Biomat 2005 : Proceedings of the International Symposium on Mathematical and Computational Biology, Rio De Janeiro, Brazil, 3-8 December 2005.
Title:
Biomat 2005 : Proceedings of the International Symposium on Mathematical and Computational Biology, Rio De Janeiro, Brazil, 3-8 December 2005.
Author:
Mondaini, Rubem P.
ISBN:
9789812773685
Personal Author:
Physical Description:
1 online resource (408 pages)
Contents:
Contents -- Preface -- Editorial Board of the BIOMAT Consortium -- Biological Modeling -- Modelling aspects of vascular cancer development -- 1. Introduction -- 2. Brief biological background -- 3. Cellular automaton model -- 4. Effects of hypoxia on cell cycle dynamics -- 5. The role of acidity -- 6. Discussion -- References -- Modelling cooperative phenomena in interacting cell systems with cellular automata -- 1. Introduction: roots of cellular automata -- 2. Cellular automaton definition -- 3. Cellular automaton models of cell interaction -- 4. An example: a cellular automaton model of a vascular tumor growth -- 5. Discussion -- References -- A mathematical analysis of cylindrical shaped aneurysms -- 1. Introduction -- 2. The Mathematical Model -- 3. The Dynamical Properties of the Model -- 4. Discussion -- References -- On the origin of metazoans -- 1. Introduction -- 2. Pattern Formation -- 3. Coupling Pattern to Cell Shape -- 4. On Urcnidaria -- 5. On Urbilateria -- Appendix A -- Appendix B -- References -- A software tool to model genetic regulatory networks: Applications to segmental patterning in Drosophila -- 1. Introduction -- 2. A model for the regulation of gene expression -- 3. The GeNetSim package -- 4. Segmental patterning in Drosophila -- References -- The mitochondrial Eve in an exponentially growing population and a critique to the out of Africa model for human evolution -- 1. Introduction -- 2. Percolation and mitochondrial DNA basics -- 3. Percolation model for mtDNA inheritance -- 4. Demographic considerations -- 5. Conclusions -- References -- A neurocomputational model of the role of cholesterol in the development process of Alzheimer's disease -- 1. Introduction -- 2. The Alzheimer's Disease -- 3. The Metabolism of the Cholesterol -- 4. The Formation Senile Amyloid Plaques.
5. The Formation of Neurofibrilary Tangles -- 6. Results -- 7. Conclusions -- References -- Theoretical study of a biofilm life cycle: Growth, nutrient depletion and detachment -- 1. Introduction -- 2. The mathematical model -- 3. Detachment -- References -- Optimal control of distributed systems applied to the problems of ambient pollution -- 1. Introduction -- 2. Pointwise Optimal Control -- 3. Computational Results, Analysis and Conclusion -- References -- Epidemiology and Immunology -- Modeling the in vivo dynamics of viral infections -- 1. Introduction -- 2. Modeling HIV infection -- 3. Conclusions -- References -- Short and long-term dynamics of childhood diseases in dynamic small-world networks -- 1. Introduction -- 2. PCA Model -- 3. Results: SIR model -- 4. Results: SEIR model -- 5. Discussion -- 6. Conclusion -- References -- Clonal expansion of cytotoxic T cell clones: The role of the immunoproteasome -- 1. Introduction -- 2. The model -- 3. A caricature of the cytotoxic T cell and peptide repertoire -- 4. Results -- 5. Discussion -- References -- Modeling plague dynamics: Endemic states, outbreaks and epidemic waves -- 1. Introduction -- 2. Natural History of the Ecology and Spread of Y. pestis -- 3. The Model -- 4. Threshold conditions for the establishment of the infection -- 5. Simulating the model -- 6. Discussion -- References -- The basic reproduction ratio for a Malaria model -- 1. Introduction -- 2. The Mathematical Model -- 3. The Basic Reproductive Rate -- 4. Numerical Simulation -- 5. Discussion -- References -- Epidemiological model with fast dispersion -- 1. Introduction -- 2. Preliminaries -- 3. The model -- 4. Conclusions -- References -- Protein Structure -- Structure prediction of alpha-helical proteins -- 1. Introduction -- 2. Theory and Modeling -- 3. Results and Discussion -- 4. Conclusions.
