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1.

電子ブック
ＥＢ
1. Numerical Computer Methods, Part C
Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2000
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2.

電子ブック
ＥＢ
2. Numerical Computer Methods, Part D
Ludwig; Johnson, Michael L. Brand, Ludwig Brand, Michael L. Johnson, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Burlington : Academic Press, 2004
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3.

電子ブック
ＥＢ
3. Numerical Computer Methods, Part E
Michael L.; Brand, Ludwig Johnson, Ludwig Brand, Michael L. Johnson, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Burlington : Academic Press, 2004
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Use of Least-Squares Techniques in Biochemistry / M.L. Johnson
Parameter Estimates from Nonlinear Models / D.G. Watts
Effects of Heteroscedasticity and Skewness on Prediction in Regression: Modeling Growth of the Human Heart / R.D. Abbott ; H.P. Gutgesell
Artifacts of Fourier Series Analysis / M. Lampl
Quantification of Evolution from Order to Randomness in Practical Time Series Analysis / S.M. Pincus
Sequential versus Simultaneous Analysis of Data: Differences in Reliability of Derived Quantitative Conclusions / M. Straume
Model-Independent Quantification of Measurement Error: Empirical Estimation of Discrete Variance Function Profiles Based on Standard Curves / J.D. Veldhuis
Impact of Variance Function Estimation in Regression and Calibration / L.-J. Hwang
Application of the Kalman Filter to Computational Problems in Statistics / E.N. Brown and ; C.H. Schmid
Modeling Chemical Reactions: Jacobian Paradigm and Related Issues / R.I. Shrager
The Mathematics of Biological Oscillators / G.B. Ermentrout
Diffusion-Modulated Energy Transfer and Quenching: Analysis by Numerical Integration of Diffusion Equation in Laplace Space / J. Kasba ; J.R. Lakowicz
Maximum Entropy Method of Data Analysis in Time-Resolved Spectroscopy / J.-C. Brochon
Analysis of Kinetic Data: Practical Applications of Computer Simulation and Fitting Programs / C. Frieden
Determination of Rate and Equilibrium Binding Constants for Macromolecular Interactions by Surface Plasmon Resonance / D.J. OShannessy ; M. Brigham-Burke ; K.K. Soneson ; P. Hensley ; I. Brooks
Analysis of Nonequilibrium Dynamics of Bound, Free, and Total Plasma Ligand Concentrations over Time Following Nonlinear Secretory Inputs: Kinetics of Two or More Hormones Pulsed into Compartments Containing Multiple Variable-Affinity Binding Proteins / L.M. Faunt
Testing Pulse Detection Algorithms with Simulations of Episodically Pulsatile Substrate, Metabolite, or Hormone Release
Error Analysis of Macromolecular Structures Determined with Nuclear MagneticResonance Data / J.W. Shriver ; S. Edmondson
Characterization of Enzyme-Complex Formation by Analysis of Nuclear Magnetic Resonance Line Shapes / C.B. Post
Computer Simulations of Nuclear Overhauser Effect Spectra of Complex Oligosaccharides / C.A. Bush
Determining Confidence Intervals for Parameters Derived from Analysis of Equilibrium Analytical Ultracentrifugation Data / D.G.Watts
Boundary Analysis in Sedimentation Velocity Experiments / W.F. Stafford, III
Statistical Thermodynamic Analysis of Differential Scanning Calorimetry Data: Structural Deconvolution of Heat Capacity Function of Proteins / E. Freire
Analysis of Two-Dimensional Differential Scanning Calorimetry Data: Elucidation of Complex Biomolecular Energetics
Monte Carlo Simulations of Membranes: Phase Transition of Small Unilamellar Dipalmitoylphosphatidylcholine Vesicles / I.P. Sugar ; R.L. Biltonen ; N. Mitchard
Analysis of Drug-DNA Binding Isotherms: A Monte Carlo Approach / J.J. Correia ; J.B. Chaires
Analysis of Multidimensional Spectroscopic Data to Monitor Unfolding of Proteins / G.D. Ramsay ; M.R. Eftink
Estimating Binding Constants for Site-Specific Interactions / B. Garcia-Moreno
Use of Least-Squares Techniques in Biochemistry / M.L. Johnson
Parameter Estimates from Nonlinear Models / D.G. Watts
Effects of Heteroscedasticity and Skewness on Prediction in Regression: Modeling Growth of the Human Heart / R.D. Abbott ; H.P. Gutgesell
4.

電子ブック
ＥＢ
4. Computer Methods Part A
Ludwig; Johnson, Michael L.; Brand, Ludwig Brand, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2009
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目次情報: 続きを見る
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
Contributors
Preface
Volumes in Series
5.

