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

An introduction to Biomodel engineering, illustrated for signal transduction pathways

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways

Some analyses of the chemistry and diffusion of SST exhaust materials during phase 3 of the wake period

In the generally stably stratified lower stratosphere, SST exhaust plumes could spend a significant length of time in a relatively undispersed state. This effort has utilized invariant modeling techniques to simulate the separate and combined effects of atmospheric turbulence, turbulent diffusion, and chemical reactions of SST exhaust materials in the lower stratosphere. The primary results to date are: (1) The combination of relatively slow diffusive mixing and rapid chemical reactions during the Phase III wake period minimizes the effect of SST exhausts on O3 depletion by the so-called NOx catalytic cycle. While the SST-produced NO is substantially above background concentrations, it appears diffusive mixing of NO and O3 is simply too slow to produce the O3 depletions originally proposed. (2) The time required to dilute the SST exhaust plume may be a significant fraction of the total time these materials are resident in the lower stratosphere. If this is the case, then prior estimates of the environmental impact of these materials must be revised significantly downward

Airport-Noise Levels and Annoyance Model (ALAMO) user's guide

A guide for the use of the Airport-Noise Level and Annoyance MOdel (ALAMO) at the Langley Research Center computer complex is provided. This document is divided into 5 primary sections, the introduction, the purpose of the model, and an in-depth description of the following subsystems: baseline, noise reduction simulation and track analysis. For each subsystem, the user is provided with a description of architecture, an explanation of subsystem use, sample results, and a case runner's check list. It is assumed that the user is familiar with the operations at the Langley Research Center (LaRC) computer complex, the Network Operating System (NOS 1.4) and CYBER Control Language. Incorporated within the ALAMO model is a census database system called SITE II

Gas chromatograph injection system

An injection system for a gas chromatograph is described which uses a small injector chamber (available in various configurations). The sample is placed in the chamber while the chamber is not under pressure and is not heated, and there is no chance of leakage caused by either pressure or heat. It is injected into the apparatus by changing the position of a valve and heating the chamber, and is volatilized and swept by a carrier gas into the analysis apparatus

Cost-effectiveness of counselling, graded-exercise and usual care for chronic fatigue: evidence from a randomised trial in primary care

Fatigue is common and has been shown to result in high economic costs to society. The aim of this study is to compare the cost-effectiveness of two active therapies, graded-exercise (GET) and counselling (COUN) with usual care plus a self-help booklet (BUC) for people presenting with chronic fatigue

Exotic Smoothness and Physics

The essential role played by differentiable structures in physics is reviewed in light of recent mathematical discoveries that topologically trivial space-time models, especially the simplest one, ${\bf R^4}$, possess a rich multiplicity of such structures, no two of which are diffeomorphic to each other and thus to the standard one. This means that physics has available to it a new panoply of structures available for space-time models. These can be thought of as source of new global, but not properly topological, features. This paper reviews some background differential topology together with a discussion of the role which a differentiable structure necessarily plays in the statement of any physical theory, recalling that diffeomorphisms are at the heart of the principle of general relativity. Some of the history of the discovery of exotic, i.e., non-standard, differentiable structures is reviewed. Some new results suggesting the spatial localization of such exotic structures are described and speculations are made on the possible opportunities that such structures present for the further development of physical theories.Comment: 13 pages, LaTe

On complex surfaces diffeomorphic to rational surfaces

In this paper we prove that no complex surface of general type is diffeomorphic to a rational surface, thereby completing the smooth classification of rational surfaces and the proof of the Van de Ven conjecture on the smooth invariance of Kodaira dimension.Comment: 34 pages, AMS-Te

Donaldson-Thomas invariants and wall-crossing formulas

Notes from the report at the Fields institute in Toronto. We introduce the Donaldson-Thomas invariants and describe the wall-crossing formulas for numerical Donaldson-Thomas invariants.Comment: 18 pages. To appear in the Fields Institute Monograph Serie

Euler number of Instanton Moduli space and Seiberg-Witten invariants

We show that a partition function of topological twisted N=4 Yang-Mills theory is given by Seiberg-Witten invariants on a Riemannian four manifolds under the condition that the sum of Euler number and signature of the four manifolds vanish. The partition function is the sum of Euler number of instanton moduli space when it is possible to apply the vanishing theorem. And we get a relation of Euler number labeled by the instanton number $k$ with Seiberg-Witten invariants, too. All calculation in this paper is done without assuming duality.Comment: LaTeX, 34 page