, pages = {184507}, abstract = {

The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. The nuclear quantization also leads to a smaller dielectric constant and a larger diffusion coefficient relative to the corresponding classical values. Collective and single molecule time correlation functions show a faster decay than their classical counterparts. Good agreement with the experimental measurements in the low-frequency region is obtained for the quantum infrared spectrum, which also shows a higher intensity and a redshift relative to its classical analog. A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. The quantum results for several thermodynamic and dynamical properties computed with the new model are shown to be in a significantly better agreement with the experimental data. Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Thermodynamic and dynamical properties computed using standard classical simulations with this effective quantum potential are found in excellent agreement with those obtained from significantly more computationally demanding full centroid molecular dynamics simulations. The present results suggest that the inclusion of nuclear quantum effects into an empirical model for water enhances the ability of such model to faithfully represent experimental data, presumably through an increased ability of the model itself to capture realistic physical effects.

}, keywords = {Chemical *Quantum Theory Water/*chemistry, Computer Simulation *Models}, doi = {10.1063/1.2386157}, author = {Paesani, F. and Zhang, W. and Case, D. A. and Cheatham, T. E., 3rd and G. A. Voth} } @article {610, title = {Amphiphilic Character of the Hydrated Proton in Methanol-Water Solutions}, journal = {J Phys Chem B}, volume = {110}, number = {14}, year = {2006}, note = {Petersen, Matt K Voth, Gregory A Letter Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2006 Apr 13;110(14):7085-9.}, pages = {7085-9}, abstract = {

The hydrated proton was studied in methanol-water solutions of varying methanol concentrations using the multistate empirical valence bond simulation method. Amphiphile-like behavior of the hydrated proton was noted from its anisotropic association with the methanol methyl groups. Molecular length immiscibility was also characterized through the enumeration of water and protonated water clusters. Excess proton diffusion was calculated across the varying methanol concentrations and found to be in good agreement with experiment after correcting for nuclear quantum effects.

}, keywords = {Anisotropy Computer Simulation Diffusion Methanol/*chemistry Models, Molecular Protons Quantum Theory Water/*chemistry}, doi = {10.1021/jp060698o}, author = {Petersen, M. K. and G. A. Voth} } @article {609, title = {Characterization of the Solvation and Transport of the Hydrated Proton in the Perfluorosulfonic Acid Membrane Nafion}, journal = {J Phys Chem B}, volume = {110}, number = {37}, year = {2006}, note = {Petersen, Matt K Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2006 Sep 21;110(37):18594-600.}, pages = {18594-600}, abstract = {

The solvation and transport properties of the sulfonate-hydronium ion pair have been studied in hydrated Nafion through molecular dynamics simulation. Explicit proton and charge delocalization of the excess proton transport, via the Grotthuss hopping mechanism, were treated using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. The nature of the sulfonate-hydronium ion pair was characterized through analysis of free-energy profiles. It was found that, in general, the excess proton is solvated between two water molecules of a Zundel moiety while in the contact ion pair position, but then it transitions to an Eigen-like configuration in the solvent-separated pair position. Furthermore, the positive charge associated with the excess proton passes between the contact and solvent-separated ion pair positions through the Grotthuss mechanism rather than simple vehicular diffusion. The total proton diffusion was decomposed into vehicular and Grotthuss components and were found to be of the same relative magnitude, but with a strong negative correlation resulting in a smaller overall diffusion. Correlated motions between the ion pair were examined through the distinct portion of the van Hove correlation function, and a characteristic time scale of approximately 425 ps was observed. Additionally, the association of the hydrated proton with the hydrophobic polymer backbone suggests its amphiphile-like behavior (see Acc. Chem. Res. 2006, 39, 143; Phys. Rev. 1954, 95, 249; J. Chem. Phys. 2005, 123, 084309).

}, keywords = {Artificial Models, Chemistry, Molecular Molecular Conformation Oxygen/chemistry Protein Structure, Physical/*methods Diffusion Fluorocarbon Polymers/*chemistry Hydrogen/*chemistry Ions Membranes, Tertiary *Protons Solvents/chemistry Thermodynamics Time Factors}, doi = {10.1021/jp062719k}, author = {Petersen, M. K. and G. A. Voth} } @article {432, title = {Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations}, journal = {Biophys J}, volume = {90}, number = {5}, year = {2006}, note = {Chu, Jhih-Wei Voth, Gregory A 1 S10RR17214-01/RR/NCRR NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2006 Mar 1;90(5):1572-82. Epub 2005 Dec 16.}, pages = {1572-82}, abstract = {

A coarse-grained (CG) procedure that incorporates the information obtained from all-atom molecular dynamics (MD) simulations is presented and applied to actin filaments (F-actin). This procedure matches the averaged values and fluctuations of the effective internal coordinates that are used to define a CG model to the values extracted from atomistic MD simulations. The fluctuations of effective internal coordinates in a CG model are computed via normal-mode analysis (NMA), and the computed fluctuations are matched with the atomistic MD results in a self-consistent manner. Each actin monomer (G-actin) is coarse-grained into four sites, and each site corresponds to one of the subdomains of G-actin. The potential energy of a CG G-actin contains three bonds, two angles, and one dihedral angle; effective harmonic bonds are used to describe the intermonomer interactions in a CG F-actin. The persistence length of a CG F-actin was found to be sensitive to the cut-off distance of assigning intermonomer bonds. Effective harmonic bonds for a monomer with its third nearest neighboring monomers are found to be necessary to reproduce the values of persistence length obtained from all-atom MD simulations. Compared to the elastic network model, incorporating the information of internal coordinate fluctuations enhances the accuracy and robustness for a CG model to describe the shapes of low-frequency vibrational modes. Combining the fluctuation-matching CG procedure and NMA, the achievable time- and length scales of modeling actin filaments can be greatly enhanced. In particular, a method is described to compute the force-extension curve using the CG model developed in this work and NMA. It was found that F-actin is easily buckled under compressive deformation, and a writhing mode is developed as a result. In addition to the bending and twisting modes, this novel writhing mode of F-actin could also play important roles in the interactions of F-actin with actin-binding proteins and in the force-generation process via polymerization.

}, keywords = {Actins/*chemistry/*ultrastructure Binding Sites Computer Simulation Dimerization *Models, Chemical *Models, Molecular Multiprotein Complexes/chemistry/ultrastructure Protein Binding Protein Conformation}, doi = {10.1529/biophysj.105.073924}, author = {Chu, J. W. and G. A. Voth} } @article {464, title = {A Comparative Study of Imaginary Time Path Integral Based Methods for Quantum Dynamics}, journal = {J Chem Phys}, volume = {124}, number = {15}, year = {2006}, note = {Hone, Tyler D Rossky, Peter J Voth, Gregory A Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2006 Apr 21;124(15):154103.}, pages = {154103}, abstract = {

The recently introduced approximate many-body quantum simulation method, ring polymer molecular dynamics (RPMD), is compared to the centroid molecular dynamics method (CMD). Comparisons of simulation results for liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point are presented. The calculated quantum correlation functions for the two methods are shown to be in good agreement with one another for a large portion of the time spectrum. However, as the quantum mechanical nature of the system increases, RPMD is less accurate in predicting the kinetic energy of the system than is CMD. A simplified and highly efficient algorithm is proposed which largely corrects this deficiency.

}, doi = {10.1063/1.2186636}, author = {Hone, T. D. and Rossky, P. J. and G. A. Voth} } @article {684, title = {Computer Simulation of Proton Solvation and Transport in Aqueous and Biomolecular Systems}, journal = {Acc Chem Res}, volume = {39}, number = {2}, year = {2006}, note = {Voth, Gregory A Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Review United States Accounts of chemical research Acc Chem Res. 2006 Feb;39(2):143-50.}, pages = {143-50}, abstract = {

The excess proton in aqueous media is critical to many aspects of chemistry, biology, and materials science. This species is at the heart of the most elementary of chemical (e.g., acid-base) and biological (e.g., bioenergetics) concepts, yet to this day, it remains mysterious, surprising, and often misunderstood. In this Account, our efforts to describe excess proton solvation and transport through computer modeling and simulation will be described. Results will be summarized for several important systems, as obtained from the multistate empirical valence bond (MS-EVB) approach, which allows for the explicit treatment of (Grotthuss) proton shuttling and charge delocalization.

}, keywords = {Biological Transport *Computer Simulation Energy Transfer Hydrophobic and Hydrophilic Interactions Lipid Bilayers/chemistry Models, Chemical Models, Molecular Proton Pumps/*chemistry *Protons Solvents/*chemistry Water/chemistry}, doi = {10.1021/ar0402098}, author = {G. A. Voth} } @article {389, title = {Direct Observation of Bin/amphiphysin/Rvs (BAR) Domain-induced Membrane Curvature by Means of Molecular Dynamics Simulations}, journal = {Proc Natl Acad Sci U S A}, volume = {103}, number = {41}, year = {2006}, note = {Blood, Philip D Voth, Gregory A 1 S10RR17214-01/RR/NCRR NIH HHS/United States GM0637-96/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15068-72. Epub 2006 Sep 28.}, pages = {15068-72}, abstract = {

The process of membrane curvature generation by BAR (Bin/amphiphysin/Rvs) domains is thought to involve the plastering of the negatively charged cell membrane to the positively charged concave surface of the BAR domain. Recent work [Peter, B. J., et al. (2004) Science, 303,495-499; Masuda, M., et al. (2006) EMBO J. 25, 2889-2897; and Gallop, J. L., et al. (2006) EMBO J. 25, 2898-2910] has demonstrated the importance of the charged, crescent-shaped surface and the N-terminal amphipathic helices (present in N-BAR domains) for generating membrane curvature. These experiments suggest that curvature is generated by the synergistic action of the N-terminal helices embedding in the lipid bilayer and the charged crescent-shaped dimer acting to "scaffold" membrane curvature. Here, we present atomistic molecular dynamics simulations that directly show membrane binding to the concave face of N-BAR domains, resulting in the generation of local membrane curvature that matches the curvature presented by the BAR domain. These simulations provide direct molecular-scale evidence that BAR domains create curvature by acting as a scaffold, forcing the membrane to locally adopt the intrinsic shape of the BAR domain. We find that BAR domains bind strongly through the maximum curvature surface and, additionally, at an orientation that presents a lesser degree of curvature, thus enabling N-BAR domains to induce a range of local curvatures. Finally, we find that the N-terminal region may play a role in biasing the orientations of N-BAR domains on the membrane surface to those that favor binding to the concave face and subsequent membrane bending.

}, keywords = {Animals Cell Membrane/*chemistry/physiology *Computer Simulation Crystallography, Biological *Models, Molecular Nerve Tissue Proteins/*chemistry/physiology Protein Structure, Tertiary Static Electricity Thermodynamics Transcription Factors/*chemistry/physiology, X-Ray Cytoskeletal Proteins/*chemistry/physiology Drosophila Proteins/*chemistry/physiology Forkhead Transcription Factors Humans Lipid Bilayers/chemistry *Models}, doi = {10.1073/pnas.0603917103}, author = {Blood, P. D. and G. A. Voth} } @article {522, title = {Evaluation of Nonlinear Quantum Time Correlation Functions within the Centroid Dynamics Formulation}, journal = {J Phys Chem B}, volume = {110}, number = {38}, year = {2006}, note = {Krishna, Vinod Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2006 Sep 28;110(38):18953-7.}, pages = {18953-7}, abstract = {

A method to evaluate nonlinear centroid correlation functions is presented that is amenable to simple numerical computation. It can be implemented with the centroid molecular dynamics method for approximate quantum dynamics with no additional assumptions. Two nonlinear correlation functions are evaluated for a model potential using this scheme and compared with results from exact quantum calculations.

}, keywords = {Models, Molecular Models, Theoretical *Quantum Theory}, doi = {10.1021/jp060073q}, author = {Krishna, V. and G. A. Voth} } @article {599, title = {Examining the Influence of Linkers and Tertiary Structure in the Forced Unfolding of Multiple-Repeat Spectrin Molecules}, journal = {Biophys J}, volume = {91}, number = {9}, year = {2006}, note = {Paramore, Sterling Voth, Gregory A Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2006 Nov 1;91(9):3436-45. Epub 2006 Aug 4.}, pages = {3436-45}, abstract = {

The unfolding pathways of multiple-repeat spectrin molecules were examined using steered molecular dynamics (SMD) simulations to forcibly unfold double- and triple-repeat spectrin molecules. Although SMD has previously been used to study other repeating-domain proteins, spectrin offers a unique challenge in that the linker connecting repeat units has a definite secondary structure, that of an alpha-helix. Therefore, the boundary conditions imposed on a double- or triple-repeat spectrin must be carefully considered if any relationship to the real system is to be deduced. This was accomplished by imposing additional forces on the system which ensure that the terminal alpha-helices behave as if there were no free noncontiguous helical ends. The results of the SMD simulations highlight the importance of the rupture of the alpha-helical linker on the subsequent unfolding events. Rupture of the linker propagates unfolding in the adjacent repeat units by destabilizing the tertiary structure, ultimately resulting in complete unfolding of the affected repeat unit. Two dominant classes of unfolding pathways are observed after the initial rupture of a linker which involve either rupture of another linker (possibly adjacent) or rupture of the basic tertiary structure of a repeat unit. The relationship between the force response observed on simulation timescales and those of experiment or physiological conditions is also discussed.

}, keywords = {Binding Sites Computer Simulation Cross-Linking Reagents/chemistry *Models, Chemical *Models, Mechanical, Molecular Multiprotein Complexes/chemistry/ultrastructure Protein Binding Protein Denaturation Protein Folding Protein Structure, Tertiary Spectrin/*chemistry/*ultrastructure Stress}, doi = {10.1529/biophysj.106.091108}, author = {S. Paramore and G. A. Voth} } @article {595, title = {Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response}, journal = {Biophys J}, volume = {90}, number = {1}, year = {2006}, note = {Paramore, Sterling Ayton, Gary S Mirijanian, Dina T Voth, Gregory A Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2006 Jan 1;90(1):92-100. Epub 2005 Oct 14.}, pages = {92-100}, abstract = {

Nonequilibrium molecular dynamics simulations were used to calculate the elastic properties of a spectrin repeat unit. A contiguous alpha-helical linker was constructed by employing periodic boundary conditions, allowing a novel scheme for evaluating the thermodynamic force as a function of extension. By measuring the force-extension response under small extensions, spectrin was observed to behave primarily as an elastic material with a spring constant of 1700 +/- 100 pN/nm. The implications of this spring constant, in terms of the properties of the spectrin tetramer, are also discussed.

}, keywords = {Algorithms Animals Biophysics/*methods Brain/metabolism Carbon/chemistry Chickens Computer Simulation Cytoskeleton/chemistry Magnetic Resonance Spectroscopy Microscopy, Atomic Force/methods Models, Biological Models, Secondary Software Spectrin/*chemistry/metabolism Thermodynamics Water/chemistry, Statistical Molecular Conformation Protein Conformation Protein Denaturation Protein Folding Protein Structure}, doi = {10.1529/biophysj.105.066969}, author = {S. Paramore and Ayton, G. S. and D. T. Mirijanian and G. A. Voth} } @article {596, title = {Extending a Spectrin Repeat Unit. II: Rupture Behavior}, journal = {Biophys J}, volume = {90}, number = {1}, year = {2006}, note = {Paramore, Sterling Ayton, Gary S Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2006 Jan 1;90(1):101-11. Epub 2005 Oct 14.}, pages = {101-11}, abstract = {

A spectrin repeat unit was subject to extension using cyclic expansion nonequilibrium molecular dynamics. Periodic boundary conditions were used to examine the effects of the contiguous alpha-helical linker on the force response. The measured force-extension curve shows a linear increase in the force response when the spectrin repeat unit is extended by approximately 0.4 nm. After that point, the force response peaks and subsequently declines. The peak in the force response marks the point where the spectrin repeat unit undergoes a change in its material properties from a strongly elastic material to a mostly viscous one, on the timescales of the simulations. The force peak is also correlated with rupture of the alpha-helical linker, and is likely the event responsible for the peaks in the sawtooth-pattern force-extension curves measured by atomic force microscopy experiments. Rupture of the linker involves simultaneously breaking approximately four hydrogen bonds that maintain the alpha-helical linker. After this initial rupture, the linker undergoes simple helix-to-coil transitions as the spectrin repeat unit continues to be extended. The implications of linker rupture in the interpretation of unfolding and atomic force microscopy experiments are also discussed.

