Deep Bayesian local crystallography

The advent of high-resolution electron and scanning probe microscopy imaging has opened the floodgates for acquiring atomically resolved images of bulk materials, 2D materials, and surfaces. This plethora of data contains an immense volume of information on materials structures, structural distortions, and physical functionalities. Harnessing this knowledge regarding local physical phenomena necessitates the development of the mathematical frameworks for extraction of relevant information. However, the analysis of atomically resolved images is often based on the adaptation of concepts from macroscopic physics, notably translational and point group symmetries and symmetry lowering phenomena. Here, we explore the bottom-up definition of structural units and symmetry in atomically resolved data using a Bayesian framework. We demonstrate the need for a Bayesian definition of symmetry using a simple toy model and demonstrate how this definition can be extended to the experimental data using deep learning networks in a Bayesian setting, namely rotationally invariant variational autoencoders.

New dualities from old: generating geometric, Petrie, and Wilson dualities and trialities of ribbon graphs

We define a new ribbon group action on ribbon graphs that uses a semidirect product of a permutation group and the original ribbon group of Ellis-Monaghan and Moffatt to take (partial) twists and duals, or twuals, of ribbon graphs. A ribbon graph is a fixed point of this new ribbon group action if and only if it is isomorphic to one of its (partial) twuals. This extends the original ribbon group action, which only used the canonical identification of edges, to the more natural setting of self-twuality up to isomorphism. We then show that every ribbon graph has in its orbit an orientable embedded bouquet and prove that the (partial) twuality properties of these bouquets propagate through their orbits. Thus, we can determine (partial) twualities via these one vertex graphs, for which checking isomorphism reduces simply to checking dihedral group symmetries. Finally, we apply the new ribbon group action to generate all self-trial ribbon graphs on up to seven edges, in contrast with the few, large, very high-genus, self-trial regular maps found by Wilson, and by Jones and Poultin. We also show how the automorphism group of a ribbon graph yields self-dual, -petrial or –trial graphs in its orbit, and produce an infinite family of self-trial graphs that do not arise as covers or parallel connections of regular maps, thus answering a question of Jones and Poulton.

Symmetries and anomalies of (1+1)d theories: 2-groups and symmetry fractionalization

We investigate the interactions of discrete zero-form and one-form global symmetries in (1+1)d theories. Focus is put on the interactions that the symmetries can have on each other, which in this low dimension result in 2-group symmetries or symmetry fractionalization. A large part of the discussion will be to understand a major feature in (1+1)d: the multiple sectors into which a theory decomposes. We perform gauging of the one-form symmetry, and remark on the effects this has on our theories, especially in the case when there is a global 2-group symmetry. We also implement the spectral sequence to calculate anomalies for the 2-group theories and symmetry fractionalized theory in the bosonic and fermionic cases. Lastly, we discuss topological manipulations on the operators which implement the symmetries, and draw insights on the (1+1)d effects of such manipulations by coupling to a bulk (2+1)d theory.

Set-theoretic Yang–Baxter & reflection equations and quantum group symmetries

Connections between set-theoretic Yang–Baxter and reflection equations and quantum integrable systems are investigated. We show that set-theoretic R-matrices are expressed as twists of known solutions. We then focus on reflection and twisted algebras and we derive the associated defining algebra relations for R-matrices being Baxterized solutions of the A-type Hecke algebra $${\mathcal {H}}_N(q=1)$$ H N ( q = 1 ) . We show in the case of the reflection algebra that there exists a “boundary” finite sub-algebra for some special choice of “boundary” elements of the B-type Hecke algebra $${\mathcal {B}}_N(q=1, Q)$$ B N ( q = 1 , Q ) . We also show the key proposition that the associated double row transfer matrix is essentially expressed in terms of the elements of the B-type Hecke algebra. This is one of the fundamental results of this investigation together with the proof of the duality between the boundary finite subalgebra and the B-type Hecke algebra. These are universal statements that largely generalize previous relevant findings and also allow the investigation of the symmetries of the double row transfer matrix.

