Physics 500-003, 501-002, 451-075, 452-075
Advanced Seminar - BioMed

Advanced Seminar - BioMed

Undergraduate students should enroll in Physics 451.075 (C/NC) or 452.075 (graded).
Graduate students should enroll in Physics 551.008 (C/NC) or 552.008 (graded).

Fall 2005 Wednesdays from 17:30 to 18:20 in room 184. My e-mail address is cahill@unm.edu. My office is room 176, and my phone number is 277-5318. My office hours are by appointment. But in fact whenever you see me, I am available for questions about this course.

The four courses cover the same material and meet in the same room at the same time. The 500-level courses are ``for graduate stuents" and the 400-level courses are ``for undergraduate stuents." The two courses, 501.002 and 452.075, are graded and students are expected to give short talks. The other two courses are CR/NC.

This course is a series of talks on biology, biochemistry, chemistry, medicine, and physical biology. The first few talks are by me and are about the basic facts and ideas of molecular biology. I try to get the best professors and researchers of the UNM School of Medicine to give the remaining talks.

The book Molecular Biology of the Cell, Fourth 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 1460 pages long and amounts to an undergraduate curriculum in molecular and cell biology. So it is not at all required for this course.

The talk schedule so far is:

24 August, "Basic Biochemistry I" by Kevin Cahill.
31 August, "Basic Biochemistry II" by Kevin Cahill.
7 September, "Basic Biochemistry III" by Kevin Cahill. These three introductory lectures are based on this pdf file and these two sets of notes. Here is a paper of mine on helices in biomolecules; it will apper soon in Phys. Rev. E.
14 September, "Regulating the Specificity of Transcription Factors" by Professor Scott Ness, Department of Molecular Genetics and Microbiology, UNM School of Medicine. Students should read his paper "Myb protein specificity: evidence of a context-specific transcription factor" before class. Here is his superb talk.
21 September, "miRNA & siRNA: Regulation of Gene Expression by RNA" by Brian Reinert, UNM School of Medicine. The paper "MicroRNAs directing siRNA biogenesis" is appropriate background material as are the sections on RNAi in Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter (Garland Pub; 4th edition (March 2002) ISBN: 0815332181). Here are pdf and ppt files of his talk.
28 September, "Lung MRI -- Part One" by Dr. Natalie Adolphi, New Mexico Resonance.
5 October, ``Magnetic Nanoparticles" by Professor Howard Bryant, Department of Physics & Astronomy, UNM, and Senior Science. Here is a link to the paper "A biomagnetic system for in vivo cancer imaging" by E R Flynn and H C Bryant in Phys. Med. Biol. 50 (21 March 2005) 1273-1293.
12 October, by Professor Stephen Jett, Electron Microscopy Facility, Department of Cell Biology and Physiology, UNM School of Medicine.
19 October, "Ultrasound Bubbles" by Professor James Thomas, Department of Physics & Astronomy, UNM. The paper "Cardiovascular Ultrasound" is suitable background material. Thanks to Mary Coyle.
26 October, "Digital X-ray Imaging" by Professor Philip Heintz, Department of Radiology, UNM School of Medicine.
2 November, "Neuroinflammation" by Professor Gary Rosenberg, Department of Neurology, UNM School of Medicine. His paper "Matrix Metalloproteinases in Neuroinflammation" is a good reference for students with a background in molecular biology. A powerpoint file of his excellent seminar is worth looking at.
9 November, "Endocrinology" by Professor Kathleen Colleran, Division of Endocrinology, UNM School of Medicine. A powerpoint file of her excellent seminar is worth reading.
16 November, "Lung MRI -- Part Two" by Dr. Natalie Adolphi, New Mexico Resonance.
23 November, "NanoMagnetic Imaging of Prostate Cancer" by Professor Laurel Sillerud, Department of Biochemistry, UNM School of Medicine.
30 November, ``A Role for Heparan Sulfate Proteoglycans in Fatty Acid Uptake and Accumulation by Adipocytes" by Professor Rob Orlando, Department of Biochemistry, UNM School of Medicine.
7 December, "Application of Ultrashort Laser Pulses in Biomedicine" by Professor Wolfgang Rudolf, Department of Physics & Astronomy, UNM.
14 December, Short Talks by students.
Physics 500-501
Advanced Seminar - BioMed
Advanced Seminar - BioMed (500-501)

