Physics 500-005 (CRN: 33424)

Seminar on Biophysics and Medicine

     This seminar is a series of talks on biology, biochemistry, chemistry, medicine, and physical biology.   Scientists in various universities and institutes, especially UNM and  the UNM Medical School will give most of the talks.   Professors Koch, Lidke, Thomas, and Cahill will fill-in when no outside speaker is available.   This course is inspired by the  BioMed Seminar.   There are no prerequisites.  Graduate students should register for 500-005, undergraduates for 451 (cr/nc) or 452 (graded).   Graduate students will give short talks on the last day of class.   The course gives one credit (CR/NC) and has a website on OpenWetWare and also on WebCT.

    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,,,  and   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.

 9 April:  Nano Cafe 

16 April:  Kevin Cahill, "Electroporation and Other Ways to Beat the Rule of Five."
          23 April:  Rebecca Hartley (Cell Biology and Physiology) 
      30 April:  Steve Koch, "Introduction to biophysical studies of the molecular motor kinesin

       7 May:  David Bear
(Cell Biology and Physiology) "Peering at the Pores: The Selective Transport of Proteins and RNAs Between the Cell Nucleus and Cytoplasm."

    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
    nucleic acids
    free energy
    glycolysis or what cells do with sugars
    the citric-acid cycle
    amino acids
    cartoons of proteins
    enzyme kinetics
    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