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DOE OSTI2023

The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1

The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or ‘PUS’ enzymes include those that rely on guide RNA molecules and others that function as ‘stand-alone’ enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Structural Analysis of 23S rRNA Methylating Enzyme Cfr Reveals RNA-Binding Determinants for Methylation Regiospecificity and Antibiotic Resistance

The 23S rRNA methylating enzyme Cfr, found in pathogens including Staphylococcus aureus, Clostridium difficile, Escherichia coli, and Klebsiella pneumoniae, confers resistance to phenicols, lincosamides, oxazolidinones (including linezolid), pleuromutilins, and streptogramins A (the PhLOPS A phenotype). Cfr catalyzes methylation of the C8 position of the A2503 base in 23S rRNA, the recognition site of the above antibiotic classes. Along with the RlmN housekeeping enzyme, Cfr can also promote methylation of the C2 position of the same base. The molecular and structural basis of Cfr’s dual substrate specificity is not known, which hinders our ability to design Cfr-targeting inhibitors necessary to curb PhLOPS A resistance. Here, we present the first crystal structure of Cfr and a detailed analysis of its possible interactions with rRNA. Using structure-guided mutagenesis, mass spectrometry analysis of in cellulo 23S rRNA methylated species, and in cellulo resistance studies, we identify the key amino acids essential for Cfr methylation and multidrug resistance activity. In particular, we found that Cfr’s Q329 residue is important for C8- specific methylation. These data provide a framework for further studies of the biochemistry, structure, and inhibition of this important resistance determinant.

AlphaFold↗

DOE OSTI2025

Electrochemical Oxidation in Garnet-Type Solid Electrolyte by Formation of Point Defects

All-solid-state batteries hold greater promise for improving safety and energy density over conventional battery technology employing organic liquid electrolytes. One of the required features of a Li + conducting solid electrolyte is electrochemical stability, attained thermodynamically or kinetically, within the targeted operating voltage and temperature ranges. Therefore, understanding of the oxidative or reductive degradation mechanism is important to allow the design of stable solid electrolyte materials. This work contributes to building an understanding of the oxidative degradation mechanism in lithium solid electrolytes at cell operating conditions. Here, we have focused on resolving the oxidative decomposition mechanism of Al-doped lithium garnet Li 6.28 Al 0.24 La 3 Zr 2 O 12 (LLZO) as a state-of-the-art inorganic ceramic electrolyte. By combining experimental and computational analyses, we show that oxidation of LLZO occurs by simultaneous loss of oxygen and lithium from the structure, resulting in substoichiometric LLZO, at a moderate temperature (80 °C) and a high electrode potential (4.3 V vs Li/Li + ). Based on X-ray absorption and diffraction analyses, we find that the zirconium coordination shells in LLZO contract while the crystal structure experiences positive chemical strain upon electrochemical oxidation. The results from ex situ structural characterization of both the local structure and crystal symmetry are supported by a substoichiometric LLZO with lithium and oxygen vacancies, modeled by density functional theory (DFT) calculations. These chemical and structural changes in LLZO suppress effective lithium-ion conductivity by an order of magnitude. Formation of lithium and oxygen vacancies in LLZO upon electrochemical oxidation is different from prior thermodynamic predictions of phase decomposition of LLZO. The difference here is that the experiments were conducted at near-room temperature, which can hinder the kinetics of phase separation, and thus, the resultant LLZO solid electrolyte is still single-phase but substoichiometric in Li and O. In conclusion, these findings contribute an important degradation mechanism of the electrolyte, relevant for practical operational conditions of solid-state batteries.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Lateral Integration of SnS and GeSe van der Waals Semiconductors: Interface Formation, Electronic Structure, and Nanoscale Optoelectronics

The emergence of atomically thin crystals has allowed extending materials integration to lateral heterostructures where different 2D materials are covalently connected in the plane. The concept of lateral heterostructures can be generalized to thicker layered crystals, provided that a suitably faceted seed crystal presents edges to which a compatible second van der Waals material can be attached layer by layer. Here, we examine the possibility of integrating multilayer crystals of the group IV monochalcogenides SnS and GeSe, which have the same crystal structure, small lattice mismatch, and similar bandgaps. In a two-step growth process, lateral epitaxy of GeSe on the sidewalls of multilayer SnS flakes (obtained by vapor transport of a SnS 2 precursor on graphite) yields heterostructures of laterally stitched crystalline GeSe and SnS without any detectable vertical overgrowth of the SnS seeds and with sharp lateral interfaces. Combined cathodoluminescence spectroscopy and ab initio calculations show the effects of small band offsets on carrier transport and radiative recombination near the interface. Further, the results demonstrate the possibility of forming atomically connected lateral interfaces across many van der Waals layers, which is promising for manipulating optoelectronics, photonics, and for managing charge- and thermal transport.

