2,819 research outputs found
Programmability of Chemical Reaction Networks
Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical systems, and with the advent of synthetic biology they become a promising language for the design of artificial biochemical circuits. Our interest here is the computational power of SCRNs and how they relate to more conventional models of computation. We survey known connections and give new connections between SCRNs and Boolean Logic Circuits, Vector Addition Systems, Petri Nets, Gate Implementability, Primitive Recursive Functions, Register Machines, Fractran, and Turing Machines. A theme to these investigations is the thin line between decidable and undecidable questions about SCRN behavior
Approximating Mexican highways with slime mould
Plasmodium of Physarum polycephalum is a single cell visible by unaided eye.
During its foraging behavior the cell spans spatially distributed sources of
nutrients with a protoplasmic network. Geometrical structure of the
protoplasmic networks allows the plasmodium to optimize transport of nutrients
between remote parts of its body. Assuming major Mexican cities are sources of
nutrients how much structure of Physarum protoplasmic network correspond to
structure of Mexican Federal highway network? To find an answer undertook a
series of laboratory experiments with living Physarum polycephalum. We
represent geographical locations of major cities by oat flakes, place a piece
of plasmodium in Mexico city area, record the plasmodium's foraging behavior
and extract topology of nutrient transport networks. Results of our experiments
show that the protoplasmic network formed by Physarum is isomorphic, subject to
limitations imposed, to a network of principle highways. Ideas and results of
the paper may contribute towards future developments in bio-inspired road
planning
Exploring the concept of interaction computing through the discrete algebraic analysis of the BelousovâZhabotinsky reaction
Interaction computing (IC) aims to map the properties of integrable low-dimensional non-linear dynamical systems to the discrete domain of finite-state automata in an attempt to reproduce in software the self-organizing and dynamically stable properties of sub-cellular biochemical systems. As the work reported in this paper is still at the early stages of theory development it focuses on the analysis of a particularly simple chemical oscillator, the Belousov-Zhabotinsky (BZ) reaction. After retracing the rationale for IC developed over the past several years from the physical, biological, mathematical, and computer science points of view, the paper presents an elementary discussion of the Krohn-Rhodes decomposition of finite-state automata, including the holonomy decomposition of a simple automaton, and of its interpretation as an abstract positional number system. The method is then applied to the analysis of the algebraic properties of discrete finite-state automata derived from a simplified Petri net model of the BZ reaction. In the simplest possible and symmetrical case the corresponding automaton is, not surprisingly, found to contain exclusively cyclic groups. In a second, asymmetrical case, the decomposition is much more complex and includes five different simple non-abelian groups whose potential relevance arises from their ability to encode functionally complete algebras. The possible computational relevance of these findings is discussed and possible conclusions are drawn
Component-based design and analysis: a case study
Š2003 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.In this paper, we introduce a component-based design methodology and present a practical analysis approach that makes use of the modular nature of component-based designs to alleviate the state space explosion problem, a well-known obstacle to system verification. In addition, the approach is illustrated by application to a non-trivial case study: the production cell. It is shown that not only the basic consistency property, viz. the freedom from unexpected reception and deadlock, but also other important safety properties in the design can be proved.Yan Jin, Charles Lakos, Robert Esse
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