Computational cell biology
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This text is an introduction to dynamical modeling in computational cell biology. The target audience is students of biology, neuroscience, or mathematics at the advanced undergraduate or beginning graduate level. There are 4 editors and 17 contributors, but the treatment is much more uniform than might be expected because the core of the book is a set of course notes written by one person, the late Joel Keizer. The book is divided into two major sections, an introductory course of 6 chapters covering the basic elements of compartmental modeling, and an additional section of 7 chapters covering divers advanced topics. Appendices contain details on mathematical and computational concepts. Topics discussed in the introductory course include voltage-gated ion currents, transporters and pumps, whole-cell calcium models, and intercellular communications. Advanced topics include diffusion in spatial modeling, modeling of calcium waves, biochemical oscillations, cell cycle controls, stochastic gating of ion channels, and molecular motors. The text was designed to be independent of any particular software, but it would be difficult to do many of the exercises without employing the recommended XPPAUT package. XPPAUT solves ordinary differential equations and plots their solutions. It also incorporates numerical bifurcation software and methods for solving stochastic equations. XPPAUT is distributed without charge. However a significant amount of computer sophistication is required to dowload and apply it.
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- Spatio-temporal modelling of the Hes1 and p53-Mdm2 intracellular signalling pathways
- The low conductance mitochondrial permeability transition pore confers excitability and CICR wave propagation in a computational model
- The influence of nuclear compartmentalisation on stochastic dynamics of self-repressing gene expression
- An alternative bifurcation analysis of the Rose--Hindmarsh model
- A distributed parameter identification problem in neuronal cable theory models
- Parameter estimation of ODE's via nonparametric estimators
- Robust master-slave synchronization of neuronal systems
- Entrained collective rhythms of multicellular systems: partial impulsive control strategy
- Discontinuity mappings for stochastic nonsmooth systems
- Into higher dimensions for nonsmooth dynamical systems
- Electrical propagation of condensed and diffuse ions along actin filaments
- Fluctuations in transcription factor binding can explain the graded and binary responses observed in inducible gene expression
- A regularization method for the parameter estimation problem in ordinary differential equations via discrete optimal control theory
- A modelling framework describing the enzyme regulation of membrane lipids underlying gradient perception in \textit{Dictyostelium} cells II: input-output analysis
- Sustained simultaneous glycolytic and insulin oscillations in \(\beta\)-cells
- An immersed boundary framework for modelling the growth of individual cells: an application to the early tumour development
- Analytical solution of linearized equations of the Morris-Lecar neuron model at large constant stimulation
- Dynamic optimization of metabolic networks coupled with gene expression
- Error analysis of a specialized numerical method for mathematical models from neuroscience
- Are buffers boring? Uniqueness and asymptotical stability of traveling wave fronts in the buffered bistable system
- Steady-state-preserving simulation of genetic regulatory systems
- Computing optimal properties of drugs using mathematical models of single channel dynamics
- Synchronized dynamics and non-equilibrium steady states in a stochastic yeast cell-cycle net\-work
- A modified Hodgkin-Huxley model
- Bioinformatics: organisms from Venus, technology from Jupiter, algorithms from Mars
- The regulation of gene expression in eukaryotes: bistability and oscillations in repressilator models
- Modelling the coupling between intracellular calcium release and the cell cycle during cortical brain development
- Amplified biochemical oscillations in cellular systems
- Hopf bifurcation analysis for models on genetic negative feedback loops
- Wiggly canards: growth of traveling wave trains through a family of fast-subsystem foci
- Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors
- Memristive model of the Barnacle giant muscle fibers
- Computing rates of Markov models of voltage-gated ion channels by inverting partial differential equations governing the probability density functions of the conducting and non-conducting states
- Probabilistic Description of Model Set Response in Neuromuscular Blockade
- The ghosts of departed quantities in switches and transitions
- On the mathematical basis of solid friction
- Kernel-based profile estimation for ordinary differential equations with partially measured state variables
- Differential Algebra and System Modeling in Cellular Biology
- Applying a Rigorous Quasi-Steady State Approximation Method for Proving the Absence of Oscillations in Models of Genetic Circuits
- Modeling secondary messenger pathways in neurovascular coupling
- A graph-based approach for the approximate solution of the chemical master equation
- Synapses and Neurons: Basic Properties and Their Use in Recognizing Environmental Signals
- Optimal control and additive perturbations help in estimating ill-posed and uncertain dynamical systems
- Microbial metabolism and growth under conditions of starvation modelled as the sliding mode of a differential inclusion
- An observer for mass-action chemical reaction networks
- On the coherent behavior of pancreatic beta cell clusters
- Mean field analysis of a spatial stochastic model of a gene regulatory network
- Tick, tock, circadian clocks
- Computational software
- Periods 1 + 2 imply chaos in steep or nonsmooth maps
- Novel phase-fitted symmetric splitting methods for chemical oscillators
- Motoneuron model of self-sustained firing after spinal cord injury
- A mathematical model for astrocytes mediated LTP at single hippocampal synapses
- Two-dimensional finite element model to study unsteady state \(\text{Ca}^{2+}\) diffusion in neuron involving ER LEAK and SERCA
- Hopf bifurcation in a gene regulatory network model: molecular movement causes oscillations
- Introduction to the geometric theory of ODEs with applications to chemical processes
- Third-order memristive Morris-Lecar model of barnacle muscle fiber
- Fractional time scale in calcium ion channels model
- BISTABILITY AND SELF-OSCILLATIONS IN CELL CYCLE CONTROL
- EXPLOITING OPTIMAL CONTROL FOR TARGET-ORIENTED MANIPULATION OF (BIO)CHEMICAL SYSTEMS: A MODEL-BASED APPROACH TO SPECIFIC MODIFICATION OF SELF-ORGANIZED DYNAMICS
- Efficient exponential methods for genetic regulatory systems
- Pacer cell response to periodic Zeitgebers
- Novel techniques in parameter estimation for fractional dynamical models arising from biological systems
- Role of coupling delay in oscillatory activity in autonomous networks of excitable neurons with dissipation
- A conservative and monotone mixed-hybridized finite element approximation of transport problems in heterogeneous domains
- Where do computational mathematics and computational statistics converge?
- A 3D-1D-0D multiscale model of the neuro-glial-vascular unit for synaptic and vascular dynamics in the dorsal vagal complex
- Ionic flux calculation by an extended Goldman-Hodgkin-Katz equation accounting for nonlinear ion channel electrostatics
- The immersed molecular finite element method
- Controlling nonlinear waves in excitable media
- An efficient method for simulation of noisy coupled multi-dimensional oscillators
- Disorder, oscillatory dynamics and state switching: the role of c-Myc
- Collective oscillations in coupled-cell systems
- Solving the chemical master equation for monomolecular reaction systems analytically
- A stochastic immersed boundary method for fluid-structure dynamics at microscopic length scales
- Partial equilibrium approximations in apoptosis. II: The death-inducing signaling complex subsystem
- A tracking approach to parameter estimation in linear ordinary differential equations
- On the dynamical behaviour of FitzHugh-Nagumo systems: revisited
- Inferring (biological) signal transduction networks via transitive reductions of directed graphs
- Perturbation approximation of solutions of a nonlinear inverse problem arising in olfaction experimentation
- Synapses as stochastic concurrent systems
- Error analysis of a stochastic immersed boundary method incorporating thermal fluctuations
- Approximations and their consequences for dynamic modelling of signal transduction pathways
- Computational cell biology: second theme issue on ``computational biology
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