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At least 127 records · Page 7

Electronic structure theory on modeling short-range noncovalent interactions between amino acids

While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the “gold standard” coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller−Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.

Chemistry↗

Tailoring electrophotonic capabilities of atomically thin GeS through controlled organometallic intercalation

The unique structure of van der Waals materials facilitates a robust mechanism for precise control of physical properties. In this study, we present a comprehensive analysis based on the intercalation of organometallics to modulate the optoelectronic behavior of two-dimensional germanium sulfide (GeS). Advanced computational exploration reveals significant and tunable features in the intercalated material. Additionally, the weak chemical interactions between organometallics and GeS support the electric-field-mediated drift and charge–discharge processes in intercalants. Controlling the concentration of organometallics in this manner enables the dynamic emergence of novel characteristics post-intercalation. These include flatbands near the Fermi level, significant enhancement of carrier mobility, and a magnetic ground state that is atypical for pristine GeS. Our findings demonstrate that organometallic intercalation offers a powerful strategy for tailoring the optoelectronic and magnetic characteristics of GeS, paving the way for harnessing emerging features for applications in next-generation devices.

Physics↗

Metabolic profiling of epidermal and mesophyll tissues under water-deficit stress in Opuntia ficus-indica reveals stress-adaptive metabolic responses

Cactus pear (Opuntia ficus-indica) is a high productivity species within the Cactaceae grown in many semiarid parts of the world for food, fodder, forage, and biofuels. O. ficus-indica utilises obligate crassulacean acid metabolism (CAM), an adaptation that greatly improves water-use efficiency (WUE) and reduces crop water usage. To better understand CAM-related metabolites and water-deficit stress responses of O. ficus-indica, comparative metabolic profiling was performed on mesophyll and epidermal tissues collected from well-watered and water-deficit stressed cladodes at 50% relative water content (RWC). Tissues were collected over a 24-h period to identify metabolite levels throughout the diel cycle and analysed using a combination of acidic/basic ultra-high-performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS) and gas chromatography/mass spectrometry (GC/MS) platforms. A total of 382 metabolites, including 210 (55%) named and 172 (45%) unnamed compounds, were characterised across both tissues. Most tricarboxylic acid (TCA) cycle and glycolysis intermediates were depleted in plants undergoing water-deficit stress indicative of CAM idling or post-idling, while the raffinose family oligosaccharides (RFO) accumulated in both mesophyll and epidermal tissues as osmoprotectants. Levels of reduced glutathione and other metabolites of the ascorbate cycle as well as oxylipins, stress hormones such as traumatic acid, and nucleotide degradation products were increased under water-deficit stress conditions. Notably, tryptophan accumulation, an atypical response, was significantly (24-fold) higher during all time points in water-deficit stressed mesophyll tissue compared with well-watered controls. Many of the metabolite increases were indicative of a highly oxidising environment under water-deficit stress. A total of 34 unnamed metabolites also accumulated in response to water-deficit stress indicating that such compounds might play important roles in water-deficit stress tolerance.

Plant Sciences↗

Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception

The vertebrate inner ear, responsible for hearing and balance, is able to sense minute mechanical stimuli originating from an extraordinarily broad range of sound frequencies and intensities or from head movements. Integral to these processes is the tip-link protein complex, which conveys force to open the inner-ear transduction channels that mediate sensory perception. Protocadherin-15 and cadherin-23, two atypically large cadherins with 11 and 27 extracellular cadherin (EC) repeats, are involved in deafness and balance disorders and assemble as parallel homodimers that interact to form the tip link. Here we report the X-ray crystal structure of a protocadherin-15 + cadherin-23 heterotetrameric complex at 2.9-Å resolution, depicting a parallel homodimer of protocadherin-15 EC1-3 molecules forming an antiparallel complex with two cadherin-23 EC1-2 molecules. In addition, we report structures for 10 protocadherin-15 fragments used to build complete high-resolution models of the monomeric protocadherin-15 ectodomain. Molecular dynamics simulations and validated crystal contacts are used to propose models for the complete extracellular protocadherin-15 parallel homodimer and the tip-link bond. Steered molecular dynamics simulations of these models suggest conditions in which a structurally diverse and multimodal protocadherin-15 ectodomain can act as a stiff or soft gating spring. These results reveal the structural determinants of tip-link–mediated inner-ear sensory perception and elucidate protocadherin-15’s structural and adhesive properties relevant in disease.

