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Physics
257: Special Topics in Biological Physics
Tue/Thur 5:30 - 7:00 pm in Broida 3302
Questions? e-mail: deborah@physics.ucsb.edu
April 1st
LECTURE NOTES: Course Info and Biophysics defined (PDF)
HOMEWORK: a take home QUIZ (PDF) due at the start of class on April 3rd.
April 3rd
LECTURE NOTES: The Basics: Energy, Length and Time Scales (PDF)
HOMEWORK: a PAPER (PDF) to read before class on April 8th.
April 8th
LECTURE NOTES: Introduction to Polymers (PDF)
HOMEWORK: a take home QUIZ (PDF) about the previous paper due at the start of class on April 10th.
HOMEWORK: an assignment based on attending a seminar (PDF) on April 10th, just before class.
April 10th
LECTURE NOTES:A Walk Through (PDF) Strick, Croquette and Bensimon,
"Single molecule analysis of DNA uncoiling by a type II topoisomerase," Nature 40:901 (2000)
HOMEWORK: a PAPER (PDF) to read before class on April 15th.
April 15th
LECTURE NOTES: continuation of April 10th & beginning of April17th
HOMEWORK: Take Home Quiz (PDF) based on Strick, et al. due at the start of class on April 22.
April 17th
LECTURE NOTES: A Walk Through (PDF) Ferrell and Machleder,
"The Biochemical Basis of an All-or-None Cell Fate Switch in Xenopus Oocytes," Science 280:895 (1998)
HOMEWORK: a PAPER (PDF) to read in time for class on April 22nd.
April 22nd
LECTURE NOTES: A Walk Through (PDF coming soon!) Hopfield,
"Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic...," PNAS 71:4135 (1974)
HOMEWORK: several PAPERS invoking kinetic proofreading, read ONE before class on April 24th.
One looks at specificity in signal transduction through the kinase cascade (PDF).
Another challenges a key assumption in the first (PDF).
A third looks at topo's bias for disentangling DNA (PDF) and leaving it that way (PDF).
April 24th
LECTURE NOTES: continuation of April 22nd
HOMEWORK: a
PAPER (PDF) chosen by Jenny Ross to read in time for class on April 29th.
April 29th
LECTURE NOTES:Jenny Ross Walks Us Through
Cameron, Footer, vanOudenaarden and Theriot,
"Motility of ActA protein-coated microspheres driven by actin polymerization," PNAS 96:4908 (1999)
HOMEWORK: a
PAPER (PDF) chosen by Jesse Berezovsky to read in time for class on May 1st.
May 1st
LECTURE NOTES:Jesse Berezovsky Walks Us Through (PDF)
Parent and Devriotes,
"A Cell's Sense of Direction," Science 284:765 (1999)
HOMEWORK: a
PAPER (PDF) chosen by Ryan Epstein to read in time for class on May 6th.
May 6th
LECTURE NOTES:Ryan Epstein Walks Us Through (PDF)
Yasuda, Noji, Yoshida, Kinosita and Itoh,
"Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase," Nature 410:898 (2001)
HOMEWORK: a
PAPER (PDF) chosen by Sara Hastings to read in time for class on May 8th.
May 8th
LECTURE NOTES:Sara Hastings Walks Us Through (PDF)
Roberts, Marsh, Weyand and Taylor,
"Muscular Force in Running Turkeys: The Economy of Minimizing Work," Science 275:1113 (1997)
HOMEWORK: a
PAPER (PDF) chosen by Miriam Friedel to read in time for class on May 13th.
May 13th
LECTURE NOTES:Miriam Friedel Walks Us Through (PDF)
Balbirnie, Grothe, and Eisenberg,
"An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated beta-sheet structure for amyloid," PNAS 98:2375 (2001)
HOMEWORK: a
PAPER (PDF) chosen by Adam Scott to read in time for class on May 15th.
May 15th
LECTURE NOTES:Adam Scott Walks Us Through (PDF)
Hubel and Weisel,
"Receptive Fields of Single Neurones in the Cats Striate Cortex," Journal of Physiology 148:574 (1959)
HOMEWORK: a
PAPER (PDF) chosen by Felix Mendoza to read in time for class on May 20th.
May 20th
LECTURE NOTES:Felix Mendoza Walks Us Through (PDF)
Zhuang, et al.,
"A Single-Molecule Study of RNA Catalysis and Folding," Science 288:2048 (2000)
HOMEWORK: a
PAPER (PDF) chosen by Corrinne Mills to read in time for class on May 22nd.
May 22nd
LECTURE NOTES:Corrinne Mills Walks Us Through (PDF)
Zeck and Fromherz,
"Noninvasive neuroelectronic interfacing with synaptically connected snail neurons immobilized on a semiconductor chip," PNAS 98:10457 (2001)
HOMEWORK: a
PAPER (PDF) chosen by Chris Santangelo to read in time for class on May 27th.
May 27th
LECTURE NOTES:A Walk Through
Okada and Hirokawa,
"A Processive Single-Headed Motor: Kinesin Superfamily Protein KIF1A," Science 283:1152 (1999)
HOMEWORK: a
PAPER (PDF) chosen by Juan Hodelin to read in time for class on May 29th.
May 29th
LECTURE NOTES:Juan Hodelin Walks Us Through (PDF)
Visscher, Schnitzer and Block,
"Single kinesin molecules studied with a molecular force clamp," Nature 400:184 (1999)
HOMEWORK: a
PAPER (PDF) chosen by David Wood to read in time for class on June 3rd.
June 3rd
LECTURE NOTES:David Wood Walks Us Through (PDF)
Dunin-Borkowski, McCartney, Frankel, Bazylinski, Posfai & Buseck,
"Magnetic Microstructure of Magnetotactic Bacteria by Electron Holography," Science 282:1868 (1998)
HOMEWORK: a
PAPER (PDF) chosen by Mark Henle to read in time for class on June 5th.
June 5th
LECTURE NOTES:A Walk Through
Lev-Maor, Sorek, Shomron and Ast
"The Birth of an Alternatively Spliced Exon: 3' Splice-Site Selection in Alu Exons," Science 300:1288 (2003)
HOMEWORK: a
PAPER (PDF) chosen by Benjamin Huff to read in time for class on June 10th.
June 10th
LECTURE NOTES:A Walk Through
Jiang, Ruta, Chen, Lee and MacKinnon
"The principle of gating charge movement
in a voltage-dependent K+ channel," Nature 423:42 (2003)
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