| Contributors |
| Preface |
| Volumes in Series |
| Phase Response Curves: Elucidating the Dynamics of Coupled Oscillators / A. Granada ; R. M. Hennig ; B. Ronacher ; A. Kramer ; H. Herzel1： |
| Introduction |
| Estimation of Phase Response Curves / 2： |
| Specific Applications / 3： |
| Discussion / 4： |
| Acknowledgments / Appendix I： |
| References |
| Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways / Kalyan C. Vinnakota ; Fan Wu ; Martin J. Kushmerick ; Daniel A. Beard |
| Biochemical Conventions and Calculations |
| Application to Physiological Systems |
| Acknowledgment |
| Analytical Methods for the Retrieval and Interpretation of Continuous Glucose Monitoring Data in Diabetes / Boris Kovatchev ; Marc Breton ; William Clarke |
| Decomposition of Sensor Errors |
| Measures of Average Glycemia and Deviation from Target |
| Risk and Variability Assessment |
| Measures and Plots of System Stability / 5： |
| Time-Series-Based Prediction of Future BG Values / 6： |
| Conclusions / 7： |
| Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing / Borries Demeler ; Emre Brookes ; Luitgard Nagel-Steger |
| Methodology |
| Job Submission |
| Results |
| Discrete Stochastic Simulation Methods for Chemically Reacting Systems / Yang Cao ; David C. Samuels |
| The Chemical Master Equation |
| The Stochastic Simulation Algorithm |
| The Tau-Leaping Method |
| Measurement of Simulation Error |
| Software and Two Numerical Experiments |
| Conclusion |
| Analyses for Physiological and Behavioral Rhythmicity / Harold B. Dowse |
| Types of Biological Data and Their Acquisition |
| Analysis in the Time Domain |
| Analysis in the Frequency Domain |
| Time/Frequency Analysis and the Wavelet Transform |
| Signal Conditioning |
| Strength and Regularity of a Signal |
| A Computational Approach for the Rational Design of Stable Proteins and Enzymes: Optimization of Surface Charge-Charge Interactions / Katrina L. Schweiker ; George I. Makhatadze8： |
| Computational Design of Surface Charge-Charge Interactions |
| Experimental Verification of Computational Predictions |
| Closing Remarks |
| Efficient Computation of Confidence Intervals for Bayesian Model Predictions Based on Multidimensional Parameter Space / Amber D. Smith ; Alan Genz ; David M. Freiberger ; Gregory Belenky ; Hans P. A. Van Dongen |
| Height of the Probability Density Function at the Boundary of the Smallest Multidimensional Confidence Region |
| Approximating a One-Dimensional Slice of the Probability Density Function by Means of Normal Curve Spline Pieces |
| Locating the Boundary of the Smallest Multidimensional Confidence Region |
| Finding the Minimum and Maximum of the Prediction Model over the Confidence Region |
| An Application: Bayesian Forecasting of Cognitive Performance Impairment during Sleep Deprivation |
| 95% Confidence Intervals for Bayesian Predictions of Cognitive Performance Impairment during Sleep Deprivation |
| Appendix |
| Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pK<a/ Calculations and Titration Curve Fitting / Jens Erik Nielsen9： |
| Calculating the pH Dependence of Protein Characteristics |
| Setting up and Running a pKa/ Calculation |
| Analyzing the Results of a pKa/ Calculation |
| How Reliable Are Calculated pKa/ Values? |
| Predicting pH Activity Profiles |
| Decomposition Analysis |
| Predicting Protein Stability Profiles |
| Fitting pH Titration Curves, pH Activity Profiles, and pH Stability Profiles |
| Least Squares in Calibration: Weights, Nonlinearity, and Other Nuisances / Joel Tellinghuisen10： |
| Review of Least Squares |
| Experiment Design Using Vprior/-Numerical Illustrations |
| Evaluation and Comparison of Computational Models / Jay I. Myung ; Yun Tang ; Mark A. Pitt11： |
| Conceptual Overview of Model Evaluation and Comparison |
| Model Comparison Methods |
| Model Comparison at Work: Choosing between Protein Folding Models |
| Desegregating Undergraduate Mathematics and Biology - Interdisciplinary Instruction with Emphasis on Ongoing Biomedical Research / Raina Robeva12： |
| Course Description |
| Mathematical Algorithms for High-Resolution DNA Melting Analysis / Robert Palais ; Carl T. Wittwer13： |
| Extracting Melting Curves from Raw Fluorescence |
| Methods Used for Clustering and Classifying Melting Curves by Genotype |
| Methods Used for Modeling Melting Curves |
| Biomathematical Modeling of Pulsatile Hormone Secretion: A Historical Perspective / William S. Evans ; Leon S. Farhy ; Michael L. Johnson14： |
| Early Attempts to Identify and Characterize Pulsatile Hormone Release |
| Impact of Sampling Protocol and Pulse Detection Algorithm on Hormone Pulse Detection |
| Application of Deconvolution Procedures for the Identification and Characterization of Hormone Secretory Bursts |
| Limitations and Subsequent Improvements in Deconvolution Procedures |
| Evaluation of Pulsatile and Basal Hormone Secretion Using a Stochastic Differential Equations Model |
| Characterization of Regulation of Signal and Response Elements: Estimation of Approximate Entropy |
| Evaluation of Coupled Systems |
| Evaluation of Hormonal Networks with Feedback Interactions |
| Future Directions |
| AutoDecon: A Robust Numerical Method for the Quantification of Pulsatile Events / Lenore Pipes ; Paula P. Veldhuis ; Ralf Nass ; Michael O. Thorner15： |
| Methods |
| Modeling Fatigue over Sleep Deprivation, Circadian Rhythm, and Caffeine with a Minimal Performance Inhibitor Model / Patrick L. Benitez ; Gary H. Kamimori ; Thomas J. Balkin ; Alexander Greene16： |
| Author Index |
| Subject Index |
