Synchrotron Radiation inMaterials Science

Synchrotron Radiation in Materials Science

Light Sources, Techniques, and Applications

Edited by Chunhai Fan and Zhentang Zhao

Volume 1

Synchrotron Radiation in Materials Science

Light Sources, Techniques, and Applications

Edited by Chunhai Fan and Zhentang Zhao

Volume 2

The Editors

Prof. Chunhai FanShanghai Institute of Applied PhysicsCAS2019 Jia Luo RoadJiading District201800 ShanghaiChina

Prof. Zhentang ZhaoShanghai Institute of Applied PhysicsCAS2019 Jia Luo RoadJiading District201800 ShanghaiChina

CoverBackgroundfotolia/Stefan Kuhn and Wikipedia/EPSIM3D/JF Santarelli, Synchrotron Soleil

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v

Contents to Volume 1

Preface xviiAbout the Editors xxi

1 Synchrotron Light Sources 1Zhentang Zhao

1.1 Introduction 11.2 Synchrotron Radiation Generation 11.2.1 Radiation from Bending Magnet 21.2.2 Radiation from Undulator 51.2.2.1 Planar Undulator Radiation 51.2.2.2 Helical Undulator Radiation 61.2.3 Radiation from Wiggler 81.3 Light Source Storage Ring and Its Beam Dynamics 91.3.1 Transverse Dynamics 101.3.2 Longitudinal Dynamics 131.3.3 Synchrotron Radiation Effects and Beam Dimensions 141.3.4 Radiation Source Parameters 171.4 Low-Emittance Lattice for Light Source Storage Ring 191.4.1 The Lattice Cell and Its Design Constraints 191.4.2 Typical Lattices for Light Source Storage Ring 201.5 Status of Storage Ring Light Sources 241.5.1 High Energy Storage Rings 251.5.2 Low Energy Storage Rings 251.5.3 Intermediate Energy Storage Rings 27

References 30

2 Beamlines for Materials Science 35Tetsuya Ishikawa

2.1 Introduction 352.2 Radiation Properties of Different Sources 362.3 SR Beamline as an Optical System 372.4 Structure of Typical X-ray Beamlines 392.5 Radiation Safety and Interlock System 452.6 Beamline X-ray Optics 47

vi Contents

2.6.1 Crystal Monochromators 472.6.2 X-ray Mirrors 542.6.3 X-ray Lenses 552.7 X-ray Beamlines for Next Generation SRs 562.8 Concluding Remarks 59

References 59

3 Synchrotron Radiation Experimental Techniques 61Renzhong Tai, Jianhua He, Yuying Huang, Jie Wang, Xingyu Gao, Tiqiao Xiao,and Jingyuan Ma

3.1 X-ray Diffraction 613.1.1 Introduction 613.1.2 Single Crystal X-ray Diffraction 623.1.3 Powder Diffraction 623.1.4 Surface Diffraction 643.1.4.1 Grazing Incidence X-ray Diffraction 653.1.4.2 Crystal Truncation Rods (CTR) 653.1.4.3 X-ray Standing-Wave (XSW) 663.1.5 High-Energy Diffraction 673.1.5.1 Compton Scattering 673.1.5.2 Atomic Pair Distribution Function (PDF) 683.1.6 Laue Micro-Diffraction 683.2 XAFS Technique 693.2.1 Introduction 693.2.2 XAFS Theory – Development of the EXAFS Equation 703.2.3 XAFS Experiments 733.2.4 Examples for Application 773.2.4.1 Nanomaterials 773.2.4.2 Metallic Glasses (MG) 793.2.4.3 Magnetic Material 823.2.4.4 Cathode Material 823.3 Small-Angle X-ray Scattering Technique 843.3.1 SAXS Theory 843.3.1.1 X-ray Scattering of Electrons 843.3.1.2 X-ray Scattering of Continuous-Distribution Electrons 853.3.1.3 X-ray Scattering of Single Particle 863.3.1.4 X-ray Scattering of Multiple Particles 883.3.2 Experimental Set-Up of SAXS 893.3.3 Examples for the Application of SAXS 923.3.3.1 Lamellar Structure 923.3.3.2 Three-Dimensional Periodic Framework 933.3.3.3 Film Morphology and Microstructure 943.3.3.4 Spatial Configuration of Self-Assembled Pyramids 943.3.3.5 Lattice of Liquid Crystallines 963.4 Imaging Technique 973.4.1 X-ray Computed Tomography 973.4.1.1 Crystal Interferometer Imaging 983.4.1.2 Diffraction-Enhanced Imaging 99

Contents vii

3.4.1.3 Grating Interferometer Imaging 993.4.1.4 Propagation-Based Imaging 993.4.2 Three-Dimensional X-ray Diffraction 993.4.3 SAXS–CT 1003.4.4 X-ray Correlated Imaging 1023.4.5 Quantitative Analysis 1033.5 Soft X-ray Methodology 1043.5.1 Scanning Transmission X-ray Microscopy (STXM) 1053.5.2 Soft X-ray Interference Lithography 1073.5.3 Angle-Resolved Photoemission Spectroscopy 1093.5.4 Photoemission Electron Microscopy 1113.5.5 Resonant Inelastic X-ray Scattering (RIXS) 114

References 116

4 Photon-In Photon-Out Spectroscopic Techniques for MaterialsAnalysis: Some Recent Developments 123Tsun-Kong Sham

4.1 Introduction 1234.2 Photon-In Photon-Out Soft X-ray Techniques 1284.2.1 2D Fluorescence Map of LiFePO4 at the Fe L3,2-Edge: XANES from

Inverse Partial Fluorescence Yield (IPFY) 1284.2.1.1 The X-ray Fluorescence Spectrum: A 2D Map 1284.2.1.2 Fe L3,2-Edge XANES Using Fe L

