Related papers: Information processing in biological molecular mac…
We examine a biomolecular machine involving a driven, observable process coupled to a hidden process in a kinetically cooperative manner. A stochastic thermodynamics framework is employed to analyze a fluctuation theorem for 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,…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
Molecular motion through pores plays a crucial role in various natural and industrial processes. One of the most fascinating features of biological channel-facilitated transport is a stochastic gating process, when the channels dynamically…
To induce transport, detailed balance must be broken. A common mechanism is to bias the dynamics with a thermodynamic fuel, such as chemical energy. An intriguing, alternative strategy is for a Maxwell demon to effect the bias using…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…
The probabilistic information flow and natural computational capability of a system with two magnetic skyrmions at room temperature have been experimentally evaluated. Based on this evaluation, an all-solid-state built-in Maxwell's demon…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
We relate the information exchange between two stochastic systems to the nonequilibrium entropy production in the whole system. By deriving a general formula that decomposes the total entropy production into the thermodynamic and…
Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on fixed networks. Here, we develop a scalable approach to…
Molecular machines consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an engine that "transduces" input energy into…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
Molecular motors convert chemical energy into mechanical work while operating in an environment dominated by Brownian motion. The aim of this paper is to explore the flow of energy between the molecular motors and its surroundings, 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…
Maxwell's demon explores the role of information in physical processes. Employing information about microscopic degrees of freedom, this "intelligent observer" is capable of compensating entropy production (or extracting work), apparently…
Information dynamics is an emerging description of information processing in complex systems which describes systems in terms of intrinsic computation, identifying computational primitives of information storage and transfer. In this paper…
The second law of thermodynamics dictates the fundamental limits to the amount of energy and information that can be exchanged between physical systems. In this work, we extend a thermodynamic formalism describing this flow of energy and…
Bio-molecules are active agents in that they consume energy to perform tasks. The standard theoretical description, however, considers only a system-external work agent. Fluctuation theorems, for example, do not allow work-exchange between…
Information plays a pivotal role in the thermodynamics of nonequilibrium processes with feedback. However, much remains to be learned about the nature of information fluctuations in small scale devices and their relation with fluctuations…