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Research Methods in Biomineralization Science
- 1st Edition, Volume 532 - October 31, 2013
- Editor: Jim De Yoreo
- Language: English
- Hardback ISBN:9 7 8 - 0 - 1 2 - 4 1 6 6 1 7 - 2
- eBook ISBN:9 7 8 - 0 - 1 2 - 4 1 6 6 5 5 - 4
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods i… Read more
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Request a sales quoteThis new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in biomineralization science, and includes sections on such topics as determining solution chemistry, structure and nucleation; probing structure and dynamics at surfaces; and interfaces mapping biomineral and morphology and ultrastructure.
- Continues the legacy of this premier serial with quality chapters authored by leaders in the field
- Covers research methods in biomineralization science
- Contains sections on such topics as and includes sections on such topics as determining solution chemistry, structure and nucleation; probing structure and dynamics at surfaces; and interfaces mapping biomineral and morphology and ultrastructure
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists.
Series Page
Contributors
Preface
Methods in Enzymology
Section I: Investigating Solution Chemistry, Structure, and Nucleation
Chapter One. Development of Accurate Force Fields for the Simulation of Biomineralization
Abstract
1 Introduction
2 Force Field Selection and Refinement
3 The Mineral–Aqueous Interface
4 Organics in Geochemical Systems
5 Summary
Acknowledgments
References
Chapter Two. The Integration of Ion Potentiometric Measurements with Chemical, Structural, and Morphological Analysis to Follow Mineralization Reactions in Solution
Abstract
1 Introduction
2 Ion Potentiometric Measurements
3 Combination of Ion Potentiometric Measurements with other Analysis Techniques
4 Comparison with Standard Analyses
5 Summary
References
Chapter Three. Investigating the Early Stages of Mineral Precipitation by Potentiometric Titration and Analytical Ultracentrifugation
Abstract
1 Introduction
2 Equipment
3 Experimental Procedures
4 Data Evaluation
5 Conclusions and Outlook
References
Chapter Four. Replica Exchange Methods in Biomineral Simulations
Abstract
1 Introduction
2 Monte Carlo Sampling
3 Replica Exchange MD
4 Application of REMD to Early Stage Mineralization
5 Summary
References
Chapter Five. SAXS in Inorganic and Bioinspired Research
Abstract
1 Introduction
2 General Considerations: How Does SAXS/WAXS Work and When It Is Applicable?
3 What Happens in a Solution When Ions Meet and How Do We Quantify it?
4 SAXS Data Processing and Interpretation
5 Case Studies
6 Outlook
Acknowledgments
References
Chapter Six. In Situ Solution Study of Calcium Phosphate Crystallization Kinetics
Abstract
1 Introduction
2 Solution Preparation and Experimental Considerations
3 In Situ Experiments
4 Data Handling/Processing
5 Summary
References
Section II: Probing Structure and Dynamics at Surfaces and Interfaces
Chapter Seven. Design, Fabrication, and Applications of In Situ Fluid Cell TEM
Abstract
1 Introduction
2 Fluid Cell Design
3 Cell Fabrication and Assembly
4 TEM Operation
5 Effects of the Electron Beam on Reactions in the Fluid Cell
6 Conclusions
Acknowledgments
References
Chapter Eight. X-ray Absorption Spectroscopy for the Structural Investigation of Self-Assembled-Monolayer-Directed Mineralization
Abstract
1 Introduction
2 Theory
3 Experimental
4 Analysis
Acknowledgments
References
Chapter Nine. Cryo-TEM Analysis of Collagen Fibrillar Structure
Abstract
1 Introduction
2 Sample Preparation for Cryo-TEM
3 Image Acquisition and Processing
4 Image Averaging
5 Summary and Outlook
Acknowledgments
References
Section III: Biomimetic Crystallization Techniques in vitro
Chapter Ten. Preparation of Organothiol Self-Assembled Monolayers for Use in Templated Crystallization
Abstract
1 Introduction
2 Crystallization Approaches Using SAMs as Templates
3 Preparation
4 Why Good SAMs Go Bad
5 SAM Preparation Procedure
6 Summary
Acknowledgments
References
