Index

1PE see single-photon excitation
3B microscopy 120
3D printing 282, 291
3T3 cells see immortal cells
6-12 potential see Lennard–Jones potential
12-6 potential see Lennard–Jones potential
Abbe limit 113–14, 126, 134, 163
ABEL trapping 252–3
absorbance 62–3
Ab initio calculations 234, 326
acousto-optic deflector see AOD
acousto-optic modulator104
acousto-optic tunable filter see AOTF
adaptive optics 138–9, 426
additive manufacturing 291
advection-diffusion equation 360
AFM 123, 135, 152, 156–7, 205, 222, 231–43, 256, 258, 260–2, 328, 369, 403, 407, 417–18, 425–6, 432
agarose 215, 244–5, 250, 256
AGT 89
airy ring 112–14, 120, 371
a/LCI see angle-resolved low-coherence interferometry
alcohol dehydrogenase 327
alkylation 266
allostery 337
α-hemolysin 249–51, 418
AMBER 334–5
amino acid 27–31, 35, 40, 52, 55–6, 64, 69, 84, 87–8, 118, 152, 169, 227, 228, 237, 244, 249, 250, 261, 266–9, 276, 278–9, 282, 298, 333, 340, 344, 348–9, 377, 389, 406, 411–12
amyloid peptides 242
analytical ultracentrifugation 207
angle-resolved low-coherence interferometry 144
animal locomotion 380
anisotropy 66–8, 106, 223
anomalous diffusion 134, 137, 361–2
antibodies see immunoglobulin
anti-DIG 268
antigen 268–9, 419
antimatter 306
AO see adaptive optics
AOD 78, 101, 104, 212–14, 216, 224–5, 230, 259
AOTF 78–9
APD 72–3, 101
apoptosis see programmed cell death
aptamers 269–70, 419
Arabidopsis 169, 272
archaea 15–16, 18, 27, 34, 37, 42. 51, 280
arc lamp 64, 78, 90
astigmatism imaging 124–5, 155
atomic force acoustic microscopy see UFM
atomic force microscopy see AFM
Auger electron spectroscopy see XPS
autocorrelation function 133–4, 147–8, 156
autofluorescence 86–7, 89, 96–7, 153, 368, 370, 376
avalanche photodiode see APD
avidin see streptavidin
axial spatial resolution 99
azide–alkyne Huisgen cycloaddition see click chemistry

back focal plane detection see BFP detection
bacteria 5, 15–20, 27, 34, 36, 40–1, 43, 45, 51–4, 56–7, 63, 65, 75, 77–8, 88, 92, 98–9, 106, 108, 117, 119, 124–6, 135, 144, 152, 164, 196, 208, 217, 227, 242, 247, 249, 251–2, 256, 259–60, 266–7, 270–1, 274–80, 282, 286, 295–7, 298, 311, 338–9, 349, 353–4, 365, 369, 372, 386, 391, 397–400, 404–5, 409, 411–14, 424–6, 428, 431–3
bacteriophages 270
Baker’s yeast see Saccharomyces
Barabási–Albert model 399
barium meal 306
base pairs 26, 33–4, 36–7, 51, 130, 192, 220, 249, 256, 269–70, 274, 276, 386, 406–7, 418, 428–9
Bayes theorem 362–3, 386–7
Beeman algorithm 318
Beer–Lambert law 62–4, 107, 180
bending free energy 384, 389
Bessel beam 99, 220–1
Bessel function 112
Bessel trap 220
BFP detection 215–16, 229, 260
BiFC 113, 118, 279, 298
bilayers 25, 27, 45, 67, 75, 135, 179, 236, 250, 254, 330, 384
binding-activated localization microscopy 120
binomial nomenclature 16
bioarcheology 181
biobattery 250
biocompatible materials 413
biocomputation 414
bioconjugation 265–6, 268–9, 276
bioelectronics 287, 290, 413, 417
biofilms 16, 41, 47, 144, 256, 296, 426–7
biofuels 410
bioinformatics 31, 368, 377, 418, 421
biological circuits 404–6, 414, 418, 432
biological transistors 413
biomarkers 416–18
biomimetic materials 256, 412–13, 420
bionanotechnology 10, 401–14, 419, 421
bioplastics 410
bioremediation 410
biosensors see lab-on-a-chip
Biot–Savart law 188–9
biotin 84, 218, 221–2, 266, 268–9, 297, 413–14
biotribology 380
biplane imaging 124
birefringence 75, 143
Bjerrum length 321
BLAST 377–8
blinking see photoblinking
blinking assisted localization microscopy 120
blood vessels 36, 145, 157, 231, 272, 305, 307–8, 421
BLS see Brillouin scattering
bond order 323
bone 9, 33, 37, 144, 152, 186, 191, 223, 253, 255, 303–6, 308, 380, 420–1
Bohr radius 86
Born–Oppenheimer approximation 320
bosons 193, 327, 424
Bragg diffraction 170, 178, 214
Bragg peak frequency 177
Bragg’s law 170, 176
bremsstrahlung radiation 173
Brenner potential 327
bright-field 72–4, 77, 81, 106, 209, 215–16, 229, 256, 299, 369
Brillouin doublet 224
Brillouin microscope 153
Brillouin scattering 154, 210
Brillouin spectroscopy 153
broadband lasers 78
Brownian diffusion 53, 100, 134, 137, 156, 252, 352, 359–60, 389–90, 392
Brownian dynamics see Langevin dynamics
Budding yeast see saccharomyces
butanol 411
butterfly wings 286–7, 412–13