59 BASIC BIOLOGICAL SCIENCES↗

Evolution-inspired design of multicolored photoswitches from a single cyanobacteriochrome scaffold

Significance Cyanobacteriochromes (CBCRs) are small cyanobacterial photoreceptors which are highly diversified and categorized into many lineages based on their primary sequences. In this study, we identified an atypical CBCR exhibiting an orange/green reversible photocycle. Step-by-step site-directed mutagenesis was performed on this native CBCR, and seven new photoconvertible variants were created. During this process, we identified residues crucial for each color tuning event. These seven molecules covering the shorter-wavelength blue-to-orange region would contribute to the future development of multicolored optogenetic tools and are complementary to recently developed molecules sensing longer wavelengths of light.

59 BASIC BIOLOGICAL SCIENCES↗

Mechanism of tethered agonist-mediated signaling by polycystin-1

Mutations of polycystin-1 (PC1) are the major cause (85% of cases) of autosomal dominant polycystic kidney disease (ADPKD), which is the fourth leading cause of kidney failure. PC1 is thought to function as an atypical G protein-coupled receptor, yet the mechanism by which PC1 regulates G-protein signaling remains poorly understood. A significant portion of ADPKD mutations of PC1 encode a protein with defects in maturation or reduced function that may be amenable to functional rescue. In this work, we have combined complementary biochemical and cellular assay experiments and accelerated molecular simulations, which revealed an allosteric transduction pathway in activation of the PC1 C-terminal fragment. Our findings will facilitate future rational drug design efforts targeting the PC1 signaling function. Polycystin-1 (PC1) is an important unusual G protein-coupled receptor (GPCR) with 11 transmembrane domains, and its mutations account for 85% of cases of autosomal dominant polycystic kidney disease (ADPKD). PC1 shares multiple characteristics with Adhesion GPCRs. These include a GPCR proteolysis site that autocatalytically divides these proteins into extracellular, N-terminal, and membrane-embedded, C-terminal fragments (CTF), and a tethered agonist (TA) within the N-terminal stalk of the CTF that is suggested to activate signaling. However, the mechanism by which a TA can activate PC1 is not known. Here, we have combined functional cellular signaling experiments of PC1 CTF expression constructs encoding wild type, stalkless, and three different ADPKD stalk variants with all-atom Gaussian accelerated molecular dynamics (GaMD) simulations to investigate TA-mediated signaling activation. Correlations of residue motions and free-energy profiles calculated from the GaMD simulations correlated with the differential signaling abilities of wild type and stalk variants of PC1 CTF. They suggested an allosteric mechanism involving residue interactions connecting the stalk, Tetragonal Opening for Polycystins (TOP) domain, and putative pore loop in TA-mediated activation of PC1 CTF. Key interacting residues such as N3074–S3585 and R3848–E4078 predicted from the GaMD simulations were validated by mutagenesis experiments. Together, these complementary analyses have provided insights into a TA-mediated activation mechanism of PC1 CTF signaling, which will be important for future rational drug design targeting PC1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Divergent evolution of extreme production of variant plant monounsaturated fatty acids

Metabolic extremes provide opportunities to understand enzymatic and metabolic plasticity and biotechnological tools for novel biomaterial production. We discovered that seed oils of many Thunbergia species contain up to 92% of the unusual monounsaturated petroselinic acid (18:1Δ6), one of the highest reported levels for a single fatty acid in plants. Supporting the biosynthetic origin of petroselinic acid, we identified a Δ6-stearoyl-acyl carrier protein (18:0-ACP) desaturase from Thunbergia laurifolia , closely related to a previously identified Δ6-palmitoyl-ACP desaturase that produces sapienic acid (16:1Δ6)-rich oils in Thunbergia alata seeds. Guided by a T. laurifolia desaturase crystal structure obtained in this study, enzyme mutagenesis identified key amino acids for functional divergence of Δ6 desaturases from the archetypal Δ9-18:0-ACP desaturase and mutations that result in nonnative enzyme regiospecificity. Furthermore, we demonstrate the utility of the T. laurifolia desaturase for the production of unusual monounsaturated fatty acids in engineered plant and bacterial hosts. Through stepwise metabolic engineering, we provide evidence that divergent evolution of extreme petroselinic acid and sapienic acid production arises from biosynthetic and metabolic functional specialization and enhanced expression of specific enzymes to accommodate metabolism of atypical substrates.

