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Oxford Uni - Biological motors glossary
Category: Sciences
Date & country: 16/12/2007, UK
Words: 29


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 (kB) 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.

Johnson noise
Thermal noise that occurs in resistors. The rms noise voltage of a resistor is given by √(4kTRB) where k is Boltzmann's constant, T is the abolute temperature, R is the resistance and B is the bandwidth in Hertz.

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
This states that 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
An arbitrary (but useful) criterion for resolution. For a microscope, this is that the resolution is equal to 1.22·λ/2·NA, where λ is the wavelength of the light and NA is the numerical aperture of an objective.

Reynolds Number (Re<-i>)
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.

Snell's law
The law in optics governing the angle of a refracted ray:
n1 ·
sin θi = n3 · sin θt
(More Details)

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).

Stoke's Law
The law giving the drag coefficient of a spherical object:
γ = 6·π·η·r

TEM00<-SUB>
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.

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.

yocto
SI prefix for 10-24 (See SI Units page at NIST)

zepto
SI prefix for 10-21 (See SI Units page at NIST)