Archive for January, 2010


2nd Year Plans

Well, it’s official. After months of agonizing over plans for my immediate future, the upcoming academic year, I have managed to narrow down the field of possibility to just three choices. Over the course of the past week, I’ve managed to visit all of the contenders and speak to some faculty and students at those various programs, as well as submitted the relevant applications. I haven’t yet decided on a particular course yet, and probably won’t until the last minute. As often is the case, I’m telling myself that there’s really no reason to set my hearts on a particular program, when at any moment I might be rejected, making my decision far easier. We’ll see if this line of logic turns out to hold any more veracity this time than in the past several times I’ve tried applying it.

Imperial College London

As some of you might know, the funding scheme I’m on both permits and obliges at least 2 years of graduate study in the U.K. For my first year, which you’ll know if you’ve been keeping up with my blog, I chose to read for an MRes in Biomedical Physical Chemistry at Imperial College. Additionally, it happens that I almost certainly have funding if I choose to continue on for a PhD at Imperial, likely in bioengineering, so there’s option 1.

Pros/Cons: I definitely like and enjoy the environs (I do so love some of the friends I’ve made here!), and thus far have gotten on well with my supervisors. The bioengineering department is arguably the best in Europe, and the research I’m doing combines to some extent my love of mathematics with applications to biochemistry. Additionally, from speaking to Kristy, a current Bioeng PhD student from Texas, I’m told there’s a “geek cachet” to being from Imperial. Whereas students might be perceived as choosing a school like Cambridge or Harvard for name recognition, coming from Imperial signals that one is extraordinarily serious about the science itself. The flip side to this of course is that because Imperial holds less recognition outside of the academy in America, it won’t help as much should I choose to pursue a non-academic career in the States. However, I’d be out with a PhD at 23 years old, which has its own associated advantages.

Imperial College Pavillion

Imperial College Pavillion

University of Warwick

Options 2 takes me back to the world of straight mathematics. Earlier today, I visited the University of Warwick (where my friend Michelle went for undergrad), located near Coventry in the Midlands. Warwick has one of the best maths departments in the U.K., despite its relative youth (it’s only about a half century old), and is also a true campus university, like IU Bloomington, and in contrast to Imperial or Cambridge (option 3). Thus, yesterday, I submitted my application for their MSc in Mathematics, and was told today by the MSc director that I should here back in about a month, and that based on my college GPA, he would find it unlikely (though not impossible) for me to be rejected.

Pros/Cons: The campus really is beautiful and reminds me very much of Bloomington. The MSc is comparatively small and offers a lot of personal attention, also requiring students to do supervised research projects. Warwick is also obviously a non-Oxbridge/London institution, and so is a bit less inundated by foreigners (though still so, and the maths department especially); it’s also a bit off the beaten path for Marshall Scholars, which holds both it’s appeals and drawbacks. There is one compelling reason not to choose the Warwick MSc over the Cambridge part III course though: the MSc director told me so, saying quite bluntly that while Warwick is a close second, the Cambridge part III course is better.

University of Warwick Modern Architecture

The buildings are obviously quite new at the University of Warwick.

University of Cambridge

Which brings us to option 3, which is part III of the Mathematical Tripos at Cambridge. Despite the anachronistic name, part III is the “equivalent of a very hard taught masters” in mathematics, and is quite international reputed. The maths department claims to be the oldest maths department(s) in the English speaking world, and with that age comes great bureaucracy, as was obvious from the even just the application procedure. The application form was 32 pages long (including instructions), and three copies were required, one for the central office, one for the department, and one for the “college”, each of which technically needs to approve of me, though the major decision will be made for the two maths departments. I visited on Friday, in the lovely rain so characteristic of England.

Pros/Cons: Cambridge obviously has the benefit of a strong reputation nearly everywhere and in most fields. Because of the reputation, it’s also harder to get in, and the part III course is much larger than Warwick’s MSc, consisting of nearly 200 students from around the world. Thus, one receives far less personal attention, and the competition can also be quite fierce for the limited number of PhD places offered, which tend to be given based on the exam results from part III. On a more visceral note, the place is also beautiful, though in a very different way than Warwick. While there isn’t as much green space, the architecture is truly astounding in some of the older Cambridge colleges. There’s also a mix of the really old gothic style with some more modernist buildings like the Centre for Mathematical Sciences, where I’d be based.

Cambridge Centre for Mathematical Sciences

Cambridge Centre for Mathematical Sciences

So there you have it, the three options I’ll possibly have to choose from for next year. A lot will depend on how well my research at Imperial goes, and on whether my applications for Warwick and Cambridge are successful, so it’ll be a while before I know for certain. Still, at least I can take comfort in knowing that even after I’ve chosen, I’ll continue to have the opportunity of agonizing over my long-term future plans!

~William~

Gromacs Genion Fix

Gromacs is a wonderful open source molecular dynamics simulation package that I will be using for some of my research here at Imperial. However, as is oftentimes the case with scientific packages (both open and closed source), there are some minor quirks that I’ve had to learn to deal with. One of those quirks was elusive and irritating enough that I’ve decided to write a short howto so that someone elsewhere might not have to spend as long as I did trying to solve it.

Warning: I am not a computer scientist or programmer, and barely even a scientist. There is no guarantee that this code will not destroy your data, so be sure to backup all files before attempting this fix (which you should be doing anyways)! Having said that, it worked for me, and I can only hope for the best.

Version: This behaviour is seen on Gromacs 4.0.7. The proposed fix uses standard unix command line utilities (and is a very ugly but working hack).

