Biophysics Tools and Techniques by Leake, Mark C. -- Read -- Imperial Library of Trantor

Index

Cover Half Title Title Page Copyright Page Dedication Table of Contents Preface Author Chapter 1 Introduction: Toolbox at the Physical–Life Science Interface

1.1 Motivation for Biophysics 1.2 What Do We Mean by a “Toolbox?” 1.3 Makeup of the Subsequent Chapters in This Book

1.3.1 Detection/Sensing/Imaging Techniques 1.3.2 Experimental Biophysical Methods Primarily Relating Especially to Force 1.3.3 Complementary Experimental Technologies 1.3.4 Theoretical Biophysics Tools

1.4 Once More, unto the Breach 1.5 Summary Points Questions References

Chapter 2 Orientation for the Bio-Curious: The Basics of Biology for the Physical Scientist

2.1 Introduction: The Material Stuff of Life 2.2 Architecture of Organisms, Tissues, and Cells and the Bits Between

2.2.1 Cells and Their Extracellular Surroundings 2.2.2 Cells Should Be Treated Only as a “Test Tube of Life” with Caution 2.2.3 Cells Categorized by the Presence of Nuclei (or Not) 2.2.4 Cellular Structures 2.2.5 Cell Membranes and Walls 2.2.6 Viruses

2.3 Chemicals That Make Cells Work

2.3.1 Importance of Carbon 2.3.2 Lipids and Fatty Acids 2.3.3 Amino Acids, Peptides, and Proteins 2.3.4 Sugars 2.3.5 Nucleic Acids 2.3.6 Water and Ions 2.3.7 Small Organic Molecules of Miscellaneous Function

2.4 Cell Processes

2.4.1 Central Dogma of Molecular Biology 2.4.2 Detection of Signals 2.4.3 Trapping “Negative” Entropy 2.4.4 Natural Selection, Neo-Darwinism, and Evolution 2.4.5 “Omics” Revolution

2.5 Physical Quantities in Biology

2.5.1 Force 2.5.2 Length, Area, and Volume 2.5.3 Energy and Temperature 2.5.4 Time 2.5.5 Concentration and Mass 2.5.6 Mobility

2.6 Summary Points Questions References

Chapter 3 Making Light Work in Biology: Basic, Foundational Detection and Imaging Techniques Involving Ultraviolet, Visible, and Infrared Electromagnetic Radiation Interactions with Biological Matter

3.1 Introduction 3.2 Basic UV–VIS–IR Absorption, Emission, and Elastic Light Scattering Methods

3.2.1 Spectrophotometry 3.2.2 Fluorimetry 3.2.3 Flow Cytometry and Fluorescence-Assisted Cell Sorting 3.2.4 Polarization Spectroscopy 3.2.5 Optical Interferometry 3.2.6 Photothermal Spectroscopy

3.3 Light Microscopy Basics

3.3.1 Magnification 3.3.2 Depth of Field 3.3.3 Light Capture from the Sample 3.3.4 Photon Detection at the Image Plane

3.4 Nonfluorescence Microscopy

3.4.1 Bright-Field and Dark-Field Microscopy 3.4.2 Contrast Enhancement Using Optical Interference 3.4.3 Digital Holographic Microscopy

3.5 Fluorescence Microscopy: The Basics

3.5.1 Excitation Sources 3.5.2 Fluorescence Emission 3.5.3 Multicolor Fluorescence Microscopy 3.5.4 Photobleaching of Fluorophores 3.5.5 Organic Dye Fluorophores 3.5.6 FlAsH/ReAsH Probes 3.5.7 Semiconductor- and Metal-Based Fluorophores 3.5.8 Fluorescent Proteins 3.5.9 SNAP- and CLIP-Tags 3.5.10 Overcoming Cellular Autofluorescence

3.6 Basic Fluorescence Microscopy Illumination Modes

3.6.1 Wide-Field Modes of Epifluorescence and Oblique Epifluorescence 3.6.2 Total Internal Reflection Fluorescence 3.6.3 Fluorescence Polarization Microscopy 3.6.4 Confocal Microscopy 3.6.5 Environmental Fluorescence Microscopy 3.6.6 Slimfield and Narrow-Field Epifluorescence Microscopy

