Entrance hall of the ICMSWhy is life so complicated?

Tell us your dream supercomputer simulation!

Marie Nostrum Supercomputer in Barcelona with a simulated DNA molecule shown in front

Marie Nostrum Supercomputer in Barcelona with a simulated DNA molecule shown in front

Do you ever wish you could see your nerve cells fire when you touch something, or watch the cosmos expanding through time? Do you struggle to fit all your activities into the day without rushing around, or feel frustrated by the energy inefficiency of your car or home?

Maybe a simulation is what you need!

Computer simulations can help us explore possibilities with greater range than purely physical experiments. They are used to improve the design of our cars, aeroplanes, buildings, cites and transport and communications infrastructure. Simulations aid the discovery of new medicines and inform surgical procedures. Computer models predict our weather and quantify our effect on the world. In research, they are used to test fundamental physical theories, and to visualise processes and events that are either too small or too large to be directly observed, to prepare for large expensive experiments or to test hazardous concepts or to help preserve rare materials.

Simulations not only help in science but in other areas. The financial industry employs them to determine the effects of price changes, tax implications and policy enactment. This is coupled to the simulation of societal responses with the increasing information available to us through social media, allowing new insights into mass population behaviours and psychology.

What would you do with simulations?

What invention would you design? What event would you choose to simulate? How about using simulation as a predictive tool for future developments? If it can be imagined, and if it can be written as a set of rules with logic, mathematics or choices, then in principle, you can simulate it.

Send your Dream Supercomputer Simulation to our text wall!

There are three ways to send you suggestions to the text wall. Let us know what you think a supercomputer could help you to do better and we will project them anonymously during our presentation at Edinburgh International Science Festival on 10 April.

  1. Send a text to 02071 838329. Put ICMS at the beginning of your message.
  2. Send an email to sms@textwall.co.uk . Put ICMS at the beginning of the subject line.
  3. Use the web form at http://textwall.co.uk/post . Put ICMS at the beginning of your message.

Come along on 10 April to see all the suggestions!

 

Biomolecules are Beautiful!

Structure of the yeast proteasome

 Yeast proteasome

The molecular structures of the structural proteins, enzymes, membranes and molecular machines that make up living cells possess an inherent beauty that is as striking as their ability to perform complex biological functions. Biomolecular scientists who discover these structures want to share them as widely as they can; so have provided free on-line resources for everyone to experience.

The Protein Data Bank (http://www.rcsb.org/pdb/home/home.do) is a free resource site which allows anyone to view and download every known protein structure. Molecule of the Month highlights a different molecule each month with an explanation of the underlying biological science for the presented molecule which is suitable for A-level/SCQF Level 5 and above.

You can download PDB files by searching for the molecule you are interested, for example, try “haemoglobin”, and you will see a list of molecules related to haemoglobin available. A Molecule of the Month article on haemoglobin can be found here: http://pdb101.rcsb.org/motm/41. The image on the right is from Molecule of the Month article on proteasome: http://pdb101.rcsb.org/motm/166.

You can view and manipulate biomolecular structures within PDB by clicking on the picture of the protein, and selecting the option to view in JSmol (a browser based viewer for molecules).
For more control and more flexibility over how you can view molecules, you use a free molecular visualisation tool. A commonly used tool for this is VMD: http://www.ks.uiuc.edu/Research/vmd/

Note that you will need to register to download VMD, the tool is free to use and this will help the developers keep up-to-date on how many users they have. To use VMD, you should follow the instructions on the website to install the software on your computer.

To view a PDB file, first download it from PDB (put it into an easily to find directory, perhaps one called molecules). Then start VMD and using the “file loadpdb” command on the drop-down menus, select your molecule from your molecules directory.

A video tutorial showing beginners how to use VMD to explore protein structures can be found here: https://www.youtube.com/watch?v=Fl3hmqCHYU4