Disentangling interacting symmetry protected phases of fermions in two dimensions

We construct fixed point lattice models for group supercohomology symmetry protected topological (SPT) phases of fermions in 2+1D. A key feature of our approach is to construct finite depth circuits of local unitaries that explicitly build the ground states from a tensor product state. We then recover the classification of fermionic SPT phases, including the group structure under stacking, from the algebraic composition rules of these circuits. Furthermore, we show that the circuits are symmetric, implying that the group supercohomology phases can be many body localized. Our strategy involves first building an auxiliary bosonic model, and then fermionizing it using the duality of Chen, Kapustin, and Radicevic. One benefit of this approach is that it clearly disentangles the role of the algebraic group supercohomology data, which is used to build the auxiliary bosonic model, from that of the spin structure, which is combinatorially encoded in the lattice and enters only in the fermionization step. In particular this allows us to study our models on 2d spatial manifolds of any topology and to define a lattice-level procedure for ungauging fermion parity.Comment: 17 + 13 pages, 16 figures, v3 published versio

Floquet codes with a twist

We describe a method for creating twist defects in the honeycomb Floquet code of Hastings and Haah. In particular, we construct twist defects at the endpoints of condensation defects, which are built by condensing emergent fermions along one-dimensional paths. We argue that the twist defects can be used to store and process quantum information fault tolerantly, and demonstrate that, by preparing twist defects on a system with a boundary, we obtain a planar variant of the $\mathbb{Z}_2$ Floquet code. Importantly, our construction of twist defects maintains the connectivity of the hexagonal lattice, requires only 2-body measurements, and preserves the three-round period of the measurement schedule. We furthermore generalize the twist defects to $\mathbb{Z}_N$ Floquet codes defined on $N$-dimensional qudits. As an aside, we use the $\mathbb{Z}_N$ Floquet codes and condensation defects to define Floquet codes whose instantaneous stabilizer groups are characterized by the topological order of certain Abelian twisted quantum doubles.Comment: 35+7 pages, 19 figures; v2 corrected typos; v3 corrected fault-tolerance argument, clarified implementation of logical S gat

Disentangling supercohomology symmetry-protected topological phases in three spatial dimensions

We build exactly solvable lattice Hamiltonians for fermionic symmetry-protected topological (SPT) phases in (3+1)D classified by group supercohomology. A central benefit of our construction is that it produces an explicit finite-depth quantum circuit (FDQC) that prepares the ground state from an unentangled symmetric state. The FDQC allows us to clearly demonstrate the characteristic properties of supercohomology phases—namely, symmetry fractionalization on fermion parity flux loops—predicted by continuum formulations. By composing the corresponding FDQCs, we also recover the stacking relations of supercohomology phases. Furthermore, we derive topologically ordered gapped boundaries for the supercohomology models by extending the protecting symmetries, analogous to the construction of topologically ordered boundaries for bosonic SPT phases. Our approach relies heavily on dualities that relate certain bosonic 2-group SPT phases with supercohomology SPT phases. We develop physical motivation for the dualities in terms of explicit lattice prescriptions for gauging a 1-form symmetry and for condensing emergent fermions. We also comment on generalizations to supercohomology phases in higher dimensions and to fermionic SPT phases outside of the supercohomology framework

Disentangling supercohomology symmetry-protected topological phases in three spatial dimensions

We build exactly solvable lattice Hamiltonians for fermionic symmetry-protected topological (SPT) phases in (3+1)D classified by group supercohomology. A central benefit of our construction is that it produces an explicit finite-depth quantum circuit (FDQC) that prepares the ground state from an unentangled symmetric state. The FDQC allows us to clearly demonstrate the characteristic properties of supercohomology phases - namely, symmetry fractionalization on fermion parity flux loops - predicted by continuum formulations. By composing the corresponding FDQCs, we also recover the stacking relations of supercohomology phases. Furthermore, we derive topologically ordered gapped boundaries for the supercohomology models by extending the protecting symmetries, analogous to the construction of topologically ordered boundaries for bosonic SPT phases. Our approach relies heavily on dualities that relate certain bosonic 2-group SPT phases with supercohomology SPT phases. We develop physical motivation for the dualities in terms of explicit lattice prescriptions for gauging a 1-form symmetry and for condensing emergent fermions. We also comment on generalizations to supercohomology phases in higher dimensions and to fermionic SPT phases outside of the supercohomology framework.Comment: 28+25 pages, 31 figure

