Related papers: Master Equation Approach to Molecular Motors
We study a Markov random process describing a muscle molecular motor behavior. Every motor is either bound up with a thin filament or unbound. In the bound state the motor creates a force proportional to its displacement from the neutral…
Within the f-deformed oscillator formalism, we derive a Markovian master equation for the description of the damped dynamics of nonlinear systems that interact with their environment. The applicability of this treatment to the particular…
With potential relevance to biomechanics, an interesting problem in statistical mechanics not previously solved is a binary mechanical model system. Discrete chemical states of proteins are often associated with discrete metastable…
Molecular motors are in charge of almost every process in the life cycle of cells, such as protein synthesis, DNA replication, and cell locomotion, hence being of crucial importance for understanding the cellular dynamics. However, given…
Measurement and feedback control are essential features of quantum science, with applications ranging from quantum technology protocols to information-to-work conversion in quantum thermodynamics. Theoretical descriptions of feedback…
Dual phospho/dephosphorylation cycles, as well as covalent enzymatic-catalyzed modifications of substrates, are widely diffused within cellular systems and are crucial for the control of complex responses such as learning, memory and…
A simple tight-coupling model of a molecular chemical engine is proposed. The efficiency of the chemical engine and its average velocity can be explicitly calculated. The diffusion constant is evaluated approximately using the fluctuation…
From the underlying Master equations we derive one-dimensional stochastic processes that describe generalized ensemble simulations as well as tempering (simulated and parallel) simulations. The representations obtained are either in the…
A geometrical model which captures the main ingredients governing atom-diatom collinear chemical reactions is proposed. This model is neither near-integrable nor hyperbolic, yet it is amenable to analysis using a combination of the recently…
We develop the stochastic approach to thermodynamics based on the stochastic dynamics, which can be discrete (master equation) continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
We discuss the force-velocity relations obtained in a two-state crossbridge model for molecular motors. They can be calculated analytically in two limiting cases: for a large number and for one pair of motors. The effect of the…
The chemical birth-death process, whose chemical master equation (CME) is exactly solvable, is a paradigmatic toy problem often used to get intuition for how stochasticity affects chemical kinetics. In a certain limit, it can be…
We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical…
We consider a multi component gas mixture with translational and internal energy degrees of freedom without chemical reactions assuming that the number of particles of each species remains constant. We will illustrate the derived model in…
We recall theoretical studies on transient transport through interacting mesoscopic systems. It is shown that a generalized master equation (GME) written and solved in terms of many-body states provides the suitable formal framework to…
We present a new kinetic equation for cell migration driven by mechanical interactions with the substrate, an effect not previously captured in kinetic models, and essential for explaining observed collective behaviors such as those in…
Engines are open systems that can generate work cyclically, at the expense of an external disequilibrium. They are ubiquitous in nature and technology, but the course of mathematical physics over the last 300 years has tended to make their…
The quantum master equation is a widespread approach to describing open quantum system dynamics. In this approach, the effect of the environment on the system evolution is entirely captured by the dynamical generator, providing a compact…
We derive Markovian master equations of single and interacting harmonic systems in different scenarios, including strong internal coupling. By comparing the dynamics resulting from the corresponding Markovian master equations with exact…