Novel Computational Methods for Systems Chemistry

Traditional text book chemistry typically operates with few purified and well mixed reagents. This convenience is lost when chemical systems increase in complexity and ultimately approach the organization of living systems, which are prone to involve a multitude of spatially arranged, interacting reagents. Particularly when molecules are able to form heteropolymers, the space of potential chemical species becomes infinite. In my talk, I will present novel computational methods that are able to overcome the limitations of well-mixing and low species count that underlie conventional modelling methods.

The first part of my talk will showcase computational methods that pay tribute to spatial organization arising from phase separation and molecular folding. Similar in spirit to Molecular Dynamics, these methods track molecular positions and interactions, but sacrifice resolution in order to apply to much larger system sizes and time scales. I will present recent research results on supra-molecular self-assembly as well as DNA folding, origami, and computation.

The second part of my talk will demonstrate how recently developed methods from algorithmic chemoinformatics can be used to tackle reactions in combinatorial chemical libraries which can give rise to potentially myriads of different chemical species. As examples, I will present recent results on a toy chemistry of self-replicating nucleic acid polymers, as well as a small peptide library that gives rise to self-replicating peptide fibres.