Related papers: Predicting Non-Equilibrium Folding Behavior of Pol…
A microscopic understanding of low-temperature thermodynamics and its relation to dynamical features such as a fragile-to-strong crossover (FSC) remains a central challenge in glass physics. Using swap Monte Carlo combined with a full…
Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…
We solve a two dimensional model for polymer chain folding in the presence of mechanical pulling force ($f$) exactly using equilibrium statistical mechanics. Using analytically derived expression for the partition function we determine the…
We study transition paths in energy landscapes over multi-categorical Potts configurations using the mean-field approach introduced by Mauri et al., {\em Phys Rev Lett 130, 158402 (2023)}. Paths interpolate between two fixed configurations…
We revisit the nature of the quasi-one-dimensional Ising model on the basis of Wang-Landau simulation. We introduce the density of states in the two-dimensional energy space corresponding to the intra- and inter-chain directions. We then…
In this work we propose a new algorithm for the computation of statistical equilibrium quantities on a cubic lattice when both an energy and a statistical temperature are involved. We demonstrate that the pivot algorithm used in situations…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
As has been shown elsewhere, a reasonable model of the loss of entanglement or correlation that occurs in quantum computations is one which assumes that they can effectively be predicted by a framework that presupposes the presence of…
Inspired by recent advances in the chromosome capture techniques, a method is proposed to study the structural organization of systems of polymers rings with topological constraints.To this purpose, the system is divided into compartments…
We apply a newly proposed Monte Carlo method, the Wang-Landau algorithm, to the study of the three-dimensional antiferromagnetic q-state Potts models on a simple cubic lattice. We systematically study the phase transition of the models with…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
Wetting and drying phenomena are studied for flexible and semiflexible polymer solutions via coarse-grained molecular dynamics simulations and density functional theory calculations. The study is based on the use of Young's equation for the…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
We present a novel approach to the regression of quantum mechanical energies based on a scattering transform of an intermediate electron density representation. A scattering transform is a deep convolution network computed with a cascade of…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
The quantum Mpemba effect is a phenomenon characterized by an exponential relaxation from a non-equililbrium state to a steady state. This effect was predicted with an analysis of the Liouvillian superoperator and experimentally…
Monte Carlo simulations using Wang-Landau sampling are performed to study three-dimensional chains of homopolymers on a lattice. We confirm the accuracy of the method by calculating the thermodynamic properties of this system. Our results…
We address the problem of constructing accurate mathematical models of the dynamics of complex systems projected on a collective variable. To this aim we introduce a conceptually simple yet effective algorithm for estimating the parameters…
Boltzmann's microcanonical entropy is the link between statistical physics and thermodynamics, forasmuch as the behavior of any thermodynamic quantity is directly related to the number of microscopic configurations. Accordingly, in this…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…