Trade-offs and design principles in the spatial organization of catalytic particles

Spatial organization of catalytic particles is ubiquitous in biological systems across different length scales, from enzyme complexes to metabolically coupled cells. Despite the different scales, these systems share common features of localized reactions with partially hindered diffusive transport, determined by the collective arrangement of the catalysts. Yet it remains largely unexplored how different arrangements affect the interplay between the reaction and transport dynamics, which ultimately determines the flux through the reaction pathway. Here we show that two fundamental trade-offs arise, the first between efficient inter-catalyst transport and depletion of substrate, and the second between steric confinement of intermediate products and accessibility of catalysts to substrate. We use a model reaction pathway to characterize the general design principles for the arrangement of catalysts that emerge from the interplay of these trade-offs. We find that the question of optimal catalyst arrangements generalizes the famous Thomson problem of electrostatics.

Patchy particles by self-assembly of star copolymers on a spherical substrate: Thomson solutions in a geometric problem with a color constraint

Star copolymers on a sphere self-assemble into patchy particles with structure and coordination corresponding to those found in the famous Thomson problem.

Nearly uniform sampling of crystal orientations

A method is presented for generating nearly uniform distributions of three-dimensional orientations in the presence of symmetry. The method is based on the Thomson problem, which consists in finding the configuration of minimal energy of N electrons located on a unit sphere – a configuration of high spatial uniformity. Orientations are represented as unit quaternions, which lie on a unit hypersphere in four-dimensional space. Expressions of the electrostatic potential energy and Coulomb's forces are derived by working in the tangent space of orientation space. Using the forces, orientations are evolved in a conventional gradient-descent optimization until equilibrium. The method is highly versatile as it can generate uniform distributions for any number of orientations and any symmetry, and even allows one to prescribe some orientations. For large numbers of orientations, the forces can be computed using only the close neighbourhoods of orientations. Even uniform distributions of as many as 106 orientations, such as those required for dictionary-based indexing of diffraction patterns, can be generated in reasonable computation times. The presented algorithms are implemented and distributed in the free (open-source) software package Neper.