Publications
] . Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes. Biophys. J. 2019 ;117(3):553–562.
. Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. J. Phys. Chem. Lett. 2019 ;10(16):4549–4557.
. Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations. Acc Chem Res. 2007 ;40:1193-9.
. Understanding Dynamics in Coarse-Grained Models: III. Roles of Rotational Motion and Translation-Rotation Coupling in Coarse-Grained Dynamics. J. Chem. Phys. 2023 ;159:164102.
. Understanding Dynamics in Coarse-Grained Models: II. Coarse-Grained Diffusion Modeled Using Hard Sphere Theory. J. Chem. Phys. 2023 ;158(3):034104.
. Understanding Dynamics in Coarse-Grained Models: I. Universal Excess Entropy Scaling Relationship. J. Chem. Phys. 2023 ;158(3):034103.
. Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems. J. Chem. Theory Comput. 2018 ;14(4):2180–2197.
. Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding. J. Chem. Theory Comput. 2018 ;14(12):6159–6174.
. The Theory of Ultra-Coarse-Graining. 3. Coarse-grained Sites with Rapid Local Equilibrium of Internal States. J. Chem. Theory Comput. 2017 ;13.
. Temperature and Phase Transferable Bottom-up Coarse-Grained Models. J. Chem. Theory Comput. 2020 ;16(11):6823–6842.
. Structure of the Liquid−Vacuum Interface of Room-Temperature Ionic Liquids: A Molecular Dynamics Study. J Phys Chem B. 2006 ;110:1800-6.
. Statistical Mechanical Design Principles for Coarse-grained Interactions Across Different Conformational Free Energy Surfaces. J. Phys. Chem. Lett. 2023 ;14(6):1354–1362.
. Simple Reversible Molecular Dynamics Algorithms for Nos[e-acute]–Hoover Chain Dynamics. The Journal of Chemical Physics. 1997 ;107:9514-9526.
. Seipin Transmembrane Segments Critically Function in Triglyceride Nucleation and Droplet Budding from the Membrane. eLife. 2022 ;11:e75808.
. A Relationship between Centroid Dynamics and Path Integral Quantum Transition State Theory. The Journal of Chemical Physics. 2000 ;112:8747-8757.
. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148(10):102335.
. Quantum Molecular Dynamics Simulations of Low-Temperature High Energy Density Matter: Solid p-H2/Li and p-H2/B. The Journal of Physical Chemistry A. 1999 ;103:9512-9520.
. Quantum Molecular Dynamics Simulations of Low-Temperature High Energy Density Matter: Solid p-H2/Li and p-H2/B. The Journal of Physical Chemistry A. 1999 ;103:9512-9520.
. Quantum Molecular Dynamics and Spectral Simulation of a Boron Impurity in Solid Para-hydrogen. The Journal of Chemical Physics. 2000 ;113:9079-9089.
. Quantum Dynamical Simulation of the Energy Relaxation Rate of the CN- Ion in Water. The Journal of Physical Chemistry A. 1999 ;103:10289-10293.
. Proton Conduction in Exchange Membranes Across Multiple Length Scales. Acc. Chem. Res. 2012 ;45:2002-2010.
. Path Integral Centroid Variables and the Formulation of their Exact Real Time Dynamics. The Journal of Chemical Physics. 1999 ;111:2357-2370.
. OpenMSCG: A Software Tool for Multiscale Coarse-graining. J. Phys. Chem. B. 2023 ;127:8537–8550.
. Non-Uniqueness of Quantum Transition State Theory and General Dividing Surfaces in the Path Integral Space. J. Chem. Phys. 2017 ;146.
. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-Body Projected Water (BUMPer). II. Temperature Transferability and Structural Properties at Low Temperature. J. Chem. Phys. 2021 ;154(4):044105.
. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-body Projected Water (BUMPer). I. General Theory and Model. J. Chem. Phys. 2021 ;154(4):044104.
. Nanostructural Organization in Acetonitrile/Ionic Liquid Mixtures: Molecular Dynamics Simulations and Optical Kerr Effect Spectroscopy. ChemPhysChem. 2012 ;13:1687-1700.
. A Multiscale Coarse-Graining Study of Liquid/Vacuum Interface of Room-Temperature Ionic Liquids with Alkyl Substituents of Different Lengths. J. Phys. Chem. C. 2008 ;112:1132-1139.
. Multiscale Coarse-Graining of the Protein Energy Landscape. PLoS Comp. Bio. 2010 ;6:e1000827.
. Molecular Dynamics Simulation of the Energetic Room Temperature Ionic Liquid 1-Hydroxyethyl-4Amino-1, 2, 4-Triazolium Nitrate (HEATN). J. Phys. Chem. B. 2008 ;112:3121-3131.
. Molecular Dynamics Simulation of Nanostructural Organization in Ionic Liquid/Water Mixtures. J Phys Chem B. 2007 ;111:4812-8.
. A Modification of Path Integral Quantum Transition State Theory for Asymmetric and Metastable Potentials. The Journal of Physical Chemistry A. 1999 ;103:9527-9538.
