Andrey V. Brukhno

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The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from(More)
By extending the cleaving method to molecular systems, we perform direct calculations of the ice Ih-water interfacial free energy for the TIP4P model. The values for the basal, prism, and {112[over]0} faces are 23.3+/-0.8 mJ m{-2}, 23.6+/-1.0 mJ m{-2}, and 24.7+/-0.8 mJ m{-2}, respectively. The closeness of these values implies a minimal role of(More)
We employ the cleaving approach to calculate directly the ice Ih-water interfacial free energy for the simple models of water, TIP4P, TIP4P-Ew, and TIP5P-E, with full electrostatic interactions evaluated via the Ewald sums. The results are in good agreement with experimental values, but lower than previously obtained for TIP4P-Ew and TIP5P-E by indirect(More)
By using a generic coarse grained polypeptide model, we perform multicanonical molecular dynamics simulations for determining the equilibrium conformation state diagram of a single homopolypeptide chain as a function of the chain length and temperature. The state diagram highlights the thermal regimes of stability for various conformational patterns in(More)
In this study, we address the questions of how important is the kinetics in protein aggregation, and what are the intrinsic properties of proteins that cause this behavior. On the basis of our recent quantitative calculation of the equilibrium phase diagram of natively folded α-helical and β-sheet forming peptides, we perform molecular dynamics simulations(More)
NEUROSCIENCE Correction for “Ischemia-induced calpain activation causes eukaryotic (translation) initiation factor 4G1 (eIF4GI) degradation, protein synthesis inhibition, and neuronal death,” by Peter S.Vosler, Yanqin Gao, Christopher S. Brennan, Akiko Yanagiya, Yu Gan, Guodong Cao, Feng Zhang, Simon J. Morley, Nahum Sonenberg, Michael V. L. Bennett, and(More)
NEUROSCIENCE Correction for “Ischemia-induced calpain activation causes eukaryotic (translation) initiation factor 4G1 (eIF4GI) degradation, protein synthesis inhibition, and neuronal death,” by Peter S.Vosler, Yanqin Gao, Christopher S. Brennan, Akiko Yanagiya, Yu Gan, Guodong Cao, Feng Zhang, Simon J. Morley, Nahum Sonenberg, Michael V. L. Bennett, and(More)
NEUROSCIENCE Correction for “Ischemia-induced calpain activation causes eukaryotic (translation) initiation factor 4G1 (eIF4GI) degradation, protein synthesis inhibition, and neuronal death,” by Peter S.Vosler, Yanqin Gao, Christopher S. Brennan, Akiko Yanagiya, Yu Gan, Guodong Cao, Feng Zhang, Simon J. Morley, Nahum Sonenberg, Michael V. L. Bennett, and(More)
Attractive interactions between like-charged aggregates (macromolecules, colloidal particles, or micelles) in solution due to electrostatic correlation effects are revisited. The associated phenomenon of phase separation in a colloidal solution of highly charged particles is directly observed in Monte Carlo simulations. We start with a simple, yet(More)
Characterization of the folding transition in polypeptides and assessing the thermodynamic stability of their structured folds are of primary importance for approaching the problem of protein folding. We use molecular dynamics simulations for a coarse grained polypeptide model in order to (1) obtain the equilibrium conformation diagram of homopolypeptides(More)
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