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 sjkoch@unm.edu, jthomas@unm.edu, klidke@unm.edu, and
cahill@unm.edu. See also Koch's OpenWetWare
site.
Some notes on mathematics are available on-line;
chapter
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
Biology
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
site Molecular
Biology
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
Adolphi
(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
Cafe
19 February: Truman Brown
(Percy
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
data.
What follows is from a prior semester
24 January, Remarks
on
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
Cahill
(physics).
7 February, Salient
points
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
Kevin Cahill
(physics).
28 February, "Something by" Diane Lidke (UNM Medical School)
6 March, "Something by" Keith
Lidke
(physics)
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
Physiology)
17 April, "Something by" David Bear (Cell
Biology
and
Physiology). Rebecca Hartley says Bear "knows everything."
24 April, "Technologies
and
Challenges in Gene Expression and Genomics"
by Scott Ness (Molecular Genetics & Microbiology)
1 May,
8 May,
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
David
Bear (cell
biology and physiology); students should read chapter 6 of Molecular Biology of the Cell which
is
available on
line.
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
sugars
fats
nucleic acids
free energy
glycolysis or what cells do with sugars
the citric-acid cycle
amino acids
cartoons of proteins
enzyme kinetics
sex
osmolarity
Nernst's equation
early axon experiments
protein translocation
transport inside cells
redox potentials
protein filaments in cells
actin and tubulin
actin filaments and tubulin microtubules
mitosis or cell division
flowers
plants