1.2k citations · 2.2k across the 19 of their papers we have counts for
19 papers
Predicting reaction coordinates in energy landscapes with diffusion anisotropy
Pratyush Tiwary, B. J. Berne
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 rea…
How wet should be the reaction coordinate for ligand unbinding?
Pratyush Tiwary, B. J. Berne
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 opt…
Kramers turnover: from energy diffusion to spatial diffusion using metadynamics
Pratyush Tiwary, B. J. Berne
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…
Caliber based spectral gap optimization of order parameters (SGOOP) for sampling complex molecular systems
Pratyush Tiwary, B. J. Berne
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…
The role of water and steric constraints in the kinetics of cavity-ligand unbinding
Pratyush Tiwary, Jagannath Mondal, Joseph A. Morrone +1
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 t…
Interface limited growth of heterogeneously nucleated ice in supercooled water
Razvan A. Nistor, Thomas E. Markland, B. J. Berne
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.…