Colloquium : Toward living matter with colloidal particles

Abstract

A fundamental unsolved problem is to understand the differences between inanimate matter and living matter. Although this question might be framed as philosophical, there are many fundamental and practical reasons to pursue the development of synthetic materials with the properties of living ones. There are three fundamental properties of living materials that we seek to reproduce: The ability to spontaneously assemble complex structures; the ability to self-replicate; and the ability to perform complex and coordinated reactions that enable transformations impossible to realize if a single structure acted alone. The conditions that are required for a synthetic material to have these properties are currently unknown. This colloquium examines whether these phenomena could emerge by programming interactions between colloidal particles, an approach that bootstraps off of recent advances in DNA nanotechnology and in the mathematics of sphere packings. We argue that the essential properties of living matter could emerge from colloidal interactions that are specific -so that each particle can be programmed to bind or not bind to any other particleand also time-dependent -so that the binding strength between two particles could increase or decrease in time at a controlled rate. There is a small regime of interaction parameters that give rise to colloidal particles with life-like properties, including self-assembly, self-replication and metabolism. The parameter range for these phenomena can be identified using a combinatorial search over the set of known sphere packings. * zorana.zeravcic@espci.fr 2 CONTENTS

Programming colloidal bonding using DNA strand-displacement circuitry

“…Combining the complex functions of DNA strand-displacement circuits (30,31) with sophisticated DNA functional building blocks such as "transmutable nanoparticles" (33), DNA-origami-based units (38,39), and the methods for regulating the attractive and repulsive forces between particles (13) can greatly increase the possibilities for the creation of complex and functional nanoscale materials and for the realization of complex phase behaviors (12,34). Moreover, this time-dependent interaction scheme may offer additional possibilities for creating artificial matter that possesses properties of living matter (14,15) to aid in new discoveries. Fig.…”

“…To date, PAEs have shown powerful programmability in building three-dimensional colloidal superlattices (8-11), realizing colloidal phase transitions (12), and regulating interactions between nanoparticles (13). Colloidal particles endowed with time-dependent interactions were also suggested as a promising way of constructing artificial systems having properties of living systems (14,15). Here we create a system that allows PAE bonding to be programmed, whereby we can explore whether it is possible to realize an ordered structure corresponding to the free-energy minimum under time-dependent interaction control.…”

Lessons from equilibrium statistical physics regarding the assembly of protein complexes

“…As in crystals, the arrangements of these components may be highly reproducible: All ribosomes in a cell are made of many different proteins, yet the arrangement of the core ribosomal proteins is basically the same. This unusual combination of properties is rarely considered in physical theories of matter, with the closest analogue being "programmable materials" of biological origin, such as DNA origami (36) or self-assembling colloidal particles (37). One of the directions of future studies could be to further explore underlying principles of reliable equilibrium and nonequilibrium assembly for synthetic materials inspired by biology.…”

Stochastic Yield Catastrophes and Robustness in Self-Assembly

“…These insights could usefully inform the design of experiments to circumvent yield catastrophes: In particular, while slow provision of constituents is a feasible strategy for experiments, it is highly susceptible to stochastic effects. On the other hand, irrespective of its robustness to stochastic effects, the experimental realization of the dimerization scenario relies on cooperative or allosteric effects in binding, and may therefore require more sophisticated design of the constituents 39,40 . Our theoretical analysis shows that stochasticity can be alleviated either by decreasing heterogeneity (presumably lowering realizable complexity) or by increasing reversibility (potentially requiring fine-tuning of binding affinities).…”