Is it true that all scientists are geeks?
Tonbridge Grammar School for Girls 1996-2001, Univeristy of Bath 2003-2006, University of Birmingham 2006-2007, University of Nottingham 2008 – now
BSc in Physics, MSc in Computer Science and about to get a PhD in Computational Chemistry
All over: a sweet shop, an investment company, a ski shop, my university, a college, in a library…
Researching proteins using expensive computers
University of Nottingham
Favourite thing to do in science Being paid to get a bit lost in my own thoughts. Then talking about them with different people.
Supercomputers vs. superbugs – I use computer simulations to understand how new antibiotics can treat illnesses that are very hard to cure.
What is a superbug?
You may have heard of hospital superbugs. They are bacteria like MRSA or c.diff that cannot be treated using ordinary medicines. People can catch these infections when they are being treated in hospital and it makes the patient very ill and sometimes leads to death.
Bacteria, like all living organisms, evolve to survive in their environment. Unfortunately, superbugs have evolved so that antibiotics no longer kill them.
How can a computer kill a superbug?
By helping scientists develop new drugs that will kill resistant bacteria.
I am working on an antibiotic called nisin. When the nisin is first made it is like a long strand but to be able to kill bacteria it must fold up into a shape with two circles. Imagine taking a straight piece of wire and bending it into a frame for a pair of spectacles, this is similar to the microscopic folding process. Small changes to the position of some of the atoms in the nisin molecule change how it folds. Making all the possible nisin molecules in the laboratory would be very expensive and time consuming. By running simulations I can see which molecules will make the shape I want and then I can tell my colleagues who are making and testing new antibiotics which ones to focus their work on – saving them time, effort and money
I run lots of different type of simulations:
Molecular dynamics simulations that look at how atoms can move.
Docking simulations that predict how molecules interact with each other.
Some simulations use Newton’s Laws of Motion…
…but others use Quantum Mechanics, a branch of physics where electrons behave in weird and unexpected ways.
This YouTube channel has animations of simulations made by scientists working in my research area:
Do you work with any other molecules?
I am also trying to understand a molecule called the ileal lipid binding protein (ILBP for short) which is in the gut and absorbs bile salts. Bile salts are made in the body from cholesterol and help us to digest fatty foods. When bile salts are absorbed by ILBP they are recycled, meaning that the body will not convert as much cholesterol into new bile salts. If we can find a way of stopping ILBP absorbing bile salts then we would decrease the amount of cholesterol in the body. This would be really good news as 6 out of 10 adults in the UK have high cholesterol and it is strongly linked to heart disease.
This is a picture of ILBP. The purple coils on top act as a gate that allows bile salts to enter and leave the inside of the protein. I have been running computer simulations of ILBP under different conditions, such as changing the type of bile salt or pH level, to understand what makes the gate open and shut. Once this is understood other scientists who work on developing medicines can use the information to find a drug that will stop ILBP absorbing so many bile salts.
What is your subject called?
Computational biophysical chemistry. This basically means I use IT, physics, biology and chemistry to understand how these molecules work. Physics so that I know how the molecules move, biology to know how they work in the body, chemistry to know how the atoms are bonded to each other and IT so I can simulate it all.
When you study science at school there is a clear distinction between physics, chemistry, biology, maths and IT. But to full-time scientists there are lots of areas where the subjects overlap.
My Typical Day
I get up early to write about my work so it can be published. This is usually the most difficult task so I like to do it in the morning when I’m feeling fresh. The hard work usually lasts until lunch time then I spend the afternoon talking with colleagues about science and playing around with simulations.
What I'd do with the money
With the help of local school students and the Periodic Videos, I will make simulations the stars of YouTube.
Do you know about the Periodic Videos?
The Periodic Videos (http://www.periodicvideos.com) is a fantastic website full of short videos about the elements, molecules and science in general. The YouTube channel has had 23 million views and, in May, the site won a ‘Webby’ – the Oscars of the internet. You may have even watched some of the videos in you science classes.
What’s special about proteins?
Proteins are very special biological molecules. All the enzymes in your body are proteins and all living things on planet Earth make and use them. In fact, most life depends on them.
Proteins have weird microscopic behaviour. They start out as long, floppy chains but always fold up into the same shape. It’s like dropping a strand of cooked spaghetti and it always landing in exactly the same position. I run simulations of proteins to try and understand and predict this strange behaviour.
What do the Periodic Videos and proteins have to do with the ‘I’m a Scientist’ prize money?
The Periodic Videos are made right here in my department at the University of Nottingham. However, they currently don’t have any videos about proteins. If I win I’m a Scientist I am going to work with some local school pupils to run simulations of proteins. We will then animate the simulations and make our own Periodic Video. Hopefully the Professor will present it for us and the students will be able to visit my work to see how the videos are made.
Professor Martyn Poliakoff, presenter of the Periodic Videos, and Brady Haran, the film maker.
How would you describe yourself in 3 words?
Funny, friendly, ambitious
Who is your favourite singer or band?
Muse, Metallica, Lady Gaga, Radiohead, Dizee Rascal, The Smiths… it’s hard to choose just one
What is the most fun thing you've done?
A few years ago I went to China and met a panda
What did you want to be after you left school?
Were you ever in trouble at school?
Sometimes – I have dyslexia so I was always handing in my homework late or being nagged about spelling words wrong
What's the best thing you've done as a scientist?
Not sure about the best, but the worst is that I once accidentally broke a £1 million supercomputer
If you had 3 wishes for yourself what would they be? - be honest!
(1) Finish my PhD so that everyone has to call me Dr Ellie (2) Get a cat, a dog and a horse (3) Win I’m a Scientist
Tell us a joke.
Did you hear about the mathematician with constipation? He worked it out with a pencil.