Related papers: Deterministic replica-exchange method without pseu…
We propose a new implementation of the replica-exchange method (REM) in which replicas follow a pre-planned route in temperature space instead of a random walk. Our method satisfies the detailed balance condition in the proposed route. The…
We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of…
The nematic-isotropic (NI) phase transition of 4-cyano-4'-pentylbiphenyl (5CB) was simulated using the generalized replica-exchange method (gREM) based on molecular dynamics simulations. The effective temperature is introduced in gREM,…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
The complete phase diagram of Random Energy Model (REM) is obtained for complex temperatures using the method proposed by Derrida. We find the density of zeroes for statistical sum. Then the method is applied to Generalized Random Energy…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
In this paper, we present a new idea for Transfer Learning (TL) based on Gibbs Sampling. Gibbs sampling is an algorithm in which instances are likely to transfer to a new state with a higher possibility with respect to a probability…
We combine replica exchange (parallel tempering) with normalizing flows, a class of deep generative models. These two sampling strategies complement each other, resulting in an efficient strategy for sampling molecular systems characterized…
Replica exchange (RE) is one of the most popular enhanced-sampling simulations technique in use today. Despite widespread successes, RE simulations can sometimes fail to converge in practical amounts of time, e.g., when sampling around…
Enhanced sampling techniques are essential for exploring biomolecular conformational dynamics that occur on timescales inaccessible to conventional molecular dynamics (MD) simulations. This study introduces a framework that combines…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
An expression for the moment of partition function valid for any finite system size $N$ and complex power $n (\Re(n)>0)$ is obtained for a simple spin glass model termed the {\em discrete random energy model} (DREM). We investigate the…
Inverse problems are of great importance in astrophysics for deriving information about the physical characteristics of hot optically thin plasma sources from their EUV and X-ray spectra. We describe and test an iterative method developed…
Efficiently generating statistically independent samples from an unnormalized probability distribution, such as equilibrium samples of many-body systems, is a foundational problem in science. In this paper, we propose Iterated Denoising…
Recently, distribution element trees (DETs) were introduced as an accurate and computationally efficient method for density estimation. In this work, we demonstrate that the DET formulation promotes an easy and inexpensive way to generate…
We propose a new method for the determination of the weight factor for the simulated tempering method. In this method a short replica-exchange simulation is performed and the simulated tempering weight factor is obtained by the…
Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynman's path integrals to overcome large barriers we…
The continuous random energy model (CREM) is a toy model of spin glasses on $\{0,1\}^N$ that, in the limit, exhibits an infinitely hierarchical correlation structure. We give two polynomial-time algorithms to approximately sample from the…
In this thesis, we consider several Random Energy Models. This includes Derrida's Random Energy Model (REM) and Generalized Random Energy Model (GREM) and a nonhierarchical version (BK-GREM) by Bolthausen and Kistler. The limiting free…
A continuous variable ping-pong scheme, which is utilized to generate deterministically private key, is proposed. The proposed scheme is implemented physically by using Gaussian-modulated squeezed states. The deterministic way, i.e., no…