相关论文: Free Energy Evaluation in Polymer Translocation vi…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
A random polymer model is a one-dimensional Jacobi matrix randomly composed of two finite building blocks. If the two associated transfer matrices commute, the corresponding energy is called critical. Such critical energies appear in…
In this article, we try to give a rather complete picture of the behavior of the free energy for a model of directed polymer in a random environment, in which the polymer is a simple symmetric random walk on the lattice $\Z^d$, and the…
In the global framework of finding an axiomatic derivation of nonequilibrium Statistical Mechanics from fundamental principles, such as the maximum path entropy -- also known as Maximum Caliber principle -- , this work proposes an…
We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and…
The free energy between a static quark and an antiquark is studied by using the color-singlet Polyakov-line correlation at finite temperature. We perform simulations on $32^3 \times 12$, 10, 8, 6, 4 lattices in the high temperature phase…
The existence of two types of internal friction wet and dry is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires…
A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…
Almost 25 years ago, Jarzynski published a paper in which it was asserted: the work done, W, in driving a system from state A to state B, characterized by the Helmholtz free energies FA and FB, satisfies an equality in which an average over…
Almost 25 years ago, Jarzynski published a paper in which it was asserted: the work done, W, in driving a system from state A to state B, characterized by the Helmholtz free energies FA and FB, satisfies an equality in which an average over…
A simple model featuring a double well potential is used to represent a liquid that is quenched from an ergodic state into a history dependent glassy state. Issues surrounding the application of the Jarzynski Equality to glass formation are…
Langevin Dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is…
This paper considers an undirected polymer chain on $\mathbb{Z}^d$, $d \geq 2$, with i.i.d.\ random charges attached to its constituent monomers. Each self-intersection of the polymer chain contributes an energy to the interaction…
The recently discovered supersymmetric generalizations of Langevin dynamics and Kramers equation can be utilized for the exploration of free energy landscapes of systems whose large time-scale separation hampers the usefulness of standard…
We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway…
We study the thermodynamic properties of a semiflexible polymer confined inside strips of widths L<=9 defined on a square lattice. The polymer is modeled as a self-avoiding walk and a short range interaction between the monomers and the…
For a class of mean-field particle systems, we formulate a criterion in terms of the free energy that implies uniform bounds on the log-Sobolev constant of the associated Langevin dynamics. For certain double-well potentials with quadratic…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces.…
Energy-based models (EBMs) are generative models inspired by statistical physics with a wide range of applications in unsupervised learning. Their performance is best measured by the cross-entropy (CE) of the model distribution relative to…