Publications
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2003. Titration \em in silico of reversible B$łeftrightarrow$A transitions in DNA. J. Am. Chem. Soc.. 125:7849–7859.
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1991. Derivation and testing of explicit equations of motion for polymers described by internal coordinates. J. Comput. Phys.. 92:261–272.
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1999. Internal correlations in minor groove profiles of experimental and computed B-DNA conformations. J. Mol. Biol.. 290:373–377.
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2014. Atomic force microscopy study of DNA flexibility on short length scales: Smooth bending versus kinking. Nucleic. Acids. Res.. 42:14006–14012.
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1990. Toward a theory of quasi-steady-state enzymatic processes. Mol. Biol.. 24:202–208.
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2008. The electrostatic origin of low-hydration polymorphism in DNA. Chemphyschem in Press. 9:2691–2694.
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2012. Torque transfer coefficient in DNA under torsional stress. Phys. Rev. E. 86:011914.
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1994. The catalytic mechanism of {$\alpha$}-amylases based upon enzyme crystal structures and model building calculations. Biochem. Biophys. Res. Commun.. 204:297–302.
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2007. Wormlike chain theory and bending of short DNA. Phys. Rev. Lett.. 98:218102.
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2002. DNA dynamics in a water drop without counterions. J. Am. Chem. Soc.. 124:14707–14715.
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2001. Internal coordinate simulation method. Computational Biochemistry and Biophysics. :115–131.
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1988. Model of spatial random movement of depolymerase when interacting with the substrate. Biophysics. 23:417–421.
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2013. Comment on ``Length Scale Dependence of DNA Mechanical Properties''. Phys. Rev. Lett.. 111
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1990. A new method for analysing of kinetic graphs in enzymatic catalysis. Mol. Biol.. 24:209–213.
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2020. Direct Homologous dsDNA-dsDNA Pairing: How, Where, and Why? J Mol Biol. 432(3):737-744.
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1989. A new approach to the modelling of the structure and dynamics of biomacromolecules and their complexes. Doklady. Biophysics. 304:456–460.
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2009. Modeling DNA dynamics under steady deforming forces and torques. J. Chem. Theory Comput.. 5:2149–2157.
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1998. Hierarchy of fast motions in protein dynamics. J. Phys. Chem. B. 102:473–479.
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2000. Theoretical studies of the possible origin of intrinsic static bends in double helical DNA. J. Am. Chem. Soc.. 122:12778–12785.
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1999. Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion. J. Chem. Phys.. 111:1407–1414.
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2013. Comment on ’Length scale dependence of DNA mechanical properties’. Phys. Rev. Lett.. 111:179801.
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1997. Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of St\H ormer-leapfrog integrators. J. Comput. Phys.. 136:354–365.
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2017. What Can Human-Guided Simulations Bring to RNA Folding? Biophys J. 113(2):302-312.
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2005. Following the aggregation of amyloid-forming peptides by computer simulations. J. Chem. Phys.. 122:174904.
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2007. Probing amyloid fibril formation of the NFGAIL peptide by computer simulations. J. Chem. Phys.. 126:065101.