相关论文: Edge-effects dominate copying thermodynamics for f…
Templated copying is the central operation by which biology produces complex molecules. Cells copy sequence information from DNA to RNA and on into proteins, which are the molecules responsible for the function and regulation of cellular…
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated…
Living systems produce "persistent" copies of information-carrying polymers, in which template and copy sequences remain correlated after physically decoupling. We identify a general measure of the thermodynamic efficiency with which these…
Information processing at the molecular scale is limited by thermal fluctuations. This can cause undesired consequences in copying information since thermal noise can lead to errors that can compromise the functionality of the copy. For…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…
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,…
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,…
The production of sequence-specific copolymers using copolymer templates is fundamental to the synthesis of complex biological molecules and is a promising framework for the synthesis of synthetic chemical complexes. Unlike the…
Natural supports of information are given by random copolymers such as DNA or RNA where information is coded in the sequence of covalent bonds. At the molecular scale, the stochastic growth of a single copolymer with or without a template…
We discuss how information encoded in a template polymer can be stochastically copied into a copy polymer. We consider four different stochastic copy protocols of increasing complexity, inspired by building blocks of the mRNA translation…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
In the recent progress in nonequilibrium thermodynamics, information has been recognized as a kind of thermodynamic resource that can drive thermodynamic current without any direct energy injection. In this paper, we establish the framework…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
In detailed microcanonical analyses of densities of states obtained by extensive multicanonical Monte Carlo computer simulations, we investigate the caloric properties of conformational transitions adsorbing polymers experience near…
The specific heat is a central property of condensed matter systems including polymers and oligomers in their condensed phases. Yet, predictions of this quantity from molecular simulations and successful comparisons to experimental data are…
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…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical…
We analyze information transmission in a recently proposed coarse-grained model of polymer replication by framing it as a communication channel between templates and copies. By calculating the mutual information in the steady-state limit of…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…