Related papers: Isothermal-isobaric molecular dynamics using stoch…
We examine stochastic processes that are used to model nonequilibrium processes (e.g, pulling RNA or dragging colloids) and so deliberately violate detailed balance. We argue that by combining an information-theoretic measure of…
We investigate the large population dynamics of a family of stochastic particle systems with three-state cyclic individual behaviour and parameter-dependent transition rates. On short time scales, the dynamics turns out to be approximated…
Starting at the mesoscopic level with a general formulation of stochastic thermodynamics in terms of Markov jump processes, we identify the scaling conditions that ensure the emergence of a (typically nonlinear) deterministic dynamics and…
We present a new hydrodynamic model for incompressible binary fluids that is thermodynamically consistent and non-isothermal. This model follows the generalized Onsager principle and Boussinesq approximation and preserves the volume of each…
In the context of the recently developed "equation-free" approach to the computer-assisted analysis of complex systems, we illustrate the computation of coarsely self-similar solutions. Dynamic renormalization and fixed point algorithms for…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
We propose here some new sampling algorithms for Path Sampling in the case when stochastic dynamics are used. In particular, we present a new proposal function for equilibrium sampling of paths with a Monte-Carlo dynamics (the so-called…
Micro- and nano-scale systems driven by rapid changes in control parameters (control protocols) dissipate significant energy. In the fast-protocol limit, we find that protocols that minimize dissipation at fixed duration are universally…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
We study microscopic engines that use a single active particle as their "working medium". Part of the energy required to drive the directed motion of the particle can be recovered as work, even at constant temperature. A wide class of…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions. We start by introducing the formalism of the new…
This work obtains the efficiency at maximum power for a stochastic heat engine performing Carnot-like, Stirling-like and Ericsson-like cycles. For the mesoscopic engine a Brownian particle trapped by an optical tweezers is considered. The…
Advanced thermostats for molecular dynamics are proposed on the base of the rigorous Langevin dynamics. Because the latter accounts for the subsystem-bath interactions in details, the bath anisotropy and nonuniformity are described via the…
In non-linear estimations, it is common to assess sampling uncertainty by bootstrap inference. For complex models, this can be computationally intensive. This paper combines optimization with resampling: turning stochastic optimization into…
It is well known that energy dissipation and finite size can deeply affect the dynamics of granular matter, often making usual hydrodynamic approaches problematic. Here we report on the experi-mental investigation of a small model system,…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
Using the density functional formalism we derive expression for the distortion free energy for systems with continuous broken symmetry and use it to derive expression for the elastic constants of smectic phases in which director is tilted…
When particles are multiply scattered by a random potential, their momentum distribution becomes isotropic on average. We study this quantum dynamics numerically and with a master equation. We show how to measure the elastic scattering time…
In the mechanics of inviscid conservative fluids, it is classical to generate the equations of dynamics by formulating with adequate variables, that the pressure integral calculated in the time-space domain corresponding to the motion of…