## Chemical Biophysics: Quantitative Analysis of Cellular SystemsChemical Biophysics provides an engineering-based approach to biochemical system analysis for graduate-level courses on systems biology, computational bioengineering and molecular biophysics. It is the first textbook to apply rigorous physical chemistry principles to mathematical and computational modeling of biochemical systems for an interdisciplinary audience. The book is structured to show the student the basic biophysical concepts before applying this theory to computational modeling and analysis, building up to advanced topics and research. Topics explored include the kinetics of nonequilibrium open biological systems, enzyme mediated reactions, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems. End-of-chapter exercises range from confidence-building calculations to computational simulation projects. |

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### Contents

Concepts from physical chemistry | 7 |

Conventions and calculations for biochemical systems | 24 |

Chemical kinetics and transport processes | 41 |

Enzymecatalyzed reactions | 69 |

Biochemical signaling modules | 105 |

Biochemical reaction networks | 128 |

Coupled biochemical systems and membrane transport | 162 |

Spatially distributed systems and reactiondiffusion modeling | 195 |

Constraintbased analysis of biochemical systems | 220 |

Biomacromolecular structure and molecular association | 240 |

Stochastic biochemical systems and the chemical master equation | 261 |

reaction networks | 267 |

the statistical basis of thermodynamics | 282 |

### Other editions - View all

Chemical Biophysics: Quantitative Analysis of Cellular Systems Daniel A. Beard,Hong Qian No preview available - 2008 |

Chemical Biophysics: Quantitative Analysis of Cellular Systems Daniel A. Beard,Hong Qian No preview available - 2010 |

### Common terms and phrases

ACCOA ADP3 analysis apparent equilibrium constant associated assumed ATP4 binding biochemical reactants biochemical reaction biochemical systems Boltzmann capillary catalyzed cell cellular Chapter chemical kinetics chemical reaction citrate synthase coefﬁcient complex computed constraints corresponding deﬁned deﬁnition dehydrogenase denote differential equations diffusion entropy enzyme kinetics equilibrium constant example ﬁeld ﬁgure ﬁrst ﬁxed ﬂow ﬂux ﬂux expression Gibbs free energy given glucose illustrated in Figure ionic kinase mass master equation mathematical matrix mechanism membrane potential metabolic Mg2+ Michaelis–Menten microstates molecular molecules myoglobin NADH NVT system obtained oxygen parameter values phosphatase phosphorylation plotted predicted protein proton rate constants reactants reaction ﬂuxes reaction system reference reaction represents Section signiﬁcant simulation solution species speciﬁc steady stochastic stoichiometric substrate systems biology TCA cycle temperature theory thermodynamic tissue transition transport variables vector zero

### Popular passages

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Page 304 - Teusink, B., Passarge, J., Reijenga, CA, Esgalhado, E., van der Weijden, CC, Schepper, M., Walsh, MC, Bakker, BM, van Dam, K., Westerhoff, HV and Snoep, JL (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes?

Page 305 - Lidstrom. 2002. Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AMI, with application to reconstruction of Ci and C4 metabolism.

Page 304 - Analysis of optimality in natural and perturbed metabolic networks, Proc. Natl. Acad. Sci.

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