Related papers: The mean velocity of two-state models of molecular…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
The muscle contraction, operation of ATP synthase, maintaining the shape of a cell are believed to be secured by motor proteins, which can be modelled using the Brownian ratchet mechanism. We consider the randomly flashing ratchet model of…
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
A method-of-moments scheme is invoked to compute the asymptotic, long-time mean (or composite) velocity and dispersivity (effective diffusivity) of a two-state particle undergoing one-dimensional convective-diffusive motion accompanied by a…
Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…
We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents…
Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
In a single molecule assay, the motion of a molecular motor is often inferred from measuring the stochastic trajectory of a large probe particle attached to it. We discuss a simple model for this generic set-up taking into account…
The control of chemical dynamics requires understanding the effect of time-dependent transition rates between states of chemo-mechanical molecular configurations. Pumping refers to generating a net current, e.g. per period in the…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
Molecular machines described in this paper are meant to be such molecular systems that make use of conformational mobility (i.e. hindered rotation around chemical bonds and molecular construction deformations with formation and breakage of…
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…
In recent literature there has been a lot of interest in the phenomena of noise induced transport in the absence of an average bias occurring in spatially periodic systems far from equilibrium. One of the main motivations in this area is to…
Cells are complex structures which require considerable amounts of organization via transport of large intracellular cargo. While passive diffusion is often sufficiently fast for the transport of smaller cargo, active transport is necessary…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
We present a theoretical treatment of energy transfer in a molecular motor described in terms of overdamped Brownian motion on a multidimensional tilted periodic potential. The tilt acts as a thermodynamic force driving the system out of…
Here we study a pumping device capable of maintaining a density gradient and a flux of particles across a membrane. Its driving mechanism is based on the flashing ratchet effect powered by the random telegraph process in the presence of…