UID:
almafu_9958132943402883
Umfang:
1 online resource (701 p.)
Ausgabe:
1st ed.
ISBN:
9786612967382
,
9781282967380
,
128296738X
,
9780123812711
,
0123812712
Serie:
Methods in enzymology, v. 487
Inhalt:
The combination of faster, more advanced computers and more quantitatively oriented biomedical researchers has recently yielded new and more precise methods for the analysis of biomedical data. These better analyses have enhanced the conclusions that can be drawn from biomedical data, and they have changed the way that experiments are designed and performed. This volume, along with the 2 previous Computer Methods volumes for the Methods in Enzymology serial, aims to inform biomedical researchers about recent applications of modern data analysis and simulation methods as applie
Anmerkung:
Description based upon print version of record.
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Front Cover; Methods in Enzymology: Research on Nitrification and Related Processes, Part C; Copyright; Contents; Contributors; Preface; Methods in Enzymology; Chapter 1: Predicting Fluorescence Lifetimes and Spectra of Biopolymers; 1. Introduction; 2. Qualitative Concepts: Developing Intuition; 3. Methods; 4. Nonexponential Fluorescence Decay; 5. Final Remarks; Appendix: Ab Initio Computation of Electron Transfer Coupling Matrix Elements; Acknowledgments; References; Chapter 2: Modeling of Regulatory Networks...; 1. Introduction; 2. Developmental History of the Drosophila Circadian Clock
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3. Comparative Analysis of Three Network Regulatory Models4. The CWO Anomaly and a New Network Regulatory Rule; 5. Concluding Remarks; References; Chapter 3: Strategies for Articulated Multibody-Based Adaptive Coarse Grain Simulation of RNA; 1. Introduction; 2. Need for the Development of Adaptive Coarse-Graining Machinery; 3. Metrics to Guide Transitions in Adaptive Modeling; 4. Adaptive Modeling Framework in DCA Scheme; 5. Conclusions; Acknowledgments; References; Chapter 4: Modeling Loop Entropy; 1. Introduction; 2. Computing Bounds on the Entropy of the Unfolded Ensemble
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3. Approximating Entropy of the Loops in the Folded Ensemble4. Examples; 5. Conclusions; Acknowledgments; References; Chapter 5: Inferring Functional Relationships and Causal Network Structure from Gene Expression Profiles; 1. Introduction; 2. Methods; 3. Results; 4. Conclusions; References; Chapter 6: Numerical Solution of the Chemical Master Equation...; 1. Introduction; 2. The Chemical Master Equation; 3. Irreducible Chemical Reaction Systems; 4. Stability of the Chemical Master Equation Stationary Probability Distribution
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5. Two Different Algorithms to Calculate Stationary Probability Distributions for the Chemical Master Equation...6. Gene Expression with Negative Feedback Regulation; 7. Concluding Remarks; References; Chapter 7: How Molecular Should Your Molecular Model Be?...; 1. Introduction; 2. Michaelis-Menten Kinetics Revisited; 3. Use of the Hill Kinetics for Transcription Rate; 4. Repressilator; 5. Toggle Switch; 6. Discussion; 7. Conclusion; Acknowledgments; Appendix: The Gillespie Algorithm; References; Chapter 8: Computational Modeling of Biological Pathways by Executable Biology; 1. Introduction
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2. Executable Modeling Languages for Biology3. Intuitive Representation of Formal Models; 4. Case Studies; 5. Conclusions and Perspectives; Acknowledgments; References; Chapter 9: Computing Molecular Fluctuations in Biochemical Reaction Systems Based on a Mechanistic, Statistical Theory...; 1. Introduction; 2. Theoretical Developments; 3. Elementary Chemical Reactions; 4. An Example of Chemical Reaction; 5. Activation of Transcriptional Factors; 6. Binding and Unbinding TF to E-boxes; 7. Binding and Unbinding of Activated TF to E-Boxes; 8. Conclusions; Acknowledgments; References
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Chapter 10: Probing the Input-Output Behavior of Biochemical and Genetic Systems...
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English
Weitere Ausg.:
ISBN 9780123812704
Weitere Ausg.:
ISBN 0123812704
Sprache:
Englisch
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