442 Index

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