Physics 581-002 and 480-001
Tuesdays and Thursdays from 4 to 5:15 in room 5.

The main textbook is Physical Biology of the Cell (2nd Edition) by Phillips and others.
The UNM bookstore and Amazon sell physical copies of this book. A pdf of it is available for free on the website bookzz.org.
We also will use my class notes.
The book Introduction to Thermal Physics by Daniel Schroeder is excellent as is the book Molecular Driving Forces by Ken Dill and Sarina Bromberg. Both are available for free on the website bookzz.org.


Two pages from Physical Mathematics on Lagrange multipliers.

An article on editing out redundant codons is here.

Janie Rae Byrum, Rebecca Hartley, and Keith Lidke have pointed out these articles on how cells use proteins and small noncoding RNAs to get RNA to fold correctly:
An article on RNA folding.
A minireview of RNA chaperones.
A review of RNA Chaperones, RNA Annealers and RNA Helicases.
A review of chaperone proteins.
A link to a website that predicts how a given strand of RNA or DNA will fold.
An article on DNA and RNA hairpins teased by optical tweezers.


Video of laminar-flow demo.


Guest lecturers:
27 October Cedric Clayrat on CRISPR-Cas9 slides

1 November Keith Lidke on Fluorescence Nanoscopy slides

10 November Fu-Sen Liang on Cell Control

6 December Marjolein Meddens
Title: Biophysical techniques to study mechanosensory podosomes in immune cells
Abstract: Various immune cells such as macrophages and dendritic cells use cytoskeletal structures called podosomes to sense and explore their environment. In this talk I will show how biophysical methods such as super-resolution microscopy, image correlation spectroscopy and FRET have deepened our understanding of the structure and function of podosomes. Slides.

8 December Laurel Sillerud
Title: Alzheimer's Disease: The long, dark tea-time of the Brain Slides.


The enzyme that cuts and rejoins DNA is topoisomerase.
Some 2500 repeats of TTAGGG at the ends of human chromosomes are telomeres.


Errata in PBoC2:
In equations (3.18) & (3.19), D should be 6D.


Last autumn, the course was on Mondays and Wednesdays at 4:30 in room 184.

Here are some of its links:
Here's a video of the demonstration in which I poured sulfuric acid onto some sugar in a beaker. On YouTube it's here.

Here are the class notes.
Here are my notes on probability and statistics.

Here's a gorgeous image of the genetic code.

Here's the article Flippin' lipids about flippase, floppase, and scramblase.

Here are some chapters on neurons: chapter one, chapter two, chapter three, chapter four, and chapter five.

Here's a paper that Gabriel Sandoval found that says that mitochondria can reproduce in axons.

Here's a video about the packing of DNA that Matt Koppa found. The YouTube website also has videos of other topics in molecular biology.

Here are chapters 10 and 11 of MBoC5.

Here's a write-up of mine on neurons. I do not guarrantee the part about action potentials, which I wrote up some years ago, but it might be right.

Here's a paper of mine on membrane electrostatics.

Here's some info on cycles on cycles of reactions.

Here's chapter 14 of MBoC6 on mitochondria.

Here's a link to Harvard's Inner Life of the Cell videos.

Link to my lecture on on the Fisher information matrix, the Cramer-Rao lower bound, and Kolmogorov's theorem and test. Also available on YouTube.

Links of Mr. Koppa's talk on exercise, on genetic prediction, and (full article) on molecular classification.



Homework due Wednesday 26 August 2015: Derive equation (1.5) of the class notes from equation (1.4).
Homework due Wednesday 9 September 2015: Compute the number of negative ions that lie just below the surface of a cell's membrane if the radius of the cell is 1 micron and the electrostatic potential across the membrane is - 50 mV.