}, keywords = {Animals Brain/metabolism Chickens Computer Simulation Hydrogen Bonding Microscopy, Atomic Force Models, Molecular Molecular Conformation Protein Conformation Protein Denaturation Protein Folding Protein Structure, Secondary Protein Structure, Tertiary Software Spectrin/*chemistry Time Factors}, doi = {10.1529/biophysj.105.066977}, author = {S. Paramore and Ayton, G. S. and G. A. Voth} } @article {706, title = {Flexible Simple Point-charge Water Model with Improved Liquid-State Properties}, journal = {J Chem Phys}, volume = {124}, number = {2}, year = {2006}, note = {Wu, Yujie Tepper, Harald L Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2006 Jan 14;124(2):024503.}, pages = {024503}, abstract = {

In order to introduce flexibility into the simple point-charge (SPC) water model, the impact of the intramolecular degrees of freedom on liquid properties was systematically studied in this work as a function of many possible parameter sets. It was found that the diffusion constant is extremely sensitive to the equilibrium bond length and that this effect is mainly due to the strength of intermolecular hydrogen bonds. The static dielectric constant was found to be very sensitive to the equilibrium bond angle via the distribution of intermolecular angles in the liquid: A larger bond angle will increase the angle formed by two molecular dipoles, which is particularly significant for the first solvation shell. This result is in agreement with the work of Hochtl et al. [J. Chem. Phys. 109, 4927 (1998)]. A new flexible simple point-charge water model was derived by optimizing bulk diffusion and dielectric constants to the experimental values via the equilibrium bond length and angle. Due to the large sensitivities, the parametrization only slightly perturbs the molecular geometry of the base SPC model. Extensive comparisons of thermodynamic, structural, and kinetic properties indicate that the new model is much improved over the standard SPC model and its overall performance is comparable to or even better than the extended SPC model.

}, keywords = {Algorithms Chemistry, Physical/*methods Computer Simulation Diffusion Electrochemistry/methods Hydrogen/chemistry Hydrogen Bonding Kinetics Models, Statistical Models, Theoretical Molecular Conformation Oxygen/chemistry Thermodynamics Viscosity Water/*chemistry}, doi = {10.1063/1.2136877}, author = {Y. Wu and H. L. Tepper and G. A. Voth} } @article {714, title = {Free Energy Profiles for H+ Conduction in the D-pathway of Cytochrome c Oxidase: A Study of the Wild Type and N98D Mutant Enzymes}, journal = {Biochim Biophys Acta}, volume = {1757}, number = {7}, year = {2006}, note = {Xu, Jiancong Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States R01 GM053148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Netherlands Biochimica et biophysica acta Biochim Biophys Acta. 2006 Jul;1757(7):852-9. Epub 2006 May 24.}, pages = {852-9}, abstract = {

The molecular mechanism for proton conduction in the D-pathway of Cytochrome c Oxidase (CcO) is investigated through the free energy profile, i.e., potential of mean force (PMF) calculations of both the native enzyme and the N98D mutant. The multistate empirical valence bond (MS-EVB) model was applied to simulate the interaction of an excess proton with the channel environment. In the study of the wild type enzyme, the PMF reveals the previously proposed proton trap inside the channel; it also shows a high free energy barrier against the passage of proton at the entry of the channel, where two conserved asparagines (ASN80/98) may be essential for the gating of proton uptake. We also present data from an investigation of the N98D mutant, which has been previously shown to completely eliminate proton pumping but significantly enhance the oxidase activity in Rhodobacter sphaeroides. These results suggest that mutating Asn98 to negatively charged aspartate will create an unfavorable energy barrier sufficiently high to prevent the overall proton uptake through the D-pathway, whereas with a protonated aspartic acid the proton conduction was found to be accelerated. Plausible explanations for the origin of the uncoupling of proton pumping from the oxidase activity will be discussed.

}, keywords = {Animals Cattle Electron Transport Complex IV/genetics/*metabolism Hydrogen/*metabolism Myocardium/enzymology Point Mutation Thermodynamics}, doi = {10.1016/j.bbabio.2006.05.028}, author = {Xu, J. and G. A. Voth} } @article {662, title = {Mechanisms of Passive Ion Permeation through Lipid Bilayers: Insights from Simulations}, journal = {J Phys Chem B}, volume = {110}, number = {42}, year = {2006}, note = {Tepper, Harald L Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States R01 GM053148/GM/NIGMS NIH HHS/United States R01 GM053148-05/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2006 Oct 26;110(42):21327-37.}, pages = {21327-37}, abstract = {

Multistate empirical valence bond and classical molecular dynamics simulations were used to explore mechanisms for passive ion leakage through a dimyristoyl phosphatidylcholine lipid bilayer. In accordance with a previous study on proton leakage (Biophys. J. 2005, 88, 3095), it was found that the permeation mechanism must be a highly concerted one, in which ion, solvent, and membrane coordinates are coupled. The presence of the ion itself significantly alters the response of those coordinates, suggesting that simulations of transmembrane water structures without explicit inclusion of the ionic solute are insufficient for elucidating transition mechanisms. The properties of H(+), Na(+), OH(-), and bare water molecules in the membrane interior were compared, both by biased sampling techniques and by constructing complete and unbiased transition paths. It was found that the anomalous difference in leakage rates between protons and other cations can be largely explained by charge delocalization effects rather than the usual kinetic picture (Grotthuss hopping of the proton). Permeability differences between anions and cations through phosphatidylcholine bilayers are correlated with suppression of favorable membrane breathing modes by cations.

}, keywords = {Computer Simulation Dimyristoylphosphatidylcholine Ions/*pharmacokinetics Kinetics Lipid Bilayers/*metabolism Permeability Solvents}, doi = {10.1021/jp064192h}, author = {H. L. Tepper and G. A. Voth} } @article {450, title = {Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics}, journal = {Biophys J}, volume = {91}, number = {10}, year = {2006}, note = {Gebremichael, Yeshitila Ayton, Gary S Voth, Gregory A GM053148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States Biophysical journal Biophys J. 2006 Nov 15;91(10):3640-52. Epub 2006 Aug 25.}, pages = {3640-52}, abstract = {

A particle-based hybrid method of elastic network model and smooth-particle hydrodynamics has been employed to describe the propulsion of bacterial flagella in a viscous hydrodynamic environment. The method explicitly models the two aspects of bacterial propulsion that involve flagellar flexibility and long-range hydrodynamic interaction of low-Reynolds-number flow. The model further incorporates the molecular organization of the flagellar filament at a coarse-grained level in terms of the 11 protofilaments. Each of these protofilaments is represented by a collection of material points that represent the flagellin proteins. A computational model of a single flexible helical segment representing the filament of a bacterial flagellum is presented. The propulsive dynamics and the flow fields generated by the motion of the model filament are examined. The nature of flagellar deformation and the influence of hydrodynamics in determining the shape of deformations are examined based on the helical filament.

}, keywords = {*Bacterial Physiological Phenomena Computer Simulation Flagella/*physiology Microfluidics/*methods *Models, Biological Motion}, doi = {10.1529/biophysj.106.091314}, author = {Gebremichael, Y. and Ayton, G. S. and G. A. Voth} } @article {642, title = {Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel}, journal = {J Phys Chem B}, volume = {110}, number = {31}, year = {2006}, note = {Shi, Qiang Izvekov, Sergei Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States R01 GM63796/GM/NIGMS NIH HHS/United States Letter Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2006 Aug 10;110(31):15045-8.}, pages = {15045-8}, abstract = {

The recently developed multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105) is used to build a mixed all-atom and coarse-grained (AA-CG) model of the gramicidin A (gA) ion channel embedded in a dimyristoylphosphatidylcholine (DMPC) lipid bilayer and water environment. In this model, the gA peptide was described in full atomistic detail, while the lipid and water molecules were described using coarse-grained representations. The atom-CG and CG-CG interactions in the mixed AA-CG model were determined using the MS-CG method. Molecular dynamics (MD) simulations were performed using the resulting AA-CG model. The results from simulations of the AA-CG model compare very favorably to those from all-atom MD simulations of the entire system. Since the MS-CG method employs a general and systematic approach to obtain effective interactions from the underlying all-atom models, the present approach to rigorously develop mixed AA-CG models has the potential to be extended to many other systems.

}, keywords = {*Computer Simulation Dimyristoylphosphatidylcholine/chemistry Gramicidin/*chemistry Ion Channels/chemistry Lipid Bilayers/chemistry Models, Molecular Peptides/*chemistry Protein Conformation Quantum Theory Water/chemistry}, doi = {10.1021/jp062700h}, author = {Shi, Q. and Izvekov, S. and G. A. Voth} } @article {484, title = {Modeling Real Dynamics in the Coarse-grained Representation of Condensed Phase Systems}, journal = {J Chem Phys}, volume = {125}, number = {15}, year = {2006}, note = {Izvekov, Sergei Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2006 Oct 21;125(15):151101.}, pages = {151101}, abstract = {

This work presents a systematic multiscale methodology to provide a more faithful representation of real dynamics in coarse-grained molecular simulation models. The theoretical formalism is based on the recently developed multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B. 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] and relies on the generalized Langevin equation approach and its simpler Langevin equation limit. The friction coefficients are determined in multiscale fashion from the underlying all-atom molecular dynamics simulations using force-velocity and velocity-velocity correlation functions for the coarse-grained sites. The diffusion properties in the resulting CG Brownian dynamics simulations are shown to be quite accurate. The time dependence of the velocity autocorrelation function is also well-reproduced relative to the all-atom model if sufficient resolution of the CG sites is implemented.

}, keywords = {*Computer Simulation Diffusion *Models, Chemical *Phase Transition Quantum Theory}, doi = {10.1063/1.2360580}, author = {Izvekov, S. and G. A. Voth} } @article {430, title = {The Multiscale Challenge for Biomolecular Systems: Coarse-grained Modeling}, journal = {Mol. Sim.}, volume = {32}, year = {2006}, pages = {211-218}, doi = {10.1080/08927020600612221}, author = {Chu, J. W. and Izvekov, S. and G. A. Voth} } @article {697, title = {Multiscale Coarse-Graining of Ionic Liquids}, journal = {J Phys Chem B}, volume = {110}, number = {8}, year = {2006}, note = {Wang, Yanting Izvekov, Sergei Yan, Tianying Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2006 Mar 2;110(8):3564-75.}, pages = {3564-75}, abstract = {

A recently developed multiscale coarse-graining (MS-CG) approach for obtaining coarse-grained force fields from fully atomistic molecular dynamics simulation is applied to the challenging case of the EMIM+NO3- ionic liquid. The force-matching in the MS-CG methodology is accomplished with an explicit separation of bonded and nonbonded forces. While the nonbonded forces are adopted from this force-matching approach, the bonded forces are obtained from fitting the statistical configurational data from the atomistic simulations. The many-body electronic polarizability is also successfully broken into effective pair interactions. With a virial constraint fixing the system pressure, the MS-CG models rebuild satisfactory structural and thermodynamic properties for different temperatures. The MS-CG model developed from a modest atomistic simulation is therefore suitable for simulating much larger systems, because the coarse-grained models show significant time integration efficiency. This approach is expected to be general for coarse-graining other ionic liquids, as well as many other liquid-state systems. The limitations of the present coarse-graining procedure are also discussed.

}, keywords = {*Algorithms Ionic Liquids/*chemistry Temperature}, doi = {10.1021/jp0548220}, author = {Wang, Y. and Izvekov, S. and T. Yan and G. A. Voth} } @article {485, title = {Multiscale Coarse-graining of Mixed Phospholipid/Cholesterol Bilayer}, journal = {J. Chem. Theory Comp.}, volume = {2}, year = {2006}, pages = {637-648}, doi = {10.1021/ct050300c}, author = {Izvekov, S. and G. A. Voth} } @article {572, title = {A Multistate Empirical Valence Bond Description of Protonatable Amino Acids}, journal = {J Phys Chem A}, volume = {110}, number = {2}, year = {2006}, note = {Maupin, C Mark Wong, Kim F Soudackov, Alexander V Kim, Sun Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States 2R01GM53148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States The journal of physical chemistry. A J Phys Chem A. 2006 Jan 19;110(2):631-9.}, pages = {631-9}, abstract = {

The multistate empirical valence bond (MS-EVB) model, which was developed for molecular dynamics simulations of proton transport in water and biomolecular systems, is extended for the modeling of protonatable amino acid residues in aqueous environments, specifically histidine and glutamic acid. The parameters of the MS-EVB force field are first determined to reproduce the geometries and energetics of the gas phase amino acid-water clusters. These parameters are then optimized to reproduce experimental pK(a) values. The free energy profiles for acid ionization and the corresponding pK(a) values are calculated by MS-EVB molecular dynamics simulations utilizing the umbrella sampling technique, with the center of excess charge coordinate chosen as the dissociation reaction coordinate. A general procedure for fitting the MS-EVB parameters is formulated, which allows for the parametrization of other amino acid residues with protonatable groups and the subsequent use of the MS-EVB approach for molecular dynamics simulations of proton transfer processes in proteins involving protonation/deprotonation of the protonatable amino acid groups.

}, keywords = {Amino Acids/*chemistry Electrons *Models, Molecular Proteins/chemistry *Protons}, doi = {10.1021/jp053596r}, author = {Maupin, C. M. and Wong, K. F. and Soudackov, A. V. and Kim, S. and G. A. Voth} } @article {425, title = {Origins of Proton Transport Behavior from Selectivity Domain Mutations of the Aquaporin-1 Channel}, journal = {Biophys J}, volume = {90}, number = {10}, year = {2006}, note = {Chen, Hanning Wu, Yujie Voth, Gregory A R01-GM53148/GM/NIGMS NIH HHS/United States Letter Research Support, N.I.H., Extramural United States Biophysical journal Biophys J. 2006 May 15;90(10):L73-5. Epub 2006 Mar 31.}, pages = {L73-5}, abstract = {

The permeation free-energy profile and maximum ion conductance of proton transport along the channel of three aquaporin-1 (AQP1) mutants (H180A/R195V, H180A, and R195V) are calculated via molecular dynamics simulations and Poisson-Nernst-Planck theory. The proton dynamics was described by the multistate empirical valence bond (MS-EVB) model. The results reveal three major contributions to the overall free-energy barrier for proton transport in AQP1: 1), the bipolar field, 2), the electrostatic repulsion due to the Arg-195 residue, and 3), the dehydration penalty due to the narrow channel pore. The double mutation (H180A/R195V) drastically drops the overall free-energy barrier by roughly 20 kcal/mol via simultaneously relaxing the direct electrostatic interaction (by R195V) and dehydration effect (by H180A).

}, keywords = {Amino Acid Substitution Aquaporin 1/*chemistry/genetics Cell Membrane/*chemistry Computer Simulation *Ion Channel Gating *Models, Chemical *Models, Molecular Mutagenesis, Site-Directed Porosity Protein Conformation Protein Structure, Tertiary *Protons Structure-Activity Relationship}, doi = {10.1529/biophysj.106.084061}, author = {Chen, H. and Y. Wu and G. A. Voth} } @article {395, title = {The Properties of Ion-water Clusters. II. Solvation Structures of Na+, Cl-, and H+ Clusters as a Function of Temperature}, journal = {J Chem Phys}, volume = {124}, number = {2}, year = {2006}, note = {Burnham, Christian J Petersen, Matt K Day, Tyler J F Iyengar, Srinivasan S Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2006 Jan 14;124(2):024327.}, pages = {024327}, abstract = {

Ion-water-cluster properties are investigated both through the multistate empirical valence bond potential and a polarizable model. Equilibrium properties of the ion-water clusters H+(H2O)100, Na+(H2O)100, Na+(H2O)20, and Cl-(H2O)17 in the temperature region 100-450 K are explored using a hybrid parallel basin-hopping and tempering algorithm. The effect of the solid-liquid phase transition in both caloric curves and structural distribution functions is investigated. It is found that sodium and chloride ions largely reside on the surface of water clusters below the cluster melting temperature but are solvated into the interior of the cluster above the melting temperature, while the solvated proton was found to have significant propensity to reside on or near the surface in both the liquid- and solid-state clusters.