2D layered crystals↗

DOE OSTI2022

Charge-ordered state satisfying the Anderson condition in LiRh 2 O 4 arising from local dimer order

Here we report on the charge-ordered structure of LiRh 2 O 4 arising below the metal-insulator transition at 170 K. Structural studies using synchrotron x rays have revealed that the charge-ordered states of Rh 3+ and Rh 4+ with dimerization are realized in the low-temperature phase below 170 K. Although the low-temperature ground state resembles that of CuIr 2 S 4 , a charge-ordering pattern satisfying the Anderson condition is realized in LiRh 2 O 4 . Based on structural information such as the short-range order of dimers appearing above the transition temperature and the weakening of the correlation between rhodium one-dimensional chains appearing in the crystal structure, we argue that the Coulomb interaction plays an important role in determining the charge-ordering patterns.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Crystal and Electronic Structures of A 2 NaIO 6 Periodate Double Perovskites (A = Sr, Ca, Ba): Candidate Wasteforms for I-129 Immobilization

The synthesis, structure, and thermal stability of the periodate double perovskites A 2 NaIO 6 (A= Ba, Sr, Ca) were investigated in the context of potential application for the immobilization of radioiodine. A combination of X-ray diffraction and neutron diffraction, Raman spectroscopy, and DFT simulations were applied to determine accurate crystal structures of these compounds and understand their relative stability. The compounds were found to exhibit rock-salt ordering of Na and I on the perovskite B-site; Ba 2 NaIO 6 was found to adopt the Fm- 3 m aristotype structure, whereas Sr 2 NaIO 6 and Ca 2 NaIO 6 adopt the P 2 1 / n hettotype structure, characterized by cooperative octahedral tilting. DFT simulations determined the Fm- 3 m and P 2 1 / n structures of Ba 2 NaIO 6 to be energetically degenerate at room temperature, whereas diffraction and spectroscopy data evidence only the presence of the Fm- 3 m phase at room temperature, which may imply an incipient phase transition for this compound. The periodate double perovskites were found to exhibit remarkable thermal stability, with Ba 2 NaIO 6 only decomposing above 1050 °C in air, which is apparently the highest recorded decomposition temperature so far recorded for any iodine bearing compound. As such, these compounds offer some potential for application in the immobilization of iodine-129, from nuclear fuel reprocessing, with an iodine incorporation rate of 25–40 wt%. The synthesis of these compounds, elaborated here, is also compatible with both current conventional and future advanced processes for iodine recovery from the dissolver off-gas.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Quasi-Two-Dimensional Heterostructures (K M 1 – x Te)(LaTe 3 ) ( M = Mn and Zn) with Charge Density Waves

Layered heterostructure materials with two different functional building blocks can teach us about emergent physical properties and phenomena arising from interactions between the layers. Here, we report intergrowth compounds KLaM 1 - x Te 4 (M = Mn and Zn; $x \approx$ 0.35) featuring two chemically distinct alternating layers [LaTe 3 ] and [KM 1 - x Te]. Their crystal structures are incommensurate, determined by single X-ray diffraction for the Mn compound and a transmission electron microscope study for the Zn compound. KLaMn 1 – x Te 4 crystallizes in the orthorhombic superspace group Pmnm(01/2 gamma)s00 with lattice parameters a = 4.4815(3) Å, b = 21.6649(16) Å, and c = 4.5220(3) Å. It exhibits charge density wave order at room temperature with a modulation wave vector q = 1/2b* + 0.3478c* originating from electronic instability of Te-square nets in [LaTe 3 ] layers. The Mn analog exhibits a cluster spin glass behavior with spin freezing temperature $T_f \approx$ 5 K attributed to disordered Mn vacancies and competing magnetic interactions in the [Mn 1 - x Te] layers. The Zn analog also has charge density wave order at room temperature with a similar q-vector having the c* component similar to 0.346 confirmed by selected-area electron diffraction. Electron transfer from [KM 1 - x Te] to [LaTe 3 ] layers exists in KLaM 1 – x Te 4 , leading to an enhanced electronic specific heat coefficient. The resistivities of KLaM 1 - x Te 4 (M = Mn and Zn) exhibit metallic behavior at high temperatures and an upturn at low temperatures, suggesting partial localization of carriers in the [LaTe 3 ] layers with some degree of disorder associated with the M atom vacancies in the [M 1 - x Te] layers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

