A
Ab initio MD simulations, 287–289
Absorbance, 55
Acousto-optic deflector (AOD), 90, 186–188
Acousto-optic modulator, 92
Acousto-optic tunable filter (AOTF), 69
Adaptive optics (AO), 120
Additive manufacturing, 257
Adenosine triphosphate (ATP), 17, 31, 37–39
Advection-diffusion equation, 319
AFM, see Atomic force microscopy
Agarose, 215
Airy ring, 98
a/LCI, see Angle-resolved low-coherence interferometry
Alcohol dehydrogenase, 288
Alkylation, 235
O6-Alkylguanine-DNA alkyltransferase (AGT), 78
Allostery, 298
α-helix, 24
AMBER, see Assisted Model Building with Energy Refinement
Amine, 234
Analytical ultracentrifugation, 180
Angle-resolved low-coherence interferometry (a/LCI), 125
Anomalous diffusion, 118, 319–320
Antibodies, see Immunoglobulin
Anti-DIG, 236
Antigen, 236
Antimatter, 271
AO, see Adaptive optics
AOD, see Acousto-optic deflector
AOTF, see Acousto-optic tunable filter
APD, see Avalanche photodiode
Apoptosis, see Programmed cell death
Aptamers, 237
Archaea, 13
Arc lamp, 68
Assisted Model Building with Energy Refinement (AMBER), 295–296
Astigmatism imaging, 109
Atomic force acoustic microscopy, see Ultrasonic force microscopy
Atomic force microscopy (AFM), 290
ATP, see Adenosine triphosphate
Auger electron spectroscopy, see X-ray photoelectron spectroscopy
Autocorrelation function, 117
Auto fluorescence, 78
Avalanche photodiode (APD), 63
Avidin, see Streptavidin
Axial spatial resolution, 87
Azide–alkyne Huisgen cycloaddition, see Click chemistry
B
Back focal plane detection (BFP detection), 188–189
Bacteria, 13
Bacteriophages, 238
Baker’s yeast, see Saccharomyces
Barabási–Albert model, 351
Barium meal, 271
Basic alignment search tool (BLAST), 335
Beeman algorithm, 281
Bending free energy, 341
Bessel beam, 87
Bessel function, 98
Bessel trap, 190
β-barrel, 24
β-sheet, 24
BFP detection, see Back focal plane detection
Bifunctional fluorescence complementation (BiFC), 103–104, 245
Binding-activated localization microscopy, 105
Binomial nomenclature, 14
Bioarcheology, 158
Biocompatible materials, 363
Biocomputation, 363
Biological circuits, 355
Biological transistor, 363–364
Biomimetic materials, 226, 337, 363
Bio nanotechnology, 354
Bioplastics, 361
Bioremediation, 361
Biosensors, see Lab-on-a-chip
Biotribology, 337
Biplane imaging, 108
Bjerrum length, 283
BLAST, see Basic alignment search tool
Blinking, see Photo blinking
Blinking assisted localization microscopy, 105
Blood vessels, 370
BLS, see Brillouin scattering
Bohr radius, 76
Bond order, 283
Bone, 370
Born–Oppenheimer approximation, 281
Bosons, 288
Bragg diffraction, 147, 186–187
Bragg peak frequency, 154
Bragg’s law, 147
Bremsstrahlung radiation, 150
Brenner potential, 289
Brillouin doublet, 196
Brillouin microscopy, 134
Brillouin scattering, 134, 196
Brillouin spectroscopy, 134
Broadband laser, 69
Brownian diffusion, 47, 117, 319–320
Brownian dynamics, see Langevin dynamics
Budding yeast, see Saccharomyces
Butanol, 361
Butterfly wings, 253
C
Cadmium selenide, 75
Cadmium telluride, 75
Caenorhabditis, see Flatworm
cAMP, see Cyclic adenosine monophosphate
Carbohydrates, see Sugars
Carboxyl, 234
Carboxysomes, 17
Cartilage, 338
CAT, see Computer-assisted tomography
Cauchy equation, 80
Caveolae, 84
CCD, see Charge-coupled device
CD, see Circular dichroism
Cell
membranes, 15, 17–18, 21–22, 66, 210
signaling, 351
squeezing, 242
Cellular differentiation, 40
Central dogma of molecular biology, 32–35
Charge-coupled device (CCD), 63–64
CHARMM, see Chemistry at HARvard Macromolecular Mechanics
Chaste, 338
Chemical imaging, see Hyperspectral imaging
Chemical potential, 250
Chemical shift, 161
Chemistry at HARvard Macromolecular Mechanics (CHARMM), 295–296
Chemoattractants, 349
Chemorepellants, 349
Chemotaxis, 68, 299–300, 324, 349
Chinese hamster ovary cells, see Immortal cells
Chirality, 23
Chlamydomonas, 239
Chromatography, 180
Cilia, 341
Circular dichroism (CD), 57–58
Clausius–Mossotti factor, 223
CLEM, see Correlative light and electron microscopy
Clustered regularly interspaced short palindromic repeat (CRISPR), 244
CMOS, see Complementary MOS
Coarse-grained simulations, 294–295
Codons, 362
Coherence beating, 373
