Related papers: Quantitative Study of Polymer Dynamics Through Hie…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
In this chapter we review concepts and theories of polymer dynamics. We think of it as an introduction to the topic for scientists specializing in other subfields of statistical mechanics and condensed matter theory, so, for the readers…
We perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along…
The Synchronized Molecular-Dynamics simulation which was recently proposed by authors [Phys. Rev. X {\bf 4}, 041011 (2014)] is applied to the analysis of polymer lubrication between parallel plates. The rheological properties,…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…
We review recent results from computer simulation studies of polymer glasses, from chain dynamics around the glass transition temperature Tg to the mechanical behaviour below Tg. These results clearly show that modern computer simulations…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…
A hierarchical (triple scale) simulation methodology is presented for the prediction of the dynamical and rheological properties of high molecular weight entangled polymer melts. The methodology consists of atomistic, moderately…
The mesoscopic modeling of three polysiloxanes in solution is reported in this work, with the purpose of predicting their physicochemical properties as functions of the quality of the solvent, so that a judicious choice of polymer/solvent…
We investigate numerically the dynamics of a single polymer in a linear shear flow. The effects of thermal fluctuations and randomly fluctuating velocity gradients are both analyzed. Angular, elongation and tumbling time statistics are…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
The properties of semidilute polymer solutions are investigated at equilibrium and under shear flow by mesoscale simulations, which combine molecular dynamics simulations and the multiparticle collision dynamics approach. In semidilute…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
Abstract polymer models are systems of weighted objects, called polymers, equipped with an incompatibility relation. An important quantity associated with such models is the partition function, which is the weighted sum over all sets of…
Semiflexible polymers in concentrated lyotropic solution are studied within a bead-spring model by molecular dynamics simulations, focusing on the emergence of a smectic A phase and its properties. We systematically vary the density of the…
A novel quantum dynamical method to simulate vibronic reaction dynamics in molecules at metal surfaces is proposed. The method is based on the hierarchical quantum master equation approach and uses a discrete variable representation of the…
The ability to perform ab initio molecular dynamics simulations using potential energies calculated on quantum computers would allow virtually exact dynamics for chemical and biochemical systems, with substantial impacts on the fields of…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…