Physical models of catalysis
Enzymes are unrivalled catalysts. Are they following special design principles? Can we make comparable artificial catalysts with programmable matter?
Simplest model of catalysis
What physically constrains catalysis? A one-dimensional elastic model already accounts for several constraints to which simple catalysts are subject: (i) an active site geometry that is complementary to the transition state of the reaction (Pauling’s principle); (ii) an interaction energy that is neither too weak nor too strong (Sabatier’s principle); (iii) a sufficiently rigid scaffold.
Reference: O. Rivoire (2020). Geometry and flexibility of optimal catalysts in a minimal elastic model.
Towards catalysis with programmable matter
Spherical building blocks interacting via programmable potentials can be realized experimentally and provide an approach to emulate biological functionality with artificial components. Previous works have demonstrated self-assembly and self-replication but these realizations are limited by the lack of catalysis. Through theory and numerical simulations, we have shown how an elementary catalyst accelerating bond cleavage could be designed with currently available experimental systems.
Reference: M. Muñoz Basagoiti, O. Rivoire. Z. Zeravcic (2023). Computational design of a minimal catalyst using colloidal particles with programmable interactions.
On the role of flexibility in catalysis
Our previous models involved rigid catalysts, but many enzymes are known to undergo conformational changes during catalysis. However, the role that flexibility plays in catalysis is highly controversial. To clarify this issue, we demonstrate with a solvable model how flexibility can play a key role. Although highly simplified and limited to a particular reaction, our model has several features that distinguish enzymes from other known catalysts.
Reference: O. Rivoire (2023). How flexibility can enhance catalysis.
With Yann Sakref & Zorana Zeravcic, we develop physical models of catalysis to investigate some of the system-level properties exibited by networks of biochemical reactions.