}, keywords = {Algorithms Calorimetry Chemistry, Molecular Models, Physical/*methods Chlorides/*chemistry Chlorine/chemistry Computer Simulation Ions Models, Statistical Models, Theoretical Monte Carlo Method *Protons Sodium/*chemistry Temperature Water/*chemistry}, doi = {10.1063/1.2149375}, author = {C. J. Burnham and Petersen, M. K. and Day, T. J. and S. S. Iyengar and G. A. Voth} } @article {371, title = {A Second Generation Mesoscopic Lipid Bilayer Model: Connections to Field-Theory Descriptions of Membranes and Nonlocal Hydrodynamics}, journal = {J Chem Phys}, volume = {124}, number = {6}, year = {2006}, note = {Ayton, Gary S McWhirter, J Liam Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States The Journal of chemical physics J Chem Phys. 2006 Feb 14;124(6):64906.}, pages = {64906}, abstract = {

A new mesoscopic membrane model is developed in order to examine long-wavelength structural and dynamical membrane phenomena. Two different explicit mesoscopic solvent models are employed. The first mesoscopic solvent is denoted the big liquid oscillating blob system, which is parametrized to model water at a coarse-grained level and is motivated by a Langevin-like approach; the resulting membrane dynamics predict a solvent viscosity dependence consistent with the known viscosity of water. The second mesoscopic solvent is a Weeks-Chandler-Anderson model. Here, it is found that the correct mesoscopic hydrodynamic scaling of the membrane undulation dynamics is still preserved, although accelerated. When the behavior of the two membranes in close proximity to one another is examined, very little correlated motion is observed. However, the theoretically predicted scaling of the entropic undulation energy is confirmed, demonstrating that the entropic interaction between two membranes becomes increasingly repulsive with decreasing separation.

}, keywords = {*Algorithms Computer Simulation Diffusion Entropy Lipid Bilayers/*chemistry *Membrane Fluidity Models, Biological Solvents/chemistry Surface Properties}, doi = {10.1063/1.2165194}, author = {Ayton, G. S. and McWhirter, J. L. and G. A. Voth} } @article {720, title = {Structure of the Liquid-Vacuum Interface of Room-Temperature Ionic Liquids: A Molecular Dynamics Study}, journal = {J Phys Chem B}, volume = {110}, number = {4}, year = {2006}, note = {Yan, Tianying Li, Shu Jiang, Wei Gao, Xueping Xiang, Bing Voth, Gregory A United States The journal of physical chemistry. B J Phys Chem B. 2006 Feb 2;110(4):1800-6.}, pages = {1800-6}, abstract = {

Molecular dynamics simulations for the liquid-vacuum interface of the ionic liquid 1-ethyl-3-methylimidazolium nitrate (EMIM+/NO3-) were performed for both electronically polarizable and nonpolarizable potential energy surfaces. The interfacial structural properties, such as the oscillation in the number density profile, the orientational ordering, and the local clustering in the interfacial region, were calculated. The simulations with both the polarizable and nonpolarizable model demonstrate the existence of an inhomogeneous interfacial structure normal to the surface layer. It was found for both models that the ethyl tail group on EMIM+ is likely to protrude outward from the surface. In the outmost surface layer, the cation is likely to lie on the surface with the imidazolium ring parallel to the interface, while there is a second region with enhanced density from that in the bulk where the cation preferably slants with the imidazolium ring tending to be perpendicular to the surface. The results also reveal that the electronic polarization effect is important for the ionic liquid interface. It is found that the cation is likely to be segregated at the ionic liquid surface for the polarizable model, while for the nonpolarizable model, the anion is found to be more likely to exhibit such behavior. The surface tension of the polarizable model (58.5 +/- 0.5 mN/m) is much smaller than that of the nonpolarizable model (82.7 +/- 0.6 mN/m), in better agreement with extrapolated experimental measurements on similar ionic liquid systems.

}, doi = {10.1021/jp055890p}, author = {T. Yan and Li, S. and Jiang, W. and Gao, X. and Xiang, B. and G. A. Voth} } @article {701, title = {Tail Aggregation and Domain Diffusion in Ionic Liquids}, journal = {J Phys Chem B}, volume = {110}, number = {37}, year = {2006}, note = {Wang, Yanting Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2006 Sep 21;110(37):18601-8.}, pages = {18601-8}, abstract = {

An extended multiscale coarse-graining model for ionic liquids is used to investigate the liquid crystal-like phase in certain ionic liquids. The tail groups of the cations with a sufficient side-chain length are found to aggregate, forming spatially heterogeneous domains, due to the competition between the electrostatic interactions between the charged head groups and the anions and the collective short-range interactions between the neutral tail groups. With a sufficiently long alkyl chain at a low enough temperature, the tail domains remain relatively stable, despite the diffusion of individual ions in the liquid phase. With increasing temperature, the average tail domains begin to diffuse, while beyond a transition temperature, their average density has an almost uniform distribution, although the tail groups still form instantaneous domains.

}, keywords = {Carbon/chemistry Cations Chemistry, Molecular Models, Physical/*methods Diffusion Gas Chromatography-Mass Spectrometry/methods *Ions Liquid Crystals Models, Statistical Software Solvents Static Electricity Temperature}, doi = {10.1021/jp063199w}, author = {Wang, Y. and G. A. Voth} } @article {483, title = {Ab Initio Molecular-dynamics Simulation of Aqueous Proton Solvation and Transport Revisited}, journal = {J Chem Phys}, volume = {123}, number = {4}, year = {2005}, note = {Izvekov, Sergei Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2005 Jul 22;123(4):044505.}, pages = {044505}, abstract = {

The solvation and transport of the hydrated excess proton is studied using the Car-Parrinello molecular-dynamics (CPMD) simulation method. The simulations were performed using BLYP and HCTH gradient-corrected exchange-correlation energy functionals. The fictitious electronic mass was chosen to be small enough so that the underlying water structural and dynamical properties were converged with respect to this important CPMD simulation parameter. An unphysical overstructuring of liquid water in the CPMD simulations using the BLYP functional resulted in the formation of long-lived hydrogen-bonding structures involving the excess proton and a particular (special) water oxygen. The excess proton was observed to be attracted to the special oxygen through the entire length of the BLYP CPMD simulations. Consequently, the excess proton diffusion was limited by the mobility of the special oxygen in the slowly diffusing water network and, in turn, the excess proton self-diffusion coefficient was found to be significantly below the experimental value. On the other hand, the structural properties of liquid water in the HCTH CPMD simulation were seen to be in better agreement with experiment, although the water and excess proton diffusions were still well below the experimental value.

}, doi = {10.1063/1.1961443}, author = {Izvekov, S. and G. A. Voth} } @article {431, title = {Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-grained Analysis}, journal = {Proc Natl Acad Sci U S A}, volume = {102}, number = {37}, year = {2005}, note = {Chu, Jhih-Wei Voth, Gregory A 1 S10RR17214-01/RR/NCRR NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13111-6. Epub 2005 Aug 31.}, pages = {13111-6}, abstract = {

The structural and mechanical properties of monomeric actin (G-actin), the trimer nucleus, and actin filaments (F-actins) are determined as a function of the conformation of the DNase I-binding loop (DB loop) by using all-atom molecular dynamics simulations and coarse-grained (CG) analysis. Recent x-ray structures of ADP-bound G-actin (G-ADP) by Otterbein et al. [Otterbein, L. R., Graceffa, P. \& Dominguez, R. (2001) Science 293, 708-711] and ATP-bound G-actin (G-ATP) by Graceffa and Dominguez [Graceffa, P. \& Dominguez, R. (2003) J. Biol. Chem. 278, 34172-34180] indicate that the DB loop of actin does not have a well defined secondary structure in the ATP state but folds into an alpha-helix in the ADP state. MD simulations and CG analysis indicate that such a helical DB loop significantly weakens the intermonomer interactions of actin assemblies and thus leads to a wider, shorter, and more disordered filament. The computed persistence lengths of F-actin composed of G-ATP (16 microm) and of G-ADP (8.5 microm) agree well with the experimental values for the two states. Therefore, the loop-to-helix transition of the DB loop may be one of the factors that lead to the changes in structural and mechanical properties of F-actin after ATP hydrolysis. This result may provide a direct connection between the conformational changes of an actin monomer and the structural and mechanical properties of the cytoskeleton. The information provided by MD simulations also helps to understand the possible origin of the special features of actin dynamics.

}, keywords = {Actin Cytoskeleton/*chemistry Actins/chemistry Adenosine Diphosphate/analogs \& derivatives/chemistry Adenosine Triphosphate/analogs \& derivatives/chemistry/metabolism *Allosteric Site Animals Binding Sites Computer Simulation Deoxyribonuclease I Humans *M, Molecular Motion Protein Binding Protein Structure, Secondary}, doi = {10.1073/pnas.0503732102}, author = {Chu, J. W. and G. A. Voth} } @article {470, title = {On the Amphiphilic Behavior of the Hydrated Proton: An Ab Initio Molecular Dynamics Study}, journal = {Int. J. Mass. Spec.}, volume = {241}, year = {2005}, pages = {197-204}, doi = {10.1016/j.ijms.2004.12.003}, author = {S. S. Iyengar and T. J. F. Day and G. A. Voth} } @article {526, title = {A Bond-order Analysis of the Mechanism for Hydrated Proton Mobility in Liquid Water}, journal = {J Chem Phys}, volume = {122}, number = {1}, year = {2005}, note = {Lapid, Hadas Agmon, Noam Petersen, Matt K Voth, Gregory A United States The Journal of chemical physics J Chem Phys. 2005 Jan 1;122(1):14506.}, pages = {14506}, abstract = {

Bond-order analysis is introduced to facilitate the study of cooperative many-molecule effects on proton mobility in liquid water, as simulated using the multistate empirical valence-bond methodology. We calculate the temperature dependence for proton mobility and the total effective bond orders in the first two solvation shells surrounding the H(5)O(2) (+) proton-transferring complex. We find that proton-hopping between adjacent water molecules proceeds via this intermediate, but couples to hydrogen-bond dynamics in larger water clusters than previously anticipated. A two-color classification of these hydrogen bonds leads to an extended mechanism for proton mobility.

}, doi = {10.1063/1.1814973}, author = {Lapid, H. and Agmon, N. and Petersen, M. K. and G. A. Voth} } @article {660, title = {A Coarse-grained Model for Double-helix Molecules in Solution: Spontaneous Helix Formation and Equilibrium Properties}, journal = {J Chem Phys}, volume = {122}, number = {12}, year = {2005}, note = {Tepper, Harald L Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2005 Mar 22;122(12):124906.}, pages = {124906}, abstract = {

A new reductionist coarse-grained model is presented for double-helix molecules in solution. As with such models for lipid bilayers and micelles, the level of description is both particulate and mesoscopic. The particulate (bead-and-spring) nature of the model makes for a simple implementation in standard molecular dynamics simulation codes and allows for investigation of thermomechanic properties without preimposing any (form of) response function. The mesoscopic level of description{\textendash}where groups of atoms are condensed into coarse-grained beads{\textendash}causes long-range interactions to be effectively screened, which greatly enhances the efficiency and scalability of simulations. Without imposing local or global order parameters, a linear initial configuration of the model molecule spontaneously assembles into a double helix due to the interplay between three contributions: hydrophobic/hydrophilic interactions between base pairs, backbone, and solvent; phosphate-phosphate repulsion along the backbone; and favorable base-pair stacking energy. We present results for the process of helix formation as well as for the equilibrium properties of the final state, and investigate how both depend on the input parameters. The current model holds promise for two routes of investigation: First, within a limited set of generic parameters, the effect of local (atomic-scale) perturbations on overall helical properties can be systematically studied. Second, since the efficiency allows for a direct simulation of both small and large (\>100 base pairs) systems, the model presents a testground for systematic coarse-graining methods.

}, keywords = {Base Pairing Computer Simulation DNA/*chemistry Hydrophobic and Hydrophilic Interactions *Models, Molecular Nucleic Acid Conformation Solutions Solvents/chemistry}, doi = {10.1063/1.1869417}, author = {H. L. Tepper and G. A. Voth} } @article {709, title = {A Computational Study of the Closed and Open States of the Influenza A M2 Proton Channel}, journal = {Biophys J}, volume = {89}, number = {4}, year = {2005}, note = {Wu, Yujie Voth, Gregory A GM53148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2005 Oct;89(4):2402-11. Epub 2005 Jul 22.}, pages = {2402-11}, abstract = {

In this study, four possible conformations of the His-37 and Trp-41 residues for the closed state of the influenza M2 ion channel were identified by a conformation scan based on a solid-state NMR restraint. In the four conformations, the His-37 residue can be of either the t-160 or t60 rotamer, whereas Trp-41 can be of either the t-105 or t90 rotamer. These conformations were further analyzed by density functional theory calculations and molecular dynamics simulations, and the data indicate that the His-37 residue most likely adopts the t60 rotamer and should be monoprotonated at the delta-nitrogen site, whereas Trp-41 adopts the t90 rotamer. This result is consistent with published experimental data and points to a simple gating mechanism: in the closed state, the His-37 and Trp-41 residues adopt the (t60, t90) conformation, which nearly occludes the pore, preventing nonproton ions from passing through due to the steric and desolvation effects. Moreover, the His-37 tetrad interrupts the otherwise continuous hydrogen-bonding network of the pore water by forcing the water molecules above and below it to adopt opposite orientations, thus adding to the blockage of proton shuttling. The channel can be easily opened by rotating the His-37 chi2 angle from 60 to 0 degrees . This open structure allows pore water to penetrate the constrictive region and to form a continuous water wire for protons to shuttle through, while being still narrow enough to exclude other ions.

}, keywords = {Biological *Models, Chemical *Models, Computer Simulation *Ion Channel Gating Ion Channels/*chemistry Models, Molecular Porosity Protein Conformation Proton Pumps/*chemistry Structure-Activity Relationship Viral Matrix Proteins/*chemistry}, doi = {10.1529/biophysj.105.066647}, author = {Y. Wu and G. A. Voth} } @article {713, title = {Computer Simulation of Explicit Proton Translocation in Cytochrome c Oxidase: the D-pathway}, journal = {Proc Natl Acad Sci U S A}, volume = {102}, number = {19}, year = {2005}, note = {Xu, Jiancong Voth, Gregory A R01 GM053148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A. 2005 May 10;102(19):6795-800. Epub 2005 Apr 27.}, pages = {6795-800}, abstract = {

Proton translocation in the D-pathway of cytochrome c oxidase has been studied by a combination of classical molecular dynamics and the multistate empirical valence bond methodology. This approach allows for explicit Grotthuss proton hopping between water molecules. According to mutagenesis experiments, the role of proton donor/acceptor along the D-pathway is carried by the highly conserved residue Glu-242. The present multistate empirical valence bond simulations indicate that the protonation/deprotonation state of Glu-242 is strongly coupled to the distance of proton propagation in the D-pathway. The proton was seen to travel the full length of the D-pathway when Glu-242 was deprotonated; however, it was trapped halfway along the path when Glu-242 was protonated. Further investigation in terms of both proton dynamical properties and free energy calculations for the pathway of proton transport provides evidence for a two-step proton transport mechanism in the D-pathway.