59 BASIC BIOLOGICAL SCIENCES↗

Spectral and photochemical diversity of tandem cysteine cyanobacterial phytochromes

The atypical trichromatic cyanobacterial phytochrome NpTP1 from Nostoc punctiforme ATCC 29133 is a linear tetrapyrrole (bilin)-binding photoreceptor protein that possesses tandem-cysteine residues responsible for shifting its light-sensing maximum to the violet spectral region. Using bioinformatics and phylogenetic analyses, in this study we established that tandem-cysteine cyanobacterial phytochromes (TCCPs) compose a well-supported monophyletic phytochrome lineage distinct from prototypical red/far-red cyanobacterial phytochromes. To investigate the light-sensing diversity of this family, we compared the spectroscopic properties of NpTP1 (here renamed NpTCCP) with those of three phylogenetically diverged TCCPs identified in the draft genomes of Tolypothrix sp. PCC7910, Scytonema sp. PCC10023, and Gloeocapsa sp. PCC7513. Recombinant photosensory core modules of ToTCCP, ScTCCP, and GlTCCP exhibited violet-blue–absorbing dark-states consistent with dual thioether-linked phycocyanobilin (PCB) chromophores. Photoexcitation generated singly-linked photoproduct mixtures with variable ratios of yellow-orange and red-absorbing species. The photoproduct ratio was strongly influenced by pH and by mutagenesis of TCCP- and phytochrome-specific signature residues. Our experiments support the conclusion that both photoproduct species possess protonated 15E bilin chromophores, but differ in the ionization state of the noncanonical “second” cysteine sulfhydryl group. We found that the ionization state of this and other residues influences subsequent conformational change and downstream signal transmission. We also show that tandem-cysteine phytochromes present in eukaryotes possess similar amino acid substitutions within their chromophore-binding pocket, which tune their spectral properties in an analogous fashion. Taken together, our findings provide a roadmap for tailoring the wavelength specificity of plant phytochromes to optimize plant performance in diverse natural and artificial light environments.

59 BASIC BIOLOGICAL SCIENCES↗

Searching for long-lived particles beyond the Standard Model at the Large Hadron Collider

Particles beyond the Standard Model (SM) can generically have lifetimes that are long compared to SM particles at the weak scale. When produced at experiments such as the Large Hadron Collider (LHC) at CERN, these long-lived particles (LLPs) can decay far from the interaction vertex of the primary proton–proton collision. Such LLP signatures are distinct from those of promptly decaying particles that are targeted by the majority of searches for new physics at the LHC, often requiring customized techniques to identify, for example, significantly displaced decay vertices, tracks with atypical properties, and short track segments. Given their non-standard nature, a comprehensive overview of LLP signatures at the LHC is beneficial to ensure that possible avenues of the discovery of new physics are not overlooked. Here we report on the joint work of a community of theorists and experimentalists with the ATLAS, CMS, and LHCb experiments—as well as those working on dedicated experiments such as MoEDAL, milliQan, MATHUSLA, CODEX-b, and FASER—to survey the current state of LLP searches at the LHC, and to chart a path for the development of LLP searches into the future, both in the upcoming Run 3 and at the high-luminosity LHC. The work is organized around the current and future potential capabilities of LHC experiments to generally discover new LLPs, and takes a signature-based approach to surveying classes of models that give rise to LLPs rather than emphasizing any particular theory motivation. We develop a set of simplified models; assess the coverage of current searches; document known, often unexpected backgrounds; explore the capabilities of proposed detector upgrades; provide recommendations for the presentation of search results; and look towards the newest frontiers, namely high-multiplicity 'dark showers', highlighting opportunities for expanding the LHC reach for these signals.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Model-agnostic search for dijet resonances with anomalous jet substructure in proton–proton collisions at $\sqrt{s}$ = 13 TeV

This paper presents a model-agnostic search for narrow resonances in the dijet final state in the mass range 1.8-6 TeV. The signal is assumed to produce jets with substructure atypical of jets initiated by light quarks or gluons, with minimal additional assumptions. Search regions are obtained by utilizing multivariate machine-learning methods to select jets with anomalous substructure. A collection of complementary anomaly detection methods - based on unsupervised, weakly supervised, and semisupervised algorithms - are used in order to maximize the sensitivity to unknown new physics signatures. These algorithms are applied to data corresponding to an integrated luminosity of 138 fb -1 , recorded by the CMS experiment at the LHC, at a center-of-mass energy of 13 TeV. No significant excesses above background expectations are seen. Exclusion limits are derived on the production cross section of benchmark signal models varying in resonance mass, jet mass, and jet substructure. Many of these signatures have not been previously sought, making several of the limits reported on the corresponding benchmark models the first ever. When compared to benchmark inclusive and substructure-based search strategies, the anomaly detection methods are found to significantly enhance the sensitivity to a variety of models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Advances in Nb 3 Sn superconducting radiofrequency cavities towards first practical accelerator applications

