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Overview
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This interdisciplinary course has been developed under the auspices
of the M.I.T. Department of Physics and the Harvard- M.I.T. Division
of Health Sciences and Technology. It is addressed to seniors and
graduate students in the Schools of Sciences, Engineering and the
Division of Health Sciences and Technology who are interested in
a detailed quantitative and analytic understanding of biological
and physiological phenomena. In addition to the blackboard lecture
presentations, students will be provided with typed notes on the
topics covered.
The principal discipline which will underlie and unify the analysis
in this course is statistical mechanics and thermodynamics. We shall
provide at the first lecture a complete set of notes reviewing those
elements of statistical mechanics and thermodynamics with emphasis
on those most useful in applications to biological phenomena. In
order to increase the time available for biophysical topics, we
urge the student to read these notes on their own. When a particular
element of statistical mechanics or thermodynamics is needed for
the development of a biological topic, a review of that element
will be provided in lecture and further explained in recitation
sections. Each of the topics covered in the course will be provided
to students in the form of typewritten text which can be found in the Lecture Notes on the course website.
The topics to be discussed during the term are as follows:
I. Review of Statistical Mechanics and Thermodynamics
Concept of entropy, microcanonical ensemble, fundamental equations
of thermodynamics, the chemical potential. The thermodynamic potentials:
equations of state, phase equilibria, Clapeyron equation, multicomponent
systems, phase equilibria, aqueous solution of biological molecules,
osmotic pressure, Poisson Boltzmann equation. Reactions and reaction
equilibria, pH and pH control-buffers. Random walk and diffusion.
Ligand binding to macromolecules - the binding polynomials. Wyman
linkage relations between interacting ligands.
II. Proteins as Stores and Transporters: The Respiratory
Proteins
Experimental data on the binding of ligands to hemoglobin. Oxygen
dissociation curve, effect of pH, effect of organic phosphates,
effect of CO2. Heterotropic and homotropic interaction, cooperativity,
allosteric control, linkage between heterotropic ligands. Statistical
thermodynamics of binding of ligands to distinct sites on multisubunit
proteins: The Pauling, and the Monod-Wyman-Changeaux models of homotropic
interactions in hemoglobin. Allosteric model for heterotropic interaction
in hemoglobin. Theory of the Bohr effect - pH as a modulator of
oxygen binding to hemoglobin.
III. Biological Physics of the Eye and Vision
Basic anatomy, physiology and pathophysiology of the visual system.
Cornea, ciliary body, aqueous humour dynamics, iris, ciliary muscles
and the lens. History of the development of spectacles. Theory of
transparency of the eye: normal and pathological corneas. Scattering
of light from the normal and cataractous lens. Discovery of high
molecular weight protein aggregates. Observation of Brownian movement
of lens proteins. The method of optical mixing spectroscopy. Liquid-liquid
and solid-liquid phase transition in concentrated protein solution.
Protein condensation diseases. Threshold detection of light at low
and high light levels. Light detection as signal to noise discrimination.
The molecular basis of phototransduction. The role of rhodopsin,
transducin (G protein), phosphodiesterase and cyclic GMP as a cascade
for the transduction of light into an electrical response. The theory
of the gain and kinetics of the G protein cascade.
IV. Theory of Action Potentials, Simplified Neural Network
Models, and Neural Basis of Short Term Memory
V. Random Walks and Diffusion in Biological Systems
VI. Feedback, Control and Homeostasis in Physiological
Systems
General role of feedback and control on a molecular level (metabolic
pathways) and an organ level (physiological control loops). The
human respiratory system and basic model of CO2 control. The system,
the controller, the concept of open and closed loop gain. Transient
behavior of CO2 proportional control system. Time delays and instability
in control. Control during exercise and at high altitudes. Control
of blood glucose and the theory of control of enzyme activity at
the molecular level.
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