Cover
Half-Title Page
Title Page
Copyright Page
Dedication
Table of Contents
Preface
About the Author
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, and 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
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 Liquid–Liquid Phase-Separated (LLPS) Biomolecular Condensates
2.2.7 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
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: The 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 Semiconductors, Metal-Based Fluorophores, and Nanodiamonds
3.5.8 Fluorescent Proteins and Amino Acids
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
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 Efficiency of FRET
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 or Thick 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
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 and CryoET
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
6 Forces: Methods that Measure and/or Manipulate Biological Forces or Use Forces in Their Principal 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 Tweezer 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
6.6.8 Tethered Particle Motion and Acoustic Trapping
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
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
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
8.3.6 Modeling Biomolecular Liquid–Liquid Phase Separation
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
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, Biomimicry, 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 The Impact of AI, ML, and Deep Learning on Biophysics and the Physics of Life
9.7 Summary Points
Questions
References
Index
Biophysics: Tools and Techniques for the Physics of Life
Cover
Half-Title Page
Title Page
Copyright Page
Dedication
Table of Contents
Preface
About the Author
1 Introduction: Toolbox at the Physical–Life Science Interface
Index
i
ii
iii
iv
v
vi
vii
viii
ix
x
xi
xii
xiii
xiv
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442