Key word in context index and bibliography on computer systems evaluation techniques

Selected bibliography of information pertinent to computer system

Key word in context index and bibliography on computer systems simulation and evaluation

Index program for bibliography on systems evaluation, simulation languages, mathematical models, and computer simulation technique

Analysis of data processing systems

Mathematical simulation models and software monitoring of multiprogramming computer syste

A Mathematical Model for DNA Damage and Repair

In cells, DNA repair has to keep up with DNA damage to maintain the integrity of the genome and prevent mutagenesis and carcinogenesis. While the importance of both DNA damage and repair is clear, the impact of imbalances between both processes has not been studied. In this paper, we created a combined mathematical model for the formation of DNA adducts from oxidative estrogen metabolism followed by base excision repair (BER) of these adducts. The model encompasses a set of differential equations representing the sequence of enzymatic reactions in both damage and repair pathways. By combining both pathways, we can simulate the overall process by starting from a given time-dependent concentration of 17β-estradiol (E2) and 2′-deoxyguanosine, determine the extent of adduct formation and the correction by BER required to preserve the integrity of DNA. The model allows us to examine the effect of phenotypic and genotypic factors such as different concentrations of estrogen and variant enzyme haplotypes on the formation and repair of DNA adducts

A Computational Model of Quantitative Chromatin Immunoprecipitation (ChIP) Analysis

Chromatin immunoprecipitation (ChIP) analysis is widely used to identify the locations in genomes occupied by transcription factors (TFs). The approach involves chemical cross-linking of DNA with associated proteins, fragmentation of chromatin by sonication or enzymatic digestion, immunoprecipitation of the fragments containing the protein of interest, and then PCR or hybridization analysis to characterize and quantify the genomic sequences enriched. We developed a computational model of quantitative ChIP analysis to elucidate the factors contributing to the method’s resolution. The most important variables identified by the model were, in order of importance, the spacing of the PCR primers, the mean length of the chromatin fragments, and, unexpectedly, the type of fragment width distribution, with very small DNA fragments and smaller amplicons providing the best resolution of TF binding. One of the major predictions of the model was also validated experimentally

Inside and out: An epicardial lead gone astray

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Complexation of DNA with Cationic Surfactant

Transfection of an anionic polynucleotide through a negatively charged membrane is an important problem in genetic engineering. The direct association of cationic surfactant to DNA decreases the effective negative charge of the nucleic acid, allowing the DNA-surfactant complex to approach a negatively charged membrane. The paper develops a theory for solutions composed of polyelectrolyte, salt, and ionic surfactant. The theoretical predictions are compared with the experimental measurements.Comment: 9 pages, 3 figure

Investigating situated cultural practices through cross-sectoral digital collaborations: policies, processes, insights

The (Belfast) Good Friday Agreement represents a major milestone in Northern Ireland's recent political history, with complex conditions allowing for formation of a ‘cross-community’ system of government enabling power sharing between parties representing Protestant/loyalist and Catholic/nationalist constituencies. This article examines the apparent flourishing of community-focused digital practices over the subsequent ‘post-conflict’ decade, galvanised by Northern Irish and EU policy initiatives armed with consolidating the peace process. Numerous digital heritage and storytelling projects have been catalysed within programmes aiming to foster social processes, community cohesion and cross-community exchange. The article outlines two projects—‘digital memory boxes’ and ‘interactive galleon’—developed during 2007–2008 within practice-led PhD enquiry conducted in collaboration with the Nerve Centre, a third-sector media education organisation. The article goes on to critically examine the processes involved in practically realising, and creatively and theoretically reconciling, community-engaged digital production in a particular socio-political context of academic-community collaboration