Using Langevin dynamics simulations, we study the hysteresis in unzipping of longer double stranded DNA chains whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ keeping other end fixed. We find that area loop, $A_{loop}$, scales as $1/\omega$ at higher frequencies, whereas it $(G-G_c)^{\alpha}\omega^{\beta}$ exponents $\alpha=1$ $\beta=1.25$ l...

Thin-film growth by sputter deposition is a manufacturing process that is well suited for study by particle simulation methods. The authors report on the development of a high performance, parallel, molecular-dynamics software package that simulates atomic metal systems under sputter deposition conditions. The package combines advanced techniques for parallel molecular dynamics with specialized...

In this paper we investigate the use of Langevin Monte Carlo methods on the probability simplex and propose a new method, Stochastic gradient Riemannian Langevin dynamics, which is simple to implement and can be applied to large scale data. We apply this method to latent Dirichlet allocation in an online minibatch setting, and demonstrate that it achieves substantial performance improvements ov...

We construct an infinite particle/infinite volume Langevin dynamics on the space of configurations in R having velocities as marks. The construction is done via a limiting procedure using N-particle dynamics in cubes (−λ, λ] with periodic boundary conditions. A main step to this result is to derive an (improved) Ruelle bound for the canonical correlation functions of N-particle systems in (−λ, ...

We study graded response attractor neural networks with asymmetrically extremely dilute interactions and Langevin dynamics. We solve our model in the thermodynamic limit using generating functional analysis, and find (in contrast to the binary neurons case) that even in statics, for T > 0 or large α, one cannot eliminate the non-persistent order parameters, atypically for recurrent neural netwo...

We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the phase-space density and are suitable for equilibrium or nonequilibrium systems in stationary state. All the methods use a series of interfaces in phase space, between the initial and final states, t...

We present theory and simulations to describe nonequilibrium stretching of semiflexible chains that serve as models of DNA molecules. Using a self-consistent dynamical variational approach, we calculate the force-extension curves for worm-like chains as a function of the pulling speed, v(0). Due to nonequilibrium effects the stretching force, which increases with v(0), shows nonmonotonic variat...

In this work, a self-consistent Langevin dynamics simulator will be presented, and computational issues unique to the simulation of charge transport through ion channels will be addressed. The simulation approach is divided into two parts; the first is the development of an efficient model to account for the charge transport in bulk electrolyte solutions, while the second is the accurate repres...