Related papers: Information processing in biological molecular mac…
The living cell expends energetic and material resources to reliably process information from its environment. To do so, it utilises unreliable molecular circuitry that is subject to thermal and other fluctuations. Here, we argue that…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
The common saying, that information is power, takes a rigorous form in stochastic thermodynamics, where a quantitative equivalence between the two helps explain the paradox of Maxwell's demon in its ability to reduce entropy. In the present…
Brownian information engines can extract work from thermal fluctuations by utilizing information. So far, the studies on Brownian information engines consider the system in a thermal bath; however, many processes in nature occur in a…
We generalize stochastic thermodynamics to include information reservoirs. Such information reservoirs, which can be modeled as a sequence of bits, modify the second law. For example, work extraction from a system in contact with a single…
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Stochastic network-dynamics are typically assumed to be memory-less. Involving prolonged dwells interrupted by instantaneous transitions between nodes such Markov networks stand as a coarse-graining paradigm for chemical reactions, gene…
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…
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…
Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined…
Motivated by the recent proposed models of the information engine [D. Mandal and C. Jarzynski, Proc. Natl. Acad. Sci. 109, 11641 (2012)] and the information refrigerator [D. Mandal, H. T. Quan, and C. Jarzynski, Phys. Rev. Lett. 111, 030602…
Living systems often function with regulatory interactions, but the question of how activity, stochasticity and regulations work together for achieving different goals still remains puzzling. We propose a stochastic model of an active…
Molecular machines composed of coupled subsystems transduce free energy between different external reservoirs, in the process internally transducing energy and information. While subsystem efficiencies of these molecular machines have been…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
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…
We report a realization of an associative memory signal/information processing system based on simple enzyme-catalyzed biochemical reactions. Optically detected chemical output is always obtained in response to the triggering input, but the…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
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…