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So….where do I start?!

I am part of a research group called ExoMol which is based at University College London in the department of physics & astronomy which has around 20 members including summer students, Masters students, Postdocs, Research Associates and, sitting at the top of the academic pyramid, Professors.

Each of us works on a molecule or two. Our aim is to produce a “linelist” for our molecules-what we mean by this is a list(a rather long list I might add, can be about 10 billion in the case of methane..) of wavelengths and intensities which astronomers can use to identify different molecules in outer space. Each moledule has a different list! Think of it like barcodes. Each of the “lines”(ie wavelength with an intensity) corresponds to a transition in the molecule-ie when a molecule changes state, due to conservation of energy, a wavelength of light at a specific(think 4 decimal places accuracy) is given off, emitted

Before I start talking quantum chemistry-the molecules I’m working on are Chromium Hydride(CrH) and Manganese Hydride(MnH). I’ve also become friendly with Beryllium, Magnesium & Calcium Hydride as these are smaller(and hence a little simpler) which helped me get my head around The Big Two, CrH & MnH whom I nickname ‘Naughty & Nice’ respectively. Basically the extra electron in MnH makes life a lot more stable….

Now….what do I mean by a state of a molecule?

In a single atom, electrons are whizzing around the nucleus. When the electrons are arranged a certain way(“configuration”) that is what we call  a state of the atom. For a molecule as well as these electronic configurations, to fully describe its state we need to also specify a) how fast it is vibrating(and what modes) and b) how fast it is rotating. When a molecule changes state to one of a lower energy(ie starts spinning slower, starts vibrating in a different way or the electrons move around) then, there will be a release in energy ie wavelength of light!

So how do we produce a linelist?

By solving Schrodingers equation! Yes Schrodinger has a very famous cat. When we start solving Schordingers equation for a particular molecule it is literally like opening up a box with a cat in it-we don’t know how friendly, easy-going or downright obtuse the molecule will be! They can be very deceptive. Like all cats, they all have their quirks-when you think you’ve ‘got them’ under control, you get some strange result which can’t be explained by logic.

So how do we solve Schroedinger equation? Computers. Big Computers. Big Rooms full of Big Computers. We use various quantum chemistry packages where people have made a lot of clever approximations which will use various procedures to effectively number crunch.

In physics a two body problem can be solved exactly-any more than two bodies and you need to start using approximations! Such as the Born-Oppenheimer approximation which uses the fact that the mass of an electron is around 10^-4 the mass of the proton. This thus allows us to split the Schroedinger equation into an equation for the motion of the wee electrons flying around and a second equation for the motion of the heavier nuclei(protons and neutrons) which are very slugglish in comparison(ie the vibrational & rotational motion of the molecule).

After we have produced a linelist we always ‘fit’ ie refine to any experimental data available-it acts a as a very good sanity check!

So now you might wonder why astronomers can’t just use experimental data to identify molecules in outer space? The reason is, as the temperature increases molecules get more energetic, more excited. The electrons reach higher energy levels & the nuclei vibrate and rotate faster. Hence molecules ventures into new states which it will transition between-ie more lines! We can’t measure the spectrum(ie list of wavelength lines with intensities) in the lab due to safety concerns-astronomers want to know what the spectrum ie linelist of molecules of different molecules will be at temperatures approaching 5000 K.

So instead of heating up experimental labs to 5000K we instead heat up server rooms with Big Computers doing theoretical calculations(when Big Computers are running they give off lots of heat! But not as hot as 5000K….the server room does have its own air conditioning system to stop the computers overheating).

On a final note, feel free to ask me how its possible to set off remotely from the other side of the world  Sonic Booms in the server room.

I work in an office which is situated in the library(UCL has a pressing shortage of space so us theory dudes get housed in the library away from all the experimental labs in the actual physics department….).

Our office has 5 residents-myself, fellow PhD student, post docs Lorenzo & Andrei and my supervisor, Dr Sergey Yurchenko aka The Trove Monster…………..eh no I mean the  Trove Master (https://twitter.com/trovemaster). Trove is the name of the program he has co-built and works on.  Think hardcore maths…all pretty epic stuff.

The 5 ‘other residents’ in the office are 5 computers which each have their own name-“Burroughs”, “Sickboy”, “Renton”, “Marvin”, “Eddie”.  It gets very hot. Even in winter when the heating is on full blast we often actually have to open windows and use fans…..

