D
David Perahia
Researcher at École Normale Supérieure
Publications - 60
Citations - 2373
David Perahia is an academic researcher from École Normale Supérieure. The author has contributed to research in topics: Molecular dynamics & Normal mode. The author has an hindex of 25, co-authored 51 publications receiving 2237 citations. Previous affiliations of David Perahia include University of Paris-Sud & University of Paris.
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Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix
TL;DR: In this article, a methode d'estimation de la difference d'entropie de configuration entre les conformations moleculaires de proteines a partir de simulations de dynamique moleculaire is presented.
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Internal and Interfacial Dielectric Properties of Cytochrome c from Molecular Dynamics in Aqueous Solution
Thomas Simonson,David Perahia +1 more
TL;DR: The Fröhlich-Kirkwood theory of dielectrics is used to analyze two 1-ns molecular dynamics simulations of ferro- and ferricytochrome c in spherical droplets of 1400 water molecules to suggest that Poisson-Boltzmann models could treat the protein bulk as a low-dielectric medium and the charged surface groups as part of the solvent region.
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Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode.
TL;DR: Estimation of the energy associated with the interdomain motion of the apoenzyme over a range of 90 degrees demonstrates that local structural relaxation makes possible large-scale rotations with relatively small energy increments.
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Microscopic Dielectric Properties of Cytochrome c from Molecular Dynamics Simulations in Aqueous Solution
Thomas Simonson,David Perahia +1 more
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Molecular dynamics of an α-helical polypeptide: Temperature dependence and deviation from harmonic behavior
TL;DR: Analysis of the time dependence of the fluctuations shows that low-frequency modes dominate the atomic fluctuations and that there is a contribution with a very long relaxation timeAbove 100 K the harmonic approximation significantly underestimates the amplitudes of the displacements.