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pro vyhledávání: '"Berne, B."'
Autor:
Tiwary, Pratyush, Berne, B. J.
Publikováno v:
J. Chem. Phys. 147, 152701 (2017)
We consider a range of model potentials with metastable states undergoing molecular dynamics coupled to a thermal bath in the high friction regime, and consider how the optimal reaction coordinate depends on the diffusion anisotropy. For this we use
Externí odkaz:
http://arxiv.org/abs/1704.03912
Autor:
Tiwary, Pratyush, Berne, B. J.
We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) (Tiwary and Berne, Proc. Natl. Acad. Sci 2016, 113, 2839 (2016)), to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a buc
Externí odkaz:
http://arxiv.org/abs/1605.07090
Autor:
Tiwary, Pratyush, Berne, B. J.
We consider the rate of transition for a particle between two metastable states coupled to a thermal environment for various magnitudes of the coupling strength, using the recently proposed infrequent metadynamics approach (Tiwary and Parrinello, Phy
Externí odkaz:
http://arxiv.org/abs/1602.06588
Autor:
Tiwary, Pratyush, Berne, B. J.
In modern day simulations of many-body systems much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CV) or reaction coordinates. A vast array of enhanced samp
Externí odkaz:
http://arxiv.org/abs/1509.06145
A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but extremely diffic
Externí odkaz:
http://arxiv.org/abs/1507.02985
Heterogeneous ice growth exhibits a maximum in freezing rate arising from the competition between kinetics and the thermodynamic driving force between the solid and liquid states. Here, we use molecular dynamics simulations to elucidate the atomistic
Externí odkaz:
http://arxiv.org/abs/1308.6541
Autor:
Markland, Thomas E., Berne, B. J.
Publikováno v:
Published in PNAS May 22, 2012 vol. 109 no. 21 7988-7991
When two phases of water are at equilibrium, the ratio of hydrogen isotopes in each is slightly altered due to their different phase affinities. This isotopic fractionation process can be utilized to analyze water's movement in the world's climate. H
Externí odkaz:
http://arxiv.org/abs/1307.7684
Longstanding mechanistic questions about the role of protecting osmolyte trimethylamine N- oxide (TMAO) which favors protein folding and the denaturing osmolyte urea are addressed by studying their effects on the folding of uncharged polymer chains.
Externí odkaz:
http://arxiv.org/abs/1306.4642
Publikováno v:
Proc. Natl. Acad. Sci. USA 110, 13277 (2013)
A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry states wi
Externí odkaz:
http://arxiv.org/abs/1305.7505
We study the kinetics of assembly of two plates of varying hydrophobicity, including cases where drying occurs and water strongly solvates the plate surfaces. The potential of mean force and molecular-scale hydrodynamics are computed from molecular d
Externí odkaz:
http://arxiv.org/abs/1208.6170