09091 Abstracts Collection -- Formal Methods in Molecular Biology

From 23. February to 27. February 2009, the Dagstuhl Seminar 09091 ``Formal Methods in Molecular Biology \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

An adequate compositional encoding of bigraph structure in linear logic with subexponentials

International audienceIn linear logic, formulas can be split into two sets: classical (those that can be used as many times as necessary) or linear (those that are consumed and no longer available after being used). Subexponentials generalize this notion by allowing the formulas to be split into many sets, each of which can then be specified to be classical or linear. This flexibility increases its expressiveness: we already have adequate encodings of a number of other proof systems, and for computational models such as concurrent constraint programming, in linear logic with subexponentials (SEL). Bigraphs were proposed by Milner in 2001 as a model for ubiquitous computing, subsuming models of computation such as CCS and the π-calculus and capable of modeling connectivity and locality at the same time. In this work we present an encoding of the bigraph structure in SEL, thus giving an indication of the expressive power of this logic, and at the same time providing a framework for reasoning and operating on bigraphs. Our encoding is adequate and therefore the operations of composition and juxtaposition can be performed on the logical level. Moreover, all the proof-theoretical tools of SEL become available for querying and proving properties of bigraph structures

Spatio-temporal logic for the analysis of biochemical models

Process algebra, formal specification, and model checking are all well studied techniques in the analysis of concurrent computer systems. More recently these techniques have been applied to the analysis of biochemical systems which, at an abstract level, have similar patterns of behaviour to concurrent processes. Process algebraic models and temporal logic specifications, along with their associated model-checking techniques, have been used to analyse biochemical systems. In this thesis we develop a spatio-temporal logic, the Logic of Behaviour in Context (LBC), for the analysis of biochemical models. That is, we define and study the application of a formal specification language which not only expresses temporal properties of biochemical models, but expresses spatial or contextual properties as well. The logic can be used to express, or specify, the behaviour of a model when it is placed into the context of another model. We also explore the types of properties which can be expressed in LBC, various algorithms for model checking LBC - each an improvement on the last, the implementation of the computational tools to support model checking LBC, and a case study on the analysis of models of post-translational biochemical oscillators using LBC. We show that a number of interesting and useful properties can be expressed in LBC and that it is possible to express highly useful properties of real models in the biochemistry domain, with practical application. Statements in LBC can be thought of as expressing computational experiments which can be performed automatically by means of the model checker. Indeed, many of these computational experiments can be higher-order meaning that one succinct and precise specification in LBC can represent a number of experiments which can be automatically executed by the model checker

Continuous-time temporal logic specification and verification for nonlinear biological systems in uncertain contexts

In this thesis we introduce a complete framework for modelling and verification of biological systems in uncertain contexts based on the bond-calculus process algebra and the LBUC spatio-temporal logic. The bond-calculus is a biological process algebra which captures complex patterns of interaction based on affinity patterns, a novel communication mechanism using pattern matching to express multiway interaction affinities and general kinetic laws, whilst retaining an agent-centric modelling style for biomolecular species. The bond-calculus is equipped with a novel continuous semantics which maps models to systems of Ordinary Differential Equations (ODEs) in a compositional way. We then extend the bond-calculus to handle uncertain models, featuring interval uncertainties in their species concentrations and reaction rate parameters. Our semantics is also extended to handle uncertainty in every aspect of a model, producing non-deterministic continuous systems whose behaviour depends either on time-independent uncertain parameters and initial conditions, corresponding to our partial knowledge of the system at hand, or time-varying uncertain inputs, corresponding to genuine variability in a system’s behaviour based on environmental factors. This language is then coupled with the LBUC spatio-temporal logic which combines Signal Temporal Logic (STL) temporal operators with an uncertain context operator which quantifies over an uncertain context model describing the range of environments over which a property must hold. We develop model-checking procedures for STL and LBUC properties based on verified signal monitoring over flowpipes produced by the Flow* verified integrator, including the technique of masking which directs monitoring for atomic propositions to time regions relevant to the overall verification problem at hand. This allows us to monitor many interesting nested contextual properties and frequently reduces monitoring costs by an order of magnitude. Finally, we explore the technique of contextual signal monitoring which can use a single Flow* flowpipe representing a functional dependency to complete a whole tree of signals corresponding to different uncertain contexts. This allows us to produce refined monitoring results over the whole space and to explore the variation in system behaviour in different contexts