Coherence length, 125
Coherent anti-stokes Raman scattering (CARS), 133
Coherent stokes Raman scattering (CSRS), 133
Coherent x-ray diffraction imaging (CXDI), 156
Colocalization analysis, 331–333
Colorimetry, 55
Comparative biomechanics, 337
Complementary MOS (CMOS), 64
Computer-assisted tomography (CAT), 268, 270–271
Computerized tomography (CT), 268
Condenser, 61, 64–68, 140, 153, 156, 189
Confocal theta microscopy, 87
Confocal volume, 86
Conformational spreading, 299
Connective tissue, 43, 210, 225, 239
Connectome, 240
Consciousness, 374
Contact mechanics, 337
Convolution modelling, 333–334
Coomassie Blue, 216
Corner frequency, 190
Correlative light and electron microscopy (CLEM), 146–147
Coulomb forces, 43, 170, 282–283, 373
Counter ions, 293
Covalent bonds, 20
CRISPR, see Clustered regularly interspaced short palindromic repeat
Critical angle, 80
Cryoembedding, 142
Cryofixation, 142
Cryosubstitution, 142
Cryptochrome, 374
robots, 250
window, 250
Crystal resonator, 224
CSRS, see Coherent stokes Raman scattering
CXDI, see Coherent x-ray diffraction imaging
Cyanobacteria, 17
Cyclic adenosine monophosphate, 349
Cyclodextrin, 220
Cyclotron, 151
Cysteine scanning mutagenesis, 243
D
DAB, see Diaminobenzidine
Danio, see Zebrafish
Dark field microscopy, 65
Dark noise, 100
Dark population, 103
Death sensors, 123
Debye–Hückel approximation, 293
Debye length, 283
Debye–Scherrer method, 154
Deconvolution, 119
Defocusing microscopy, 64
Deformable mirrors, 120
Delayed-coincidence methods, 272
Dementia, 163
Dendritic fibers, 174
Density gradient, 181
Deoxyribose nucleic acid (DNA), 27–30
absorbance, 54
ligase, 241
mechanics, 194
sequencing, 368
Depth of field, 62
Depth of focus, 62
Depth of penetration, 81
Deuterium, 162
Dialysis, see Osmosis
Diaminobenzidine (DAB), 145
DIC, see Differential interference contrast microscopy
Dielectric heating, see Radio frequency heating
Dielectric spectroscopy, see Electrical impedance spectroscopy
Differential interference contrast microscopy (DIC), 66–67
Differential scanning calorimetry, 268
Diffraction before destruction, 152
limited, 310
-to-capture, 319
DIG, see Digoxigenin
Digital holographic microscopy, 68
Digitalis, 236
Digital micromirror array, 188
Digoxigenin (DIG), 236
Dihedrals, 283
Dipole moment, 162, 184, 200–201, 206, 222, 224
Dipole orientation factor, 113
Directed diffusion, 319
Disequilibrium, 312
DLS, see Dynamic light scattering
DNA, see Deoxyribose nucleic acid
DNA sequencing, 368
Doob–Gillespie algorithm, see Gillespie algorithm
DPI, see Dual polarization interferometry
Drosophila, 240
Drug delivery, 369
Dual polarization interferometry (DPI), 59–60
Dynamic light scattering (DLS), 126, 128–129
E
ECM, see Extracellular matrix
E. coli, see Escherichia coli
Edge-preserving filters, 336–337
EDL, see Electrical double layer
Effective potentials, see Pseudopotentials
Eigenfaces, 146
EIS, see Electrical impedance spectroscopy
Electrical double layer (EDL), 43, 130
Electrical impedance spectroscopy, 268
Electrocardiography, 268
Electroencephalography, 268
Electromyography, 272
Electron gun, 140
Electron microscopy (EM), 140–149, 358
Electron multiplying CCD (EMCCD), 63–64
Electron paramagnetic resonance (EPR), 168; see also Electron spin resonance
Electron spectroscopy, see X-ray photoelectron spectroscopy
Electron spin resonance (ESR), 159
Electron tomography (ET), 144
Electronystagmography, 272
Electrophoretic light scattering, 129–130
Electrophoretic mobility, 129
Electroporation, 242
Elemental analysis, 144
Ellipticity, 57
EM, see Electron microscopy
Embedded-atom method, 289
EMCCD, see Electron multiplying CCD
Emergent structures, 14
Empirical potentials, 282
Enantiomers, 23
Endoplasmic reticulum (ER), 16, 19
Endoscopy, 273
Entropic springs, 16, 226, 302–308
Environmental scanning electron microscope (ESEM), 145
Enzymes, 25
Epitaxy, 256
Epithelial cervical cells, see Immortal cells
Epitope, 236
EPS, see Extracellular polymeric substances
Equipartition theorem, 44, 190, 201, 205, 223
ER, see Endoplasmic reticulum
Erithacus, 374
Erosion, 327
Escherichia coli, 14, 312, 352
ESEM, see Environmental scanning electron microscope