cadmium selenide 85
cadmium telluride 85
Caenorhabditis see flatworm
cAMP see cyclic adenosine monophosphate
cancer 142, 144, 193, 400, 416, 418, 419, 426
carbon nanotubes 152, 240
carboxyl 27, 29, 41, 43, 84, 218, 251, 266, 425
CARS 153
cartilage 223, 380
Cauchy equation 91
caveolae 95
CCD 70, 72–3, 90, 106, 130, 139, 150–2, 155, 166, 170–1, 177, 197, 215, 229, 433
cell membranes 3, 8, 10, 37, 48, 50, 75, 103, 106, 143, 165, 177, 193, 204, 224, 239, 246, 249, 275, 279–80, 302, 338–9, 418, 432
cell signaling 400
cell squeezing 275
cellular biophysics 395–6
centrifugation 52, 206–7, 221
CHARMM 334–5
Chaste 381
chemical fixation 164, 169
chemical imaging see hyperspectral imaging
chemical potential 42, 44, 51, 146, 233–4, 246, 285, 352, 384, 423
chemical shift 182, 185–7, 191, 195, 200
chemoattractants 397
chemorepellants 397
chemotaxis 78, 365–6, 397–400, 404–5, 432
Chinese hamster ovary cells see immortal cells
chlamydomonas 271
chloroplasts 19, 27, 41, 411, 423
chromatography 206, 208, 282, 296
Chung–Kennedy filter 378–9, 392
cilia 77–8, 384
circular dichroism 66
Clausius–Mossotti factor 252
CLEM 165, 168–9
click chemistry 84, 268
clustered regularly interspaced short palindromic repeat see CRISPR
CMOS 72–3
coarse-grained simulations 333, 381, 427
codons 40, 279, 412
coherence beating 423
coherence length 143–4
coherent anti-Stokes Raman scattering see CARS
coherent Stokes Raman scattering see CSRS
coherent x-ray diffraction imaging see CXDI
collagen 75, 143, 181, 223, 303, 308, 362, 420, 426
colocalization analysis 373
colorimetry 63
comparative biomechanics 380
computer-assisted tomography see CT
condenser 73–7, 179, 216
confocal microscopy 70, 90, 98–9, 101, 108, 133, 135, 138, 142, 150, 420, 426
confocal theta microscopy 99, 143
confocal volume 6, 98–101, 103, 108, 130, 133–5, 138, 144, 156, 166, 213, 354–5
conformational spreading 338–9
connective tissue 49, 223, 239, 255, 272, 420
connectome 273
consciousness 424
contact mechanics 337
contact mode 235–6, 242, 260
contrast reagent 163, 165–7, 305–6
convolution model 375–6
Coomassie Blue 245
copy number 89, 117, 125, 242–3, 296, 316, 355, 368, 374–7, 379, 419
corner frequency 216, 218, 225
correlative light and electron microscopy see CLEM
Coulomb forces 193
counter ions 331
CRISPR 277
critical angle 90–1, 93–7, 299
cryo-EM 167–9, 370, 409
cryoembedding 164
cryofixation 164, 167, 169
cryosubstitution 164
cryptochrome 425–6
crystal resonator 254
crystallization 15, 198, 282–4, 286, 299
CSRS 153
CT scan 303, 305, 308
CXDI 179–80
cyclic adenosine monophosphate 397
cyclodextrin 249
cyclotron 173–4, 193, 226–7
cysteine mutagenesis 84, 267
cytoplasm 18, 21, 40, 44–5, 53, 57, 68, 102–8, 116–17, 122, 124–5, 135, 168, 280, 311, 353–5, 364–5, 381, 390–1
cytoskeleton 19–20, 143, 223, 239, 381

DAB 169
danio see zebrafish
dark field microscopy 73–5, 362
dark noise 114–15, 136
dark population 117
dark states 83, 86
death sensors 142
De Broglie relation 163, 171, 210
Debye–Hückel approximation 331
Debye length 221, 321
Debye–Scherrer method 176
deconvolution 137–8
defocusing microscopy 73
deformable mirror 138–9
degron 278, 412
delayed-coincidence method 309
deletion mutant 276
dementia 186, 242, 416
dendritic fibers 198
density gradient 207
deoxyribose nucleic acid see DNA
depth of field 71–2, 97–8, 107, 124, 311, 375
depth of focus see depth of field
depth of penetration 68, 92, 97, 143, 197
deuterium 185, 198
dialysis 208, 282
diaminobenzidine see DAB
dichroic mirror 79–81, 95–6, 101, 107, 154, 156, 222, 287, 299, 433
dictyostelium 271, 397–8
dielectric heating 303
dielectric spectroscopy see electrical impedance spectroscopy
differential interference contrast 76
differential scanning calorimetry 302
diffraction before destruction 176
diffusion 10, 20, 21, 53, 67, 68, 95, 99–100, 103–5, 109, 117, 122, 131, 133–5, 137, 147–8, 154, 156, 181, 206–8, 252, 258, 261, 275, 284, 286, 294, 300–1, 316, 328–9, 333, 344, 351–4, 359–3, 365–9, 371, 374, 382, 388–92, 406, 413, 432
DIG 268
digital holographic microscopy 77
digital micromirror array 215
digitalis 268
digoxigenin see DIG
dihedrals 320–2
dipole moment 61, 66–7, 88, 94, 121, 129, 151, 228–9, 234, 252, 303
dipole orientation factor 129
directed diffusion 361
disequilibrium 353
DLS see dynamic light scattering
DNA 5–7, 18–19, 23, 26–7, 29, 32–41, 45–8, 50–1, 54–6, 62, 83–4, 87–9, 100–1, 108–9, 117, 119, 130, 152, 155, 178, 192–3, 210, 219–22, 228, 230, 238–9, 241, 245, 247–9, 253, 256–9, 261, 267–72, 274–7, 279, 282, 290, 295–6, 298, 302, 308–9, 311, 332, 335, 349, 386, 404, 406–14, 418–19, 428–9, 432–3
Doob–Gillespie algorithm see Gillespie algorithm
Doppler shift 148, 196
DPI 68–9
Drosophila 273
drug delivery 419
dual polarization interferometry see DPI
duplex 35, 409–10
dynamic light scattering 145, 147

