MODELS OF CELLULAR REGULATION
CONTENTS GENERAL INTRODUCTION GOALS INTRACELLULAR PROCESSES, CELL STATES AND CELL FATE: OVERVIEW OF THE CHAPTERS ON MATHEMATICAL MODELLING OF BIOLOGICAL PHENOMENA A BRIEF NOTE ON THE ORGANIZATION AND USE OF THE BOOK REFERENCES FROM MOLECULES TO A LIVING CELL CELL COMPARTMENTS AND ORGANELLES THE MOLECULAR MACHINERY OF GENE EXPRESSION MOLECULAR PATHWAYS AND NETWORKS THE OMICS REVOLUTION REFERENCES & FURTHER READINGS MATHEMATICAL AND COMPUTATIONAL MODELLING TOOLS CHEMICAL KINETICS ORDINARY DI?ERENTIAL EQUATIONS (ODES) THEOREMS ON UNIQUENESS OF SOLUTIONS VECTOR ?ELDS, PHASE SPACE, AND TRAJECTORIES STABILITY OF STEADY STATES PHASE PORTRAITS ON THE PLANE BIFURCATIONS BISTABILITY AND HYSTERESIS HOPF BIFURCATION SINGULAR PERTURBATIONS PARTIAL DI?ERENTIAL EQUATIONS (PDES) REACTION-DI?USION EQUATIONS CAUCHY PROBLEM DIRICHLET, NEUMANN AND THIRD-BOUNDARY-VALUE PROBLEMS WELL POSED AND ILL POSED PROBLEMS CONSERVATION LAWS CONSERVATION OF MASS EQUATION METHOD OF CHARACTERISTICS STOCHASTIC SIMULATIONS COMPUTER SOFTWARE PLATFORMS FOR CELL MODELLING CONTENTS REFERENCES EXERCISES GENE-REGULATORY NETWORKS: FROM DNA TO METABOLITES AND BACK GENOME STRUCTURE OF ESCHERICHIA COLI THE TRP OPERON A MODEL OF THE TRP OPERON ROLES OF THE NEGATIVE FEEDBACKS IN THE TRP OPERON THE LAC OPERON EXPERIMENTAL EVIDENCE AND MODELLING OF BISTABLE BEHAVIOR OF THE LAC OPERON A REDUCED MODEL DERIVED FROM THE DETAILED LAC OPERON NETWORK THE CHALLENGE AHEAD: COMPLEXITY OF THE GLOBAL TRANSCRIPTIONAL NETWORK CONTROL OF DNA REPLICATION IN A PROKARYOTE THE CELL CYCLE OF E COLI OVERLAPPING CELL CYCLES: COORDINATING GROWTH AND DNA REPLICATION THE ORIC AND THE INITIATION OF DNA REPLICATION THE INITIATION-TITRATION-ACTIVATION MODEL OF REPLICATION INITIATION DNAA PROTEIN SYNTHESIS DNAA BINDING TO BOXES AND INITIATION OF REPLICATION CHANGING NUMBERS OF ORICS AND DNAA BOXES DURING CHROMOSOME REPLICATION DEATH AND BIRTH OF ORICS INACTIVATION OF DNAA-ATP MODEL DYNAMICS ROBUSTNESS OF INITIATION CONTROL THE EUKARYOTIC CELL-CYCLE ENGINE PHYSIOLOGY OF THE EUKARYOTIC CELL CYCLE THE BIOCHEMISTRY OF THE CELL-CYCLE ENGINE EMBRYONIC CELL CYCLES CONTROL OF MPF ACTIVITY IN EMBRYONIC CELL CYCLES ESSENTIAL ELEMENTS OF THE BASIC EUKARYOTIC CELL-CYCLE ENGINE SUMMARY CELL-CYCLE CONTROL CELL-CYCLE CHECKPOINTS THE RESTRICTION POINT MODELLING THE RESTRICTION POINT THE G1–S REGULATORY NETWORK A SWITCHING MODULE THE G2 DNA DAMAGE CHECKPOINT THE MITOTIC SPINDLE CHECKPOINT CELL DEATH BACKGROUND ON THE BIOLOGY OF APOPTOSIS INTRINSIC AND EXTRINSIC CASPASE PATHWAYS A BISTABLE MODEL FOR CASPASE-3 ACTIVATION DISC FORMATION AND CASPASE-8 ACTIVATION COMBINED INTRINSIC AND EXTRINSIC APOPTOSIS PATHWAYS SUMMARY AND FUTURE MODELLING CELL DI?ERENTIATION CELL DI?ERENTIATION IN THE HEMATOPOIETIC SYSTEM MODELLING THE DI?ERENTIATION OF TH LYMPHOCYTES CYTOKINE MEMORY IN SINGLE CELLS POPULATION OF DI?ERENTIATING TH LYMPHOCYTES EQUATION FOR POPULATION DENSITY ? DETERMINING THE POPULATION DENSITY ? HIGH-DIMENSIONAL SWITCHES IN CELLULAR DI?ERENTIATION CELL AGING AND RENEWAL CELLULAR SENESCENCE AND TELOMERES MODELS OF TISSUE AGING AND MAINTENANCE THE PROBABILISTIC MODEL OF OP DEN BUIJS ET AL A CONTINUUM MODEL ASYMMETRIC STEM-CELL DIVISION MAINTAINING THE STEM-CELL RESERVOIR THE ROEDER–LOE?ER MODEL A DETERMINISTIC MODEL MULTISCALE MODELLING OF CANCER ATTRIBUTES OF CANCER A MULTISCALE MODEL OF AVASCULAR TUMOR GROWTH CELLULAR SCALE EXTRACELLULAR SCALE SUBCELLULAR SCALE A MULTISCALE MODEL OF COLORECTAL CANCER GENE LEVEL: A BOOLEAN NETWORK CELL LEVEL: A DISCRETE CELL-CYCLE MODEL TISSUE LEVEL: COLONIES OF CELLS AND OXYGEN SUPPLY CONTINUUM MODELS OF SOLID TUMOR GROWTH THREE TYPES OF CELLS ONE TYPE OF CELLS