Take 10 with... Shamim Shadfar

1.    Describe your research topic to us in 10 words or less.

Studying interactions of biochemical systems using computational methods.

2.    Now explain it in everyday terms!

My research is mainly on inter-molecular interactions between different systems, such as host-guest complexes, protein-protein, protein-DNA, protein-ligand and protein-membrane. The work is all computer-based, using molecular dynamics (MD) simulations to investigate the binding modes and analysing the behaviours of these systems, as well as studying how these biological molecules move and function. I am currently a postdoctoral Research fellow in A/Prof Jane Allison’s group. 

3.    Describe some of your day-to-day research activities.

I mostly work on the main project I am involved in, which is entirely computational. This means that I am seated in front of a high-spec desktop computer with access to a supercomputer. I work with a range of computer programs, most of which are operated from the command line (no graphical user interface) to set up, run and analyse my simulations of biological and biochemical systems.

Apart from preparation, simulation and analysis, I also need to figure out how to quantify what is seen, and how to visualise it so that could be published. Besides, I am one of the co-chairs of the Faculty of Science Research Fellow Society, which means going to meetings, sending emails, setting up budgets, organising events, etc. 

4.    What do you enjoy most about your research?

I enjoy challenging and non-routine positions! To me research in science is something which satisfies me, and I believe it is always alive and on-going! I graduated BSc and MSc in chemistry and I was drawn to biochemistry and biology during the course of my PhD. Computers were always my favourites! Therefore, I became a fan of using computational methods to understand biochemistry. I also really enjoy working in a group and as a team-member.

5.    Tell us something that has surprised or amused you in the course of your research.

“How great a bond in a work team could be” has really amazed and surprised me. I had never expected such ties before I started my PhD. “Allison group” is without doubt one of the most positive, productive, and at the same time fun groups I have ever been part of! We are all like a family, and I am sure one of the main reasons for this is our manager A/Prof Jane Allison, who supervises us patiently and efficiently, making sure everyone in the group is equally feeling appreciated, valued and encouraged. I really enjoy being part of such an amazing team.

6.    How have you approached any challenges you’ve faced in your research?

In the early days of my research, when I faced challenges, I used to get frustrated. But as I grew to be a more experienced researcher, I started to like it! My approach is to always make a mind map, and organise and prioritise the issues first. Taking notes, and creating ReadMe files in every folder can help with tracking what I do while solving a problem. Of course, my supervisor is always the best help for me.

Also, I try to fit going for a short walk, stretching my body and taking deep breaths in my daily plan, which can all be a great help when facing challenges at work. I can also reach out to my team-mates and discuss the issue with them.

7.    What questions have emerged as a result?

As an example, in one of the chapters of my PhD course, the system I was studying was a kinase protein binding to RAS interacting to a membrane bilayer. I did many trial simulations, but did not get the sensible results I expected. This initially was frustrating, but finally became a building block for another PhD student’s research project and we realised maybe there are other methods (such as coarse-graining) work better for this system.

8.    What kind of impact do you hope your research will have?

In addition to validation experimental results, our research can cut down a large amount of experimentation costs, as in docking and rapid screening methods, one can scan 1000s of drug molecules and investigate the binding mode and filter out only a few favourable ones, and in collaboration with experimental colleagues, the given test could be done only with those few samples.

9.    If you collaborate across the faculty or University, or outside the University, who do you work with and how does it benefit your research?

I have been collaborating extensively with experimental groups both within the University and at other Universities and Crown Research Institutes (CRIs), such as Environmental Science and Research Institute (ESR). Our group can often propose hypotheses that can be tested experimentally, and we can study aspects of a system that are difficult or impossible to study experimentally, such as short time-scales and specific (atomic-level) interactions. Ultimately, however, our simulations are only as good as the models and methods that we use, and working with experimentalists gives us a chance to validate these.

10.    What one piece of advice would you give your younger, less experienced research self?

Take notes of every step and everything you do, and try to be as organised as possible. Even if you do great research and generate a huge amount of data, if you are disorganised, you may not be able to get a clear and publishable outcome! Use simple apps such as Trello, calendar, etc., or even a physical notebook and a pen! Creating ReadMe files in each folder can also really facilitate your workflow.