ESR, see Electron spin resonance
ET, see Electron tomography
Etalon, see Fabry–Pérot interferometer
Ethidium bromide, 216
European robin, see Erithacus
Evanescent field, 193
Evanescent wave equation, 81
Evaporative deposition, 256
Everhart–Thornley detector, 144
Evolution, 40
Excitation filters, 69
Extended x-ray absorption fine structure, 157
Extracellular matrix (ECM), 13–14, 66
Extracellular polymeric substances (EPS), 376
F
Fabry–Pérot interferometer, 69–70, 134
FACS, see Fluorescence-assisted cell sorting
Faraday cage, 144
FCS, see Fluorescence correlation spectroscopy
FEA, see Finite element analysis
Feedback, 177, 188, 191, 203, 206–209, 353
Fermions, 288
Ferromagnetic materials, 198
FIB, see Focused ion beam
Field flow fractionation, 181
Finesse coefficient, 70
Finite element analysis, 226, 270
Finnis–Sinclair model, see Embedded-atom method
FISH, see Fluorescence in situ hybridization
Fixed charge explicit solvent model, 291
FlAsH, see Fluorescein arsenical helix
FLIM, see Fluorescence lifetime imaging microscopy
FLIP, see Fluorescence loss in photobleaching
Flocking, 377
Flory’s mean field theory, 309
Flow cytometry, see Fluorescence-assisted cell sorting
Fluctuation–dissipation theorem, 12
Fluid force microscopy, 210
Fluidic circuits, 260
Fluid mosaic model, see Singer–Nicholson model
Fluid reservoirs, 260
Fluorescein arsenical helix (FlAsH), 74, 146
Fluorescence-assisted cell sorting (FACS), 56–57
Fluorescence correlation spectroscopy (FCS), 116–119
Fluorescence imaging with one nanometer accuracy, 100
Fluorescence in situ hybridization (FISH), 73–74, 236, 262
Fluorescence intermittency, see Photoblinking
Fluorescence lifetime imaging microscopy (FLIM), 89–90
Fluorescence loss in photobleaching (FLIP), 87
Fluorescence recovery after photobleaching (FRAP), 87, 312–313
Fluorescent proteins, 24, 73, 76–77, 101, 237, 245–246
Fluorescent speckle microscopy, 103
Fluorophore, 55
Foam physics, 339
Focal drift, 264
Fokker–Planck equation, see Smoluchowski equation
Förster radius, 112
Förster resonance energy transfer (FRET), 83, 90, 111–116, 195, 351
Fourier transform, 109, 120–121, 166–167, 199, 283, 326
Fourier transforms infrared spectrometer, 52–53
4Pi microscopy, 105
Franck–Condon principle, 56
FRAP, see Fluorescence recovery after photobleaching
Free-electron lasers, 168; see also X-ray free-electron laser
Free-electron maser, 168
Free energy, 12
Free induction decay, 167
Freely rotating chain, 303
Free radical quencher, 101
Free spectral range, 70
Freeze-fracture, 142
Frequency doubling, 124
Fresnel zone plates, 156
FRET, see Förster resonance energy transfer
Fruit fly, see Drosophila
FT, see Fourier transform
FTIR, see Fourier transform infrared spectrometer
Functional imaging, 270
G
Gabor hologram, 144
Gating optical intensifier, 89
Gaussian polymer coil, 128
Geiger counter, 172
Generalized Born approximation, 292
circuits, 355
concatemerization, 244
editing, 244
knockouts (see Deletion mutants)
Genome, 28
Genotype, 348
Geometrical light scattering, 123
Geonavigation, 374
G-factor, 58
Gillespie algorithm, 352
Gliding, 190
Glutaraldehyde, 141
Glycocalyx, 14
Goldman equation, 218
Golgi body, 16
GPUs, see Graphics processor units
Gram-negative, 18
Gram-positive, 18
Granocentric model, 339
Graphics processor units (GPUs), 297–298
Gray goo, see Nanobots
GROningen MAchine for Chemical Simulations (GROMACS), 295–296
Ground state depletion, 105
Guinier model, 127
Gyromagnetic ratio, 160
H
Hagen–Poiseuille flow, see Poiseuille flow
Hahn echo, see Spin-echo
Half potential, 283
Hamaker constant, 206
Hamiltonian operator, 287
Hard x-rays, 157
Hartree–Fock approximations, 288
H-bonding, see Hydrogen bonding
HeLa cells, see Immortal cells
Helfrich forces, 44
Hertz model, 204
HF, see Hartree–Fock approximations
Hidden Markov model (HMM), 105
Highly inclined and laminated optical sheet illumination (HILO), see Oblique epifluorescence
High-speed spinning disk confocal microscopy, 86
High-throughput techniques, 253–267
Hill equation, 298
HIO algorithm, see Hybrid input–output algorithm
HMM, see Hidden Markov model
Hoffmann modulation contrast (HMC) microscopy, 67