𝛼FLY and IPFY of O K

𝛼Fluorescence

X-ray 1304.2.2 2D XANES-XEOL Studies of GaN–ZnO (GZNO) Solid Solution

Light-Emitting Nanostructures 1314.2.2.1 2D XANES–XEOL Map for GaN–ZnO Solid Solution 1314.2.2.2 Time-Resolved XEOL (TRXEOL) Using an Optical Streak

Camera 1334.3 Prospects 134

Acknowledgments 135References 135

5 Quantitative Femtosecond Charge Transfer Dynamics atOrganic/Electrode Interfaces Studied by Core-Hole ClockSpectroscopy 137Liang Cao, Xing-Yu Gao, Andrew T. S. Wee, and Dong-Chen Qi

5.1 Introduction 1375.2 Basic Principles of Core-Hole Clock Spectroscopy 1395.2.1 Photoexcitation Excitation–De-excitation Processes 1395.2.2 Determining Charge Transfer Times 1425.3 Energetic Condition for Probing Dynamic Charge Transfer 1435.4 Experimental Realization 1455.4.1 Sample Preparation: Forming Well-Defined Organic/Electrode

Interfaces 1455.4.1.1 Organic Molecular Beam Deposition (OMBD) 1455.4.1.2 Self-Assembled Monolayers (SAMs) 1465.4.2 Synchrotron-Based CHC Measurements 147

viii Contents

5.5 Charge Transfer Dynamics at Organic/Electrode Interfaces 1485.5.1 Charge Transfer Times between Organic Semiconductor and Metal

Substrates 1485.5.1.1 Physisorbed Organic Molecule on Metal 1485.5.1.2 Chemisorbed Molecules on Metal 1505.5.1.3 Electrons Tunneling through Inorganic Buffer Layer at Organic/Metal

Interface 1525.5.2 Charge Transfer Times between Organic Molecules and Metal Oxide

Substrates 1555.5.2.1 Charge Transfer Timescale between Organic Dyes and TiO2

Substrates 1555.5.2.2 Molecular Orientation and Site Dependence 1565.5.3 Charge Transfer Dynamics in Self-Assembled Monolayers on Metal

Substrates 1595.5.4 Charge Transfer Dynamics through-Space within π Coupled

Molecules 1645.6 Conclusions and Outlook 166

Acknowledgments 167References 167

6 Experimental Study of Ferroelectric Materials by CoherentX-ray Scattering 179Renzhong Tai and Kazumichi Namikawa

6.1 Introduction 1796.2 Soft X-ray Speckle 1806.2.1 X-ray Speckle from Surface a/c Domains 1806.2.2 Soft X-ray Speckle from Polarization Clusters 1816.3 Temporal Intensity Correlation 1836.4 Concluding Remarks 189

References 189

7 Probing Organic Solar Cells with Grazing Incidence ScatteringTechniques 191Peter Müller-Buschbaum

7.1 Introduction 1917.2 Grazing Incidence Small Angle X-ray Scattering (GISAXS) 1947.3 Grazing Incidence Wide Angle X-ray Scattering (GIWAXS) 1997.4 Probing the Active Layer Morphology with GIWAXS 2047.5 Probing the Active Layer Morphology with GISAXS 2157.6 Summary 223

Acknowledgments 224References 224

8 Investigation Strain in Silicon-on-Insulator Nanostructures byCoherent X-ray Diffraction 239Gang Xiong, Oussama Moutanabbir, Manfred Reiche, Ross Harder, and IanRobinson

8.1 Introduction 239

Contents ix

8.2 Coherence 2398.2.1 Transverse (or Spatial) Coherence Length 2408.2.2 Longitudinal (or Temporal) Coherence Length 2408.3 Coherent X-ray Diffraction Imaging (CDI) 2418.3.1 Fundamental Concepts of Lens-Less Imaging 2418.3.2 Phase Retrieval 2438.3.3 Forward Coherent Diffraction Imaging 2468.3.4 Bragg Coherent Diffraction Imaging 2498.4 Strain Distribution in Silicon-on-Insulator (SOI)

Structures 2548.4.1 Silicon on Insulator 2548.4.2 Strain Distribution in sSOI Structures 2578.4.2.1 Strain Relaxation in Individual sSOI Structures 2588.4.2.2 Strain Relaxation in Multiple sSOI Nanostructures 2648.5 Conclusion 265

Acknowledgments 266References 266

9 Synchrotron Soft X-ray Absorption Spectroscopy Study ofCarbon and Silicon Nanostructures for EnergyApplications 275Jun Zhong, Hui Zhang, Xuhui Sun, and Shuit-tong Lee

9.1 Introduction 2759.1.1 The Energy Applications of Carbon and Si Nanostructures 2769.1.2 Introduction to Synchrotron Techniques 2779.2 Carbon Nanostructures in Energy Applications 2809.2.1 Fuel Cell Application 2809.2.2 Li Battery 2849.2.3 Solar Cell 2889.2.4 Catalyst 2899.3 Si Nanostructures in Energy Applications 2939.3.1 Si Nanowires 2949.3.1.1 Bottom-Up VLS Si Nanowires 2949.3.1.2 Top-Down, Electroless, and Chemically Etched

Si Nanowires 2969.3.1.3 Metal Nanoparticles Modified Si Nanowires 2989.3.2 Si Quantum Dots 3019.4 Conclusions and Prospective 303

Acknowledgments 306References 306

10 Synchrotron-Radiation-Based Soft X-ray ElectronSpectroscopies Applied to Structural and ChemicalCharacterization of Isolated Species, from Molecules toNano-objects 321Catalin Miron, Minna Patanen, and Safia Benkoula