}, keywords = {Animals Biophysics/*methods Cattle Computer Simulation Crystallography, Molecular Models, Statistical Mutagenesis Protons Serine/chemistry Static Electricity Thermodynamics Time Factors Water/chemistry, X-Ray Electron Transport Complex IV/*chemistry Glutamic Acid/chemistry Mitochondria/metabolism Models}, doi = {10.1073/pnas.0408117102}, author = {Xu, J. and G. A. Voth} } @article {370, title = {Coupling Field Theory with Continuum Mechanics: A Simulation of Domain Formation in Giant Unilamellar Vesicles}, journal = {Biophys J}, volume = {88}, number = {6}, year = {2005}, note = {Ayton, Gary S McWhirter, J Liam McMurtry, Patrick Voth, Gregory A GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2005 Jun;88(6):3855-69. Epub 2005 Mar 25.}, pages = {3855-69}, abstract = {

Domain formation is modeled on the surface of giant unilamellar vesicles using a Landau field theory model for phase coexistence coupled to elastic deformation mechanics (e.g., membrane curvature). Smooth particle applied mechanics, a form of smoothed particle continuum mechanics, is used to solve either the time-dependent Landau-Ginzburg or Cahn-Hilliard free-energy models for the composition dynamics. At the same time, the underlying elastic membrane is modeled using smooth particle applied mechanics, resulting in a unified computational scheme capable of treating the response of the composition fields to arbitrary deformations of the vesicle and vice versa. The results indicate that curvature coupling, along with the field theory model for composition free energy, gives domain formations that are correlated with surface defects on the vesicle. In the case that external deformations are included, the domain structures are seen to respond to such deformations. The present simulation capability provides a significant step forward toward the simulation of realistic cellular membrane processes.

}, keywords = {Biomechanics Biophysical Phenomena Biophysics Elasticity Liposomes/*chemistry Models, Chemical Thermodynamics}, doi = {10.1529/biophysj.105.059436}, author = {Ayton, G. S. and McWhirter, J. L. and P. McMurtry and G. A. Voth} } @article {499, title = {The Dynamic Stress Responses to Area Change in Planar Lipid Bilayer Membranes}, journal = {Biophys J}, volume = {88}, number = {2}, year = {2005}, note = {Jeon, Jonggu Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2005 Feb;88(2):1104-19. Epub 2004 Nov 12.}, pages = {1104-19}, abstract = {

The viscoelastic properties of planar phospholipid (dimyristoylphosphatidylcholine) bilayer membranes at 308 K are studied, many of them for the first time, using the nonequilibrium molecular dynamics simulation (NEMD) method for membrane area change. First, we present a unified formulation of the intrinsic three-dimensional (3D) and apparent in-plane viscoelastic moduli associated with area change based on the constitutive relations for a uniaxial system. The NEMD simulations of oscillatory area change process are then used to obtain the frequency-domain moduli. In the 4-250 GHz range, the intrinsic 3D elastic moduli of 20-27 kbar and viscous moduli of 0.2-9 kbar are found with anisotropy and monotonic frequency dispersion. In contrast, the apparent in-plane elastic moduli (1-9 kbar) are much smaller than, and the viscous moduli (2-6 kbar) comparable to, their 3D counterparts, due to the interplay between the lateral and normal relaxations. The time-domain relaxation functions, separately obtained by applying stepwise strains, can be fit by 4-6 exponential decay modes spanning subpicosecond to nanosecond timescale and are consistent with the frequency-domain results. From NEMD with varying strain amplitude, the linear constitutive model is shown to be valid up to 6 and 20\% area change for the intrinsic 3D elastic and viscous responses, respectively, and up to 20\% area change for the apparent in-plane viscoelasticity. Inclusion of a gramicidin A dimer (approximately 1 mol \%) yields similar response properties with possibly smaller (\<10\%) viscous moduli. Our results agree well with available data from ultrasonic experiments, and demonstrate that the third dimension (thickness) of the planar lipid bilayer is integral to the in-plane viscoelasticity.

}, keywords = {Artificial *Models, Chemical *Models, Dimyristoylphosphatidylcholine/*chemistry Elasticity Kinetics Linear Models Lipid Bilayers/*chemistry *Membrane Fluidity Membranes, Mechanical Surface Tension, Molecular Models, Statistical Motion Oscillometry/methods Physical Stimulation/methods Stress}, doi = {10.1529/biophysj.104.052183}, author = {J. Jeon and G. A. Voth} } @article {481, title = {Effective Force Field for Liquid Hydrogen Fluoride from Ab Initio Molecular Dynamics Simulation Using the Force-Matching Method}, journal = {J Phys Chem B}, volume = {109}, number = {14}, year = {2005}, note = {Izvekov, Sergei Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2005 Apr 14;109(14):6573-86.}, pages = {6573-86}, abstract = {

A recently developed force-matching method for obtaining effective force fields for condensed matter systems from ab initio molecular dynamics (MD) simulations has been applied to fit a simple nonpolarizable two-site pairwise force field for liquid hydrogen fluoride. The ab initio MD in this case was a Car-Parrinello (CP) MD simulation of 64 HF molecules at nearly ambient conditions within the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure included a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The performance of the force-match potential was examined for the gas-phase dimer and for the liquid phase at various temperatures. The model was able to reproduce correctly the bent structure and energetics of the gas-phase dimer, while the results for the structural properties, self-diffusion, vibrational spectra, density, and thermodynamic properties of liquid HF were compared to both experiment and the CP MD simulation. The force-matching model performs well in reproducing nearly all of the liquid properties as well as the aggregation behavior at different temperatures. The model is computationally cheap and compares favorably to many more computationally expensive potential energy functions for liquid HF.

}, keywords = {Chemical Models, Chemistry, Physical/*methods Computer Simulation Dimerization Electrons Hydrofluoric Acid/*chemistry Models, Statistical Models, Theoretical Molecular Conformation Probability Software Temperature Thermodynamics}, doi = {10.1021/jp0456685}, author = {Izvekov, S. and G. A. Voth} } @article {509, title = {An Efficient and Accurate Implementation of Centroid Molecular Dynamics Using a Gaussian Approximation}, journal = {J Phys Chem A}, volume = {109}, number = {50}, year = {2005}, note = {Ka, Being J Voth, Gregory A United States The journal of physical chemistry. A J Phys Chem A. 2005 Dec 22;109(50):11609-17.}, pages = {11609-17}, abstract = {

An approximate method for Centroid Molecular Dynamics (CMD) is presented which uses a Gaussian approximation. The resulting method, called Gaussian CMD (GCMD), is 100-1000 times faster than CMD because it replaces explicit path-integral sampling, which is the most time-consuming part of CMD, with a Gaussian averaging, which can be done analytically. Several methods for computing the Gaussian width parameter in the GCMD approach are also presented. This new method is shown to give satisfactory results for the position correlation function in simple one-dimensional systems when CMD itself is consistent with the exact result. The GCMD and CMD results are also compared for the case of 1-dimensional systems coupled to harmonic baths, with good success. GCMD is further compared to CMD with good success for liquid para-hydrogen at two different temperatures, 14 K and 25 K, and for ortho-deuterium at 20.7 K.

}, doi = {10.1021/jp053919j}, author = {Ka, B. J. and G. A. Voth} } @article {611, title = {Excess Proton Solvation and Delocalization in a Hydrophilic Pocket of the Proton Conducting Polymer Membrane Nafion}, journal = {J Phys Chem B}, volume = {109}, number = {9}, year = {2005}, note = {Petersen, Matt K Wang, Feng Blake, Nick P Metiu, Horia Voth, Gregory A Letter Research Support, Non-U.S. Gov{\textquoteright}t United States The journal of physical chemistry. B J Phys Chem B. 2005 Mar 10;109(9):3727-30.}, pages = {3727-30}, abstract = {

Solvation properties of the hydrated excess proton are studied in a hydrophilic pocket of Nafion 117 through a series of molecular dynamics simulations. The multistate empirical valence bond (MS-EVB) methodology, which enables the delocalization of the excess proton through the Grotthuss hopping mechanism, was employed for one of the excess protons in the simulation cell. Simulations were performed such that "classical" nondissociable hydronium cations and a single excess proton treated with the MS-EVB methodology were at a concentration ratio of 39:1. Two degrees of hydration of the Nafion polymer electrolyte membrane were simulated, each displaying the same marked difference between the solvation structures of the classical versus MS-EVB treated (Grotthuss shuttling) excess proton species. These differences are attributed to the solvent dynamics needed to transfer the cation between the solvent separated and contact pair positions about the sulfonic acid counterion. The results demonstrate that it is generally impossible to describe the low pH conditions in the hydrophilic domains of Nafion without the explicit treatment of Grotthuss delocalization in the underlying molecular dynamics model for the excess protons.

}, keywords = {Fluorocarbon Polymers/*chemistry Models, Molecular Polymers/*chemistry *Protons Solubility}, doi = {10.1021/jp044535g}, author = {Petersen, M. K. and Wang, F. and Blake, N. P. and Metiu, H. and G. A. Voth} } @article {463, title = {Fast Centroid Molecular Dynamics: a Force-matching Approach for the Predetermination of the Effective Centroid Forces}, journal = {J Chem Phys}, volume = {122}, number = {5}, year = {2005}, note = {Hone, Tyler D Izvekov, Sergei Voth, Gregory A United States The Journal of chemical physics J Chem Phys. 2005 Feb 1;122(5):54105.}, pages = {54105}, abstract = {

A fast centroid molecular dynamics (CMD) methodology is proposed in which the effective centroid forces are predetermined through a force-matching algorithm applied to a standard path integral molecular dynamics simulation. The resulting method greatly reduces the computational cost of generating centroid trajectories, thus extending the applicability of CMD. The method is applied to the study of liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The static and dynamical results are compared to those obtained from full adiabatic CMD simulations and found to be in excellent agreement for all three systems; the transport properties are also compared to experiment and found to have a similar level of agreement.

}, doi = {10.1063/1.1836731}, author = {Hone, T. D. and Izvekov, S. and G. A. Voth} } @article {695, title = {A Linear-scaling Self-consistent Generalization of the Multistate Empirical Valence Bond Method for Multiple Excess Protons in Aqueous Systems}, journal = {J Chem Phys}, volume = {122}, number = {14}, year = {2005}, note = {Wang, Feng Voth, Gregory A United States The Journal of chemical physics J Chem Phys. 2005 Apr 8;122(14):144105.}, pages = {144105}, abstract = {

An extension to the multistate empirical valence bond (MS-EVB) method is presented in this paper that is capable of treating multiple excess protons within the context of molecular-dynamics simulation. The computational cost of the method scales linearly with respect to the number of excess protons. Calculations for a 0.44 M HCl systems are carried out to illustrate the multiproton extension of the MS-EVB method. A significant decrease in the Eigen-type H(9)O(4)(+) cation is observed in the contact ion-pair configuration formed between Cl(-) and hydronium ions.

}, doi = {10.1063/1.1881092}, author = {Wang, F. and G. A. Voth} } @article {480, title = {Multiscale Coarse Graining of Liquid-state Systems}, journal = {J Chem Phys}, volume = {123}, number = {13}, year = {2005}, note = {Izvekov, Sergei Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2005 Oct 1;123(13):134105.}, pages = {134105}, abstract = {

A methodology is described to systematically derive coarse-grained (CG) force fields for molecular liquids from the underlying atomistic-scale forces. The coarse graining of an interparticle force field is accomplished by the application of a force-matching method to the trajectories and forces obtained from the atomistic trajectory and force data for the CG sites of the targeted system. The CG sites can be associated with the centers of mass of atomic groups because of the simplicity in the evaluation of forces acting on these sites from the atomistic data. The resulting system is called a multiscale coarse-grained (MS-CG) representation. The MS-CG method for liquids is applied here to water and methanol. For both liquids one-site and two-site CG representations without an explicit treatment of the long-ranged electrostatics have been derived. In addition, for water a two-site model having the explicit long-ranged electrostatics has been developed. To improve the thermodynamic properties (e.g., pressure and density) for the MS-CG models, the constraint for the instantaneous virial was included into the force-match procedure. The performance of the resulting models was evaluated against the underlying atomistic simulations and experiment. In contrast with existing approaches for coarse graining of liquid systems, the MS-CG approach is general, relies only on the interatomic interactions in the reference atomistic system.

}, keywords = {Chemical *Models, Computer Simulation Methanol/*chemistry Models, Molecular Molecular Conformation Water/*chemistry}, doi = {10.1063/1.2038787}, author = {Izvekov, S. and G. A. Voth} } @article {482, title = {A Multiscale Coarse-Graining Method for Biomolecular Systems}, journal = {J Phys Chem B}, volume = {109}, number = {7}, year = {2005}, note = {Izvekov, Sergei Voth, Gregory A Letter Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2005 Feb 24;109(7):2469-73.}, pages = {2469-73}, abstract = {

A new approach is presented for obtaining coarse-grained (CG) force fields from fully atomistic molecular dynamics (MD) trajectories. The method is demonstrated by applying it to derive a CG model for the dimyristoylphosphatidylcholine (DMPC) lipid bilayer. The coarse-graining of the interparticle force field is accomplished by an application of a force-matching procedure to the force data obtained from an explicit atomistic MD simulation of the biomolecular system of interest. Hence, the method is termed a "multiscale" CG (MS-CG) approach in which explicit atomistic-level forces are propagated upward in scale to the coarse-grained level. The CG sites in the lipid bilayer application were associated with the centers-of-mass of atomic groups because of the simplicity in the evaluation of the forces acting on them from the atomistic data. The resulting CG lipid bilayer model is shown to accurately reproduce the structural properties of the phospholipid bilayer.

}, keywords = {Chemical Models, Chemistry, Molecular Models, Physical/*methods Computer Simulation Dimyristoylphosphatidylcholine/*chemistry Lipid Bilayers/*chemistry Models, Statistical Molecular Conformation Phospholipids/*chemistry}, doi = {10.1021/jp044629q}, author = {Izvekov, S. and G. A. Voth} } @article {419, title = {Multiscale Coupling of Mesoscopic- and Atomistic-level Lipid Bilayer Simulations}, journal = {J Chem Phys}, volume = {122}, number = {24}, year = {2005}, note = {Chang, Rakwoo Ayton, Gary S Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States R01-GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States The Journal of chemical physics J Chem Phys. 2005 Jun 22;122(24):244716.}, pages = {244716}, abstract = {

A multiscale method is presented to bridge between the atomistic and mesoscopic membrane systems. The atomistic model in this case is the united atom dimyristoylphosphatidylcholine membrane system, although the method is completely general. Atomistic molecular dynamics provides the expansion modulus which is used to parametrize a mesoscopic elastic membrane model. The resulting elastic membrane model, including explicit mesoscopic solvent, shows appropriate static and dynamic undulation behaviors. Large membranes of approximately 100 nm in length can then be easily simulated using the mesoscopic membrane system. The critical feedback from the mesoscopic system back down to the atomistic-scale system is accomplished by bridging the stress (or surface tension) of a small region in the mesoscopic membrane to the corresponding atomistic membrane system. Because of long length-scale modes of membranes such as undulation and buckling, the local tension responds differently from the frame tension, when subjected to external perturbations. The effect of these membrane modes is shown for the stress response of a local membrane region and therefore the atomistic membrane system. In addition, certain equilibrium static and dynamic properties of stand-alone and multiscale coupled systems are presented for several different membrane sizes. Although static properties such as two-dimensional pair-correlation function and order parameters show no noticeable discrepancy for the different systems, lipid self-diffusion and the rotational relaxation of lipid dipoles have a strong dependence on the membrane size (or long-wavelength membrane motions), which is properly modeled by the present multiscale method.

}, keywords = {*Algorithms Carbon/chemistry *Computer Simulation Diffusion Dimyristoylphosphatidylcholine/chemistry Lipid Bilayers/*chemistry *Membrane Fluidity Stress, Mechanical Surface Properties Surface Tension Time Factors}, doi = {10.1063/1.1931651}, author = {R. Chang and Ayton, G. S. and G. A. Voth} } @article {644, title = {Multi-Scale Modeling of Phase Separation in Mixed Lipid Bilayers}, journal = {Biophys J}, volume = {89}, number = {4}, year = {2005}, note = {Shi, Qiang Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2005 Oct;89(4):2385-94. Epub 2005 Jul 29.}, pages = {2385-94}, abstract = {

An approach to bridging the phenomenological field theory description of phase separation in binary mixed lipid bilayers with coarse-grained (CG) molecular dynamics (MD) simulation is presented. CG MD simulation is carried out for a 1:1 dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylethanolamine lipid mixture at the liquid-gel phase coexistence condition. The liquid-gel phase separation can be characterized by the bilayer thickness, area per lipid molecule, and orientation parameter of the lipid tails. After a local order parameter is defined using the lipid tail bond orientation parameter, the CG MD data are bridged to a mesoscopic model based on the phenomenological Landau-Ginzberg free-energy functional. All parameters in this mesoscopic model are defined from the information of the phase boundary structure and the distributions of the order parameter in the liquid and gel phases. It is found that the mesoscopic model reproduces the equilibrium properties of the system very well, including collective fluctuations in both phases, spatial correlation functions of the order parameter, and the line tension. The possibility of using a time-dependent Landau-Ginzberg model to mimic the phase-separation dynamics is also investigated, using the relaxation time constant obtained by fitting the time-dependent correlation functions of the order parameter.

