Publications
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1985. Dry deposition of nitric acid to grass. J. Geophys. Res.. 90:2085–2090.
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2010. Single-spanning transmembrane domains in cell growth and cell-cell interactions: More than meets the eye? Cell Adh. Migr.. 4:313–324.
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2018. Controlling Redox Enzyme Orientation at Planar Electrodes. Catalysts. 8
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2014. Molecular simulations and visualization: introduction and overview. Faraday Discuss.. 169:9–22.
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2004. DNA in Virtuo: Visualization and Virtual Manipulation of 3D Genomic Structures. International CODATA Conference, The Information Society: New Horizons for Science.
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2004. DNA in Virtuo: Visualization and Exploration of 3D Genomic Structures. International Conference on Virtual Reality, Computer Graphics, Visualization and Interaction (Afrigraph 2005 - ACM-SIGRAPH sponsored).
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2008. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys. J.. 94:832–839.
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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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2010. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J. Chem. Theory Comput.. 6:35–47.
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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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2004. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J. Chem. Phys.. 121:2904–2914.
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2009. Models for phosphatidylglycerol lipids put to a structural test. J. Phys. Chem. B. 113:6958–6963.
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2014. A predicted binding site for cholesterol on the GABAA receptor.. Biophys. J.. 106:1938–1949.
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2006. Hydrogen-bonding patterns of cholesterol in lipid membranes. Chem. Phys. Lett.. 425:329–335.
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2021. Fast and Accurate Multidimensional Free Energy Integration.. J Chem Theory Comput. 17(11):6789-6798.
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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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2022. Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD.. J Chem Theory Comput. 18(3):1945-1956.
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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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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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2006. Probing a model of a GPCR/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor. Biophys. J.. 90:1232–1240.
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2008. United-Atom Acyl Chains for CHARMM Phospholipids. J. Phys. Chem. B.. 112:7008–7015.
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2007. How complex is the dynamics of peptide folding? Phys. Rev. Lett.. 98
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2010. Sequence-dependent DNA flexibility mediates DNase I cleavage. J. Mol. Biol.. 395:123–133.
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2008. Importance of accurate DNA structures in solution: the Jun-Fos model.. J. Mol. Biol.. 382:956–70.
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2010. Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res.. 38:1034–1047.