Fall 2004 Wednesdays from 17:30 to 18:20 in room 184. My e-mail address is cahill@unm.edu. My office is room 176, and my phone number is 277-5318. My office hours are by appointment. But in fact whenever you see me, I am available for questions about this course.

Each student will be expected to give a short talk sometime during the semester.

The recommended text is Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter (Garland Pub; 4th edition (March 2002) ISBN: 0815332181). This book is not required and is too long to be the expected reading in a one-credit course. It costs $110 at amazon.com and 45 pounds = $81 at amazon.co.uk, not including shipping.

25 August, "Basic Biochemistry" by Kevin Cahill.
1 September, "Molecular Machines" by David Keller, Chemistry, UNM.
8 September, "Basic Biochemistry and Neurons" by Kevin Cahill.
15 September, "Proteins and Nanotechnology" by Kevin Cahill.
22 September, "MINING LARGE CHEMICAL SPACES IN LEAD AND DRUG DISCOVERY" by Tudor Oprea, School of Medicine, UNM.
29 September, "Xrays and Mammography" by Paul Schwoebel.
6 October, "NMR-based Development of Itegrin-Related Cell Adhesion Inhibitors" by Professor Laurel O. Sillerud, Biochemistry and Molecular Biology, UNM School of Medicine.
13 October, "Introduction to NMR" by Dmitri Sergatskov.
20 October, "Application of Ultrashort Laser Pulses in Biomedicine" by Wolfgang Rudolph.
27 October, "Biomagnetic Cancer Imaging" by Howard Bryant and Ed Flynn.
3 November, "Energy Landscapes and Accelerated Molecular-Dynamical Techniques for the Study of Protein Folding" by John Prentice.
10 November, "Biophysics of Cell Adhesion" by Gordon Zwartz, School of Medicine, UNM.
17 November, "Bcl-2 Family Proteins in Cancer Apoptosis" by Chien-an Andy Hu, School of Medicine, UNM.
24 November, "Molecular Mechanisms of Prostate Cancer Progression" by Marco Bisoffi, School of Medicine, UNM.
1 December, ``The Functional-Genomics Inverse Problem" by Susan R. Atlas, CAS and P&A.
8 December, Talks by students.
Physics 500-003
Advanced Seminar - Biophysics
Advanced Seminar - Biophysics (500-003)

Spring 2004 Wednesdays from 17:30 to 18:45 in room 5. My e-mail address is cahill@unm.edu. My office is room 176, and my phone number is 277-5318. My office hours are by appointment. But in fact whenever you see me, I am available for questions about this course.

This course will introduce students of physics to the more important facts, methods, and ideas of molecular biology and biophysics. It will consist mainly of lectures by UNM professors of physics, biochemistry, biophysics, and medicine. But the course will begin with a review by Kevin Cahill of carbohydrates, fats, nucleic acids, proteins, cells, viruses, and recombinant-DNA technology.

The recommended text is Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter (Garland Pub; 4th edition (March 2002) ISBN: 0815332181). This book costs $110 at amazon.com and 45 pounds at amazon.co.uk. A few months ago, 45 pounds was $76; now due to Bush's cowboy economics, it is $83.

No prior knowledge of biology or chemistry will be assumed. Molecular biology and biophysics provide the main basis for both molecular medicine and nanotechnology.

Notes of my first two lectures are available as the pdf files, pages 1 - 12 and pages 12 - 18.
Slides of my third and fourth lectures are available as part of the pdf file, Biophysics.
Advice about healthy living is given in the pdf file Healthy.

