Spontaneous chiral symmetry breaking in a random driven chemical system.

Living systems have evolved to efficiently consume available energy sources using an elaborate circuitry of chemical reactions which, puzzlingly, bear a strict restriction to asymmetric chiral configurations. While autocatalysis is known to promote such chiral symmetry breaking, whether a similar phenomenon may also be induced in a more general class of configurable chemical systems-via energy exploitation-is a sensible yet underappreciated possibility. This work examines this question within a model of randomly generated complex chemical networks.

Inverse design of nonequilibrium steady states: A large-deviation approach.

The design of small scale nonequilibrium steady states (NESS) is a challenging, open ended question. While similar equilibrium problems are tractable using standard thermodynamics, a generalized description for nonequilibrium systems is lacking, making the design problem particularly difficult. Here we show we can exploit the large-deviation behavior of a Brownian particle and design a variety of geometrically complex steady-state density distributions and flux field flows.

Kinetic proofreading and the limits of thermodynamic uncertainty.

To mitigate errors induced by the cell's heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively studied KPR circuits, DNA replication by the T7 DNA polymerase and translation by the E. coli ribosome.

Inverse design of multicomponent assemblies.

Inverse design can be a useful strategy for discovering interactions that drive particles to spontaneously self-assemble into a desired structure. Here, we extend an inverse design methodology-relative entropy optimization-to determine isotropic interactions that promote assembly of targeted multicomponent phases, and we apply this extension to design interactions for a variety of binary crystals ranging from compact triangular and square architectures to highly open structures with dodecagonal and octadecagonal motifs. We compare the resulting optimized (self- and cross) interactions for the binary assemblies to those obtained from optimization of analogous single-component systems.

Inverse Design of Self-Assembling Frank-Kasper Phases and Insights Into Emergent Quasicrystals.

We discuss how a machine learning approach based on relative entropy optimization can be used as an inverse design strategy to discover isotropic pair interactions that self-assemble single- or multicomponent particle systems into Frank-Kasper phases. In doing so, we also gain insights into the self-assembly of quasicrystals.

Designing pairwise interactions that stabilize open crystals: Truncated square and truncated hexagonal lattices.

Using a recently introduced formulation of the ground-state inverse design problem for a targeted lattice [W. Piñeros et al., J.

Designing convex repulsive pair potentials that favor assembly of kagome and snub square lattices.

Building on a recently introduced inverse strategy, isotropic and convex repulsive pair potentials were designed that favor assembly of particles into kagome and equilateral snub square lattices. The former interactions were obtained by a numerical solution of a variational problem that maximizes the range of density for which the ground state of the potential is the kagome lattice. Similar optimizations targeting the snub square lattice were also carried out, employing a constraint that required a minimum chemical potential advantage of the target over select competing structures.

Breadth versus depth: Interactions that stabilize particle assemblies to changes in density or temperature.

We use inverse methods of statistical mechanics to explore trade-offs associated with designing interactions to stabilize self-assembled structures against changes in density or temperature. Specifically, we find isotropic, convex-repulsive pair potentials that maximize the density range for which a two-dimensional square lattice is the stable ground state subject to a constraint on the chemical potential advantage it exhibits over competing structures (i.e.