ECM 16
E. coli see Escherichia coli
ecomechanics 427
edge-preserving filters 379
EDL 149
effective potentials see pseudopotentials
eigenfaces see eigenimages
eigenimages 168
EIS see electrical impedance spectroscopy
elastic scattering 5, 63, 84, 106, 147, 150, 166, 176, 212
electrical double layer see EDL
electrical impedance spectroscopy 303
electrocardiography 303
electroencephalography 303
electromyography 308
electron diffraction 169–70, 176
electron gun 162
electron microscopy see EM
electron multiplying CCD see EMCCD
electron paramagnetic resonance see ESR
electron spectroscopy see XPS
electron spin resonance see ESR
electron tomography see ET
electronystagmography 308
electrophoretic light scattering 148
electrophoretic mobility 148
electrophysiology 246, 248, 381
electroporation 275
electrorotation 244, 251–2
elemental analysis 167, 180–1
ellipticity 66
EM 9, 23, 106, 162–70
embedded-atom method 327
EMCCD 72–3, 90, 106, 130, 152, 155
emergent structures 14
emission filter 76, 79–81, 107, 128, 154, 287, 299, 433
empirical potentials 320, 327
endoscopy 308
entropic spring 7, 18, 255, 341, 349, 382
environmental scanning electron microscope see ESEM
epifluorescence 90–1, 93, 95, 97, 102–3, 108, 115, 125–6, 258
epithelial cervical cells see immortal cells
epitope 268
epitaxy 290
EPR see ESR
EPS 426
equipartition theorem 50, 218, 229, 233, 252, 260, 317, 392
ergodic hypothesis 204, 324, 356
Erithacus 425
erosion 368
Escherichia coli 16, 108, 117, 270, 338, 353, 398
ESEM 167
ESR 161, 182, 191–2, 267
ET 166
etalon see Fabry–Pérot interferometer
ethidium bromide 245
eukaryote 15, 16, 18–19, 34, 36, 38, 40–1, 43–4, 46, 95, 124, 227, 271, 276, 286, 309, 390, 397
European robin see Erithacus
exciton 85–6, 142, 423
excitation filter 78–9
excitation volume 95, 98–9, 120–1, 130–3, 142, 156, 353
excluded volume 18, 117, 126, 348–50, 382, 288
explicit solvent 329–31, 388
extended x-ray absorption fine structure 180
extracellular matrix see ECM
extracellular polymeric substances see EPS
evanescent field 68, 91–7, 131, 220, 291, 417
evanescent wave equation 92
evaporative deposition 290
Everhart–Thornley detector 167

fab region 268
Fabry–Pérot interferometer 76, 79, 153
FACS 65, 106, 295, 419
Faraday cage 167
Fc region 267–8, 297
FCS 129, 132–5, 147, 154
FEA see finite element analysis
feedback 16–17, 54, 65, 106, 112, 203, 214, 219, 235–6, 238, 241, 246, 252–3, 277, 299. 333, 353, 365, 381, 396, 399–401, 405, 414, 428, 432–3
fermions 326–7
ferromagnetic materials 226
FT see Fourier transform
FIB see focused ion beam
fibroblasts 239, 272
field flow fractionation 181
finesse coefficient 70
finite element analysis 207
Finnis–Sinclair model see embedded-atom method
FISH 83–4
fixed charge explicit solvent model 329
FlAsH/ReAsH 84
flatworm 138, 272, 310
flavins 89
FLIM 101–2, 129, 155
FLIM-FRET 129, 155
FLIP 99
flocking 338, 428
Flory’s mean field theory 349
flow cytometry see FACS
fluctuation–dissipation theorem 14
fluid force microscopy 239
fluid reservoirs 294
fluidic circuits 294
fluorescence-assisted cell sorting see FACS
fluorescence correlation spectroscopy see FCS
fluorescence imaging with one nanometer accuracy115
fluorescence in situ hybridization see FISH
fluorescence intermittency see photoblinking
fluorescence lifetime imaging see FLIM
fluorescence loss in photobleaching see FLIP
fluorescence recovery after photobleaching see FRAP
fluorescent proteins 29, 83, 87–8, 115, 169, 224, 241, 269–70, 279, 372, 412
fluorescent speckle microscopy 117
fluorimetry 63–5
fluorophore 64–7, 78–90, 93–5, 99, 101–4, 107, 109, 113, 115–25, 128–30, 133–5, 137–8, 140, 143, 150, 155–6, 169, 209–10, 254, 265, 268–9, 291, 372, 276
foam physics 381
focal drift 299
focused ion beam 168, 248, 287
Fokker–Planck equation see Smoluchowski equation
force clamp 215, 328
Förster radius 128, 131, 155–6, 428, 433
Förster resonance energy transfer see FRET
Fourier transform 3, 60, 78, 112, 122, 125, 139, 170, 177, 180, 189–90, 216, 218, 227, 322, 368
Fourier transform infrared spectrometer 60
Franck–Condon principle 64
FRAP 99, 353, 355
free-electron lasers 168; see also XFEL
free-electron masers 193
free energy 13–14, 21–2, 25, 30, 41–2, 44, 55–6, 204, 285, 302, 320, 324–6, 329, 345–7, 349–51, 355–9, 382–5, 389, 391, 405, 410, 422, 424–5, 428–9
free induction decay 190
free spectral range 80
freely jointed chain 255, 341–2, 386
freely rotating chain 341
freeradical quencher 116
freeze-fracture 164–5
frequency doubling 143
Fresnel zone plates 179
FRET 94, 101–2, 121, 127–32, 135, 154–6, 159, 210, 223–4, 239, 253, 399, 409, 411, 429, 433
FRET-FCS 135
Fröhlich condensate 193, 424
fruit fly see Drosophila
FT see Fourier transform
FTIR see Fourier transform infrared spectrometer
functional imaging 5, 305–6

