New Beginnings

As Natural Sciences students, we’re no strangers to laboratory work. Practical experiments are something we’ve all so far encountered, to a larger or smaller extent. On the other hand, despite it being something very desirable by many employers, we’ve realised that modelling what happens on a molecular level in theory is not a strong skillset of ours at all. Therefore, we believe that both gaining insight into molecular dynamics and modelling, as well as attempting to convey that knowledge to others will be a valuable experience as much as it will surely prove to be an exciting challenge. We’ll be documenting the progress of this journey of ours on this blog, so make sure to refresh the page for any updates. 

 

Now, without further ado: 

 

What exactly is molecular dynamics?

 

Computer simulations can be used to assess the behaviour of a constantly changing, in other words a dynamic, system. Thanks to our current understanding of classical mechanics, this system can be comprised of atoms or molecules and their interactions, providing insight into possible properties of the study subject. Running simulations of atoms or molecules before performing practical experiments is a great cost-effective tool for the materials and pharmaceutical industries, as well as for research purposes in biophysics or chemical physics. Thanks to the improvements in computational technology, molecular dynamics is a continually improving tool – beginning with a small simulation run in 1957 by Alder & Wainwright and up to this day, with modelling systems involving even millions of atoms. 

 

Various brilliant pieces of software have been developed for performing molecular mechanics calculations, though we’ve decided to focus on one in particular – LAMMPS. The acronym of this modelling software stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is an open source code which allows for much freedom within running simulations, on which more information can be found here. The large community involved in developing, improving and using LAMMPS ensures easier troubleshooting with the possibility to improve our networking skills. We are yet to decide on the visualisation software we’ll be using for the code. 

 

Tutorials

 

Our main aim is to create a series of easy-to-follow, enticing and informative tutorials regarding the use of LAMMPS. By embracing our role as science communicators, we’re not only hoping for others to benefit from our efforts but expecting to improve ourselves as teachers as well.

 

Our case-study

 

Since for the entirety of this project we’re all stranded in our own homes, we’ve decided to gain insight into the very efforts to alleviate this situation. The main theme of our case-study for our modelling efforts is COVID-19 treatment. We’ve identified some possible treatments of interest – namely dexamethasone and GS-44152, a metabolite of remdesivir - and rejected some which we deemed overly complicated to model with our equipment and resources, like lenzilumab or type 1 interferons. The next post will provide more insight into our agenda within this case-study. 

~ MW, on behalf of the whole team