Volume I of this two-volume, interdisciplinary work is a unified presentation of a broad range of state-of-the-art topics in the rapidly growing field of mathematical modeling in the biological sciences. Highlighted throughout the work are mathematical and computational approaches to solving central problems in the life sciences, ranging from the organizational principles of individual cells to the dynamics of large populations.The chapters are thematically organized into the following main areas: Cellular Biophysics; Regulatory Networks; Developmental Biology; Biomedical Applications; Data Analysis and Model Validation.The work will be an excellent reference text for a broad audience of researchers, practitioners, and advanced students in this rapidly growing field at the intersection of applied mathematics, experimental biology and medicine, computational biology, biochemistry, computer science, and physics. This edited volume contains a selection of chapters that are an outgrowth of the - ropean Conference on Mathematical and Theoretical Biology (ECMTB05, Dresden, Germany, July 2005). The peer-reviewed contributions show that mathematical and computational approaches are absolutely essential for solving central problems in the life sciences, ranging from the organizational level of individual cells to the dynamics of whole populations. The contributions indicate that theoretical and mathematical biology is a diverse and interdisciplinary ?eld, ranging from experimental research linked to mathema- cal modeling to the development of more abstract mathematical frameworks in which observations about the real world can be interpreted, and with which new hypotheses for testing can be generated. Today, much attention is also paid to the development of ef?cient algorithms for complex computation and visualisation, notably in molecular biology and genetics. The ?eld of theoretical and mathematical biology and medicine has profound connections to many current problems of great relevance to society. The medical, industrial, and social interests in its development are in fact indisputable. Preface Part I Cellular Biophysics 1 1 Multiparticle Direct Simulation of Photosynthetic Electron Transport Processes Ilya B. Kovalenko, Galina Yu. Riznichenko 3 2 Selective Regulation of Protein Activity by Complex Ca + Oscillations: A lheoretical Study Beate Knoke, Marko Marhl, Stefan Schuster 11 3 Phase Separation in Eukaryotic Directional Sensing Indrea Gamba, Antonio de Candia, Stefano Di Talia, Antonio Coniglio, Federico Bussolino, Guido Serini 23 4 Protein Domains of GTPases on Membranes: Do They Rely on Turing's Mechanism? Lutz Brusch, Perla Del Conte-Zerial, Yannis Kalaidzidis, Jochen Rink, Bianca Habermann, Marino Zerial, Andreas Deutsch 33 5 In Vitro Tubulogenesis of Endothelial Cells: Analysis of a Bifurcation Process Controlled by a Mechanical Switch Philippe Tracqui, Patrick Namy, Jacques Ohayon 47 6 Nonexponential Time Distributions in Biocatalytic Systems: Mass Service Replacing Mass Action Peter W. K hl, Manfred Jobmann 59 Part II Regulatory Networks 69 7 A Stochastic Model of Gene Regulation Using the Chemical Master Equation Hilary S. Booth, Conrad J. Burden, Markus Hegland, Lucia Santoso 71 8 Piecewise-Linear Models of Genetic Regulatory Networks: Analysis of the Carbon Starvation Response in Escherichia coli Delphine Ropers, Hidde de Jong, Jean-Luc Gouz Michel Page, Dominique Schneider, Johannes Geiselmann 83 9 Predicting Gene Expression from Combined Expression and Promoter Profile Similarity with Application to Missing Value Imputation Laura L. Elo, Johannes Tuikkala, Olli S. Nevalainen, Tero Aittokallio 97 10 Chemical Organizations in the Central Sugar Metabolism of Escherichia coli Florian Centler, Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich 105 11 Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science Frank No Jeremy C. Smith 121 Part III Development 139 12 Pigmentation Pattern Formation in Butterfly Wings: Global Patterns on Fore- and Hindwing Toshio Sekimura, Anotida Madzvamuse, Philip K. Maini 141 13 Agent-Based Model for Developmental Pattern Formation with Multiscale Dynamics and Varying Cell Geometry Scott Christley, Stuart A. Newman, Mark S. Alber 149 14 Bacterial Swarming Driven by Rod Shape J rn Starru Fernando Peruani, Markus B Andreas Deutsch 163 15 Stability Properties of Some Tissue-Growth Models John R. King, Susan J. Franks 175 16 A Modified Backward Euler Scheme for Advection-Reaction-Diffusion Systems Anotida Madzvamuse 183 Part IV Biomedical Applications 191 17 Fractional Transport of Cancer Cells Due to Self-Entrapment by Fission Alexander Iomin 193 18 Mathematical Modelling of Vascular Tumour Growth and Implications for Therapy Jasmina Panovska, Helen M. Byrne, Philip K. Maini 205 19 A Stochastic Model of Glioblastoma Invasion Andrew M. Stein, David A. Vader, Leonard M. Sander, David A. Weitz 217 20 Morphology of Tumor Vasculature: A Theoretical Model Katalin Bartha, Heiko Rieger 225 21 A Mathematical Model of the Cell Cycle and Its Circadian Control Jean Clairambault, Philippe Michel, Benoit Perthame 239 22 Bone Turnover Cycle Model with a Torus-Like Steady State Adam Moroz, David Ian Wimpenny 253 23 Modelling the Early Stages of Atherosclerosis Michael J. Plank, Andrew Comerford, David J.N. Wall, Tom David 263 24 Magnetic Nanoparticles for In Vivo Applications: A Numerical Modeling Study Carlos Trenado, Daniel J. Strauss 275 25 Fluid Transport in Peritoneal Dialysis: A Mathematical Model and Numerical Solutions Roman Cherniha, Vasyl' Dutka, Joanna Stachowska-Pietka, Jacek Waniewski 281 26 Relevance of Intracellular Replication to the Evolution of Chagas' Disease G.J. Sibona, C.A. Condat, S. Cossy Isasi 289 27 A Finite Volume Spatial Discretisation for Taxis-Diffusion-Reaction Systems with Axi-Symmetry: Application to Fracture Healing Alf Gerisch, Liesbet Geris 299 28 Information Content Toward a Neonatal Disease Severity Score System Giulia Menconi, Marco Franciosi, Claudio Bonanno, Jacopo Bellazzini 313 Part V Data Analysis and Model Validation 321 29 Statistical Analysis and Physical Modelling of Oligonucleotide Microarrays Conrad J. Burden, Yvonne E. Pittelkow, and Susan R. Wilson 323 30 Validation of Human Alternative Splice Forms Using the EASED Platform and Multiple Splice Site Discriminating Features Ralf Bortfeldt, Alexander Herrmann, Heike Pospisil, Stefan Schuster 337 31 Gaussian Mixture Decomposition of Time-Course DNA Microarray Data Joanna Pol ka, Piotr Widlak, Joanna Rzeszowska-Wolny, Marek Kimmel, Andrzej Pol ki 351 32 SVD Analysis of Gene Expression Data Krzysztof Simek, Michaf Jarzab 361 Index 373