Guest Lectures:

18 February, "Cell Membranes: Physics and Fluorescence" by Professor James Thomas. His talk is available as the pdf file Cell Membranes. He also has a position open for a student.
25 February, "The challenges of genes, gene expression and genomics" by Professor Scott A. Ness, Molecular Genetics & Microbiology, School of Medicine, UNM. The slides of his talk are available as the pdf file Gene Expression.
3 March, "MRI Imaging" by Professor Philip Heintz, Radiology, School of Medicine, UNM.
10 March, "Pre-messenger RNA splicing in eukaryotes" by Professor Stephanie Ruby, Molecular Genetics & Microbiology, School of Medicine, UNM.
17 March, Spring Break.
24 March, "Magnetoencephalography in Epilepsy: What can it see and do?" by Professor Julia Stephen, Radiology, School of Medicine, UNM. The slides of her talk are available as the pdf file MEG & Eplilepsy.
31 March, "Applications of Ultrashort Laser Pulses in Biomedicine" by Professor Wolfgang Rudolph. The slides of his talk are available as the pdf file Microscopy.
7 April at 4 pm, "Ligand-Receptor Interactions" Professor Hugo Kubinyi, Department of Pharmaceutical Chemistry, University of Heidelberg.
7 April at 5:30 pm, "NMR Imaging and Spectroscopy in Prostate-Cancer Diagnosis" by Professor Laurel O. Sillerud, Biochemistry and Molecular Biology, UNM School of Medicine.
14 April, "Cellular clearance mechanisms for triglyceride-rich lipoproteins" by Professor Robert Orlando, Biochemistry and Molecular Biology, UNM School of Medicine.
21 April, "Empirical potentials in biophysical simulations: From Hooke's law to nonlinear quantum 'charge springs'" by Dr. Steve Valone, LANL.
28 April, "Electric and magnetic fields from the brain: Their origins and importance" by Dr. Shingo Murakami, Neurology, UNM SoM.
5 May, "Mining the Chemistry-Biology Interface" by Professor Tudor I. Oprea, Division of Biocomputing, UNM SoM.
12 May is in the middle of final exams: no seminar. But there will be seminars throughout the summer at 4:30 PM on Wednesdays in room 5 (unless we get a better room).
19 May, Professor Glew, Biochemistry and Molecular Biology, UNM SoM, will describe recent findings on the levels and significance of trans and conjugated fatty acids in the breast milk of Fulani women and their "food chain."
26 May, "Alternative Splicing and Genomic Stability" by Kevin Cahill, Department of Physics and Astronomy. (4:30 PM)
2 June, "Mirror Charges, Hydrogen Bonds, and the Water-Dielectric Interface" by Kevin Cahill, Department of Physics and Astronomy. (4:30 PM)
9 June, "Search for the Higgs at the Tevatron" by Professor Michael Gold, Department of Physics and Astronomy (4:30 PM).
16 June, "Majorana Fields without Tears" by Kevin Cahill, Department of Physics and Astronomy. (4:30 PM)
23 June, no class because some students are away.
30 June, "Dirac Fields without Tears" by Kevin Cahill, Department of Physics and Astronomy. (4:30 PM)
7 July, Thursday, a talk on medical imaging by Professor Duric, presently scheduled for 2 pm in room 1131.
14 July, "Real-Time Functional Magnetic-Resonance Imaging: Methods and Applications" by Professor Stefan Posse, MIND Imaging Center, Psychiatry, SoM, and ECE. His course Magnetic-Resonance Imaging and Spectroscopy: From Methods to Functional Brain Imaging is open to you.
21 July, Thursday, 4:30 pm, a talk on computer networks by our own Michael Malik.
29 July, Thursday, "Monte Carlo Methods" by Kevin Cahill, Department of Physics and Astronomy. (4:30 PM).