A parallel-in-time, multiscale interaction procedure is introduced for systems described at molecular scales by time-dependent random variables that obey Langevin dynamics. At larger, kinetic scales, the system is described by a probability distribution function that obeys an associated Fokker-Planck equation. It is assumed that the main quantity of interest is the kinetic-scale probability dis...

In recent years, stochastic gradient Markov Chain Monte Carlo (SG-MCMC) methods have been raised to process large-scale dataset by iterative learning from small minibatches. However, the high variance caused by naive subsampling usually slows down the convergence to the desired posterior distribution. In this paper, we propose an effective subsampling strategy to reduce the variance based on a ...

Abstract: The generalized elastic model encompasses several linear stochastic models describing the dynamics of polymers, membranes, rough surfaces, and fluctuating interfaces. While usually defined in the overdamped case, in this paper we formally include the inertial term to account for the initial diffusive stages of the stochastic dynamics. We derive the generalized Langevin equation for a ...

Medicinal chemistry depends on many other disciplines ranging from organic chemistry andpharmacology to computational chemistry. Typically medicinal chemists use the moststraightforward ways to prepare compounds. The validation of any design project comes from thebiological testing.Studies of the binding site of vinblastine by a single cross—linking experiment identified it asbeing between resi...

We consider numerical methods for thermodynamic sampling, i.e., computing sequences of points distributed according to the Gibbs–Boltzmann distribution, using Langevin dynamics and overdamped Langevin dynamics (Brownian dynamics). A wide variety of numerical methods for Langevin dynamics may be constructed based on splitting the stochastic differential equations into various component parts, ea...

Starting from the kinetic equations for the fluctuations and correlations of a dilute gas of inelastic hard spheres or disks, a Boltzmann-Langevin equation for the one-particle distribution function of the homogeneous cooling state is constructed. This equation is the linear Boltzmann equation with a fluctuating white-noise term. Balance equations for the fluctuating hydrodynamic fields are der...

The results of a molecular dynamics (MD) computer simulation are presented for the solvation dynamics of an ion pair instanteously produced from a neutral pair, in a model polar aprotic solvent. These time-dependent fluorescence dynamics are analyzed theoretically to examine the validity of several linear response theory approaches, as well as of various theoretical descriptions (e.g., Langevin...