相关论文: Master curve of boosted diffusion for ten catalyti…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an intracellular transport system consisting of a cargo attached to two cooperative but not identical molecular motors (for example, kinesin-1…
Molecular dynamics simulations are used to study the mechanism and kinetics of hydrated electron diffusion. The electron center of mass is found to exhibit Brownian-type behavior with a diffusion coefficient considerably greater than that…
The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on…
Diffusion of transported particles in the intracellular medium is described by means of a generalized diffusion equation containing forces due to the cytoskeleton network and to the protein motors. We find that the enhanced diffusion…
We propose a minimal mathematical model to explain long-range coordination of dynamics of multiple cells in epithelial spreading, which may be induced, under different conditions, by a chemical signal, or mechanical stress, or both. The…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
We develop a theory of enzyme catalysis within biological cells where the substrate concentration [S](t) is time dependent, in contrast to the Michaelis-Menten theory that assumes a steady state. We find that the time varying concentration…
Situations where a spontaneous process of energy or matter transfer is enhanced by an external device are widespread in nature (human sweating system, enzyme catalysis, facilitated diffusion across bio-membranes, industrial heat…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
Energy transfer plays a vital role in many natural and technological processes. In this work, we study the effects of mechanical motion on the excitation transfer through a chain of interacting molecules with application to biological…
Classical descriptions of enzyme kinetics ignore the physical nature of the intracellular environment. Main implicit assumptions behind such approaches are that reactions occur in compartment volumes which are large enough so that molecular…
Micrometer-sized objects are widely known to exhibit chemically-driven motility in systems away from equilibrium. Experimental observation of reaction-induced motility or enhancement in diffusivity at the much shorter length scale of small…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
The hyperbolic dependence of catalytic rate on substrate concentration is a classical result in enzyme kinetics, quantified by the celebrated Michaelis-Menten equation. The ubiquity of this relation in diverse chemical and biological…
A prime example of non-equilibrium or active environment is a biological cell. In order to understand in-vivo functioning of biomolecules such as proteins, chromatins, a description beyond equilibrium is absolutely necessary. In this…
Recent fluorescence spectroscopy measurements of single-enzyme kinetics have shown that enzymatic turnovers form a renewal stochastic process in which the inverse of the mean waiting time between turnovers follows the Michaelis-Menten…
Catalytically active macromolecules are envisioned as key building blocks in development of artificial nanomotors. However, theory and experiments report conflicting findings regarding their dynamics. The lack of consensus is mostly caused…
Catalysis-driven synthetic molecular motors operate in a loose mechanochemical coupling regime, one in which a decomposition of a fuel molecule does not reliably produce a forward step. In that regime, stochastic backward steps can…