Gabor hologram 166, 170
gamma rays 195–8, 305–6, 309
gating optical intensifier 101
Gaussian chain 256–7, 341, 344
Gaussian polymer coil see Gaussian chain
Geiger counter 196–7
gel electrophoresis 244–6, 251, 365, 407, 418
generalized born approximation 330
genes 17, 19, 34, 37–9, 45–8, 56, 84, 117, 192, 230, 268, 270–1, 273–9, 353, 396–7, 400, 405, 407, 412, 414
genotype 296, 330, 397, 419
geometrical light scattering 140–1
geonavigation 424
Gillespie algorithm 400–1
gliding 217, 365
glutaraldehyde 164
Goldman equation 246
GPUs 334, 336–7
Granocentric model 383
gray goo see nanobots
GROMACS 334
ground state depletion 120
Guinier model 146
gyromagnetic ratio 183

Hagen–Poiseuille flow see Poiseuille flow
Hahn echo see spin-echo
half potential 323
Hamaker constant 235
hamiltonian operator 326
hard x-rays 174, 176
Hartree–Fock approximations 326
HeLa cells see immortal cells
Hertz model 232
HF see Hartree–Fock approximations
hidden Markov model see HMM
high performance computing see supercomputing
high-speed spinning disk confocal microscopy 98, 135
high-throughput techniques 287–301
Hill equation 337
HILO see oblique epifluorescence
HIO algorithm 177
HMC 77
HMM 120
Hoffmann modulation contrast microscopy see HMC
holographic optical traps 215
homeostasis 42, 381, 395, 411
Hooke’s law 243, 346–7, 382
human embryonic kidney cells see immortal cells
hydration layer see solvation shell
hydration pockets 330
hydration shell see solvation shell
hydraulic radius 294
hydrodynamic radius see stokes radius
hydrodynamics see rheology
hybrid classical and quantum mechanical methods see QM/MM
hybrid QM/MM see QM/MM
hydrogels 350, 427
hydrophobic forces 50, 87, 164, 221, 250
hyperfine interactions 186
hyperspectral imaging152
hyperspace 370

ICCD see intensified CCD
ideal chain limit 345
Ig see immunoglobulin
image classes 370
image denoising 368
image segmentation 369–70
immortal cells 272
immune system 267
immunogenic 268–9, 419–20
immunoglobulin 237, 267
immunostaining 165–6
impalefection 275
implicit solvent 330–2, 334, 388
in silico drug design 316, 333, 416, 421
inelastic scattering 62, 141, 150, 152–4, 166, 178, 224
inner filter effect 65
insertion mutant 276
integrationist 396
intensified CCD 73
intensity centroid 114, 118, 125, 216, 371
interaction energy 337–9
interchangeable parts 404
interfacial free energy 285
interference filter 79
interferometric light scattering microscopy 149
internal conversion 64, 80
intersystem crossing 64, 80
ion trap 227
ionic strength 206, 221, 226, 282, 296, 321, 350, 407, 428
IPTG 278–9, 311
IR imaging 308
IR spectroscopy 61, 151
iSCAT see interferometric light scattering microscopy
Ising model 317, 337–8, 397
isopropyl-β-D-thio-galactoside see IPTG
isothermal titration calorimetry see ITC
isotropic emissions 66, 131
ITC 302
Jablonski diagram 64, 141
Jarzynski equality 357
Joule–Thompson effect 189
Jurkat cells see immortal cells

Kappa squared factor see dipole orientation factor
KDE see kernel density estimation
Kelvin probe microscopy 212
Kernel density estimation 372
Kerr effect see two-photon absorption
K-means 399
Knudsen cell 290
Köhler illumination 73
Kolmogorov equation see Smoluchowski equation
Kramers theory 328, 357
Kratky–Porod model see Wormlike chain
Kuhn length 386

lab-on-a-chip 287, 291, 301, 410, 416–17, 421, 432
label-free methods 124, 143, 150–1, 153–4
Lac operon 277–8
LacI 99–101, 277–9, 311
Laguerre–Gaussian beam 221
lambda DNA 5
lambda phage 270, 274
laminar flow 207, 288, 293–4, 300, 312, 365
Langevin dynamics 332
Langevin equation 216, 332, 350
Langevin force 49, 217–18, 254, 260, 332
lanthanides 86
Larmor frequency 184
laser dark field see dark field microscopy
laser diffraction 255
laser-induced optoacoustic spectroscopy 69
laser microsurgery 308
laser tweezers see optical tweezers
lateral spatial resolution 123, 126, 169, 236
Laue method 177
LD 66
LeapFrog algorithm 318
Lennard-Jones potential 50, 55, 234, 320–4, 329, 348
leucine zipper 113, 118
level-broadening effect 424
Levinthal’s paradox 357
light sheet microscopy 143, 272, 380
LINAC 175
linear accelerator see LINAC
linear dichroism see LD
lipid vesicle 20, 253, 383–4
liposomes 25, 275, 412
liquid crystals 75, 186, 206
localization microscopy 114–20, 124–6, 135, 209, 215, 352, 371, 388, 399
lock-in amplifier 242
logic gates 414
lone pair electrons 329
Lorentz oscillators 91
Lorentzian 216–18, 225, 260
low-voltage electron microscopy see LVEM
lymphocyte 272
lysozyme 193, 296, 424
LVEM 166

