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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…
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.…
How hydrophobic drying forces impact the kinetics of molecular recognition
Jagannath Mondal, Joseph A. Morrone, B. J. Berne
A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solv…
Are hydrodynamic interactions important in the kinetics of hydrophobic collapse?
Jingyuan Li, Joseph A. Morrone, B. J. Berne
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…