Holographic optical traps, 188
Homeostasis, 347
Hooke’s law, 204, 307, 340–341
Human embryonic kidney cells, see Immortal cells
Hybrid classical and quantum mechanical methods (Hybrid QM/MM), 289, 293
Hybrid input–output algorithm (HIO algorithm), 154
Hydration layer, see Solvation shell
Hydration pockets, 292
Hydration shell, see Solvation shell
Hydrodynamic radius, see Stokes radius
Hydrodynamics, see Rheology
Hydrogen bonding (H-bonding), 23–25, 46, 291
Hydrophobic forces, 21, 25, 56
Hyperfine interactions, 163, 172
Hyperspace, 328
Hyperspectral imaging, 133
I
ICCD, see Intensified CCD
Ideal chain limit, 306
Ig, see Immunoglobulin
Image classes, 328
Image denoising, 326
Image segmentation, 326
Immortal cells, 239
Immunogenic, 236
Immunoglobulin (Ig), 43, 209, 235–236
Impalefection, 242
imaging, 273
Inner filter effect, 56
Insertion mutant, 243
In silico drug design, 371
Integrationist, 348
Intensified CCD (ICCD), 64
Interaction energy, 298
Interchangeable parts, 355
Interfacial free energy, 250
Interference filters, 69
Interferometric light scattering microscopy, 130–131
Intermediate filaments, 17
Internal conversion, 55
Intersystem crossing, 56
Ionicity, 283
Ionic strength, 283
Ion trap, 199
iSCAT, see Interferometric light scattering microscopy
Isopropyl-ß-D-thio-galactoside (IPTG), 244
Isothermal titration calorimetry (ITC), 268
Isotropic emissions, 58
J
Jablonski diagram, 55
Jarzynski equality, 316
Joule–Thompson effect, 165
Jurkat cells, see Immortal cells
K
Kappa squared factor, see Dipole orientation factor
KDE, see Kernel density estimation
Kelvin probe microscopy, 212
Kernel density estimation (KDE), 330
Kerr effect, see Two-photon absorption
Knudsen cell, 256
Köhler illumination, 64
Kolmogorov equation, see Smoluchowski equation
Kratky–Porod model, see Wormlike chain
Kuhn length, 302
L
Label-free methods, 97, 108, 120, 124, 131–132, 133
Laguerre–Gaussian beams, 194
Lambda DNA, 238
Lambda phage, 238
Lamellipodia, 17
Laminar flow, 259
Lamor frequency, 161
Langevin equation, 189
Lanthanides, 76
Laser dark field, see Dark field microscopy
Laser diffraction, 225
Laser-induced optoacoustic spectroscopy, 60
Laser microsurgery, 273
Laser tweezers, see Optical tweezers
Lateral spatial resolution, 87
Laue method, 154
LD, see Linear dichroism
LeapFrog algorithm, 281
Lennard–Jones potential, 44, 282
Leucine zipper, 104
Level-broadening effect, 373
Levinthal’s paradox, 316
Light sheet microscopy, 124–125
Linear accelerator (LINAC), 152
Linear dichroism (LD), 57
Lipid rafts, 21
Liposomes, 22
Localization microscopy, 90, 100–103, 329; see also Colocalization analysis
Lock-in amplifier, 213
Lone pair electrons, 291
Lorentzian, 190
Lorentz oscillators, 80
Low-voltage electron microscopy (LVEM), 143
Lymphocytes, 239
Lysosomes, 17
Lysozyme, 262
M
Magnetic beads, 198
Magnetic resonance imaging (MRI), 268–270
Magnetofection, 242
Magnetoreception, 374
Magnetospirilum, 374
Magnetotaxis, see Magnetoreception
Magnetron, 256
MALDI, see Matrix-assisted laser desorption ionization
Maleimide, 235
Many-body potential energy function, 283
Markov processes, 105, 310–311
Matrix-assisted laser desorption ionization (MALDI), 199
Matter waves, 141
Maximum a posteriori, 327
Maximum entropy, 327
Maximum likelihood methods, 328
Maxwell–Boltzmann distribution, 279
Maxwell’s electromagnetic equations, 80–82, 184
Maxwell’s relations, 267
MCPs, see Methyl-accepting chemotaxis proteins
MD, see Molecular dynamics
Mean free collision path, 142–143
Median filters, 336
Membrane fence model, 18
Membrane proteins, 58, 142, 147
MEMS, see Microelectromechanical systems
Merodiploid, 246
Mesoscale, 341
Messenger RNA (mRNA), 29
Metalloproteins, 157
Metal-oxide semiconductor (MOS), 63
Methanethiosulfonate, 235
Methicillin-resistant S. aureus, 18, 220
Methyl-accepting chemotaxis proteins (MCPs), 352
Metropolis criterion, 285
Micelles, 21
Michaelis–Menten kinetics, 316–317
Microbial flora, 262
Microdomains, 22
Microelectromechanical systems (MEMS), 254
Microfilaments, 17
Microfluidics, 56, 181, 259–261, 266–267
Microlenses, 119
Microplate reader, 262
MicroRNA, 244
Microtome, 142
Microtubules, 17