Symptoms: While trying to neutralize the charge on a solvated system using genion to add X ions, genion insists on instead adding kX ions, where k is an integer. Additionally, attempts to use genion’s own “-neutral” option also fail, with it calculating the correct number of ions to add, but then adding it multiple times.

Cause: The reason this happens is due to the way the topology files are constructed. Near the end of the topology file is a section that details the type and number of molecules in the system. For instance, it might look something like this:

[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 27550

When genion runs, if one selects option 12, “solvent”, genion will replace some of the solvent “SOL” molecules with the specified ions, perhaps resulting in the following, where we specified the addition of 8 NA+ ions:

[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 27542
NA+ 8
CL- 0

However, sometimes, due to prior processing with other tools, there will be multiple “SOL” lines, like so:

[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 72
SOL 75
SOL 27403

Notice that the total number of solvent molecules is the same in both examples. However, genion gets confused when multiple solvent lines are present, and seemingly acts on each line! This causes the resulting topology file to look like this:

[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 64
NA+ 8
CL- 0
SOL 67
NA+ 8
CL- 0
SOL 27395
NA+ 8
CL- 0

Notwithstanding the fact that the resulting topology file is decidedly not neutral, the topology file also then for some reason does not match up with the .gro file, which causes additional problems down the line.

Of course, by now, you’ve probably figured out how to solve the problem yourself: just make sure to consolidate multiple SOL lines before running genion, and you’re golden! Since I am lazy and do not like doing that by hand (and because I’ll probably need to bulk process many proteins sometime in the future), I hacked together a really ugly but working bash script to do just that. Following:

#!/bin/bash
# Consolidate the solvent molecules in the topology file.
filename=example.top
sol_mol=0
cp $filename $filename-new
while read line; do
sed "/$line/d" $filename-new > $filename-new2
mv $filename-new2 $filename-new
add=$(echo $line | sed 's/SOL//')
sol_mol=$(($sol_mol+$add))
done < <( tail -n $(( $(cat $filename | wc -l) - $(grep " molecules " $filename -n | sed 's/:\[ molecules \]//') + 1 )) $filename | grep SOL )
echo "SOL $sol_mol" >> $filename-new
mv $filename-new $filename

If anyone actually stumbles across this page and finds it useful (which I rather doubt, but you never know), I’d love to hear about it.

~William~

Final Examinations

Though the bulk of the degree is research—as befits an MRes (Master of Research)—there was still a taught component, and this past week final exams marked the end of the assessed classes. I should first state the caveat that I should not generalize too much from this one experience taking English final exams, but having said that, I will now proceed and do exactly that.

Over the course of 7 weeks, we had 7 taught modules of about 8-10 hours of lecture each. The lectures themselves were quite interesting, and covered a wide range of topics, though not in very much depth given the time constraints. Each module was taught by 2-3 lecturers in sequence on related topics; for instance, in a biophysical techniques module, one lecturer spent 4 hours on NMR and another 4 hours on X-ray diffraction. The final exams were given by module, with 30 minutes being allocated for each, though in a fuzzy way—we had 2 hours last Tuesday for 4 modules worth of questions and 1.5 hours yesterday for the other 3 modules. For each module, we had a choice between two multi-part essay questions, usually one set by each lecturer of a module, though in the modules with 3 lecturers, we still only had two choices. Each subquestion would be worth some fraction of the total points for that module, and whether or not we passed the exams as a whole depended on a simple summation of the points we earned from all modules. The passmark for us is 50%, and more points are need to get merit (60%) or distinction (70%). For any American readers, I should remark that it is supposedly far more difficult to get 100% here than in the U.S., but will have to wait until I get my own results back before commenting on the grading scale.

As for the questions, I must say that I am in a way quite disappointed with the level of difficulty. Perhaps it’s because I’ve already taken full semester classes in biochemistry, genetics, etc., so I have an unfair advantage over chemistry/physics/electrical engineering graduates who haven’t taken any biology since A-levels. However, it felt like even for the subjects I hadn’t previously had, the level of the questions was only about that of CHEM-S117 (honors general chemistry) at IU, which I took when I was a fresher way back when. I suppose the grading might be extremely harsh, but I’d be hard pressed to figure out how they’d pull that off given the questions set.

Of course, this is a postgraduate course, and the primary purpose of the lectures was to give physical science graduates a crash-course in biology so that they’ll have some inkling of the why behind their research projects for the next 3 years and 9 months (or only 9 months, for the few of us overseas students who are on the 1-year MRes instead of the 1+3 MRes + PhD). Indeed, one of the lecturers (my supervisor, actually) explicitly stated that her question would be easy because the thrust of the program is the research component. The course directors themselves stated that it was largely due to University of London regulations that the exams took the form they did, and that they were looking into changing them now that Imperial has unaffiliated. Still, I had assumed classes and exams would get significantly harder upon going to grad school, which turns out not to be the case. Oh well, at least the research component is considerably more challenging and exciting.

I should now state that a decent number of the British students also felt somewhat disappointed by the exams. Hence, it might just be the postgraduate philosophy of this particular program to place little emphasis on taught material that’s behind how easy it was, and not British higher education in general. Still, this experience stands in marked contrast to the perception of some a few Imperial students, who have argued to me before that the coursework is harder and more in depth than at most American universities, due to the specialization inherent in British higher education and the better secondary school education (the A-levels every university-bound student take correspond roughly to American AP classes content-wise).

I’ll be following up this post when I get my exam results back, to compare and contrast the grading system. It’s also possible I’ll have to eat my words if I end up miserably failing, but I’ll deal with that then. In any event, I’ll be beginning my research project on Monday, so wish me luck!! ::squeals of excitement::

~William~

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