3.7 Summary Points Questions References

Chapter 4 Making Light Work Harder in Biology: Advanced, Frontier UV–VIS–IR Spectroscopy and Microscopy for Detection and Imaging

4.1 Introduction 4.2 Super-Resolution Microscopy

4.2.1 Abbe Optical Resolution Limit 4.2.2 Localization Microscopy: The Basics 4.2.3 Making the Most Out of a Limited Photon Budget 4.2.4 Advanced Applications of Localization Microscopy 4.2.5 Limiting Concentrations for Localization Microscopy 4.2.6 Substoichiometric Labeling and Delimited Photobleaching 4.2.7 Genetic Engineering Approaches to Increase the Nearest-Neighbor Distance 4.2.8 Stochastic Activation and Switching of Fluorophores 4.2.9 Stochastic Blinking 4.2.10 Reshaping the PSF 4.2.11 Patterned Illumination Microscopy 4.2.12 Near-Field Excitation 4.2.13 Super-Resolution in 3D and 4D

4.3 Förster Resonance Energy Transfer

4.3.1 FRET Efficiency 4.3.2 Förster Radius and the Kappa-Squared Orientation Factor 4.3.3 Single-Molecule FRET

4.4 Fluorescence Correlation Spectroscopy

4.4.1 Determining the Autocorrelation of Fluorescence Data 4.4.2 FCS on Mixed Molecule Samples 4.4.3 FCS on More Complex Samples

4.5 Light Microscopy of Deep Samples

4.5.1 Deconvolution Analysis 4.5.2 Adaptive Optics for Correcting Optical Inhomogeneity 4.5.3 Ptychography Methods for Numerical Focusing 4.5.4 Multiphoton Excitation 4.5.5 Second-Harmonic Imaging 4.5.6 Light Sheet Microscopy 4.5.7 Optical Coherence Tomography 4.5.8 Removing the Deep Tissue Barrier

4.6 Advanced Biophysical Techniques Using Elastic Light Scattering

4.6.1 Static Light Scattering 4.6.2 Dynamic Light Scattering 4.6.3 Electrophoretic Light Scattering 4.6.4 Interferometric Elastic Light Scattering for Molecular Imaging

4.7 Tools Using the Inelastic Scattering of Light

4.7.1 Raman Spectroscopy 4.7.2 Resonance Raman Spectroscopy 4.7.3 Raman Microscopy 4.7.4 Coherent Raman Spectroscopy Methods 4.7.5 Brillouin Light Scattering

4.8 Summary Points Questions References

Chapter 5 Detection and Imaging Tools That Use Nonoptical Waves: Radio and Microwaves, Gamma and X-Rays, and Various High-Energy Particle Techniques

5.1 Introduction 5.2 Electron Microscopy

5.2.1 Electron Matter Waves 5.2.2 Fixing a Sample for Electron Microscopy and Generating Contrast 5.2.3 Generating Contrast in Electron Microscopy 5.2.4 Transmission Electron Microscopy 5.2.5 Scanning Electron Microscopy 5.2.6 Cryo-EM 5.2.7 Correlative Light and Electron Microscopy 5.2.8 Electron Diffraction Techniques

5.3 X-Ray Tools

5.3.1 X-Ray Generation 5.3.2 X-Ray Diffraction by Crystals 5.3.3 X-Ray Diffraction by Noncrystalline Samples 5.3.4 X-Ray Microscopy Methods 5.3.5 X-Ray Spectroscopy 5.3.6 Radiation Damage of Biological Samples by X-Rays and Ways on How to Minimize It

5.4 NMR and Other Radio Frequency and Microwave Resonance Spectroscopies

5.4.1 Principles of NMR 5.4.2 NMR Chemical Shift 5.4.3 Other NMR Energy Coupling Processes 5.4.4 Nuclear Relaxation 5.4.5 NMR in Practice 5.4.6 NMR Spectroscopy Pulse Sequences 5.4.7 Multidimensional NMR 5.4.8 Electron Spin Resonance and Electron Paramagnetic Resonance 5.4.9 Terahertz Radiation Applications and Spectroscopies