Mie/Tyndall light scattering, 55, 122–123, 125
Mini call, 312
Minimal model, 311
MiniSOG, 146
Missing wedge, 144
Mitochondria, 17
MM, see Molecular mechanics
Molecular clock, 16
Molecular confinement, 17
Molecular docking, 295
Molecular dynamics (MD), 279–298
Molecular heterogeneity, 12, 178–179
Molecular interaction maps, 90
Molecular mechanics (MM), 12–13, 83, 225, 281, 324–326, 360
Molecular motors, 13, 25, 83, 194, 311, 338
Molecular ruler, 114
Molecular signature, 209
Molecular statics, 278
Molecular weight, 46, 118, 126
Monochromator, 151
Monoclonal, 236
Monod–Wyman–Changeux (MWC) model, 298
Moore’s law, 296
Morphogensis, 312
Morse potential, 205
MOS, see Metal-oxide semiconductor
Moseley’s law, 150
Mössbauer spectroscopy, 172–173
Motility assay, 83
Mouse ear cress, see Arabidopsis
MPE, see Multiphoton excitation
MRI, see Magnetic resonance imaging
mRNA, see Messenger RNA
MS, see Molecular statics
MSA, see Multivariate statistical analysis
Multicellularity, 14
Multilayered solvent model, 293
Multiphoton excitation, 121–124
Multiplane imaging, 108
Multivariate statistical analysis, 328
Mu phage, 238
Muscle, 83, 191–192, 209, 225, 272–273, 370
N
NAMD, see Nanoscale molecular dynamics
Nanobots, 369
Nanoeye, 221
Nanofluidics, see Microfluidics
Nanoimprimpt, 255
Nanoscale molecular dynamics (NAMD), 296
Nanostructures, 356
Nanothermometers, 123
Navier–Stokes equation, 254–255, 323–324
N@C60, 375
ND, see Neutral density
Near-field optical microscopy (NFOM), 108
Near-TIRF, see Oblique epifluorescence
Nerves, 145, 174, 348, 369–370, 374
Neuroengineering, 248
Neutral density (ND), 68
NeutrAvidin, see Streptavidin
Newtonian fluid, 259
NFOM, see Near-field optical microscopy
Nipkow disk, see High-speed spinning disk confocal microscopy
Nitroxide, 168
NMR, see Nuclear magnetic resonance
Nonequilibrium states, 18, 289–290
Normal modes, 328
NSOM, see Near-field optical microscopy
Nuclear imaging, 271
Nuclear magnetic resonance (NMR), 12, 146, 159–168
Nuclear overhauser effect, 164
Nucleoid, 16
Numerical aperture, 61–63, 141, 192
Numerical focusing, see Ptychography
Nyquist theory, 101
O
Objective lens, 61–63, 65–67, 83, 86–87, 91
Oblique epifluorescence, 79–80
OCT, see Optical coherence tomography
OD, see Optical density
OLID, see Optical lock-in detection
Oligo inserts, see Oligonucleotide labelling
Oligonucleotide labelling, 74, 236–237
One-hybrid assay, 264
1PE, see Single-photon excitation
Onsager reaction field potential, 293
Ophthalmology, 125
Optical activity, see Birefringence
Optical coherence tomography (OCT), 125
Optical density, 54
Optical lithography, see Photolithography
Optical lock-in detection (OLID), 78
Optical resolution limit, see Abbe limit
Optical spanners, 194
Optical stretcher, 192
Optical switches, 361
Optical tweezers, 57, 183–197, 219, 225, 290, 369
Optogenetics, 124, 239, 246–238
Organelles, 17
Osmotic chamber, 182
Osteoblasts, 370
Over-damped simple harmonic motion, 189
Overhang, see Toehold
Overstretch transition, 191
P
PALM, see Photoactivatable localization microscopy
Paraffin wax, 142
Parallel tempering, see Replica exchange MCMC sampling
Paramagnetic materials, 198
Particle in a box, 75
Particle mesh Ewald (PME), 43, 284
Particle-particle-particle-mesh (PPPM), 283
Pascal’s triangle, 163
Patch clamping, 217
Patterned illumination microscopy, see Structured illumination microscopy
Pattern formation, 312
Patterson function, 154
Pauli exclusion principle, 44, 206
PBCs, see Periodic boundary conditions
PCA, see Principal component analysis
PDMS, see Polydimethylsiloxane
PEG, see Polyethylene glycol
Periodic boundary conditions (PBCs), 291
Personalized medicine, 366–371
PET, see Positron emission tomography
Phase contrast microscopy, 65–66
Phase modulation plate, 109
Phase problem, 154
Phase ring, 66
Phenol extraction, 241
pHlourin, 77
Phospholipids, 17, 20–22, 220, 341
Phosphorescence, 56
Photoacoustic imaging, 272
Photoactivatable localization microscopy (PALM), 104
Photoactivation, see Stochastic activation
Photobleaching, 72–73, 101, 103
Photoblinking, 73, 76, 104–105
Photoelasticity, 186
Photoelectric effect, 63
Photomultiplier tube (PMT), 61, 144
Photon budget, 101
