Related papers: Effective equations for reaction coordinates in po…

We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…

In this study, we present a comprehensive analysis of the motion of a tagged monomer within a Gaussian semiflexible polymer model. We carefully derived the generalized Langevin Equation (GLE) that governs the motion of a tagged central…

A model has two main aims: predicting the behavior of a physical system and understanding its nature, that is how it works, at some desired level of abstraction. A promising recent approach to model building consists in deriving a…

Entangled networks of stiff biopolymers exhibit complex dynamic response, emerging from the topological constraints that neighboring filaments impose upon each other. We propose a class of reference models for entanglement dynamics of stiff…

By means of computer simulations and solution of the equations of the Mode Coupling Theory (MCT), we investigate the role of the intramolecular barriers on several dynamic aspects of non-entangled polymers. The investigated dynamic range…

We study the dynamics of an heteropolymeric chain relaxing toward a new equilibrium configuration after the action of an external perturbation. We compare the results from Monte Carlo simulations with the results of a Langevin normal mode…

A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a…

Individual components such as cells, particles, or agents within a larger system often require detailed understanding of their relative position to act accordingly, enabling the system as a whole to function in an organised and efficient…

We study the Langevin dynamics of diffusive particles with regular pairwise interactions under mean-field scaling. By approximating empirical distributions with conditional distributions, we establish coercive and contractive properties for…

The structural dynamics of a biopolymer is governed by a process of diffusion through its conformational energy landscape. In pulling experiments using optical tweezers, features of the energy landscape can be extracted from the probability…

We describe the Loewner chains of the real locus of a class of real rational functions whose critical points are on the real line. Our main result is that the poles of the rational function lead to explicit formulas for the dynamical system…

The distance-resolved effective interaction between two star polymers in a good solvent is calculated by Molecular Dynamics computer simulations. The results are compared with a pair potential proposed recently by Likos et al. [Phys. Rev.…

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of external driving force, we consider a polymer which is initially placed in the middle of the pore…

A method to generate reactive trajectories, namely equilibrium trajectories leaving a metastable state and ending in another one is proposed. The algorithm is based on simulating in parallel many copies of the system, and selecting the…

Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…

The ability to deal with systems parametric uncertainties is an essential issue for heavy self-driving vehicles in unconfined environments. In this sense, robust controllers prove to be efficient for autonomous navigation. However,…

This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…

We apply well-established concepts of Langevin sampling to derive a new class of algorithms for the efficient computation of free energy differences of fluctuating particles embedded in a 'fast' membrane, i.e., a membrane that…

A stochastic field theory approach is applied to a coarse-grained polymer model that will enable studies of polymer behavior under non-equilibrium conditions. This article is focused on the validation of the new model in comparison to…

The transport of molecules for chemical reactions is critically important in various cellular biological processes. Despite thermal diffusion being prevalent in many biochemical processes, it is unreliable for any sort of directed transport…