Related papers: Dynamic Phase Transitions in Coupled Motor Protein…
The diffusion of a two-dimensional array of particles driven by a constant force in the presence of a periodic external potential exhibits a hierarchy of dynamical phase transitions when the driving force is varied. This behavior can be…
We discuss effects of the stepping kinetics of molecular motors on their traffic behavior on crowded filaments using a simple two-state chemomechanical cycle. While the general traffic behavior is quite robust with respect to the detailed…
Interactions often require the proximity between particles. The movement of particles, thus, drives the change of the neighbors which are located in their proximity, leading to a sequence of interactions. In pathogenic contagion, infections…
Allostery refers to the puzzling phenomenon of long-range communication between distant sites in proteins. Despite its importance in biomolecular regulation and signal transduction, the underlying dynamical process is not well understood.…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
Particles moving in oscillating potential with broken mirror symmetry are considered. We calculate their energetic efficiency, when acting as molecular motors carrying a load against external force. It is shown that interaction between…
Cooperative binding affects many processes in biology, but it is commonly addressed only in equilibrium. In this work we explore dynamical cooperativity in driven systems, where the cooperation occurs because some of the bonds change the…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
We investigate the transport of interacting active run-and-tumble particles moving under an external drift force through a periodic array of obstacles for increasing drive amplitudes. For high activity where the system forms a motility…
The purpose of this work is to use active particles to study the effect of facilitation on supercooled liquids. To this end we investigate the behavior of a model supercooled liquid doped with intermittently active and intermittently slowed…
We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load…
Non-reciprocal systems exhibit diverse dynamical phases whose character depends on the type and degree of non-reciprocity. In this study, we theoretically investigate dynamical structures in a mixture of non-reciprocally aligning polar…
Systems with two species of active molecular motors moving on (cytoskeletal) filaments into opposite directions are studied theoretically using driven lattice gas models. The motors can unbind from and rebind to the filaments. Two motors…
Recent work on stochastic interacting particle systems with two particle species (or single-species systems with kinematic constraints) has demonstrated the existence of spontaneous symmetry breaking, long-range order and phase coexistence…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
This letter investigates the molecular dynamics of inelastic disks without external forcing. By introducing a new observation frame with a rescaled time, we observe the virtual steady states converted from asymptotic energy dissipation…
Driven diffusive systems have provided simple models for non-equilibrium systems with non-trivial structures. Steady state behaviour of these systems with constant boundary conditions have been studied extensively. Comparatively less work…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
We show that optomechanical quantum systems can undergo dissipative phase transitions within the limit of small nonlinear interaction and strong external drive. In such a defined thermodynamical limit, the nonlinear interaction stabilizes…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…