(111) Faceted Metal Oxides: A Review of Synthetic Methods

Material design and synthesis have made tremendous impacts in the scientific community by unleashing a material's true potential via enhanced properties and applications. Over the years, advanced synthetic strategies have emerged and have been expanded to not only control the size and shape of nanoparticles but also to control the preferential growth of surface facets, paving the way for new materials with facet-dependent properties. Metal oxide (111) facets as compared to their potentially more stable counterpart facets (e.g., (100), (110)) have recently exhibited enriched chemical properties owing to their unique surface arrangement. As a result, metal oxide (111) faceted surfaces have been used in applications such as catalysis, sorbents, batteries, etc. This work aims to provide a perspective on the synthetic processes utilized to expose (111) surfaces and the governing factors/synthetic parameters that expose them across various metal oxides of different crystal structures as well as some of their applications.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Tuning chemical precompression: Theoretical design and crystal chemistry of novel hydrides in the quest for warm and light superconductivity at ambient pressures

Over the past decade, a combination of crystal structure prediction techniques and experimental synthetic work has thoroughly explored the phase diagrams of binary hydrides under pressure. The fruitfulness of this dual approach is demonstrated in the recent identification of several superconducting hydrides with T c s approaching room temperature. We start with an overview of the computational procedures for predicting stable structures and estimating their propensity for superconductivity. A survey of phases with high T c reveals some common structural features that appear conducive to the strong coupling of the electronic structure with atomic vibrations that leads to superconductivity. We discuss the stability and superconducting properties of phases containing two of these—molecular H 2 units mixed with atomic H and hydrogenic clathrate-like cages—as well as more unique motifs. Lastly, we argue that ternary hydride phases, whose exploration is still in its infancy, are a promising route to achieve simultaneous superconductivity at high temperatures and stability at low pressures. Several ternary hydrides arise from the addition of a third element to a known binary hydride structure through site mixing or onto a new site, and several more are based on altogether new structural motifs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Effect of nitrogen doping and pressure on the stability of $\mathrm{LuH_3}$

A report on the near-ambient superconductivity in a nitrogen-doped lutetium hydride has stimulated great interest in this material [Dasenbrock-Gammon et al. , Nature (London) 615, 244 (2023)]. While its superconductivity is still a subject of debate, the structure of the claimed cubic phase remains uncertain. In this work, we study the effect of nitrogen doping and pressure on the energetic and dynamic stability of cubic $\mathrm{LuH_3}$. Our findings indicate that both pressure and nitrogen doping can enhance the stability of the cubic $\mathrm{LuH_3}$ phase. Here, we propose a $\mathrm{Lu_8}$$\mathrm{H_{21}}$$\mathrm{Lu}$ structure that exhibits a stable phonon, reasonable thermodynamic stability at 1 GPa, and an x-ray diffraction pattern similar to the experimental data. However, we do not observe electron-phonon coupling in the zone-center phonon modes of these crystal structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Structure and lattice excitations of the copper substituted lead oxyapatite Pb 9.06⁢(7)⁢ Cu 0.94⁢(6)⁢ (PO 3.92⁢(4) ) 6 ⁢O 0.96⁢(3)