電子ブック
ＥＢ
5. Fluorescence Spectroscopy
Michael L; Brand, Ludwig; Johnson, Michael L. Johnson, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2008
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Contributors
Preface
Volumes in Series
A Method in Enzymology for Measuring Hydrolytic Activities in Live Cell Environments / Beverly Z. Packard ; Akira Komoriya1：
Protease Substrate Design
Protease Specificity / 2：
Cell-Permeable Fluorogenic Probes / 3：
Conclusions / 4：
References
Heterogeneity of Fluorescence Determined by the Method of Area-Normalized Time-Resolved Emission Spectroscopy / N. Periasamy
Introduction
TRES and TRANES Methods
TRES and TRANES Spectra of Simple Cases
Physical Significance of TRANES and Isoemissive Point
TRES and TRANES of Fluorophores in Microheterogeneous Media / 5：
Fluorescence in Microheterogeneous and Biological Media: Special Cases / 6：
Acknowledgment
Multiparametric Probing of Microenvironment with Solvatochromic Fluorescent Dyes / Andrey S. Klymchenko ; Alexander P. Demchenko
"Universal" and "Specific" Noncovalent Interactions
The Methodology of Multiparametric Approach with Application of 3-Hydroxyflavone Dyes
Correlations of Spectroscopic Data with Solvatochromic Variables
Algorithm for Multiparametric Probing Based on Parameters of Absorption and Dual Emission
Application of Multiparametric Probing
Limitations of the Multiparametric Approach
Concluding Remarks / 7：
Site-Selective Red-Edge Effects
Molecular Disorder and the Origin of Red-Edge Effects
The Principle of Photoselection
Ground-State Heterogeneity
The Magnitude of Red-Edge Excitation Fluorescence Shift and Its Connection with Dielectric Relaxations
Red-Edge Effect with High Resolution in Time
Red-Edge Effects in Excited-State Reactions
Fluorescent Probes for Optimal Observation of Red-Edge Effects / 8：
Peculiarities of the Red-Edge Effects of Indole and Tryptophan / 9：
Fluorescence Approaches to Quantifying Biomolecular Interactions / Catherine A. Royer ; Suzanne F. Scarlata10：
Fluorescence Observables
Designing a Fluorescence Experiment
Forster Resonance Energy Transfer Measurements of Transmembrane Helix Dimerization Energetics / Mikhail Merzlyakov ; Kalina Hristova
Challenges in Quantitative Measurements of Interactions Between TM Helices in Bilayers
Bilayer Platforms for Measuring TM Helix Interactions Using FRET
FRET Due to Random Colocalization of Donors and Acceptors (Proximity FRET)
FRET Efficiencies and Energetics of TM Helix Dimerization
Biological Insights from FRET Measurements
Conclusion
Application of Single-Molecule Spectroscopy in Studying Enzyme Kinetics and Mechanism / Jue Shi ; Joseph Dertouzos ; Ari Gafni ; Duncan Steel
Experimental Considerations
Sample Preparation
Instrumentation
Data Analysis of Single-Molecule Trajectories
Additional Considerations
Summary
Ultrafast Fluorescence Spectroscopy via Upconversion: Applications to Biophysics / Jianhua Xu ; Jay R. Knutson
Basic Concepts
Upconversion Spectrophotofluorometer and Experimental Considerations
Ultrafast Photophysics of Single Tryptophan, Peptides, Proteins, and Nucleic Acids
Summary and Future Directions
Use of Fluorescence Resonance Energy Transfer (FRET) in Studying Protein-induced DNA Bending / Anatoly I. Dragan ; Peter L. Privalov
Preparation of Labeled DNA Duplexes
Fluorescence Resonance Energy Transfer
FRET in Studying Large Protein-Induced DNA Bends
Dependence of the Protein-induced DNA Bend on the Forces Involved in Binding
FREt in Studying Small Protein-Induced DNA Bends
Fluorescent Pteridine Probes for Nucleic Acid Analysis / Mary E. Hawkins
Pteridine Analog Characteristics
Procedures for Oligonucleotide Synthesis with Pteridine Analogs
Characterization of Pteridine-Containing Sequences
Applications
Acknowledgments
Single-Molecule Fluorescence Methods for the Analysis of RNA Folding and Ribonucleoprotein Assembly / Goran Pljevaljcic ; David P. Millar11：
Labeling Methods
Single-Molecule Fluorescence Detection Methods
Diffusion Single-Pair FRET for RNA Based Systems
Total Internal Reflection Fluorescence (TIRF) for RNA Based Systems
Application 1: Folding of the Hairpin Ribozyme