Photon correlation spectroscopy, see Dynamic light scattering
crystals, 253
waveguides, 108
Photoselection rule, 58
Photoswitching, 104
Photosynthesis, 17, 36, 361, 372
Photothermal deflection spectroscopy, 60
Photothermal diffraction, 60
Phototoxicity, 68
Piezoelectric effect, 224
Pixelation noise, 100
Pixel thresholding, 327
Planctomycetes, 17
Plant biomechanics, 338
Plasma ashing, 363
Plasma medicine, 274
Plasmids, 29
PME, see Particle mesh Ewald
PMT, see Photomultiplier tube
Podosomes, 17
Point mutation, 243
Point spread function (PSF), 62, 98–100
corkscrew, 109
double-helix, 109
Poiseuille flow, 259
Poisson–Boltzmann model, 292–293
Poisson sampling, 89, 131, 188–189, 191, 328
Polarizable explicit solvent model, 291
Polarization spectroscopy, 57–59
Polarized light microscopy, 66
Polyacrylamide, 215
Polyclonal, 236
Polydimethylsiloxane (PDMS), 226, 260–261
Polydisperse diffusion, 118
Polyethylene glycol (PEG), 195
Positron emission tomography (PET), 173, 271–272
Potential of mean force (PMF), 282
PPPM, see Particle-particle-particle-mesh
Primary antibody, 73
Primary hydration shell method, 291
Primary structure, 23
Principal component analysis, 146, 328
Prism method, 83
Programmed cell death, 239
Protein circuit, 355
Proteolysis, 245; see also Degrons
Proton motive force (PMF), 39
Protoplast fusion, 242
Pseudopotentials, 281
Pseudo-TIRF, 82; see also Oblique epifluorescence
PSF, see Point spread function
Pull-down assay, 262
Purines, 27
Pyridyl disulfide, 235
Q
QCM, see Quartz crystal microbalance
QCM-D, see Quartz crystal microbalance with dissipation monitoring
QDs, see Quantum dots
QM/MM, see Quantum mechanical/molecular mechanics
Quadrant photodiode (QPD), 61, 188–189, 201
Quality factor, 367
Quantum chromodynamics, 159
Quantum coherence, 373
Quantum electrodynamics, 353
Quantum mechanical/molecular mechanics (QM/MM), 281
Quantum numbers, 150, 160, 165, 170–171, 288
Quantum rods, 74
Quantum tunneling, 36, 211–212, 288, 361, 372
Quartz crystal microbalance (QCM), 224–225
Quartz crystal microbalance with dissipation monitoring (QCM-D), 224–225
Quasielastic light scattering, see Dynamic light scattering
Quasi-TIRF, see Oblique epifluorescence
R
Radio frequency heating, 268
Radioisotope, see Radionuclide
Radiology, 270
Radius of gyration, 126, 128, 303–304
Ramachandran plot, 24
Raman–Nath diffraction, 186
Random coil, 24
Random flight model, see Freely jointed chain
Random telegraph model, 335
Ratiometric pH indicators, 77
Rayleigh criterion, 98–100, 332
Rayleigh equation, 126
Rayleigh light scattering, 122–123, 126
Ray-optics, 184
Reaction-diffusion equation, 310–312
Reaction-diffusion processes, 92, 310–322
Reaction limited, 310
Reactive force field (ReaxFF), 289
Readout noise, 64
ReAsH, see Resorufin arsenical helix
Recombinant DNA, 241
Redox enzymes, 361
Reduced mass, 52
Reduced model, see Minimal model
Reductionist, 347
Regenerative medicine, 226, 363, 370–371
Relativistic relation, 140
Relaxation pathways, 73
Replica exchange MCMC sampling, 287
Resonance Raman spectroscopy, 132
Resonant inelastic soft x-ray scattering (RIXS), 155
Resorufin arsenical helix (ReAsH), 74
Restriction endonucleases, 241
Restriction sites, 241
Reverse engineering, 354
Ribonucleic acid (RNA), 16, 29–30
absorbance, 54
interference, 244
Ribosomal RNA (rRNA), 16
Ribosomes, 16
Ribozymes, 25
Ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO), 36
RIXS, see Resonant inelastic soft x-ray scattering
RNA, see Ribonucleic acid
Rodlike limit, 306
Rotational correlation time, 58
rRNA, see Ribosomal
RNA RuBisCO, see Ribulose-1,5-bisphosphate carboxylase oxygenase
S
Saffman–Delbrück equations, 18, 59
Salmonella, 352
Salt bridges, 25
Salting out, 249
SAM instrument, see Simple analysis at Mars instrument
Sanger shotgun, see DNA sequencing
SANS, see Small-angle neutron scattering
Satellite lines, 151
Satellite transitions, 161
Saturated pattern excitation microscopy, 107
Saturated structured illumination microscopy (SSIM), 105
Sawtooth pattern, 209
SAXS, see Small-angle x-ray scattering
Scaffolds, 358
Scale-free networks, 351
Scanning electron microscopy (SEM), 207
