Computational Chemistry by Maya M (Continued)

Continued from her previous post, Maya tells us about the rest of her week in a Computational Chemistry research group…

Day 3: I spent the third day drawing more molecules on the computer.  I also began to optimize the molecules that I had drawn. Optimizing a molecule on Molden meant that I had to use the software to run a program which ensured that each atom and bond utilized the space around it properly and that the bond angle between carbon and hydrogen atoms, for example, was correct. I was already used to Molden by this day so I didn’t encounter any problems using it or carrying out the instructions that my supervisor gave me. I also got to know the PhD students in the ICT room in which I was based.

Image: the graphs are the details of the optimization test

Optimization
Day 4: Two students who had gained a research placement from the Nuffield Science Work Experience program, joined me on my placement. I was really happy because I was able to speak to students who were of a similar age to me and we all shared ideas and thoughts of how to best use Molden. I felt quite proud of myself, as I was able to demonstrate and explain to the students how they should go about using the software and what we were trying to achieve. On this day, my supervisor, Dr Rosta, decided to show me how you would carry a reaction out on the computer. Dr Rosta’s current research is based on Hydroboration,  so she made me draw a cyclic hydrocarbon and a small BH3 molecule. Then we placed them next to each other and ran the program. The program was a bit like a movie, as it show the BH3 molecule moving towards the nearest double bond, an area of high electron density,  and breaking the double bond to form a new bond. I was really impressed when I saw this occur as it was a visual aid to what normally occurs on an atomic level, which our eyes can’t normally see when we carry out experiments in beakers.

Image: The red and white molecule is the BH3 molecule and it is moving towards the blue and white molecule, which is a cyclic hydrocarbon

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Day 5: This was my final day and I was very sad to leave. I had enjoyed my time at the department and I didn’t want to leave. My supervisor and I decided to talk about her life and how she arrived at the place where she is now. Dr Rosta had started out studying for a chemistry degree when she decided that she wanted to study Maths. She started her Maths degree and had done three years of her degree when she decided to get a PhD in Chemistry. Dr Rosta is now a lecturer at King’s College,  where she teaches third year students Computational Chemistry. She is very intelligent and I was grateful that I was able to learn how her. I also had my picture taken to go in the in2science records, and I had to strive for a casual pose in the picture, but somehow I don’t think I managed that! Overall I had a great time and learnt new skills.  I have even downloaded Molden on my home computer so I can explore some of the features I didn’t use in my placement. I enjoyed myself immensely and I would do it again if I was given the chance.

By Maya M

University of Bath August Placements

Becky Mead updates us about the varied and exciting range of placements taking place at the University of Bath

Another fantastic mixture of placements @UniofBath this month! First, the Department of Pharmacy and Pharmacology @PharmUnivBath. Our in2scienceUK student has been busy working alongside Dr Chris Bailey’s PhD students, investigating neuronal changes caused by drugs of abuse, and how they relate to drug tolerance and addiction. During my visit she was working with PhD student @AnnelisaSadler and preparing her first gel electrophoresis (see photo below). She has really enjoyed all aspects of the practical work and has a clearer idea about what degree she would like to study.

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Next, the Department of Biology and Biochemistry where two students have been working with Dr Momna Hedjmadi. Both students have completed practical work with Momna into the effectiveness of anti-cancer drugs and have also worked with MSc student Grace, who investigates behaviour and genetic changes in the worm C. elegans (seen with the microscope in the photo below). Both students have thoroughly enjoyed the experience, especially the practical lab work, and don’t want to leave!

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On to the Department of Chemistry where one student has been working in the group of Professor Aron Walsh @lonepair alongside Dr Keith Butler and other post docs and PhD students. Based mainly in a theoretical chemistry lab, out student has been learning to code and create scripts which search through the periodic table for possible new materials (see photo below). He has also been able to visit an organic chemistry lab. The lab have been incredibly welcoming and have helped our student to focus on which degree he wants to apply for and he is really grateful to all the researchers who have spoken to him about their degrees and shared their advice.

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Staying in the Department of Chemistry, I visited Dr Judith Brown and her in2scienceUK student, who is hoping to study Dentistry. One of Judith’s current research themes is culturing biofilms to examine the effect of ultrasonic cavitation on plaque so this was a really interesting project for our student to be part of. He has been able to visit a Biochemistry lab and has learnt a number of lab techniques during his two weeks at Bath.

