Spring 2009 Thursdays from 4:00 to 4:50 pm in room 1131 of
the northwest wing of the physics building on
Lomas near Yale.
Our e-mail addresses are firstname.lastname@example.org, email@example.com, firstname.lastname@example.org, and
email@example.com. See also Koch's OpenWetWare
Some notes on mathematics are available on-line;
15 discusses probability and Langevin's theory of diffusion and
Brownian motion. You may find there a simple derivation of
Einstein's relation D = b k T
in which D is the diffusion
constant and b the mobility,
which is the inverse of the viscous-friction coefficient.
The book Molecular
of the Cell, Fifth Edition by Bruce Alberts,
Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter
Walter is a wonderful source of background material
for any course on biophysics.
But it is very long and amounts to an
undergraduate curriculum in molecular and cell biology.
So it is not required for this course. You can read
it online thru the PubMed
of the Cell.
Some basic facts of biochemistry appear
after the list of talks.
Students are encouraged to ask all sorts of questions during the talks.
With tentative titles in italics,
the talk schedule so far is:
22 January: Kevin Cahill (Physics) "The
Standard Model of Biology"
29 January: Fang Huang (Physics) "Photobleaching, Mobility, and Compartmentalisation:Inferences in Fluorescence Correlation Spectroscopy."
5 February: Natalie
(Biochemistry and Molecular Biology) "SQUID-relaxometry as a novel
detection method for disease-targeted magnetic
nanoparticles." Her talk
and her paper,
"Characterization of Magnetite Nanoparticles for SQUID-relaxometry and
Magnetic Needle Biopsy."
12 February: Nano
19 February: Truman Brown
Kay and Vida L.W. Hudson Professor of Biomedical Engineering
and Professor of Radiology, Columbia University) "Probing Brain Metabolism and Function."
26 February: Kevin Cahill, "Pathogens: Bacteria,
Fungi, Protozoa, Viruses, and Prions." Slides and text.
5 March: Biophysics Group, "Highlights of
the Annual Meeting of the Biophysical Society."
12 March: Nano Cafe
19 March: Spring Break
26 March: Kevin Cahill, "Some electrostatic
problems relevant to cells."
2 April: Diane Lidke, "Studying ERK1 Nuclear-Cytoplasmic Shuttling Using Fluorescence Microscopy."
will discuss new ERK
What follows is from a prior semester
24 January, Remarks
medicinal chemistry and on the rule of 5
by Christopher Kipinski in the auditorium of the Domenici Center.
31 January, "Elements of Brownian Motion" by Kevin
7 February, Salient
of the 52d annual meeting of the Biophysical Society reported by
Cahill, Lidke, and Lidke with incisive remarks by Thomas. Kornberg's paper on the trigger loop of the
DNA and RNA polymerases.
Friday 15 February, "Probing the Very Small in
Biology! Mechanical Unfolding and Refolding of Protein Domains" by Evan Evans (B.U. & U.B.C.)
at 2 pm in room 101 of CHTM, which is 338 on map.
Abstract of his talk.
21 February, "Fluctuation and Dissipation" by
28 February, "Something by" Diane Lidke (UNM Medical School)
6 March, "Something by" Keith
13 March, on the Quake paper by Steve Koch (physics)
20 March, Spring Break, no seminar.
Many dates remain open:
27 March, "How to Make Optical Tweezers" by Steve Koch (physics)
3 April, "Something by" James Thomas (physics)
10 April, "Cold-inducible RNA binding protein's
role in breast cancer" by Rebecca Hartley (Cell Biology and
17 April, "Something by" David Bear (Cell
Physiology). Rebecca Hartley says Bear "knows everything."
24 April, "Technologies and Challenges in Gene Expression and Genomics" by Scott Ness (Molecular Genetics & Microbiology)
What follows is from a previous semester.
1 March,"Protease-Mediated Blood-Brain Barrier Injury in Stroke and Vascular Dementia," Professor Gary A. Rosenberg (neurology) A recent paper by him on proteins that use metal ions to cut other proteins.
8 March, "Microscope Optics and Phase-Contrast Microscopy," Professor James Thomas (physics).
15 March, Spring Break, no class
22 March, "Nuclear-Resonance Single-Cell Detection," Professor Laurel Sillerud (biochemistry and molecular biology)
29 March, "Smart Drugs," Kevin Cahill (physics), pdf of talk. Two questions and two answers.
5 April, "DNA Packing Pressure in vitro vs. in viro," Dr. Adrian Parsegian, Laboratory of Physical and Structural Biology of NICHD, NIH.
12 April, "RNA Interference," Professor Rebecca Hartley (cell biology and physiology), ppt of talk.
19 April, "Synthetic Polymers for Tissue Engineering," Professor Elizabeth Dirk (chemical & nuclear engineering), abstract of talk.
26 April, "OPMD: A Complex Genetic Disease of
Protein Aggregation," Professor
biology and physiology); students should read chapter 6 of Molecular Biology of the Cell which
3 May, "Cytometry," Dr. James Jett (LANL)
10 May, Short talks by graduate students and eager undergraduates.
Here are some basic facts of biochemistry from MBoC5:
carbon bonds and basic organic groups
water, acids, and bases
weak chemical bonds
glycolysis or what cells do with sugars
the citric-acid cycle
cartoons of proteins
early axon experiments
transport inside cells
protein filaments in cells
actin and tubulin
actin filaments and tubulin microtubules
mitosis or cell division