}, keywords = {Biological *Models, Cell Membrane/*chemistry Computer Simulation Lipid Bilayers/*chemistry *Membrane Fluidity Models, Chemical *Models, Molecular Molecular Conformation Phase Transition Phospholipids/*chemistry}, doi = {10.1529/biophysj.105.063784}, author = {Shi, Q. and G. A. Voth} } @article {387, title = {Probing the Molecular-Scale Lipid Bilayer Response to Shear Flow Using Nonequilibrium Molecular Dynamics}, journal = {J Phys Chem B}, volume = {109}, number = {39}, year = {2005}, note = {Blood, Philip D Ayton, Gary S Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States The journal of physical chemistry. B J Phys Chem B. 2005 Oct 6;109(39):18673-9.}, pages = {18673-9}, abstract = {

A nonequilibrium molecular dynamics simulation of the response of dimyristoylphosphatidylcholine (DMPC) bilayers to a solvent shear flow is presented. Application of shear flow to planar, stationary DMPC bilayers results in a redistribution of the membrane density profile along the bilayer normal due to the alignment of the lipids in the direction of flow and an increase in average lipid chain length. An increase in the intermolecular and intramolecular order of the lipids in response to the shear flow is also observed. This study provides groundwork for understanding the mechanism of the full response of lipid bilayers to externally imposed solvent shear flows, beginning with the response in the absence of collective lipid motions such as undulations and bilayer flow.

}, keywords = {*Lipid Bilayers *Molecular Probes}, doi = {10.1021/jp0530449}, author = {Blood, P. D. and Ayton, G. S. and G. A. Voth} } @article {471, title = {The Properties of Ion-water Clusters. I. The Protonated 21-water Cluster}, journal = {J Chem Phys}, volume = {123}, number = {8}, year = {2005}, note = {Iyengar, Srinivasan S Petersen, Matt K Day, Tyler J F Burnham, Christian J Teige, Virginia E Voth, Gregory A Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2005 Aug 22;123(8):084309.}, pages = {084309}, abstract = {

The ab initio atom-centered density-matrix propagation approach and the multistate empirical valence bond method have been employed to study the structure, dynamics, and rovibrational spectrum of a hydrated proton in the "magic" 21 water cluster. In addition to the conclusion that the hydrated proton tends to reside on the surface of the cluster, with the lone pair on the protonated oxygen pointing "outwards," it is also found that dynamical effects play an important role in determining the vibrational properties of such clusters. This result is used to analyze and complement recent experimental and theoretical studies.

}, keywords = {Adsorption Algorithms Binding Sites Chemistry, Physical/methods Fourier Analysis Hydrogen/chemistry *Ions Models, Theoretical Molecular Conformation Protons Software Thermodynamics Time Factors Water/*chemistry}, doi = {10.1063/1.2007628}, author = {S. S. Iyengar and Petersen, M. K. and Day, T. J. and C. J. Burnham and Teige, V. E. and G. A. Voth} } @article {661, title = {Protons May Leak through Pure Lipid Bilayers via a Concerted Mechanism}, journal = {Biophys J}, volume = {88}, number = {5}, year = {2005}, note = {Tepper, Harald L Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States R01 GM053148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2005 May;88(5):3095-108. Epub 2005 Feb 4.}, pages = {3095-108}, abstract = {

Protons are known to permeate pure lipid bilayers at a rate that is anomalous compared to those of other small monovalent cations. The prevailing mechanism via which they cross the membrane is still unclear, and it is unknown how to probe the mechanism directly by experiment. One of the more popular theories assumes the formation of membrane-spanning single-file water wires providing a matrix along which the protons can "hop" over the barrier. However, free energy calculations on such structures (without the presence of an excess proton) suggest that this mechanism alone cannot account for the observed permeation rates. We use the multistate empirical valence bond method to directly study water structures surrounding a (delocalized) excess proton on its way through the membrane. We find that membrane-spanning networks, rather than single-file chains, are formed around the proton. We also find that such structures are considerably stabilized in the presence of the proton, with lifetimes of several hundreds of picoseconds. The observed structures are suggestive of a new, concerted, mechanism and provide some direction for further investigation.

}, keywords = {Biophysics/*methods Hydrogen Bonding Ion Channels Lipid Bilayers/*chemistry Membrane Lipids/chemistry Models, Molecular Models, Statistical Oxygen/chemistry Phospholipids/chemistry *Protons Thermodynamics Time Factors Water/chemistry}, doi = {10.1529/biophysj.104.056184}, author = {H. L. Tepper and G. A. Voth} } @inbook {737, title = {Quantum Rate Theory: A Path Integral Centroid Perspective}, booktitle = {Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods}, year = {2005}, author = {Geva, E. and S. Jang and G. A. Voth}, editor = {Yip, S.} } @article {385, title = {Structure of Hydrated Na-Nafion Polymer Membranes}, journal = {J Phys Chem B}, volume = {109}, number = {51}, year = {2005}, note = {Blake, Nick P Petersen, Matt K Voth, Gregory A Metiu, Horia United States The journal of physical chemistry. B J Phys Chem B. 2005 Dec 29;109(51):24244-53.}, pages = {24244-53}, abstract = {

We use molecular dynamics simulations to investigate the structure of the hydrated Na-Nafion membranes. The membrane is "prepared" by starting with the Nafion chains placed on a cylinder having the water inside it. Minimizing the energy of the system leads to a filamentary hydrophilic domain whose structure depends on the degree of hydration. At 5 wt \% water the system does not have enough water molecules to solvate all the ions that could be formed by the dissociation of the -SO3Na groups. As a result, the -SO3Na groups aggregate with the water to form very small droplets that do not join into a continuous phase. The size of the droplets is between 5 and 8 A. As the amount of water present in the membrane is increased, the membrane swells, and SO3Na has an increasing tendency to dissociate into ions. Furthermore, a transition to a percolating hydrophilic network is observed. In the percolating structure, the water forms irregular curvilinear channels branching in all directions. The typical dimension of the cross section of these channels is about 10-20 A. Calculated neutron scattering from the simulated system is in qualitative agreement with experiment. In all simulations, the pendant sulfonated perfluorovinyl side chains of the Nafion hug the walls of the hydrophilic channel, while the sulfonate groups point toward the center of the hydrophilic phase. The expulsion of the side chains from the hydrophilic domain is favored because it allows better interaction between the water molecules. We have also examined the probability of finding water molecules around the Na+ and the -SO3(-) ions as well as the probability of finding other water molecules next to a given water molecule. These probabilities are much broader than those found in bulk water or for one ion in bulk water (calculated with the potentials used in the present simulation). This is due to the highly inhomogeneous nature of the material contained in the small hydrophilic pores.

}, doi = {10.1021/jp054687r}, author = {Blake, N. P. and Petersen, M. K. and G. A. Voth and Metiu, H.} } @article {671, title = {Superposition State Molecular Dynamics}, journal = {J. Chem. Theory Comp.}, volume = {1}, year = {2005}, pages = {36-40}, doi = {10.1021/ct0499175}, author = {A. Venkatnathan and G. A. Voth} } @article {477, title = {Systematic Coarse-Graining of Nanoparticle Interactions in Molecular Dynamics Simulation}, journal = {J Phys Chem B}, volume = {109}, number = {36}, year = {2005}, note = {Izvekov, Sergei Violi, Angela Voth, Gregory A Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2005 Sep 15;109(36):17019-24.}, pages = {17019-24}, abstract = {

A recently developed multiscale coarse-graining procedure [Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469] is extended to derive coarse-grained models for nanoparticles. The methodology is applied to C(60) and to carbonaceous nanoparticles produced in combustion environments. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to data obtained from trajectories and forces from all-atom MD simulations. The CG models are shown to reproduce accurately the structural properties of the nanoparticle systems studied, while allowing for MD simulations of much larger self-assembled nanoparticle systems.

}, keywords = {Models, Molecular *Nanoparticles}, doi = {10.1021/jp0530496}, author = {Izvekov, S. and Violi, A. and G. A. Voth} } @article {700, title = {Unique Spatial Heterogeneity in Ionic Liquids}, journal = {J Am Chem Soc}, volume = {127}, number = {35}, year = {2005}, note = {Wang, Yanting Voth, Gregory A United States Journal of the American Chemical Society J Am Chem Soc. 2005 Sep 7;127(35):12192-3.}, pages = {12192-3}, abstract = {

A multiscale coarse-graining model for ionic liquids has been extended to investigate the unique aggregation of cations in ionic liquids through computer simulation. It has been found that, with sufficiently long side chains, the tail groups of cations aggregate to form spatially heterogeneous domains, while headgroups of the cations and the anions distribute as uniformly as possible. This is understood as the result of competition between the charged electrostatic interactions between headgroups and anions and the collective short-range interactions between the neutral tail groups. This aggregation can help to explain a number of experimentally observed physical phenomena in ionic liquids.

}, doi = {10.1021/ja053796g}, author = {Wang, Y. and G. A. Voth} } @article {465, title = {A Centroid Molecular Dynamics Study of Liquid Para-hydrogen and Ortho-deuterium}, journal = {J Chem Phys}, volume = {121}, number = {13}, year = {2004}, note = {Hone, Tyler D Voth, Gregory A United States The Journal of chemical physics J Chem Phys. 2004 Oct 1;121(13):6412-22.}, pages = {6412-22}, abstract = {

Centroid molecular dynamics (CMD) is applied to the study of collective and single-particle dynamics in liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The CMD results are compared with the results of classical molecular dynamics, quantum mode coupling theory, a maximum entropy analytic continuation approach, pair-product forward- backward semiclassical dynamics, and available experimental results. The self-diffusion constants are in excellent agreement with the experimental measurements for all systems studied. Furthermore, it is shown that the method is able to adequately describe both the single-particle and collective dynamics of quantum liquids.

}, doi = {10.1063/1.1780951}, author = {Hone, T. D. and G. A. Voth} } @article {508, title = {Combining the Semiclassical Initial Value Representation with Centroid Dynamics}, journal = {J. Phys. Chem. B}, volume = {108}, year = {2004}, pages = {6883-6892}, doi = {10.1021/jp037862h}, author = {Ka, B. J. and G. A. Voth} } @inbook {744, title = {Computer Simulations of Proton Transport Through the M2 Channel of the Influenza A Virus}, booktitle = {Viral Membrane Proteins: Structure, Function and Drug Design}, year = {2004}, publisher = {Kluwer Academic/Plenum Publishers}, organization = {Kluwer Academic/Plenum Publishers}, chapter = {10}, address = {New York}, author = {Y. Wu and G. A. Voth}, editor = {Fischer, W.} } @article {575, title = {Coupling Field Theory with Mesoscopic Dynamical Simulations of Multicomponent Lipid Bilayers}, journal = {Biophys J}, volume = {87}, number = {5}, year = {2004}, note = {McWhirter, J Liam Ayton, Gary Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2004 Nov;87(5):3242-63. Epub 2004 Sep 3.}, pages = {3242-63}, abstract = {

A method for simulating a two-component lipid bilayer membrane in the mesoscopic regime is presented. The membrane is modeled as an elastic network of bonded points; the spring constants of these bonds are parameterized by the microscopic bulk modulus estimated from earlier atomistic nonequilibrium molecular dynamics simulations for several bilayer mixtures of DMPC and cholesterol. The modulus depends on the composition of a point in the elastic membrane model. The dynamics of the composition field is governed by the Cahn-Hilliard equation where a free energy functional models the coupling between the composition and curvature fields. The strength of the bonds in the elastic network are then modulated noting local changes in the composition and using a fit to the nonequilibrium molecular dynamics simulation data. Estimates for the magnitude and sign of the coupling parameter in the free energy model are made treating the bending modulus as a function of composition. A procedure for assigning the remaining parameters in the free energy model is also outlined. It is found that the square of the mean curvature averaged over the entire simulation box is enhanced if the strength of the bonds in the elastic network are modulated in response to local changes in the composition field. We suggest that this simulation method could also be used to determine if phase coexistence affects the stress response of the membrane to uniform dilations in area. This response, measured in the mesoscopic regime, is already known to be conditioned or renormalized by thermal undulations.

}, keywords = {Chemical *Models, Computer Simulation Lipid Bilayers/*chemistry Macromolecular Substances/chemistry *Membrane Fluidity *Models, Molecular Molecular Conformation Motion Phase Transition Surface Properties}, doi = {10.1529/biophysj.104.045716}, author = {McWhirter, J. L. and G. Ayton and G. A. Voth} } @article {476, title = {Effective Force Fields for Condensed Phase Systems from ab initio Molecular Dynamics Simulation: a New Method for Force-matching}, journal = {J Chem Phys}, volume = {120}, number = {23}, year = {2004}, note = {Izvekov, Sergei Parrinello, Michele Burnham, Christian J Voth, Gregory A United States The Journal of chemical physics J Chem Phys. 2004 Jun 15;120(23):10896-913.}, pages = {10896-913}, abstract = {

A novel least-squares fitting approach is presented to obtain classical force fields from trajectory and force databases produced by ab initio (e.g., Car-Parrinello) molecular dynamics (MD) simulations. The method was applied to derive effective nonpolarizable three-site force fields for liquid water at ambient conditions from Car-Parrinello MD simulations in the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure includes a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The various parameterizations of the water force field differ by an enforced smooth cut-off applied to the short-ranged interaction term. These were obtained by fitting to the trajectory and force data produced by Car-Parrinello MD simulations of systems of 32 and 64 H(2)O molecules. The new water force fields were developed assuming both flexible or rigid molecular geometry. The simulated structural and self-diffusion properties of liquid water using the fitted force fields are in close agreement with those observed in the underlying Car-Parrinello MD simulations. The resulting empirical models compare to experiment much better than many conventional simple point charge (SPC) models. The fitted potential is also shown to combine well with more sophisticated intramolecular potentials. Importantly, the computational cost of the new models is comparable to that for SPC-like potentials.

}, doi = {10.1063/1.1739396}, author = {Izvekov, S. and M. Parrinello and C. J. Burnham and G. A. Voth} } @article {620, title = {Hybrid Ab Initio Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach}, journal = {J. Phys. Chem. B}, volume = {108}, year = {2004}, pages = {4210 - 4220}, doi = {10.1021/jp0370829}, author = {Rega, N. and S. S. Iyengar and G. A. Voth and H. B. Schlegel and Vreven, T. and M. J. Frisch} } @article {607, title = {The Hydrated Proton at the Water Liquid/Vapor Interface}, journal = {J. Phys. Chem. B}, volume = {108}, year = {2004}, pages = {14804-14806}, doi = {10.1021/jp046716o }, author = {Petersen, M. K. and S. S. Iyengar and T. J. F. Day and G. A. Voth} } @article {672, title = {Kinetic Monte Carlo-Molecular Dynamics Approach To Model Soot Inception}, journal = {Combust. Sci. and Tech.}, volume = {176}, year = {2004}, pages = {991-1005}, doi = {10.1080/00102200490428594}, author = {Violi, A. and Sarofim, A. F. and G. A. Voth} } @article {466, title = {The Mechanism of Proton Exclusion in Aquaporin Channels}, journal = {Proteins}, volume = {55}, number = {2}, year = {2004}, note = {Ilan, Boaz Tajkhorshid, Emad Schulten, Klaus Voth, Gregory A P41 RR05969/RR/NCRR NIH HHS/United States R01 GM067887/GM/NIGMS NIH HHS/United States R01-GM53148/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Proteins Proteins. 2004 May 1;55(2):223-8.}, pages = {223-8}, abstract = {

The mechanism of proton exclusion in aquaporin channels is elucidated through free energy calculations of the pathway of proton transport. The second generation multistate empirical valence bond (MS-EVB2) model was applied to simulate the interaction of an excess proton with the channel environment. Jarzynski{\textquoteright}s equality was employed for rapid convergence of the free energy profile. A barrier sufficiently high to block proton transport is located near the channel center at the NPA motif-a site involved in bi-orientational ordering of the embedded water-wire in absence of the excess proton. A second and lower barrier is observed at the selectivity filter near the periplasmic outlet where the channel is narrowest. This secondary barrier may be essential in filtering other large solutes and cations.

