Related papers: Escorted free energy simulations
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
I develop a numerical algorithm for stochastic impulse control in the spirit of Regression Monte Carlo for optimal stopping. The approach consists in generating statistical surrogates (aka functional approximators) for the continuation…
We perform a fully self-consistent 3-D numerical simulation for a compressible, dissipative magneto-plasma driven by large-scale perturbations, that contain a fairly broader spectrum of characteristic modes, ranging from largest scales to…
We introduce a variational algorithm to estimate the likelihood of a rare event within a nonequilibrium molecular dynamics simulation through the evaluation of an optimal control force. Optimization of a control force within a chosen basis…
We formulate theoretical modeling approaches and develop practical computational simulation methods for investigating the non-equilibrium statistical mechanics of fluid interfaces with passive and active immersed particles. Our approaches…
Monte Carlo methods are now a definitively well established methods for studying the transport of charges in semiconductors. A lot of drawbacks are however present about the correct reconstruction of the distribution function, which has to…
We derive an extended fluctuation theorem for a geometric pumping in a spin-boson system under a periodic control of environmental temperatures by using a Markovian quantum master equation. We perform the Monte-Carlo simulation and obtain…
We present a strategy to construct guiding distribution functions (GDFs) based on variance minimization. Auxiliary dynamics via GDFs mitigates the exponential growth of variance as a function of bias in Monte Carlo estimators of large…
Estimating free-energy differences using nonequilibrium work relations, such as the Jarzynski equality, is hindered by poor convergence when work fluctuations are large. For systems governed by overdamped Langevin dynamics, we propose the…
We study the statistics of the dissipated energy in the two-dimensional random fuse model for fracture under different imposed strain conditions. By means of extensive numerical simulations we compare different ways to compute the…
The entropy per particle in most Monte-Carlo simulations is size dependent due to correlated energy fluctuations. Guided by nanothermodynamics, we find a constraint for the Ising model that enhances the fluctuations and lowers the free…
We analyze a new Monte Carlo method which uses transition matrix in the space of energy. This method gives an efficient reweighting technique. The associated artificial dynamics is a constrained random walk in energy, producing the result…
We discuss the optimized switching free energy simulations in an analogy with the systems which are driven under nonequilibrium feedback control. We find an on-the-fly simulation approach of switching optimization is a special case of the…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
We develop a systematic procedure to approximate generalized free energy in out of equilibrium stochastic systems. The procedure only requires knowledge of the averages of macroscopic observables and uses quasi-equilibrium distribution to…
The fluctuation theorems have remained one of the cornerstones in the study of systems that are driven far out of equilibrium, and they provide strong constraints on the fraction of trajectories that behave atypically in light of the second…
For systems in equilibrium at a temperature $T$, thermal noise and energy damping are related to $T$ through the fluctuation-dissipation theorem (FDT). We study here an extension of the FDT to an out of equilibrium steady state: a…
Systems that are driven out of thermal equilibrium typically dissipate random quantities of energy on microscopic scales. Crooks fluctuation theorem relates the distribution of these random work costs with the corresponding distribution for…
The basic problem in equilibrium statistical mechanics is to compute phase space average, in which Monte Carlo method plays a very important role. We begin with a review of nonlocal algorithms for Markov chain Monte Carlo simulation in…
Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means…