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Present-day atomistic simulations generate long trajectories of ever more complex systems. Analyzing these data, discovering metastable states, and uncovering their nature is becoming increasingly challenging. In this paper, we first use…
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…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
Very often, models in biology, chemistry, physics, and engineering are systems of polynomial or power-law ordinary differential equations, arising from a reaction network. Such dynamical systems can be generated by many different reaction…
The connection between domain relaxations at individual scales and the collective heterogeneous response in non-equilibrium systems is a topic of profound interest in recent times. In a model sys- tem of constantly driven oppositely charged…
We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants can be described by deterministic, acyclic automata with a…
We investigate the heterogeneous dynamics in a model, where chemical gelation and glass transition interplay, focusing on the dynamical susceptibility. Two independent mechanisms give raise to the correlations, which are manifested in the…
Dual phospho/dephosphorylation cycles, as well as covalent enzymatic-catalyzed modifications of substrates, are widely diffused within cellular systems and are crucial for the control of complex responses such as learning, memory and…
A simple phenomenological model of a binary granular mixture is developed and investigated numerically. We attempt to model the experimental system of [1,2] where a horizontally vibrated binary monolayer was found to exhibit a transition…
Dense suspensions of fine particles are significant in numerous biological, industrial, and natural phenomena. They also provide an ideal tool to develop statistical mechanics description for out-of-equilibrium systems. Predicting the bulk…
Mixtures of several macromolecular species can lead to the formation of higher-order structures that often display non-ideal mixing behavior. In this work, we propose a minimal model of a quaternary system which considers the formation of a…
Evidence from experimental studies shows that oscillations due to electro-mechanical coupling can be generated spontaneously in smooth muscle cells. Such cellular dynamics are known as \textit{pacemaker dynamics}. In this article we address…
A long standing puzzle in the rheology of living cells is the origin of the experimentally observed long time stress relaxation. The mechanics of the cell is largely dictated by the cytoskeleton, which is a biopolymer network consisting of…
We will derive here the relaxation behavior of a simple quantum random matrix model. The aim is to derive the effective equations which rise when a random matrix interaction is taken in the weak coupling limit. The physical situation this…
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
We develop efficient asymptotic-preserving time discretization schemes to solve the disparate mass kinetic system of a binary gas or plasma in the "relaxation time scale" relevant to the epochal relaxation phenomenon. Since the resulting…