Related papers: Dynamic Phase Transitions in Coupled Motor Protein…
Kinesins are processive motor proteins that move along microtubules in a stepwise manner, and their motion is powered by the hydrolysis of ATP. Recent experiments have investigated the coupling between the individual steps of single kinesin…
Transport of molecular motors, stimulated by interactions with specific links between consecutive binding sites (called ``bridges''), is investigated theoretically by analyzing discrete-state stochastic ``burnt-bridge'' models. When an…
Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we…
Many-variable differential equations with random coefficients provide powerful models for the dynamics of many interacting species in ecology. These models are known to exhibit a dynamical phase transition from a phase where population…
A general system of particles (of one or several species) on a one dimensional lattice with boundaries is considered. Two general behaviors of such systems are investigated. The stationary behavior of the system, and the dominant way of the…
We have numerically studied the trapping problem in a two-dimensional lattice where particles are continuously generated. We have introduced interaction between particles and directionality of their movement. This model presents a critical…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
The movement of motor particles consisting of one or several molecular motors bound to a cargo particle is studied theoretically. The particles move on patterns of immobilized filaments. Several patterns are described for which the motor…
Using numerical simulations we study the pinning and dynamics of interacting colloids on periodic one-dimensional substrates. As a function of colloid density, temperature, and substrate strength, we find a variety of pinned and dynamic…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Under an external field a double-stranded peptide chain can separate in a fragile or ductile transition. It is usually believed that these two regimes are driven either by chemical and thermal fields, or through non-local mechanical…
We overview the concept of dynamical phase transitions in isolated quantum systems quenched out of equilibrium. We focus on non-equilibrium transitions characterized by an order parameter, which features qualitatively distinct temporal…
Motivated by the recent experimental observations on clustering of motor proteins on microtubule filament, we study an open system of two parallel totally asymmetric simple exclusion processes under asymmetric coupling conditions, which…
We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical…
Active particles may undergo phase separation when interactions oppose self-propulsion, in the absence of any cohesive forces. The corresponding Motility-Induced Phase Separation (MIPS) is arguably the simplest non-trivial collective…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We study dynamical phase transitions in a model supercooled liquid. These transitions occur in ensembles of trajectories that are biased towards low (or high) dynamical activity. We compare two different measures of activity that were…
The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…
Phase transitions are emergent phenomena where microscopic interactions drive a disordered system into a collectively ordered phase. Near the boundary between two phases, the system can exhibit critical, scale-invariant behavior. Here, we…