Application 2: Assembly of the Rev-RRE Complex
Using Fluorophore-Labeled Oligonucleotides to Measure Affinities of Protein-DNA Interactions / Brian J. Anderson ; Chris Larkin ; Kip Guja ; Joel F. Schildbach12：
Definitions of Fluorescence Anisotropy and Intensity
Advantages of Fluorescence Measurements
Disadvantages of Fluorescence Measurements
Designing the Oligonucleotide
Designing the Experiment
Competition Assays for Determining Specificity
Identifying Small Pulsatile Signals within Noisy Data: A Fluorescence Application / Michael L. Johnson ; Leon S. Farhy ; Paula P. Veldhuis ; Joseph R. Lakowicz13：
Methods
Results
Discussion
Determination of Zinc Using Carbonic Anhydrase-Based Fluorescence Biosensors / Rebecca Bozym ; Tamiika K. Hurst ; Nissa Westerberg ; Andrea Stoddard ; Carol A. Fierke ; Christopher J. Frederickson ; Richard B. Thompson14：
Principles of CA-Based Zinc Sensing
Transducing Zinc Binding as a Fluorescence Change
"Free" Versus Bound Zinc Ion: Speciation
Metal Ion Buffers
Kinetics
Applications: Ratiometric Determination of Free Zinc in Solution
Preparation of Apocarbonic Anhydrase
Intracellular Sensing with TAT Tag
Intracellular Sensing with an Expressible CA Sensor
Instrumentation for Fluorescence-Based Fiber Optic Biosensors / Hui-Hui Zeng ; Daniel Ohnemus ; Bryan McCranor ; Michele Cramer ; James Moffett15：
Introduction and Rationale for Fluorescence-Based Fiber Optic Sensors
Basic Principles of Fiber Optics for Fluorescence Sensors
Optics and Mechanics of Fluorescence-Based Fiber Optic Sensors
Mounting and Alignment of the Instrument
Standards for Ratiometric and Lifetime-Based Fiber Optic Fluorescence Sensors
Construction of Fiber Optic Probes
Zn[superscript 2+] Probe
Cu[superscript 2+] Probe
Use of Fiber Optic Probes for Discrete Samples
Operating Issues: Noise, Background, Thermal Drift, and Mode Hopping
Field and Shipboard Use
Author Index
Subject Index
Contributors
Preface
Volumes in Series
6.

電子ブック
ＥＢ
6. Computer Methods Part B
Michael L. John, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2009
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Contributors
Preface
Volumes in Series
Correlation Analysis: A Tool for Comparing Relaxation-Type Models to Experimental Data / Maurizio Tomaiuolo ; Joel Tabak ; Richard Bertram1：
Introduction
Scatter Plots and Correlation Analysis / 2：
Example 1: Relaxation Oscillations / 3：
Example 2: Square Wave Bursting / 4：
Example 3: Elliptic Bursting / 5：
Example 4: Using Correlation Analysis on Experimental Data / 6：
Summary / 7：
Acknowledgments
References
Trait Variability of Cancer Cells Quantified by High-Content Automated Microscopy of Single Cells / Vito Quaranta ; Darren R. Tyson ; Shawn P. Garbett ; Brandy Weidow ; Mark P. Harris ; Walter Georgescu
Background
Experimental and Computational Workflow
Application to Traits Relevant to Cancer Progression
Conclusions
Matrix Factorization for Recovery of Biological Processes from Microarray Data / Andrew V. Kossenkov ; Michael F. Ochs
Overview of Methods
Application to the Rosetta Compendium
Results of Analyses
Discussion
Modeling and Simulation of the Immune System as a Self-Regulating Network / Peter S. Kim ; Doron Levy ; Peter P. Lee
Mathematical Modeling of the Immune Network
Two Examples of Models to Understand T Cell Regulation
How to Implement Mathematical Models in Computer Simulations
Concluding Remarks
Acknowledgmentss
Entropy Demystified: The ôThermoö-dynamics of Stochastically Fluctuating Systems / Hong Qian
Energy
Entropy and ôThermoö-dynamics of Markov Processes
A Three-State Two-Cycle Motor Protein
Phosphorylation-Dephosphorylation Cycle1 Kinetics
Summary and Challenges
Effect of Kinetics on Sedimentation Velocity Profiles and the Role of Intermediates / John J. Correia ; P. Holland Alday ; Peter Sherwood ; Walter F. Stafford
Methods
ABCD Systems
Monomer-Tetramer Model
Algebraic Models of Biochemical Networks / Reinhard Laubenbacher ; Abdul Salam Jarrah
Computational Systems Biology
Network Inference
Reverse-Engineering of Discrete Models: An Example
High-Through put Computing in the Sciences / Mark Morgan ; Andrew Grimshaw8：
What is an HTC Application?
