APH 161

About the class

Historic advances in molecular biology, structural biology and the use of biophysical techniques such as optical traps have provided an unprecedented window on the mechanics of the cell. The aim of this course is to study the cell and its components using whatever tools we need in order to make quantitative and predictive statements about cellular life. The main intellectual thread of the course will be the idea that the type of quantitative data which is becoming routine in biology calls for a corresponding quantitative modeling framework. The objective of this course is to elucidate general principles with exciting case studies.

Note that science is driven by experiment--nowhere is this more evident than in the life sciences. As a result, those who are most serious are encouraged to enroll in BE/APh 162: Physical Biology Laboratory concurrently. This laboratory class is built around a series of experiments which are designed to correspond with material covered in the BE/APh 161 lectures.



2/22/09: Clarification of 1(a) of HW5 part A: In (a) of HW 5 part A we ask you to derive the dynamical equations for the repressilator and then to put these equations in dimensionless form--the dynamical equations we're referring to are found in equation 19.45 in section 19.3.3 of PBoC, and their dimensionless form is given in equation 19.46.

2/21/09: HW5 part A has been posted; part B will be posted on Tuesday.  Both parts are due 3/9 by 5pm in the box outside Rob's office.

Part A of the homework requires you to solve differential equations numerically using Matlab or some other program of your choice.  The TAs will be giving tutorials on solving equations numerically in Matlab on Sunday night from 5-7 pm in the third-floor multimedia room in SFL, and on Monday night during Steph's and Maja's usual office hours (7-9pm, SFL 229).  The code we will be going over has been posted on the website.  If you're planning on attending one of these sessions please try to look over the problem set and the sample code beforehand.  We'll definitely go over basic Matlab syntax at the beginning of both sessions so don't worry if you've never used Matlab before.

Also please note that there's a mistake in figure 19.31 in PBoC, which the problem set asks you to reproduce; a corrected version has been posted on the website with the problem set.  There's also a mistake in eqn. 19.52 in PBoC; the correct equation is given in the problem set.

2/19/09: Important announcements:

- There will only be one more homework (HW5).  It will be posted next Tuesday, 2/24, and will be due the Thursday of the following week, 3/5.  It will be fairly long and difficult so please don't wait till the last minute to get started on it!

- As a reminder next week is the last week of class (Rob will be out of town after that).  We're no longer having a Friday make-up lecture either this week or next week (or any other week!), only the two regular lectures next Tuesday and Thursday mornings.

- The TAs made a mistake in grading HW2, problem 3b.  If you got points deducted from your eigenvectors and/or for your energy diagram on that problem, please bring your problem set to Steph after next Tuesday's class and we'll check to see if we can give you some points back.

2/12/09: Clarification and correction on HW4, and some announcements:

- There's a mistake in part (c) of problem 3 on HW4: the last sentence of the first paragraph of 3(c) should read "Show that sqrt{<(N_1-N_2)^2>}=sqrt{N}", not "Show that sqrt{<(N_1-N_2)^2>}=N."  A corrected version has been posted on the website.

- Rob has posted the following clarification regarding the Excel spreadsheet of data that is posted for problem 1: "On problem 1 of HW4 you will need to use data from the Fiebig et al. experiments.  We have provided you both the "raw" data which comes from taking the data points from their graphs as well as a second version of the data that is properly normalized such that the integral of p(x,N) over the length (or radius) is one.   You will probably want to use the second version of the data when you make your fits."  Please ask one of the TAs if the format of the spreadsheet isn't clear--that shouldn't be the tricky part of the problem!

- As a reminder once again, we won't have class next Tuesday, so the problem set will be due by 5 pm on Tuesday 2/17 in the box outside Rob's office.  We're still working on scheduling a make-up lecture; it probably will be postponed once more until the last week of class, Friday 2/27.  We'll let you know the details once they've been finalized.

- Rob will be out of town next Monday and so won't be holding office hours that day (2/16).

2/10/09 Announcement from class: 

-HW3 is due on Thursday 2/12 at the beginning of class; as announced last week, there will be a party and a special lecture on Thursday in celebration of Darwin's birthday.  You are strongly urged to come to lecture on Thursday!  Also please find Stephanie after class if you didn't pick up your homework on Tuesday.

HW4 will be posted as soon as possible and will be due next Tuesday at 5pm in a box outside Rob's office. As a reminder we won't have class next Tuesday (Rob will be out of town); we had originally scheduled a make-up lecture for this Friday at 5pm but we're going to have to reschedule the make-up for next Friday 2/20 at 5 pm in Broad 100.

Finally, the TAs will be holding extra office hours on Wednesday to help with HW3.  Steph and Maja will have office hours from 1:30-2:30pm and Bill and Jonathan will have office hours 2:30-3:30 pm.  Both sets of office hours will be held in the Phillips lab conference room (down the hall from Rob's office).

2/6/09: HW3 extension and clarification: Because of midterms week next week and our delay in posting HW3 this week we've extended the deadline for HW3 to next Thursday, Feb. 12th.  Please remember that the homework is due at the beginning of class.  Also next Thursday we are having a party and you are all strongly urged to come because there will be a special lecture that day.

