Publications
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2011. Dynamics of water in concentrated solutions of amphiphiles: Key roles of local structure and aggregation. J. Phys. Chem. B. 115:3254–3262.
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2018. Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions.. J Biol Chem. 293(18):6637-6646.
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2002. Effect of binding of Cd2+ on bacterial reaction center mutants: proton-transfer uses interdependent pathways. Biochemistry. 41:9132–9138.
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1997. Effect of cytosine methylation on DNA-DNA recognition at CpG steps. J. Mol. Biol.. 270:328–335.
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2015. Epock: rapid analysis of protein pocket dynamics. Bioinformatics. 31:1478–1480.
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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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2014. ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations. Faraday Discuss.. 169:119–142.
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2012. Early Stage of the Dehydrogenation of NaAlH4 by Ab Initio Rare Event Simulations. The Journal of Physical Chemistry C. 116:19636–19643.
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2004. Early steps of amyloid-petide oligomerisation explored by simulations. Neurobiol. Aging. 25:S143.
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2023. Editorial: In Celebration of Women in Science: Biological Modeling and Simulation. Front Mol Biosci. 10:1175325.
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2019. Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions. J Phys Chem B. 123:3312-3324.
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2013. The effect of protein composition on hydration dynamics. Phys. Chem. Chem. Phys.. 15:3570–3576.
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2014. Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A beta 40 and A beta 42. Acs Chem. Neurosci.. 5:646–657.
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2013. Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42). Acs Chem. Neurosci.. 4:1446–1457.
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1991. EFFECT OF UREY-BRADLEY-SHIMANOUCHI FORCE-FIELD ON THE HARMONIC DYNAMICS OF PROTEINS. Proteins-structure Function and Genetics. 11:120–132.
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2011. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
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2019. Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16–22 dimer. Journal of chemical theory and computation. 15:1440–1452.
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2011. Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations. J. Phys. Chem. B. 115:1282–1288.
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2010. Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70-86 of Glycophorin A: An All-Atom Molecular Dynamics Study. J. Phys. Chem. B. 114:1004–1009.
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1995. Efficient conformational space sampling for nucleosides using internal coordinate Monte-Carlo simulations and a modified furanose description. J. Comput. Chem.. 16:667–680.
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2001. Elastic constants from direct correlation functions in nematic liquid crystals: A computer simulation study. J. Chem. Phys.. 115:7227–7234.
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2015. The elastic free energy of a tandem modular protein under force.. Biochem. Biophys. Res. Comm.. :1–5.
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2013. Elasticity, structure, and relaxation of extended proteins under force.. Proc. Natl. Acad. Sci. U.s.a. 110:3847–52.
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2008. The electrostatic origin of low-hydration polymorphism in DNA. Chemphyschem in Press. 9:2691–2694.
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2005. Electrostatic polymer condensation and the A/B polymorphism in DNA: Sequence effects. J. Chem. Theory Comput.. 1:325–336.