}, keywords = {Aquaporins/*chemistry/*metabolism Biological Transport Cations/metabolism Computer Simulation Escherichia coli Proteins/*chemistry/*metabolism Models, Biological Models, Molecular Protein Conformation *Protons Substrate Specificity Thermodynamics Water/*metabolism}, doi = {10.1002/prot.20038}, author = {B. Ilan and E. Tajkhorshid and K. Schulten and G. A. Voth} } @article {375, title = {Mesoscopic Lateral Diffusion in Lipid Bilayers}, journal = {Biophys J}, volume = {87}, number = {5}, year = {2004}, note = {Ayton, Gary S Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2004 Nov;87(5):3299-311. Epub 2004 Aug 31.}, pages = {3299-311}, abstract = {

The lateral diffusion in bilayers is modeled with a multiscale mesoscopic simulation. The methodology consists of two simulations, where the first employs atomistic models to obtain exact results for the mesoscopic model. The second simulation takes the results obtained from the first to parameterize an effective force field that is employed in a new coarse-grained model. The multiscale aspect of this scheme occurs at the point where the microscopic time-averaged results of the first simulation are employed to parameterize the second simulation that operates in a higher spatial and temporal domain. The results of both simulation schemes give quantitative information on the details associated with lipid lateral diffusion.

}, keywords = {Artificial *Models, Chemical *Models, Cholesterol/chemistry Computer Simulation *Diffusion Dimyristoylphosphatidylcholine/chemistry Lipid Bilayers/*chemistry *Membrane Fluidity Membranes, Molecular Molecular Probes/*chemistry Motion Nanotubes/*chemistry}, doi = {10.1529/biophysj.104.047811}, author = {Ayton, G. S. and G. A. Voth} } @article {719, title = {Molecular Dynamics Simulation of Ionic Liquids: The Effect of Electronic Polarizability}, journal = {J. Phys. Chem. B}, volume = {108}, year = {2004}, pages = {11877-11881}, doi = {10.1021/jp047619y}, author = {T. Yan and C. J. Burnham and Popolo, M. G. Del and G. A. Voth} } @article {374, title = {A New Perspective on the Coarse-grained Dynamics of Fluids}, journal = {J Chem Phys}, volume = {120}, number = {9}, year = {2004}, note = {Ayton, Gary S Tepper, Harald L Mirijanian, Dina T Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States The Journal of chemical physics J Chem Phys. 2004 Mar 1;120(9):4074-88.}, pages = {4074-88}, abstract = {

A computational methodology is presented that is designed to model, at a coarse-grained level, the mesoscale dynamics of fluids and potentially other forms of soft matter. Within a molecular dynamics simulation, "ghost" particles of a specific size, corresponding to the fundamental length-scale of coarse-graining, are used as micro-probes designed to respond to local mesoscale fluid flows and stress gradients. A subsequent coarse-grained model is then developed that incorporates both the coarse-grained mesoscale dynamics and isothermal compressibility of the original microscopic system. The method is applied to water and methanol. A contrast with dissipative particle dynamics (DPD) is also presented.

}, keywords = {Chemical *Models, Colloids/*chemistry Computer Simulation Microfluidics/*methods *Models, Mechanical, Molecular Models, Statistical Molecular Conformation Motion Nanostructures/*chemistry Phase Transition Stress}, doi = {10.1063/1.1644092}, author = {Ayton, G. S. and H. L. Tepper and D. T. Mirijanian and G. A. Voth} } @article {376, title = {The Simulation of Biomolecular Systems at Multiple Length and Time Scales}, journal = {Int. J. for Multiscale Comp. Eng.}, volume = {2}, year = {2004}, pages = {291-311}, doi = {10.1615/IntJMultCompEng.v2.i2.80 }, author = {Ayton, G. S. and G. A. Voth} } @article {617, title = {On the Structure and Dynamics of Ionic Liquids}, journal = {J. Phys. Chem. B}, volume = {108}, year = {2004}, pages = {1744-1752}, doi = {10.1021/jp0364699}, author = {Popolo, M. G. Del and G. A. Voth} } @article {474, title = {Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. IV. Formal Analysis of the Deviations from Born-Oppenheimer Dynamics}, journal = {Israel. J. Chem.}, volume = {42}, year = {2003}, pages = {191-202}, doi = {10.1560/GLW2-8NVQ-4N6T-6C92}, author = {S. S. Iyengar and H. B. Schlegel and G. A. Voth and J. M. Millam and G. E. Scuseria and M. J. Frisch} } @article {473, title = {Atom-centered Density Matrix Propagation (ADMP): Generalizations using Bohmian Mechanics}, journal = {J. Phys. Chem.}, volume = {107}, year = {2003}, pages = {7269-7277}, doi = {10.1021/jp034633m}, author = {S. S. Iyengar and H. B. Schlegel and G. A. Voth} } @article {708, title = {Computational Studies of Proton Transport through the M2 Channel}, journal = {FEBS Lett}, volume = {552}, number = {1}, year = {2003}, note = {Wu, Yujie Voth, Gregory A GM53148/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. Review Netherlands FEBS letters FEBS Lett. 2003 Sep 18;552(1):23-7.}, pages = {23-7}, abstract = {

The M2 ion channel is an essential component of the influenza A virus. This low-pH gated channel has a high selectivity for protons. Evidence from various experimental data has indicated that the essential structure responsible for the channel is a parallel homo-tetrameric alpha-helix bundle having a left-handed twist with each helix tilted with respect to the membrane normal. A backbone structure has been determined by solid state nuclear magnetic resonance (NMR). Though detailed structures for the side chains are not available yet, evidence has indicated that His37 and Trp41 in the alpha-helix are implicated in the local molecular structure responsible for the selectivity and channel gate. More definitive conformations for the two residues were recently suggested based on the known backbone structure and recently obtained NMR data. While two competitive proton-conductance mechanisms have been proposed, the actual proton-conductance mechanism remains an unsolved problem. Computer simulations of an excess proton in the channel and computational studies of the His37/Trp41 conformations have provided insights into these structural and mechanism issues.

}, keywords = {Computer Simulation DNA/chemistry Histidine/chemistry Hydrogen-Ion Concentration Ions Magnetic Resonance Spectroscopy Models, Molecular Peptides/chemistry Protein Conformation Protein Structure, Secondary *Protons Tryptophan/chemistry Ultraviolet Rays Viral Matrix Proteins/*chemistry/metabolism}, doi = {10.1016/S0014-5793(03)00779-8}, author = {Y. Wu and G. A. Voth} } @article {683, title = {The Computer Simulation of Proton Transport in Biomolecular Systems}, journal = {Front Biosci}, volume = {8}, year = {2003}, note = {Voth, Gregory A GM-53148/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Research Support, U.S. Gov{\textquoteright}t, P.H.S. Review United States Frontiers in bioscience : a journal and virtual library Front Biosci. 2003 Sep 1;8:s1384-79.}, pages = {s1384-79}, abstract = {

A Molecular Dynamics computer simulation model for describing proton transport in biomolecular systems will be reviewed. The development of the underlying computational method which allows us to study the structural and dynamical properties of excess protons in these channels will first be discussed. Several applications of the methodology to study proton transport in channel environments will then be described. In each case, insight will be provided into the atomistic factors which determine the proton transport rate and the underlying mechanism(s) for the proton hopping process. More extensive background and results for the M2 channel in the influenza A virus will also be presented.

}, keywords = {Active *Computer Simulation Influenza A virus/chemistry/physiology Ion Channels/chemistry/physiology *Models, Amino Acid Sequence Biological Transport, Molecular Molecular Sequence Data *Protons Thermodynamics}, doi = {10.2741/1213}, author = {G. A. Voth} } @article {707, title = {A Computer Simulation Study of the Hydrated Proton in a Synthetic Proton Channel}, journal = {Biophys J}, volume = {85}, number = {2}, year = {2003}, note = {Wu, Yujie Voth, Gregory A GM53148/GM/NIGMS NIH HHS/United States Comparative Study Evaluation Studies Research Support, U.S. Gov{\textquoteright}t, P.H.S. Validation Studies United States Biophysical journal Biophys J. 2003 Aug;85(2):864-75.}, pages = {864-75}, abstract = {

Classical molecular dynamics simulations using the multistate empirical valence bond model for aqueous proton transport were performed to characterize the hydration structure of an excess proton inside a leucine-serine synthetic ion channel, LS2. For such a nonuniform pore size ion channel, it is found that the Zundel ion (H(5)O(2)(+)) solvation structure is generally more stable in narrow channel regions than in wider channel regions, which is in agreement with a recent study on idealized hydrophobic proton channels. However, considerable diversity in the relative stability of the Zundel to Eigen cation (H(9)O(4)(+)) was observed. Three of the five wide channel regions, one located at the channel{\textquoteright}s center and the other two located near the channel mouths, are found to show extraordinary preference for the Eigen solvation structure. This implies that proton hopping is inhibited in these regions and therefore suggests that these regions may behave as barriers in the proton conducting pathway inside the channel. The proton solvation is also greatly influenced by the local molecular environment of the protein. In particular, the polar side chains of the Ser residues, which are intimately involved in the solvation structure, can greatly influence proton solvation. However, no preference of the influence by the various Ser side chains was found; they can either promote or prevent the formation of certain solvation structures.

}, keywords = {Computer Simulation Ion Channel Gating Ion Channels/*chemistry Leucine/*chemistry Membrane Lipids/*chemistry *Models, Molecular Porosity Protein Conformation Proton Pumps/*chemistry *Protons Serine/*chemistry Water/*chemistry}, doi = {10.1016/S0006-3495(03)74526-3}, author = {Y. Wu and G. A. Voth} } @article {498, title = {An Improved Polarflex Water Model}, journal = {J. Chem. Phys.}, volume = {118}, year = {2003}, pages = {7504-7518}, doi = {10.1063/1.1560934}, author = {J. Jeon and Lefohn, A. E. and G. A. Voth} } @article {641, title = {Massively Parallel Linear-scaling Algorithm in an ab initio Local-orbital Total-energy Method}, journal = {J. Comp. Phys}, volume = {188}, year = {2003}, pages = {1-15}, doi = {10.1016/S0021-9991(03)00069-X}, author = {Shellman, S. D. and Lewis, J. P. and Glaesemann, K. R. and Sikorski, K. and G. A. Voth} } @article {469, title = {Modeling Condensed Phase Chemistry Through Molecular Dynamics Simulation}, journal = {Computers in Science and Engineering}, volume = {5}, year = {2003}, pages = {31-35}, doi = {10.1109/MCISE.2003.1208639}, author = {S. S. Iyengar and C. J. Burnham and Petersen, M. K. and G. A. Voth} } @article {646, title = {The Theory of Electron Transfer Reactions: What May Be Missing?}, journal = {J Am Chem Soc}, volume = {125}, number = {24}, year = {2003}, note = {Small, David W Matyushov, Dmitry V Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Journal of the American Chemical Society J Am Chem Soc. 2003 Jun 18;125(24):7470-8.}, pages = {7470-8}, abstract = {

Molecular dynamics simulations are presented for condensed-phase electron transfer (ET) systems where the electronic polarizability of both the solvent and the solute is incorporated. The solute polarizability is allowed to change with electronic transition. The results display notable deviation from the standard free energy parabolas of traditional ET theories. A new three-parameter ET model is applied, and the theory is shown to accurately model the free energy surfaces. This paper presents conclusive evidence that the traditional theory for the free energy barrier of ET reactions requires modification.

}, keywords = {Chemical *Thermodynamics, Computer Simulation Electrons *Models}, doi = {10.1021/ja029595j}, author = {Small, D. W. and Matyushov, D. V. and G. A. Voth} } @article {633, title = {Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born-Oppenheimer Dynamics}, journal = {J. Chem. Phys.}, volume = {117}, year = {2002}, pages = {8694-8704}, doi = {10.1063/1.1514582}, author = {H. B. Schlegel and S. S. Iyengar and X. Li and J. M. Millam and G. A. Voth and G. E. Scuseria and M. J. Frisch} } @article {582, title = {Ab initio Molecular Dynamics Simulation of the H/InP(100){\textendash}Water Interface}, journal = {J. Chem. Phys.}, volume = {117}, year = {2002}, pages = {872-884}, doi = {10.1063/1.1483070}, author = {Narayanan, G. and Izvekov, S. and G. A. Voth} } @article {365, title = {Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers}, journal = {Biophys J}, volume = {83}, number = {6}, year = {2002}, note = {Ayton, Gary Voth, Gregory A GM 63796/GM/NIGMS NIH HHS/United States Evaluation Studies Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2002 Dec;83(6):3357-70.}, pages = {3357-70}, abstract = {

A lipid bilayer is modeled using a mesoscopic model designed to bridge atomistic bilayer simulations with macro-scale continuum-level simulation. Key material properties obtained from detailed atomistic-level simulations are used to parameterize the meso-scale model. The fundamental length and time scale of the meso-scale simulation are at least an order of magnitude beyond that used at the atomistic level. Dissipative particle dynamics cast in a new membrane formulation provides the simulation methodology. A meso-scale representation of a dimyristoylphosphatidylcholine membrane is examined in the high and low surface tension regimes. At high surface tensions, the calculated modulus is found to be slightly less than the atomistically determined value. This result agrees with the theoretical prediction that high-strain thermal undulations still persist, which have the effect of reducing the value of the atomistically determined modulus. Zero surface tension simulations indicate the presence of strong thermal undulatory modes, whereas the undulation spectrum and the calculated bending modulus are in excellent agreement with theoretical predictions and experiment.

}, keywords = {*Algorithms Cell Membrane/chemistry Computer Simulation Dimyristoylphosphatidylcholine/chemistry Elasticity Lipid Bilayers/*chemistry *Membrane Fluidity Membranes, Artificial *Models, Chemical *Models, Mechanical Surface Tension, Molecular Molecular Conformation Molecular Structure Motion Stress}, doi = {10.1016/S0006-3495(02)75336-8}, author = {G. Ayton and G. A. Voth} } @article {364, title = {Calculating the Bulk Modulus for a Lipid Bilayer with Nonequilibrium Molecular Dynamics Simulation}, journal = {Biophys J}, volume = {82}, number = {3}, year = {2002}, note = {Ayton, Gary Smondyrev, Alexander M Bardenhagen, Scott G McMurtry, Patrick Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2002 Mar;82(3):1226-38.}, pages = {1226-38}, abstract = {

Nonequilibrium molecular dynamics (NEMD) computer simulations are used to calculated the bulk modulus for a dimyristoylphosphatidylcholine bilayer. A methodology is developed whereby NEMD can be effectively used to calculate material properties for complex systems that undergo long time-scale conformational changes. It is found that the bulk modulus upon expansion from a zero stress state agrees well with experimental estimates. However, it is also found that the modulus upon contraction from a zero stress state is larger. From a molecular perspective, it is possible to explain this phenomena by examining the molecular origins of the pressure response. The finding that the two moduli are not equal upon compression and expansion is in apparent contradiction to osmotic stress experiments where the area modulus was found to be the same upon expansion and contraction. This issue is addressed.

