PHYSICS 146A/230A
Quarter: Fall Quarter 2006
Goals of the course:
This course has three main goals. It will
introduce students to basic concepts and language of biology that are necessary
to engage in a meaningful dialogue with biological researchers. Emphasis will
be on overarching concepts, challenges, and principles rather than cataloguing
details. The student will see several examples of biological problems and
approaches to their solution that require a true interplay between physics,
computation, and biology (not just adding numbers, equations or standard
physics approaches to biological questions). All examples are chosen such that
molecular information is important, but also such that an understanding of
biological function requires description of the system and its properties.
Examples include: regulation of gene transcription in bacteria, transport of
molecules by free diffusion and across membranes, bacterial chemotaxis,
photosynthetic systems and transduction of nerve impulses. The third goal is to
give the student a brief overview of state-of-the art experimental and modeling
approaches as a starting point for further studies.
Materials
Lecture materials will be posted on this webpage.
There is no one book that covers the scope and goals of this course. We will
draw from Alberts et al: Molecular
Biology of the Cell for some of the background biology, and from Philip Nelson: Biological Physics, Howard
Berg: Random Walks in Biology, Jonathon Howard: Mechanics of Motor Proteins and
the Cytoskeleton for some of the physics descriptions.
Grading
Grades will be determined based on completion of homework assignments (60%), class participation (10%) and the final examination (30%). There will be no midterm exam. Homework sets stimulate quantitative analysis of the concepts discussed in the lecture and can involve small programming effort. The final exam will test mostly for acquired knowledge.
Schedule
Week 1 (Sep 25-Sep29) What are the
building blocks? (aka Review of Molecular Microbiology)
Mon, Sep 25: genomic
information, central dogma, notes, ppt
Wed, Sep 27: flow of genomic information; proteins, cells, notes
Fri, Sep 29: DNA-transcription factors in bacteria:
biological facts, notes
Week 2 (Oct 2-Oct 7)
Example:
Transcription regulation through protein DNA-interactions (lac-repressor)
Mon, Oct 2: DNA-TF interactions I,
notes
Wed, Oct 4: DNA-TF interactions II, notes
Fri, Oct 6: DNA-TF interactions III, notes
Week 3 (Oct 9-Oct 13) How do
things move in cells?
Mon, Oct 9: free diffusion, first mean passage times, notes
Wed, Oct 11: diffusion to multiple absorbers, glimpse into
more general statistical mechanics, notes
Fri, Oct 13: lecture cancelled
Week 4 (Oct 16-Oct 20) Molecular Level information: X-ray crystallography, NMR
Mon, Oct 16: DNA-TF interactions with dynamics, notes
Wed, Oct 18: X-ray crystallography, slides
Fri, Oct 20: Structure determination with NMR
Week 5 (Oct 23-Oct 27)
Electrical energy in cells
Biological membranes, ion transport, ion channels, ion pumps
Week 6 (Oct 30-Nov 3) How do we
model biological systems?
Mon, Oct 30: Molecular Dynamics, notes
Wed, Nov 1: Brownian Dynamics, Monte-Carlo, Poisson
Boltzmann
Fri, Nov 3: Sampling: Jarzynski equality, autocorrelation, notes
Week 7 (Nov 6-Nov10) Signaling
Mon, Nov 6: Signaling overview, notes
Wed, Nov 8: Bacterial chemotaxis: slides
Fri, Nov 10: Bacterial chemotaxis: Leibler
paper
Week 8 (Nov 13-Nov17) Control
Theory
Mon, Nov 13: no lecture
Wed, Nov 15: Control theory I, notes
Fri, Nov 17: Control theory II,
notes
Week 9 (Nov 20-Nov24)
Example: Photosynthesis: harvesting sun light and bioelectronics
Week 10 (Nov 27-Dec 1)