Reactive Turing Machines

We propose reactive Turing machines (RTMs), extending classical Turing machines with a process-theoretical notion of interaction, and use it to define a notion of executable transition system. We show that every computable transition system with a bounded branching degree is simulated modulo divergence-preserving branching bisimilarity by an RTM, and that every effective transition system is simulated modulo the variant of branching bisimilarity that does not require divergence preservation. We conclude from these results that the parallel composition of (communicating) RTMs can be simulated by a single RTM. We prove that there exist universal RTMs modulo branching bisimilarity, but these essentially employ divergence to be able to simulate an RTM of arbitrary branching degree. We also prove that modulo divergence-preserving branching bisimilarity there are RTMs that are universal up to their own branching degree. Finally, we establish a correspondence between executability and finite definability in a simple process calculus

Computing Solution Operators of Boundary-value Problems for Some Linear Hyperbolic Systems of PDEs

We discuss possibilities of application of Numerical Analysis methods to proving computability, in the sense of the TTE approach, of solution operators of boundary-value problems for systems of PDEs. We prove computability of the solution operator for a symmetric hyperbolic system with computable real coefficients and dissipative boundary conditions, and of the Cauchy problem for the same system (we also prove computable dependence on the coefficients) in a cube $Q\subseteq\mathbb R^m$. Such systems describe a wide variety of physical processes (e.g. elasticity, acoustics, Maxwell equations). Moreover, many boundary-value problems for the wave equation also can be reduced to this case, thus we partially answer a question raised in Weihrauch and Zhong (2002). Compared with most of other existing methods of proving computability for PDEs, this method does not require existence of explicit solution formulas and is thus applicable to a broader class of (systems of) equations.Comment: 31 page

Toward accurate polynomial evaluation in rounded arithmetic

Given a multivariate real (or complex) polynomial $p$ and a domain $\cal D$, we would like to decide whether an algorithm exists to evaluate $p(x)$ accurately for all $x \in {\cal D}$ using rounded real (or complex) arithmetic. Here ``accurately'' means with relative error less than 1, i.e., with some correct leading digits. The answer depends on the model of rounded arithmetic: We assume that for any arithmetic operator $op(a,b)$, for example $a+b$ or $a \cdot b$, its computed value is $op(a,b) \cdot (1 + \delta)$, where $| \delta |$ is bounded by some constant $\epsilon$ where $0 < \epsilon \ll 1$, but $\delta$ is otherwise arbitrary. This model is the traditional one used to analyze the accuracy of floating point algorithms.Our ultimate goal is to establish a decision procedure that, for any $p$ and $\cal D$, either exhibits an accurate algorithm or proves that none exists. In contrast to the case where numbers are stored and manipulated as finite bit strings (e.g., as floating point numbers or rational numbers) we show that some polynomials $p$ are impossible to evaluate accurately. The existence of an accurate algorithm will depend not just on $p$ and $\cal D$, but on which arithmetic operators and which constants are are available and whether branching is permitted. Toward this goal, we present necessary conditions on $p$ for it to be accurately evaluable on open real or complex domains ${\cal D}$. We also give sufficient conditions, and describe progress toward a complete decision procedure. We do present a complete decision procedure for homogeneous polynomials $p$ with integer coefficients, {\cal D} = \C^n, and using only the arithmetic operations $+$, $-$ and $\cdot$.Comment: 54 pages, 6 figures; refereed version; to appear in Foundations of Computational Mathematics: Santander 2005, Cambridge University Press, March 200

Sticker systems over monoids

Molecular computing has gained many interests among researchers since Head introduced the first theoretical model for DNA based computation using the splicing operation in 1987. Another model for DNA computing was proposed by using the sticker operation which Adlemanused in his successful experiment for the computation of Hamiltonian paths in a graph: a double stranded DNA sequence is composed by prolonging to the left and to the right a sequence of (single or double) symbols by using given single stranded strings or even more complex dominoes with sticky ends, gluing these ends together with the sticky ends of the current sequence according to a complementarity relation. According to this sticker operation, a language generative mechanism, called a sticker system, can be defined: a set of (incomplete) double-stranded sequences (axioms) and a set of pairs of single or double-stranded complementary sequences are given. The initial sequences are prolonged to the left and to the right by using sequences from the latter set, respectively. The iterations of these prolongations produce “computations” of possibly arbitrary length. These processes stop when a complete double stranded sequence is obtained. Sticker systems will generate only regular languages without restrictions. Additional restrictions can be imposed on the matching pairs of strands to obtain more powerful languages. Several types of sticker systems are shown to have the same power as regular grammars; one type is found to represent all linear languages whereas another one is proved to be able to represent any recursively enumerable language. The main aim of this research is to introduce and study sticker systems over monoids in which with each sticker operation, an element of a monoid is associated and a complete double stranded sequence is considered to be valid if the computation of the associated elements of the monoid produces the neutral element. Moreover, the sticker system over monoids is defined in this study

Changing a semantics: opportunism or courage?