Rob has also posted the following clarification for HW3, problem 5: "In problem 5 of the HW (i.e. problem 8.4 of PBoC) what I am asking you to do is to work out a partial differential equation for the probability that the polymer ends at position x after N steps.  This derivation was essentially sketched in class.   The clarification that I want to propose is this: p(x,N) is the generic solution and a special name (G(x,N), known as the Green function) is given when the "initial condition" is a spike (or delta function) like we have chosen. Remember, we said that G(x,0)=delta(x-x0).   Further, I described G(x,N) as a "counter" that tells us the number of configurations that are of length N and end at position x.  More precisely, G(x,N) should be thought of as the statistical weight of the polymer configurations with N links that end at x.   Because of the absorbing boundary conditions, once we find the result for G(x,N) (or if you prefer to call it p(x,N)), we need to normalize the solution as I discussed in class.   I am happy to talk about this in more detail at today's help session."

2/4/09: HW3 has been posted, and HW2 solutions will be posted as soon as possible.

2/3/09: Announcements from class today:

- There will be no class on Feb. 17th (Rob will be out of town); instead there will be a make-up lecture at 5 pm on 2/13 in Broad 100.  HW4 will still be due on the 17th, but you can turn it in as late as 10:30 am outside Rob's office (we'll put a box there).  A note on late homeworks: except for HW4, homework is due at 8:30 am and will be considered one day late after 8:30.  Your grade on a late homework will drop by 10% every day that it's late.

-Rob will also be out of town on 2/9 and so will not be holding office hours that day; instead he'll be holding an extra help session at 5 pm on 2/6 in Broad 100.

-If you didn't get HW1 back today please see Stephanie after class on Thursday.  Please email Stephanie with any questions about grading.

1/25/09: Rob has added office hours from 1-3 pm on Fridays, in addition to his Monday office hours.  NOTE: Stephanie and Maja now hold their office hours in SFL room 229, and Jonathan and Bill at the Broad cafe.  Please refer to the "People" page for the most updated information about office hour times and locations.

1/22/09: Another quantum mechanics review session will be held this Friday, 1/23/09, at 5 pm in 100 Broad.  There will be pizza!  Also, there's a typo on Problem 3a of HW1: the problem currently reads "Using the schematic in Fig. 1 and the facts that carbon-carbon single bonds are about 1.3 A and double bonds about 1.5 A, estimate the area ..."  The question should read "Using the schematic in Fig. 1 and the facts that carbon carbon DOUBLE bonds are 1.3 A and SINGLE bonds about 1.5 A, estimate the area ..."  A corrected version has been posted on the homework page.

1/19/09: Rob's office hours on 1/26 will be 1-2 pm, NOT 12-2!

1/16/09: Quantum Mechanics: Several additional resources for quantum mechanics have been posted on the syllabus page, including the TAs' notes for those who missed the review.  Rob, Steph, and Maja all have office hours on Monday, so please come talk to us if there were parts of the review session you weren't comfortable with!

1/14/09: More announcments:

- We have two new TAs, Bill Dempsey and Jonathan Sternberg.  We're working on adding their contact info and office hours to the website.

- READING for Tuesday 1/20/09: Please read the following by next Tuesday's lecture: Physical Biology of the Cell ("PBoC") Chs. 2 and 3, and the Paul Nurse article on "The Great Ideas of Biology."  Rob will not be going over this material in class but will assume it is part of your working knowledge from Tuesday on!

- The schedule for the remaining lectures have been posted on the syllabus page.  Note that the last lecture is on 2/26!

1/13/09:  Several logistical announcements from class today:

- Beginning Thursday, January 15, class will start at 8:30 am instead of 9 am.  This will allow Rob to cover all the material he needs to without holding make-up lectures in the evenings, as originally planned (so no Tuesday/Thursday evening classes!)

- There will be an optional quantum mechanics review session this Friday, January 16th, at 5 pm in 100 Broad.

- Homeworks for the course will be posted online and will be due a week later, at the beginning of class.  The first homework will be posted either this Thursday or next Tuesday.

- Office hours: Rob's office hours will be Mondays 12-1 pm (159 Broad); Steph and Maja will hold joint office hours Mondays 7-9 pm in the Phillips lab conference room (across from Rob's office).

12/19/08: The first day of class for BE/APh 161 will be on Tuesday, January 13, NOT January 6th, in 100 Broad. All classes will be held in 100 Broad, NOT 104 Watson! Rob and several members of his group will be at a meeting the first week of classes, so we will start classes a week late,but with an aggressive plan of mandatory makeup lectures in the evenings. There will also be an optional review of quantum mechanics held one evening early in the course. The makeup lectures and the quantum mechanics review will be from 7-8:30 pm in 100 Broad, Tuesday and Thursday for the first two weeks of class (so the evenings of 1/13, 1/15, 1/20, and 1/22); the specific schedule for which nights will be makeup lectures and which will be review has yet to be determined, but we'll let you know as soon as possible.