Related papers: Dynamical Aspects of Information in Copolymerizati…
Allostery plays a fundament role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The…
The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…
We characterize the information dynamics of strongly disordered systems using a combination of analytics, exact diagonalization, and matrix product operator simulations. More specifically, we study the spreading of quantum information in…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
Hydrogels are soft materials engineered to suit a multitude of applications that exploit their tunable mechanochemical properties. Dynamic hydrogels employing noncovalent, physically crosslinked networks dominated by either enthalpic or…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Protection of the sensitive content is crucial for extensive information sharing. We present a technique of information concealing, based on introduction and maintenance of families of repeats. Repeats in DNA constitute a basic obstacle for…
Thermodynamics is a macroscopic physical theory whose two very general laws are independent of any underlying dynamical laws and structures. Nevertheless, its generality enables us to understand a broad spectrum of phenomena in physics,…
Information flow is central to contemporary accounts of cognition, yet its physical basis in living neural matter remains poorly specified. Here, we develop a multiscale resource-theoretical framework motivated by the \textit{thermocoherent…
Living microorganisms have evolved dedicated sensory machinery to detect environmental perturbations, processing these signals through biochemical networks to guide behavior. Replicating such capabilities in synthetic active matter remains…
We perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along…
The paper moves a step towards the full integration of statistical mechanics and information theory. Starting from the assumption that the thermodynamical system is composed by particles whose quantized energies can be modelled as…
We describe, at the microscopic level, the dynamics of N interacting components where the probability is very small when N is large that a given component interact more than once, directly or indirectly, up to time t, with any other…
We analyze a (1+1)-dimension directed random walk model of a polymer dipped in a medium constituted by two immiscible solvents separated by a flat interface. The polymer chain is heterogeneous in the sense that a single monomer may…