Computer Methods Part A

Name: Computer Methods Part A
Brand: Academic Press
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Academic Press

Published on 10. March 2009

488 pages

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978-0-08-092329-1 (ISBN)

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Front Cover
Computer Methods, Part A
Copyright Page
Contents
Contributors
Preface
Methods in Enzymology
Chapter 1: Phase Response Curves: Elucidating the Dynamics of Coupled Oscillators
1. Introduction
2. Estimation of Phase Response Curves
3. Specific Applications
4. Discussion
Appendix I
Appendix II
Acknowledgments
References
Chapter 2: Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways
1. Introduction
2. Biochemical Conventions and Calculations
3. Application to Physiological Systems
4. Discussion
Acknowledgment
References
Chapter 3: Analytical Methods for the Retrieval and Interpretation of Continuous Glucose Monitoring Data in Diabetes
1. Introduction
2. Decomposition of Sensor Errors
3. Measures of Average Glycemia and Deviation from Target
4. Risk and Variability Assessment
5. Measures and Plots of System Stability
6. Time-Series-Based Prediction of Future BG Values
7. Conclusions
Acknowledgments
References
Chapter 4: Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing
1. Introduction
2. Methodology
3. Job Submission
4. Results
5. Conclusions
Acknowledgments
References
Chapter 5: Discrete Stochastic Simulation Methods for Chemically Reacting Systems
1. Introduction
2. The Chemical Master Equation
3. The Stochastic Simulation Algorithm
4. The Tau-Leaping Method
5. Measurement of Simulation Error
6. Software and Two Numerical Experiments
7. Conclusion
Acknowledgments
References
Chapter 6: Analyses for Physiological and Behavioral Rhythmicity
1. Introduction
2. Types of Biological Data and their Acquisition
3. Analysis in the Time Domain
4. Analysis in the Frequency Domain
5. Time/Frequency Analysis and the Wavelet Transform
6. Signal Conditioning
7. Strength and Regularity of a Signal
8. Conclusions
References
Chapter 7: A Computational Approach for the Rational Design of Stable Proteins and Enzymes: Optimization of Surface Charge-Charge Interactions
1. Introduction
2. Computational Design of Surface Charge-Charge Interactions
3. Experimental Verification of Computational Predictions
4. Closing Remarks
Acknowledgments
References
Chapter 8: Efficient Computation of Confidence Intervals for Bayesian Model Predictions Based on Multidimensional Parameter Space
1. Introduction
2. Height of the Probability Density Function at the Boundary of the Smallest Multidimensional Confidence Region
3. Approximating a One-Dimensional Slice of the Probability Density Function by Means of Normal Curve Spline Pieces
4. Locating the Boundary of the Smallest Multidimensional Confidence Region
5. Finding the Minimum and Maximum of the Prediction Model over the Confidence Region
6. An Application: Bayesian Forecasting of Cognitive Performance Impairment during Sleep Deprivation
7. 95% Confidence Intervals for Bayesian Predictions of Cognitive Performance Impairment during Sleep Deprivation
8. Conclusion
Acknowledgments
Appendix Proof that the Boundary of the Confidence Region for a Multidimensional, Continuous PDF is a Level Contour
References
Chapter 9: Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pKa Calculations and Titration Curve Fitting
1. Introduction
2. Calculating the pH Dependence of Protein Characteristics
3. Setting up and Running a pKa Calculation
4. Analyzing the Results of a pKa Calculation
5. How Reliable are Calculated pKa Values?
6. Predicting pH Activity Profiles
7. Decomposition Analysis
8. Predicting Protein Stability Profiles
9. Fitting pH Titration Curves, pH Activity Profiles, and pH Stability Profiles
10. Conclusion
References
Chapter 10: Least Squares in Calibration: Weights, Nonlinearity, and Other Nuisances
1. Introduction
2. Review of Least Squares
3. Experiment Design Using Vprior - Numerical Illustrations
4. Conclusion
References
Chapter 11: Evaluation and Comparison of Computational Models
1. Introduction
2. Conceptual Overview of Model Evaluation and Comparison
3. Model Comparison Methods
4. Model Comparison at Work: Choosing between Protein Folding Models
5. Conclusions
Acknowledgments
References
Chapter 12: Desegregating Undergraduate Mathematics and Biology-Interdisciplinary Instruction with Emphasis on Ongoing Biomedical Research
1. Introduction
2. Course Description
3. Discussion
Acknowledgments
References
Chapter 13: Mathematical Algorithms for High-Resolution DNA Melting Analysis
1. Introduction
2. Extracting Melting Curves from Raw Fluorescence
3. Methods Used for Clustering and Classifying Melting Curves by Genotype
4. Methods Used for Modeling Melting Curves
References
Chapter 14: Biomathematical Modeling of Pulsatile Hormone Secretion: A Historical Perspective
1. Introduction
2. Early Attempts to Identify and Characterize Pulsatile Hormone Release
3. Impact of Sampling Protocol and Pulse Detection Algorithm on Hormone Pulse Detection
4. Application of Deconvolution Procedures for the Identification and Characterization of Hormone Secretory Bursts
5. Limitations and Subsequent Improvements in Deconvolution Procedures
6. Evaluation of Pulsatile and Basal Hormone Secretion Using a Stochastic Differential Equations Model
7. Characterization of Regulation of Signal and Response Elements: Estimation of Approximate Entropy
8. Evaluation of Coupled Systems
9. Evaluation of Hormonal Networks with Feedback Interactions
10. Future Directions
Acknowledgments
References
Chapter 15: Autodecon: a Robust Numerical Method for the Quantification of Pulsatile Events
1. Introduction
2. Methods
3. Results
4. Discussion
Acknowledgments
References
Chapter 16: Modeling Fatigue over Sleep Deprivation, Circadian Rhythm, and Caffeine with a Minimal Performance Inhibitor Model
1. Introduction
2. Methods
3. Results
4. Discussion
Acknowledgments
References
Author Index
Subject Index

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Computer Methods Part A

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