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What is included with this book?
General introduction | p. 1 |
Goals | p. 1 |
Intracellular processes, cell states and cell fate: overview of the chapters | p. 2 |
On mathematical modelling of biological phenomena | p. 3 |
A brief note on the organization and use of the book | p. 5 |
References | p. 5 |
From molecules to a living cell | p. 6 |
Cell compartments and organelles | p. 6 |
The molecular machinery of gene expression | p. 9 |
Molecular pathways and networks | p. 12 |
The omics revolution | p. 15 |
References & further readings | p. 16 |
Mathematical and computational modelling tools | p. 18 |
Chemical kinetics | p. 18 |
Ordinary differential equations (ODEs) | p. 22 |
Theorems on uniqueness of solutions | p. 22 |
Vector fields, phase space, and trajectories | p. 23 |
Stability of steady states | p. 24 |
Phase portraits on the plane | p. 25 |
Bifurcations | p. 27 |
Bistability and hysteresis | p. 29 |
Hopf bifurcation | p. 30 |
Singular perturbations | p. 32 |
Partial differential equations (PDEs) | p. 33 |
Reaction-diffusion equations | p. 33 |
Cauchy problem | p. 34 |
Dirichlet, Neumann and third-boundary-value problems | p. 35 |
Well posed and ill posed problems | p. 36 |
Conservation laws | p. 37 |
Conservation of mass equation | p. 37 |
Method of characteristics | p. 38 |
Stochastic simulations | p. 40 |
Computer software platforms for cell modelling | p. 41 |
References | p. 42 |
Exercises | p. 42 |
Gene-regulatory networks: from DNA to metabolites and back | p. 44 |
Genome structure of Escherichia coli | p. 44 |
The Trp operon | p. 45 |
A model of the Trp operon | p. 47 |
Roles of the negative feedbacks in the Trp operon | p. 50 |
The lac operon | p. 52 |
Experimental evidence and modelling of bistable behavior of the lac operon | p. 54 |
A reduced model derived from the detailed lac operon network | p. 55 |
The challenge ahead: complexity of the global transcriptional network | p. 61 |
References | p. 62 |
Exercises | p. 63 |
Control of DNA replication in a prokaryote | p. 65 |
The cell cycle of E. coli | p. 65 |
Overlapping cell cycles: coordinating growth and DNA replication | p. 67 |
The oriC and the initiation of DNA replication | p. 67 |
The initiation-titration-activation model of replication initiation | p. 69 |
DnaA protein synthesis | p. 70 |
DnaA binding to boxes and initiation of replication | p. 71 |
Changing numbers of oriCs and dnaA boxes during chromosome replication | p. 73 |
Death and birth of oriCs | p. 74 |
Inactivation of dnaA-ATP | p. 74 |
Model dynamics | p. 74 |
Robustness of initiation control | p. 75 |
References | p. 77 |
Exercises | p. 78 |
The eukaryotic cell-cycle engine | p. 79 |
Physiology of the eukaryotic cell cycle | p. 79 |
The biochemistry of the cell-cycle engine | p. 80 |
Embryonic cell cycles | p. 82 |
Control of MPF activity in embryonic cell cycles | p. 85 |
Essential elements of the basic eukaryotic cell-cycle engine | p. 87 |
Summary | p. 93 |
References | p. 95 |
Exercises | p. 95 |
Cell-cycle control | p. 96 |
Cell-cycle checkpoints | p. 96 |
The restriction point | p. 97 |
Modelling the restriction point | p. 98 |
The G1-S regulatory network | p. 98 |
A switching module | p. 100 |
The G2 DNA damage checkpoint | p. 101 |
The mitotic spindle checkpoint | p. 104 |
References | p. 106 |
Exercises | p. 107 |
Cell death | p. 108 |
Background on the biology of apoptosis | p. 108 |
Intrinsic and extrinsic caspase pathways | p. 109 |
A bistable model for caspase-3 activation | p. 111 |
DISC formation and caspase-8 activation | p. 115 |
Combined intrinsic and extrinsic apoptosis pathways | p. 120 |
Summary and future modelling | p. 122 |
References | p. 124 |
Exercises | p. 124 |
Cell differentiation | p. 125 |
Cell differentiation in the hematopoietic system | p. 126 |
Modelling the differentiation of Th lymphocytes | p. 127 |
Cytokine memory in single cells | p. 130 |
Population of differentiating Th lymphocytes | p. 131 |
Equation for population density [Phi] | p. 131 |
Determining the population density [Phi] | p. 133 |
High-dimensional switches in cellular differentiation | p. 134 |
Summary | p. 136 |
References | p. 137 |
Exercises | p. 137 |
Cell aging and renewal | p. 139 |
Cellular senescence and telomeres | p. 139 |
Models of tissue aging and maintenance | p. 140 |
The probabilistic model of Op den Buijs et al. | p. 140 |
A continuum model | p. 142 |
Asymmetric stem-cell division | p. 145 |
Maintaining the stem-cell reservoir | p. 148 |
The Roeder-Loeffler model | p. 148 |
A deterministic model | p. 151 |
References | p. 153 |
Exercises | p. 153 |
Multiscale modelling of cancer | p. 155 |
Attributes of cancer | p. 155 |
A multiscale model of avascular tumor growth | p. 156 |
Cellular scale | p. 157 |
Extracellular scale | p. 158 |
Subcellular scale | p. 159 |
A multiscale model of colorectal cancer | p. 160 |
Gene level: a Boolean network | p. 161 |
Cell level: a discrete cell-cycle model | p. 163 |
Tissue level: colonies of cells and oxygen supply | p. 164 |
Continuum models of solid tumor growth | p. 167 |
Three types of cells | p. 167 |
One type of cells | p. 172 |
References | p. 174 |
Exercises | p. 174 |
Glossary | p. 176 |
Index | p. 181 |
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The Used, Rental and eBook copies of this book are not guaranteed to include any supplemental materials. Typically, only the book itself is included. This is true even if the title states it includes any access cards, study guides, lab manuals, CDs, etc.