相关论文: Exploring the free energy gain of phase separation…
Many state of the art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are…
In this paper, we review the physical concepts of the nonequilibrium techniques for the calculation of free energies applied to magnetic systems using Monte Carlo simulations of different nonequilibrium processes. The methodology allows the…
Markov state models (MSMs) have been broadly adopted for analyzing molecular dynamics trajectories, but the approximate nature of the models that results from coarse-graining into discrete states is a long-known limitation. We show…
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…
Non-equilibrium Markov State Modeling (MSM) has recently been proposed [Phys. Rev. E 94, 053001 (2016)] as a possible route to construct a physical theory of sliding friction from a long steady state atomistic simulation: the approach…
By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent…
Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
An oft-used concept in modeling macromolecules is the free energy landscape, obtained by coarse-graining a vast number of microstates into a low-dimensional mesh of mesostates. If the landscape contains two or more local minima…
Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In…
This paper explores a discrete energy state transition model for energy harvesting (EH) in cell-free massive multiple-input multiple-output (CF-mMIMO) networks. Multiple-antenna access points (APs) provide wireless power and information to…
We explore the cooperative behaviour and phase transitions of interacting networks by studying a simplified model consisting of Ising spins placed on the nodes of two coupled Erd\"os-R\'enyi random graphs. We derive analytical expressions…
Because of their multimodality, mixture posterior distributions are difficult to sample with standard Markov chain Monte Carlo (MCMC) methods. We propose a strategy to enhance the sampling of MCMC in this context, using a biasing procedure…
Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations, for example…
We study mean-field Ising models whose coupling depends on the magnetization via a feedback function. We identify mixed phases (MPs) and show that they can be stable at zero temperature for sufficiently strong feedback. Moreover, stable MPs…
The evaluation of the free energy of a stochastic model is considered a significant issue in various fields of physics and machine learning. However, the exact free energy evaluation is computationally infeasible because the free energy…
We consider an Ising model with quenched surface disorder, the disorder average of the free energy is the main object of interest. Explicit expressions for the free energy distribution are difficult to obtain if the quenched surface spins…
Free energy as a function of polarization is calculated for the square-lattice $J_1$-$J_2$ Ising model for $J_2 < |J_1|/2$ using the random local field approximation (RLFA) and Monte Carlo (MC) simulations. Within RLFA, it reveals a…
The description of a three-dimensional Ising-like magnet in the presence of an external field in the vicinity of the critical point by the collective variables method is proposed. Using the renormalization group transformations, the scaling…
We study a class of non-equilibrium quasi-stationary states for a Markov system interacting with two different thermal baths. We show that the work done under a slow, external change of parameters admits a potential, i.e., the free energy.…