5.5 Tools That Use Gamma Rays, Radioisotope Decays, and Neutrons

5.5.1 Mössbauer Spectroscopy 5.5.2 Radioisotope Decay 5.5.3 Neutron Diffraction and Small-Angle Scattering

5.6 Summary Points Questions References

Chapter 6 Forces: Methods That Measure and/or Manipulate Biological Forces or Use Forces in Their Principle Mode of Operation on Biological Matter

6.1 Introduction 6.2 Rheology and Hydrodynamics Tools

6.2.1 Chromatography Techniques 6.2.2 Centrifugation Tools 6.2.3 Tools That Utilize Osmotic Forces 6.2.4 Deforming Biological Matter with Flow

6.3 Optical Force Tools

6.3.1 Basic Principles of Optical Tweezers 6.3.2 Optical Tweezers Designs in Practice 6.3.3 Characterizing Displacements and Forces in Optical Tweezers 6.3.4 Applications of Optical Tweezers 6.3.5 Non-Gaussian Beam Optical Tweezers 6.3.6 Controlling Rotation Using “Optical Spanners” 6.3.7 Combining Optical Tweezers with Other Biophysical Tools 6.3.8 Optical Microscopy and Scattering Methods to Measure Biological Forces

6.4 Magnetic Force Methods

6.4.1 Magnetic Bead–Mediated Purification Methods 6.4.2 Mass Spectrometry 6.4.3 Magnetic Tweezers

6.5 Scanning Probe Microscopy and Force Spectroscopy

6.5.1 Principles of AFM Imaging 6.5.2 Forces Experienced during AFM Imaging 6.5.3 AFM Imaging Modes 6.5.4 Single-Molecule AFM Force Spectroscopy 6.5.5 AFM “Cut and Paste” 6.5.6 AFM and Fluorescence Microscopy 6.5.7 AFM to Measure Cellular Forces 6.5.8 Scanning Tunneling Microscopy 6.5.9 Scanning Ion Conductance Microscopy 6.5.10 Ultrasonic Force Microscopy

6.6 Electrical Force Tools

6.6.1 Gel Electrophoresis 6.6.2 Electrophysiology 6.6.3 Solid-State Nanopores 6.6.4 Synthetic Soft-Matter Nanopores 6.6.5 Electrorotation 6.6.6 ABEL Trapping 6.6.7 Piezoelectric Technologies

6.7 Tools to Mechanically Probe Cells and Tissues

6.7.1 Mechanical Stretch Techniques on Muscle Fibers and Myofibrils 6.7.2 Mechanical Stress Techniques on Nonmuscle Tissues

6.8 Summary Points Questions References

Chapter 7 Complementary Experimental Tools: Valuable Experimental Methods That Complement Mainstream Research Biophysics Techniques

7.1 Introduction 7.2 Bioconjugation

7.2.1 Biotin 7.2.2 Carboxyl, Amine, and Sulfhydryl Conjugation 7.2.3 Antibodies 7.2.4 “Click” Chemistry 7.2.5 Nucleic Acid Oligo Inserts 7.2.6 Aptamers

7.3 Model Organisms

7.3.1 Model Bacteria and Bacteriophages 7.3.2 Model Unicellular Eukaryotes or “Simple” Multicellular Eukaryotes 7.3.3 Model Plants 7.3.4 Model Animals

7.4 Molecular Cloning

7.4.1 Cloning Basics 7.4.2 Site-Directed Mutagenesis 7.4.3 Controlling Gene Expression 7.4.4 DNA-Encoded Reporter Tags

7.5 Making Crystals

7.5.1 Biomolecule Purification 7.5.2 Crystallization 7.5.3 Treatment after Crystallization 7.5.4 Photonic Crystals

7.6 High-Throughput Techniques

7.6.1 Smart Fabrication Techniques 7.6.2 Microfluidics 7.6.3 Optical “Omics” Methods 7.6.4 “Smart” Sample Manipulation

7.7 Characterizing Physical Properties of Biological Samples in Bulk

7.7.1 Calorimetry 7.7.2 Electrical and Thermal Properties of Tissues 7.7.3 Bulk Magnetic Properties of Tissues 7.7.4 Tissue Acoustics

