Defect structures and torque on an elongated colloidal particle immersed in a liquid crystal host

Combining molecular dynamics and Monte Carlo simulation we study defect structures around an elongated colloidal particle embedded in a nematic liquid crystal host. By studying nematic ordering near the particle and the disclination core region we are able to examine the defect core structure and the difference between two simulation techniques. In addition, we also study the torque on a particle tilted with respect to the director, and modification of this torque when the particle is close to the cell wall

Particle-based simulation of ellipse-shaped particle aggregation as a model for vascular network formation

Computational modelling is helpful for elucidating the cellular mechanisms driving biological morphogenesis. Previous simulation studies of blood vessel growth based on the Cellular Potts model (CPM) proposed that elongated, adhesive or mutually attractive endothelial cells suffice for the formation of blood vessel sprouts and vascular networks. Because each mathematical representation of a model introduces potential artifacts, it is important that model results are reproduced using alternative modelling paradigms. Here, we present a lattice-free, particle-based simulation of the cell elongation model of vasculogenesis. The new, particle-based simulations confirm the results obtained from the previous Cellular Potts simulations. Furthermore, our current findings suggest that the emergence of order is possible with the application of a high enough attractive force or, alternatively, a longer attraction radius. The methodology will be applicable to a range of problems in morphogenesis and noisy particle aggregation in which cell shape is a key determining factor.Comment: 9 pages, 11 figures, 2 supplementary videos (on Youtube), submitted to Computational Particle Mechanics, special issue: Jos\'e-Manuel Garcia Aznar (Ed.) Particle-based simulations on cell and biomolecular mechanic

Weibel instability and associated strong fields in a fully 3D simulation of a relativistic shock

Plasma instabilities (e.g., Buneman, Weibel and other two-stream instabilities) excited in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a new 3-D relativistic particle-in-cell code, we have investigated the particle acceleration and shock structure associated with an unmagnetized relativistic electron-positron jet propagating into an unmagnetized electron-positron plasma. The simulation has been performed using a long simulation system in order to study the nonlinear stages of the Weibel instability, the particle acceleration mechanism, and the shock structure. Cold jet electrons are thermalized and slowed while the ambient electrons are swept up to create a partially developed hydrodynamic (HD) like shock structure. In the leading shock, electron density increases by a factor of 3.5 in the simulation frame. Strong electromagnetic fields are generated in the trailing shock and provide an emission site. We discuss the possible implication of our simulation results within the AGN and GRB context.Comment: 4 pages, 3 figures, ApJ Letters, in pres

Particle In Cell Simulation of Combustion Synthesis of TiC Nanoparticles

A coupled continuum-discrete numerical model is presented to study the synthesis of TiC nanosized aggregates during a self-propagating combustion synthesis (SHS) process. The overall model describes the transient of the basic mechanisms governing the SHS process in a two-dimensional micrometer size geometry system. At each time step, the continuum (micrometer scale) model computes the current temperature field according to the prescribed boundary conditions. The overall system domain is discretized with a desired number of uniform computational cells. Each cell contains a convenient number of computation particles which represent the actual particles mixture. The particle-in-cell (discrete) model maps the temperature field from the (continuum) cells to the respective internal particles. Depending on the temperature reached by the cell, the titanium particles may undergo a solid-liquid transformation. If the distance between the carbon particle and the liquid titanium particles is within a certain tolerance they will react and a TiC particle will be formed in the cell. Accordingly, the molecular dynamic method will update the location of all particles in the cell and the amount of transformation heat accounted by the cell will be entered into the source term of the (continuum) heat conduction equation. The new temperature distribution will progress depending on the cells which will time-by-time undergo the chemical reaction. As a demonstration of the effectiveness of the overall model some paradigmatic examples are shown.Comment: submitted to Computer Physics Communication