HTC Technologies
High-Throughput Computing Examples
Advanced Topics
Large Scale Transcriptome Data Integration Across Multiple Tissues to Decipher Stem Cell Signatures / Ghislain Bidaut ; Christian J. Stoeckert9：
Systems and Data Sources
Data Integration
Artificial Neural Network Training and Validation
Future Development and Enhancement Plans
DynaFit-A Software Package for Enzymology / Petr Kuzmiĉ10：
Equilibrium Binding Studies
Initial Rates of Enzyme Reactions
Time Course of Enzyme Reactions
General Methods and Algorithms
Discrete Dynamic Modeling of Cellular Signaling Networks / Réka Albert ; Rui-Sheng Wang11：
Cellular Signaling Networks
Boolean Dynamic Modeling
Variants of Boolean Network Models
Application Examples
Conclusion and Discussion
The Basic Concepts of Molecular Modeling / Akansha Saxena ; Diana Wong ; Karthikeyan Diraviyam ; David Sept12：
Homology Modeling
Molecular Dynamics
Molecular Docking
Deterministic and Stochastic Models of Genetic Regulatory Networks / Ilya Shmulevich ; John D. Aitchison13：
Boolean Networks
Differential Equation Models
Probabilistic Boolean Networks
Stochastic Differential Equation Models
Bayesian Probability Approach to ADHD Appraisal / Raina Robeva ; Jennifer Kim Penberthy14：
Bayesian Probability Algorithm
The Value of Bayesian Probability Approach as a Meta-Analysis Tool
Discussion and Future Directions
Simple Stochastic Simulation / Maria J. Schilstra ; Stephen R. Martin15：
Understanding Reaction Dynamics
Graphical Notation
Reactions
Reaction Kinetics
Transition Firing Rules
Notes
Monte Carlo Simulation in Establishing Analytical Quality Requirements for Clinical Laboratory Tests: Meeting Clinical Needs / James C. Boyd ; David E. Bruns16：
Modeling Approach
Methods for Simulation Study
Results
Nonlinear Dynamical Analysis and Optimization for Biological/Biomedical Systems / Amos Ben-Zvi ; Jong Mm Lee17：
Hypothalamic-Pituitary-Adrenal Axis System
Development of a Clinically Relevant Performance-Assessment Tools
Dynamic Programming
Computation of Optimal Treatments for HPA Axis System
Modeling of Growth Factor-Receptor Systems: From Molecular-Level Protein Interaction Networks to Whole-Body Compartment Models / Florence T. H. Wu ; Marianne O. Stefanini ; Feilim Mac Gabhann ; Aleksander S. Popel18：
Molecular-Level Kinetics Models: Simulation of In Vitro Experiments
Mesoscale Single-Tissue 3D Models: Simulation of In Vivo Tissue Regions
Single-Tissue Compartmental Models: Simulation at In Vivo Tissue
Multitissue Compartmental Models: Simulation of Whole Body
The Least-Squares Analysis of Data from Binding and Enzyme Kinetics Studies: Weights, Bias, and Confidence Intervals in Usual and Unusual Situations / Joel Tellinghuisen19：
Least Squares Review
Statistics of Reciprocals
Weights When y is a True Dependent Variable
Unusual Weighting: When x is the Dependent Variable
Assessing Data Uncertainty: Variance Function Estimation
Conclusion
Nonparametric Entropy Estimation Using Kernel Densities / Douglas E. Lake20：
Motivating Application: Classifying Cardiac Rhythms
Renyi Entropy and the Friedman-Tukey Index
Kernel Density Estimation
Mean-Integrated Square Error
Estimating the FT Index
Connection Between Template Matches and Kernel Densities
Summary and Future Work
Pancreatic Network Control of Glucagon Secretion and Counterregulation / Leon S. Farhy ; Anthony L. McCall21：
Mechanisms of Glucagon Counterregulation (GCR) Dysregulation in Diabetes
Interdisciplinary Approach to Investigating the Defects in the GCR
Initial Qualitative Analysis of the GCR Control Axis
Mathematical Models of the GCR Control Mechanisms in STZ-Treated Rats
Approximation of the Normal Endocrine Pancreas by a Minimal Control Network (MCN) and Analysis of the GCR Abnormalities in the Insulin Deficient Pancreas
Advantages and Limitations of the Interdisciplinary Approach
Enzyme Kinetics and Computational Modeling for Systems Biology / Pedro Mendes ; Hanan Messiha ; Naglis Malys ; Stefan Hoops22：
Computational Modeling and Enzyme Kinetics
Yeast Triosephosphate Isomerase (EC 5.3.1.1)
Initial Rate Analysis
Progress Curve Analysis
Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer / Kenneth A. Johnson23：
Challenges of Fitting by Simulation
Progress Curve Kinetics
Fitting Full Progress Curves
Slow Onset Inhibition Kinetics
Author Index
Subject Index
Contributors
Preface
Volumes in Series
7.

