Mini Tour of Tom Schneider's Theory
Banff
is an overview video.
paperlist
my papers are listed by name.
Below is a suggested reading order of the papers
that leads progressively deeper into the theory.
- Basics:
-
primer
A short primer on information theory.
-
schneider1986
Using information theory to measure the information at binding sites
(Rsequence) and to predict that information from the size of the
genome and number of sites (Rfrequency).
-
logo
A sequence logo graphically shows for binding sites the average
information at each position in the site.
-
walker
Sequence walksers graphically show the information of individual
binding sites. They are extremely useful!!!
-
ri
The math underlying sequence walkers.
-
ev
Demonstration of the results of schneider1986 that Rsequence evolves
to match Renergy: the ev and evj models. Run the java - complete
evolution in a few seconds!
-
Advanced theory:
-
ccmm
Molecular machines defined, channel capacity for molecular machines,
noise, energy dissipation, biological states are high dimensional
hyperspheres:
-
edmm
Building on ccmm, derive minimum energy per bit (Emin)
from channel capacity and second law of thermodynamics:
-
emmgeo
Information (in bits) versus energy (converted to bits using
Emin) gives efficiency, often 70% for molecular machines.
-
lattice
The theory depends on high dimensional space. Find the dimensionality
for restriction enzymes. 6 base restriction enzymes have apparently
discovered the best sphere packing, the 24 dimensional Leech lattice!
Schneider Lab
origin: 2021 Jun 29
updated: 2021 Jun 29