Abstract Nb 3 Sn is a promising next-generation material for superconducting radiofrequency cavities, with significant potential for both large scale and compact accelerator applications. However, so far, Nb 3 Sn cavities have been limited to continuous wave accelerating fields <18 MV m −1 . In this paper, new results are presented with significantly higher fields, as high as 24 MV m −1 in single cell cavities. Results are also presented from the first ever Nb 3 Sn-coated 1.3 GHz 9-cell cavity, a full-scale demonstration on the cavity type used in production for the European XFEL and LCLS-II. Results are presented together with heat dissipation curves to emphasize the potential for industrial accelerator applications using cryocooler-based cooling systems. The cavities studied have an atypical shiny visual appearance, and microscopy studies of witness samples reveal significantly reduced surface roughness and smaller film thickness compared to typical Nb 3 Sn films for superconducting cavities. Possible mechanisms for increased maximum field are discussed as well as implications for physics of RF superconductivity in the low coherence length regime. Outlook for continued development is presented.

43 PARTICLE ACCELERATORS↗

The mystery of photometric twins DES17X1boj and DES16E2bjy

In this paper, we present an analysis of DES17X1boj and DES16E2bjy, two peculiar transients discovered by the Dark Energy Survey (DES). They exhibit nearly identical double-peaked light curves that reach very different maximum luminosities ($M_r$ = -15.4 and -17.9, respectively). The light-curve evolution of these events is highly atypical and has not been reported before. The transients are found in different host environments: DES17X1boj was found near the nucleus of a spiral galaxy, while DES16E2bjy is located in the outskirts of a passive red galaxy. Early photometric data are well fitted with a blackbody and the resulting moderate photospheric expansion velocities (1800 km s –1 for DES17X1boj and 4800 km s –1 for DES16E2bjy) suggest an explosive or eruptive origin. Additionally, a feature identified as high-velocity Ca II absorption ($v ≈$ 9400 km s –1 ) in the near-peak spectrum of DES17X1boj may imply that it is a supernova. While similar light-curve evolution suggests a similar physical origin for these two transients, we are not able to identify or characterize the progenitors.

79 ASTRONOMY AND ASTROPHYSICS↗

Radio fossils, relics, and haloes in Abell 3266: cluster archaeology with ASKAP-EMU and the ATCA

ABSTRACT Abell 3266 is a massive and complex merging galaxy cluster that exhibits significant substructure. We present new, highly sensitive radio continuum observations of Abell 3266 performed with the Australian Square Kilometre Array Pathfinder (0.8–1.1 GHz) and the Australia Telescope Compact Array (1.1–3.1 GHz). These deep observations provide new insights into recently reported diffuse non-thermal phenomena associated with the intracluster medium, including a ‘wrong-way’ relic, a fossil plasma source, and an as-yet unclassified central diffuse ridge, which we reveal comprises the brightest part of a large-scale radio halo detected here for the first time. The ‘wrong-way’ relic is highly atypical of its kind: it exhibits many classical signatures of a shock-related radio relic, while at the same time exhibiting strong spectral steepening. While radio relics are generally consistent with a quasi-stationary shock scenario, the ‘wrong-way’ relic is not. We study the spectral properties of the fossil plasma source; it exhibits an ultrasteep and highly curved radio spectrum, indicating an extremely aged electron population. The larger scale radio halo fills much of the cluster centre, and presents a strong connection between the thermal and non-thermal components of the intracluster medium, along with evidence of substructure. Whether the central diffuse ridge is simply a brighter component of the halo, or a mini-halo, remains an open question. Finally, we study the morphological and spectral properties of the multiple complex radio galaxies in this cluster in unprecedented detail, tracing their evolutionary history.

