Related papers: Fast convergence to equilibrium for long-chain pol…
A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important…
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength…
We examine the long-term behaviour of non-integrable, energy-conserved, 1D systems of macroscopic grains interacting via a contact-only generalized Hertz potential and held between stationary walls. We previously showed that in homogeneous…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…
A linear copolymer made of two reciprocally attracting N-monomer blocks collapses to a compact phase through a novel transition, whose exponents are determined with extensive MC simulations in two and three dimensions. In the former case,…
We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional…
We describe a simulation method for the accurate study of the equilibrium freezing properties of polydisperse fluids under the experimentally relevant condition of fixed polydispersity. The approach is based on the phase switch Monte Carlo…
An infinite hierarchy of layering transitions exists for model polymers in solution under poor solvent or low temperatures and near an attractive surface. A flat histogram stochastic growth algorithm known as FlatPERM has been used on a…
The convergence to equilibrium for renormalised solutions to nonlinear reaction-diffusion systems is studied. The considered reaction-diffusion systems arise from chemical reaction networks with mass action kinetics and satisfy the complex…
The purpose of this work is to study mortar methods for linear elasticity using standard low order finite element spaces. Based on residual stabilization, we introduce a stabilized mortar method for linear elasticity and compare it to the…
Polymer simulation with both accuracy and efficiency is a challenging task. Machine learning (ML) forcefields have been developed to achieve both the accuracy of ab initio methods and the efficiency of empirical force fields. However,…
We formulate and test a hybrid fluid-Monte Carlo scheme for the treatment of elastic collisions in gases and plasmas. While our primary focus and demonstrations of applicability are for moderately collisional plasmas, as described by the…
The aim of hybrid methods in simulations is to communicate regions with disparate time and length scales. Here, a fluid described at the atomistic level within an inner region P is coupled to an outer region C described by continuum fluid…
We investigate the effect of hydrodynamic interactions on the non-equilibrium drift dynamics of an ideal flexible polymer pulled by a constant force applied at one end of the polymer using the perturbation theory and the renormalization…
Helical motifs are ubiquitious in macromolecular systems. The mechanism of spontaneous emergence of helicity is unknown, especially in cases where torsional interactions are absent. Emergence of helical order needs coordinated organization…
Letting free polymers diffuse from solution into a crosslinked polymer gel is often a crucial processing step in the synthesis of multiphase polymer-based gels, e.g., core-shell microgels. Here we use coarse-grained molecular dynamics…
The Fermi liquid-Wigner crystal transition in a two dimensional electronic system is revisited with a focus on the nature of the fixed node approximation done in quantum Monte Carlo calculations. Recently, we proposed (Phys. Rev. Lett. 94,…
This work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct collisions (short-range) or through harmonic…
Equilibrium quantum systems are often described by a gas of weakly-interacting normal modes. Bringing such systems far from equilibrium, however, can drastically enhance mode-to-mode interactions. Understanding the resulting liquid is a…
We introduce a numerical workflow to model and simulate transient close-contact melting processes based on the space-time finite element method. That is, we aim at computing the velocity at which a forced heat source melts through a…