Publications
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2010. Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys.. 132
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2011. Real Time Observation of Ultrafast Peptide Conformational Dynamics: Molecular Dynamics Simulation vs Infrared Experiment. J. Phys. Chem. B. 115:13084–13092.
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2013. Conformational Ensemble and Polymorphism of the All-Atom Alzheimer's A beta(37-42) Amyloid Peptide Oligomers. J. Phys. Chem. B. 117:5831–5840.
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2006. Photoinduced conformational dynamics of a photoswitchable peptide: A nonequilibrium molecular dynamics simulation study. Biophys. J.. 91:1224–1234.
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2013. Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
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2019. Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution.. J Phys Chem B. 123(31):6750-6756.
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2006. Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys.. 323:36–44.
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2007. Monomer adds to preformed structured oligomers of A beta-peptides by a two-stage dock-lock mechanism. Proc. Natl. Acad. Sci. U.s.a.. 104:111–116.
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2012. Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
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2006. Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces. J. Chem. Phys.. 124
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2014. Understanding Amyloid Fibril Nucleation and A beta Oligomer/Drug Interactions from Computer Simulations. Acc. Chem. Res.. 47:603–611.
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2013. Replica-exchange molecular dynamics simulations of the amyloid-beta(16-22) fragments. European Biophysics Journal with Biophysics Letters. 42:S68.
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2015. Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol. Simul.. 41:1041–1044.
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2001. Induction-independent recruitment of CREB-binding protein to the c-fos serum response element through interactions between the bromodomain and Elk-1. J. Biol. Chem.. 276:5213–5221.
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2010. One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc. Natl. Acad. Sci. U.s.a.. 107:6275–6280.
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2011. X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature. 469:428–431.
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2022. Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions. Proteins: Structure, Function, and Bioinformatics. 90:858-868.
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2008. Anomalous diffusion of ions at the surface of hydrated DNA molecule. Europhys. Lett.. 82:46002.
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2014. Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans. J. Phys. Chem. B. 118:13800–13811.
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2014. The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes. Phys. Chem. Chem. Phys.. 16:11318–11322.
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2009. Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J. Chem. Phys.. 131
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1987. Calorimetric studies of oxygen and carbon monoxide binding to human hemoglobin. Sequential binding heats for oxygen. J. Biol. Chem.. 262:10994–10999.
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1987. Calorimetric analysis of oxygen binding to lobster hemocyanin. Invertebrate Oxygen Carriers.
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2013. Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations. Plos Comput. Biol.. 9:e1003034.
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2008. Numerical methods for fluctuation driven interactions between dielectrics. Phys. Rev. E. 77:016705.