Related papers: Free Energy Evaluation in Polymer Translocation vi…
Using a recently developed technique to estimate the equilibrium free energy of glassy materials, we explore if equilibrium simulation methods can be used to estimate the solubility of amorphous solids. As an illustration, we compute the…
We describe a simple Monte Carlo simulation method to calculate the free-energy cost of localizing a single monomer of a polymer confined to a cavity. The localization position is chosen to be on the inside surface of the confining cavity.…
We use the method of dimensional reduction to show that a branching polymer with excluded volume interaction confined between two flat plates has, in the thermodynamic limit, a confinement free energy and density profile that is the same as…
We present a generalization of Jarzynski's Equality, applicable to quantum systems, relating discretized mechanical work and free-energy changes. The theory is based on a step-wise pulling protocol. We find that work distribution functions…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
In this paper, we study Jarzynski's equality and fluctuation theorems for diffusion processes. While some of the results considered in the current work are known in the (mainly physics) literature, we review and generalize these…
Long linear polymers in dilute solutions are known to undergo a collapse transition from a random coil (expand itself) to a compact ball (fold itself up) when the temperature is lowered, or the solvent quality deteriorates. A natural model…
We study the driven translocation of a flexible polymer through an interacting conical pore using Langevin dynamics simulations. We find that, for a fixed value of externally applied force and pore polymer interaction strength, the mean…
We calculate exactly the first cumulants of the free energy of a directed polymer in a random medium for the geometry of a cylinder. By using the fact that the n-th moment <Z^n> of the partition function is given by the ground state energy…
The transition between a regime in which thermodynamic relations apply only to ensembles of small systems coupled to a large environment and a regime in which they can be used to characterize individual macroscopic systems is analyzed in…
In this short communication, I give a very simple derivation of the Jarzynski equality, which allows to compute the free energy difference of a body, which is driven between two equilibrium states $A$ and $B$ by an external (time-dependent)…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
The aim of this paper is twofold: - To give an elementary and self-contained proof of an explicit formula for the free energy for a general class of polymer chains interacting with an environment through periodic potentials. This…
The solid-liquid interface free energy \gamma sl is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous…
We study the free energy and its relevant quantity for the directed polymer in random environment. The polymer is allowed to make unbounded jumps and the environment is given by the Bernoulli variables. We first establish the concentration…
In this paper we study multi-matrix models whose potentials are perturbations of the quadratic potential associated with independent GUE random matrices. More precisely, we compute the free energy and the expectation of the trace of…
The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were…
Free energies are fundamental quantities governing phase behavior and thermodynamic stability in polymer systems, yet their accurate computation often requires extensive simulations and post-processing techniques such as the Bennett…
The influence of monomer-monomer interactions on the scaling exponents and shape characteristics of a single polymer chain in a selective solvent is investigated using Langevin dynamics simulations. By systematically increasing the…
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a polynomial that optimally fits the thermodynamic integration…