Condensed Matter Theory

Abstract:

This chapter will provide an overview of how characterising free energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The landscapes for these complex systems are accessible through the use of accurate coarse-grained descriptions of DNA. Particular foci will be the landscapes associated with DNA self-assembly and mechanical deformation, where the latter can arise from either externally imposed forces or internal stresses.

Abstract:

We construct models hosting classical fractal spin liquids on two realistic three-dimensional (3D) lattices of corner-sharing triangles: trillium and hyperhyperkagome (HHK). Both models involve the same form of three-spin Ising interactions on triangular plaquettes as the Newman-Moore (NM) model on the 2D triangular lattice. However, in contrast to the NM model and its 3D generalizations, their degenerate ground states and low-lying excitations cannot be described in terms of scalar cellular automata (CA), because the corresponding fractal structures lack a simplifying algebraic property, often termed the "freshman's dream."By identifying a link to matrix CAs - that makes essential use of the crystallographic structure - we show that both models exhibit fractal symmetries of a distinct class to the NM-type models. We devise a procedure to explicitly construct low-energy excitations consisting of finite sets of immobile defects or "fractons,"by flipping arbitrarily large self-similar subsets of spins, whose fractal dimensions we compute analytically. We show that these excitations are associated with energetic barriers which increase logarithmically with system size, leading to "fragile"glassy dynamics, whose existence we confirm via classical Monte Carlo simulations. We also discuss consequences for spontaneous fractal symmetry breaking when quantum fluctuations are introduced by a transverse magnetic field, and propose multispin correlation function diagnostics for such transitions. Our findings suggest that matrix CAs may provide a fruitful route to identifying fractal symmetries and fractonlike behavior in lattice models, with possible implications for the study of fracton topological order.

Abstract:

A common feature of biological self-organization is how active agents communicate with each other or their environment via chemical signaling. Such communications, mediated by self-generated chemical gradients, have consequences for both individual motility strategies and collective migration patterns. Here, in a purely physicochemical system, we use self-propelling droplets as a model for chemically active particles that modify their environment by leaving chemical footprints, which act as chemorepulsive signals to other droplets. We analyze this communication mechanism quantitatively both on the scale of individual agent-trail collisions as well as on the collective scale where droplets actively remodel their environment while adapting their dynamics to that evolving chemical landscape. We show in experiment and simulation how these interactions cause a transient dynamical arrest in active emulsions where swimmers are caged between each other's trails of secreted chemicals. Our findings provide insight into the collective dynamics of chemically active particles and yield principles for predicting how negative autochemotaxis shapes their navigation strategy.