Related papers: A general efficiency relation for molecular machin…
An equilibrium reversible cycle with a certain engine to transduce the energy of any chemical reaction into mechanical energy is proposed. The efficiency for chemical energy transduction is also defined so as to be compared with Carnot…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
We consider a molecular machine described as a Brownian particle diffusing in a tilted periodic potential. We evaluate the absorbed and released power of the machine as a function of the applied molecular and chemical forces, by using the…
A system responding to a stochastic driving signal can be interpreted as computing, by means of its dynamics, an implicit model of the environmental variables. The system's state retains information about past environmental fluctuations,…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Life relies on a sophisticated metabolic molecular machinery that turns over high-energy molecules to evolve complex macromolecules and assemblies. At the molecular origin of life, such machinery was absent, implying the need for simple yet…
The excess work required to drive a stochastic system out of thermodynamic equilibrium through a time-dependent external perturbation is directly related to the amount of entropy produced during the driving process, allowing excess work and…
We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of…
In recent literature there has been a lot of interest in the phenomena of noise induced transport in the absence of an average bias occurring in spatially periodic systems far from equilibrium. One of the main motivations in this area is to…
Molecular motors fulfill critical functions within all living beings. Understanding their underlying working principles is therefore of great interest. Here we develop a simple model inspired by the two-component biomolecular motor Fo-F1…
Recent experiments demonstrate that molecular motors from the Myosin II family serve as cross-links inducing active tension in the cytoskeletal network. Here we revise the Brownian ratchet model, previously studied in the context of active…
Stochastic fluctuations of molecular abundances are a ubiquitous feature of cellular processes and lead to significant cell-to-cell variability. Recent theoretical work established lower bounds for stochastic fluctuations in cells for broad…
We study the thermodynamic efficiency of the Malkus-Lorenz waterwheel. For this purpose, we derive an exact analytical formula that describes the efficiency of this dissipative structure as a function of the phase space variables and the…
An expression for the energetic efficiency of a molecular motor is presented in terms of an effective temperature, which was defined based on the ratio of the correlation function to the susceptibility of its velocity. We also present a…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in…
The main physical features and operating principles of isothermal nanomachines in microworld are reviewed, which are common for both classical and quantum machines. Especial attention is paid to the dual and constructive role of dissipation…
Recent developments in nanoscale experimental techniques made it possible to utilize single molecule junctions as devices for electronics and energy transfer with quantum coherence playing an important role in their thermoelectric…
Biological systems sense and extract information from fluctuating signals while operating under energetic constraints and limited resolution. We introduce a general chemical model in which a sensor, coupled to a signaling pathway activated…
Understanding noisy information engines is a fundamental problem of non-equilibrium physics, particularly in biomolecular systems agitated by thermal and active fluctuations in the cell. By the generalized second law of thermodynamics, the…