440 Index

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