8.592 - Spring 2018 - Anonymous Comments


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From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 13 May. 2018

How (hard copy or electric one) and where can we hand in the final project?

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Response: The final projects (PDF format preferred) should be submitted by Email to Professors Kardar and Mirny.


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 8 May. 2018

In lecture note 22, section 4.4.1 "Attractive fixed point", after adding noise, why the 1D steady state probability distribution is p*(x)~(-V(x)/D) but not p*(x)~exp(-V(x)/D)? (line 5, page coded 9)  I suppose it's somewhat like a Boltzmann distribution with external potential. Please correct me if I'm wrong.

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Response: You are correct; it is a typo.


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 7 May. 2018

On problem 1c, what is meant by, "for starting values close to P(p)?" What value is the problem referring to? 

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Response: ... for "starting value" of the recursion $P_1(p)$ close to $P(p)$ defined in part 1b...


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 30 Apr. 2018

For problem 2a, we are still assuming distinct R and T states, correct? So the binding affinities not only differ from each other in the same state across sites, but differ for the same site across states?

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Response: For problem 2(a) of PS#7, the R and T states of hemoglobin are still proportioned with the factor c. Given either R or T state, the 4 sites have affinities, K_1,K_2,K_3,K_4 irrespective of R or T.


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 30 Apr. 2018

Where is the gene_table.txt file for problem 5?

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Response: Thank you for bringing up this omission, gene_table.txt has now been added to the assignment page.


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 27 Apr. 2018

I just wanted to clarify what you are looking for in question 1a of Assignment 7. They ask for the Hill coefficient. So basically we should use one of the two methods mentioned to solve ln(Y/1-Y) for both the MWC model and the Hill model. Then, our final answer would be the Hill coefficient in terms of the parameters for the MWC model?

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Response: Yes, by taking apprpriate derivates of ln(Y/1-Y), evaluate the Hill coefficient as a function of the MWC model parameters.


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 27 Apr. 2018

Could you please upload the Lecture Notes for this week (Lecture 19 and 20)?

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Response: Lecture 19 was posted previously; always clear the cache of your browser if a page appears as absent. Lecture 20 was posted today, and again I advise clearing browser cache.


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 13 Apr. 2018

The lecture note 16 is not available online.

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Response: Thanks, reposted.


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 5 Mar. 2018

On problem set 2, question 2c, when do the mutations (the convolution step) occur?   Does it occur prior to step i, prior to removal of lower-fitness individuals (convolution of two Gaussians).  Or does it occur prior to reproduction in step ii (convolution of a Gaussian and "half-Gaussian")?

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Response: Mutuations are assumed to occur prior prior to step (i).


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 23 Feb. 2018

Where is the problem set submitting bins setup located? 

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Response: The Physics Homework bins are located at the intersection of buildings 8 and 16, on 3rd floor on building 8 (connecting to 4th floor of building 16). There is a box that is marked 8.592.


From: anonymous-8.592-student@MIT.EDU
Subject: comments on 8.592
Date: 20 Feb. 2018

I have two questions regards to Q1 in pset1. First, is "a sequence of N non-stop triplets" meaning a sequence of 3N bp or meaning a sequence of N bp? Second, "how many ORFs of length 600", should we calculate the number of ORFs with the exact length of 600, or roughly 600, or the number of ORFs that are longer than 600?

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Response: 1. N triplets=3N bp;   2. exact length of 600


8.592 Anonymous Discussions- last updated  5/14/18 by M. Kardar