Reversible Computation: Extending Horizons of Computing

This open access State-of-the-Art Survey presents the main recent scientific outcomes in the area of reversible computation, focusing on those that have emerged during COST Action IC1405 "Reversible Computation - Extending Horizons of Computing", a European research network that operated from May 2015 to April 2019. Reversible computation is a new paradigm that extends the traditional forwards-only mode of computation with the ability to execute in reverse, so that computation can run backwards as easily and naturally as forwards. It aims to deliver novel computing devices and software, and to enhance existing systems by equipping them with reversibility. There are many potential applications of reversible computation, including languages and software tools for reliable and recovery-oriented distributed systems and revolutionary reversible logic gates and circuits, but they can only be realized and have lasting effect if conceptual and firm theoretical foundations are established first

Reversible Computation: Extending Horizons of Computing

This open access State-of-the-Art Survey presents the main recent scientific outcomes in the area of reversible computation, focusing on those that have emerged during COST Action IC1405 "Reversible Computation - Extending Horizons of Computing", a European research network that operated from May 2015 to April 2019. Reversible computation is a new paradigm that extends the traditional forwards-only mode of computation with the ability to execute in reverse, so that computation can run backwards as easily and naturally as forwards. It aims to deliver novel computing devices and software, and to enhance existing systems by equipping them with reversibility. There are many potential applications of reversible computation, including languages and software tools for reliable and recovery-oriented distributed systems and revolutionary reversible logic gates and circuits, but they can only be realized and have lasting effect if conceptual and firm theoretical foundations are established first

Communication in membrana Systems with symbol Objects.

