Related papers: Molecular dynamics simulation of reversibly self-a…
Magnetic nanoparticles in a colloidal solution self-assemble in various aligned structures, which has a profound influence on the flow behavior. However, the precise role of the microstructure in the development of the rheological response…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
Depending on the pH value and salt concentration of Al2O3 suspensions different microstructures can form. Especially the clustered one is of major interest for industrial purposes as found in the production of ceramics. In this paper we…
While evaporating solvent is a widely used technique to assemble nano-sized objects into desired superstructures, there has been limited work on how the assembled structures are affected by the physical aspects of the process. We present…
We perform numerical simulations of athermal repulsive frictionless disks and spheres in two and three spatial dimensions undergoing cyclic quasi-static simple shear to investigate particle-scale reversible motion. We identify three classes…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
Cowpea chlorotic mottle virus (CCMV) is a widely used model for virus replication studies. A major challenge lies in distinguishing between the roles of the interaction between coat proteins and that between the coat proteins and the viral…
Patchy particles have proven to be a prominent model for studying the self-assembly behavior of various systems, ranging from finite clusters to bulk crystal assemblies, and from synthetic colloidal particles to viruses. The patchy particle…
A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is…
Discrete particle simulations are used to model segregation in granular mixtures of three different particle species in a horizontal rotating drum. Axial band formation is observed, with medium-size particles tending to be located between…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
In the field of freezing colloidal suspensions, it is important to understand the particle-scale behavior of particle packing. Here, we reveal the dynamics of particle packing by identifying the behavior of each single particle in situ. The…
The self-assembly of DNA-coated colloids controlled by enzymatic reactions has the potential to enable the formation of materials with hierarchical organization and switchable configurations. However, the problem of designing such…
The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…
In a granular gas, inelastic collisions produce an instability in which the constituent particles cluster heterogeneously. These clusters then interact with each other, further decreasing their kinetic energy. We report experiments of the…
Preliminary results are presented about a fully self-consistent N-body simulation of a sample of four massive globular clusters in close interaction within the central region of a galaxy. The N-body representation (with N=1.5x10^6 particles…
Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities…
The formation mechanism of planetesimals in protoplanetary discs is hotly debated. Currently, the favoured model involves the accumulation of meter-sized objects within a turbulent disc, followed by a phase of gravitational instability. At…
Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which…