Related papers: Dynamical Aspects of Information in Copolymerizati…
We investigate fundamental connections between thermodynamics and quantum information theory. First, we show that the operational framework of thermal operations is nonequivalent to the framework of Gibbs-preserving maps, and we comment on…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
How can the information that a set ${X_{1},...,X_{n}}$ of random variables contains about another random variable $S$ be decomposed? To what extent do different subgroups provide the same, i.e. shared or redundant, information, carry unique…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
This paper presents the computational methods of information cohomology applied to genetic expression in and in the companion paper and proposes its interpretations in terms of statistical physics and machine learning. In order to further…
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…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Active matter agents consume internal energy or extract energy from the environment for locomotion and force generation. Already rather generic models, such as ensembles of active Brownian particles, exhibit phenomena, which are absent at…
Thermodynamics is based on the notions of energy and entropy. While energy is the elementary quantity governing physical dynamics, entropy is the fundamental concept in information theory. In this work, starting from first principles, we…
Molecular machines transduce free energy between different forms throughout all living organisms. While truly machines in their own right, unlike their macroscopic counterparts molecular machines are characterized by stochastic…
We apply the formalism of dynamical system analysis to investigate the evolution of interacting dark energy scenarios at the background and perturbation levels in a unified way. Since the resulting dynamical system contains the extra…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
Using information theory we derive a thermodynamics for systems evolving under a collective motion, i.e. under a time-odd constraint. An illustration within the Lattice gas Model is given for two model cases: a collision between two complex…
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
We propose a decomposition of information flow into housekeeping and excess components for autonomous bipartite systems described by Markov jump processes. We introduce this decomposition using the geometric structure of probability…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that…