Related papers: Molecular dynamics simulation of reversibly self-a…
Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially bind to the genome through an en masse mechanism and form nucleoprotein complexes in a…
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that…
Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse…
Colloidal particles with mobile binding molecules constitute a powerful platform for probing the physics of self-assembly. Binding molecules are free to diffuse and rearrange on the surface, giving rise to spontaneous control over the…
We describe a robust, fast, and memory-efficient procedure that can cluster millions of structures derived from molecular dynamics simulations. The essence of the method is based on a peak-picking algorithm applied to three- and…
In this thesis, we aim to further elucidate the phenomenon of galaxy evolution in the environment of galaxy clusters using the methodology of numerical simulations. For that, we have developed hydrodynamic models in which idealized gas-rich…
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed…
The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The…
Three dimensional molecular dynamics simulations of cohesive dissipative powders under a plane shear are performed. We find the various phases depending on the dimensionless shear rate and the dissipation rate as well as the density. We…
Deposition of smaller granular particles on a larger nucleus particle has been simulated in two-dimension using molecular dynamics method. Variation of sequences of velocity of deposited particles is conducted and reported in this work. The…
We report a detailed computational study by Brownian Dynamics simulations of the structure and dynamics of a liquid of patchy particles which develops an amorphous tetrahedral network upon decreasing temperature. The highly directional…
In three-dimensional electromagnetic configurations that result from unstable resistive tearing modes particles can efficiently be accelerated to relativistic energies. To prove this resistive magnetohydrodynamic simulations are used as…
Gels in soft-matter systems are an important nonergodic state of matter. We study a colloid-polymer mixture which is quenched by increasing the polymer concentration, from a fluid to a gel. Using confocal microscopy, we study both the…
Polymer self-consistent field theory techniques are used to find radial electron densities and total binding energies for isolated atoms. Quantum particles are modelled as Gaussian threads with ring-polymer architecture in a four…
As an extension of the former study on 2-dimensional systems, we simulate phase behavior of polymer-grafted colloidal particles in 3 dimensions by molecular Monte Carlo technique in the canonical ensemble. We use a spherically symmetric…
Colloidal molecules are ideal model systems for mimicking real molecules and can serve as versatile building blocks for the bottom-up self-assembly of flexible and smart materials. While most colloidal molecules are rigid objects, the…
We present a coarse-grained model of clathrin that is simple enough to be computationally tractable yet includes key observed qualitative features: a triskelion structure with excluded volume between legs; assembly of polymorphic cages in…
In this paper, we present a 2D numerical model developed to simulate the dynamics of soft, deformable particles. To accommodate significant particle deformations, the particle surface is represented as a narrow shell composed of mass points…
Mutually repelling particles form spontaneously ordered clusters when forced into confinement. The clusters may adopt similar spatial arrangements even if the underlying particle interactions are contrastingly different. Here we demonstrate…
Multi-component aggregates are being intensively researched in various fields because of their highly tunable properties and wide applications. Due to the complex configurational space of these systems, research would greatly benefit from a…