10.1 Introduction 321

x Contents

10.1.1 XPS: A Multiscale Experimental Tool 32210.1.2 Soft X-ray Instrumentation at Third Generation Light Sources 32410.2 Relevant Information in Photoelectron Spectra 32510.2.1 Linewidths in Small Atomic and Molecular Systems 32510.3 Photoionization Cross Sections: A Structural Probe for Simple

Molecules 32910.3.1 Electron Diffraction and Relative Photoionization Cross Sections 32910.3.2 Vibrational Resolution in Photoelectron Spectra for the Observation of

Intramolecular Diffraction Effects 33210.3.3 Interference Effects due to Coherent Multicenter Photoemission 33310.4 Imaging Molecular Potentials 33710.5 Photoelectron Spectroscopy-Based Structural Investigations of

Clusters 33810.5.1 Polarization Screening 33910.5.2 Exchange Interaction 34010.5.3 Interatomic Coulombic Decay 34110.6 Soft X-ray Spectroscopy Applied to Even Larger Systems: Physical

Properties of Isolated Nanoparticles 34210.6.1 Insight on Light/Matter Interaction 34210.6.2 Toward Concrete Applications 34210.6.2.1 Atmospheric Sciences 34310.6.2.2 Heterogeneous Catalysis 34510.7 Conclusion 346

References 347

11 X-ray Imaging for Nondestructive Analysis of MaterialMicrostructures 357Yanan Fu, Honglan Xie, Biao Deng, Guohao Du, and Tiqiao Xiao

11.1 Introduction 35711.2 Methodology Development 35811.2.1 Quantitative Phase-Contrast Micro-CT 35811.2.1.1 Phase Retrieval 35811.2.1.2 Data-Constrained Modeling 36211.2.2 Dynamic Microtomography 36311.2.2.1 Dynamic Micro-CT Based on CS 36411.2.2.2 Dynamic Micro-CT Based on EST 36411.2.3 Three-Dimensional X-ray Diffraction 36411.2.4 SAXS-CT 36711.3 Applications in Material Science 36711.3.1 Alloys 36911.3.2 Welding 37211.3.3 Biomaterials 37511.3.4 Polymers 37711.3.5 Amorphous Materials 37711.3.6 Composite Materials 380

References 382

Contents xi

Contents to Volume 2

Preface xviiAbout the Editors xxi

12 Exploring Actinide Materials through Synchrotron RadiationTechniques 389Wei-Qun Shi, Li-Yong Yuan, Cong-Zhi Wang, Lin Wang, Lei Mei, Cheng-LiangXiao, Li Zhang, Zi-Jie Li, Yu-Liang Zhao, and Zhi-Fang Chai

12.1 Introduction 38912.2 The Redox and Coordination Chemistry of Actinide 39112.3 Challenges for Actinide Measurements at SR Facilities 39312.3.1 Managing Radioactive Samples under Radiation Protection

Standards 39312.3.2 Design and Execution of in situ Experiments with Modular

Experimental Platforms 39512.4 Determination of Actinide Speciation by XAFS 39812.4.1 Characterization of the Local Structures of Actinide Solid Materials

by EXAFS 39812.4.1.1 Actinide Materials Associated with Nuclear Fuels 39812.4.1.2 Actinide Materials Associated with Nuclear Waste Disposal 40012.4.1.3 Structural Analysis of Novel Actinide Materials 40212.4.2 Applications of EXAFS to Investigate Actinides in Molten Salts and

Ionic Liquids 40412.4.2.1 Actinide Materials in Molten Salts 40412.4.2.2 Actinide Materials in Ionic Liquids 40612.4.3 Solution Structural Chemistry of Actinides 41012.4.3.1 Species of Actinides in Aqueous Solution 41012.4.3.2 Species of Actinides in Organic Solutions 41812.4.4 Actinide EXAFS of Environmental Concern 42012.4.4.1 Interactions of Actinides with Minerals 42012.4.4.2 Interactions of Actinides with Microorganisms 43412.5 Applications of XANES in Actinide Characterization 43912.5.1 Uranium 43912.5.2 Plutonium 44412.5.3 Neptunium 44612.5.4 Other Actinides 44712.6 Actinide Computational Chemistry Associated with EXAFS

and XANES Results 44812.6.1 XAFS Simulations 44812.6.2 Quantum Mechanical (QM) Method 44912.6.2.1 Actinide Hydrate Complexes 44912.6.2.2 Actinide Hydroxide Complexes 45212.6.2.3 Actinide Complexes with Inorganic Ligands 45312.6.2.4 Actinide Complexes with Organic Ligands 45412.6.2.5 Solid-State Actinide Complexes 455

xii Contents

12.6.3 Molecular Dynamics (MD) Method 45612.7 Applications of SR-Based XRD in Actinide Material 45712.7.1 SR Single Crystal XRD (SR-SCXRD) Characterization of

Actinide Materials 45812.7.2 SR Powder XRD (SR-PXRD) Characterization of Actinide

Materials 45812.7.3 Actinide Materials under High Pressures 46012.7.3.1 Actinide Metals under High Pressures 46012.7.3.2 Actinide Oxides and Nitrides under High Pressures 46012.7.3.3 Other Actinide Complexes under High Pressures 46112.8 Applications of SR-Based X-ray Scattering (XRS) in Actinide

Material 46212.8.1 Research Progress of Actinide Materials with HEXS 46212.8.1.1 Uranium-Containing Solutions 46212.8.1.2 Thorium-Containing Solutions 46312.8.1.3 Other Actinide-Containing Solutions 46312.8.2 SR-Based SAXS for Actinide Materials 46412.8.3 SR-Based RXS for Actinide Materials 46512.8.4 Phonon Dispersion Properties of Actinide Materials with

SR-Based IXS 46612.9 Synchrotron Radiation X-ray Fluorescence (SR-XRF) for Elemental

