Glossary

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A

Acousto-optic Deflector: A solid-state device used for steering laser beams. Consists of a crystal of a material such as Tellurium dioxide (TeO₂) and a piezoelectric transducer. A radio frequency signal input to the transducer generates a sound wave in the crystal which acts as a diffraction grating. The frequency of the signal determines the angle of deflection; the amplitude determines the intensity of the deflected spot. More details.

Boltzmann's constant: The value of Boltzmann's constant is 1.380 6503 × 10^-23 J·K^-1 ( NIST)
Boltzmann's Law: The law that relates the probability of a particle being in a particular state to the energy of that state (see, for example, Howard, 2001).

Critical Angle: The minimum angle of incidence at which Total Internal Reflection can occur. More details.

Evanescent Wave: The oscillating electric field produced at an interface where total internal reflection occurs; hence Evanescent Wave Microscopy (another name for TIRFM).
External Reflection: Reflection that occurs when light encounters a medium with a higher optical density (refractive index). More details.

Faxen's Law: A correction to Stoke's law for the drag coefficient of a spherical object near a surface. (See Svoboda and Block, 1994)

HMM (Heavy Meromyosin): A proteolytic fragment of myosin II which is commonly used in experimental work because it is soluble (i.e., does not form filaments). It consists of two motor domain which dimerise through an α-helical coiled coil.

Internal reflection: Reflection that occurs when light encounters a medium with a lower optical density (refractive index). More details.

Lorentzian: A curve describing the power spectrum of the motion of a trapped bead.

Numerical Aperture (NA): The numerical aperture of an objective lens is given by NA = n sin θ where n is the refractive index of the medium between objective and cover slip and θ is the half angle of rays entering the objective. (Interactive tutorial on NA). The greater the NA, the higher is the light gathering power and resolution of the lens. The higher angle of the outermost rays is also essential for stable optical trapping.

Oil immersion objectives: These objectives use an immersion oil between cover slip and lens to achieve a higher NA than is possible with dry objectives. They are corrected to yield the best results when looking through the thickness of a standard cover slip. (Focussing deeper into an aqueous specimen will cause spherical aberration).
Optical spanner: A specialised form of optical trap which allows torque to be exerted on the trapped object (Simpson et al., 1997).
Opticution: The death of an organism due to intense light (usually a laser). (presumably by analogy with electrocution, itself derived from electro- + (exe)cution). (Ashkin and Dziedzic, 1989). Appears to be mainly due to photochemical effects in the presence of oxygen, and can be minimised by careful choice of laser wavelength (Neuman et al., 1999).

Parseval's Theorem: The integral of the power spectrum is equal to the total variance of a signal.
Power Spectrum: A plot which shows how the amount of power in a signal is distributed across different frequencies. The power spectrum is calculated using the Fourier transform. For a good discussion of the use of spectral analysis in trapping, see Gittes and Schmidt (1998). For a discussion of the power spectrum in optical trap data, see this page.

Rayleigh Criterion: Criterion for resolution
Reynolds Number (Re): The ratio of inertial and viscous forces acting on an object. At Re >> 1 inertial forces are dominant; at Re << 1, viscous drag, and not inertia, is most important. The latter scenario applies to a typical object in an optical trap, e.g. bacterium, latex bead. See Howard (2001) p. 38.

S1 (Subfragment 1): A proteolytic fragment of myosin II consisting of a single motor domain and accompanying regulatory domain.
Shot noise: The statistical noise that arises in a signal which counts a number of discrete objects per time interval, e.g. photons at low light intensities.
Spherical aberration: Lens aberration where rays entering a lens at different positions come to a focus at different points. Often seen when focussing into a thick specimen with oil immersion objectives (Interactive tutorial).
Snell's law: The law in optics governing the angle of a refracted ray:
n₁· sin θ_i = n₃ · sin θ_t_{(More Details)}
Stoke's Law: The law giving the drag coefficient of a spherical object:
γ = 6·π·η·r

TEM₀₀: The most commonly used transverse laser mode, which has a gaussian distribution of intensity across the beam.
TIR - Total Internal Reflection: An optical phenomenon occurring at the interface between a medium of high refractive index and one of lower refractive index (e.g. quartz and water respectively). An incident ray of light will be totally reflected if it meets the interface at an angle greater than the critical angle.
TIRF(M) - Total Internal Reflection Fluorescence (Microscopy): A form of fluorescence microscopy using the phenomenon of Total Internal Reflection. This form of fluorescence microscopy takes advantage of the small penetration depth and exponential decay of the evanescent wave to greatly increase the signal to noise ratio. This is particularly useful for observing low level signals (e.g. single molecules) and/or looking specifically at processes occurring close to a surface.

Water Immersion objectives: Like oil immersion objectives, these lenses use an immersion medium to increase the possible NA. Water (n = 1.33) offers lower NA than oil immersion, but allows focussing into thick aqueous specimens without spherical aberration.