. Mesoscale Simulation of Proton Transport in Proton Exchange Membranes. J. Phys. Chem. C. 2012 ;116:935-944.
. Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain. J. Mol. Biol. 2012 ;423:800-817.
. Mechanism of Targeting of Amphipathic Helix-Containing Proteins to Lipid Droplets. Dev. Cell. 2018 ;44(1):73–86.
Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
. Lithium Impurity Recombination in Solid Para-hydrogen: A Path Integral Quantum Transition State Theory Study. The Journal of Chemical Physics. 1998 ;108:4098-4106.
. Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins. Biophys. J. 2021 ;120(1):46–54.
. Ligand-Dependent Activation and Deactivation of a G Protein-Coupled Receptor. J. Am. Chem. Soc. 2013 ;135:8749-8759.
. Key Factors Governing Initial Stages of Lipid Droplet Formation. J. Phys. Chem. B. 2022 ;126(2):453–462.
. Key Computational Findings Reveal Proton Transfer as Driving the Functional Cycle in the Phosphate Transporter PiPT. Proc. Natl. Acad. Sci. USA. 2021 ;118(25):e2101932118.
. An Improved Polarflex Water Model. J. Chem. Phys. 2003 ;118:7504-7518.
. How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes. Proc. Nat. Acad. Sci. USA. 2016 .
. Gaussian Representation of Coarse-Grained Interactions of Liquids: Theory, Parametrization, and Transferability. J. Chem. Phys. 2023 ;159:184105.
. Gating of the Mechanosensitive Channel Protein MscL: The Interplay of Membrane and Protein. Biophys. J. 2008 ;94:3497-3511.
. Feynman Path Centroid Dynamics for Fermi–Dirac Statistics. The Journal of Chemical Physics. 1999 ;111:5303-5305.
. A Feynman Path Centroid Dynamics Approach for the Computation of Time Correlation Functions Involving Nonlinear Operators. The Journal of Chemical Physics. 2000 ;113:919-929.
. Extending the Range and Physical Accuracy of Coarse-grained Models: Order Parameter Dependent Interactions. J. Chem. Phys. 2017 .
. An Electrochemically and Thermally Switchable Donor-Acceptor [c2]Daisy Chain Rotaxane. Angewandte Chemie. 2014 ;53:1953-1958.
. The Dynamic Stress Responses to Area Change in Planar Lipid Bilayer Membranes. Biophys J. 2005 ;88:1104-19.
. A Derivation of Centroid Molecular Dynamics and Other Approximate Time Evolution Methods for Path Integral Centroid Variables. The Journal of Chemical Physics. 1999 ;111:2371-2384.
. Constructing Many-body Mesoscopic Models of Fluids from Bottom-up Coarse-graining. J. Chem. Phys. 2021 ;154(8):084122.
. Coarse-Graining Involving Virtual Sites: Centers of Symmetry Coarse-Graining. J. Chem. Phys. 2019 ;150(15):154103.
. Coarse-grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly. Nat. Comm. 2016 ;7(1156):1-11.
. Coarse-Grained Simulation of Full-Length Integrin Activation. Biophys. J. 2019 ;116(6):1000–1010 .
. Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover. J. Chem. Theory Comput. 2021 ;17(2):1170–1180.
. Cholesterol Alters the Membrane Orientation and Activity of the Influenza Virus M2 Amphipathic Helix. J. Phys. Chem. B. 2020 ;124(31):6738–6747 .
. Centroid Molecular Dynamics: A Quantum Dynamics Method Suitable for the Parallel Computer. Parallel Computing. 2000 ;26:1025-1041.
. Can the Ring Polymer Molecular Dynamics Method be Interpreted as Real Time Quantum Dynamics?. J. Chem. Phys. 2014 ;140:1-11.
. Can Quantum Transition State Theory be Defined as a t = 0+ Limit?. J. Chem. Phys. 2016 ;144(084110):1-12.
. Bottom-up Coarse-Graining: Principles and Perspectives. J. Chem. Theory Comput. 2022 ;18(10):5759–5791.
. Atomistic Modeling of the Electrode-Electrolyte Interface in Li-ion Energy Storage Systems: Electrolyte Structuring. J. Phys. Chem. C. 2013 ;17.
. Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6). Sci. Adv. 2020 ;6(36).
. Applications Of Higher Order Composite Factorization Schemes In Imaginary Time Path Integral Simulations. J. Chem. Phys. 2001 ;115:7832-7842.
. Applications Of Higher Order Composite Factorization Schemes In Imaginary Time Path Integral Simulations. J. Chem. Phys. 2001 ;115:7832-7842.
Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
. Spatial Heterogeneity in Ionic Liquids. In: Ionic Liquids IV. Not Just Solvents Anymore. Ionic Liquids IV. Not Just Solvents Anymore. Washington DC: American Chemical Society; 2007. pp. 272-307.
. Quantum Rate Theory: A Path Integral Centroid Perspective. In: Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods. Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods. ; 2005.