Mathematical Terms of Biological Information Theory

Thomas D. Schneider *

version = 1.08 of bitt.tex 2011 Nov 12

B = log2M (bits) Number of bits for M symbols [1]

Cy = dspace log2(Py∕Ny + 1) (bits/mmo)Molecular machine capacity [23]

D = 2dspace 3n- 6 Dimensionality of a molecular machine coding space [2]

dspace = D∕2 Number of ‘pins’ a molecular machine uses [23]

ΔG (joules/mmo) Free energy dissipated by a molecular machine in an operation [23]

d.f. = 3n- 6 Degrees of freedom for n atoms [2]

Emin = 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 [45]

ϵt =  (Py  )
  Ny = ln(ρ+1)
   ρ Theoretical maximum molecular efficiency [45]

ϵr ϵt Real (or measured) molecular efficiency [45]

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 [26]

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 [278]

Py = -ΔG (joules/mmo) Energy dissipated by a molecular machine in an opertion [23]

p(x) = -√1---
  2πσ 2e-   2
(x-2σμ2) Probabilty of x for a Gaussian distribution

quincunx Galton’s Quincunx - a device that demonstrates the formation of a Gaussian distribution. See

R (bits/mmo) Information gained during a molecular machine operation, often of a binding site[9]

Renergy ≡-ΔGEmin (bits per mmo)The maximum bits that can be gained for the given free energy dissipation [45]

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

y See x



[1]    T. D. Schneider. Information theory primer. Published on the web at, 2010.

[2]    T. D. Schneider. Theory of molecular machines. I. Channel capacity of molecular machines. J. Theor. Biol., 148:83–123, 1991.

[3]    T. D. Schneider. Theory of molecular machines. II. Energy dissipation from molecular machines. J. Theor. Biol., 148:125–137, 1991.

[4]    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,

[5]    T. D. Schneider. A brief review of molecular information theory. Nano Communication Networks, 1:173–180, 2010.,

[6]    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.

[7]    J. B. Johnson. Thermal agitation of electricity in conductors. Physical Review, 32:97–109, 1928.

[8]    H. Nyquist. Thermal agitation of electric charge in conductors. Physical Review, 32:110–113, 1928.

[9]    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.