|B = log2M (bits)||Number of bits for M symbols|||
|Cy = dspace log2(Py∕Ny + 1) (bits/mmo)||Molecular machine capacity||[2, 3]|
|D = 2dspace ≪ 3n- 6||Dimensionality of a molecular machine coding space|||
|dspace = D∕2||Number of ‘pins’ a molecular machine uses||[2, 3]|
|ΔG (joules/mmo)||Free energy dissipated by a molecular machine in an operation||[2, 3]|
|d.f. = 3n- 6||Degrees of freedom for n atoms|||
|min = kBT ln2 (joules per bit)||A version of the Second Law of Thermodynamics that can be used as an ideal conversion factor between energy and bits||[4, 5]|
|ϵt = =||Theoretical maximum molecular efficiency||[4, 5]|
|ϵr ≤ ϵt||Real (or measured) molecular efficiency||[4, 5]|
|kB (joules/kelvin)||Boltzmann’s constant|
|λ = R∕2||Compressed bases: the number of bases a binding site would take up if the information of the site was compressed as small as possible.|
|M = 2B||Number of symbols corresponding to B bits|
|mmo||Molecular machine operation||[2, 6]|
|μ||Mean of Gaussian distribution|
|σ||Standard deviation of Gaussian distribution|
|π||Circle circumference/radius, something to eat|
|n||Number of atoms in a molecular machine. see d.f.|
|Ny (joules/mmo)||Thermal noise flowing through a molecular machine during an opertion||[2, 7, 8]|
|Py = -ΔG (joules/mmo)||Energy dissipated by a molecular machine in an opertion||[2, 3]|
|p(x) = e-||Probabilty of x for a Gaussian distribution|
|quincunx||Galton’s Quincunx - a device that demonstrates the formation of a Gaussian distribution. See http://tinyurl.com/GaltonQuincunx|
|R (bits/mmo)||Information gained during a molecular machine operation, often of a binding site|||
|Renergy ≡-ΔG∘∕min (bits per mmo)||The maximum bits that can be gained for the given free energy dissipation||[4, 5]|
|ρ = Py∕Ny||Energy dissipation of a molecular machine normalized by the thermal noise flowing through the machine|
|T (K)||Absolute temperture, Kelvin|
|x||Voltage (for a communications system) or total potental and kinetic energy for a molecular machine|
 T. D. Schneider. Information theory primer. Published on the web at http://alum.mit.edu/www/toms/papers/primer/, 2010.
 T. D. Schneider. Theory of molecular machines. I. Channel capacity of molecular machines. J. Theor. Biol., 148:83–123, 1991. http://alum.mit.edu/www/toms/papers/ccmm/.
 T. D. Schneider. Theory of molecular machines. II. Energy dissipation from molecular machines. J. Theor. Biol., 148:125–137, 1991. http://alum.mit.edu/www/toms/papers/edmm/.
 T. D. Schneider. 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence. Nucleic Acids Res., 38:5995–6006, 2010. doi:10.1093/nar/gkq389, http://alum.mit.edu/www/toms/papers/emmgeo/.
 T. D. Schneider. A brief review of molecular information theory. Nano Communication Networks, 1:173–180, 2010. http://dx.doi.org/10.1016/j.nancom.2010.09.002, http://alum.mit.edu/www/toms/papers/brmit/.
 T. D. Schneider. Sequence logos, machine/channel capacity, Maxwell’s demon, and molecular computers: a review of the theory of molecular machines. Nanotechnology, 5:1–18, 1994. http://alum.mit.edu/www/toms/papers/nano2/.
 T. D. Schneider, G. D. Stormo, L. Gold, and A. Ehrenfeucht. Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188:415–431, 1986. http://alum.mit.edu/www/toms/papers/schneider1986/.