Publications
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2013. The effect of protein composition on hydration dynamics. Phys. Chem. Chem. Phys.. 15:3570–3576.
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2017. Configurational Disorder of Water Hydrogen Bond Network at the Protein Dynamical Transition. J. Phys. Chem. B. 121:6792−6798.
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2006. HDAC1 acetylation is linked to progressive modulation of steroid receptor-induced gene transcription.. Mol. Cell. 22:669–679.
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2022. Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
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1993. Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers. 33:335–50.
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2009. Deforming DNA: from physics to biology. Chemphyschem. 10:1399–404.
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1997. Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: An internal coordinate molecular modeling study. J. Biomol. Struct. Dyn.. 14:703–714.
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2012. A novel Locally Closed Conformation of a Bacterial Pentameric Proton-gated Ion Channel. Nature Structural & Molecular Biology.
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2008. Recombination and Meiosis : Models, Means and Evolution Coll. Genome Dynamics \& Stability. Genome Dynamics \& Stability. 3:65–84.
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2021. Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces.. Proteins.
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2003. Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination. Q. Rev. Biophys.. 36:429–53.
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2008. Searching for Homology by Filaments of RecA-like Proteins. Genome Dynamics & Stability. Recombination and Meiosis. Models, Means and Evolution:65–89.
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2015. Structure/function relationships in RecA protein-mediated homology recognition and strand exchange. Crit. Rev. Biochem. Mol. Biol.. 50:453–76.
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2008. Insights on protein-DNA recognition by coarse grain modelling. J. Comput. Chem.. 29:2582–92.
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2004. Critical role of the C-terminal segment in the maturation and export to the cell surface of the homopentameric $\alpha$7–5HT3A receptor. Eur. J. Neurosci.. 20:2022–2030.
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2007. How protein surfaces induce anomalous dynamics of hydration water. J. Phys. Chem. B. 111:7584–90.
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2003. Local structure in nematic and isotropic liquid crystals. J. Chem. Phys.. 119:1214–1222.
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2002. The direct correlation function in nematic liquid crystals from computer simulation. Comput. Phys. Commun.. 147:350–353.
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2001. Elastic constants from direct correlation functions in nematic liquid crystals: A computer simulation study. J. Chem. Phys.. 115:7227–7234.
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2020. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153
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1995. Investigation of the conformational properties of a {$\beta$}-(1-3) branched {$\beta$}-(1-6) heptasacchardie elicitor and its analogues by internal coordinate stochastic dynamics. Carbohydr. Res.. 279:41–57.
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1992. Global optimization of conformation energy of polypeptides by tunnel algorithm. Biophysics. 37:226–230.
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1992. Modeling of the possible binding modes of substrates in the active site of Taka-Amylase A. Mol. Biol.. 26:292–299.
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2022. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13
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1989. RAMAN-SPECTROSCOPY, MOLECULAR-FORCE FIELDS, AND THE DYNAMICS OF BIOLOGICAL MOLECULES. Chemica Scripta. 29A:113–122.