}, keywords = {Algorithms Computer Simulation Lipid Bilayers/*chemistry Osmosis Protein Conformation Temperature Time Factors Water/chemistry}, doi = {10.1016/S0006-3495(02)75479-9}, author = {G. Ayton and Smondyrev, A. M. and Bardenhagen, S. G. and P. McMurtry and G. A. Voth} } @article {479, title = {Car-Parrinello Molecular Dynamics Simulation of Liquid Water: New Results}, journal = {J. Chem. Phys.}, volume = {116}, year = {2002}, pages = {10372-10376}, doi = {10.1063/1.1473659}, author = {Izvekov, S. and G. A. Voth} } @article {540, title = {A Centroid Molecular Dynamics Approach for Nonadiabatic Dynamical Processes in Condensed Phases: The Spin-Boson Case}, journal = {J. Phys. Chem. B}, volume = {106}, year = {2002}, pages = {8449-8455}, doi = {10.1021/jp020978d}, author = {Liao, J. L. and G. A. Voth} } @article {363, title = {Interfacing Molecular Dynamics and Macro-scale Simulations for Lipid Bilayer Vesicles}, journal = {Biophys J}, volume = {83}, number = {2}, year = {2002}, note = {Ayton, Gary Smondyrev, Alexander M Bardenhagen, Scott G McMurtry, Patrick Voth, Gregory A United States Biophysical journal Biophys J. 2002 Aug;83(2):1026-38.}, pages = {1026-38}, abstract = {

A continuum-level model for a giant unilamellar vesicle (GUV) is bridged to a corresponding atomistic model of a dimyristoylphosphatidylcholine (DMPC) bilayer at various cholesterol concentrations via computation of the bulk modulus. The bulk modulus and other microscopically determined parameters are passed to a continuum-level model operating in time- and length-scales orders of magnitude beyond that which is accessible by atomistic-level simulation. The continuum-level simulation method used is the material point method (MPM), and the particular variation used here takes advantage of the spherical nature of many GUVs. An osmotic pressure gradient due to a solvent concentration change is incorporated into the continuum-level simulation, resulting in osmotic swelling of the vesicle. The model is then extended to treat mixtures of DMPC and cholesterol, where small domains of different composition are considered.

}, keywords = {Algorithms Biophysical Phenomena Biophysics Carbon/chemistry Cholesterol/chemistry Computer Simulation Dimyristoylphosphatidylcholine/chemistry Lipid Bilayers/*chemistry Membranes/chemistry Models, Statistical Osmosis Protein Structure, Tertiary Time Factors}, doi = {10.1016/S0006-3495(02)75228-4}, author = {G. Ayton and Smondyrev, A. M. and Bardenhagen, S. G. and P. McMurtry and G. A. Voth} } @article {648, title = {Molecular Dynamics Simulation of Proton Transport Near the Surface of a Phospholipid Membrane}, journal = {Biophys J}, volume = {82}, number = {3}, year = {2002}, note = {Smondyrev, Alexander M Voth, Gregory A GM53148/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2002 Mar;82(3):1460-8.}, pages = {1460-8}, abstract = {

The structural and dynamical properties of a hydrated proton near the surface of DMPC membrane were studied using a molecular dynamics simulation. The proton transport between water molecules was modeled using the second generation multistate empirical valence bond model. The proton diffusion was found to be inhibited at the membrane surface. The potential of mean force for the proton adsorption to the membrane surface and its release back into the bulk water was also determined, yielding a small barrier in each direction. An efficient algorithm for Ewald summation calculations for the multistate empirical valence bond model is also introduced.

}, keywords = {Adsorption Algorithms Biological Transport Cell Membrane/*metabolism Diffusion Dimyristoylphosphatidylcholine/chemistry Lipids/chemistry Models, Molecular Models, Statistical Phospholipids/*chemistry *Protons Water/chemistry}, doi = {10.1016/S0006-3495(02)75500-8}, author = {Smondyrev, A. M. and G. A. Voth} } @article {647, title = {Molecular Dynamics Simulation of Proton Transport through the Influenza A Virus M2 Channel}, journal = {Biophys J}, volume = {83}, number = {4}, year = {2002}, note = {Smondyrev, Alexander M Voth, Gregory A GM-53148/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2002 Oct;83(4):1987-96.}, pages = {1987-96}, abstract = {

The structural and dynamical properties of a solvated proton in the influenza A virus M2 channel are studied using a molecular dynamics (MD) simulation technique. The second-generation multi-state empirical valence bond (MS-EVB2) model was used to describe the interaction between the excess proton and the channel environment. Solvation structures of the excess proton and its mobility characteristics along the channel were determined. It was found that the excess proton is capable of crossing the channel gate formed by the ring of four histidine residues even though the gate was only partially open. Although the hydronium ion itself did not cross the channel gate by traditional diffusion, the excess proton was able to transport through the ring of histidine residues by hopping between two water molecules located at the opposite sides of the gate. Our data also indicate that the proton diffusion through the channel may be correlated with the changes in channel conformations. To validate this observation, a separate simulation of the proton in a "frozen" channel has been conducted, which showed that the proton mobility becomes inhibited.

}, keywords = {Biological Transport Biophysical Phenomena Biophysics Carbon/chemistry Computer Simulation Diffusion Dimyristoylphosphatidylcholine/chemistry Influenza A virus/*metabolism Ion Channel Gating Ion Channels/chemistry/physiology Lipid Bilayers/*chemistry Mode, Molecular Models, Statistical Protons Time Factors Viral Matrix Proteins/*chemistry/*physiology}, doi = {10.1016/S0006-3495(02)73960-X}, author = {Smondyrev, A. M. and G. A. Voth} } @inbook {739, title = {New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases}, booktitle = {Reviews in Computational Chemistry}, volume = {18}, year = {2002}, pages = {147-210}, publisher = {John Wiley and Sons}, organization = {John Wiley and Sons}, address = {New York}, author = {Matyushov, D. V. and G. A. Voth}, editor = {Lipkowitz, K. B. and Boyd, D. B.} } @article {541, title = {Numerical Approaches for Computing Nonadiabatic Electron Transfer Rate Constants}, journal = {J. Chem. Phys.}, volume = {116}, year = {2002}, pages = {9174-9187}, doi = {10.1063/1.1474584}, author = {Liao, J. L. and G. A. Voth} } @article {578, title = {Path Integral Molecular Dynamics Simulation of Solid Para-Hydrogen with an Aluminum Impurity}, journal = {Chem. Phys. Lett.}, volume = {365}, year = {2002}, pages = {487-493}, doi = {10.1016/S0009-2614(02)01505-1}, author = {D. T. Mirijanian and Alexander, M. H. and G. A. Voth} } @article {441, title = {A Second Generation Multi-State Empirical Valence Bond Model for Proton Transport in Aqueous Systems}, journal = {J. Chem. Phys.}, volume = {117}, year = {2002}, pages = {5839-5849}, doi = {10.1063/1.1497157}, author = {T. J. F. Day and Soudackov, A. V. and Cuma, M. and Schmitt, U. W. and G. A. Voth} } @article {510, title = {The Vibrational Spectrum of the Hydrated Proton: Comparison of Experiment, Simulation, and Normal Mode Analysis}, journal = {J. Chem. Phys.}, volume = {116}, year = {2002}, pages = {737-746}, doi = {10.1063/1.1423327}, author = {Kim, J. and Schmitt, U. W. and Gruetzmacher, J. A. and G. A. Voth and Scherer, N. F.} } @article {634, title = {Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals}, journal = {J. Chem. Phys.}, volume = {114}, year = {2001}, pages = {9758-9763}, doi = {10.1063/1.1372182}, author = {H. B. Schlegel and J. M. Millam and S. S. Iyengar and G. A. Voth and A. D. Daniels and G. E. Scuseria and M. J. Frisch} } @article {472, title = {Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. II. Generalization based on Mass-weighting, Idempotency, Energy Conservation, and Choice of Initial Conditions}, journal = {J. Chem. Phys.}, number = {115}, year = {2001}, pages = {10291-10302}, doi = {10.1063/1.1416876}, author = {S. S. Iyengar and H. B. Schlegel and J. M. Millam and G. A. Voth and G. E. Scuseria and M. J. Frisch} } @article {478, title = {Ab initio Molecular Dynamics Simulation of the Ag(111){\textendash}Water Interface}, journal = {J. Chem. Phys.}, volume = {115}, year = {2001}, pages = {7196-7206}, doi = {10.1063/1.1403438}, author = {Izvekov, S. and G. A. Voth} } @article {475, title = {Ab initio Molecular Dynamics Simulation of the Cu(110){\textendash}Water Interface}, journal = {J. Chem. Phys.}, volume = {114}, year = {2001}, pages = {3248}, doi = {10.1063/1.1342859}, author = {Izvekov, S. and A. Mazzolo and K. VanOpdorp and G. A. Voth} } @article {490, title = {Applications Of Higher Order Composite Factorization Schemes In Imaginary Time Path Integral Simulations}, journal = {J. Chem. Phys.}, volume = {115}, year = {2001}, pages = {7832-7842}, doi = {10.1063/1.1410117}, author = {S. Jang and S. Jang and G. A. Voth} } @article {393, title = {The Formation and Dynamics of Proton Wires in Channel Environments}, journal = {Biophys J}, volume = {80}, number = {4}, year = {2001}, note = {Brewer, M L Schmitt, U W Voth, G A GM-53148/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2001 Apr;80(4):1691-702.}, pages = {1691-702}, abstract = {

By virtue of an accurate interaction model, the equilibrium and dynamical properties of an excess proton in aqueous systems are studied, in which the water and excess proton are confined to hydrophobic cylindrical channels. Solvation structures of the excess proton and its mobility along the channel are considered as a function of the channel radius. It is found that when the aqueous proton systems are sufficiently constricted there is a substantial increase in the diffusion of the excess proton charge accompanied by a decrease in the diffusion of water molecules along the channel. Such systems present clear evidence for the possible existence of "proton wires."

}, keywords = {Biophysical Phenomena Biophysics Cations Computer Simulation Diffusion Kinetics Onium Compounds/chemistry Oxygen/chemistry *Protons Thermodynamics Water/*chemistry}, doi = {10.1016/S0006-3495(01)76140-1}, author = {Brewer, M. L. and Schmitt, U. W. and G. A. Voth} } @article {533, title = {Further Developments in the Local-Orbital Density-Functional-Theory Tight-Binding Method}, journal = {Phys. Rev. B}, volume = {64}, year = {2001}, pages = {195103}, doi = {10.1103/PhysRevB.64.195103}, author = {Lewis, J. P. and Glaesemann, K. R. and G. A. Voth and Fritsch, J. and Demkov, A. A. and Ortega, J. and O. F. Sankey, ", " 64, 195103-1:10 (2001).} } @article {361, title = {Interfacing Continuum and Molecular Dynamics: An Application to Lipid Bilayers}, journal = {J. Chem. Phys.}, volume = {114}, year = {2001}, pages = {6913-6924}, doi = {10.1063/1.1356001}, author = {G. Ayton and S Bardenhagen and P. McMurtry and D. Sulsky and G. A. Voth} } @article {362, title = {Interfacing Molecular Dynamics with Continuum Dynamics in Computer Simulation: Toward an Application to Biological Membranes}, journal = {IBM J. Res. Dev.}, volume = {45}, year = {2001}, pages = {417-426}, doi = {10.1147/rd.453.0417}, author = {G. Ayton and S Bardenhagen and P. McMurtry and D. Sulsky and G. A. Voth} } @article {531, title = {A Multi-State Empirical Valence Bond Approach to a Polarizable and Flexible Water Model}, journal = {J. Phys. Chem. B}, volume = {105}, year = {2001}, pages = {6628-6637}, doi = {10.1021/jp010103j}, author = {Lefohn, A. E. and Ovchinnikov, M. V. and G. A. Voth} } @article {438, title = {A Multi-State Empirical Valence Bond Model for Weak Acid Dissociation in Aqueous Solution}, journal = {J. Phys. Chem. A}, volume = {105}, year = {2001}, pages = {2814-2823}, doi = {10.1021/jp0038207}, author = {Cuma, M. and Schmitt, U. W. and G. A. Voth} } @article {386, title = {Path Integral Formulation of Centroid Dynamics for Systems Obeying Bose-Einstein Statistics}, journal = {J. Chem. Phys.}, volume = {115}, year = {2001}, pages = {4484}, doi = {10.1063/1.1392355}, author = {Blinov, N. V. and Roy, P. N. and G. A. Voth} } @article {452, title = {Quantum Mechanical Reaction Rate Constants from Centroid Molecular Dynamics Simulations}, journal = {J. Chem. Phys.}, volume = {115}, year = {2001}, pages = {9209-9222}, doi = {10.1063/1.1412870}, author = {Geva, E. and Shi, Q. and G. A. Voth} } @article {586, title = {Semiclassical Molecular Dynamics Computation of Spontaneous Light Emission in the Condensed Phase: Resonance Raman Spectra}, journal = {J. Chem. Phys.}, volume = {114}, year = {2001}, pages = {7130-7143}, doi = {10.1063/1.1357205}, author = {Ovchinnikov, M. and Apkarian, V. A. and G. A. Voth} } @article {602, title = {Centroid Molecular Dynamics: A Quantum Dynamics Method Suitable for the Parallel Computer}, journal = {Parallel Computing}, volume = {26}, year = {2000}, pages = {1025-1041}, doi = {10.1016/S0167-8191(00)00025-9}, author = {Pavese, M. and S. Jang and G. A. Voth} } @inbook {741, title = {Feynman Path Centroid Dynamics}, booktitle = {Progress in Theoretical Chemistry and Physics}, volume = {5}, year = {2000}, pages = {47-68}, publisher = {Kluwer}, organization = {Kluwer}, address = {Dordrecht}, doi = {10.1007/0-306-46949-9_2}, author = {G. A. Voth}, editor = {Schwartz, S. D.} } @article {638, title = {The Isotope Substitution Effect on the Hydrated Proton}, journal = {Chem. Phys. Lett.}, volume = {329}, year = {2000}, pages = {36-41}, doi = {10.1016/S0009-2614(00)00995-7}, author = {Schmitt, U. W. and G. A. Voth} } @article {561, title = {Modeling the Free Energy Surfaces of Electron Transfer in Condensed Phases}, journal = {J. Chem. Phys.}, volume = {113}, year = {2000}, pages = {5413-5424}, doi = {10.1063/1.1289886}, author = {Matyushov, D. and G. A. Voth} } @article {437, title = {A Multi-State Empirical Valence Bond Model for Acid-Base Chemistry in Aqueous Solution}, journal = {Chem. Phys. Lett.}, volume = {258}, year = {2000}, pages = {187}, doi = {10.1016/S0301-0104(00)00071-9}, author = {Cuma, M. and Schmitt, U. W. and G. A. Voth} } @article {460, title = {Simulating Accidental Fires and Explosions}, journal = {Computing in Science and Engineering}, volume = {2}, year = {2000}, pages = {64-76}, doi = {10.1109/5992.825750}, author = {Henderson, T. C. and McMurtry, P. A. and Smith, P. J. and G. A. Voth and Wight, C. A. and Pershing, D. W.} } @article {397, title = {Largescale Computer Simulation of an Electrochemical Bond Breaking Reaction}, journal = {Chem. Phys. Lett.}, volume = {305}, year = {1999}, pages = {94-100}, doi = {10.1016/S0009-2614(99)00353-X}, author = {A. Calhoun and Koper, M. T. M. and G. A. Voth} } @article {619, title = {Molecular Dynamics of Synthetic Leucine-serine Ion Channels in a Phospholipid Membrane}, journal = {Biophys J}, volume = {77}, number = {5}, year = {1999}, note = {Randa, H S Forrest, L R Voth, G A Sansom, M S GM-53148/GM/NIGMS NIH HHS/United States Wellcome Trust/United Kingdom Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t United States Biophysical journal Biophys J. 1999 Nov;77(5):2400-10.}, pages = {2400-10}, abstract = {

Molecular dynamics calculations were carried out on models of two synthetic leucine-serine ion channels: a tetrameric bundle with sequence (LSLLLSL)(3)NH(2) and a hexameric bundle with sequence (LSSLLSL)(3)NH(2). Each protein bundle is inserted in a palmitoyloleoylphosphatidylcholine bilayer membrane and solvated by simple point charge water molecules inside the pore and at both mouths. Both systems appear to be stable in the absence of an electric field during the 4 ns of molecular dynamics simulation. The water motion in the narrow pore of the four-helix bundle is highly restricted and may provide suitable conditions for proton transfer via a water wire mechanism. In the wider hexameric pore, the water diffuses much more slowly than in bulk but is still mobile. This, along with the dimensions of the pore, supports the observation that this peptide is selective for monovalent cations. Reasonable agreement of predicted conductances with experimentally determined values lends support to the validity of the simulations.