電子ブック
ＥＢ
7. Computer Methods, Part C
Melvin I. Simon, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Burlington : Academic Press, 2011
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Predicting Fluorescence Lifetimes and Spectra of Biopolymers / Patrik R. Callis
Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock / Elizabeth Y. Scribner ; Hassan M. Fathallah-Shaykh
Strategies for articulated multibody-based adaptive coarse grain simulation of RNA / Mohammad Poursina ; Kishor D. Bhalerao ; Samuel C. Flores ; Kurt S. Anderson ; Alain Laederach
Modeling Loop Entropy / Gregory S. Chirikjian
Inferring Functional Relationships and Causal Network Structure from Gene Expression Profiles / Radhakrishnan Nagarajan
Numerical solution of the chemical master equation: uniqueness and stability of the stationary distribution for chemical networks, and mRNA bursting in a gene network with negative feedback regulation / E. S. Zeron ; M. Santill_an
How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology / Didier Gonze ; Wassim Abou-Jaoud´e ; Adama Ouattara ; Jos´e Halloy
Computational modelling of biological pathways by executable biology / Maria Luisa Guerriero John K. Heath
Computing Molecular Fluctuations in Biochemical Reaction Systems Based on A Mechanistic, Statisitical Theory of Irreversible Processes / Don Kulasiri
Probing the input-output behaviour of biochemical and genetic systems: system identification methods from control theory / David McMillen ; Brian Ingalls ; Jordan Ang
Biochemical pathway modelling tools for drug target detection in cancer and other complex diseases / Alberto Marin-Sanguino ; Shailendra K. Gupta ; Eberhard O. Voit ; Julio Vera
Deterministic and Stochastic Simulation and Analysis of Biochemical Reaction Networks: The Lactose Operon Example / Necmettin Yildirim ; Caner Kazanci F.
Multivariate Neighborhood Sample Entropy: A method for data reduction and prediction of complex data / Joshua S. Richman MD, PhD
Scaling differences of heartbeat excursions between wake and sleep periods / L. Guzm´an-Vargas ; I. Reyes-Ram´irez ; R. Hern´andez-P´erez ; F. Angulo-Brown
Changepoint analysis for single-molecule polarized totalinternal reflection fluorescence microscopy experiments / John F. Beausang ; Yale E. Goldman ; Philip C. Nelson
Inferring mechanisms from dose-response curves / Carson C. Chow ; Karen M. Ong ; Edward J. Dougherty ; S. Stoney Simons, Jr
Spatial Aspects in Biological System Simulations / Haluk Resat ; Michelle N. Costa ; Harish Shankaran
Computational Approaches to Modeling Viral Structure and Assembly / Stephen C. Harvey ; Anton S. Petrov ; Batsal Devkota ; Mustafa Burak Boz
An Object-Oriented Software Suite for the Simulation and Design of Macromolecules / Andrew Leaver-Fay ; Michael Tyka ; Steven M. Lewis ; Oliver F. Lange ; James Thompson ; Ron Jacak ; Kristian Kaufman ; P. Douglas Renfrew ; Colin A. Smith ; Will Sheffler ; Ian W. Davis ; Seth Cooper ; Adrien Treuille ; Daniel J. Mandell ; Florian Richter ; Yih-En Andrew Ban ; Sarel J. Fleishman ; Jacob E. Corn ; David E. Kim ; Sergey Lyskov ; Monica Berrondo ; Stuart Mentzer ; Zoran Popovic ; James J. Havranek ; John Karanicolas ; Rhiju Das ; Jens Meiler ; Tanja Kortemme ; Jeffrey J. Gray ; Brian Kuhlman1 ; David Baker ; Philip Bradley
Computational Design of Intermolecular Stability and Specificity in Protein Self-Assembly / Vikas Nanda ; Sohail Zahid ; Fei Xu ; Daniel Levine
Predicting Fluorescence Lifetimes and Spectra of Biopolymers / Patrik R. Callis
Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock / Elizabeth Y. Scribner ; Hassan M. Fathallah-Shaykh
Strategies for articulated multibody-based adaptive coarse grain simulation of RNA / Mohammad Poursina ; Kishor D. Bhalerao ; Samuel C. Flores ; Kurt S. Anderson ; Alain Laederach
8.

電子ブック
ＥＢ
8. Computer Methods Part A
Ludwig; Johnson, Michael L.; Brand, Ludwig Brand, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
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目次情報: 続きを見る
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
Contributors
Preface
Volumes in Series
9.