Distribution and Quantitative Analysis of Actinide Materials 46612.9.1 SR Micro-XRF (SR-μ-XRF) 46712.9.2 Total Reflection Synchrotron X-ray and Confocal SR-μ-XRF 47012.10 Scanning Transmission X-ray Microscopy for Actinide Imaging 47112.11 Summary 472

Acknowledgments 475Abbreviations 475References 478

13 Techniques and Demonstrations of Synchrotron-Based In situSoft X-ray Spectroscopy for Studying Energy Materials 511Wanli Yang and Zhi Liu

13.1 Introduction 51113.2 Ambient Pressure Photoelectron Spectroscopy 51413.2.1 AP-PES Principles and Recent Instrumentation Developments 51413.2.2 Recent Progress in Energy Material Applications 51713.2.2.1 Catalysis: CO Oxidation over Single Crystal Pd(100) 51713.2.2.2 Operando Study of Electrochemical Devices 51913.3 Soft X-ray Absorption, Nonresonant X-ray Emission Spectroscopy,

and Resonant Inelastic Soft X-ray Scattering 52713.3.1 Soft X-ray XAS, XES, and RIXS 52813.3.2 Progress and Applications of XAS, XES, and RIXS in Energy

Research 52913.3.2.1 Gas and Liquid Cells for in situ Soft X-ray PIPO XAS

Spectroscopy 53013.3.2.2 High-Efficiency XES and RIXS System 532

Contents xiii

13.3.2.3 Soft X-ray Optics and High-Efficiency XAS Detectors 53513.3.2.4 In situ RIXS to Study the Ion Solvation Effect 53713.3.2.5 In situ and Operando XAS of Solid-State Li Ion Batteries 53913.3.2.6 Operando Soft X-ray PIPO Microscopy 54013.4 Conclusions and Future Outlook 542

References 544

14 Synchrotron-Based Bioimaging in Cells and In vivo 563Ying Zhu, Jichao Zhang, Lihua Wang, and Chunhai Fan

14.1 Introduction 56314.2 Overview of Synchrotron-Based X-ray Microscopy 56314.3 Synchrotron-Based Bioimaging in Cells 56414.3.1 Imaging of the Cellular and Subcellular Structures 56414.3.2 X-ray-Sensitive Nanoprobe for Cellular Imaging 56614.3.2.1 Brief Description of Existing Microscopy for Cellular Imaging 56614.3.2.2 Synchrotron-Based X-ray Microscopy for Cellular Imaging 56814.3.3 Cell Effects of Nanomaterials 57214.4 Synchrotron-Based Bioimaging In vivo 57614.4.1 Imaging of the Tissue Structures 57614.4.2 In vivo Bioeffects of Nanomaterials 57914.4.2.1 In Model Organisms 57914.4.2.2 In Animals 58114.4.2.3 In Plants 58314.5 Summary 588

References 588

15 Study on the Toxicology of Nanomaterials by SynchrotronRadiation Techniques 597Yu-Feng Li, Jiating Zhao, Yuxi Gao, Bai Li, and Chunying Chen

15.1 Introduction 59715.2 Characterization of Nanomaterials 59815.2.1 Characterization of As-Manufactured Nanomaterials 59815.2.2 Characterization of Nanomaterials in Simulated Biological

Systems 60115.3 In vitro and In vivo Behaviors of Nanomaterials 60215.3.1 The Cellular Uptake, Distribution, Transformation, and Expulsion of

Nanomaterials 60215.3.2 The Absorption, Distribution, Metabolism, and Excretion of

Nanomaterials In vivo 60515.4 Toxicological Effects of Nanomaterials in Ecosystems 60915.4.1 Fate of Nanomaterials in Natural Environment 60915.4.2 Toxicity of Nanomaterials in Model Organisms in Ecosystems 61115.4.2.1 Plants 61115.4.2.2 Aquatic Animals 61215.4.2.3 Terrestrial Animals 61415.4.2.4 Atmospheric Animals 61515.5 Conclusions 616

xiv Contents

Acknowledgments 617References 618

16 Synchrotron Radiation X-ray Imaging in BiomedicalResearch 633Liping Wang, Guo-Yuan Yang, and Lisa X. Xu

16.1 History of Synchrotron Radiation Imaging 63316.2 Principle of Synchrotron Radiation Imaging 63316.3 Advantage of SR X-ray Imaging 63416.4 SR X-ray Absorption-Contrast Imaging 63516.4.1 SR Angiography in Cerebral Vascular Disease 63616.4.1.1 Experimental Ischemic Stroke 63616.4.1.2 Detection of the Collateral Circulation in Rodents 63816.4.1.3 Application of Functional SR Angiography (fSRA) 63816.4.1.4 Examination of Functional Angiogenesis in vivo 64016.4.1.5 Evaluation of Cerebral Vasospasm in Subarachnoid Hemorrhage 64116.4.2 Applications in Other Diseases 64116.4.2.1 SR Angiography in Diabetes Research 64116.4.2.2 SR Angiography in Hypertension Research 64116.4.2.3 Brain Metastasis of Breast Cancer 64216.4.2.4 Detection of Hepatocellular Carcinoma 64316.4.2.5 SR Imaging in Spinal Cord Vasculature 64316.5 Phase-Contrast Imaging 64416.5.1 Detection of Early-Stage Lung Cancer 64416.5.2 Visualization of Spinal Cord Microvasculature 64416.5.3 In-Line PCI of Hepatic Portal Vein Embolization 64516.6 Development of SR Molecular Imaging 64516.6.1 Tumor Angiogenesis Imaging Using a Magnetite Nanocluster

Probe 64616.6.2 Characterization of Gold Nanorods in vivo 64716.6.3 Microbubble-Based SRPCI 64716.7 Microbeam Radiation Therapy (MRT) 64816.8 The Safety of SR Imaging 64816.9 Prospects 649

