Better late than never……. During summer 2017 I was asked to play at the Cornerstone, Beer and Music festival in Didcot UK. The Cornerstone theatre has become a real hub of the Didcot community and the summer festival has become an annual event with bands and musicians from all over Oxfordshire. I played mixed set of original songs and covers and even dusted off my mandolin to accompany Rob Traynor on a traditional english folk song. This was also my opportunity to test the new camera I brought for recording my performances….. mixed results ;). Heres a link to a song which might be familiar.
We recently published a paper on a new method to accelerate kinetics simulations entitled “A Simple “Boxed Molecular Kinetics” Approach To Accelerate Rare Events in the Stochastic Kinetic Master Equation”. The fundamental question of how quickly chemicals react, or more generally transform, from one state to another, underpins countless scientific fields. If you want to understand how long some pollutant sticks around in the earths atmosphere then you need to understand what other chemicals may interact with this pollutant and the rate or speed at which these interactions occur. In the human body floppy proteins wrap themselves into different shapes and the rate at which they transform from shape to shape is vital to our understanding issues such as Alzheimer’s. These problems, and many, more are encapsulated by the field of chemical kinetics.
A long-standing research interest of ours is in methods to calculate the rate of chemical reactions theoretically, using a computer. We have been involved in the development of the open source master equation code MESMER and for this paper we developed a method for accelerating certain types kinetics calculations. This method attempts to alleviate the so-called “rare-event” problem, which is common to a number of disciplines. This problem occurs when some process of interest, in this case a chemical reaction, occurs on a timescale, which is very long compared to some fundamental timescale associated with the type of calculation or simulation. For this method we took inspiration from the “boxed molecular dynamics” method, which is used in the related field of molecular dynamics and adapted it to form the “boxed molecular kinetics”, (BXK) method. Using this we demonstrate that this method can accelerate the time taken to calculate the rates of certain reactions by several orders of magnitude! For more information check out the paper here: https://pubs.acs.org/doi/pdfplus/10.1021/acs.jpca.7b12521?src=recsys
Recently I made the trip up to the University of Leeds along with fellow Glowacki group member Dasha Shchepanovska. These meetings used to be an annual occurrence and have been revitalised this year thanks to the hard work of Dr Dan Stone and Dr Julia Lehman. Gas kinetics is not a subject that often breaches into the public consciousness. Kinetics is simply the study of how quickly given molecules react with each other and what new molecule is produced. In the gas phase we are interested in diverse environments such as the earths atmosphere, the inside of a combustion engine and the chemistry in the cold depths of space and as such this field is at the forefront of efforts to understand and predict climate change and to probe the origins of life in outer space.
This meeting gathered researchers from all over the UK, from Bristol, Oxford and London up to York, and Edinburgh and was a great environment to present work and exchange ideas. I signed up to give a talk and took the opportunity to unveil the software I have been writing over the past year called ChemDyME ( name subject to change) designed to automatically map complex networks of reactions and calculate the rate at which the system evolves. This code is designed to work in a black box manner to compliment experimental measurments and this was a great opportunity to introduce my code to the wide array of experimental groups who were present is Leeds. The picture above shows ChemDyME mapping the various reactions in a key combustion system. Watch this space for more details about ChemDyME or contact me.