COMPUTER SIMULATION AND COMPUTABILITY OF BIOLOGICAL SYSTEMS

The ability to simulate a biological organism by employing a computer is related to the ability of the computer to calculate the behavior of such a dynamical system, or the "computability" of the system.* However, the two questions of computability and simulation are not equivalent. Since the question of computability can be given a precise answer in terms of recursive functions, automata theory and dynamical systems, it will be appropriate to consider it first. The more elusive question of adequate simulation of biological systems by a computer will be then addressed and a possible connection between the two answers given will be considered. A conjecture is formulated that suggests the possibility of employing an algebraic-topological, "quantum" computer (Baianu, 1971b) for analogous and symbolic simulations of biological systems that may include chaotic processes that are not, in genral, either recursively or digitally computable. Depending on the biological network being modelled, such as the Human Genome/Cell Interactome or a trillion-cell Cognitive Neural Network system, the appropriate logical structure for such simulations might be either the Quantum MV-Logic (QMV) discussed in recent publications (Chiara, 2004, and references cited therein)or Lukasiewicz Logic Algebras that were shown to be isomorphic to MV-logic algebras (Georgescu et al, 2001)

Turing Automata and Graph Machines

Indexed monoidal algebras are introduced as an equivalent structure for self-dual compact closed categories, and a coherence theorem is proved for the category of such algebras. Turing automata and Turing graph machines are defined by generalizing the classical Turing machine concept, so that the collection of such machines becomes an indexed monoidal algebra. On the analogy of the von Neumann data-flow computer architecture, Turing graph machines are proposed as potentially reversible low-level universal computational devices, and a truly reversible molecular size hardware model is presented as an example

A Bibliography on Fuzzy Automata, Grammars and Lanuages

This bibliography contains references to papers on fuzzy formal languages, the generation of fuzzy languages by means of fuzzy grammars, the recognition of fuzzy languages by fuzzy automata and machines, as well as some applications of fuzzy set theory to syntactic pattern recognition, linguistics and natural language processing

Behavioural equivalences for timed systems

Timed transition systems are behavioural models that include an explicit treatment of time flow and are used to formalise the semantics of several foundational process calculi and automata. Despite their relevance, a general mathematical characterisation of timed transition systems and their behavioural theory is still missing. We introduce the first uniform framework for timed behavioural models that encompasses known behavioural equivalences such as timed bisimulations, timed language equivalences as well as their weak and time-abstract counterparts. All these notions of equivalences are naturally organised by their discriminating power in a spectrum. We prove that this result does not depend on the type of the systems under scrutiny: it holds for any generalisation of timed transition system. We instantiate our framework to timed transition systems and their quantitative extensions such as timed probabilistic systems

Organismic Supercategories and Qualitative Dynamics of Systems

The representation of biological systems by means of organismic supercategories, developed in previous papers, is further discussed. The different approaches to relational biology, developed by Rashevsky, Rosen and by Baianu and Marinescu, are compared with Qualitative Dynamics of Systems which was initiated by Henri Poincaré (1881). On the basis of this comparison some concrete results concerning dynamics of genetic system, development, fertilization, regeneration, analogies, and oncogenesis are derived

Organismic Supercategories: III. Qualitative Dynamics of Systems

The representation of biological systems by means of organismic supercategories, developed in previous papers, is further discussed. The different approaches to relational biology, developed by Rashevsky, Rosen and by Baianu and Marinescu, are compared with Qualitative Dynamics of Systems which was initiated by Henri Poincaré (1881). On the basis of this comparison some concrete results concerning dynamics of genetic system, development, fertilization, regeneration, analogies, and oncogenesis are derived

Minimization via duality

We show how to use duality theory to construct minimized versions of a wide class of automata. We work out three cases in detail: (a variant of) ordinary automata, weighted automata and probabilistic automata. The basic idea is that instead of constructing a maximal quotient we go to the dual and look for a minimal subalgebra and then return to the original category. Duality ensures that the minimal subobject becomes the maximally quotiented object

The compositional construction of Markov processes II

In an earlier paper we introduced a notion of Markov automaton, together with parallel operations which permit the compositional description of Markov processes. We illustrated by showing how to describe a system of n dining philosophers, and we observed that Perron-Frobenius theory yields a proof that the probability of reaching deadlock tends to one as the number of steps goes to infinity. In this paper we add sequential operations to the algebra (and the necessary structure to support them). The extra operations permit the description of hierarchical systems, and ones with evolving geometry