PHD Defense - Maitane Muñoz Basagoiti - 20/12/2022 - Bio-inspired design from the bottom-up: Catalysis and Self-Assembly through Folding

Maitane Muñoz Basagoiti’s PhD Defense will take place on:
December 20th at 2pm
IPGG amphitheatre
6 Rue Jean Calvin, 75005 Paris

Bio-inspired design from the bottom-up: Catalysis and Self-Assembly through Folding

Biological matter is highly sophisticated: using a limited range of building blocks, living organisms perform complex functions like replication, adaptation, learning and evolution. Understanding how these functionalities emerge and how they can be reproduced in the lab will revolutionise Materials Science. Towards this ultimate goal, in this thesis we investigate the design principles for catalysis and self-assembly through folding using coarse-grained physical models of spherical particles interacting via programmable potentials.

Catalysis, the acceleration of chemical reactions by molecules that are not consumed in the reaction, is central to living organisms and a cornerstone of the chemical industry. Despite its ubiquity, the geometrical and physical constraints that give rise to catalysis are not fully understood. Furthermore, there is no theoretical framework to rationally design catalysis from scratch. Consequently, elucidating the design principles of efficient catalysis remains a major challenge, with artificial enzymes failing to meet the capabilities of their natural counterparts. Here we introduce a theoretical framework for bottom-up catalysis design based on the theory of First-Passage Times and apply the framework to design a minimal catalyst that accelerates dissociation reactions in a model based on artificial chemistry. We show that a minimal rigid dimer accelerates the cleaving of a bond in a narrow range of the parameter space spanned by the geometry and physical interactions of the catalyst with the substrate, as well as the reaction conditions. Our results open the door to the design of self-regulated artificial systems with bio-inspired functionalities.

Self-assembly refers to the process in which subunits autonomously organise into orderly patterns and functional structures. An efficient self-assembly strategy is embodied by natural proteins, which reversibly fold into their native state starting from a chain with a specific amino acid sequence. The prevailing self-assembly strategy is the assembly from a gas of particles. Instead, in this work we introduce a new paradigm for materials design by studying the folding of short, freely-jointed colloidal chains, colloidomers, where interactions are mediated by DNA. Control over the final folded state is achieved by designing non-equilibrium temperature protocols which funnel the polymer configuration space, guiding the folding of the chain towards a unique geometry that we call a (colloidal) foldamer. In order to systematically identify all foldamer solutions, we develop an algorithm that selects unique folds in two dimensions by searching in sequence, particle species and interaction space. Our approach reveals folding modes reminiscent of those proposed in the context of proteins and allows for the design of novel supra-colloidal building blocks.


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