References -- Quality and effectiveness of protein structure comparative models -- 1. Introduction -- 2. How good are comparative models? the CASP experiment -- 3. Can we evaluate the quality of a protein comparative model a priori? -- 4. Useful applications of comparative models: molecular replacement in x-ray crystallography -- 5. Conclusions -- References -- Steiner minimal trees and twist angles in folded protein structures -- 1. Motivation -- 2. Problem Background -- 3. Mathematical Models and Properties -- 4. Amino Acid Results -- 5. Dipeptide Structures -- 6. Summary and Conclusions -- References -- Steiner trees as intramolecular networks of the biomacromolecular structures -- 1. An Analytical approach to the search of Minimal Potential Energy configurations -- 2. The Stability of Networks under Elastic Force Deformations -- 3. The Measure of Chirality as the Constraint of a Constrained Optimization Problem -- 4. Concluding Remarks -- References -- Bioinformatics -- Exploring chemical space with computers: Informatics challenges for AI and machine learning -- 1. Introduction -- 2. Small Molecules in Organic Chemistry -- 3. Chemoinformatics Challenges -- 4. Data: Database, Datasets, and Annotations -- 5. Similarity Measures and Kernels -- References -- Optimization of between group analysis of gene expression disease class prediction -- 1. Introduction -- 2. Methods -- 3. Results -- 4. Discussion -- Bibliography -- On biclustering with feature selection for microarray data sets -- 1. Introduction -- 2. Problem Statement and the Algorithm -- 3. Computational Experiments -- References -- Simple and effective classifiers to model biological data -- 1. Introduction -- 2. Ensemble Methods -- 3. Methodology -- 4. Results -- 5. Discussion -- 6. Conclusions and Future Work -- References -- Index.
Abstract:
This volume contains the contributions of the keynote speakers to the BIOMAT 2005 symposium, as well as a collection of selected papers by pioneering researchers. It provides a comprehensive review of the mathematical modeling of cancer development, Alzheimer's disease, malaria, and aneurysm development. Various models for the immune system and epidemiological issues are analyzed and reviewed. The book also explores protein structure prediction by optimization and combinatorial techniques (Steiner trees). The coverage includes bioinformatics issues, regulation of gene expression, evolution, development, DNA and array modeling, and small world networks. Sample Chapter(s). Chapter 1: Modelling Aspects of Vascular Cancer Development (581 KB). Contents: Biological Modeling: A Mathematical Analysis of Cylindrical Shaped Aneurysms (T A Kwembe & S N Jones); On the Origin of Metazoans (F W Cummings); Optimal Control of Distributed Systems Applied to the Problems of Ambient Pollution (S F Arantes & J E M Rivera); Epidemiology and Immunology: Modeling the in Vivo Dynamics of Viral Infections (R M Ribeiro); The Basic Reproductive Rate in the Malaria Model (A P Wyse et al.); Epidemiological Model with Fast Dispersion (M R Ricard et al.); Protein Structure: Structure Prediction of Alpha-Helical Proteins (S R McAllister & C A Floudas); Steiner Minimal Trees, Twist Angles, and the Protein Folding Problem (J M Smith); Steiner Trees as Intramolecular Networks of the Biomacromolecular Structures (R P Mondaini); Bioinformatics: Optimization of Between Group Analysis of Gene Expression Disease Class Prediction (F Baty et al.); On Biclustering with Features Selection for Microarray Data Sets (P M Pardalos et al.); Simple and Effective Classifiers to Model Biological Data (R L Salvini et al.); and other papers. Readership: Graduate students and researchers in biology,
mathematics and physics.
Local Note:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
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