Related papers: Master Equation Approach to Molecular Motors
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…
The master equation plays an important role in many scientific fields including physics, chemistry, systems biology, physical finance, and sociodynamics. We consider the master equation with periodic transition rates. This may represent an…
Molecular motors convert chemical energy into mechanical work while operating in an environment dominated by Brownian motion. The aim of this paper is to explore the flow of energy between the molecular motors and its surroundings, in…
We provide a mathematical analysis of appearance of the concentrations (as Dirac masses) of the solution to a Fokker-Planck system with asymmetric potentials. This problem has been proposed as a model to describe motor proteins moving along…
Linear bio-molecular motors move unidirectionally along a track by coordinating several different processes, such as fuel (ATP) capture, hydrolysis, conformational changes, binding and unbinding from a track, and center-of-mass diffusion. A…
Generalized quantum master equations (GQMEs) are an important tool in modeling chemical and physical processes. For a large number of problems it has been shown that exact and approximate quantum dynamics methods can be made dramatically…
Molecular motors transduce chemical energy obtained from hydrolizing ATP into mechanical work exerted against an external force. We calculate their efficiency at maximum power output for two simple generic models and show that the…
We derive a master equation for the motion of a polarizable particle weakly interacting with one or several strongly pumped cavity modes. We focus here on massive particles with complex internal structure such as large molecules and…
We consider the asymptotic behavior of an evolving weakly coupled Fokker-Planck system of two equations set in a periodic environment. The magnitudes of the diffusion and the coupling are respectively proportional and inversely proportional…
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…
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 stochastic driving force exerted by a single molecular motor (e.g., a kinesin, or myosin) moving on a periodic molecular track (microtubule, actin filament, etc.) is discussed from a general viewpoint open to experimental test. An…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
We consider a molecular aggregate consisting of $N$ identical monomers. Each monomer comprises two electronic levels and a single harmonic mode. The monomers interact with each other via dipole-dipole forces. The monomer vibrational modes…
Structures of quantum Fokker-Planck equations are characterized with respect to the properties of complete positivity, covariance under symmetry transformations and satisfaction of equipartition, referring to recent mathematical work on…
We explore quantization of the response of a molecular motor to periodic modulation of control parameters. We formulate the Pumping-Quantization Theorem (PQT) that identifies the conditions for robust integer quantized behavior of a…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
A quantum system interacting with a dilute gas experiences irreversible dynamics. The corresponding master equation can be derived within two different approaches: The fully quantum description in the low-density limit and the semiclassical…
The nonequilibrium response and fluctuations of Markovian systems, both near and far from equilibrium, are best understood by varying their parameters along dynamical equivalence classes. In this note, I illustrate this approach for an…
The master equation for a linear open quantum system in a general environment is derived using a stochastic approach. This is an alternative derivation to that of Hu, Paz and Zhang, which was based on the direct computation of path…