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| Biological
and Medical Physics: An introductory overview
(early draft of syllabus for spring 2003)
PHY315 for
undergraduates PHY615 for graduates
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Tuesday & Thursday 10:00
to 11:20 am |
Taught by Biological Physicist
Prof. Ken Foster with guests |
Prerequisite PHY212 or equivalent |
The goal is to learn to how to think physically
about biology and medicine. The course provides an overview
of how both abstract and practical aspects of physical thinking
applied to the study of biology and medicine. |
Required Textbooks:
1. Random Walks in Biology, H. Berg, 2nd ed. Princeton Univ.Pr
$16.95 Paperback - 152 pages Rv/Nw/expn edition (September
1993) Princeton Univ Pr; ISBN: 0691000646 referred to as B
2. Biophysics: an Introduction, R. Cotterill, 1st ed. Wiley,
$39.95 Paperback 395 pages (2002) referred to as C
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| Requirements: Weekly exercises, two midterms
and a final, extra project for those in PHY615 |
I. Derive from first principles
how life evolved to the 3 bit codon stage. (Before most biochemistry
books begin) readings from C2-4, 7 & 8)
A. Origin and Philosophy of science (L. Fry), beginning of
tradition of evaluation, modification and testing of past
ideas, scientific reasoning, probability, Bayesian inference
- C appendix D
B. Concepts of Markov process, Evolution, natural selection,
first and second laws of thermodynamics, free energy and information,
natural emergence of complexity
C. Genetic definition of life
D. Physiological definition (S. Turner)
E. Initial Metabolism - no membrane, but surface, carbon and
nitrogen fixation (bottom up approach)
F. The building materials and interactions that made it all
possible.
1. Protein folding, C7.5
G. How complex to be a self-sustaining chemical system?
H. Introduction of the 3 bit code (presently there is a 4.4
bit code) and life at this transition (top down approach)
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II. The cell
A. Evolution. Natural selection. Free energy. A dynamic dissipative
machine.
B. Diffusion - particle, molecular, & cell diffusion, transport,
application to sensing, chap. C5, B1-3
C. Viscosity (momentum diffusion) C5
D. Thermal conductivity (energy diffusion) C5
E. Devices based on diffusion - B4-5
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III. The network and complexity
concepts
A. The phylogenetic tree, network
B. Biocomplexity, the cell, the brain, the ecology as networks
C. Introduction to bioinformatics (neural network, Hidden Markov)
D. The control networks, e.g. sensory and control of gene expression.
Non-adaptive, self adaptive and learning. Nonlinear multi-input
output control. Cell decisions.
E. Scale, Dimensionality, Fractal behavior. |
IV. Bionanotechnology
A. Molecular: field effect ion channels - fractal
1. Patch clamping - C6.6
2. Defects and disease, Cystic fibrosis
B. Membrane receptors, sensory transduction - rhodopsin
1. Structure, Diffraction, x-ray, electron - C6.1
2. Optical spectroscopy
3. Activation and Charge displacements
4. Acoustic spectroscopy
a) electrostriction and thermodynamics
5. Molecular dynamics - C6.7
6. Defects and disease, Retinitis pigmentosa
C. Microscopies
1. Optical and electron
2. STM - C6.3
3. AFM - C6.4
D. Energy machines -
1. Photosynthetic reaction center - C9.3
2. F0F1-ATP-synthase - C9.4
E. Cellular movement
1. Self-propelled cells - B6
2. Bacterial motors - C10.1
3. Cilia and force measurement
4. Optical tweezers - C6.5
5. Muscles - C10.3
F. Neurons
1. Excitable membranes - C11-12
a) H-H model of action potential
b) Phase-space model of action potential |
V. Humans and medicine
A. Learning and memory- C13
1. Making a sensory device, making it learn, inverse problem
2. Downside of learning - Cognitive illusions, delusions
B. Control of movement - C14
a) Optical-Vestibular control system
b) Transfer functions and convolutions
C. Imaging techniques - tomography, functional NMR C6.2
D. The integration of whole sensory systems
1. Hearing
2. Vision - sensory approximation
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