電子ブック
ＥＢ
9. Fluorescence Spectroscopy
Michael L; Brand, Ludwig; Johnson, Michael L. Johnson, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2008
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Contributors
Preface
Volumes in Series
A Method in Enzymology for Measuring Hydrolytic Activities in Live Cell Environments / Beverly Z. Packard ; Akira Komoriya1：
Protease Substrate Design
Protease Specificity / 2：
Cell-Permeable Fluorogenic Probes / 3：
Conclusions / 4：
References
Heterogeneity of Fluorescence Determined by the Method of Area-Normalized Time-Resolved Emission Spectroscopy / N. Periasamy
Introduction
TRES and TRANES Methods
TRES and TRANES Spectra of Simple Cases
Physical Significance of TRANES and Isoemissive Point
TRES and TRANES of Fluorophores in Microheterogeneous Media / 5：
Fluorescence in Microheterogeneous and Biological Media: Special Cases / 6：
Acknowledgment
Multiparametric Probing of Microenvironment with Solvatochromic Fluorescent Dyes / Andrey S. Klymchenko ; Alexander P. Demchenko
"Universal" and "Specific" Noncovalent Interactions
The Methodology of Multiparametric Approach with Application of 3-Hydroxyflavone Dyes
Correlations of Spectroscopic Data with Solvatochromic Variables
Algorithm for Multiparametric Probing Based on Parameters of Absorption and Dual Emission
Application of Multiparametric Probing
Limitations of the Multiparametric Approach
Concluding Remarks / 7：
Site-Selective Red-Edge Effects
Molecular Disorder and the Origin of Red-Edge Effects
The Principle of Photoselection
Ground-State Heterogeneity
The Magnitude of Red-Edge Excitation Fluorescence Shift and Its Connection with Dielectric Relaxations
Red-Edge Effect with High Resolution in Time
Red-Edge Effects in Excited-State Reactions
Fluorescent Probes for Optimal Observation of Red-Edge Effects / 8：
Peculiarities of the Red-Edge Effects of Indole and Tryptophan / 9：
Fluorescence Approaches to Quantifying Biomolecular Interactions / Catherine A. Royer ; Suzanne F. Scarlata10：
Fluorescence Observables
Designing a Fluorescence Experiment
Forster Resonance Energy Transfer Measurements of Transmembrane Helix Dimerization Energetics / Mikhail Merzlyakov ; Kalina Hristova
Challenges in Quantitative Measurements of Interactions Between TM Helices in Bilayers
Bilayer Platforms for Measuring TM Helix Interactions Using FRET
FRET Due to Random Colocalization of Donors and Acceptors (Proximity FRET)
FRET Efficiencies and Energetics of TM Helix Dimerization
Biological Insights from FRET Measurements
Conclusion
Application of Single-Molecule Spectroscopy in Studying Enzyme Kinetics and Mechanism / Jue Shi ; Joseph Dertouzos ; Ari Gafni ; Duncan Steel
Experimental Considerations
Sample Preparation
Instrumentation
Data Analysis of Single-Molecule Trajectories
Additional Considerations
Summary
Ultrafast Fluorescence Spectroscopy via Upconversion: Applications to Biophysics / Jianhua Xu ; Jay R. Knutson
Basic Concepts
Upconversion Spectrophotofluorometer and Experimental Considerations
Ultrafast Photophysics of Single Tryptophan, Peptides, Proteins, and Nucleic Acids
Summary and Future Directions
Use of Fluorescence Resonance Energy Transfer (FRET) in Studying Protein-induced DNA Bending / Anatoly I. Dragan ; Peter L. Privalov
Preparation of Labeled DNA Duplexes
Fluorescence Resonance Energy Transfer
FRET in Studying Large Protein-Induced DNA Bends
Dependence of the Protein-induced DNA Bend on the Forces Involved in Binding
FREt in Studying Small Protein-Induced DNA Bends
Fluorescent Pteridine Probes for Nucleic Acid Analysis / Mary E. Hawkins
Pteridine Analog Characteristics
Procedures for Oligonucleotide Synthesis with Pteridine Analogs
Characterization of Pteridine-Containing Sequences
Applications
Acknowledgments
Single-Molecule Fluorescence Methods for the Analysis of RNA Folding and Ribonucleoprotein Assembly / Goran Pljevaljcic ; David P. Millar11：
Labeling Methods
Single-Molecule Fluorescence Detection Methods
Diffusion Single-Pair FRET for RNA Based Systems
Total Internal Reflection Fluorescence (TIRF) for RNA Based Systems
Application 1: Folding of the Hairpin Ribozyme