The generalized models for higher-order logics introduced by Leon Henkin, and their multiple offspring over the years, have become a standard tool in many areas of logic. Even so, discussion has persisted about their technical status, and perhaps even their conceptual legitimacy. This paper gives a systematic view of generalized model techniques, discusses what they mean in mathematical and philosophical terms, and presents a few technical themes and results about their role in algebraic representation, calibrating provability, lowering complexity, understanding fixed-point logics, and achieving set-theoretic absoluteness. We also show how thinking about Henkin's approach to semantics of logical systems in this generality can yield new results, dispelling the impression of adhocness. This paper is dedicated to Leon Henkin, a deep logician who has changed the way we all work, while also being an always open, modest, and encouraging colleague and friend.Comment: 27 pages. To appear in: The life and work of Leon Henkin: Essays on his contributions (Studies in Universal Logic) eds: Manzano, M., Sain, I. and Alonso, E., 201

Modeling and evolving biochemical networks: insights into communication and computation from the biological domain

This paper is concerned with the modeling and evolving of Cell Signaling Networks (CSNs) in silico. CSNs are complex biochemical networks responsible for the coordination of cellular activities. We examine the possibility to computationally evolve and simulate Artificial Cell Signaling Networks (ACSNs) by means of Evolutionary Computation techniques. From a practical point of view, realizing and evolving ACSNs may provide novel computational paradigms for a variety of application areas. For example, understanding some inherent properties of CSNs such as crosstalk may be of interest: A potential benefit of engineering crosstalking systems is that it allows the modification of a specific process according to the state of other processes in the system. This is clearly necessary in order to achieve complex control tasks. This work may also contribute to the biological understanding of the origins and evolution of real CSNs. An introduction to CSNs is first provided, in which we describe the potential applications of modeling and evolving these biochemical networks in silico. We then review the different classes of techniques to model CSNs, this is followed by a presentation of two alternative approaches employed to evolve CSNs within the ESIGNET project. Results obtained with these methods are summarized and discussed

Generalized Communicating P Systems Working in Fair Sequential Model

In this article we consider a new derivation mode for generalized communicating P systems (GCPS) corresponding to the functioning of population protocols (PP) and based on the sequential derivation mode and a fairness condition. We show that PP can be seen as a particular variant of GCPS. We also consider a particular stochastic evolution satisfying the fairness condition and obtain that it corresponds to the run of a Gillespie's SSA. This permits to further describe the dynamics of GCPS by a system of ODEs when the population size goes to the infinity.Comment: Presented at MeCBIC 201

Oscillator model for dissipative QED in an inhomogeneous dielectric

The Ullersma model for the damped harmonic oscillator is coupled to the quantised electromagnetic field. All material parameters and interaction strengths are allowed to depend on position. The ensuing Hamiltonian is expressed in terms of canonical fields, and diagonalised by performing a normal-mode expansion. The commutation relations of the diagonalising operators are in agreement with the canonical commutation relations. For the proof we replace all sums of normal modes by complex integrals with the help of the residue theorem. The same technique helps us to explicitly calculate the quantum evolution of all canonical and electromagnetic fields. We identify the dielectric constant and the Green function of the wave equation for the electric field. Both functions are meromorphic in the complex frequency plane. The solution of the extended Ullersma model is in keeping with well-known phenomenological rules for setting up quantum electrodynamics in an absorptive and spatially inhomogeneous dielectric. To establish this fundamental justification, we subject the reservoir of independent harmonic oscillators to a continuum limit. The resonant frequencies of the reservoir are smeared out over the real axis. Consequently, the poles of both the dielectric constant and the Green function unite to form a branch cut. Performing an analytic continuation beyond this branch cut, we find that the long-time behaviour of the quantised electric field is completely determined by the sources of the reservoir. Through a Riemann-Lebesgue argument we demonstrate that the field itself tends to zero, whereas its quantum fluctuations stay alive. We argue that the last feature may have important consequences for application of entanglement and related processes in quantum devices.Comment: 24 pages, 1 figur