Esta tesis está dedicada a los sistemas de membranas con objetos-símbolo como marco teórico de los sistemas paralelos y distribuidos de procesamiento de multiconjuntos.Una computación de parada puede aceptar, generar o procesar un número, un vector o una palabra; por tanto el sistema define globalmente (a través de los resultados de todas sus computaciones) un conjunto de números, de vectores, de palabras (es decir, un lenguaje), o bien una función. En esta tesis estudiamos la capacidad de estos sistemas para resolver problemas particulares, así como su potencia computacional. Por ejemplo, las familias de lenguajes definidas por diversas clases de estos sistemas se comparan con las familias clásicas, esto es, lenguajes regulares, independientes del contexto, generados por sistemas 0L tabulados extendidos, generados por gramáticas matriciales sin chequeo de apariciones, recursivamente enumerables, etc. Se prestará especial atención a la comunicación de objetos entre regiones y a las distintas formas de cooperación entre ellos.Se pretende (Sección 3.4) realizar una formalización los sistemas de membranas y construir una herramienta tipo software para la variante que usa cooperación no distribuida, el navegador de configuraciones, es decir, un simulador, en el cual el usuario selecciona la siguiente configuración entre todas las posibles, estando permitido volver hacia atrás. Se considerarán diversos modelos distribuidos. En el modelo de evolución y comunicación (Capítulo 4) separamos las reglas tipo-reescritura y las reglas de transporte (llamadas symport y antiport). Los sistemas de bombeo de protones (proton pumping, Secciones 4.8, 4.9) constituyen una variante de los sistemas de evolución y comunicación con un modo restrictivo de cooperación. Un modelo especial de computación con membranas es el modelo puramente comunicativo, en el cual los objetos traspasan juntos una membrana. Estudiamos la potencia computacional de las sistemas de membranas con symport/antiport de 2 o 3 objetos (Capítulo 5) y la potencia computacional de las sistemas de membranas con alfabeto limitado (Capítulo 6).El determinismo (Secciones 4.7, 5.5, etc.) es una característica especial (restrictiva) de los sistemas computacionales. Se pondrá especial énfasis en analizar si esta restricción reduce o no la potencia computacional de los mismos. Los resultados obtenidos para sistemas de bombeo del protones están transferidos (Sección 7.3) a sistemas con catalizadores bistabiles. Unos ejemplos de aplicación concreta de los sistemas de membranas (Secciones 7.1, 7.2) son la resolución de problemas NP-completos en tiempo polinomial y la resolución de problemas de ordenación.This thesis deals with membrane systems with symbol objects as a theoretical framework of distributed parallel multiset processing systems.A halting computation can accept, generate or process a number, a vector or a word, so the system globally defines (by the results of all its computations) a set of numbers or a set of vectors or a set of words, (i.e., a language), or a function. The ability of these systems to solve particular problems is investigated, as well as their computational power, e.g., the language families defined by different classes of these systems are compared to the classical ones, i.e., regular, context-free, languages generated by extended tabled 0L systems, languages generated by matrix grammars without appearance checking, recursively enumerable languages, etc. Special attention is paid to communication of objects between the regions and to the ways of cooperation between the objects.An attempt to formalize the membrane systems is made (Section 3.4), and a software tool is constructed for the non-distributed cooperative variant, the configuration browser, i.e., a simulator, where the user chooses the next configuration among the possible ones and can go back. Different distributed models are considered. In the evolution-communication model (Chapter 4) rewriting-like rules are separated from transport rules. Proton pumping systems (Sections 4.8, 4.9) are a variant of the evolution-communication systems with a restricted way of cooperation. A special membrane computing model is a purely communicative one: the objects are moved together through a membrane. We study the computational power of membrane systems with symport/antiport of 2 or 3 objects (Chapter 5) and the computational power of membrane systems with a limited alphabet (Chapter 6).Determinism (Sections 4.7, 5.5, etc.) is a special property of computational systems; the question of whether this restriction reduces the computational power is addressed. The results on proton pumping systems can be carried over (Section 7.3) to the systems with bi-stable catalysts. Some particular examples of membrane systems applications are solving NP-complete problems in polynomial time, and solving the sorting problem

Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

On Algebraic Singularities, Finite Graphs and D-Brane Gauge Theories: A String Theoretic Perspective

In this writing we shall address certain beautiful inter-relations between the construction of 4-dimensional supersymmetric gauge theories and resolution of algebraic singularities, from the perspective of String Theory. We review in some detail the requisite background in both the mathematics, such as orbifolds, symplectic quotients and quiver representations, as well as the physics, such as gauged linear sigma models, geometrical engineering, Hanany-Witten setups and D-brane probes. We investigate aspects of world-volume gauge dynamics using D-brane resolutions of various Calabi-Yau singularities, notably Gorenstein quotients and toric singularities. Attention will be paid to the general methodology of constructing gauge theories for these singular backgrounds, with and without the presence of the NS-NS B-field, as well as the T-duals to brane setups and branes wrapping cycles in the mirror geometry. Applications of such diverse and elegant mathematics as crepant resolution of algebraic singularities, representation of finite groups and finite graphs, modular invariants of affine Lie algebras, etc. will naturally arise. Various viewpoints and generalisations of McKay's Correspondence will also be considered. The present work is a transcription of excerpts from the first three volumes of the author's PhD thesis which was written under the direction of Prof. A. Hanany - to whom he is much indebted - at the Centre for Theoretical Physics of MIT, and which, at the suggestion of friends, he posts to the ArXiv pro hac vice; it is his sincerest wish that the ensuing pages might be of some small use to the beginning student.Comment: 513 pages, 71 figs, Edited Excerpts from the first 3 volumes of the author's PhD Thesi