Related papers: Comparing open and closed molecular self-assembly
In this work, we study the long time asymptotics of a coagulation model which describes the evolution of a system of particles characterized by their volume and surface area. The aggregation mechanism takes place in two stages: collision…
We present a systematic investigation of the distribution of normal forces at the boundaries of static packings of spheres. A new method for the efficient construction of large hexagonal-close-packed crystals is introduced and used to study…
We study aggregation driven by a localized source of monomers. The densities become stationary and have algebraic tails far away from the source. We show that in a model with mass-independent reaction rates and diffusion coefficients, the…
We consider a porous mediaum flow in which the gas is initially distributed in the exterior of an empty region (a hole) and study the final stage of the hole-filling process. Hole-filling is asymptotically described by a self-similar…
In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…
Motivated by observations of heterogeneous domain structure on the surface of cells, we consider a minimal model to describe the dynamics of phase separation on the surface of a spherical particle. Finite-size effects on the curved particle…
The paper introduces a general framework for derivation of continuum equations governing meso-scale dynamics of large particle systems. The balance equations for spatial averages such as density, linear momentum, and energy were previously…
Capsids of many viruses assemble around nucleic acids or other polymers. Understanding how the properties of the packaged polymer affect the assembly process could promote biomedical efforts to prevent viral assembly or nanomaterials…
Mutually conjugated synergetic schemes are assumed to address evolution of nonequilibrium self-organizing system. Within framework of the former, the system is parameterized by a conserving order parameter being a density, a conjugate field…
We present a detailed study of the static and dynamic behavior of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [{\it Zhang et al.} ACS Macro Lett. 3,…
Anomalous coarsening in far-from equilibrium one-dimensional systems is investigated by simulation and analytic techniques. The minimal hard core particle (exclusion) models contain mechanisms of aggregated particle diffusion, with rates…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
Studying physical mechanisms and common geometric principles underlying known spherical packings is crucial for rational design of synthetic nanocontainers. Here we model the growth of small spherical shells containing n<72 identical…
Motivated by some problems in genome assembling, we investigate properties of spacings from absolutely continuous distributions. Several results on the asymptotic behavior of the maximal uniform and non-uniform $k$-spacings are presented.…
We consider a model system in which anomalous diffusion is generated by superposition of underlying linear modes with a broad range of relaxation times. In the language of Gaussian polymers, our model corresponds to Rouse (Fourier) modes…
We study the fragment size distributions after crushing of single and many particles under uniaxial compression inside a cylindrical container by means of numerical simulations. Under the assumption that breaking goes through the bulk of…
An off-lattice Monte Carlo algorithm for solutions of equilibrium polymers (EP) is proposed. At low and moderate densities this is shown to reproduce faithfully the (static) properties found recently for flexible linear EP using a lattice…
As a generic model for liquid-vapour type transitions in random porous media, the Asakura-Oosawa model for colloid-polymer mixtures is studied in a matrix of quenched spheres using extensive Monte Carlo (MC) simulations. Since such systems…