Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

The evolution of rhythmic cognition: New perspectives and technologies in comparative research

Music is a pervasive phenomenon in human culture, and musical rhythm is virtually present in all musical traditions. Research on the evolution and cognitive underpinnings of rhythm can benefit from a number of approaches. We outline key concepts and definitions, allowing fine-grained analysis of rhythmic cognition in experimental studies. We advocate comparative animal research as a useful approach to answer questions about human music cognition and review experimental evidence from different species. Finally, we suggest future directions for research on the cognitive basis of rhythm. Apart from research in semi-natural setups, possibly allowed by “drum set for chimpanzees” prototypes presented here for the first time, mathematical modeling and systematic use of circular statistics may allow promising advances

Environmental performance of spaces enclosed or semi-enclosed by fabric membrane structures

. Since the 1960s a large evolution took place in the fabric structures industry, as they became more complex with time, and designers have been able to keep up with the structural implications of this changing situation. Sophisticated analytical models and computer software have facilitated the structural design of tensile membrane structures (TMS) and this has produced a diverse and complex range of design and form solutions. However, environmental issues continue to be dealt with in a cursory manner, which is still today unable to fully satisfy the client’s requirements. With the vast interest in these structures, designers and manufacturers alike realised that if membrane enclosed spaces is to compete with other more conventional enclosures, a clear understanding of their environmental behaviour should be available to them. Moreover that if membrane enclosed spaces were to aspire to the same level of environmental performance as more conventional buildings, it would be necessary to develop tailored analytical techniques, which could be used to assess the likely performance of various design alternatives. This paper explores the thermal performance of membrane structures, and how these structures can be used as climate modifiers in spaces enclosed or semi enclosed by fabric membrane skins, providing thermal comfort for the occupiers. Analytical techniques that are used to investigate the environmental behaviour of fabric membranes and assessing their liability will be reviewed. The paper also looks at some of the work done by other researchers in the investigation of the thermal behaviour of fabric membranes by different techniques

A solution strategy to include the opening of the opercular slits in moving-mesh CFD models of suction feeding

The gill cover of fish and pre-metamorphic salamanders has a key role in suction feeding by acting as a one-way valve. It initially closes to avoid an inflow of water through the gill slits, after which it opens to allow outflow of the water that was sucked through the mouth into the expanded buccopharyngeal cavity. However, due to the inability of analytical models (relying on the continuity principle) to calculate a fluid flow through a shape-and-size-changing cavity with two openings, stringent boundary conditions had to be used in previously developed mathematical models after the moment of valve opening. By solving additionally for momentum conservation, computational fluid dynamics (CFD) has the capacity to dynamically simulate these flows, but this technique also faces complications to model a transition from closed to open valves. Here, I present a relatively simple solution strategy to incorporate valve opening, exemplified in an axisymmetrical model of a suction-feeding sunfish in ANSYS Fluent software. By controlling viscosity of a separately defined fluid entity at the opercular cavity region, early inflow can be blocked (high viscosity assigned) and later outflow can be allowed (changing viscosity to that of water). Finally, by analysing the CFD solution obtained for the sunfish model, a few new insights in the biomechanics of suction feeding will be discussed

Fault Slip and Exhumation History of the Willard Thrust Sheet, Sevier Fold‐Thrust Belt, Utah: Relations to Wedge Propagation, Hinterland Uplift, and Foreland Basin Sedimentation

Zircon (U‐Th)/He (ZHe) and zircon fission track thermochronometric data for 47 samples spanning the areally extensive Willard thrust sheet within the western part of the Sevier fold‐thrust belt record enhanced cooling and exhumation during major thrust slip spanning approximately 125–90 Ma. ZHe and zircon fission track age‐paleodepth patterns along structural transects and age‐distance relations along stratigraphic‐parallel traverses, combined with thermo‐kinematic modeling, constrain the fault slip history, with estimated slip rates of ~1 km/Myr from 125 to 105 Ma, increasing to ~3 km/Myr from 105 to 92 Ma, and then decreasing as major slip was transferred onto eastern thrusts. Exhumation was concentrated during motion up thrust ramps with estimated erosion rates of ~0.1 to 0.3 km/Myr. Local cooling ages of approximately 160–150 Ma may record a period of regional erosion, or alternatively an early phase of limited... (see full abstract in article)

Enterprise application reuse: Semantic discovery of business grid services

Web services have emerged as a prominent paradigm for the development of distributed software systems as they provide the potential for software to be modularized in a way that functionality can be described, discovered and deployed in a platform independent manner over a network (e.g., intranets, extranets and the Internet). This paper examines an extension of this paradigm to encompass ‘Grid Services’, which enables software capabilities to be recast with an operational focus and support a heterogeneous mix of business software and data, termed a Business Grid - "the grid of semantic services". The current industrial representation of services is predominantly syntactic however, lacking the fundamental semantic underpinnings required to fulfill the goals of any semantically-oriented Grid. Consequently, the use of semantic technology in support of business software heterogeneity is investigated as a likely tool to support a diverse and distributed software inventory and user. Service discovery architecture is therefore developed that is (a) distributed in form, (2) supports distributed service knowledge and (3) automatically extends service knowledge (as greater descriptive precision is inferred from the operating application system). This discovery engine is used to execute several real-word scenarios in order to develop and test a framework for engineering such grid service knowledge. The examples presented comprise software components taken from a group of Investment Banking systems. Resulting from the research is a framework for engineering servic

Construction and Verification of Performance and Reliability Models

Over the last two decades formal methods have been extended towards performance and reliability evaluation. This paper tries to provide a rather intuitive explanation of the basic concepts and features in this area. Instead of striving for mathematical rigour, the intention is to give an illustrative introduction to the basics of stochastic models, to stochastic modelling using process algebra, and to model checking as a technique to analyse stochastic models

Bayesian inference for pulsar timing models

The extremely regular, periodic radio emission from millisecond pulsars makes them useful tools for studying neutron star astrophysics, general relativity, and low-frequency gravitational waves. These studies require that the observed pulse times of arrival be fit to complex timing models that describe numerous effects such as the astrometry of the source, the evolution of the pulsar's spin, the presence of a binary companion, and the propagation of the pulses through the interstellar medium. In this paper, we discuss the benefits of using Bayesian inference to obtain pulsar timing solutions. These benefits include the validation of linearized least-squares model fits when they are correct, and the proper characterization of parameter uncertainties when they are not; the incorporation of prior parameter information and of models of correlated noise; and the Bayesian comparison of alternative timing models. We describe our computational setup, which combines the timing models of Tempo2 with the nested-sampling integrator MultiNest. We compare the timing solutions generated using Bayesian inference and linearized least-squares for three pulsars: B1953+29, J2317+1439, and J1640+2224, which demonstrate a variety of the benefits that we posit.Comment: 13 pages, 4 figures, RevTeX 4.1. Revised in response to referee's suggestions; contains a broader discussion of model comparison, revised Monte Carlo runs, improved figure