magnetic bead 226–30, 259
magnetic resonance 9, 15, 161, 168, 182, 190–1, 200, 303–4, 409
magnetic resonance imaging see MRI
magnetic tweezers 9, 209–10, 226, 228–31, 233, 237, 239, 255–6, 258–9, 263, 266, 271, 328, 356–7, 406
magnetofection 275, 424–6
magnetoreception 424–6
magnetospirilum 424
magnetotaxis see magnetoreception
magnetron 290
magnification 59, 70–2, 98, 103, 107, 114–16, 125, 154, 166, 295, 299, 376, 419
MALDI 227
maleimide 266
many-body potential energy function 323
Markov process 352
mass spectrometry 226–8, 246, 296, 411
mass-to-charge ratio 227
matter waves 145, 150, 162
matrix-assisted laser desorption ionization see MALDI
maximum a posteriori 369
maximum entropy methods 369
maximum likelihood methods 369
Maxwell–Boltzmann distribution 317
Maxwell’s electromagnetic equations 211
Maxwell’s relations 267
MDS 316–19, 387
mean free collision path 165
median filter 378
membrane protein 20, 53, 67, 104–6, 108, 164, 170, 186, 260, 180, 365, 369, 392, 409
MEMS 287, 289
merodiploid 279
mesoscale 255, 333, 335, 384
metalloproteins 180
metal-oxide semiconductor 73, 420
metamaterials 287, 412
methanethiosulfonate 267
methicillin-resistant S. aureus 249, 416
methyl-accepting chemotaxis proteins 400
metropolis criterion 324
Michaelis-Menten kinetics 358
microbial flora 296
microelectromechanical systems see MEMS
microfabrication 287–93
microfluidics 9, 65, 95, 152, 207, 239, 253, 256, 286–7, 293–6, 299–300, 311–12, 365, 417, 419
microlenses 138
microplate reader 296, 299
microRNA 277
microtome 164
Mie/Tyndall light scattering 63, 140–1, 144–6, 150
mini cell 353
minimal model 352–3, 360
MiniSOG 169
missing wedge 144
MM see MDS
model organisms 9, 270–3, 277, 310, 421
modularity 399, 404
molecular combing 209–10
molecular docking 333, 421
molecular dynamics see MD
molecular heterogeneity 14, 30, 177, 204
molecular interaction maps 101
molecular machines 1, 14–15, 19, 30, 35, 39, 44, 49, 51, 53, 117, 128, 130, 164, 204–5, 210, 230, 252–3, 370, 379, 403–4, 410, 420
molecular mechanics see MD
molecular motors see molecular machines
molecular ruler 114
molecular signature 62, 152, 191, 199, 237, 239, 249, 260, 368
molecular statics 316
molecular weight 52, 54–5, 87, 89, 135, 145, 155, 168, 191, 206, 208, 237, 244–5, 258, 266–7, 269, 282, 339, 388, 390, 409, 418
monochromator 60, 174, 180
monoclonal 268
Monod–Wyman–Changeux (MWC) model 337
Monte Carlo methods 323–6, 328, 334, 336
Moore’s law 335, 413
morphogenesis 353
Morse potential 233
MOS see metal oxide semiconductor
Moseley’s law 173, 180
Mössbauer spectroscopy 195–6
motifs 60, 66, 219, 269, 316, 333, 357, 377, 399, 406
motility assay 94
Mouse ear cress see Arabidopsis
MPE see multiphoton excitation
MRI 191, 303–8
MS see molecular statics
MSA see multivariate statistical analysis
Mu phage 271
multidimensional NMR 191
multilayered solvent model 331–2
multiphoton excitation 101, 140, 279, 426
multiplane imaging 124
multivariate statistical analysis 370
muscle 2–3, 15–16, 29–31, 37, 49, 95, 120, 142–4, 149, 162, 165, 178, 204, 209, 218–19, 222, 224, 236–7, 245, 248, 255, 262, 303–4, 307–8, 342, 349, 352, 370, 380–1, 390, 420–1
Mycoplasma 37, 413–14

N@C60 425
NAMD 335
nanobots 420
nanodroplets 63, 250, 403
nanoeye 250
nanofluidics see microfluidics
nanoimprimpt 289
nanomedicine 416, 419–21, 432
nanostructures 35, 286, 407–10, 420–1, 432
nanowires 411
narrow-field 102–3, 125–6, 135, 376, 390
Navier–Stokes equation 254–5, 323–4
ND 78, 96
near-field optical microscopy 231
near-TIRF see oblique epifluorescence
Nernst equation 44, 246, 391
nerves 2–3, 37, 198, 272, 279, 281
neuroengineering 281
neutral density filter see ND
NeutrAvidin see Streptavidin
neutron diffraction 9, 197–8
Newtonian fluid 293
Nipkow disk see high-speed spinning disk confocal microscopy
nitroxide 192
NSOM see near-field optical microscopy
numerical aperture 70–2, 93–4, 98–9, 103–4, 106–8, 112, 121, 139, 163, 220
numerical focusing see ptychography
NMR 161, 168–9, 171, 178, 182–94, 196, 199–200, 226, 304, 317, 356, 377, 409
noncontact mode 235–6
nonequilibrium states 328
normal modes 328, 357
nuclear imaging 306
nuclear magnetic resonance see NMR
nuclear overhauser effect 187
Nyquist theory 115

