Related papers: Entropy and efficiency of a molecular motor model
Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use molecular simulations to show how slight alterations of a molecular motor's structure can cause the motor's typical dynamical…
We consider in this paper a solvable model for the motion of molecular motors. Based on the averaging principle, we reduce the problem to a diffusion process on a graph. We then calculate the effective speed of transportation of these…
In living cells, molecular motors convert chemical energy into mechanical work. Its thermodynamic energy efficiency, i.e. the ratio of output mechanical work to input chemical energy, is usually high. However, using two-state models, we…
Molecular motors are single macromolecules that generate forces at the piconewton range and nanometer scale. They convert chemical energy into mechanical work by moving along filamentous structures. In this paper, we study the velocity of…
The aim of this paper is to determine lost works in a molecular engine and compare results with macro (classical) heat engines. Firstly, irreversible thermodynamics are reviewed for macro and molecular cycles. Secondly, irreversible…
A hopping model for molecular motors is presented consisting of a state with asymmetric hopping rates with period 2 and a state with uniform hopping rates. State changes lead to a stationary unidirectional current of a particle. The current…
Multi-component molecular machines are ubiquitous in biology. We review recent progress on describing their thermodynamic properties using autonomous bipartite Markovian dynamics. The first and second laws can be split into local versions…
We quantify the prior information to infer the optimal characteristics for a constrained thermodynamic process of maximum work extraction for a pair of non-identical finite systems. The total entropy of the whole system remains conserved.…
Typical man-made locomotive devices use reversible gears, as cranks, for transforming reciprocating motion into directed one. Such gears are holonomic and have the transduction efficiency of unity. On the other hand, a typical gear of…
We study the behavior of a single spin in the presence of a time-varying magnetic field utilizing Glauber dynamics. We engineer the system to function as an engine by changing the magnetic field according to specific protocols.…
Quantifying energy flows at nanometer scales promises to guide future research in a variety of disciplines, from microscopic control and manipulation, to autonomously operating molecular machines. A general understanding of the…
We present a family of algorithms for the fast determination of reaction paths and barriers in phase space and the computation of the corresponding rates. The method requires the reaction times be large compared to the microscopic time,…
We study the existing algorithms that solve the multidimensional martingale optimal transport. Then we provide a new algorithm based on entropic regularization and Newton's method. Then we provide theoretical convergence rate results and we…
Feynman's ratchet and pawl is a paradigmatic model for energy conversion using thermal fluctuations in the mesoscopic regime. Here, we optimize the power output of the ratchet as a heat engine in the high temperatures limit, and derive the…
Intracellular transport along microtubules or actin filaments, powered by molecular motors such as kinesins, dyneins or myosins, has been recently modeled using one-dimensional driven lattice gases. We discuss some generalizations of these…
Several stochastic models called thermal ratchet models have been recently proposed to analyze the motor proteins such as myosin and kinesin,etc. We propose a method to study the energetics of those models, and show how the rate of energy…
We study the problem of synthesizing a policy that maximizes the entropy of a Markov decision process (MDP) subject to a temporal logic constraint. Such a policy minimizes the predictability of the paths it generates, or dually, maximizes…
Quantitative predictions are presented of a depletion-induced torque and force acting on a single colloidal hard rod immersed in a solvent of hard spheres close to a planar hard wall. This torque and force, which are entirely of entropic…
Using stochastic thermodynamics, the properties of interacting linear chains subject to periodic drivings are investigated. The systems are described by Fokker-Planck-Kramers equation and exact (explicit) solutions are obtained for periodic…
Modern technologies could soon make it possible to investigate the operation cycles of quantum heat engines by counting the photons that are emitted and absorbed by their working systems. Using the quantum jump approach to open-system…