The copper substituted lead oxyapatite, Pb 10-x⁢ Cu x (PO 3.92⁢(4) ) 6 ⁢O 0.96⁢(3) [x = 0.94(6)] was studied using neutron and x-ray diffraction and neutron spectroscopy techniques. The crystal structure of the main phase of our sample, which has come to be colloquially known as LK-99, is verified to possess a hexagonal structure with space group P6 3 /m, alongside the presence of impurity phases Cu and Cu 2 ⁢S. We determine the primary substitution location of the Cu as the Pb1 (6⁢ℎ) site, with a small substitution at the Pb2 (4⁢f) site. Consequently, no clear Cu-doping-induced structural distortion was observed in the investigated temperature region between 10 K and 300 K. Specially, we did not observe a reduction of coordinate number at the Pb2 site or a clear tilting of PO 4 tetrahedron. Magnetic characterization reveals a diamagnetic signal in the specimen, accompanied by a very weak ferromagnetic component at 2 K. No long-range magnetic order down to 10 K was detected by the neutron diffraction. Inelastic neutron scattering measurements did not show magnetic excitations for energies up to 350 meV. There is no sign of a superconducting resonance in the excitation spectrum of this material. The measured phonon density of states compares well with density functional theory calculations performed for the main LK-99 phase and its impurity phases. Our study may shed some insight into the role of the favored substitution site of copper in the absence of structural distortion and superconductivity in LK-99.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Lead-Free Cs 4 CuSb 2 Cl 12 Layered Double Perovskite Nanocrystals

Concerns about the toxicity of lead-based perovskites have aroused great interest for the development of alternative lead-free perovskite-type materials. Recently, theoretical calculations predict that Pb 2+ cations can be substituted by a combination of Cu 2+ and Sb 3+ cations to form a vacancy-ordered layered double perovskite structure with superior optoelectronic properties. However, accessibilities to this class of perovskite-type materials remain inadequate, hindering their practical implementations in various applications. Here, we report the first colloidal synthesis of Cs 4 CuSb 2 Cl 12 perovskite-type nanocrystals (NCs). The resulting NCs exhibit a layered double perovskite structure with ordered vacancies and a direct bandgap of 1.79 eV. A composition-structure-property relationship has been established by investigating a series of Cs 4 Cu x Ag 2-2x Sb 2 Cl 12 perovskite-type NCs (0 ≤ x ≤ 1). The composition-induced crystal structure transformation, thus the electronic bandgap evolution has been explored by experimental observations and further confirmed by theoretical calculations. Taking advantages of both the unique electronic structure and solution processability, we demonstrate that the Cs 4 CuSb 2 Cl 12 NCs can be solution-processed as high-speed photodetectors with ultrafast photo-response and narrow bandwidth. We anticipate that our study will prompt future research to design and fabricate novel and high-performance lead-free perovskite-type NCs for a range of applications.

25 ENERGY STORAGE↗

DOE OSTI2024

Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1

Glycosylation is a predominant strategy plants use to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are utilized in human health. Small molecule glycosylation is largely carried out by family 1 glycosyltransferases. Here, we report a structural and biochemical investigation of UGT95A1, a family 1 GT enzyme from Pilosella officinarum that exhibits a strong, unusual regiospecificity for the 3'-O position of flavonoid acceptor substrate luteolin. We obtained an apo crystal structure to help drive the analyses of a series of binding site mutants, revealing that while most residues are tolerant to mutations, key residues M145 and D464 are important for overall glycosylation activity. Interestingly, E347 is crucial for maintaining the strong preference for 3'-O glycosylation, while R462 can be mutated to increase regioselectivity. The structural determinants of regioselectivity were further confirmed in homologous enzymes. Our study also suggests that the enzyme contains large, highly dynamic, disordered regions. We showed that while most disordered regions of the protein have little to no implication in catalysis, the disordered regions conserved among investigated homologs are important to both the overall efficiency and regiospecificity of the enzyme. This report represents a comprehensive in-depth analysis of a family 1 GT enzyme with a unique substrate regiospecificity and may provide a basis for enzyme functional prediction and engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

An investigation on the structural stability of $\mathrm{ZIF}$-8 in water versus water-derived oxidative species in aqueous environment