Application 2: Assembly of the Rev-RRE Complex
Using Fluorophore-Labeled Oligonucleotides to Measure Affinities of Protein-DNA Interactions / Brian J. Anderson ; Chris Larkin ; Kip Guja ; Joel F. Schildbach12：
Definitions of Fluorescence Anisotropy and Intensity
Advantages of Fluorescence Measurements
Disadvantages of Fluorescence Measurements
Designing the Oligonucleotide
Designing the Experiment
Competition Assays for Determining Specificity
Identifying Small Pulsatile Signals within Noisy Data: A Fluorescence Application / Michael L. Johnson ; Leon S. Farhy ; Paula P. Veldhuis ; Joseph R. Lakowicz13：
Methods
Results
Discussion
Determination of Zinc Using Carbonic Anhydrase-Based Fluorescence Biosensors / Rebecca Bozym ; Tamiika K. Hurst ; Nissa Westerberg ; Andrea Stoddard ; Carol A. Fierke ; Christopher J. Frederickson ; Richard B. Thompson14：
Principles of CA-Based Zinc Sensing
Transducing Zinc Binding as a Fluorescence Change
"Free" Versus Bound Zinc Ion: Speciation
Metal Ion Buffers
Kinetics
Applications: Ratiometric Determination of Free Zinc in Solution
Preparation of Apocarbonic Anhydrase
Intracellular Sensing with TAT Tag
Intracellular Sensing with an Expressible CA Sensor
Instrumentation for Fluorescence-Based Fiber Optic Biosensors / Hui-Hui Zeng ; Daniel Ohnemus ; Bryan McCranor ; Michele Cramer ; James Moffett15：
Introduction and Rationale for Fluorescence-Based Fiber Optic Sensors
Basic Principles of Fiber Optics for Fluorescence Sensors
Optics and Mechanics of Fluorescence-Based Fiber Optic Sensors
Mounting and Alignment of the Instrument
Standards for Ratiometric and Lifetime-Based Fiber Optic Fluorescence Sensors
Construction of Fiber Optic Probes
Zn[superscript 2+] Probe
Cu[superscript 2+] Probe
Use of Fiber Optic Probes for Discrete Samples
Operating Issues: Noise, Background, Thermal Drift, and Mode Hopping
Field and Shipboard Use
Author Index
Subject Index
Contributors
Preface
Volumes in Series
10.

電子ブック
ＥＢ
10. Computer Methods Part B
Michael L. John, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
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Contributors
Preface
Volumes in Series
Correlation Analysis: A Tool for Comparing Relaxation-Type Models to Experimental Data / Maurizio Tomaiuolo ; Joel Tabak ; Richard Bertram1：
Introduction
Scatter Plots and Correlation Analysis / 2：
Example 1: Relaxation Oscillations / 3：
Example 2: Square Wave Bursting / 4：
Example 3: Elliptic Bursting / 5：
Example 4: Using Correlation Analysis on Experimental Data / 6：
Summary / 7：
Acknowledgments
References
Trait Variability of Cancer Cells Quantified by High-Content Automated Microscopy of Single Cells / Vito Quaranta ; Darren R. Tyson ; Shawn P. Garbett ; Brandy Weidow ; Mark P. Harris ; Walter Georgescu
Background
Experimental and Computational Workflow
Application to Traits Relevant to Cancer Progression
Conclusions
Matrix Factorization for Recovery of Biological Processes from Microarray Data / Andrew V. Kossenkov ; Michael F. Ochs
Overview of Methods
Application to the Rosetta Compendium
Results of Analyses
Discussion
Modeling and Simulation of the Immune System as a Self-Regulating Network / Peter S. Kim ; Doron Levy ; Peter P. Lee
Mathematical Modeling of the Immune Network
Two Examples of Models to Understand T Cell Regulation
How to Implement Mathematical Models in Computer Simulations
Concluding Remarks
Acknowledgmentss
Entropy Demystified: The ôThermoö-dynamics of Stochastically Fluctuating Systems / Hong Qian
Energy
Entropy and ôThermoö-dynamics of Markov Processes
A Three-State Two-Cycle Motor Protein
Phosphorylation-Dephosphorylation Cycle1 Kinetics
Summary and Challenges
Effect of Kinetics on Sedimentation Velocity Profiles and the Role of Intermediates / John J. Correia ; P. Holland Alday ; Peter Sherwood ; Walter F. Stafford
Methods
ABCD Systems
Monomer-Tetramer Model
Algebraic Models of Biochemical Networks / Reinhard Laubenbacher ; Abdul Salam Jarrah
Computational Systems Biology
Network Inference
Reverse-Engineering of Discrete Models: An Example
High-Through put Computing in the Sciences / Mark Morgan ; Andrew Grimshaw8：
What is an HTC Application?
