Publications
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2009. Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis. J. Phys. Chem. B. 113:16660–16668.
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2008. Free energy surface of Abeta(16-22) complexed by N-methylated Abeta16-22 inhibitors. Publication Series of the John von Neumann Institute for Computing NIC Series. 40:177–179.
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2011. Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening. J. Chem. Theor. Comput.. 7:2348–52.
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2005. Free energy landscape and folding mechanism of a beta-hairpin in explicit water: A replica exchange molecular dynamics study. Proteins: Struct., Funct., Bioinf.. 61:795–808.
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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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2018. Forcing the reversibility of a mechanochemical reaction. Nat Commun. 9:3155.
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1994. FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .2. MALTOSE MONOHYDRATE, CELLOBIOSE AND GENTIOBIOSE. Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy. 50:105–118.
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1994. FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .1. TREHALOSE DIHYDRATE, SOPHOROSE MONOHYDRATE AND LAMINARIBIOSE. Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy. 50:87–104.
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2018. The force-dependent mechanism of DnaK-mediated mechanical folding. Sci Adv. 4:eaaq0243.
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2005. Following the aggregation of amyloid-forming peptides by computer simulations. J. Chem. Phys.. 122:174904.
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2005. Following the aggregation of amyloid-forming peptides by computer simulations.. Abstracts of Papers of the American Chemical Society. 229:U735.
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2015. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J. Phys. Chem. B. 119:6941–6951.
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1998. Folding and Aggregation of Designed Protein Chains. Proc. Natl. Acad. Sci. Usa. 95:12930–1293.
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1997. Folding a 20 amino acid alpha beta peptide with the diffusion process-controlled Monte Carlo method. J. Chem. Phys.. 107:1941–1947.
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2002. Fluids confined by nanopatterned substrates of low symmetry. Mol. Phys.. 100:2971–2982.
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2003. Fluid phase transitions at chemically heterogeneous, nonplanar solid substrates: Surface versus confinement effects. J. Chem. Phys.. 118:1453–1465.
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2008. Fluctuation-induced interactions between dielectrics. J. Chem. Phys.. 129:014703.
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2012. Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. Journal of the Royal Society Interface. 9:20–33.
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1998. Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method. J. Chem. Phys.. 109:1567–1574.
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1996. Finding and visualizing nucleic acid base stacking. J Mol Graph. 14:6–11.
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2010. A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction. J. Comput. Chem.. 31:726–738.
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2009. A fast method for large-scale De Novo peptide and miniprotein structure prediction.. J. Comput. Chem..
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2017. Fast coarse-grained model for RNA titration.. J Chem Phys. 146(3):035101.
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2021. Fast and Accurate Multidimensional Free Energy Integration.. J Chem Theory Comput. 17(11):6789-6798.