Speedy molecules! Accelerating the calculation of reaction rates.


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


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