  I believe an atomic biology is needed to supplement present day molecular
biology, if we are to design and understand proteins, as well as define, make,
and use them. Topics in the paper are molecular biology and atomic biology.
Electrodiffusion in the open channel. Electrodiffusion in mixed electrolytes.
Models of permeation. State Models of Permeation are Inconsistent with the
Electric Field. Making models in atomic biology. Molecular dynamics. Temporal
Limitations; Spatial Limitations; Periodic boundary conditions. Hierarchy of
models of the open channel. Stochastic Motion of the Channel. Langevin
Dynamics. Simulations of the Reaction Path: the Permion. Chemical reactions.
What was wrong? Back to the hierarchy: Occam's razor can slit your throat.
Poisson-Nernst-Planck PNP Models Flux Ratios; Pumping by Field Coupling. Gating
in channels of one conformation. Gating by Field Switching; Gating Current;
Gating in Branched Channels; Blocking. Back to the hierarchy: Linking levels.
Is there a theory? At what level will the adaptation be found? Simplicity,
evolution, and natural function.
