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)

Effective Theories for Circuits and Automata

Abstracting an effective theory from a complicated process is central to the study of complexity. Even when the underlying mechanisms are understood, or at least measurable, the presence of dissipation and irreversibility in biological, computational and social systems makes the problem harder. Here we demonstrate the construction of effective theories in the presence of both irreversibility and noise, in a dynamical model with underlying feedback. We use the Krohn-Rhodes theorem to show how the composition of underlying mechanisms can lead to innovations in the emergent effective theory. We show how dissipation and irreversibility fundamentally limit the lifetimes of these emergent structures, even though, on short timescales, the group properties may be enriched compared to their noiseless counterparts.Comment: 11 pages, 9 figure

M\"obius Functions and Semigroup Representation Theory II: Character formulas and multiplicities

We generalize the character formulas for multiplicities of irreducible constituents from group theory to semigroup theory using Rota's theory of M\"obius inversion. The technique works for a large class of semigroups including: inverse semigroups, semigroups with commuting idempotents, idempotent semigroups and semigroups with basic algebras. Using these tools we are able to give a complete description of the spectra of random walks on finite semigroups admitting a faithful representation by upper triangular matrices over the complex numbers. These include the random walks on chambers of hyperplane arrangements studied by Bidigare, Hanlon, Rockmere, Brown and Diaconis. Applications are also given to decomposing tensor powers and exterior products of rook matrix representations of inverse semigroups, generalizing and simplifying earlier results of Solomon for the rook monoid.Comment: Some minor typos corrected and references update

Some views on information fusion and logic based approaches in decision making under uncertainty

Decision making under uncertainty is a key issue in information fusion and logic based reasoning approaches. The aim of this paper is to show noteworthy theoretical and applicational issues in the area of decision making under uncertainty that have been already done and raise new open research related to these topics pointing out promising and challenging research gaps that should be addressed in the coming future in order to improve the resolution of decision making problems under uncertainty

Eilenberg Theorems for Free

Eilenberg-type correspondences, relating varieties of languages (e.g. of finite words, infinite words, or trees) to pseudovarieties of finite algebras, form the backbone of algebraic language theory. Numerous such correspondences are known in the literature. We demonstrate that they all arise from the same recipe: one models languages and the algebras recognizing them by monads on an algebraic category, and applies a Stone-type duality. Our main contribution is a variety theorem that covers e.g. Wilke's and Pin's work on $\infty$-languages, the variety theorem for cost functions of Daviaud, Kuperberg, and Pin, and unifies the two previous categorical approaches of Boja\'nczyk and of Ad\'amek et al. In addition we derive a number of new results, including an extension of the local variety theorem of Gehrke, Grigorieff, and Pin from finite to infinite words