Quantifying the kinetics of macromolecular self-assembly via stochastic simulations

School Colloquium

   A material may exist in its thermodynamic equilibrium structure, but often materials are driven into non-equilibrium meta-stable configurations during their assembly. Even though the perfect crystalline state may be the thermodynamic equilibrium, the kinetics of nucleation and growth of crystalline domains during cooling may create distinct domains that intersect at grain boundaries. Dislocations and vacancies may also be locked in during processing. Non-equilibrium structures vastly increase the space of possible structures, and could be intentionally exploited to achieve novel properties.

   Stochastic simulations provide a quantitative framework in which to predict the overall organization of millions of atoms, based on local pair-wise interactions between individual atoms or small molecules. The events included in these kinetic Monte Carlo simulations may be selected using first-principles calculations, experimental measurements, or ideally their combination.  Past studies in our group will be summarized, including surface diffusion in crystal growth and condensation polymerization of hyperbranched polymers.

   The talk will then focus on a kinetic Monte Carlo simulation that combines surface diffusion and polymerization reactions to investigate a model for the earliest stages of chemical evolution, prior to the onset of functional selection.  The model includes regular environmental cycles, such as dehydration-hydration cycles.  New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for regularly varying monomer/polymer diffusivities.

For more information contact Prof. Ken Brown (404-385-3125).