79 ASTRONOMY AND ASTROPHYSICS↗

Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure

The ribose 2'-hydroxyl is the key chemical difference between RNA and DNA and primary source of their divergent structural and functional characteristics. Macromolecular X-ray diffraction experiments typically do not reveal the positions of hydrogen atoms. Thus, standard crystallography cannot determine 2'-OH orientation (H2'-C2'-O2'-HO2' torsion angle) and its potential roles in sculpting the RNA backbone and the expansive fold space. Here, we report the first neutron crystal structure of an RNA, the Escherichia coli rRNA Sarcin-Ricin Loop (SRL). 2'-OD orientations were established for all 27 residues and revealed O-D bonds pointing toward backbone (O3', 13 observations), nucleobase (11) or sugar (3). Most riboses in the SRL stem region show a 2'-OD backbone-orientation. GAGA-tetraloop riboses display a 2'-OD base-orientation. An atypical C2'-endo sugar pucker is strictly correlated with a 2'-OD sugar-orientation. Neutrons reveal the strong preference of the 2'-OH to donate in H-bonds and that 2'-OH orientation affects both backbone geometry and ribose pucker. We discuss 2'-OH and water molecule orientations in the SRL neutron structure and compare with results from a solution phase 10 μs MD simulation. We demonstrate that joint cryo-neutron/X-ray crystallography offers an all-in-one approach to determine the complete structural properties of RNA, i.e. geometry, conformation, protonation state and hydration structure.

59 BASIC BIOLOGICAL SCIENCES↗

Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium

ABSTRACTSulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.

Trotter, Valentine V↗

Magic state distillation from entangled states

We report that magic can be distributed non-locally in many-body entangled states, such as the low energy states of condensed matter systems. Using the Bravyi-Kitaev magic state distillation protocol, we find that non-local magic is distillable and can improve the distillation outcome. We analyze a few explicit examples and show that spin squeezing can be used to convert non-distillable states into distillable ones. Our analysis also suggests that the conventional product input states assumed by magic distillation protocols are extremely atypical among general states with distillable magic. It further justifies the need for studying a diverse range of entangled inputs that yield magic states with high probability.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Current-driven transverse domain wall oscillations in perpendicular spin-valve structures

Spin-transfer-driven oscillations of a transverse domain wall confined to a perpendicular spin-valve structure are investigated using a one-dimensional model. The stack consists of a polarizer, nonmagnetic spacer, soft free layer, and pinned magnetic layer. It is found that the domain-wall oscillation frequency is a nonmonotonic, highly asymmetrical function of applied electric current, showing a strong dependence on the current direction and the relative strengths of the interfacial and bulk spin-transfer torques. Micromagnetic analysis reveals that the surprising and atypical oscillator response is due to an interplay between the interfacial spin-transfer torque, the bulk spin-transfer torque, the exchange torque, and the damping torque. The underlying physical and material responses are examined, including the important role of the domain-wall twist. The competitions between the involved torques under different operating conditions suggest that the oscillator could serve as a model system to investigate magnetic and spintronic phenomena at the nanoscale. Finally, the observed current-dependent twisting of the free-layer magnetization about the axis of precession may further be found interesting for investigations of the interaction between spin-polarized current and chiral spin structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Motif magnetism and quantum many-body scars

In this work, we generally expect quantum systems to thermalize and satisfy the eigenstate thermalization hypothesis (ETH), which states that finite-energy-density eigenstates are thermal. However, some systems, such as many-body localized systems and systems with quantum many-body scars, violate ETH and have high-energy athermal eigenstates. In systems with scars, most eigenstates thermalize, but a few atypical scar states do not. Scar states can give rise to a periodic revival when time-evolving particular initial product states, which can be detected experimentally. Recently, a family of spin Hamiltonians was found with magnetically ordered three-colored eigenstates that are quantum many-body scars [Lee et al., Phys. Rev. B 101, 241111(R) (2020)]. These models can be realized in any lattice that can be tiled by triangles, such as the triangular or kagome lattices, and have been shown to have close connections to the physics of quantum spin liquids in the Heisenberg kagome antiferromagnet. In this paper, we introduce a generalized family of n-colored Hamiltonians with “spiral colored” eigenstates made from n-spin motifs such as polygons or polyhedra. We show how these models can be realized in many different lattice geometries and provide numerical evidence that they can exhibit quantum many-body scars with periodic revivals that can be observed by time-evolving simple product states. The simple structure of these Hamiltonians makes them promising candidates for future experimental studies of quantum many-body scars.

36 MATERIALS SCIENCE↗