Title Modeling cellular systems / Frederik Graw, Franziska Matthäus, Jürgen Pahle, editors

Published Cham : Springer, 2017

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Description 1 online resource Series Contributions in mathematical and computational sciences ; volume 11 Contributions in mathematical and computational sciences ; v. 11. Contents Preface; Organisation; Programme Chairs; Contents; 1 Spatiotemporal Modeling of Membrane Receptors; 1 Introduction; 1.1 Background: Chemical Reaction Networks, ODE Simulations; 2 Reactions (Stochastic); 2.1 Dealing with the Molecular Nature of Chemical Reactions; 2.2 Stochastic Simulation Algorithm; 3 Diffusion; 3.1 Diffusion Basics; 3.2 Brownian or Not Brownian?; 3.3 Brownian Motion Based Simulations; 3.4 Anomalous Diffusion/Barriers to Movement; 4 Reaction -- Diffusion Systems; 4.1 First-Order Reactions and Diffusion; 4.2 Second-Order Reactions 4.3 Smoluchowski Model -- Binding Radius Approach to Bimolecular Reactions5 Conclusion; References; 2 Distribution Approximations for the Chemical Master Equation: Comparison of the Method of Moments and the System Size Expansion; 1 Introduction; 2 Stochastic Chemical Kinetics; 3 Method of Moments; 3.1 Equations for Conditional Moments; 3.2 Maximum Entropy Distribution Reconstruction; 4 System Size Expansion of the Probability Distribution; 5 Results; 5.1 Example 1: Bursty Protein Production; 5.2 Example 2: Cooperative Self-Activation of Gene Expression; 5.3 Comparison of Numerical Results 6 DiscussionReferences; 3 Sampling from T Cell Receptor Repertoires; 1 Introduction; 1.1 Sampling from a Repertoire; 2 Results; 2.1 The Mean Number of Repeats; 2.2 Number of Draws to Find the First Repeat; 2.3 Poisson Distribution of Number of Repeats in a Sample; 2.4 Estimating the Size of the Repertoire from One Repeat; 2.5 The Observed Distribution of Clonal Sizes; 2.6 Expansion of a Fraction of the Repertoire; 3 Discussion; References; 4 IL-2 Stimulation of Regulatory T Cells: A Stochastic and Algorithmic Approach; 1 Introduction; 2 Stochastic Model; 3 Stochastic Descriptors 3.1 Time to Reach a Threshold Number of Bound Complexes on the Cell Surface3.2 Number of Receptors Synthesised During the Time to Reach a Threshold Number of Bound Complexes on the Cell Surface; 4 Numerical Results; 5 Discussion; References; 5 Understanding the Role of Mitochondria Distribution in Calcium Dynamics and Secretion in Bovine Chromaffin Cells; 1 Introduction; 2 Experimental Results; 2.1 Experimental Materials and Methods; 2.2 Mitochondria Distribution in Bovine Chromaffin Cells in Culture; 3 Theoretical Model 3.1 Modeling Mitochondria as Obstacles for Diffusion of Calcium IonsReferences; 6 Dynamical Features of the MAP Kinase Cascade; 1 Introduction; 2 The Simple Futile Cycle; 3 The Dual Futile Cycle; 4 The MAPK Cascade; 5 Embedding the Cascade in Feedback Loops; 6 Alternative Phosphorylation Mechanisms; 7 Summary and Outlook; References; 7 Numerical Treatment of the Filament-Based Lamellipodium Model (FBLM); 1 Introduction; 2 Mathematical Modeling; 3 Numerical Method; 3.1 Reparametrization; 3.2 The Finite Element Formulation; 3.3 Time Discretization -- Implementation Issues Summary This contributed volume comprises research articles and reviews on topics connected to the mathematical modeling of cellular systems. These contributions cover signaling pathways, stochastic effects, cell motility and mechanics, pattern formation processes, as well as multi-scale approaches. All authors attended the workshop on "Modeling Cellular Systems" which took place in Heidelberg in October 2014. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students Notes Includes author index Bibliography Includes bibliographical references and author index Notes Print version record Subject Cells -- Mathematical models TECHNOLOGY & ENGINEERING -- Engineering (General) TECHNOLOGY & ENGINEERING -- Reference. Biomathematics Biomedical engineering Engineering Neural networks (Computer science) Systems biology Form Electronic book Author Graw, Frederik Matthäus, Franziska Pahle, Jürgen ISBN 9783319458335 3319458337

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