O6-alkylguanine-DNA alkyltransferase see AGT
objective lens 70–2, 74–7, 79–80, 90–4, 96–9, 103–4, 106–8, 112–14, 120–1, 125, 135–6, 139, 152, 154–6, 180, 211, 213, 290, 299, 311, 433
objective lens method 83
oblique epifluorescence 90–1, 103
OCT 143
OD see optical density
Ohm’s law 246, 410
OLID 89
oligo inserts see oligonucleotide labeling
oligonucleotide labeling 268
one-hybrid assay 298
Onsager reaction field potential 331
ophthalmology 144
optical activity see birefringence
optical coherence tomography see OCT
optical density 63, 143, 145, 296
optical dispersion 60
optical interferometry 68–9
optical lithography see photolithography
optical lock-in detection see OLID
optical path length 74, 144, 174, 430
optical resolution limit see Abbe limit
optical sectioning 143
optical spanners 221
optical stretcher 210, 220–1, 418
optical switch 411
optical trap see optical tweezers
optical tweezers 5, 65, 77–8, 210–13, 215–27, 229–30, 237, 242–3, 249, 255, 258–60, 263–4, 328, 342, 347, 388, 419
optogenetics 142, 144, 273, 279–81
organic dyes 73–4
osmosis 20, 206
osmotic chamber 208
osteoblast 420
over-damped simple harmonic motion 217
overhang see toehold
overstretch transition 219

P3M see particle-particle-particle-mesh
PALM 118–20, 122–3, 135, 155, 384
paraffin wax 164
parallel tempering see replica exchange MCMC sampling
paramagnetic materials 226
particle in a box 85
particle mesh Ewald 50, 322, 339
particle-particle-particle-mesh 322
Pascal’s triangle 187
patch clamping 205, 241, 244, 246–8
Pattern formation 353, 364, 384, 388, 412
patterned illumination microscopy see SIM
Patterson function 177
Pauli exclusion principle 50, 234, 321
PCA see principal component analysis
PDMS 254, 256, 294–5
PEG 224, 282, 286, 297
periodic boundary conditions 330
persistence length 219, 254, 256–7, 259, 342, 345, 349, 386, 407, 428–9
personalized medicine 295
PET 197, 306, 309
pHlourin 88
phase contrast microscopy 27, 70, 74–5, 78, 94, 106
phase modulation plate 125
phase problem 177
phase ring 75
phenol extraction 274
phenotype 37, 46–7, 296, 397, 419
phospholipids 25–7, 67–8
phosphorescence 64
photoacoustic imaging 307
photoactivatable localization microscopy see PALM
photoactivation see stochastic activation
photobleaching 72–3, 101, 103
photoblinking 78, 82–3, 85–6, 97, 99–100, 102, 104–5, 115–17, 119, 120, 122, 135–6, 150, 155, 254, 298, 311, 311, 353, 362, 371–2, 374, 378, 398, 419
photoelasticity 214
photoelectric effect 72
photolithography 231, 287–9
photomultiplier tube see PMT
photon budget 103–4, 115, 124, 216
photon correlation spectroscopy see DLS
photonics 95, 287, 290–1, 404, 411, 417, 433
photoresist 288–90, 292
photoselection rule 66
photoswitching 118
photosynthesis 19, 41, 65, 179, 181, 271, 411, 423
photothermal deflection spectroscopy 69
photothermal diffraction 69
phototoxicity 78
piezoelectric effect 253
pixel thresholding 368
pixelation noise 115
plant biomechanics 380
plasma ashing 413
plasma medicine 309
PM see particle mesh Ewald
PME see particle mesh Ewald
PMF see potential of mean force; proton motive force
PMT 70, 167
point mutation 276, 411
point spread function see PSF
Poiseuille flow 207, 293, 365
Poisson–Boltzmann model 331
Poisson sampling 115, 150, 370
polarizable explicit solvent model 329
polarization spectroscopy 66–8
polarized light microscopy 75
polyacrylamide 244
polyclonal 268
polydimethylsiloxane see PDMS
polydisperse diffusion 134
polyethylene glycol see PEG
positron emission tomography see PET
potential of mean force 320
PPPM see particle-particle-particle-mesh
primary antibody 82–3, 268, 245, 249, 297
primary hydration shell method 330
principal component analysis 168, 369, 399
Prism method 94
programmed cell death 271, 406, 418
protein circuit 404
protein data bank 31, 56, 174, 281
proteins 3, 15–16, 18–21, 27–31, 33–4, 37–40, 43, 45–6, 48, 51–4, 62, 64, 66–7, 69, 75, 83–4, 87, 108, 115–19, 135, 137, 142, 144, 149, 151, 154–5, 164, 169–70, 180, 183, 186, 191–2, 199–200, 206, 208, 219–22, 224, 227–8, 230, 237, 241, 244–5, 253, 256, 259, 266, 269, 271, 273–4, 276–82, 286, 296–8, 302, 309, 311–12, 316–17, 329–30, 334, 339, 341, 344, 349–51, 353–4, 362, 365–6, 372, 377, 384, 386, 388, 392, 396, 399–400, 404–6, 428, 409, 411–12, 423, 431
proteolysis 278
proteomics 48, 228, 296
proton motive force 44, 56, 249, 280
protoplast fusion 275
pseudopotentials 319
pseudo-TIRF see oblique epifluorescence
PSF 71, 98–9, 103–5, 112–14, 116–17, 120–1, 124–6, 133–4, 136–7, 154, 156, 376
p-TIRF 91, 93, 95, 97
ptychography 138–40, 166, 170, 179
pull-down assay 296
purines 32
pyridyl disulfide 266
pyrimidines 32, 89