The group structure of dynamical transformations between quantum reference frames

Recently, it was shown that when reference frames are associated to quantum systems, the transformation laws between such quantum reference frames need to be modified to take into account the quantum and dynamical features of the reference frames. This led to a relational description of the phase space variables of the quantum system of which the quantum reference frames are part of. While such transformations were shown to be symmetries of the system's Hamiltonian, the question remained unanswered as to whether they enjoy a group structure, similar to that of the Galilei group relating classical reference frames in quantum mechanics. In this work, we identify the canonical transformations on the phase space of the quantum systems comprising the quantum reference frames, and show that these transformations close a group structure defined by a Lie algebra, which is different from the usual Galilei algebra of quantum mechanics. We further find that the elements of this new algebra are in fact the building blocks of the quantum reference frames transformations previously identified, which we recover. Finally, we show how the transformations between classical reference frames described by the standard Galilei group symmetries can be obtained from the group of transformations between quantum reference frames by taking the zero limit of the parameter that governs the additional noncommutativity introduced by the quantum nature of inertial transformations.

Design of multi-scale protein complexes by hierarchical building block fusion

A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.

Structural and Thermal Investigations of L-CuC4H4O6·3H2O and DL-CuC4H4O6·2H2O Single Crystals

Copper(II) L-tartrate trihydrate, L-CuC4H4O6·3H2O, and copper(II) DL-tartrate dihydrate, DL-CuC4H4O6·2H2O, crystals were grown at room temperature by the gel method using silica gels as the growth medium. Differential scanning calorimetry, thermogravimetric-differential thermal analysis, and X-ray diffraction measurements were performed on both crystals. The space group symmetries (monoclinic P21 and P21/c) and structural parameters of the crystals were determined at room temperature and at 114 K. Both structures consisted of slightly distorted CuO6 octahedra, C4H4O6 and H2O molecules, C4H4O6–Cu–C4H4O6 chains linked by Cu–O bonds, and O–H–O hydrogen-bonding frameworks between adjacent molecules. Weight losses due to thermal decomposition of the crystals were found to occur in the temperature range of 300–1250 K. We inferred that the weight losses were caused by the evaporation of bound water molecules and the evolution of H2CO, CO, and O2 gases from C4H4O6 molecules, and that the residual reddish-brown substance left in the vessels after decomposition was copper(I) oxide (Cu2O).

Generalized global symmetries of T[M] theories. Part I

We study reductions of 6d theories on a d-dimensional manifold Md, focusing on the interplay between symmetries, anomalies, and dynamics of the resulting (6 −d)-dimensional theory T[Md]. We refine and generalize the notion of “polarization” to polarization on Md, which serves to fix the spectrum of local and extended operators in T[Md]. Another important feature of theories T[Md] is that they often possess higher-group symmetries, such as 2-group and 3-group symmetries. We study the origin of such symmetries as well as physical implications including symmetry breaking and symmetry enhancement in the renormalization group flow. To better probe the IR physics, we also investigate the ’t Hooft anomaly of 5d Chern-Simons matter theories. The present paper focuses on developing the general framework as well as the special case of d = 0 and 1, while an upcoming paper will discuss the case of d = 2, 3 and 4.

Visualizing the double-gyroid twin

Periodic gyroid network materials have many interesting properties (band gaps, topologically protected modes, superior charge and mass transport, and outstanding mechanical properties) due to the space-group symmetries and their multichannel triply continuous morphology. The three-dimensional structure of a twin boundary in a self-assembled polystyrene-b-polydimethylsiloxane (PS-PDMS) double-gyroid (DG) forming diblock copolymer is directly visualized using dual-beam scanning microscopy. The reconstruction clearly shows that the intermaterial dividing surface (IMDS) is smooth and continuous across the boundary plane as the pairs of chiral PDMS networks suddenly change their handedness. The boundary plane therefore acts as a topological mirror. The morphology of the normally chiral nodes and strut loops within the networks is altered in the twin-boundary plane with the formation of three new types of achiral nodes and the appearance of two new classes of achiral loops. The boundary region shares a very similar surface/volume ratio and distribution of the mean and Gaussian curvatures of the IMDS as the adjacent ordered DG grain regions, suggesting the twin is a low-energy boundary.

2-Group Symmetries of 6D Little String Theories and T-Duality

We determine the 2-group structure constants for all the six-dimensional little string theories (LSTs) geometrically engineered in F-theory without frozen singularities. We use this result as a consistency check for T-duality: the 2-groups of a pair of T-dual LSTs have to match. When the T-duality involves a discrete symmetry twist, the 2-group used in the matching is modified. We demonstrate the matching of the 2-groups in several examples.