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Economic modelling using constraint logic programming
This paper investigates the use of constraint logic programming (CLP) in economic modelling
through the design and implementation of two economic models. The first model, the Desai-
Henry model contains only linear equations while the second model, constructed by the author,
contains non-linear elements. In order to implement the second model, a non-linear constraint
solver was constructed. This was necessary because, although CLP is a very powerful
programming paradigm, currently available implementations lack any on-linear constraint
solving mechanisms
The algebra of rewriting for presentations of inverse monoids
We describe a formalism, using groupoids, for the study of rewriting for
presentations of inverse monoids, that is based on the Squier complex
construction for monoid presentations. We introduce the class of pseudoregular
groupoids, an example of which now arises as the fundamental groupoid of our
version of the Squier complex. A further key ingredient is the factorisation of
the presentation map from a free inverse monoid as the composition of an
idempotent pure map and an idempotent separating map. The relation module of a
presentation is then defined as the abelianised kernel of this idempotent
separating map. We then use the properties of idempotent separating maps to
derive a free presentation of the relation module. The construction of its
kernel - the module of identities - uses further facts about pseudoregular
groupoids.Comment: 22 page
Grid-enabled SIMAP utility: Motivation, integration technology and performance results
A biological system comprises large numbers of functionally diverse and frequently multifunctional sets of elements that interact selectively and nonlinearly to produce coherent behaviours. Such a system can be anything from an intracellular biological process (such as a biochemical reaction cycle, gene regulatory network or signal transduction pathway) to a cell, tissue, entire organism, or even an ecological web. Biochemical systems are
responsible for processing environmental signals, inducing the appropriate cellular responses and sequence of
internal events. However, such systems are not fully or even poorly understood. Systems biology is a scientific field that is concerned with the systematic study of biological and biochemical systems in terms of complex interactions rather than their individual molecular components. At the core of systems biology is computational
modelling (also called mathematical modelling), which is the process of constructing and simulating an abstract
model of a biological system for subsequent analysis. This methodology can be used to test hypotheses via insilico experiments, providing predictions that can be tested by in-vitro and in-vivo studies. For example, the ERbB1-4 receptor tyrosine kinases (RTKs) and the signalling pathways they activate, govern most core cellular processes such as cell division, motility and survival (Citri and Yarden, 2006) and are strongly linked to cancer when they malfunction due to mutations etc. An ODE (ordinary differential equation)-based mass action ErbB model has been constructed and analysed by Chen et al. (2009) in order to depict what roles of each protein plays and ascertain to how sets of proteins coordinate with each other to perform distinct physiological functions. The
model comprises 499 species (molecules), 201 parameters and 828 reactions. These in silico experiments can often be computationally very expensive, e.g. when multiple biochemical factors are being considered or a variety of complex networks are being simulated simultaneously. Due to the size and complexity of the models
and the requirement to perform comprehensive experiments it is often necessary to use high-performance computing (HPC) to keep the experimental time within tractable bounds. Based on this as part of an EC funded
cancer research project, we have developed the SIMAP Utility that allows the SImulation modeling of the MAP kinase pathway (http://www.simap-project.org). In this paper we present experiences with Grid-enabling SIMAP using Condor
Exons, introns and DNA thermodynamics
The genes of eukaryotes are characterized by protein coding fragments, the
exons, interrupted by introns, i.e. stretches of DNA which do not carry any
useful information for the protein synthesis. We have analyzed the melting
behavior of randomly selected human cDNA sequences obtained from the genomic
DNA by removing all introns. A clear correspondence is observed between exons
and melting domains. This finding may provide new insights in the physical
mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev.
Focus 15, story 1
Groupoids and the algebra of rewriting in group presentations
Presentations of groups by rewriting systems (that is, by monoid
presentations), have been fruitfully studied by encoding the rewriting system
in a --complex -- the Squier complex -- whose fundamental groupoid then
describes the derivation of consequences of the rewrite rules. We describe a
reduced form of the Squier complex, investigate the structure of its
fundamental groupoid, and show that key properties of the presentation are
still encoded in the reduced form.Comment: 15 page
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