Abbreviations 649References 649

17 Integrative SAXS-Driven Computational Modeling ofBiomolecular Complexes 657Lingshuang Song, Lanyuan Lu, Wei Huang, Krishnakumar M. Ravikumar,Jie Meng, and Sichun Yang

17.1 Introduction 65717.2 Theoretical SAXS Computing for Protein, RNA/DNA, and Their

Complexes 66117.2.1 Scattering from a Solute Biomolecule Itself 66217.2.1.1 Atomic-Level Representation 662

Contents xv

17.2.1.2 Residue/Nucleotide-Simplified Representation 66217.2.2 Scattering from a Surrounding Hydration Layer 66417.3 Computational Generation of Candidate Conformations for SAXS

Data Interpretation 66617.3.1 Space-Filling Bead Modeling 66617.3.2 Rigid-Body Docking 66717.3.3 Flexible-Docking Simulations 66717.4 Structural Determination from Experimental SAXS Data 66817.4.1 Exhaustive Conformational Search 66817.4.2 The Use of SAXS Data in MD Simulations and Rigid-Body

Docking 66917.4.3 Strategies for SAXS-Based Ensemble Fitting 67017.5 Examples of SAXS Applications and Integration with Other

Biophysical Techniques 67217.5.1 Structural Characterization of Intrinsically Disordered Proteins 67217.5.2 Examples of Integrating SAXS, Hydroxyl Radical Footprinting, and

Docking Simulations 67317.6 Conclusions and Perspectives 675

Acknowledgments 676References 676

18 Applications of Synchrotron-Based Spectroscopic Techniquesin Studying Nucleic Acids and Nucleic-Acid-BasedNanomaterials 687Peiwen Wu, Yang Yu, Claire E. McGhee, Li H. Tan, Abhijit Mishra, Gerard Wong,and Yi Lu

18.1 Introduction 68718.2 Synchrotron-Based Spectroscopic Techniques in the Characterization

of Nucleic Acids 68918.2.1 Use of XAS and XES Spectroscopy in Studying Electronic Structures of

Nucleobases 69018.2.2 XAS and XES in Characterizing Electronic Structures of

Double-Stranded DNA 69118.2.3 SRCD for Probing the Secondary Structure of DNA Molecules 69218.2.4 Synchrotron-Based Spectroscopic Methods for Studying the

Structures of Surface-Bound Nucleic Acids 69418.2.5 XAS in Characterizing the Structures of Metal–Nucleic Acid

Complexes 69518.3 SAXS for Studying Electrostatics of Nucleic Acids 69718.3.1 Theories for Counterion Distribution 69918.3.2 Contemporary Theoretical Approaches to Polyelectrolyte

Electrostatics 70018.3.3 Ordered DNA Structures with Multivalent Ions 70118.3.4 Measurements of Counterion Distributions around DNA 70218.3.5 Folded RNA Structures with Multivalent Ions 70318.3.6 DNA Compaction by Osmotic Pressure 70318.3.7 Liquid Crystalline DNA Complexes and Autoimmune Diseases 704

xvi Contents

18.4 SAXS in Studying Conformations of Nucleic Acids 70618.4.1 Use of SAXS for Probing Intermediates in RNA Folding 70618.4.2 Use of SAXS for Studying Noncanonical Structures of DNA and RNA

Molecules 71118.5 Time-Resolved Synchrotron X-ray Footprinting in Studying the

Folding of Nucleic Acid Structures 71318.6 Synchrotron-Based Methods in Studying DNA-Functionalized

Nanomaterials 71618.6.1 Use of SAXS for Characterizing DNA Nanostructures 71718.6.2 Use of SAXS for Studying DNA-Functionalized Nanoparticle 3D

Assemblies 71818.7 Synchrotron Radiation for Studying DNA–Lipid Interaction 72518.8 Summary and Outlook 727

Acknowledgments 728References 728

19 X-ray Microscopy for Nanoscale 3D Imaging of Biological Cellsand Tissues 757Zhili Wang, Kun Gao, Dajiang Wang, Chunhai Fan, Ziyu Wu, and Shiqiang Wei

19.1 Introduction 75719.2 Intermediate-Energy X-ray Microscope 75919.2.1 Design of Intermediate-Energy TXM 75919.2.2 Image Contrast 76019.2.3 Radiation Dose 76119.2.4 Depth of Focus 76319.3 Discussions and Conclusion 763

Acknowledgments 765References 765

20 Synchrotron-Based X-ray Microscopy for NanoscaleBioimaging 767Ying Zhu, Lihua Wang, and Chunhai Fan

20.1 Introduction 76720.2 Synchrotron-Based Nanoscale Bioimaging in Cells 76820.2.1 Intracellular Distribution of Nanomaterials 76820.2.2 Cellular Effects of Nanodiamond–ion Complexes 77020.2.3 Nanodiamonds Mediated Sustained Drug Release in Cells 77320.3 Synchrotron-Based Nanoscale Bioimaging in Animals 77520.4 Synchrotron-Based Nanoscale Bioimaging in Plants 77920.5 Summary 779

References 781

Index 785

xvii

Preface

Synchrotron radiation is the electromagnetic radiation emitted when chargedparticles are accelerated radially. The most notable property of synchrotronradiation lies in its high brightness and high intensity, excelling conventionalX-rays by many orders of magnitude. Synchrotron radiation also features highlevel of polarization, wide tunability in energy/wavelength, and pulsed lightemission at tens of picoseconds. Hence, synchrotron light holds great promisefor a wide range of applications in many areas, especially in materials science,condensed matter physics, biology, and medicine. By exploiting the unparalleledproperties of synchrotron light, scientists from academia and industry havedeveloped a great number of techniques for probing material structures at almostall levels ranging from subnanometer (e.g., electronic structures), nanometer(e.g., nanomaterials), and micrometer to centimeter (e.g., medical imaging).

