Physics and computer science: quantum computation and other approaches

This is a position paper written as an introduction to the special volume on quantum algorithms I edited for the journal Mathematical Structures in Computer Science (Volume 20 - Special Issue 06 (Quantum Algorithms), 2010)

Benchmarks for Parity Games (extended version)

We propose a benchmark suite for parity games that includes all benchmarks that have been used in the literature, and make it available online. We give an overview of the parity games, including a description of how they have been generated. We also describe structural properties of parity games, and using these properties we show that our benchmarks are representative. With this work we provide a starting point for further experimentation with parity games.Comment: The corresponding tool and benchmarks are available from https://github.com/jkeiren/paritygame-generator. This is an extended version of the paper that has been accepted for FSEN 201

Logics of Finite Hankel Rank

We discuss the Feferman-Vaught Theorem in the setting of abstract model theory for finite structures. We look at sum-like and product-like binary operations on finite structures and their Hankel matrices. We show the connection between Hankel matrices and the Feferman-Vaught Theorem. The largest logic known to satisfy a Feferman-Vaught Theorem for product-like operations is CFOL, first order logic with modular counting quantifiers. For sum-like operations it is CMSOL, the corresponding monadic second order logic. We discuss whether there are maximal logics satisfying Feferman-Vaught Theorems for finite structures.Comment: Appeared in YuriFest 2015, held in honor of Yuri Gurevich's 75th birthday. The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-23534-9_1

Artificial life meets computational creativity?

I review the history of work in Artificial Life on the problem of the open-ended evolutionary growth of complexity in computational worlds. This is then put into the context of evolutionary epistemology and human creativity

Protocol for the Reconstructing Consciousness and Cognition (ReCCognition) Study

Important scientific and clinical questions persist about general anesthesia despite the ubiquitous clinical use of anesthetic drugs in humans since their discovery. For example, it is not known how the brain reconstitutes consciousness and cognition after the profound functional perturbation of the anesthetized state, nor has a specific pattern of functional recovery been characterized. To date, there has been a lack of detailed investigation into rates of recovery and the potential orderly return of attention, sensorimotor function, memory, reasoning and logic, abstract thinking, and processing speed. Moreover, whether such neurobehavioral functions display an invariant sequence of return across individuals is similarly unknown. To address these questions, we designed a study of healthy volunteers undergoing general anesthesia with electroencephalography and serial testing of cognitive functions (NCT01911195). The aims of this study are to characterize the temporal patterns of neurobehavioral recovery over the first several hours following termination of a deep inhaled isoflurane general anesthetic and to identify common patterns of cognitive function recovery. Additionally, we will conduct spectral analysis and reconstruct functional networks from electroencephalographic data to identify any neural correlates (e.g., connectivity patterns, graph-theoretical variables) of cognitive recovery after the perturbation of general anesthesia. To accomplish these objectives, we will enroll a total of 60 consenting adults aged 20–40 across the three participating sites. Half of the study subjects will receive general anesthesia slowly titrated to loss of consciousness (LOC) with an intravenous infusion of propofol and thereafter be maintained for 3 h with 1.3 age adjusted minimum alveolar concentration of isoflurane, while the other half of subjects serves as awake controls to gauge effects of repeated neurobehavioral testing, spontaneous fatigue and endogenous rest-activity patterns

Mathematical models in physiology

Computational modelling of biological processes and systems has witnessed a remarkable development in recent years. The search-term (modelling OR modeling) yields over 58000 entries in PubMed, with more than 34000 since the year 2000: thus, almost two-thirds of papers appeared in the last 5–6 years, compared to only about one-third in the preceding 5–6 decades.\ud \ud The development is fuelled both by the continuously improving tools and techniques available for bio-mathematical modelling and by the increasing demand in quantitative assessment of element inter-relations in complex biological systems. This has given rise to a worldwide public domain effort to build a computational framework that provides a comprehensive theoretical representation of integrated biological function—the Physiome.\ud \ud The current and next issues of this journal are devoted to a small sub-set of this initiative and address biocomputation and modelling in physiology, illustrating the breadth and depth of experimental data-based model development in biological research from sub-cellular events to whole organ simulations