6,112 research outputs found
Splicing system in Automata Theory: A review
The study of formal language theory rapidly evolves after Tom Head introduce his research on formal language theory in 1987. Splicing system involves the process of cutting and pasting on DNA molecules with the presence of restriction enzymes and ligase, respectively. A mathematical model of the splicing system has been developed by using the concept of formal language theory, which is a branch of theoretical computer science and applied discrete mathematics, and informational macromolecules. Over the year, theoretical results in splicing systems have contributed to new research in formal language theory focused on modelling of biochemical processes. In this paper, the relation between formal language theory and some related molecular biological terms are explored. In addition, new ideas in the framework of biomolecular science, for example, the design of automated enzymatic processes are then discussed. Then, a mutual relation that exist in these field is then explained. The regular language can be implemented in the splicing system to show the DFA structure in the splicing system
Biomolecular aspects of second order limit language
The study on the recombinant behavior of double-stranded DNA molecules has led to the mathematical modelling of DNA splicing system. The interdisciplinary study is founded from the knowledge of informational macromolecules and formal language theory. A splicing language is resulted from a splicing system. Recently, second order limit language, a type of the splicing language, has been extensively explored. Before this, several types of splicing languages have been experimentally proven. Therefore, in this paper, a laboratory experiment was conducted to validate the existence of a second order limit language. To accomplish it, an initial strand of double-stranded DNA, amplified from bacteriophage lambda, was generated through polymerase chain reaction to generate thousands of copies of double-stranded DNA molecules. A restriction enzyme and ligase were added to the solution to complete the reaction. The reaction mixture was then subjected to polyacrylamide gel electrophoresis to separate biological macromolecules according to their sizes. A mathematical model derived at the early study was used to predict the approximate length of each string in the splicing language. The results obtained from the experiment are then used to verify the mathematical model of a second order limit language. This study shows that the theory on the second order limit language is biologically proven hence the model has been validated
Collective behaviours: from biochemical kinetics to electronic circuits
In this work we aim to highlight a close analogy between cooperative
behaviors in chemical kinetics and cybernetics; this is realized by using a
common language for their description, that is mean-field statistical
mechanics. First, we perform a one-to-one mapping between paradigmatic
behaviors in chemical kinetics (i.e., non-cooperative, cooperative,
ultra-sensitive, anti-cooperative) and in mean-field statistical mechanics
(i.e., paramagnetic, high and low temperature ferromagnetic,
anti-ferromagnetic). Interestingly, the statistical mechanics approach allows a
unified, broad theory for all scenarios and, in particular, Michaelis-Menten,
Hill and Adair equations are consistently recovered. This framework is then
tested against experimental biological data with an overall excellent
agreement. One step forward, we consistently read the whole mapping from a
cybernetic perspective, highlighting deep structural analogies between the
above-mentioned kinetics and fundamental bricks in electronics (i.e.
operational amplifiers, flashes, flip-flops), so to build a clear bridge
linking biochemical kinetics and cybernetics.Comment: 15 pages, 6 figures; to appear on Scientific Reports: Nature
Publishing Grou
A Multi-scale View of the Emergent Complexity of Life: A Free-energy Proposal
We review some of the main implications of the free-energy principle (FEP) for the study of the self-organization of living systems – and how the FEP can help us to understand (and model) biotic self-organization across the many temporal and spatial scales over which life exists. In order to maintain its integrity as a bounded system, any biological system - from single cells to complex organisms and societies - has to limit the disorder or dispersion (i.e., the long-run entropy) of its constituent states. We review how this can be achieved by living systems that minimize their variational free energy. Variational free energy is an information theoretic construct, originally introduced into theoretical neuroscience and biology to explain perception, action, and learning. It has since been extended to explain the evolution, development, form, and function of entire organisms, providing a principled model of biotic self-organization and autopoiesis. It has provided insights into biological systems across spatiotemporal scales, ranging from microscales (e.g., sub- and multicellular dynamics), to intermediate scales (e.g., groups of interacting animals and culture), through to macroscale phenomena (the evolution of entire species). A crucial corollary of the FEP is that an organism just is (i.e., embodies or entails) an implicit model of its environment. As such, organisms come to embody causal relationships of their ecological niche, which, in turn, is influenced by their resulting behaviors. Crucially, free-energy minimization can be shown to be equivalent to the maximization of Bayesian model evidence. This allows us to cast natural selection in terms of Bayesian model selection, providing a robust theoretical account of how organisms come to match or accommodate the spatiotemporal complexity of their surrounding niche. In line with the theme of this volume; namely, biological complexity and self-organization, this chapter will examine a variational approach to self-organization across multiple dynamical scales
Towards a Model of Life and Cognition
What should be the ontology of the world such that life and cognition are possible? In this essay, I undertake to outline an alternative ontological foundation which makes biological and cognitive phenomena possible. The foundation is built by defining a model, which is presented in the form of a description of a hypothetical but a logically possible world with a defined ontological base.
Biology rests today on quite a few not so well connected foundations: molecular biology based on the genetic dogma; evolutionary biology based on neo-Darwinian model; ecology based on systems view; developmental biology by morphogenetic models; connectionist models for neurophysiology and cognitive biology; pervasive teleonomic
explanations for the goal-directed behavior across the discipline; etc. Can there be an underlying connecting theme or a model which could make these seemingly disparate domains interconnected? I shall atempt to answer this question.
By following the semantic view of scientific theories, I tend to believe that the models employed by the present physical sciences are not rich enough to capture biological (and some of the non-biological) systems. A richer theory that could capture biological reality could also capture physical and chemical phenomena as limiting cases, but
not vice versa
The view from elsewhere: perspectives on ALife Modeling
Many artificial life researchers stress the interdisciplinary character of the field. Against such a backdrop, this report reviews and discusses artificial life, as it is depicted in, and as it interfaces with, adjacent disciplines (in particular, philosophy, biology, and linguistics), and in the light of a specific historical example of interdisciplinary research (namely cybernetics) with which artificial life shares many features. This report grew out of a workshop held at the Sixth European Conference on Artificial Life in Prague and features individual contributions from the workshop's eight speakers, plus a section designed to reflect the debates that took place during the workshop's discussion sessions. The major theme that emerged during these sessions was the identity and status of artificial life as a scientific endeavor
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