A synchrotron light source with specialized electron accelerators produceselectromagnetic radiation with characteristic polarization and generatedfrequencies covering the entire electromagnetic spectrum. Across the world,there are more than 70 synchrotron light sources that are in service for scientificand technical purposes. Most synchrotrons are located in the United States,Europe, and East Asia. After decades of development, the third generation syn-chrotron has become the mainstream and state of the art. The third generationsynchrotron is characteristic in its use special magnetic insertion devices (e.g.,wiggler and undulator), which are placed in the straight sections of the storagering. Consequently, third generation light sources typically have much brighterphoton beams than previous ones.

China has a long history of synchrotron studies. The first generation syn-chrotron light source, Beijing Synchrotron Radiation Facility (BSRF), whichstarted from 1984, is part of the Beijing Electron Positron Collider (BEPC)that was designed primarily for the purpose of high-energy physics. NationalSynchrotron Radiation Laboratory (NSRL) at the University of Science andTechnology of China (USTC) in Hefei hosts a second generation synchrotronlight source, which was opened for the public in 1991. This synchrotron has anelectron storage ring specifically designed to generate synchrotron radiation.After the successful construction and use of the two generations of synchrotronin mainland China, the Chinese government initiated the construction of theShanghai Synchrotron Radiation Facility (SSRF, or Shanghai Lightsource), thethird generation synchrotron radiation source, in 2004. This relatively new

xviii Preface

synchrotron with extremely bright X-rays was opened for the public in 2009.Since its opening, it has been one of the major players in the synchrotron club.To date, SSRF is the biggest scientific platform ever constructed for R&D inChina. It provides invaluable tools for scientists and engineers from universities,institutes, and industries in China and overseas. SSRF has a storage ring withthe energy of 3.5 GeV, which is the highest in medium-energy light sources.By taking advantage of insertion devices, SSRF can produce high brilliance,hard X-rays with 5–20 keV photon energy. SSRF produces full-wavelengthhomochromatic lights ranging from the far-infrared to the hard X-ray. Thetotal radiation power of SSRF at full is about 600 kW, its light flux is over1015 photon/(S 10−3 bw), and the light brilliance in the main spectra region is1017–1020 photon/(S mm2 mrad2 10−3 bw). Hence, it can offer high spatial reso-lution, high momentum resolution, and high temporal resolution for scientificresearch.

After the first-phase construction in 2009, SSRF hosted seven beamlinesincluding macromolecular crystallography, X-ray absorption fine structure(XAFS), hard X-ray microfocus, X-ray imaging, soft X-ray spectromicroscopy,X-ray diffraction (XRD), and small-angle X-ray scattering (SAXS). Afterthat, SSRF constructed five new beamlines dedicated to studies on proteinsciences, and a beamline dubbed “DREAMline” for high-resolution andwide-energy-range photoemission spectroscopy. Two more beamlines forangel-resolved and ambient-pressure photon electron spectroscopy are underconstruction. The Chinese government has approved of the second-phaseconstruction of SSRF beamlines, which comprises 16 new beamlines covering awide range of techniques and capabilities for materials, physical, and biologicalstudies. In addition, there will be five more user-funded beamlines for highpressure and energy sciences. By taking these into account, SSRF will possess∼40 beamlines by 2020.

In respect of the increasing popularity and impact of SSRF in China and overthe world, and to celebrate the 5-year anniversary of the operation of SSRF,the 10-year anniversary for her foundation, Advanced Materials (Wiley-VCH)launched a special issue on “Synchrotron for Materials Science” in 2014, underencouragement and great support from Dr Peter Gregory, the Editor-in-Chief.In this special issue, renowned researchers from main synchrotron centers allover the world were invited to contribute review papers on materials studieswith synchrotron. The topics of this thematic issue covers a wide range inmaterials science, including functional materials, biological materials, energymaterials, optical materials, and interfacial materials. They reflect cutting edgeresearch in these areas, demonstrating the power of using advanced synchrotrontechnologies for materials characterization and fabrication.

This special issue on Advanced Materials has not only shown high impact andvisibility in the synchrotron society but also attracted widespread attention invarious areas. However, due to space constraints in this single issue, we couldonly have 14 papers published, covering only a small portion of important areaswhere synchrotron can play key roles. Fortuitously, when we were having dinnerwith Peter and his wife, Dr Gudrun Walter, during the preparation of our specialissue, this topic came to the attention of Gudrun, who, as a book editor in Wiley,

Preface xix

kindly offered us to expand the special issue to a book. This is clearly a wise andelegant solution! Most authors of the issue almost instantly replied with positiveattitude when we approached them with this possibility. We also received thepromise to contribute chapters from several other leading experts who are notin the list of the special issue, for which we are very thankful. Editing this bookhas been a great honor for us. We very much appreciate the invitation and thesupport from Dr Gudrun Walter and the kind support from the staff members ofWiley-VCH. Our special thanks go to Dr Peter Gregory, without whose initiationnone of these could happen, and to Dr Duoduo Liang, who generously supportedthe editing and publishing of the special issue on Advanced Materials.