7.8 Biomedical Physics Tools

7.8.1 Magnetic Resonance Imaging 7.8.2 X-Rays and Computer-Assisted (or Computerized) Tomography 7.8.3 Single-Photon Emission CT and Positron Emission Tomography 7.8.4 Ultrasound Techniques 7.8.5 Electrical Signal Detection 7.8.6 Infrared Imaging and Thermal Ablation 7.8.7 Internalized Optical Fiber Techniques 7.8.8 Radiotherapy Methods 7.8.9 Plasma Physics in Biomedicine

7.9 Summary Points Questions References

Chapter 8 Theoretical Biophysics: Computational Biophysical Tools, and Methods That Require a Pencil and Paper

8.1 Introduction 8.2 Molecular Simulation Methods

8.2.1 General Principles of MD 8.2.2 Classical MD Simulations 8.2.3 Monte Carlo Methods 8.2.4 Ab Initio MD Simulations 8.2.5 Steered MD 8.2.6 Simulating the Effects of Water Molecules and Solvated Ions 8.2.7 Langevin and Brownian Dynamics 8.2.8 Coarse-Grained Simulation Tools 8.2.9 Software and Hardware for MD 8.2.10 Ising Models

8.3 Mechanics of Biopolymers

8.3.1 Discrete Models for Freely Jointed Chains and Freely Rotating Chains 8.3.2 Continuum Model for the Gaussian Chain 8.3.3 Wormlike Chains 8.3.4 Force Dependence of Polymer Extension 8.3.5 Real Biopolymers

8.4 Reaction, Diffusion, and Flow

8.4.1 Markov Models 8.4.2 Reaction-Limited Regimes 8.4.3 Diffusion-Limited Regimes 8.4.4 Fluid Transport in Biology

8.5 Advanced In Silico Analysis Tools

8.5.1 Image Processing, Segmentation, and Recognition 8.5.2 Particle Tracking and Molecular Stoichiometry Tools 8.5.3 Colocalization Analysis for Determining Molecular Interactions in Images 8.5.4 Convolution Modeling to Estimate Protein Copy Numbers in Cells 8.5.5 Bioinformatics Tools 8.5.6 Step Detection

8.6 Rigid-Body and Semirigid-Body Biomechanics

8.6.1 Animal Locomotion 8.6.2 Plant Biomechanics 8.6.3 Tissue and Cellular Biomechanics 8.6.4 Molecular Biomechanics

8.7 Summary Points Questions References

Chapter 9 Emerging Biophysics Techniques: An Outlook of the Future Landscape of Biophysics Tools

9.1 Introduction 9.2 Systems Biology and Biophysics: “Systems Biophysics”

9.2.1 Cellular Biophysics 9.2.2 Molecular Networks

9.3 Synthetic Biology and Bionanotechnology

9.3.1 Common Principles: Templates, Modularity, Hierarchy, and Self-Assembly 9.3.2 Synthesizing Biological Circuits 9.3.3 DNA Origami 9.3.4 Biofuels, Bioplastics, and a Greener Environment 9.3.5 Engineering Artificial Peptides, Proteins, and Larger Protein Complexes 9.3.6 Biomimetic Materials 9.3.7 Hybrid Bio/Bio–Bio Devices

9.4 Personalizing Healthcare

9.4.1 Lab-on-a-Chip and Other New Diagnostic Tools 9.4.2 Nanomedicine 9.4.3 Designer Drugs through In Silico Methods

9.5 Extending Length and Time Scales to Quantum and Ecological Biophysics

9.5.1 Quantum Biology 9.5.2 From Cells to Tissues 9.5.3 From Organisms to Ecosystems

9.6 Summary Points Questions References

Index

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