Publications
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2008. User Needs Analysis to Design a 3D Multimodal Protein-Docking Interface. Symposium on 3D User Interfaces 2008 (3DUI 2008 - IEEE). :125–132.
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2008. A VR Framework for Interacting with Molecular Simulations. Symposium on Virtual Reality Software and Technology (ACM-VRST 2008). :91–94.
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2008. Water-water hydrogen bond studied by QMC. J. Chem. Theory. Comput.. 4:1428–1432.
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2009. Analysis of accordion DNA stretching revealed by the gold cluster ruler. Phys. Rev. E. 80:010901.
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2009. Charge Recombination Kinetics and Protein Dynamics in Wild Type and Carotenoid-less Bacterial Reaction Centers: Studies in Trehalose Glasses. J. Phys. Chem. B. 113:10389–1398.
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2009. Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states. Chemphyschem. 10:1548–1552.
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2009. Complex molecular assemblies at hand via interactive simulations. J. Comput. Chem.. 30:2375–2387.
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2009. Coarse-graining protein mechanics. Coarse-Graining of Condensed Phase and Biomolecular Systems
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2009. The Conversion of Helix H2 to beta-Sheet Is Accelerated in the Monomer and Dimer of the Prion Protein upon T183A Mutation. J. Phys. Chem. B. 113:6942–6948.
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2009. Deforming DNA: from physics to biology. Chemphyschem. 10:1399–404.
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2009. Disulfide bond substitution by directed evolution in an engineered binding-protein scaffold.. Chembiochem. 10:1349–1359.
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2009. Ets-1 p51 and p42 isoforms differentially modulate Stromelysin-1 promoter according to induced DNA bend orientation. Nucleic Acids Res.. 37:4341–4352.
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2009. Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study. J. Phys. Chem. B. 113:9340–9347.
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2009. Estimating configurational entropy of complex molecules: A novel variable transformation approach. Chem. Phys. Lett.. 468:90–93.
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2009. Exploring amyloid aggregates with the OPEP coarse-grained force field. Abstracts of Papers of the American Chemical Society. 238
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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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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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2009. The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15 N chemical shifts. Biophys. Chem.. 143:111–123.
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2009. Induced beta-Barrel Formation of the Alzheimer’s A beta 25-35 Oligomers on Carbon Nanotube Surfaces: Implication for Amyloid Fibril Inhibition. Biophys. J.. 97:1795–1803.
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2009. Induced beta-barrel formation of the Alzheimer's Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition.. Biophys. J.. 97:1795–1803.
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2009. Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. Plos Comput. Biol.. 5:e1000267.
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2009. Key role of proximal water in regulating thermostable proteins. J. Phys. Chem. B. 113:131–7.
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2009. Kinetic and thermodynamic DNA elasticity at micro- and mesoscopic scales. J. Phys. Chem. B. 113:2077–2089.
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2009. Modeling the Mechanical Response of Proteins to Anisotropic Deformation. Chemphyschem. 10:115–118.
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2009. Mean field and the confined single homopolymer. Mol. Phys.. 107:1303–1312.