Zhentang Zhao and Chunhai FanOctober 2017Shanghai

xxi

About the Editors

Zhentang Zhao is a research professor of acceleratorscience and technology at Shanghai Institute of AppliedPhysics (SINAP), Chinese Academy of Sciences (CAS).After receiving his PhD degree from Tsinghua University,Beijing, Dr Zhao was working on Beijing Electron andPositron Collider (BEPC) operation and its luminosityupgrading program at the Institute of High EnergyPhysics, CAS, from 1990 to 1998. During this period,

he was working on LHC accelerator R&D at CERN from 1995 to 1996. Lateron, he was working on Shanghai Synchrotron Radiation Facility (SSRF) atSINAP as deputy project director and in charge of the SSRF accelerator designand construction from 1999 to 2009. Since 2002, he has been working on theSDUV-FEL and SXFEL as the project director. He has served KEK-PF, Japan,Pohang Accelerator Laboratory, Korea, Synchrotron Light Research Institute,Thailand, and LNLS Sirius Accelerator, Brazil, as a member of their InternationalAdvisory Committees, and he is a member of ACFA. He became the director ofSINAP in 2009 and the director of SSRF in 2010.

Chunhai Fan obtained his BSc and PhD from the Depart-ment of Biochemistry at Nanjing University in 1996 and2000. After his postdoctoral research at the University ofCalifornia, Santa Barbara (UCSB), he joined the faculty atShanghai Institute of Applied Physics (SINAP), ChineseAcademy of Sciences (CAS) in 2004. He is now professorand chief of the Division of Physical Biology at SINAP andthe Center of Bioimaging at the Shanghai SynchrotronRadiation Facility (SSRF). He is also an adjunct in theSchool of Molecular Sciences, and the Biodesign Institute

at Arizona State University. He is an elected fellow of the International Societyof Electrochemistry (ISE) and a fellow of the Royal Society of Chemistry (FRSC).He also serves as an associate editor of ACS Applied Materials & Interfaces, andis on the editorial board of more than 10 international journals. His researchinterests focus on biosensors, biophotonics, and DNA nanotechnology. He haspublished more than 300 papers in peer-reviewed journals. He was recognizedas High Cited Researchers in 2014 and in 2015 by Thomson Reuters.

1

1

Synchrotron Light SourcesZhentang Zhao

Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences,239 Zhangheng Road, Pudong New District, Shanghai, 201204, China

1.1 Introduction

Synchrotron light sources or storage ring light sources are indispensablelarge-scale scientific tools for basic and applied frontier research in variousfields, ranging from materials science, energy science, life science, environmentalscience, to archaeological applications. Their development has evolved fromthe first generation to the third generation in the past five decades, and hasnow entered into the fourth generation phase with even higher brightnessand coherence radiation based on the diffraction limited storage ring concept.Currently, there are over 50 synchrotron light sources in operation in morethan 20 countries, and over 15 new synchrotron radiation facilities have beenset up worldwide in various stages of commissioning, construction, design, orplanning. In this chapter, we will introduce the basics of synchrotron radiationgeneration, storage ring physics, and radiation characteristics, which are ofinterest to synchrotron radiation users. We will also present the current statusof the storage ring light source development across the world. This chapteris intended to cover only the basic concepts of synchrotron light source andreview the current status on its development. For readers who are interestedin the detailed physics and related technologies, we recommend the books ormonographs in Refs [1–15].

1.2 Synchrotron Radiation Generation

When a relativistic electron moves on a curved path at nearly the speed of light, itemits electromagnetic radiation. This radiation was theoretically predicated andstudied by Lienard, Wiechert, and Schott in around 1900, and its visible part wasfirst observed at the 70 MeV GE electron synchrotron in 1947. Since then, thiselectromagnetic radiation has been called synchrotron radiation.

Synchrotron, a kind of circular particle accelerator, can accelerate charged par-ticles from low energy to high energy or keep the particles circulating on the

Synchrotron Radiation in Materials Science: Light Sources, Techniques, and Applications, First Edition.Edited by Chunhai Fan and Zhentang Zhao.© 2018 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2018 by Wiley-VCH Verlag GmbH & Co. KGaA.

2 1 Synchrotron Light Sources

e–

e–

e–

1γ

γ

γ

1

1

N

λ

λ

λ

>>

F Bending magnetradiation

Wiggler radiation

Undulator radiation

F

F

hω

hω

hω

Figure 1.1 Synchrotron radiation from bending magnets, wigglers, and undulators [3].(Cambridge University Press.)

circular orbit at a constant energy for hours and days, which is referred to asstorage ring. The electron storage ring is the core part of synchrotron light source.Relativistic electrons, circulating in the storage ring, generate synchrotron radia-tion when passing through three on-path major source components: the bendingmagnet, wiggler, and undulator magnets, as shown in Figure 1.1.

This synchrotron radiation is extremely intense over a broad range of wave-lengths from infrared through the visible and ultraviolet range, to the soft andhard X-ray part of the electromagnetic spectrum. Bending magnet radiation hasbroad spectrum and good photon flux; wiggler radiation provides higher photonenergies and more photon flux; and undulator provides brighter radiation withsmaller spot size and partial coherence.

1.2.1 Radiation from Bending Magnet

A bending magnet, also called a dipole magnet, consists of opposite poles, namelythe north and south poles, which are on opposite sides of the magnet providinga homogeneous magnetic field.

As shown in Figure 1.2, when a relativistic electron of energy E travels on acircular trajectory in a dipole magnet of main field By =B and bending radius 𝜌,where G=B𝜌= p/e, the ratio of momentum to charge, is often called the magneticrigidity, it radiates electromagnetic power confined in a cone with ±1/𝛾 openingtoward its moving direction. Its radiation power can be expressed as,

Ps =23

r0m0c2 c𝛽4𝛾

4

𝜌2 ,

1.2 Synchrotron Radiation Generation 3

S

N

Synchrotron

radiation

Electron beam

y

x

z

Electron beam

Photon

Δφ

ρ

Figure 1.2 Synchrotron radiation from bending magnet.

where e is the electron charge, m0 is the electron rest mass, 𝛽c is the electronmoving speed, 𝛾 = E/(m0c2) is the Lorentz factor, and r0 = e2∕(4𝜋𝜖0m0c2) is theelectron classical radius. Integrating the radiated power over an isomagnetic stor-age ring with constant 𝜌 gives an electron energy loss in one turn due to thesynchrotron radiation as follows,

U0 = 4𝜋3

r0m0c2𝛽

3 𝛾4

𝜌.

