Related papers: Master Equation Approach to Molecular Motors
A quantum master equation (QME) is derived for the many-body density matrix of an open current-carrying system weakly coupled to two metal leads. The dynamics and the steady-state properties of the system for arbitrary bias are studied…
A new tool for modeling electrochemical kinetics is presented. An extension of the Stochastic Simulation Algorithm framework to electrochemical systems is proposed. The physical justifications and constraints for the derivation of a…
In this paper we consider deterministic limits of molecular stochastic systems with finite and infinite degrees of freedom. The method to obtain the deterministic vector field is based on the continuum limit of such microscopic systems…
The energetics and efficiency of a linear molecular motor model proposed by Mogilner et al. (Phys. Lett. 237, 297 (1998)) is analyzed from an analytical point of view. The model which is based on protein friction with a track is described…
Movements of molecular motors on cytoskeletal filaments are described by directed walks on a line. Detachment from this line is allowed to occur with a small probability. Motion in the surrounding fluid is described by symmetric random…
Aiming to establish a rigorous link between macroscopic random motion (described e.g. by Langevin-type theories) and microscopic dynamics, we have undertaken a kinetic-theoretical study of the dynamics of a classical test-particle weakly…
Three problems in the statistical mechanics of models for an assembly of molecular motors interacting with cytoskeletal filaments are reviewed. First, a description of the hydrodynamical behaviour of density-density correlations in…
An exact quantum master equation formalism is constructed for the efficient evaluation of quantum non-Markovian dissipation beyond the weak system-bath interaction regime in the presence of time-dependent external field. A novel truncation…
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
A model multilevel molecule described by two sets of rotational internal energy levels of different parity and degenerate ground states, coupled by a constant interaction, is considered, by assuming that the random collisions in a gas of…
Stochastic mechanics---the study of classical stochastic systems governed by things like master equations and Fokker-Planck equations---exhibits striking mathematical parallels to quantum mechanics. In this article, we make those parallels…
Matrix mechanics is developed to describe the bound state spectra in few- and many-electron atoms, ions and molecules. Our method is based on the matrix factorization of many-electron (or many-particle) Coulomb Hamiltonians which are…
How stochastic, microscopic events generate deterministic, macroscopic properties is a fundamental question in physics. We address this question by developing a quantum master equation model for concentrated radical solutions, where random…
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 consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an engine that "transduces" input energy into…
In analogy to Brownian computers we explicitly show how to construct stochastic models, which mimic the behaviour of a general purpose computer (a Turing machine). Our models are discrete state systems obeying a Markovian master equation,…
In this paper, we introduce a real symmetric and positive semi-definite matrix, which we call the non-equilibrium conductance matrix, and which generalizes the Onsager response matrix for a system in a non-equilibrium stationary state. We…
It has been recently shown that collisional models can be used to derive a general form for the master equations which describe the reduced time evolution of a composite multipartite quantum system, whose components "propagate" in an…
We derive a quantum master equation in the context of a polymerized open quantum mechanical system for the scattering of a Brownian particle in an ideal gas environment. The model is formulated in a top-down approach by choosing a…
Generalized master equations valid for the third order response of an optically driven multi-level electronic system are derived within Zwanzig projection formalism. Each of three time intervals of the response function is found to require…