Related papers: Packaging stiff polymers in small containers: A mo…
In both nature and engineering, loosely packed granular materials are often compacted inside confined geometries. Here, we explore such behaviour in a quasi-two dimensional geometry, where parallel rigid walls provide the confinement. We…
Dense packing of particles has provided important models to study the structure of matter in various systems such as liquid, glassy and crystalline phase, etc. The simplest sphere packing models are able to represent and capture salient…
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the…
An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branched model polymers, or `colloidomers'. The distribution of…
Direct numerical simulations (DNS) of particle-laden turbulent flow in straight, mildly curved and strongly bent pipes are performed in which the solid phase is modelled as small heavy spherical particles. A total of seven populations of…
We characterize the self-assembly of colloidal particles with surface mobile DNA linkers under kinetically limited valence conditions. For this, we put forward a computer simulation model that captures quantitatively the interplay between…
Random packings of granular chains are presented as a model polymer system to investigate the contribution of entanglements to strain-stiffening in the absence of Brownian motion. The chain packings are sheared in triaxial compression…
Using molecular dynamics simulations, we provide chain-level insights into the dissimilarities in rearrangements of polymers under uniaxial tensile and compressive deformation in glassy and semicrystalline samples of varying chain lengths.…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
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…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit…
Soft colloids allow to explore high density states well beyond random close packing. An important open question is whether softness controls the dynamics under these dense conditions. While experimental works reported conflicting results,…
In this paper, we investigate a stochastic model describing the time evolution of a polymerization process. A polymer is a macro-molecule resulting from the aggregation of several elementary sub-units called monomers. Polymers can grow by…
Packing problems have been of great interest in many diverse contexts for many centuries. The optimal packing of identical objects has been often invoked to understand the nature of low temperature phases of matter. In celebrated work,…
Slow dynamics in a fluid are studied in one of the most basic systems possible: polydisperse hard spheres. Monodisperse hard spheres cannot be studied as the slow down in dynamics as the density is increased is preempted by crystallisation.…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…
We study the dynamics of a single chain polymer confined to a two dimensional cell. We introduce a kinetically constrained lattice gas model that preserves the connectivity of the chain, and we use this kinetically constrained model to…
The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a…
The effect of ring stiffness and pressure on the glassy dynamics of a thermal assembly of two-dimensional ring polymers is investigated using extensive coarse-grained molecular dynamics simulations. In all cases, dynamical slowing down is…