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FMS Seminar by Omer Markovitch in Eindhoven
June 27, 2018 @ 1:00 pm - 2:00 pm
On Wednesday June 27, dr. Omer Markovitch (RUG) will give a FMS Seminar on ‘A quantitative mass-action model of the dynamics of formation, interconversion & self-replication of macrocycles made from peptide-functionalized dithiol building block’ at the Eindhoven University of Technology.
A system comprised of peptide-functionalized dithiol building block have been previously shown to spontaneously give rise to complex dynamics and eventually self-replication. The building block are rapidly oxidized and form a combinatorial library of small to large macrocycles, which can dynamically interconvert via reversible exchange reactions. A particular size macrocycle, hexamer, was found to grow exponentially and form fibers, and seeding a fresh library with pre-formed hexamers immediately lead to exponential growth of the hexamer and its fibers. Here, we address the dynamics of the different species in the system with a mass-action chemical modelling in order to underpin the reactions occurring in this system and their rate-constants.
A total conversion of the system’s mass into hexamers is achieved only when fibers are allowed to serve as catalysts for the reactions between cyclic and non-cyclic species, in a tri-molecular reaction. Such a non-intuitive interaction is supported by a recent real-time AFM study showing that cyclic species tend to amass on fibers as part of fiber elongation. The effective exponential growth rate following simulated seeding shows a linear dependency on the seed concentration with a slope close to 1, in line with previous experiments. Furthermore, such dependency is lost when the fiber-catalyzed reaction is removed.
Using parameters estimation via a fitting between the computation model and experiments, experimentally-verified apparent rate-constants are assigned to all of the reactions. Fitting with data from similar experiments give rise to similar rate-constants.
Overall, the results shown here are the first time a detailed and experimentally verified model of such a complex system is reported, and are expected to facilitate modelling of similar systems.