Publications
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2001. Internal coordinate phase space analysis of macromolecular systems. Comput. Theor. Polym. Sci.. 11:35–47.
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2001. Molecular dynamics studies of sequence-directed curvature in bending locus of Trypanosome kinetoplast DNA. J. Biomol. Struct. Dyn.. 18:832–843.
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2016. Homologous Pairing between Long DNA Double Helices. Phys. Rev. Lett.. 116:158101.
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2001. Molecular dynamics of minimal B-DNA. J. Comput. Chem.. 22:457–467.
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2006. Evaluation of elastic properties of atomistic DNA models. Biophys. J.. 91:4507–4518.
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2008. Statistics of time-limited ensembles of bent DNA conformations. J. Phys. Chem. B. 112:4975–4982.
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2007. Wormlike chain theory and bending of short DNA. Phys. Rev. Lett.. 98:218102.
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1991. A probabilistic view on steady state enzyme kinetics. J. Theor. Biol.. 148:229–242.
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2015. Algebraic Statistics of Poincaré Recurrences in a DNA Molecule.. Phys. Rev. Lett.. 115:188104.
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1989. New methodology for computer-aided modelling of biomolecular structure and dynamics: 1. Non-cyclic structures. J. Biomol. Struct. Dyn.. 6:815–832.
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1985. Oligomer distribution of depolymerase digests: Comparison of theory and experiments. Febs Lett.. 192:43–46.
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1984. Mathematical models of depolymerization of amylose by alpha-amylases. Biopolymers. 23:1735–1756.
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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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1985. On the possible mechanism of multiple enzyme attack in polysaccharide degradation. Mol. Biol.. 19:1400–1408.
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2011. Local elasticity of strained DNA studied by all-atom simulations. Phys. Rev. E. 84:021903.
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1997. Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers. J. Comput. Chem.. 18:1354–1364.
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2013. On the origin of thermal untwisting of DNA. J. Phys. Chem. B. 117:1857–1861.
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1993. Multiple attack in the porcine pancreatic alpha-amylase hydrolysis of amylose and amylopectine. Arch. Biochem. Biophys.. 306:29–38.
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1992. Schematic methods for probabilistic enzyme kinetics. J. Theor. Biol.. 155:387–407.
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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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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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2008. Role of the region 23-28 in A beta fibril formation: Insights from simulations of the monomers and dimers of Alzheimer's peptides A beta 40 and A beta 42. Curr. Alzheimer Res.. 5:244–250.