Scanning ion conductance microscopy (SICM), 211–212
Scanning IR spectrophotometers, 52
Scanning near-field optical microscopy (SNOM), see Near-field optical microscopy
Scanning transmission x-ray microscope (STXM), 156
Scanning tunneling microscopy (STM), 202, 211
Scattering formula, see Rayleigh equation
Scattering vector, 128
Schrödinger’s equation, 75, 281
SDM, see Site-directed mutagenesis
SDS, see Sodium dodecyl sulfate
SDS-Page, see Gel electrophoresis
SE, see Spin-echo
Secondary antibody, 73
Secondary structure, 23
Second harmonic imaging, 124, 253
Second-order nonlinear optical imaging of chiral crystals, 253
Sector mass spectrometer, 198
Sedimentation coefficient, 180
Seed crystals, 252
Selectively permeable membrane, 18, 181
Selective plane illumination microscopy, see Light sheet microscopy
Selective pressures, 14
Selfish genes, 14
Sellmeier equation, 80
SEM, see Scanning electron microscopy
Semiempirical potentials, 289
Semipermeable membrane, see Selectively permeable membrane
SERS, see Surface-enhanced Raman spectroscopy
SHI, see Second harmonic imaging
SICM, see Scanning ion conductance microscopy
SILAC, see Stable isotopic labeling by amino acids in cell culture
Silver staining, 216
SIM, see Structured illumination microscopy
Simple analysis at Mars (SAM) instrument, 199
Simulated annealing, 287
Singer–Nicholson model, 18
Single-beam gradient force trap, see Optical tweezers
Single crystal monochromatic radiation method, 154
Single-molecule FRET (smFRET), 113–116
Single-molecule high-resolution colocalization, 102
Single-particle tracking, see Localization microscopy
Single-particle tracking localization microscopy (TALM), 102
Single-photon emission CT (SPECT), 271–272
Single-photon excitation, 55
Single point charge (SPC), 291
Site-directed mutagenesis, 235
6–12 potential, see Lennard–Jones potential
Sleeping sickness, 239
SLM, see Spatial light modulator
SLS, see Static light scattering
Small-angle neutron scattering (SANS), 174
Small-angle x-ray scattering (SAXS), 5, 155, 225
Small interfering RNA, 244
SMD, see Steered MD
smFRET, see Single-molecule FRET
Smoluchowski equation, 294, 310–311
Snap freezing, see Cryofixation
Snell’s law, 80
Sodium dodecyl sulfate (SDS), 215
Soft-matter nanopores, 220–222
Solid-state nanopores, 219–220
Solvation shell, 291
Solvation sphere, see Solvation shell
Solvent evaporation method, 250
Sonication, 242
Sonoporation, 242
SOS response, 274
Spatial light modulator (SLM), 109, 120, 188
Spatial sampling, 349
SPECT, see Single-photon emission CT
Spectral imaging, 90
Spin-echo (SE), 167
Spin-flip, 161
Spin labels, 168
Spin–lattice relaxation, 164
Spin-1/2 nuclei, 159
Spin–spin relaxation, 164
SPR, see Surface plasmon resonance
SPRAIPAINT, see Super resolution by power-dependent active intermittency and points accumulation for imaging in nanoscale topography
Sputtering, 256
Squid giant axon, 268
SSIM, see Saturated structured illumination microscopy
Stable isotopic labeling by amino acids in cell culture (SILAC), 199
Standard model, 159
Staples, 358
Static light scattering (SLS), 126–128
STED, see Stimulated-emission depletion microscopy
Stepper motors, 264
Sticky end, see Toehold
Stillinger–Weber potential, 205
Stimulated-emission depletion microscopy (STED), 105–107
STM, see Scanning tunneling microscopy
Stochastic activation, 104
Stochastic optical reconstruction microscopy (STORM), 104
Stokes–Einstein relation, 46, 59, 129
Stokes radius, 73, 128, 130, 189, 305
Stokes shift, 69
Stopped-flow techniques, 173
STORM, see Stochastic optical reconstruction microscopy
Streitz–Mintmire model, 289
Streptavidin, 234
Strobing, 92
Structured illumination microscopy (SIM), 107
Student t-test, see T-test
STXM, see Scanning transmission x-ray microscope
SU-8, 256
Subdiffusion, see Anomalous diffusion
Substoichiometric labeling, 103
Subtractive manufacturing, 257
Sulfhydryl, 234
Supercoiling, 29
Superconductivity, 152, 164–165, 170, 361
Super resolution by power-dependent active intermittency and points accumulation for imaging in nanoscale topography (SPRAIPAINT), 105
Surface-enhanced Raman spectroscopy (SERS), 132
Surface plasmon resonance (SPR), 59–60
