Publications
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2010. Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys.. 132
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2010. Sequence-dependent DNA flexibility mediates DNase I cleavage. J. Mol. Biol.. 395:123–133.
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2010. Side-chain rotamer transitions at protein-protein interfaces. Proteins: Struct., Funct., Bioinf.. 78:3219–25.
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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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2010. The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif. J. Phys. Chem. B. 114:13839–13846.
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2010. Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues. J. Physiol. (lond.). 588:565–572.
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2010. The VLITL aggregation-prone motif might trigger amyloid fibril formation of fibrinogen A alpha-chain frameshift variants in vivo. Amyloid-journal of Protein Folding Disorders. 17:96–97.
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2010. Water around thermophilic proteins: the role of charged and apolar atoms. J Phys: Cond Matt. 22:284113.
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2010. Water hydrogen bond dynamics in aqueous solutions of amphiphiles. J. Phys. Chem. B. 114:3052–3059.
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2010. Water hydrogen-bond dynamics around amino acids: the key role of hydrophilic hydrogen-bond acceptor groups. J. Phys. Chem. B. 114:2083–9.
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2010. Water reorientation, hydrogen-bond dynamics and 2D-IR spectroscopy next to an extended hydrophobic surface.. Farad. Discuss.. 146:263–281.
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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..