Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology

Part I: Stochastic Chemical Reactions.- Test Models for Statistical Inference: Two-Dimensional Reaction Systems Displaying Limit Cycle Bifurcations and Bistability.- Importance Sampling for Metastable and Multiscale Dynamical Systems.- Multiscale Simulation of Stochastic Reaction-diffusion Networks.- Part II: Stochastic Numerical Approaches, Algorithms and Coarse-Grained Simulations.- Numerical Methods for Ergodic SDEs: When Stochastic Integration Meets Geometric Integration.- Stability and Strong Convergence for Spatial Stochastic Kinetics.- The T cells in an Ageing Virtual Mouse.- Part III: Analysis of Stochastic Dynamical Systems for Modeling Cell Biology.- Model reduction for Stochastic Reaction Systems.- ZI-closure Scheme: A Method to Solve and Study Stochastic Reaction Networks.- Deterministic and Stochastic Becker-Döring Equations: Past and Recent Mathematical Developments.- Coagulation-Fragmentation with a Finite Number of Particles: Models, Stochastic Analysis and Applications to Telomere Clustering and Viral Capsid Assembly.- A Review of Stochastic and Delay Simulation Approaches in both Time and Space in Computational Cell Biology.- Part IV: Diffusion Processes and Stochastic Modeling.- Recent Mathematical Models of Axonal Transport.- Stochastic Models for Evolving Cellular Populations of Mitochondria: Disease, Development, and Ageing.- Modeling and Stochastic Analysis of the Single Photon Response.- A Phenomenological Spatial Model for Macro-ecological Patterns in Species-rich Ecosystems.