}, keywords = {Amino Acid Sequence Cell Membrane/chemistry/*metabolism Ion Channels/chemical synthesis/*chemistry/*metabolism *Leucine *Molecular Dynamics Simulation Molecular Sequence Data Phosphatidylcholines/chemistry/*metabolism Porosity Protein Structure, Secondary *Serine Substrate Specificity Water/chemistry/metabolism}, doi = {10.1016/S0006-3495(99)77077-3}, author = {H. S. Randa and L. R. Forrest and G. A. Voth and Sansom, M. S.} } @article {637, title = {Quantum Properties of the Excess Proton in Liquid Water}, journal = {Israeli J. Chem.}, volume = {39}, year = {1999}, pages = {483-492}, doi = {10.1002/ijch.199900053}, author = {Schmitt, U. W. and G. A. Voth} } @article {594, title = {Reactive Flux Calculations of Methyl Vinyl Ketone Reacting with Cyclopentadiene in Water}, journal = {J. Phys. Chem.}, volume = {103}, year = {1999}, pages = {925-931}, doi = {10.1021/jp983785s}, author = {Pak, Y. and G. A. Voth} } @article {669, title = {Temperature Dependence of the Solvent Reorganization Energy of Electron Transfer in Highly Polar Solvents}, journal = {J. Phys. Chem. B}, volume = {103}, year = {1999}, pages = {9130-9140}, doi = {10.1021/jp990494q}, author = {Vath, P. and Zimmt, M. B. and Matyushov, D. V. and G. A. Voth} } @article {402, title = {The Computer Simulation of Electron Transfer Processes Across the Electrode/Electrolyte Interface: A Treatment of Solvent and Electrode Polarizability}, journal = {J. Electroanal. Chem.}, volume = {450}, year = {1998}, pages = {253-264}, doi = {10.1016/S0022-0728(97)00644-X}, author = {A. Calhoun and G. A. Voth} } @article {551, title = {Molecular Dynamics Simulations of Human Carbonic Anhydrase II: Insight into Experimental Results and the Role of Solvation}, journal = {Proteins}, volume = {33}, number = {1}, year = {1998}, note = {Lu, D Voth, G A 1RO1-GM-53148/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United states Proteins Proteins. 1998 Oct 1;33(1):119-34.}, pages = {119-34}, abstract = {

In this paper, the carbonic anhydrase II (CA II) enzyme active site is modeled using ab initio calculations and molecular dynamics simulations to examine a number of important issues for the enzyme function. It is found that the Zn2+ ion is dominantly tetrahedrally coordinated, which agrees with X-ray crystallographic studies. However, a transient five-fold coordination with an extra water molecule is also found. Studies of His64 conformations upon a change in the protonation states of the Zn-bound water and the His64 residue also confirm the results of an X-ray study which suggest that the His64 conformation is quite flexible. However, the degree of water solvation is found to affect this behavior. Water bridge formation between the Zn-bound water and the His64 residue was found to involve a free energy barrier of 2-3 kcal/mol and an average lifetime of several picoseconds, which supports the concept of a proton transfer mechanism through such a bridge. Mutations of various residues around the active site provide further insight into the corresponding experimental results and, in fact, suggest an important role for the solvent water molecules in the CA II catalytic mechanism.

}, keywords = {Carbonic Anhydrases/*chemistry *Computer Simulation Histidine Humans Ligands *Models, Molecular Mutagenesis, Site-Directed *Protein Conformation Solvents Threonine Water Zinc}, doi = {10.1021/ja983579y}, author = {Lu, D. and G. A. Voth} } @article {604, title = {Quantum and Classical Simulations of an Excess Proton in Water}, journal = {Ber. Bunsenges. Phys. Chem.}, volume = {102}, year = {1998}, pages = {527-532}, doi = {10.1002/bbpc.19981020336}, author = {Pavese, M. and G. A. Voth} } @article {462, title = {Quantum Time Correlation Functions and Classical Coherence}, journal = {Chem. Phys.}, volume = {233}, year = {1998}, pages = {243-255}, doi = {10.1016/S0301-0104(98)00027-5}, author = {R. Hernandez and G. A. Voth} } @article {519, title = {A Theory for Adiabatic Bond Breaking Electron Transfer Reactions at Metal Electrodes}, journal = {Chem. Phys. Lett.}, volume = {282}, year = {1998}, pages = {100-106}, doi = {10.1016/S0009-2614(97)01155-X}, author = {Koper, M. T. M. and G. A. Voth} } @article {390, title = {A Theory for Electron Transfer between an Electrode and a Multilevel Acceptor/Donor Species in an Electrolyte Solution}, journal = {J. Electroanal. Chem.}, volume = {450}, year = {1998}, pages = {95-107}, doi = {10.1016/S0022-0728(97)00620-7}, author = {Boroda, Y. and G. A. Voth} } @article {666, title = {Classical Molecular Dynamics Simulation of the Photoinduced Electron Transfer Dynamics of Plastocyanin}, journal = {Biophys J}, volume = {72}, number = {1}, year = {1997}, note = {Ungar, L W Scherer, N F Voth, G A Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United states Biophysical journal Biophys J. 1997 Jan;72(1):5-17.}, pages = {5-17}, abstract = {

Classical molecular dynamics simulations are used to investigate the nuclear motions associated with photoinduced electron transfer in plastocyanin. The blue copper protein is modeled using a molecular mechanics potential; potential parameters for the copper-protein interactions are determined using an x-ray crystallographic structure and absorption and resonance Raman spectra. Molecular dynamics simulations yield a variety of information about the ground (oxidized) and optically excited (charge-transfer) states: 1) The probability distribution of the potential difference between the states, which is used to determine the coordinate and energy displacements, places the states well within the Marcus inverted region. 2) The two-time autocorrelation function of the difference potential in the ground state and the average of the difference potential after instantaneous excitation to the excited state are very similar (confirming linear response in this system); their decay indicates that vibrational relaxation occurs in about 1 ps in both states. 3) The spectral densities of various internal coordinates begin to identify the vibrations that affect the optical transition; the spectral density of the difference potential correlation function should also prove useful in quantum simulations of the back electron transfer. 4) Correlation functions of the protein atomic motions with the difference potential show that the nuclear motions are correlated over a distance of more than 20 A, especially along proposed electron transport paths.

}, keywords = {Binding Sites Computer Simulation Copper Electron Transport Mathematics Models, Molecular Photochemistry Plastocyanin/*chemistry/*metabolism/radiation effects Probability *Protein Conformation}, doi = {10.1016/S0006-3495(97)78642-9}, author = {Ungar, L. W. and Scherer, N. F. and G. A. Voth} } @article {398, title = {Hyper-Parallel Algorithms for Centroid Molecular Dynamics: Application to Liquid para{\textendash}Hydrogen}, journal = {Chem. Phys. Lett.}, volume = {262}, year = {1996}, pages = {415-420}, doi = {10.1016/0009-2614(96)01109-8}, author = {A. Calhoun and Pavese, M. and G. A. Voth} } @article {682, title = {Path Integral Centroid Methods in Quantum Statistical Mechanics and Dynamics}, journal = {Adv. Chem. Phys.}, volume = {93}, year = {1996}, pages = {135-218}, doi = {10.1002/9780470141526.ch4}, author = {G. A. Voth} } @article {603, title = {Pseudopotentials for Centroid Molecular Dynamics: Application to Self-Diffusion in Liquid para-Hydrogen}, journal = {Chem. Phys. Lett.}, volume = {249}, year = {1996}, pages = {231-236}, doi = {10.1016/0009-2614(95)01378-4}, author = {Pavese, M. and G. A. Voth} } @article {627, title = {Structure and Dynamics of Hydronium in the Ion Channel Gramicidin A}, journal = {Biophys J}, volume = {70}, number = {5}, year = {1996}, note = {Sagnella, D E Voth, G A Research Support, Non-U.S. Gov{\textquoteright}t United states Biophysical journal Biophys J. 1996 May;70(5):2043-51.}, pages = {2043-51}, abstract = {

The effects of the hydronium ion, H(3)0+, on the structure of the ion channel gramicidin A and the hydrogen-bonded network of waters within the channel were studied to help elucidate a possible mechanism for proton transport through the channel. Several classical molecular dynamics studies were carried out with the hydronium in either the center of a gramicidin monomer or in the dimer junction. Structural reorganization of the channel backbone was observed for different hydronium positions, which were most apparent when the hydronium was within the monomer. In both cases the average O-O distance between the hydronium ion and its nearest neighbor water molecule was found to be approximately 2.55 A, indicating a rather strong hydrogen bond. Importantly, a subsequent break in the hydrogen-bonded network between the nearest neighbor and the next-nearest neighbor(approximately 2.7 -3.0 A) was repeatedly observed. Moreover, the carbonyl groups of gramicidin A were found to interact with the charge on the hydronium ion, helping in its stabilization. These facts may have significant implications for the proton hopping mechanism. The presence of the hydronium ion in the channel also inhibits to some degree the reorientational motions of the channel water molecules.

}, keywords = {Alanine Dimerization Gramicidin/*chemistry Hydrogen Bonding *Ion Channels Kinetics Models, Molecular Onium Compounds/*chemistry *Protein Conformation Tryptophan Valine}, doi = {10.1016/S0006-3495(96)79773-4}, author = {Sagnella, D. E. and G. A. Voth} } @article {415, title = {A Theory for the Quantum Activated Rate Constant in Dissipative Systems}, journal = {Chem. Phys. Lett.}, volume = {261}, year = {1996}, pages = {111-116}, doi = {10.1016/0009-2614(96)00940-2}, author = {J. Cao and G. A. Voth} } @article {657, title = {Vibrational Energy Relaxation Dynamics of Si{\textendash}H Stretching Modes on Stepped H/Si(111)1x1 Surfaces}, journal = {Chem. Phys.}, volume = {20}, year = {1995}, pages = {357-368}, doi = {10.1016/0301-0104(95)00270-7}, author = {Sun, Y.-C. and H. Gai and G. A. Voth} } @article {538, title = {Calculation of ESR Linewidths for Hydrogen Atom Impurities in Solid para-Hydrogen}, journal = {J. Chem. Phys.}, volume = {100}, year = {1994}, pages = {1785-1796}, doi = {10.1063/1.466531}, author = {Li, D. H. and G. A. Voth} } @inbook {738, title = {Quantum Mechanical Calculations of Tunneling Rates in Condensed Phases Systems}, booktitle = {Reaction Dynamics in Clusters and Condensed Phases}, year = {1994}, pages = {411-422}, publisher = {Kluwer Academic Publishers}, organization = {Kluwer Academic Publishers}, address = {The Netherlands}, author = {J. Lobaugh and G. A. Voth} } @article {626, title = {A Semiclassical Reactive Flux Method for the Calculation of Condensed Phase Activated Rate Constants}, journal = {Chem. Phys.}, volume = {180}, year = {1994}, pages = {167-180}, doi = {10.1016/0301-0104(93)E0419-V}, author = {Sagnella, D. E. and J. Cao and G. A. Voth} } @inbook {740, title = {A Feynman Path Integral Formulation of Quantum Mechanical Transition State Theory}, booktitle = {New Trends in Kramers{\textquoteright} Reaction Rate Theory}, year = {1993}, publisher = {Kluwer Academic Publishers}, organization = {Kluwer Academic Publishers}, address = {The Netherlands}, doi = {10.1021/j100134a002}, author = {G. A. Voth}, editor = {Talkner, P. and H{\"a}nggi, P.} } @article {458, title = {A Theory for the Thermally Activated Rate Constant in Systems with Spatially Dependent Friction}, journal = {Chem. Phys. Lett.}, volume = {207}, year = {1993}, pages = {309-316}, doi = {10.1016/0009-2614(93)89005-3}, author = {Haynes, G. R. and G. A. Voth and Pollak, E.} } @article {537, title = {A Variational Model for the Thermodynamical and Structural Properties of Impurities in Low Temperature Solids}, journal = {J. Chem. Phys.}, volume = {98}, year = {1993}, pages = {5734-5746}, doi = {10.1063/1.464866}, author = {Li, D. H. and G. A. Voth} } @article {448, title = {Vibrational Energy Relaxation Dynamics of Si{\textendash}H Stretching Modes on the H/Si(111)11 Surface}, journal = {J. Chem. Phys.}, volume = {99}, year = {1993}, pages = {740-743}, doi = {10.1063/1.465748}, author = {H. Gai and G. A. Voth} } @article {547, title = {Calculation of Quantum Activation Free Energies for Proton Transfer Reactions in Polar Solvents}, journal = {Chem. Phys. Lett.}, volume = {198}, year = {1992}, pages = {311-315}, doi = {10.1016/0009-2614(92)85057-H}, author = {J. Lobaugh and G. A. Voth} } @article {455, title = {Effect of Nonlinear Dissipation on Quantum-activated Rate Processes in Condensed Phases}, journal = {Phys Rev A}, volume = {46}, number = {4}, year = {1992}, note = {Haynes Voth Journal article Physical review. A Phys Rev A. 1992 Aug 15;46(4):2143-2146.}, pages = {2143-2146}, doi = {10.1103/PhysRevA.46.2143}, author = {Haynes, G. R. and G. A. Voth} } @article {677, title = {Calculation of Equilibrium Averages with Feynman-Hibbs Effective Classical Potentials and Similar Variational Approximations}, journal = {Phys Rev A}, volume = {44}, number = {8}, year = {1991}, note = {Voth Journal article Physical review. A Phys Rev A. 1991 Oct 15;44(8):5302-5305.}, pages = {5302-5305}, doi = {10.1103/PhysRevA.44.5302}, author = {G. A. Voth} } @article {679, title = {A Feynman Path Integral Approach for Calculating Quantum Rate Constants in Complex Systems}, journal = {Ber. Bunsenges. Phys. Chem.}, volume = {95}, year = {1991}, pages = {393-399}, doi = {10.1002/bbpc.19910950330}, author = {G. A. Voth} } @article {676, title = {Analytic Expression for the Transmission Coefficient in Quantum Mechanical Transition State Theory}, journal = {Chem. Phys. Lett.}, volume = {170}, year = {1990}, pages = {289-296}, doi = {10.1016/0009-2614(90)87130-J}, author = {G. A. Voth} } @inbook {742, title = {A New Perspective on Quantum Mechanical Transition State Theory}, booktitle = {Quantum Simulations of Condensed Matter Phenomena}, year = {1990}, pages = {391-400}, publisher = {World Scientific}, organization = {World Scientific}, address = {Singapore}, author = {G. A. Voth and D. Chandler and W. H. Miller}, editor = {Doll, J. D. and Gubernatis, J. E.} } @article {528, title = {Vibrational Energy Redistribution Across a Heavy Atom}, journal = {Chem. Phys.}, volume = {139}, year = {1989}, pages = {171-184}, doi = {10.1016/0301-0104(89)90010-4}, author = {Lederman, S. M. and Lopez, V. and Fairen, V. and G. A. Voth and Marcus, R. A.} } @article {673, title = {Approximate Coupled Equations for Multiphoton Processes Induced by One or More Lasers}, journal = {Chem. Phys. Lett.}, volume = {129}, year = {1986}, pages = {315-320}, doi = {10.1016/0009-2614(86)80219-6}, author = {G. A. Voth} } @article {511, title = {Iteratively Determined Effective Hamiltonians for the Adiabatically Reduced Coupled Equations Approach to Intramolecular Dynamics Calculations}, journal = {J. Chem. Phys.}, volume = {85}, year = {1986}, pages = {5019-5026}, doi = {10.1063/1.451691}, author = {Klippenstein, S. J. and G. A. Voth and Marcus, R. A.} } @article {529, title = {Quantum and Classical Energy Transfer Between Ligands of a Heavy Metal Atom}, journal = {Chem. Phys. Lett.}, volume = {124}, year = {1986}, pages = {93-98}, doi = {10.1016/0009-2614(86)85020-5}, author = {Lederman, S. M. and Lopez, V. and G. A. Voth and Marcus, R. A.} } @article {691, title = {The Highly Excited C-H Stretching States of CHD3, CHT3, and CH3D}, journal = {J. Chem. Phys.}, volume = {81}, year = {1984}, pages = {5494-5507}, doi = {10.1063/1.447650}, author = {G. A. Voth and Marcus, R. A. and Zewail, A. H.} }