Related papers: Solvent-quality dependent contact formation dynami…
This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of…
This paper constructs and analyzes a model for the dynamic frictional contact between a viscoelastic body and a moving foundation. The contact involves wear of the contacting surface and the diffusion of the wear debris. The relationships…
In recent years, thermophoresis has emerged as a promising tool for quantifying biomolecular interactions. The underlying physical effect is still not understood. To gain deeper insight, we investigate whether non-equilibrium coefficients…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
We consider a reaction-diffusion process with retardation. The particles, immersed in traps initially, remain inactive until another particle is annihilated spontaneously with a rate $\lambda$ at a certain point $\vec x$. In that case the…
We study two non-Markovian gene-expression models in which protein production is a stochastic process with a fat-tailed non-exponential waiting time distribution (WTD). For both models, we find two distinct scaling regimes separated by an…
We investigate the one-dimensional mixture of scalar bosons and spin polarized fermions interacting through a $\delta$-function potential. Using a thermodynamic description derived by employing a lattice embedding of the continuum model and…
We analyze (2+1)-dimensional Gross-Neveu model with a Thirring interaction, where a vector-vector type four-fermi interaction is on equal terms with a scalar-scalar type one. The Dyson-Schwinger equation for fermion self-energy function is…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and…
Motivated by the experimental search for the QCD critical point we perform simulations of a stochastic field theory with purely relaxational dynamics (model A). We verify the expected dynamic scaling of correlation functions. Using a finite…
Classically, the quantity of contact area $A_R$ between two bodies is considered a proxy for the force of friction. However, bond density across the interface - quality of contact - is also relevant, and contemporary debate often centers…
Dense suspensions often exhibit a dramatic response to large external deformation. The recent body of work has related this behavior to transition from an unconstrained lubricated to a constrained frictional state. Here, we use numerical…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
We study the nonequilibrium phase transition in the one-dimensional contact process with quenched spatial disorder by means of large-scale Monte-Carlo simulations for times up to $10^9$ and system sizes up to $10^7$ sites. In agreement with…
We report a computer simulation study of a model gel-former obtained by modifying the three-body interactions of the Stillinger-Weber potential for silicon. This modification reduces the average coordination number and consequently shifts…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
We have performed a molecular dynamics computer simulation of a supercooled binary Lennard-Jones system in order to compare the dynamical behavior of this system with the predictions of the idealized version of mode-coupling theory (MCT).…
We investigate theoretically a diffusion-limited reaction between a reactant attached to a Rouse polymer and an external fixed reactive site in confinement. The present work completes and goes beyond a previous study [T. Gu\'erin, O.…
We study the relaxation dynamics of a nonequilibrium Luttinger liquid after a sudden interaction switch-on ("quench"), focussing on a double-step initial momentum distribution function. In the framework of the non-equilibrium bosonization,…