So my typical day in the office can consist of any of the following in about possible orders. Or to use the more scientific phrase ‘combinations & permutations’.

1. Browsing the “archive” for new papers released in the field of Exoplanets-check out http://arxiv.org/archive/astro-ph

Anyone can access this resource and read about the latest discoveries. Yahoo for open source publishing!

2. Searching for scientific papers on the molecules I’m working on, reading through & summarizing this literature, extracting relevant figures and comparing my results to this to see if we agree (or not!)

3. Doing small ‘test’ calculations-this usually involved a lot of debugging! Then after copying files to the Big Computers in the server room to run the full-scale calculations. Very often I will set off small test calculations around mid afternoon, then go home then later in evening once they have finished log in to see the results.

Working at home! Yes it is quite possible-the beauty of the computing system in the department(and many departments) is that it is possible to ‘log in’ remotely and thus do work in any location provided you have a decent(ish) internet connection. I have friends who travel the world whilst doing their PhDs as it can becheaper than living in London…..

One point to make is office is very rarely fully occupied-we all work ‘funny hours’-it is one virtue of academia is that you are largely free to choose which hours you work-provided you get the work done! Nocturnal working hours is surprisingly not that uncommon……(Postdocs & Professors I’m looking at yoooouuuu). Also weekend working does happen quite often-research goes on at all hours not just Mon-Fri 9-5.  And some nights ‘work-off’s happen where two people in the office are ‘in the zone, on a roll’ getting results done and end up not leaving until midnight. Other days, nothing seems to work-that’s when its best to head home(or go to the pub and talk to someone who may have ideas) and try again the next day.

4. Once these calculations have finished then copy the output files back to my computer. Yes PhD involves a fair bit of moving files around the computing system in order to a) run calculations b) have them ‘backed up’. We’re talking Terabytes of data here!

5. Analyse the results of these calculations. This can involve me writing scripts that ‘grep out’ all the numbers I want from an output file and then plot them to produce some nice pretty colour-coded graphs.

6. Plan further calculations. Go back to step 3 and repeat steps 3 to 6.

7. Meeting supervisor. Discussing latest results, deciding what to do(or not do) next.

8. Checking email, replying, putting event(such as IASGMOOH) into diary

9. Backing up work. Get into the habbit! The Physics computing system automatically does this if you store files in certain places. But always best to keep your own.

And finally

9. Did I mention writing up my PhD?! 😀 For anyone that ever embarks on a project, I strongly advice you to write up as you go along!! At present I am reading through textbooks on molecular spectroscopy and writing my theory chapter explaining(in my own words, plagiarism=don’t do it….) the relevant theory involved in my PhD.

Of course in the middle I have lunch, have some breaks for hot chocolate(with double cream and marshmallows, of course), chatting to fellow PhD students. Also chatting to undergraduates who visit the office to see Sergey. And also library users who are lost and looking for a department!

On a Wednesday our research group have our weekly ExoMol Coffee-yes think (highly calorific) biscuits, donuts, tea, coffee, fruit juice, cake, ice cream where we all get together and discuss(amongst other things) the latest bureaucracy imposed by our grant providers(and more importantly how to get around it)MATOMO_URL Each of us follow a scientific journal and will report any published scientific papers from the last week that are of interest to the group.

Or alternatively any new scientific stories that are of interest such as the IgNoble prizes and the related website: http://www.improbable.com/ (check it out, its good). Then after it will be someone’s turn to speak for 20 minutes on their research-there are 20 of us in the group so every few months. The conversations are very light hearted(aka not scientific grillings) and is a very good way for everyone to ask questions and share ideas-particularly if people are coming up against similar problems in their research.

Wednesday evenings I travel to Mill Hill Observatory in North London where I do demonstrating for the “certificate in astronomy course” which ICL offers to members of the public who would like to study astronomy for interest. Mixture of helping with computing problems, supervising telescope usage, chatting about my research, teaching new concepts.

Thursday & Fridays we often have seminars given by visiting academics or fellow students in the physics department.

So yes in summary, no day in research is the same!

*Our group has at random been chosen to be audited by accountants to make the research money is getting put to good use. Think lots of rules and regulations. Ah the joys…..