Related papers: Equilibrium and nonequilibrium effects in the coll…
Conserved growth models that exhibit a nonlinear instability in which the height (depth) of isolated pillars (grooves) grows in time are studied by numerical integration and stochastic simulation. When this instability is controlled by the…
In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
We analyse the dynamics of different routes to collapse of a constrained polyelectrolyte gel in contact with an ionic bath. The evolution of the gel is described by a model that incorporates non-linear elasticity, Stefan-Maxwell diffusion…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…
The collapse of non-collisional dark matter and the formation of pancake structures in the Universe are investigated approximately. Collapse is described by a system of ordinary differential equations, in the model of a uniformly rotating,…
We examine nonequilibrium features of collapse behavior in model polymers with competing crystallization and glass transitions using extensive molecular dynamics simulations. By comparing to "colloidal" systems with no covalent bonds but…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Nonequilibrium molecular dynamics simulations are used to study the deformation behavior of disperse polymer melts by tracking test chains of length N = Mw, the weight average molecular weight, in melts of varying dispersity. At high strain…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
Coupling between chemical fuel consumption and phase separation can lead to condensation at a nonequilibrium steady state, resulting in phase behaviors that are not described by equilibrium thermodynamics. Theoretical models of such…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
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…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
The statistical properties of turbulent flows are fundamentally different from those of systems at equilibrium due to the presence of an energy flux from the scales of injection to those where energy is dissipated by the viscous forces: a…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
The dynamics of colloidal particles in potential energy landscapes have mainly been investigated theoretically. In contrast, here we discuss the experimental realization of potential energy landscapes with the help of light fields and the…
Fluid phase equilibria involving nano-dispersed phases, where at least one of the coexisting phases is confined to a small volume, are investigated by molecular dynamics simulation. Complementing previous studies on nanoscopic droplets,…
We have performed multicanonical chain-growth simulations of a polymer interacting with an adsorbing surface. The polymer, which is not explicitly anchored at the surface, experiences a hierarchy of phase transitions between conformations…