Finally, back to the Department of Biology and Biochemistry for our final two placements. Dr Stephanie Diezmann @diezmannlab has provided a fascinating project involving research into the yeast Candida albicans and the Manduca caterpillar. Our in2scienceUK student has been able to work alongside different researchers and complete lots of lab work and use techniques such as PCR. Stephanie arranged an interesting Q&A session for our student () and also for our student to meet with the department admissions tutor, both of which proved really helpful. Thank you to everyone in Stephanie’s lab for such an inspiring placement!

Last but certainly not least, Dr Daniel Henk and his lab hosted a placement looking into different aspects of fungal ecology and evolution. Our student has been directly involved in Dan’s research and has completed fieldwork collecting diseased fruit from which he has then isolated the disease-causing yeast Botrytis. This data will help Dan and his group to understand more about the ecology and genetics of this yeast and its biocontrol. Our student has spent a lot of time in the lab and has learnt many new techniques such as PCR and used equipment new to him, including pipettes. Talks with Dan and other lab members have helped him to think about his which degree to study at university and have inspired him work hard during his A Level studies in the forthcoming year.

This summer’s placements have been a huge success, thanks mainly to the incredible support and dedication from our supervisors and their groups, and also due to the enthusiasm and commitment of out students. Thank you again to everyone who has been involved this year! I look forward to seeing you all at our Celebration Evening next month.

By Becky Mead, in2scienceUK Bath Coordinator

Attempting to successfully design and synthesise a Benzothiophene antibiotic a third year Chemistry research project, carried out by Umar Warsame

As soon I heard “third year”, I was thinking how intellectually stimulating this placement has already been, but, for me to carry out a high-level project aimed at students who have covered inorganic, organic, physical and analytical Chemistry to great detail – WAY more than myself – made me realise for a brief moment that I wasn’t capable and that I didn’t have the skill to – I was wrong.

Starting the second week of my Chemistry placement and reminiscing about the insightful Chemistry I have learnt: from observations, techniques and methods, theory and mechanisms, and also the things I have learnt from the discussions I had with my supervisor, Dr Barry Marsh, and the PhD students, working with on topics ranging from catalysis to bio sensing. The experience gained from a small framework of time has implemented the idea that I have the ability to successfully synthesise the precursor (finally understand what precursor means, and why “the methylamine keeps flowing”) needed and then from there, start to design my OWN Benzothiophene antibiotic through several intricate steps.

With the whole group behind me and the whole lab open for my use, I put on my safety glasses and lab coat, put on gloves and started reading the instructions intently and began the AWESOME project…

by Umar Warsame

Schrödinger’s Equation—¿after that session was I dead or alive or both?

My In2science placement took place between the 21st and the 25th of July at the London Centre for Nanotechnology, UCL. As the week began I was both nervous and excited. I was happy with the placement I’d been given—working alongside PhD students, experts in Physics, both theoretical and experimental. I could not have been placed anywhere better! On the first day, we had a tour of UCL and we were introduced to our Supervisors; Michael, Phil and Tom. They were very helpful and patient with us, myself and the two other students. By the second day we got into some hard-core experimental physics (or so it felt). Scanning-tunnelling microscopy is what we were introduced to by Toby, an experimental physicist who gave us in-depth explanations yet were very easy to understand (see photo below). This was fun, the aim was to scan the surface of graphite and with some luck try to see as close to the atoms as we could get. The tunnelling part comes from quantum physics and psi, the probability amplitude.

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Although we didn’t get to see a perfect picture of the atoms, we got to be very hands on! As the week progressed we got to see various labs and experiments of physicists working with lasers, dust-free microscopes and liquid helium. We got talks on Quantum Physics Really Exists! and the creation (or not) of a quantum computer in the USA.  We also learnt about the differences between Classical Physics and Quantum Physics. But for myself, leaning more towards theoretical physics, the week really got exciting when we began work on differential equations and Schrödinger’s Equation, by which I was feeling very excited yet somewhat intimidated by the complexity I thought such an equation would carry.