QCM 254
QCM-D see QCM
QDs 81, 85–6, 112, 115, 142, 419
QM/MM 327–8, 331, 333–4, 339–40
QPD 215–16, 229, 260
quadrant photodiode see QPD
quadrupole 186, 196, 227
quality factor 417
quantum biology 422–6
quantum chromodynamics 182
quantum coherence 319
quantum computing 424
quantum dots see QDs
quantum electrodynamics 401
quantum numbers 187, 326
quantum rods 85
quantum tunneling 30, 42–3, 286, 327, 335, 411, 422–3
quartz crystal microbalance see QCM
quasielastic light scattering see DLS
quasi-TIRF see oblique epifluorescence

radiation damage 170, 176–7, 180–2, 198
radioisotope see radionuclide
radiology 304
radionuclide 306–7, 309
radiotherapy 308–9
radius of gyration 145, 147, 178, 342–3, 349, 386
Raman microscopy 152–3
Raman–Nath diffraction 214
Raman spectroscopy 62, 150–3, 222, 224, 322, 417
random flight model see freely jointed chain
random telegraph model 377, 391
random walk 78, 339, 342, 344, 350, 365–6, 395, 400
ratiometric pH indicator 88
Rayleigh criterion 113, 126, 374
Rayleigh equation 145
Rayleigh light scattering 145–6, 151, 157
reaction-diffusion equation 351–2, 354, 359
reaction-diffusion processes 353
reaction-limited 351, 353–5, 358, 401, 406, 414–15
reactive force field 327
readout noise 73
ReaxFF see reactive force field
recombinant DNA 274
redox enzymes 410
reduced mass 60
reduced model see minimal model
reductionist 396
regenerative medicine 256, 413
relativistic relation 163
relaxation pathways 83
replica exchange MCMC sampling 326
resonance Raman spectroscopy 151–2
resonant inelastic soft x-ray scattering see RIXS
restriction endonucleases 269
restriction sites 274
reverse engineering 403
Reynolds number 217, 293, 301, 365, 428
rheology 21, 206, 208–10, 254
rhodopsin 31, 251, 280
RIXS 179
RNA 19, 21, 23, 30, 32, 34–6, 38–42, 45–8, 51–2, 55, 62, 83, 88, 152, 193, 219, 245, 268–70, 274, 276–7, 298, 335, 350–1, 390–1, 413–14
robustness 47, 164, 302, 379, 399, 405, 427, 432
Rodlike limit 256–8, 345
rotational correlation time 66

Saccharomyces 16, 96, 271
Saffman–Delbrück equations 68
Salmonella 400
salting out 282
Sanger shotgun see DNA sequencing
SANS 198
satellite lines 174
satellite transitions 185
saturated pattern excitation microscopy 123
saturated structured illumination microscopy see SSIM
saturation curve 283–4
Sawtooth pattern 237, 260
SAXS 5, 175, 178–9, 198
scaffolds 404, 421
scale-free networks 399
scanning electron microscopy see SEM
scanning ion conductance microscopy see SICM
scanning IR spectrophotometer 60
scanning tunneling microscopy see STM
scanning transmission x-ray microscope see STXM
scattering formula see Rayleigh equation
scattering vector 146
Schrödinger’s equation 85, 319
SDM see site-directed mutagenesis
SDS-page see gel electrophoresis
SE see spin-echo
second harmonic imaging 143, 286
second-order nonlinear optical imaging of chiral crystals 286
sector mass spectrometer 227
secondary antibody 268
sedimentation coefficient 52, 207
seed crystals 286
selective plane illumination microscopy see light sheet microscopy
selectively permeable membrane 208
Sellmeier equation 91
SEM 165–7, 236
semiempirical potentials 327
semipermeable membrane see selectively permeable membrane
SERS 151–2
SHI see second harmonic imaging
shot noise 189, 215–16
signal transduction 41, 48, 365, 380, 382, 384, 397, 400, 405–6
SICM 231
SILAC 227
silver staining 245
SIM 120, 122
simple analysis at mars instrument 228
simulated annealing 326
single-beam gradient force trap see optical tweezers
single crystal monochromatic radiation method 177
single-molecule FRET see smFRET
single-molecule high-resolution colocalization 116
single-particle tracking see localization microscopy
single-photon emission CT see SPECT
single-photon excitation 82, 106, 140, 376
single point charge 329
site-directed mutagenesis 192, 276
skin 37, 171, 188, 255, 273, 307, 421
sleeping sickness 18, 271
slimfield 90–1, 102–6, 311, 376
SLM see spatial light modulator
SLS see static light scattering
small-angle neutron scattering see SANS
small-angle x-ray scattering see SAXS
small interfering RNA 277
SMD see steered MD
smFRET 129–32
Smoluchowski equation 352
SNAP/CLIP tags 89, 279
Snap freezing see cryofixation
Snell’s law 92, 430
SNOM see near-field optical microscopy
sodium dodecyl sulfate 244
soft condensed matter 13, 15
soft-matter nanopores 249–51
solid-state nanopores 248–9
solvent evaporation method 284
solvation shell 330
solvation sphere see solvation shell
sonication 275
sonoporation 275
SOS response 309
sparrow limit 100
spatial light modulator 125, 215
spatial sampling 397
SPECT 306–7
spectral imaging 102
spectrophotometery 52–5
spin-1/2 nuclei 185
spin-echo 190
spin-flip 185
spin labels 192
spin–lattice relaxation 187
spin–spin relaxation 187
SPR 68, 151, 292, 417
SPRAIPAINT 120
sputtering 290
squid axon 303, 396
SSIM 123
stable isotopic labelling by amino acids in cell culture see SILAC
standard model 182
Staphylococcus 20, 55, 249, 416
staples 409
static light scattering 141, 145, 178, 283
STED 120–2
steered MD 328–9
stem cells 46, 99, 420–1
stepper motor 299
sticky end see toehold
Stillinger–Weber potential 234
stimulated-emission depletion microscopy see STED
STM 239–41
stochastic activation 118
stochastic optical reconstruction microscopy see STORM
Stokes–Einstein relation 53, 67–8, 103, 105, 148, 207, 258, 392
Stokes radius 83, 100, 103, 106, 135, 147–9, 165, 217, 256, 258, 269, 344, 390–1
Stokes shift 79, 87, 107, 153
stopped-flow techniques 204
STORM 118–20, 122–3
Streitz–Mintmire model 327
streptavidin 221, 266, 297, 413–14
strobing 104
structured illumination microscopy see SIM
student’s t-test see T-test
STXM 179
SU-8 289, 292
subclass averaging 168
subdiffusion see anomalous diffusion
substoichiometric labeling 117–18
subtractive manufacturing 291
sulfhydryl 84, 266–7
supercomputing 324
superconductivity 175, 188–9, 193, 411
super-resolution 22, 112–27, 369, 384
supersaturation 283–5, 350
surface-enhanced Raman spectroscopy see SERS
surface plasmon resonance see SPR
surface plasmons 69, 74, 151, 291
swarming 338, 428
synapse 36, 281
synchrotron radiation 62, 173–7, 180, 198
synovial fluid 380
synthetic biology 238, 401–16
syringe pumps 294
systems biophysics 10, 248, 395–401

