How to Upscale The Kinetics of Complex Microsystems [article]

Ivan Kryven, Ariana Torres-Knoop
2019 arXiv   pre-print
The rate constants of chemical reactions are typically inferred from slopes and intersection points of observed concentration curves. In small systems that operate far below the thermodynamic limit, these concentration profiles become stochastic and such an inference is less straightforward. By using elements of queuing theory, we introduce a procedure for inferring (time dependent) kinetic parameters from microscopic observations that are given by molecular simulations of many simultaneously
more » ... acting species. We demonstrate that with this procedure it is possible to assimilate the results of molecular simulations in such a way that the latter become descriptive on the macroscopic scale. As an example, we upscale the kinetics of a molecular dynamics system that forms a complex molecular network. Incidentally, we report that the kinetic parameters of this system feature a peculiar time and temperature dependences, whereas the probability of a network strand to close a cycle follows a universal distribution.
arXiv:1810.06173v2 fatcat:gzb735vgkrdyddlcpp23bm4au4