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Using Langevin simulations, we numerically investigate the dynamics of driven two-dimensional colloids subject to randomly distributed pointlike pinning centers. Increasing the strength of pinning centers, we find a crossover from elastic to plastic depinnings, where a substantial increase in the depinning force is observed. The influence of temperature is examined, and we find a dynamic melting transition from the moving smectic to the moving liquid at high driving forces. A peak is found in the dynamic critical driving force across the transition, accompanied by a crossing of velocity-force dependence curves.

Using Langevin simulations, we numerically study the dynamics of two-dimensional colloids on a disordered substrate. With a decreasing strength of the interaction between colloids, we find a crossover from elastic to plastic depinnings, where a substantial increase in the depinning force is observed. Furthermore, we find a dynamical phase transition from the moving liquid to the moving smectic at high driving forces by decreasing the temperature. Peak effect occurs in the dynamical critical driving force across the transition, accompanied by a clear crossing of velocity-force dependence curves.

In a generic model of excitable media, we study the behavior of spiral waves interacting with obstacles and their dynamics under the influences of simple periodic mechanical deformation (PMD). Depending on the characteristics of the obstacles, i.e., size and excitability, the rotation of a pinned spiral wave shows different scenarios, e.g., embedding into or anchoring on an obstacle. Three different drift phenomena induced by PMD are observed: scattering on small partial-excitable obstacles, meander-induced unpinning on big partial-excitable obstacles, and drifting around small unexcitable obstacles. Their underlying mechanisms are discussed. The dependence of the threshold amplitude of PMD on the characteristics of the obstacles to successfully remove pinned spiral waves on big partial-excitable obstacles is studied.

Spiral waves may be pinned to anatomical heterogeneities in the cardiac tissue, which leads to monomorphic ventricular tachycardia. Wave emission from heterogeneities (WEH) induced by electric pulses in one direction (EP) is a promising method for liberating such waves by using heterogeneities as internal virtual pacing sites. Here, based on the WEH effect, a new mechanism of liberation by means of a rotating electric pulse (REP) is proposed in a generic model of excitable media. Compared with the EP, the REP has the advantage of opening wider time window to liberate pinned spiral. The influences of rotating direction and frequency of the REP, and the radius of the obstacles on this new mechanism are studied. We believe this strategy may improve manipulations with pinned spiral waves in heart experiments.

We construct a coarse-grained model in terms of the multiple particles collision (MPC) method to study the translocation dynamics of a linear polymer through a crowded channel full of fixed obstacles. The influences of a crowded environment are focused on. We explore the power-law dependence of the polymer mobility coefficient on its length and on the crowded environment. It is shown that the crowded environment may benefit the length-dependent separation of polymer chains. The exponents characterizing the power-law behavior are discussed to distinguish different dynamical regimes. The properties of the translocating polymer, such as trajectory, moving configuration, and radius of gyration, are investigated. The influences of the radius of obstacles and hydrodynamics interaction on the translocating process are also studied. We believe our studies can shed light on the understanding of complex transport processes in many biological systems.

The experimential evidences confirm that spiral waves are observed in the disinhibited mammalian neocortex. The scheme of ceullar networks is used to simulate the formation and the evolution of spiral wave in the neocortical slices. The regular networks of neurons are constructed in the two-dimensional space, the dynamical properties of thermosensitive neurons is described by temperature factor, and the effect of membrane temperature on the evolution of spiral wave is investigated in detail. A statistical factor of synchronization is defined to measure the critical condition inducing phase transition of spiral wave (death or breakup) by the factor of temperature of membrane. It is confirmed that spiral wave is removed and the whole networks become homogeneous and synchronous completely when the membrane temperature exceeds a certain threshold; the breakup of spiral wave is induced in the presence of weak channel noise being considered. Furthermore, it is suggested that the mechanism of temporary heat stupor could be the blocking of spiral wave propagation in some functional domain.

A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t(-1/2) and t(-3/2) power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

Breakup of spiral wave and consequent patterns induced by a strong polarized advective field are studied numerically. The dependences of the critical amplitude of the polarized advective field on its polarized modes and the frequency of the spiral wave are obtained. The effects of the circularly polarized advective field (CPAF, one of the polarized modes) are investigated especially. Under the modulation of a suitable CPAF, a new spiral may be reorganized after breakup, with rotating direction determined by the applied external CPAF. Moreover, hexagonal patterns are observed when the frequency of the CPAF is equal to that of the spiral and the amplitude is suitable. Our finding shows that the symmetry and chirality of the applied external field are important to the organization and selection of new-formed patterns.