Description
Springer Modelling And Simulation Exploring Dynamic System Behaviour by Louis G. Birta , Gilbert Arbez
This book provides a balanced and integrated presentation of modelling and simulation activity for both Discrete Event Dynamic Systems (DEDS) and Continuous Time Dynamic Systems (CYDS). The authors establish a clear distinction between the activity of modelling and that of simulation, maintaining this distinction throughout. The text offers a novel project-oriented approach for developing the modelling and simulation methodology, providing a solid basis for demonstrating the dependency of model structure and granularity on project goals. Comprehensive presentation of the verification and validation activities within the modelling and simulation context is also shown. PREFACE.- CHAPTER 1 BASIC PRINCIPLES OF NMR: Introduction.- Nuclear Spin in a Static Magnetic Field.- Rotating Frame.- Bloch Equations.- Fourier Transformation and its Applications in NMR.- Nyquist Theorem and Digital Filters.- Chemical Shift.- Nuclear Coupling.- Nuclear Overhauser Effect.- Relaxation.- Selection of Coherence Transfer Pathways.- Approaches to Understanding NMR Experiments.- Questions.- Appendix A: Product Operators.- Uncoupled Spins.- A2. Two Coupled Spins.- References.- CHAPTER 2 INSTRUMENTATION: System Overview.- Magnet.- Transmitter.- Receiver.- Probe.- Quarter-wavelength Cable.- Analog/Digital Converters.- Instrument specifications.- Test or Measurement Equipment.- Spectrum Analyzer.- System Noise Measurement.- Questions.- References.- CHAPTER 3 NMR SAMPLE PREPARATION: Introduction.- Expression Systems.- Overexpression of Isotope-Labeled Proteins.- Purification of Isotope-Labeled Proteins.- NMR Sample Preparation.- Examples of Protocols for Preparing 15N/13C Labeled Proteins.- Questions.- References.- CHAPTER 4 PRACTICAL ASPECTS: Tuning the Probe.- Shimming and Locking.- Instrument Calibrations.- Selective Excitation with Narrow Band and Off-Resonance Shape Pulses.- Composite Pulses.- Adiabatic Pulses.- Pulsed Field Gradients.- Solvent Suppression.- NMR Data Processing.- Two-Dimensional Experiments.- Questions.- References.- CHAPTER 5 MULTIDIMENSIONAL HETERONUCLEAR NMR EXPERIMENTS: Two-dimensional heteronuclear experiments.- Overview of Triple-Resonance Experiments.- General Procedure of Setup and Data Processing for 3D Experiments.- Experiments for Backbone Assignments.- Experiments for Side-Chain Assignment.- 3D Isotope-Edited Experiments.- Sequence-Specific Resonance Assignments of Proteins.- Assignment of NOE Cross-Peaks.- Questions.- References.- CHAPTER 6 STUDIES OF SMALL BIOLOGICAL MOLECULES: Ligand-protein Complexes.- Study of Metabolic Pathways by NMR.- Questions.- References.- CHAPTER 7 PROTEIN STRUCTURE DETERMINATION FROM NMR DATA: Introduction and Historical Overview.- NMR Structure Calculation Methods.- NMR Parameters for Structure Calculation.- Preliminary Secondary Structural Analysis.- Tertiary Structure Determination.- Protein Complexes.- Questions.- Appendix B1. Sa.inp-XPLOR Protocol for Protein Structure Calculation.- Appendix B2. Example of NOE Table.- Appendix B3. Example of Dihedral Angle Restraint Table.- Appendix B4. Example of Chemical Shift Table for TALOS.- Appendix B5. Example of Hydrogen Bond Table.- Appendix B6. Example of Input File to Generate a Random-Coil Coordinates.- Appendix B7. Example of Input File to Generate a Geometric PSF File.- References.- CHAPTER 8 PROTEIN DYNAMICS: Theory of Spin Relaxation in Proteins.- Experiments for Measurements of Relaxation Parameters.- Relaxation Data Analysis.- Questions.- References.- MULTIPLE-CHOICE QUESTIONS.- ANSWERS TO MULTIPLE CHOICE QUESTIONS.- NOMENCLATURE AND SYMBOLS.- INDEX.