Related papers: Simulated tempering with irreversible Gibbs sampli…
Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics…
Restricted Boltzmann Machines (RBMs) are one of the fundamental building blocks of deep learning. Approximate maximum likelihood training of RBMs typically necessitates sampling from these models. In many training scenarios, computationally…
In this paper we develop a new general Bayesian methodology that simultaneously estimates parameters of interest and the marginal likelihood of the model. The proposed methodology builds on Simulated Tempering, which is a powerful algorithm…
Dynamics under which a system of Ising spins relaxes to a stationary state with Bolzmann-Gibbs measure and which do not fulfil the condition of detailed balance are irreversible and asymmetric. We revisit the problem of the determination of…
Parallel tempering is a generic Markov chain Monte Carlo sampling method which allows good mixing with multimodal target distributions, where conventional Metropolis-Hastings algorithms often fail. The mixing properties of the sampler…
The equilibrium ensemble approach to disordered systems is used to investigate the critical behaviour of the two dimensional Ising model in presence of quenched random site dilution. The numerical transfer matrix technique in semi- infinite…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
We show that the acceptance probability for swaps in the parallel tempering Monte Carlo method for classical canonical systems is given by a universal function that depends on the average statistical fluctuations of the potential and on the…
New algorithm of the finite lattice method is presented to generate the high-temperature expansion series of the Ising model. It enables us to obtain much longer series in three dimensions when compared not only to the previous algorithm of…
Using MCMC to sample from a target distribution, $\pi(x)$ on a $d$-dimensional state space can be a difficult and computationally expensive problem. Particularly when the target exhibits multimodality, then the traditional methods can fail…
We implement a variational quantum algorithm for Gibbs state preparation of a transverse-field Ising model on IonQ's quantum computers. To this end, we train the variational parameters via classical simulation and perform state tomography…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
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…
The spin system of the $2d$ Ising model having a hexagonal-lattice is simulated using non-deterministic Cellular Automata. The method to implement this program is outlined and our results show a good approximation to the exact analytic…
The development of physical simulators, called Ising machines, that sample from low energy states of the Ising Hamiltonian has the potential to drastically transform our ability to understand and control complex systems. However, most of…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…
Composite systems, where couplings are of two types, a combination of strong dilute and weak dense couplings of Ising spins, are examined through the replica method. The dilute and dense parts are considered to have independent canonical…
We demonstrate the applicability of the $\epsilon$-convergence algorithm in extracting the critical temperatures and critical exponents of three-dimensional Ising models. We analyze the low temperature magnetization as well as high…
We study the efficiency of parallel tempering Monte Carlo technique for calculating true ground states of the Edwards-Anderson spin glass model. Bimodal and Gaussian bond distributions were considered in two and three-dimensional lattices.…
We propose a method for efficient simulations in extended ensembles, useful, e.g., for the study of problems with complex energy landscapes and for free energy calculations. The main difficulty in such simulations is the estimation of the a…