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Understanding the transport of driven nano- and micro-particles in complex fluids is of relevance for many biological and technological applications. Here we perform hydrodynamic multiparticle collision dynamics simulations of spherical and…
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 use stochastic rotation dynamics to examine the dynamics of the ejection of an initially strongly confined flexible polymer from a spherical capsid with and without hydrodynamics. The results obtained using SRD are compared to similar…
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…
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces.…
We use numerical simulation to investigate and analyze the way that rigid disks and spheres arrange themselves when compressed next to incommensurate substrates. For disks, a movable set is pressed into a jammed state against an ordered…
Assemblies of purely repulsive and frictionless particles, such as emulsions or hard spheres, display very curious properties near their jamming transition, which occurs at the random close packing for mono-disperse spheres. Although such…
As a model of soft confinement for polymers, we investigated equilibrium shapes of a flexible vesicle that contains a phase-separating polymer solution. To simulate such a system, we combined the phase field theory (PFT) for the vesicle and…
In this paper we study the shape characteristics of star-like polymers in various solvent quality using a mesoscopic level of modeling. The dissipative particle dynamics simulations are performed for the homogeneous and four different…
The phase behavior of helical packings of thermoresponsive microspheres inside glass capillaries is studied as a function of volume fraction. Stable packings with long-range orientational order appear to evolve abruptly to disordered states…
It is commonly believed that the most efficient way to pack a finite number of equal-sized spheres is by arranging them tightly in a cluster. However, mathematicians have conjectured that a linear arrangement may actually result in the…
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.…
Transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers could be passive, such as colloids or active (self-propelled), such as synthetic…
We enumerate all minimal energy packings (MEPs) for small single linear and ring polymers composed of spherical monomers with contact attractions and hard-core repulsions, and compare them to corresponding results for monomer packings. We…
The non-equilibrium structural and dynamical properties of a semiflexible polymer confined in a cylindrical microchannel and exposed to a Poiseuille flow is studied by mesoscale hydrodynamic simulations. For a polymer with a length half of…
The estimation of CME arrival time strongly depends on the CME propagation models in interplanetary space and the geometrical aspects of the CME model. We conducted ensemble simulations of CMEs propagation with various elliptical cone…
Granular matter takes many paths to pack. Gentle compression, compaction or repetitive tapping can happen in natural and industrial processes. The path influences the packing microstructure, and thus macroscale properties, particularly for…
Packing spheres efficiently in large dimension $d$ is a particularly difficult optimization problem. In this paper we add an isotropic interaction potential to the pure hard-core repulsion, and show that one can tune it in order to maximize…
Elastic properties and internal states of isotropic sphere packings are studied by numerical simulations. Several numerical protocols to assemble dense configurations are compared. One, which imitates experiments with lubricated contacts,…
Monte Carlo simulations are used to study the translocation of a polymer into and out of a ellipsoidal cavity through a narrow pore. We measure the polymer free energy F as a function of a translocation coordinate, s, defined to be the…