Related papers: Folding kinetics of a polymer [corrigendum]
We present a new approach to analyze homogeneous nucleation based on non-equilibrium thermodynamics. The starting point is the formulation of a Gibbs equation for the variations of the entropy of the system, whose state is characterized by…
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is…
Wetting and drying phenomena are studied for flexible and semiflexible polymer solutions via coarse-grained molecular dynamics simulations and density functional theory calculations. The study is based on the use of Young's equation for the…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
We utilize the lattice cluster theory (LCT) of polymer fluids to show that the configurational entropy, enthalpy, and internal energy are all closely interrelated, as suggested by recent measurements by Caruthers and Medvedev, so that the…
We probe the temperature dependence of friction at the interface between a glassy poly(methylmethacrylate) lens and a flat substrate coated with a methyl-terminated self-assembled monolayer. The monolayer exhibits density defects which act…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…
We use computer simulations to study the glass transition of dense fluids made of polydisperse, repulsive spheres. For hard particles, we vary the volume fraction, phi, and use compressible particles to explore finite temperatures, T>0. In…
We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and…
We present a quantum mechanical / molecular mechanics (QM/MM) to tackle chemical reactions with substantial molecular reorganization. For this, molecular dynamics simulations with smoothly switched interaction models are used to suggest…
The glassy dynamics of soft harmonic spheres is often mapped onto the dynamics of hard spheres by considering an effective diameter for the soft particles and therefore an effective packing fraction. While in this approach the thermal…
We consider a two-letter self-avoiding (square) lattice heteropolymer model of N_H (out ofN) attracting sites. At zero temperature, permanent links are formed leading to collapse structures for any fraction rho_H=N_H/N. The average chain…
A microscopic understanding of low-temperature thermodynamics and its relation to dynamical features such as a fragile-to-strong crossover (FSC) remains a central challenge in glass physics. Using swap Monte Carlo combined with a full…
A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form…
We study the finite volume approximation of strong solutions to nonlinear systems of conservation laws. We focus on time-explicit schemes on unstructured meshes, with entropy satisfying numerical fluxes. The numerical entropy dissipation is…
Efficient and accurate algorithm for partition function, free energy and thermal entropy calculations is of great significance in statistical physics and quantum many-body physics. Here we present an unbiased but low-technical-barrier…
Using the Continuous Time Quantum Monte Carlo Loop algorithm, we calculate the temperature dependence of the uniform susceptibility, and the specific heat of a spin-1/2 chain with random antiferromagnetic and ferromagnetic couplings, down…
Monte Carlo simulations have been used to study phase transitions on coupled anisotropic ferro/antiferromagnetic (FM/AFM) films of classical Heisenberg spins. We consider films of different thicknesses, with fully compensated exchange…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…