TALENs 277
TALM 116
tapping mode 235–6
TCSPC 101
technetium 306
tellurium dioxide 214
TEM 23, 106, 165–6, 261
template matching 369
templates see scaffolds
temporal sampling 397
tensor interaction 182
terahertz gap 192
terahertz imaging 193
terahertz radiation see T-rays
terahertz spectroscopy 168–9
TERS 152
Tersoff potential 234
tetramethylsilane see TMS
thermal ablation 308
thermal bath 205, 350, 356
thermal equilibrium 13, 42, 184, 187, 189, 197, 338, 349, 353, 355–7
thermal imaging see IR imaging
thermal neutrons 195, 197–8
thermal ratchet 14, 353
thermalization 193
thermionic emission 162
thermistor 302
thermoacoustic imaging 307
thermoplastics 291
thermostats 333
thin-film optics 79–80, 403, 429–30
third-harmonic imaging 143
Thompson elastic scattering 176
three-hybrid assay 287
three-photon excitation (3PE) microscopy 142
tight-binding potentials see semiempirical potentials
tight-binding second-moment approximation see embedded-atom method
time-correlated single-photon counting see TCSPC
tip broadening convolution artifact 235
tip-enhanced Raman spectroscopy see TERS
TIRF microscopy 68, 90, 95–6, 107, 124, 154, 220, 297
tissue resection 144
titin 29, 52, 209, 218, 224–5, 237, 255, 262, 342, 347, 349
TMS 185
toehold 408, 410
tomogram 305
topoisomerase 34, 230
torsional AFM 236, 426
torsional constraints 230
total internal reflection fluorescence see TIRF microscopy
transautophosphorylation 400
transcription factor 39, 117, 277, 297–8, 353, 404–5
transcriptor see biological transistor
transduction 242; see also signal transduction
transfection 274–6, 279
transformation 3, 25, 125, 177, 275–6, 322, 369
transition dipole moment 66–7, 129
transmission electron microscopy see TEM
transmission x-ray microscope see TXM
transverse relaxation optimized spectroscopy see TROSY
T-rays 192–3
triangulation 122, 130
TROSY 191
Trypanosoma 271
tryptophan fluorescence 64
T-test 372
turbulent flow 293
Turing model 353
two-photon absorption 140, 142, 275
two-photon excitation (2PE) microscopy 140–2
TXM 179

UFM 241
ultrafiltration see osmosis
ultrasonic force microscopy see UFM
ultrasound techniques 307
umbrella sampling 324, 326
undulator 175
UV spectroscopy 62

Van der Waals forces 50, 268
vapor diffusion methods 284
variable-angle epifluorescence see oblique epifluorescence
VdW see Van der Waals forces
velocity selector 227
Verlet algorithm 318
vertical transitions 64
virial coefficient 146
virtual objective lens 139
virtual state 140
viruses 22–4 168, 227, 253, 259, 267, 269–71, 274–5, 277, 392, 411
vitrification temperature 168
VMD 335

water immersion objective lens 125
watershed methods 369
waveguides 95, 124, 220, 290, 308
wavelet transform 370
weighted histogram analysis 326
western blot 245, 279
whispering gallery mode 124
white-light supercontinuum lasers see broadband laser
Wormlike chain 341–2, 245
WT see Wavelet transform

XAS 180
XFEL 174–6, 178, 182
XPS 181
X-ray absorption near edge structure 180
X-ray absorption spectroscopy see XAS
X-ray crystallography 3, 5, 9, 15, 147, 155, 168–70, 174, 176–8, 181–2, 191, 193, 199–200, 281, 287, 317, 322, 409
X-ray diffraction 182, 186, 197–8
X-ray fluorescence 172–3, 181
X-ray free-electron laser see XFEL
X-ray photoelectron spectroscopy see XPS
X-ray pump-probe 176
X-ray spectrometer 167
X-ray spectroscopy 180–1
X-ray tube 172–4, 177, 181

Y2H see yeast two-hybrid assay
yeast two-hybrid assay 297–8
Young’s modulus 232–3, 239, 242, 255, 333, 347, 382

zebrafish 107, 143, 272–3, 277, 310, 381, 411
Zeeman interaction 184
Zimm model 146, 283
zirconia see zirconium dioxide
zirconium dioxide 144
Z-stacks 138