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We model a particulate flow of constant velocity through confined geometries, ranging from a single channel to a bundle of $N_c$ identical coupled channels, under conditions of reversible blockage. Quantities of interest include the exiting…
The process of ion transport through a locust potassium channel is described by means of the Fokker-Planck equation (FPE). The deterministic and stochastic components of the process of switching between various conducting states of the…
We propose an alternative mechanism for the gating of biological membrane channels in response to membrane tension that involves a change in the slope of the membrane near the channel. Under biological membrane tensions we show that the…
Nonlinear dynamical systems may be exposed to tipping points, critical thresholds at which small changes in the external inputs or in the systems parameters abruptly shift the system to an alternative state with a contrasting dynamical…
Stop-and-go waves are commonly observed in traffic and pedestrian flows. In traffic theory they are described by phase transitions of metastable models. The self-organization phenomenon occurs due to inertia mechanisms but requires fine…
The flow of ions through permeable channels causes voltage drop in physiological nanodomains such as synapses, dendrites and dendritic spines, and other protrusions. How the voltage changes around channels in these nanodomains has remained…
An intense controversy has surrounded the mechanism of voltage-gating in ion channels. We interpreted the two leading models of voltage-gating with respect to the thermodynamic energetics of membrane insertion of the voltage-sensing…
Diverse complex dynamical systems are known to exhibit abrupt regime shifts at bifurcation points of the saddle-node type. The dynamics of most of these systems, however, have a stochastic component resulting in noise driven regime shifts…
Entanglement behavior for different classes of two qubit systems passing through a generalized amplitude damping channel is discussed. The phenomena of sudden single, double changes and the sudden death of entanglement are reported for…
Stochastic oscillations in individual cells are usually characterized by a non-monotonic power spectrum with an oscillatory autocorrelation function. Here we develop an analytical approach of stochastic oscillations in a minimal hybrid…
The sudden arrest of motion due to confinement is commonly observed via the clogging transition in the flow of particles through a constriction. We present results of a simple experiment to elucidate a similar transition in the…
By using a propagation scheme for current matrices and an auxiliary mode expansion method, we investigate the transient dynamics of a single molecular junction coupled with a vibrational mode. Our approach is based on the Anderson-Holstein…
Steady state properties of a driven tracer moving in a narrow two dimensional (2D) channel of quiescent medium are studied. The tracer drives the system out of equilibrium, perturbs the density and pressure fields, and gives the bath…
Waves and oscillations are commonly observed in the dynamics of self-driven agents such as pedestrians or vehicles. Interestingly, many factors may perturb the stability of space homogeneous streaming, leading to the spontaneous formation…
Bubbles in ion channel proteins have been proposed to be the bistable gates that control current flow. Gating currents associated with channel gating would then be an electrical signature of bubble breaking and formation, arising from the…
We study condensation transitions in the steady state of a zero-range process with two species of particles. The steady state is exactly soluble -- it is given by a factorised form provided the dynamics satisfy certain constraints -- and we…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
In a stochastic process, noise often modifies the picture offered by the mean field dynamics. In particular, when there is an absorbing state, the noise erases a stable fixed point of the mean field equation from the stationary…
Ionic models, the set of ordinary differential equations (ODEs) describing the time evolution of the state of excitable cells, are the cornerstone of modeling in neuro- and cardiac electrophysiology. Modern ionic models can have tens of…
The motion of several self-propelled boats in a narrow channel displays spontaneous pattern formation and kinetic phase transitions. In contrast with previous studies on self-propelled particles, this model does not require stochastic…