Engineering Floquet codes by rewinding

Floquet codes are a novel class of quantum error-correcting codes with dynamically generated logical qubits, which arise from a periodic schedule of non-commuting measurements. We engineer new examples of Floquet codes with measurement schedules that $\textit{rewind}$ during each period. The rewinding schedules are advantageous in our constructions for both obtaining a desired set of instantaneous stabilizer groups and for constructing boundaries. Our first example is a Floquet code that has instantaneous stabilizer groups that are equivalent -- via finite-depth circuits -- to the 2D color code and exhibits a $\mathbb{Z}_3$ automorphism of the logical operators. Our second example is a Floquet code with instantaneous stabilizer codes that have the same topological order as the 3D toric code. This Floquet code exhibits a splitting of the topological order of the 3D toric code under the associated sequence of measurements i.e., an instantaneous stabilizer group of a single copy of 3D toric code in one round transforms into an instantaneous stabilizer group of two copies of 3D toric codes up to nonlocal stabilizers, in the following round. We further construct boundaries for this 3D code and argue that stacking it with two copies of 3D subsystem toric code allows for a transversal implementation of the logical non-Clifford $CCZ$ gate. We also show that the coupled-layer construction of the X-cube Floquet code can be modified by a rewinding schedule such that each of the instantaneous stabilizer codes is finite-depth-equivalent to the X-cube model up to toric codes; the X-cube Floquet code exhibits a splitting of the X-cube model into a copy of the X-cube model and toric codes under the measurement sequence. Our final example is a generalization of the honeycomb code to 3D, which has instantaneous stabilizer codes with the same topological order as the 3D fermionic toric code.Comment: 20+3 pages, 27 figures, $\texttt{Mathematica}$ files are available at https://github.com/dua-arpit/floquetcodes, v2 changes: added more details on the rewinding X-cube Floquet code and made minor updates in color code figures in the appendi

Identification of genes conferring tolerance to lignocellulose-derived inhibitors by functional selections in soil metagenomes

The production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. These harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. We applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple inhibitory compounds. Having screened over 248 Gb of DNA cloned from 16 diverse soil metagenomes, we describe gain-of-function tolerance against acid, alcohol, and aldehyde inhibitors derived from hemicellulose and lignin, demonstrating that uncultured soil microbial communities hold tremendous genetic potential to address the toxicity of pretreated lignocellulose. We recovered genes previously known to confer tolerance to lignocellulosic inhibitors as well as novel genes that confer tolerance via unknown functions. For instance, we implicated galactose metabolism in overcoming the toxicity of lignin monomers and identified a decarboxylase that confers tolerance to ferulic acid; this enzyme has been shown to catalyze the production of 4-vinyl guaiacol, a valuable precursor to vanillin production. These metagenomic tolerance genes can enable the flexible design of hardy microbial catalysts, customized to withstand inhibitors abundant in specific bioprocessing applications

Pauli topological subsystem codes from Abelian anyon theories

We construct Pauli topological subsystem codes characterized by arbitrary two-dimensional Abelian anyon theories--this includes anyon theories with degenerate braiding relations and those without a gapped boundary to the vacuum. Our work both extends the classification of two-dimensional Pauli topological subsystem codes to systems of composite-dimensional qudits and establishes that the classification is at least as rich as that of Abelian anyon theories. We exemplify the construction with topological subsystem codes defined on four-dimensional qudits based on the $\mathbb{Z}_4^{(1)}$ anyon theory with degenerate braiding relations and the chiral semion theory--both of which cannot be captured by topological stabilizer codes. The construction proceeds by "gauging out" certain anyon types of a topological stabilizer code. This amounts to defining a gauge group generated by the stabilizer group of the topological stabilizer code and a set of anyonic string operators for the anyon types that are gauged out. The resulting topological subsystem code is characterized by an anyon theory containing a proper subset of the anyons of the topological stabilizer code. We thereby show that every Abelian anyon theory is a subtheory of a stack of toric codes and a certain family of twisted quantum doubles that generalize the double semion anyon theory. We further prove a number of general statements about the logical operators of translation invariant topological subsystem codes and define their associated anyon theories in terms of higher-form symmetries.Comment: 67 + 35 pages, single column forma