Related papers: Atomistic study of macroscopic analogs to short ch…
A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between…
The dynamic behavior of polyelectrolyte chains in the oligomer range is investigated with coarse-grained molecular dynamics simulation and compared to data obtained by two different experimental methods, namely capillary electrophoresis and…
We study the self-organization of spherical particles in an oscillating flow through experiments inside an oscillating box. The interactions between the particles and the time-averaged (steady streaming) flow lead to the formation of either…
Numerically optimized reduced descriptions of macromolecular liquids often present thermodynamic inconsistency with atomistic level descriptions even if the total correlation function, i.e. the structure, appears to be in agreement. An…
A version of the time-parallel algorithm parareal is analyzed and applied to stochastic models in chemical kinetics. A fast predictor at the macroscopic scale (evaluated in serial) is available in the form of the usual reaction rate…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…
We investigate thermal avalanche dynamics in amorphous solids using elastoplastic models with local activation rules and no external driving. Dynamical heterogeneities, quantified through persistence measurements and the associated…
Using the quantum Monte Carlo Loop algorithm, we calculate the temperature dependence of the uniform susceptibility, the specific heat, the correlation length, the generalized staggered susceptibility and magnetization of a spin-1/2 chain…
Atoms trapped in the evanescent field around a nanofiber experience strong coupling to the light guided in the fiber mode. However, due to the intrinsically strong positional dependence of the coupling, thermal motion of the ensemble limits…
Molecular dynamic simulation enables one to correlate the evolution of the micro-structure with anisotropic stress when a material is subject to strain. The anisotropic stress due to a constant strain-rate load in a cross-linked polymer is…
In this paper we present a classical Monte Carlo simulation of the orthorhombic phase of crystalline polyethylene, using an explicit atom force field with unconstrained bond lengths and angles and periodic boundary conditions. We used a…
The endpoint distribution and dynamics of semiflexible fibers is studied by numerical simulation. A brief overview is given over the analytical theory of flexible and semiflexible polymers. In particular, a closed expression is given for…
We generalize the quantum random walk protocol for a particle in a one-dimensional chain, by using several types of biased quantum coins, arranged in aperiodic sequences, in a manner that leads to a rich variety of possible wave function…
A colloidal particle is a prominent example of a stochastic system, and, if suspended in a simple viscous liquid, very closely resembles the case of an ideal random walker. A variety of new phenomena have been observed when such colloid is…
The configurations taken by polymers embedded in out-of-equilibrium baths may have broad effects in a variety of biological systems. As such, they have attracted considerable interest, particularly in simulation studies. Here we analyze the…
We numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear…
In this work we illustrate our novel quantitative simulation approach for dense amorphous polymer systems, as discussed in our previous work[Kulkarni et al., A Novel Approach for Lattice Simulations of Polymer Chains in Dense Amorphous…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
We describe a chain of unidirectionally coupled adaptive excitable elements slowly driven by a stochastic process from one end and open at the other end, as a minimal toy model of unresolved irreducible uncertainty in a system performing…
We investigate thermalization in a tight-binding chain with an on-site defect subject to local dephasing noise implemented as random phase kicks. For a single linear defect of strength $\epsilon$, we obtain an exact analytical description…