Swarming, 377
Synapse, 248
Synchrotron radiation, 53, 151
Synovial fluid, 337
Synthetic biology, 210, 353–366
Syringe pumps, 260
Systems biophysics, 219, 347–353
T
TALENs, see Transcription activator-like effector nucleases
TCSPC, see Time-correlated single-photon counting
Technetium, 271
Tellurium dioxide, 186
TEM, see Transmission electron microscopy
Template matching, 328
Templates, see Scaffolds
Temporal sampling, 349
Tensor interaction, 159
Terahertz gap, 168
Terahertz imaging, 168
Terahertz radiation (T-rays), 168
Terahertz spectroscopy, 168–169
TERS, see Tip-enhanced Raman spectroscopy
Tersoff potential, 283
Tertiary structure, 23
Tetramethylsilane (TMS), 162
Thermal ablation, 273
Thermal bath, 179
Thermal imaging, see Infrared
Thermalization, 169
Thermionic emission, 140
Thermistor, 267
Thermoacoustic imaging, 272
Thermodynamic potentials, 267
Thermoplastics, 257
Thermostats, 294
Thin-film optics, 253
Third-harmonic imaging, 124
Thompson elastic scattering, 152
3B microscopy, 105
Three-hybrid assay, 264
3PE, see Three-photon excitation microscopy
Three-photon excitation microscopy (3PE), 123
3T3 cells, see Immortal cells
Tight-binding potentials, see Semiempirical potentials
Tight-binding second-moment approximation, see Embedded-atom method
Time-correlated single-photon counting (TCSPC), 89
Tip broadening convolution artifact, 207
Tip-enhanced Raman spectroscopy (TERS), 132
TIRF microscopy, see Total internal reflection fluorescence microscopy
acoustics, 269
decolorization, 125
impedance tomography, 268
resection, 126
TMS, see Tetramethylsilane
Toehold, 360
Tomogram, 271
Topoisomerases, 201
Torsional AFM, 207
Torsional constraints, 201
Total internal reflection fluorescence (TIRF) microscopy, 60, 80–83, 192–194
Transautophosphorylation, 352
Transcription, 16
activator-like effector nucleases, 244
initiation complex, 263
Transcription activator-like effector nucleases (TALENs), 244
Transcriptor, see Biological transistor
Transduction, 242; see also Signal transduction
Transfection, 242
magnet-assisted (see Magnetofection)
optical transfection, 242
Transfer RNA (tRNA), 30
Transformation, 242
Transition dipole moment, 58
Transmission electron microscopy (TEM), 143–144
Transmission x-ray microscope (TXM), 156
Transverse relaxation optimized spectroscopy (TROSY), 168
T-rays, see Terahertz radiation
Triangulation, 114
tRNA, see Transfer RNA
TROSY, see Transverse relaxation optimized spectroscopy
Trypanosoma, 239
Tryptophan fluorescence, 56
T-test, 337
Turbulent flow, 259
Turing machine, 312
12–6 potential, see Lennard–Jones potential
2PE, see Two-photon excitation microscopy
Two-photon absorption, 121–122
Two-photon excitation microscopy, 121–122
TXM, see Transmission x-ray microscope
U
UFM, see Ultrasonic force microscopy
Ultrafiltration, see Osmosis
Ultrasonic force microscopy (UFM), 212–213
Ultrasound techniques, 272
Ultraviolet (UV) spectroscopy, 54
Umbrella sampling, 287
Undulators, 152
Unicellularity, 14
V
Vacuoles, 17
van der Waals forces (VdW), 25, 43, 282
Vapor diffusion methods, 250
Variable-angle epifluorescence, see Oblique epifluorescence
VdW, see van der Waals forces
Vector, 241
Velocity selector, 199
Verlet algorithm, 281
Vertical transitions, 56
Virial coefficients, 128
Virtual objective lens, 121
Visual molecular dynamics (VMD), 296
Vitrification temperature, 145
W
Water-immersion objective lens, 83
Watershedding, 327
Wavelet transform (WT), 328
Weighted histogram analysis, 287
Western blotting, 216
Whispering gallery mode, 108
White-light supercontinuum lasers, see Broadband laser
WT, see Wavelet transform
X
XAS, see X-ray absorption spectroscopy
XFEL, see X-ray free-electron laser
XPS, see X-ray photoelectron spectroscopy
X-ray absorption near edge structure, 157
X-ray absorption spectroscopy (XAS), 157
X-ray diffraction, 225
X-ray free-electron laser (XFEL), 152
X-ray photoelectron spectroscopy (XPS), 157
X-ray pump-probe, 152
X-ray spectrometer, 144
X-ray spectroscopy, 144, 157–158
Y
Yeast two-hybrid assay (Y2H), 262–264
Young’s modulus, 204
Z
Zebrafish, 240
Zeeman interaction, 160
Zimm model, 127
Zirconia, 126
Zirconium dioxide, 126
Z-stacks, 119