HTC Technologies
High-Throughput Computing Examples
Advanced Topics
Large Scale Transcriptome Data Integration Across Multiple Tissues to Decipher Stem Cell Signatures / Ghislain Bidaut ; Christian J. Stoeckert9：
Systems and Data Sources
Data Integration
Artificial Neural Network Training and Validation
Future Development and Enhancement Plans
DynaFit-A Software Package for Enzymology / Petr Kuzmiĉ10：
Equilibrium Binding Studies
Initial Rates of Enzyme Reactions
Time Course of Enzyme Reactions
General Methods and Algorithms
Discrete Dynamic Modeling of Cellular Signaling Networks / Réka Albert ; Rui-Sheng Wang11：
Cellular Signaling Networks
Boolean Dynamic Modeling
Variants of Boolean Network Models
Application Examples
Conclusion and Discussion
The Basic Concepts of Molecular Modeling / Akansha Saxena ; Diana Wong ; Karthikeyan Diraviyam ; David Sept12：
Homology Modeling
Molecular Dynamics
Molecular Docking
Deterministic and Stochastic Models of Genetic Regulatory Networks / Ilya Shmulevich ; John D. Aitchison13：
Boolean Networks
Differential Equation Models
Probabilistic Boolean Networks
Stochastic Differential Equation Models
Bayesian Probability Approach to ADHD Appraisal / Raina Robeva ; Jennifer Kim Penberthy14：
Bayesian Probability Algorithm
The Value of Bayesian Probability Approach as a Meta-Analysis Tool
Discussion and Future Directions
Simple Stochastic Simulation / Maria J. Schilstra ; Stephen R. Martin15：
Understanding Reaction Dynamics
Graphical Notation
Reactions
Reaction Kinetics
Transition Firing Rules
Notes
Monte Carlo Simulation in Establishing Analytical Quality Requirements for Clinical Laboratory Tests: Meeting Clinical Needs / James C. Boyd ; David E. Bruns16：
Modeling Approach
Methods for Simulation Study
Results
Nonlinear Dynamical Analysis and Optimization for Biological/Biomedical Systems / Amos Ben-Zvi ; Jong Mm Lee17：
Hypothalamic-Pituitary-Adrenal Axis System
Development of a Clinically Relevant Performance-Assessment Tools
Dynamic Programming
Computation of Optimal Treatments for HPA Axis System
Modeling of Growth Factor-Receptor Systems: From Molecular-Level Protein Interaction Networks to Whole-Body Compartment Models / Florence T. H. Wu ; Marianne O. Stefanini ; Feilim Mac Gabhann ; Aleksander S. Popel18：
Molecular-Level Kinetics Models: Simulation of In Vitro Experiments
Mesoscale Single-Tissue 3D Models: Simulation of In Vivo Tissue Regions
Single-Tissue Compartmental Models: Simulation at In Vivo Tissue
Multitissue Compartmental Models: Simulation of Whole Body
The Least-Squares Analysis of Data from Binding and Enzyme Kinetics Studies: Weights, Bias, and Confidence Intervals in Usual and Unusual Situations / Joel Tellinghuisen19：
Least Squares Review
Statistics of Reciprocals
Weights When y is a True Dependent Variable
Unusual Weighting: When x is the Dependent Variable
Assessing Data Uncertainty: Variance Function Estimation
Conclusion
Nonparametric Entropy Estimation Using Kernel Densities / Douglas E. Lake20：
Motivating Application: Classifying Cardiac Rhythms
Renyi Entropy and the Friedman-Tukey Index
Kernel Density Estimation
Mean-Integrated Square Error
Estimating the FT Index
Connection Between Template Matches and Kernel Densities
Summary and Future Work
Pancreatic Network Control of Glucagon Secretion and Counterregulation / Leon S. Farhy ; Anthony L. McCall21：
Mechanisms of Glucagon Counterregulation (GCR) Dysregulation in Diabetes
Interdisciplinary Approach to Investigating the Defects in the GCR
Initial Qualitative Analysis of the GCR Control Axis
Mathematical Models of the GCR Control Mechanisms in STZ-Treated Rats
Approximation of the Normal Endocrine Pancreas by a Minimal Control Network (MCN) and Analysis of the GCR Abnormalities in the Insulin Deficient Pancreas
Advantages and Limitations of the Interdisciplinary Approach
Enzyme Kinetics and Computational Modeling for Systems Biology / Pedro Mendes ; Hanan Messiha ; Naglis Malys ; Stefan Hoops22：
Computational Modeling and Enzyme Kinetics
Yeast Triosephosphate Isomerase (EC 5.3.1.1)
Initial Rate Analysis
Progress Curve Analysis
Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer / Kenneth A. Johnson23：
Challenges of Fitting by Simulation
Progress Curve Kinetics
Fitting Full Progress Curves
Slow Onset Inhibition Kinetics
Author Index
Subject Index
Contributors
Preface
Volumes in Series
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