Time Independent Equation:

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Time Dependent Equation:

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Using calculus as a starting point we found and solved differential equations for exponential radioactive decay and more, leading to the point of using coding on the computer to create a interactive diagram of the quantum tunnelling process using Schrödinger’s Equation.

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All in all I can say that it was a very productive and fascinating week which not only assured me of my passion for physics but opened my eyes to the wide array of possibilities a career in science could lead to.

By Maria B

A Computational Chemistry placement at King’s College London, By Maya M

Maya undertook a placement in Computational Chemistry at King’s College London,  supervised by Dr Edina Rosta.  

On Monday the 14th of July,  I arrived at King’s College London to take part in my Computational Chemistry placement. It was a daunting task. As my supervisor showed me my task for the week, I looked on in confusion. My task was to use computer software to display and optimise a chemical reaction. The hardest part was that the software could only be operated through a command-line interface, which was something I had never used before. I was in for an interesting and eye-opening week!

I spent the second day of my placement trying to learn how to use Linux and how to understand coding, as this was a crucial step for me to be able to use the software programs. My supervisor taught me the basic commands I would need to operate the software. However, to ensure that I had complete understanding of the software I watched a YouTube video which highlighted and explained how to draw and optimize chemical molecules. The software I used was called Molden and it is used by people in the Computational Chemistry field to draw software and to run virtual reactions so they can have a visual idea of what would happen if a reaction was to take place (see photo).

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By Maya M

A placement in Epidemiology & Public Health

Jennifer tells us about her placement in UCL’s Department of Epidemiology and Public Health…

During my week at UCL Department of Epidemiology I learnt in depth how scientific research projects on a cross-disciplinary basis are constructed and can be completed successfully. I also learnt about applying for funding and appealing to organisations such as the National institute for Health Research and looked at how current research taking place progresses and becomes published and cited in journals.

Research in the department included looking at age cohort differences in health. I found this interesting and was able to directly help Stephen Jivraj, who is carrying out the research by collecting relevant literature such as ‘Lifetime prevalence and age-of-onset distributions of mental disorders ‘, which used the WHO’s World Mental Health Survey Initiative.   This research opened up many further questions of curiosity such as ‘why do mental disorders arise more or less commonly in certain areas or cultures’. Learning how to find upcoming and intriguing scientific studies and research will help me to further explore my interest surrounding different areas in psychology.

By Jennifer B

Rods and Cones – a placement at the UCL Institute of Ophthalmology

Lucky recently undertook a placement at UCL’s Institute of Ophthalmology. Here she explains a little of what she learnt about vision…

The retina is the part of the eye that senses light. It consists of two types of photoreceptor cells: rods and cones. Rod cells work in low light levels, and as their name implies, they are rod shaped. This type of photoreceptor cell is responsible for what we would call night vision; they allow us to see in the dark. Rods use a chemical called rhodopsin to absorb photons. Rhodopsin molecules split into a retinal and an opsin molecule when they absorb photons. Rhodopsin then reforms from these molecules at a constant rate but this process is very slow. This is the reason why our eyes take time to adjust to the dark. When the light is on and there are high light levels, rhodopsin molecules are broken down so when the light is switched off and there is less intense light we can’t really see until rhodopsin starts to reform. Gradually our night vision, in a sense, activates. Rod cells are unable to perceive colour, unlike cone cells and so our night vision is black and white.

Cone cells are responsible for our ability to perceive colour. The cone cells of our retina function at higher light levels than rods and have a cone-like shape. There are three types of cone cells, all of which respond to different wavelengths. S-cones respond to short wavelengths and peak at a bluish colour; M-cones to medium wavelengths and peak at green; L-cones to long wavelengths and peak at red.

Our colour vision or perception of colour is based on the wavelengths of light that objects reflect. Take the example of a plant leaf; the cells of a plant leaf contain the green pigment chlorophyll. As a result, plant leaves are green and so absorb other colours of the spectrum such as blue and red, reflecting green visible light into our colour perceiving cone cells. Green light has a medium range wavelength so it is responded to by M-cone cells. Your brain then interprets signals it receives from your cone cells. People without all three cone types functioning correctly have colour blindness. So, if a person’s L-cone isn’t functioning properly they won’t be able to see the colour red properly as L-cones respond to long wavelengths like red light.

By Lucky G