Related papers: Particle-based Multiscale Modeling of Calcium Puff…
Certain geological features have been interpreted as evidence of channelized magma flow in the mantle, which is a compacting porous medium. Aharonov et al. (1995) developed a simple model of reactive porous flow and numerically analysed its…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Proteins' fuzziness are features for communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene…
This tutorial introduces the dynamics of charged particles in a radiofrequency trap in a very general manner to point out the differences between the dynamics in a quadrupole and in a multipole trap. When dense samples are trapped, the…
A simple model accounting for the ejection of heavy particles from the vortical structures of a turbulent flow is introduced. This model involves a space and time discretization of the dynamics and depends on only two parameters: the…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
A simple model of a trapped ion cloud cooled by collisions in a buffer gas in a Paul trap is presented. It is based on the customary decomposition of the ion motion in micro- and macro- (or secular) motions and a statistical treatment of…
Single-particle tracking allows to infer the motion of single molecules in living cells. When we observe a long trajectory (more than 100 points), it is possible that the particle switches mode of motion over time. Then, fitting a single…
In a uniform radio-frequency (RF) plasma between a large electrode pair, the addition of an axial magnetic field induces diverse longitudinal filaments. To reveal its pattern dynamics, we conduct two-dimensional (2D) Particle-In-Cell (PIC)…
In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion…
Active emulsions can spontaneously form self-propelled droplets or phoretic micropumps. It has been predicted that the interaction with their self-generated chemical fields can lead to multistable higher-order flows and chemodynamic…
A linear ion trap setup has been developed for studying the dynamics of trapped ion cloud and thereby realizing possible systematics of a high precision measurement on a single ion within it. The dynamics of molecular nitrogen ion cloud has…
We use numerical simulations to examine two-dimensional particle mixtures that strongly phase separate in equilibrium. When the system is externally driven in the presence of quenched disorder, plastic flow occurs in the form of meandering…
Microparticles migrate in response to gradients in solute concentration through diffusiophoresis and diffusioosmosis. Merging streams of fluid with distinct solute concentrations is a common strategy for producing a steady concentration…
In vertebrates, insufficient availability of calcium and phosphate ions in extracellular fluids leads to loss of bone density and neuronal hyper-excitability. To counteract this problem, calcium ions are present at high concentrations…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…
Mitochondrial calcium handling is a particularly active research area in the neuroscience field, as it plays key roles in the regulation of several functions of the central nervous system, such as synaptic transmission and plasticity,…
We numerically study the dynamics and the phases of self-propelled disk-shaped particles of different sizes with soft repulsive potential in two dimensions. Size diversity is introduced by the polydispersity index (PDI) $\epsilon$, which is…
During early development, waves of activity propagate across the retina and play a key role in the proper wiring of the early visual system. During the stage II these waves are triggered by a transient network of neurons, called Starburst…
We have used the Nernst chemical potential treatment to couple the time domains of sodium and calcium ion channel opening and closing rates to the spatial domain of the diffusing waves of the travelling calcium ions inside single cells. The…