Related papers: Single molecule pulling with large time steps
We study the effects of interatomic interactions on the quantum dynamics of a dense, nanoscale, atomic ensemble driven by a strong electromagnetic field. We use a self-consistent, mean-field technique based on the pseudo-spectral…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
In this paper, a physics-oriented stochastic kinetic scheme will be developed that includes random inputs from both flow and electromagnetic fields via a hybridization of stochastic Galerkin and collocation methods. Based on the BGK-type…
We introduce and study a class of particle hopping models consisting of a single box coupled to a pair of reservoirs. Despite being zero-dimensional, in the limit of large particle number and long observation time, the current and activity…
By conditioning a stochastic process on the value of an observable, one obtains a new stochastic process with different properties. We apply this idea in the context of active matter, and condition interacting self-propelled particles on…
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the…
We study the energy landscape of the Random Energy model (REM) integrated along trajectories of the simple random walk on the hypercube. We show that the quenched cumulant generating function of the time integral of the REM energy undergoes…
Chemical reactions are usually studied under the assumption that both substrates and catalysts are well mixed (WM) throughout the system. Although this is often applicable to test-tube experimental conditions, it is not realistic in…
Active Flux is a modified Finite Volume method that evolves additional Degrees of Freedom for each cell that are located on the interface by a non-conservative method to compute high-order approximations to the numerical fluxes through the…
Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to…
Complex systems often show macroscopic coherent behavior due to the interactions of microscopic agents like molecules, cells, or individuals in a population with their environment. However, simulating such systems poses several…
A challenging and fundamental research problem is the better understanding and control of the turbulent transport of heat in present-day tokamak fusion experiments. Recent developments in numerical methods along with enormous gains in…
The athermal quasistatic deformation method provides an elegant solution to overcome the limitation of short time spans in molecular simulations. It provides overdamped conditions, allowing for the extraction of purely structural responses…
Application of Jarzynski nonequilibrium work relation to free energy calculation is limited by the very slow convergence of the estimate when dissipation is high. We present a novel perturbation protocol able to improve the convergence of…
We propose a unified method for the large space-time scaling limit of \emph{linear} collisional kinetic equations in the whole space. The limit is of \emph{fractional} diffusion type for heavy tail equilibria with slow enough decay, and of…
We study nonlinear mean-field dynamics of ultracold molecule formation in the case when the external field configuration is defined by the level-crossing Demkov-Kunike model, characterized by a bell-shaped coupling and finite variation of…
In this short communication, I give a very simple derivation of the Jarzynski equality, which allows to compute the free energy difference of a body, which is driven between two equilibrium states $A$ and $B$ by an external (time-dependent)…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…