Related papers: Free Energy Transduction in a Chemical Motor Model
Molecular motors do not work in isolation {\it in-vivo}. We highlight some of the coordinations, cooperations and competitions that determine the collective properties of molecular motors in eukaryotic cells. In the context of traffic-like…
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest…
A novel mechanism of reaction-induced active molecular motion, not involving any kind of self-propulsion, is proposed and analyzed. Because of the momentum exchange with the surrounding solvent, conformational transitions in…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create inhomogeneities that…
We report a realization of an associative memory signal/information processing system based on simple enzyme-catalyzed biochemical reactions. Optically detected chemical output is always obtained in response to the triggering input, but the…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Results in the field of mechanochemistry are summarized. For example under mechanical load often a solvolysis is observed instead of a simple homolytic bond rupture. Also a mechanically induced redox reaction was reported experimentally and…
Using Brownian dynamics simulations, the motion of active Brownian particles (ABPs) in the presence of fuel (or 'food') sources is studied. It is an established fact that within confined stationary systems, the activity of ABPs generates…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
The cellular milieu is teeming with biochemical nano-machines whose activity is a strong source of correlated non-thermal fluctuations termed active noise. Essential elements of this circuitry are enzymes, catalysts that speed up the rate…
A cyclically operating chemical engine is considered that converts chemical energy into mechanical work. The working fluid is a gas of finite-sized spherical particles interacting through elastic hard collisions. For a generic transport law…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand…
The dynamics of a spherical chemically-powered synthetic colloidal motor that operates by a self-diffusiophoretic mechanism and has a catalytic domain of arbitrary shape is studied using both continuum theory and particle-based simulations.…
Molecular motors transport various cargos along cytoskeletal filaments, analogous to trucks on roads. In contrast to vehicles, however, molecular motors do not work alone but in small teams. We describe a simple model for the transport of a…
Mechanochemical coupling was studied for two different types of myosin motors in cells: myosin V, which carries cargo over long distances by as a single molecule; and myosin II, which generates a contracting force in cooperation with other…
Anomalously slow passive diffusion, $\langle \delta x^2(t)\rangle\simeq t^{\alpha}$, with $0<\alpha<1$, of larger tracers such as messenger RNA and endogenous submicron granules in the cytoplasm of living biological cells has been…