8.593J - Biological Physics Spring 2010

Lecture Notes:

Lecture notes will be posted here throughout the semester.

Table of Contents
Chapter 1, Sections 1-2
Chapter 1, Sections 3-5
Chapter 1, Sections 6-8
Chapter 2, Sections 1-3
Chapter 2, Sections 4-5
Chapter 2, Sections 6-7
Chapter 2, Sections 8-9
Chapter 2, Sections 10-12
Chapter 2, Pages 204-205
Chapter 3, Section 1
Chapter 3, Section 2
Chapter 3, Sections 1-2 (updated)
Chapter 3, Section 3
Chapter 3, Section 4

May 6th Lecture by Leonid Mirny:
How a protein searches for its site on DNA: the mechanism of facilitated diffusion
J. Phys. A: Math. Theor. 42 No 43 (30 October 2009) 434013

May 11th Lecture by Leonid Mirny:
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
Science. 2009 Oct 9;326(5950):289-93.

If you print lecture notes and want to save paper and space, the notes are still pretty legible when printed two pages per side of the paper, on both sides of paper. I could not find a way to do this from an Athena workstation (it would default to low resolution halftone, and SIPB couldn't help), but I could print this way from a Windows XP computer to an Athena printer. Instructions for setting up the printer can be found here. To enable duplex printing, go to Control Panel -> Printers and Faxes, right-click on the Athena printer you have installed previously, and choose Properties. Go to the Device Settings tab, and under the Installable Options branch, change the Duplex Unit option to Installed, click OK, and close the Control Panel. Open the document you want to print, and go to File -> Print. Select the Athena printer you installed previously. Click the Properties button, and go to the Layout tab. Select Orientation: Portrait, Print on Both Sides: Flip on Long Edge (so that the pages can be read nicely in a binder), and Pages Per Sheet: 2. Then click OK on the Properties dialog and OK on the Print dialog to begin printing.

I am unaware of other efficent methods of printing. If you would like to pass on your knowledge so that following students may benefit, please email the course instructors and they will update this section of the website.

Other Notes:

Recitation 1: A Mnemonic Scheme for Thermodynamics from MRS Bulletin, Vol. 34, pages 92-94 (2009).

Lecture 2 Supplemental: Jeffries Wyman Biographical Memoir from the National Academies of Sciences (2003).

Goldman, Benedek, Dohlman, and Kravitt (1968): Structural alterations affecting transparency in swollen human corneas

Goldman and Benedek (1968): The relationship between morphology and transparency in the nonswelling corneal stroma of the shark

Tanaka and Benedek (1975): Observation of protein diffusivity in intact human and bovine lenses with application to cataract

Nogi et. al. (2009): Optically transparent nanofiber paper

Errata:

Chapter 1, Page 26, Line 2,7: The reference to equation (2.5-2) should be replaced by (1.2-25).

Chapter 1, Page 26, Line 3: The reference to Fig. 2.5-1 should be replaced by Fig. 1-2.

Chapter 1, Page 32, Figure 1-3: The vertical axis label t should be replaced by p.

Chapter 2, Page 24, Equation (2.2-30a): The rhs numerator 1 should be replaced by R.

Chapter 2, Page 112, Line 14: The character alpha should be replaced by the character z.

Chapter 2, Page 117, Table 2.6-2: In the header the variable Δμ0RT should be replaced by Δμ0T.

Chapter 2, Page 118, Line 16: Between "energy ladder" and "9.11" should be inserted "for R forms".

Chapter 2, Page 118, Line 16: "is the top of the R ladder" should be replaced by "the top of the T ladder".

Chapter 2, Page 121, Line 4: The reference to Figure 2.6-5 should be replaced by Figure 2.6-6 (hand correction already made in notes).

Chapter 2, Page 146, Line 12: The word "occasional" should be replaced by "possible".

Chapter 2, Page 147, Line 10: The word "as" should be replaced by the word "an".

Chapter 2, Page 148, Equation (2.8-3): The variable μ0R should be replaced by Δμ0R in both instances.

Chapter 2, Page 157, Line 4: The words "and is" should be deleted from "pCO and is relative to the pO2 asis...".

Chapter 2, Page 162, Line 6: The word "the" should be deleted from "... each of the these...".

Chapter 2, Page 165, Line 14: The phrase should be updated as (changes in bold) "Thus in this domain of saturation, the...".

Chapter 2, Page 172, Figure 2.8-5: The values given in the caption label the curves from top to bottom.

Chapter 2, Page 174, Line 8: Between the word "converted" and the comma should be placed the phrase "into HCO3-.