Related papers: Entropy and efficiency of a molecular motor model
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
We introduce a pathwise approach to analyze the relative performance of an equity portfolio with respect to a benchmark market portfolio. In this energy-entropy framework, the relative performance is decomposed into three components: a…
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…
Interpreting partial information collected from systems subject to noise is a key problem across scientific disciplines. Theoretical frameworks often focus on the dynamics of variables that result from coarse-graining the internal states of…
We explore the properties of run-and-tumble particles moving in a piecewise-linear "ratchet" potential by deriving analytic results for the system's steady-state probability density, current, entropy production rate, extractable power, and…
We identify generic protocols achieving optimal power extraction from a single active particle subject to continuous feedback control under the assumption that its spatial trajectory, but not its instantaneous self-propulsion force, is…
Motivated by entropic optimal transport, time reversal of diffusion processes is revisited. An integration by parts formula is derived for the carr\'e du champ of a Markov process in an abstract space. It leads to a time reversal formula…
Molecular motors convert chemical energy derived from the hydrolysis of ATP into mechanical energy. A well-studied model of a molecular motor is the flashing ratchet model. We show that this model exhibits a fluctuation relation known as…
Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance with entropy production. But this alone is not sufficient…
We develop a perturbation theory of quantum (and classical) master equations with slowly varying parameters, applicable to systems which are externally controlled on a time scale much longer than their characteristic relaxation time. We…
The metriplectic formalism is useful for describing complete dynamical systems which conserve energy and produce entropy. This creates challenges for model reduction, as the elimination of high-frequency information will generally not…
Molecular motors are macromolecular complexes which use some form of input energy to perform mechanical work. The filamentary tracks, on which these motors move, are made of either proteins (e.g., microtubules) or nucleic acids (DNA or…
Stochastic thermodynamics has revolutionized our understanding of heat engines operating in finite time. Recently, numerous studies have considered the optimal operation of thermodynamic cycles acting as heat engines with a given profile in…
Molecular motors perform active movements along cytoskeletal filaments and drive the traffic of organelles and other cargo particles in cells. In contrast to the macroscopic traffic of cars, however, the traffic of molecular motors is…
The concepts of weighted reciprocal of temperature and weighted thermal flux are proposed for a heat engine operating between two heat baths and outputting mechanical work. With the aid of these two concepts, the generalized thermodynamic…
Many types of molecular motors have been proposed and synthesized in recent years, displaying different kinds of motion, and fueled by different driving forces such as light, heat, or chemical reactions. We propose a new type of molecular…
Molecular motors do not work in isolation {\it in-vivo}. We highlight some of the coordinations, cooperations and competitions that determine the collective properties of molecular motors in eukaryotic cells. In the context of traffic-like…
Although instantaneous interactions are unphysical, a large variety of maximum entropy statistical inference methods match the model-inferred and the empirically-measured equal-time correlation functions. Focusing on collective motion of…
We study single commodity network flows with suitable robustness and efficiency specs. An original use of a maximum entropy problem for distributions on the paths of the graph turns this problem into a steering problem for Markov chains…
Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice gas model we study how the interplay between active and…