Publications
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2014. Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins. Membrane Proteins Production for Structural Analysis. :347–392.
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2015. The adaptive biasing force method: everything you always wanted to know but were afraid to ask.. J. Phys. Chem. B. 119:1129–51.
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2014. Allosteric regulation of pentameric ligand-gated ion channels: An emerging mechanistic perspective. Channels. 8:350–360.
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2010. An atomistic model for simulations of the general anesthetic isoflurane. J. Phys. Chem. B. 114:604–612.
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2020. Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys. Chem. Chem. Phys.. 22:24014-24027.
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2021. Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry. The Journal of Chemical Physics. 154:204101.
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2014. CHARMM36 united atom chain model for lipids and surfactants.. J. Phys. Chem. B. 118:547–556.
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2006. Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations. J. Phys. Chem. B. 110:16718–16723.
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2022. Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
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2008. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys. J.. 94:832–839.
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2008. Embedded cholesterol in the nicotinic acetylcholine receptor. Proc. Natl. Acad. Sci. U.s.a.. 105:14418–14423.
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2022. Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 4:1583.
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2016. Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors.. Plos One. 11:e0151934.
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2010. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J. Chem. Theory Comput.. 6:35–47.
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2005. Exploring the free energy landscape of a short peptide using an average force. J. Chem. Phys.. 123:244906.
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2021. Fast and Accurate Multidimensional Free Energy Integration.. J Chem Theory Comput. 17(11):6789-6798.
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2012. General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity. Plos Comput. Biol.. 8:e1002532.
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2022. Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD.. J Chem Theory Comput. 18(3):1945-1956.
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2006. Hydrogen-bonding patterns of cholesterol in lipid membranes. Chem. Phys. Lett.. 425:329–335.
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2005. Insights into the recognition and association of transmembrane $\alpha$-helices. The free energy of $\alpha$-helix dimerization in glycophorin A. J. Am. Chem. Soc.. 127:8478–8484.
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2014. Lipid concentration and molar ratio boundaries for the use of isotropic bicelles.. Langmuir. 30:6162–6170.
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2021. Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.. Front Chem. 9:650651.
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2015. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.. J. Membr. Biol.. 248
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2017. A membrane-inserted structural model of the yeast mitofusin Fzo1. Sci Rep. 7(1):10217.
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2009. Models for phosphatidylglycerol lipids put to a structural test. J. Phys. Chem. B. 113:6958–6963.