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Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
A soft particle model for diblock (AB) copolymer melts is proposed. Each molecule is mapped onto two soft spheres built by Gaussian A- and B-monomer distributions. An approximate analytical expression for the joint distribution function for…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias…
By quantitative studies of statistics of polymer stretching in a random flow and of a flow field we demonstrate that the stretching of polymer molecules in a 3D random flow occurs rather sharply via the coil-stretch transition at the value…
We present a theoretical study of the phase diagram and the structure of a fluid adsorbed in high-porosity aerogels by means of an integral-equation approach combined with the replica formalism. To simulate a realistic gel environment, we…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
In a recent letter, a simple method was proposed to generate solvable models that predict the critical properties of statistical systems in hyperspherical geometries. To that end, it was shown how to reduce a random walk in $D$ dimensions…
We study conformations assumed by single diblock star copolymers in a poor solvent by means of the Gaussian variational theory and Monte Carlo simulation in continuous space. Cases of stars with internal and external hydrophobic blocks are…
We introduce an off-lattice model with continuous particle distances and pair-potential interactions which allows for the efficient simulation of strained heteroepitaxial growth by means of kinetic Monte Carlo (KMC) simulations. We discuss…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
The non-equilibrium structural and dynamical properties of semiflexible polymers confined to two dimensions are investigated by molecular dynamics simulations. Three different scenarios are considered: The force-extension relation of…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
Molecular dynamics simulations are used to study the behavior of closely-fitting spherical and ellipsoidal particles moving through a fluid-filled cylinder at nanometer scales. The particle, the cylinder wall and the fluid solvent are all…
We use the Fokker-Planck equation and its moment equations to study the collective behavior of interacting particles in unsteady one-dimensional flows. Particles interact according to a long-range attractive and a short-range repulsive…
Characteristics of relaxed density profile and conformation of polymer chains are studied by a Monte Carlo simulation on a discrete lattice in three dimensions using different segmental (kink-jump $K$, crank-shaft $C$, reptation $R$)…
We derive the fully time-dependent solution to a run-and-tumble model for a particle which has tumbling restricted to the boundaries of a one-dimensional interval. This is achieved through a field-theoretic perturbative framework by…
We obtain an exact result for the midpoint probability distribution function (pdf) of the stationary continuum directed polymer, when averaged over the disorder. It is obtained by relating that pdf to the linear response of the stochastic…
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…