Related papers: Master Equation Approach to Molecular Motors
Particles moving in oscillating potential with broken mirror symmetry are considered. We calculate their energetic efficiency, when acting as molecular motors carrying a load against external force. It is shown that interaction between…
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…
Future developments of lighter, more compact and powerful motors-driven by environmental and sustainability considerations in the transportation industry-involve higher stresses, currents and electromagnetic fields. Strong couplings between…
In this paper, we derive a general master equation for continuous feedback based on arbitrary linear signals. This result is an extension of the Quantum Fokker-Planck Master Equation derived by Annby-Andersson et al (Phys. Rev. Lett. 129,…
Many single molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom…
While accurate simulations of dense gas flows far from the equilibrium can be achieved by Direct Simulation adapted to the Enskog equation, the significant computational demand required for collisions appears as a major constraint. In order…
We investigate the multi-chain version of the Chemical Master Equation, when there are transitions between different states inside the long chains, as well as transitions between (a few) different chains. In the discrete version, such a…
We consider the mean field Fokker-Planck equation subject to nonlinear no-flux boundary conditions, which necessarily arise when subjecting a system of Brownian particles interacting via a pair potential in a bounded domain. With the…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
We illustrate the equivalence between the non-unitary evolution of an open quantum system governed by a Markovian master equation and a process of continuous measurements involving this system. We investigate a system of two coupled modes,…
Aim of this note is to analyse branching Brownian motion within the class of models introduced in the recent paper [4] and called chemical diffusion master equations. These models provide a description for the probabilistic evolution of…
Master equation could be applied to model various kinds of biochemical systems. A general theory for its time-dependent nonequilibrium thermodynamics is rigorously derived. We not only introduce a concept of general internal energy, but…
Concepts of everyday use like energy, heat, and temperature have acquired a precise meaning after the development of thermodynamics. Thermodynamics provides the basis for understanding how heat and work are related and with the general…
We use machine learning to enable large-scale molecular dynamics (MD) of a correlated electron model under the Gutzwiller approximation scheme. This model exhibits a Mott transition as a function of on-site Coulomb repulsion $U$. The…
Motivated by claims about the nature of the observed timescales in protein systems said to fold downhill, we have studied the finite, linear master equation which is a model of the downhill process. By solving for the system eigenvalues, we…
The Dougherty model Fokker-Planck operator is extended to describe nonlinear full-f collisions between multiple species in plasmas. Simple relations for cross-species interactions are developed which obey conservation laws, and reproduce…
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…
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,…
We study an approximation scheme based on a second quantization method for a chemical master equation. Small systems, such as cells, could not be studied by the traditional rate equation approach because fluctuation effects are very large…
The stochastic dynamics of biochemical networks are usually modelled with the chemical master equation (CME). The stationary distributions of CMEs are seldom solvable analytically, and numerical methods typically produce estimates with…