In engineering units,

U0[keV] = 88.5 E4[GeV]𝜌[m]

.

For an electron beam traveling through a dipole magnet of bending angle Δ𝜑with average current of Ib, the radiated power is,

Pd = 23

r0m0c2 c𝛽4𝛾

4

e𝜌Δ𝜑Ib.

For an electron beam circulating in storage ring (with average current of Ib andrevolution time of T0), the total radiated power per turn is,

P0 =IbU0

e= 4𝜋

3r0m0c2

𝛽3 𝛾

4

e𝜌Ib.

When an electron travels on the circular path in a dipole magnet, its emit-ting radiation on a fixed target outside the orbit circle comes only from a shortarc of electron trajectory, this short synchrotron radiation pulse covers a widecontinuous spectrum of photon energies from infrared to X-rays depending onthe electron energy and the bending magnetic field. A so-called critical photonenergy 𝜀c (or critical frequency 𝜔c) is defined as the photon energy which dividesthe synchrotron radiation into two spectral regions with equal radiated power,

𝜔c =32

c𝛾3

𝜌,

𝜀c =h

2𝜋𝜔c =

3hc4𝜋

𝛾3

𝜌.

In engineering units,𝜀c [keV] = 0.665E2 [GeV]B [T].

The significance of the critical photon energy is that it sets up the upper bundfor the synchrotron radiation spectrum, and the spectral power falls rapidly for

4 1 Synchrotron Light Sources

photon energies above this critical value. The complete spectral distribution ofsynchrotron radiation can be calculated using the Fourier transform of the radi-ation electric field,

dPs

d𝜔=

Ps

𝜔cS(𝜔

𝜔c

),

S(𝜔

𝜔c

)=

9√

38𝜋

𝜔

𝜔c ∫∞

𝜔∕𝜔c

K5∕3(x)dx.

The K5/3(x) above and K2/3(x) below are the modified Bessel functions. Theon-axis spectral photon flux Nph (defined as the number of photons per unit time)per unit solid angle in a bandwidth Δ𝜔/𝜔 and for a circulating beam current Ib isa more useful parameter. It can be written as,

dNph

dΩ=

d2Nph

d𝜃d𝜓=

3𝛼E2Ib

4𝜋2e(mc2)2Δ𝜔𝜔

(𝜔

𝜔c

)2

K22∕3

(𝜔

2𝜔c

),

where 𝛼 = e2/(2ch𝜀0) is the fine structure constant. In engineering units, and with0.1% bandwidth,

dNph

dΩ[photons/sec/mrad2] = 1.33 × 1013E2 [GeV]Ib [A]

(𝜔

𝜔c

)2

K22∕3

(𝜔

2𝜔c

).

The on-axis photon flux per unit deflection angle is,

dNph

d𝜓=

Ps

𝜔chΔ𝜔𝜔

S(𝜔

𝜔c

).

The photon flux at energy 𝜀 is given by,

Nph, 𝜀 =Ps

𝜀c𝜀S(𝜔

𝜔c

)=

9√

3𝜋2

Ps

h2𝜔2c ∫

∞

𝜔∕𝜔c

K5∕3(x)d x

and by integrating the photon flux for 𝜀 from zero to infinity, the total number ofradiating photons per unit time is,

Nph = ∫+∞

0Nph, 𝜀d𝜀 =

15√

38

Ps

𝜀c.

The total photon flux at energy 𝜀 for the storage ring with average beam currentIb is,

Nph, 𝜀 =3√

32

r0m0c2𝛽

3𝛾

4

e𝜌𝜀2c

Ib ∫∞

𝜔∕𝜔c

K5∕3(x)d x.

The total photon flux

Nph =5𝜋

√3

2e𝜀cr0m0c2

𝛽3 𝛾

4

𝜌Ib.

1.2 Synchrotron Radiation Generation 5

1.2.2 Radiation from Undulator

Undulator and wiggler, or so-called insertion devices, consisting of a series ofalternating magnet poles, deflect the electron periodically in opposite directions.They are installed in the storage ring straight sections and optimized for gener-ating specific synchrotron radiation characteristics.

1.2.2.1 Planar Undulator RadiationThe radiation from planar undulator with Nu period has the same physical pro-cess as a short bending magnet, but the Nu times of oscillations that an elec-tron performs in an undulator transform the radiation into quasi-monochramaticwith finite line width and within a cone of 1∕(𝛾N1∕2

u ). This makes the planar undu-lator radiation intensity effectively enhanced with reasonable radiation power(Figure 1.3).

In a planar undulator with period length 𝜆u and peak field B0, the main mag-netic field is By =B0 sin(2𝜋s/𝜆u), and the average instantaneous radiation powerof an electron traveling in planar undulator is,

Pu =r0cm0c2

𝛾2K2

3

(2𝜋𝜆u

)2

,

where K is the so-called deflection parameter and is defined as,

K =ecB0𝜆u

2𝜋m0c2 .

The total energy emitted by an electron from the undulator with a length ofLu = Nu𝜆u is,

Uu =r0m0c2

𝛾2K2Lu

3

(2𝜋𝜆u

)2

.

The total average radiated power of an electron beam with current of Ib passingthrough the undulator is,

Pu, I =r0m0c2

𝛾2K2LuIb

3e

(2𝜋𝜆u

)2

.

In engineering units,

Pu, I [kW] = 0.633E2 [GeV]B20 [T]Lu[m]Ib [A] .

Electronbeam Synchrotron

radiation

y

x

Photon

θ

z

S

N NS S

NNS

Figure 1.3 Synchrotron radiation from undulator.