Research Methods in Biomineralization Science

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