Condensed Matter Theory

Abstract:

We present a thermodynamically consistent model describing the dynamics of a multicomponent mixture where one enzyme component catalyzes a reaction between other components. We find that the catalytic activity alone can induce phase separation for sufficiently active systems and large enzymes, without any equilibrium interactions between components. In the limit of fast reaction rates, binodal lines can be calculated using a mapping to an effective free energy. We also explain how this catalysis-induced phase separation can act to autoregulate the enzymatic activity, which points at the biological relevance of this phenomenon.

Abstract:

Fitness landscapes are often described in terms of 'peaks' and 'valleys', indicating an intuitive low-dimensional landscape of the kind encountered in everyday experience. The space of genotypes, however, is extremely high dimensional, which results in counter-intuitive structural properties of genotype-phenotype maps. Here we show that these properties, such as the presence of pervasive neutral networks, make fitness landscapes navigable. For three biologically realistic genotype-phenotype map models-RNA secondary structure, protein tertiary structure and protein complexes-we find that, even under random fitness assignment, fitness maxima can be reached from almost any other phenotype without passing through fitness valleys. This in turn indicates that true fitness valleys are very rare. By considering evolutionary simulations between pairs of real examples of functional RNA sequences, we show that accessible paths are also likely to be used under evolutionary dynamics. Our findings have broad implications for the prediction of natural evolutionary outcomes and for directed evolution.

Abstract:

We show that the gapless boundary signatures - namely, chiral/helical hinge modes or localized zero modes - of three-dimensional higher-order topological insulators and superconductors with inversion symmetry can be gapped without symmetry breaking upon the introduction of non-Abelian surface topological order. In each case, the fractionalization pattern that appears on the surface is "anomalous"in the sense that it can be made consistent with symmetry only on the surface of a three-dimensional higher-order insulator/superconductor. Our results show that the interacting manifestation of higher-order topology is the appearance of "anomalous gapped boundaries"between distinct topological orders whose quasiparticles are related by inversion, possibly in conjunction with other protecting symmetries such as time-reversal symmetry and charge conservation.

Abstract:

We show that the gapless boundary signatures—namely, chiral/helical hinge modes or localized zero modes—of three-dimensional higher-order topological insulators and superconductors with inversion symmetry can be gapped without symmetry breaking upon the introduction of non-Abelian surface topological order. In each case, the fractionalization pattern that appears on the surface is “anomalous” in the sense that it can be made consistent with symmetry only on the surface of a three-dimensional higher-order insulator/superconductor. Our results show that the interacting manifestation of higher-order topology is the appearance of “anomalous gapped boundaries” between distinct topological orders whose quasiparticles are related by inversion, possibly in conjunction with other protecting symmetries such as time-reversal symmetry and charge conservation.

Abstract:

We study classical dimers on two-dimensional quasiperiodic Ammann-Beenker (AB) tilings. Using the discrete scale-symmetry of quasiperiodic tilings, we prove that each infinite tiling admits “perfect matchings”, where every vertex is touched by one dimer. We show the appearance of so-called monomer pseudomembranes. These are sets of edges, which collectively host exactly one dimer, which bound certain eightfold-symmetric regions of the tiling. Regions bounded by pseudomembranes are matched together in a way that resembles perfect matchings of the tiling itself. These structures emerge at all scales, suggesting the preservation of collective dimer fluctuations over long distances. We provide numerical evidence, via Monte Carlo simulations, of dimer correlations consistent with power laws over a hierarchy of different lengthscales. We also find evidence of rich monomer correlations, with monomers displaying a pattern of attraction and repulsion to different regions within pseudomembranes, along with signatures of deconfinement within certain annular regions of the tiling.