Chapter Eleven. Experimental Techniques for the Growth and Characterization of Silica Biomorphs and Silica Gardens
Abstract
1 Introduction
2 Silica Biomorphs
3 Chemical Gardens
4 Conclusions and Outlook
Acknowledgments
References
Chapter Twelve. Precipitation in Liposomes as a Model for Intracellular Biomineralization
Abstract
1 Introduction
2 Model Systems for Studying the Influence of Confinement on Biomineralization
3 Preparation of Liposomes
4 Precipitation Inside Liposomes
5 Characterization Methods
6 Conclusions
Acknowledgments
References
Chapter Thirteen. Polymer-Mediated Growth of Crystals and Mesocrystals
Abstract
1 Introduction
2 Insoluble Polymers
3 Soluble Polymers
4 Conclusion
References
Chapter Fourteen. Phage Display for the Discovery of Hydroxyapatite-Associated Peptides
Abstract
1 Introduction
2 Methods
3 Summary
References
Section IV: Protein Structure, Interactions and Function
Chapter Fifteen. Quantitatively and Kinetically Identifying Binding Motifs of Amelogenin Proteins to Mineral Crystals Through Biochemical and Spectroscopic Assays
Abstract
1 Introduction
2 Strategy and Rationale
3 Experimental Components and Considerations
4 Experimental Approaches
5 Data Handling and Processing
6 Summary
Acknowledgments
References
Chapter Sixteen. Using the RosettaSurface Algorithm to Predict Protein Structure at Mineral Surfaces
Abstract
1 Introduction
2 Algorithm Evolution and Prior Results
3 Computational Methods
4 Protocol Capture
5 Future Challenges
Acknowledgments
References
Chapter Seventeen. Investigating Protein Function in Biomineralized Tissues Using Molecular Biology Techniques
Abstract
1 Introduction
2 Discovery of Proteins Involved in Biomineralization
3 Analysis of Function
Acknowledgments
References
Section V: Mapping Biomineral Morphology and Ultrastructure
Chapter Eighteen. Imaging the Nanostructure of Bone and Dentin Through Small- and Wide-Angle X-Ray Scattering
Abstract
1 Introduction
2 Experimental Setup
3 Overview of Parameters
4 Treatment of SAXS Data from Mineralized Tissue
5 Treatment of WAXD Data from Mineralized Tissues
6 Analysis Tools
7 Combination of Scanning SAXS/WAXD with Other Methods
8 Conclusions
References
Chapter Nineteen. Synchrotron X-Ray Nanomechanical Imaging of Mineralized Fiber Composites
Abstract
1 Introduction
2 Molecular and Nanoscale Strains and Stresses in a Prototypical Biomineralized Composite
3 Relation between X-Ray Spectra and Nanomechanics
4 Sample Preparation for In Situ Mechanical Testing with Synchrotron X-Rays
5 Mechanical Tester Design
6 Synchrotron Setup
7 In Situ Experimental Procedure
8 Data Analysis
9 Case Studies
10 Model Interpretation
11 Summary
Acknowledgments
References
Section VI: Mapping Mineral Chemistry
Chapter Twenty. Application of Total X-Ray Scattering Methods and Pair Distribution Function Analysis for Study of Structure of Biominerals
Abstract
1 Introduction
2 Total Scattering Methodology
3 The PDF
4 Extracting Information from the PDF
5 PDF Studies of Biominerals
6 Summary
Links
Acknowledgments
References
Chapter Twenty-One. X-Ray Microdiffraction of Biominerals
Abstract
1 Introduction
2 Elements of X-Ray (Micro)Diffraction
3 Synchrotron, X-Ray Focusing Optics, and Area Detectors
4 Sample Preparation
5 Powder X-Ray Microdiffraction
6 White-Beam X-Ray Microdiffraction
7 Microbeam Small-Angle X-Ray Scattering
8 Future Developments
References
Chapter Twenty-Two. FTIR and Raman Studies of Structure and Bonding in Mineral and Organic–Mineral Composites
Abstract
1 Introduction
2 FTIR and Raman Spectroscopies Overview
3 The Raman Effect
4 Measuring Biomimetic Crystals and Biominerals
5 Future Directions
Acknowledgments
References
Chapter Twenty-Three. A Mixed Flow Reactor Method to Synthesize Amorphous Calcium Carbonate Under Controlled Chemical Conditions
Abstract
1 Introduction
2 Method
3 Characterization
4 Results
References
Author Index
Subject Index
- No. of pages: 704
- Language: English
- Edition: 1
- Volume: 532
- Published: October 31, 2013
- Imprint: Academic Press
- Hardback ISBN: 9780124166172
- eBook ISBN: 9780124166554
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