7,657 research outputs found

    Reaction Cycles in Membrane Systems and Molecular Dynamics

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    We are considering molecular dynamics and (sequential) membrane systems from the viewpoint of Markov chain theory. The first step is to understand the structure of the configuration space, with respect to communicating classes. Instead of a reachability analysis by traditional methods, we use the explicit monoidal structure of this space with respect to rule applications. This leads to the notion of precycle, which is an element of the integer kernel of the stoichiometric matrix. The generators of the set of precycles can be effectively computed by an incremental algorithm due to Contejean and Devie. To arrive at a characterization of cycles, we introduce the notion of defect, which is a set of geometric constraints on a configuration to allow a precycle to be enabled, that is, be a cycle. An important open problem is the effcient calculation of the defects. We also discuss aspects of asymptotic behavior and connectivity, as well as give a biological example, showing the usefulness of the method for model checking

    Mammalian Brain As a Network of Networks

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    Acknowledgements AZ, SG and AL acknowledge support from the Russian Science Foundation (16-12-00077). Authors thank T. Kuznetsova for Fig. 6.Peer reviewedPublisher PD

    Communication as the Main Characteristic of Life

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    A semiotic analysis of the genetic information

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    Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biologists as basically ‘the carriers of hereditary information.’ Nevertheless, a number of researchers consider such talk as inadequate and ‘just metaphorical,’ thus expressing a skepticism about the use of the term ‘information’ and its derivatives in biology as a natural science. First, because the meaning of that term in biology is not as precise as it is, for instance, in the mathematical theory of communication. Second, because it seems to refer to a purported semantic property of genes without theoretically clarifying if any genuinely intrinsic semantics is involved. Biosemiotics, a field that attempts to analyze biological systems as semiotic systems, makes it possible to advance in the understanding of the concept of information in biology. From the perspective of Peircean biosemiotics, we develop here an account of genes as signs, including a detailed analysis of two fundamental processes in the genetic information system (transcription and protein synthesis) that have not been made so far in this field of research. Furthermore, we propose here an account of information based on Peircean semiotics and apply it to our analysis of transcription and protein synthesis

    Symposium on Frontiers of Molecular Neurobiology

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    Membrane structure, synaptic transmission, and fibrous proteins of neurons - conferenc

    The Biosemiotic Approach in Biology : Theoretical Bases and Applied Models

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    Biosemiotics is a growing fi eld that investigates semiotic processes in the living realm in an attempt to combine the fi ndings of the biological sciences and semiotics. Semiotic processes are more or less what biologists have typically referred to as “ signals, ” “ codes, ”and “ information processing ”in biosystems, but these processes are here understood under the more general notion of semiosis, that is, the production, action, and interpretation of signs. Thus, biosemiotics can be seen as biology interpreted as a study of living sign systems — which also means that semiosis or sign process can be seen as the very nature of life itself. In other words, biosemiotics is a field of research investigating semiotic processes (meaning, signification, communication, and habit formation in living systems) and the physicochemical preconditions for sign action and interpretation. (...

    Omnipresent Maxwell’s demons orchestrate information management in living cells

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    The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the informationmanaging agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell’s demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers
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