Mathematical Modeling of Biological Systems, Volume I

1. Front Matter

   Pages I-XVIII

   PDF

2. Cellular Biophysics

   1. Front Matter

      Pages 1-1

      PDF

   2. Multiparticle Direct Simulation of Photosynthetic Electron Transport Processes

      • Ilya B. Kovalenko, Galina Yu. Riznichenko

      Pages 3-9

   3. Selective Regulation of Protein Activity by Complex Ca2+ Oscillations: A Theoretical Study

      • Beate Knoke, Marko Marhl, Stefan Schuster

      Pages 11-22

   4. Phase Separation in Eukaryotic Directional Sensing

      • Andrea Gamba, Antonio de Candia, Stefano Di Talia, Antonio Coniglio, Federico Bussolino, Guido Serini

      Pages 23-32

   5. 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 et al.

      Pages 33-46

   6. In Vitro Tubulogenesis of Endothelial Cells: Analysis of a Bifurcation Process Controlled by a Mechanical Switch

      • Philippe Tracqui, Patrick Namy, Jacques Ohayon

      Pages 47-57

   7. Nonexponential Time Distributions in Biocatalytic Systems: Mass Service Replacing Mass Action

      • Peter W. Kühl, Manfred Jobmann

      Pages 59-67

3. Regulatory Networks

   1. Front Matter

      Pages 69-69

      PDF

   2. A Stochastic Model of Gene Regulation Using the Chemical Master Equation

      • Hilary S. Booth, Conrad J. Burden, Markus Hegland, Lucia Santoso

      Pages 71-81

   3. Piecewise-Linear Models of Genetic Regulatory Networks: Analysis of the Carbon Starvation Response in Escherichia coli

      • Delphine Ropers, Hidde de Jong, Jean-Luc Gouzé, Michel Page, Dominique Schneider, Johannes Geiselmann

      Pages 83-95

   4. Predicting Gene Expression from Combined Expression and Promoter Profile Similarity with Application to Missing Value Imputation

      • Laura L. Elo, Tuikkala Johannes, Olli S. Nevalainen, Tero Aittokallio

      Pages 97-104

   5. Chemical Organizations in the Central Sugar Metabolism of Escherichia coli

      • Florian Centler, Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich

      Pages 105-119

   6. Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science

      • Frank Noé, Jeremy C. Smith

      Pages 121-137

4. Development

   1. Front Matter

      Pages 139-139

      PDF

   2. Pigmentation Pattern Formation in Butterfly Wings: Global Patterns on Fore- and Hindwing

      • Toshio Sekimura, Anotida Madzvamuse, Philip K. Maini

      Pages 142-148

   3. Agent-Based Model for Developmental Pattern Formation with Multiscale Dynamics and Varying Cell Geometry

      • Scott Christley, Stuart A. Newman, Mark S. Alber

      Pages 149-161

   4. Bacterial Swarming Driven by Rod Shape

      • Jörn Starruß, Fernando Peruani, Markus Bär, Andreas Deutsch

      Pages 163-174

   5. Stability Properties of Some Tissue-Growth Models

      • John R. King, Susan J. Franks

      Pages 175-182

   6. A Modified Backward Euler Scheme for Advection-Reaction-Diffusion Systems

      • Anotida Madzvamuse

      Pages 183-189

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.

• Excel
• biochemistry
• biology
• biomedical applications
• biomedicine
• biophysics
• calculus
• cells
• data analysis
• developmental biology
• dynamics
• life sciences
• mathematical modeling
• model
• modeling

"[This book] has thirty-two papers that address topics in five broad areas: cellular biophysics, regulatory networks, development, biomedical applications and data analysis...A general theme is the progression in each application area from experimental research to mathematical modeling, from there to construction of a more abstract mathematical framework and thence to new biological hypotheses. Desirable tools are efficient algorithms for complex computations and visualization, especially in the areas of molecular biology and genetics...This is a volume directed at specialists, but it is possible to find one's way to interesting results without too much specialized knowledge. The range of applications is enormous, and this is just Volume 1. Topics addressed in Volume 2 include epidemiology, immunology, evolution and ecology."   —MAA Reviews

• Center for Information Services and High Performance Computing, Technische Universität Dresden, 01062 Dresden, Germany

  Andreas Deutsch, Lutz Brusch

• Centre for Mathematical Medicine School of Mathematical Sciences, University of Nottingham, Nottingham, U.K

  Helen Byrne

• Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Canada

  Gerda de Vries

• Institute of Theoretical Biology, Humboldt-Universität zu Berlin Invalidenstraße 43, 10115 Berlin, Germany

  Hanspeter Herzel

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