We report the zeolitic-imidazolate-framework-8 (ZIF-8) is one of the extensively studied metal-organic frameworks (MOF) materials because of its unique structure. For its potential applicability in numerous fields, it becomes crucial to have detailed studies on the structural stability of ZIF-8, especially in aqueous environments. A number of studies have been conducted to investigate the breakdown process of the ZIF-8 structure in water; which is known as the hydrolysis of ZIF-8. However, those studies reported different opposing experimental observations on the role of water on the structural stability of ZIF-8, which created obscurity in understanding this phenomenon. This study explored the effects of different water-derived species on the structural stability of ZIF-8; specifically, examined the effects of only water and water with different oxidative species that may be generated by water molecules' dissociation under external energy or catalyst presence. To this effort, we experimentally probed the physical and chemical structural changes of ZIF-8 in DI water and three different solutions of hydrogen peroxides (H 2 O 2 ); taking H 2 O 2 as the source of oxidative species. To assess the changes in elemental compositions, chemical bonds, functional groups, crystal structure, and morphology, all the samples were analyzed by X-ray photoelectron spectroscopy (XPS), energy-dispersive x-ray (EDX) spectroscopy, Fourier Transform Infrared (FTIR) spectroscope, X-ray diffractometer (XRD), and scanning electron microscope (SEM). Significant structural changes in ZIF-8 occurred mainly in the presence of oxidative species in water. Notably, oxidative species' concentration exceeding 1 M heightened the deformation of the ZIF-8 structure.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Compositional heterogeneity in Cs y FA 1- y Pb(Br x I 1- x ) 3 perovskite films and its impact on phase behavior

Hybrid organic inorganic lead halide perovskite semiconductors of the form Cs y FA 1-y Pb(Br x I 1-x ) 3 are promising candidate materials for high-efficiency photovoltaics. Notably, cation and anion substitution can be used to tune the band gaps to optimize performance and improve stability. However, multi-component materials can be prone to compositional and structural inhomogeneity and the extent, length scale and impact of this heterogeneity on lead halide perovskite properties are not well understood. Here we use synchrotron X-ray diffraction to probe the evolution of crystal structure across the tetragonal-to-cubic phase transition for a series of Cs y FA 1-y Pb(Br x I 1-x ) 3 thin films with x = 0.05 to 0.3 and y = 0.17 to 0.40. We find that the transition occurs across a broad temperature range of approximately 40 °C, much larger than for pure compounds such as MAPbI 3 and MAPbBr 3 . Finally, we hypothesize that this smearing of the phase transition is due to compositional inhomogeneities that give rise to a distribution of local transition temperatures and we estimate the composition varies by about 10% to 15% with likely greater heterogeneity for the halide anion than the cation. This approach of mapping the transition is a simple and effective method of assessing heterogeneity, enabling evaluation of its impact.

36 MATERIALS SCIENCE↗

DOE OSTI2024

High-temperature structure, elasticity, and thermal expansion of ε-ZrH 1.8

Zirconium hydride is a promising candidate material for nuclear microreactor applications as a solid-state moderator component, owing to its favorable neutronics properties and good thermal stability over other metal hydrides. Here, in the present work, the crystal structure, thermal expansion, and elastic properties of the hydrogen-rich ε phase hydride were measured at elevated temperatures in the range 300–900 K. Samples were prepared by direct hydriding Zircaloy-4 metal – a nuclear-grade zirconium alloy. Room-temperature lattice parameters agree well with those reported from literature for unalloyed zirconium hydride and fall within an observed quadratic H-content dependence. The coefficients of thermal expansion, determined from lattice expansion and dilatometry, agree well within our work but were about 30 % lower than those reported by others for unalloyed hydrides. Density functional theory-based molecular dynamics simulations were used to compare with thermal expansion and elasticity measurements. Results showed lattice parameter temperature dependence and slope of thermal expansion align with those from measurements. Based on diffraction scans at select temperatures, ε phase remained stable in air up to at least 770 K. Likewise, dilatometry showed smooth thermal expansion up to the thermal decomposition temperature around 950 K. The precise decomposition temperature was not determined via diffraction due to sparse scanning. The complete elastic property measurements were gathered for ε-phase Ziracloy-4 hydride for the first time. Young's modulus was lower compared to the metal and δ hydride phases. High-temperature elasticity measurements were limited to <350 K due to acoustic dissipation effects.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Crystallographic Insight of Reduced Lattice Volume Expansion in Mesoporous Cu 2+ -Doped TiNb 2 O 7 Microspheres during Li + Insertion

TiNb 2 O 7 represents a promising anode material for lithium-ion batteries (LIBs), but its practical applications are currently hampered by the non-negligible volumetric expansion and contraction during the charge/discharge process and the sluggish ion/electron kinetics. Here a combination technique is reported by systematically optimizing the porous and spherical morphology, crystal structure, and surface decoration of mesoporous Cu 2+ -doped TiNb 2 O 7 microspheres to enhance the electrochemical Li + storage performance and stability simultaneously. The Cu 2+ dopants preferentially replace Ti 4+ in crystal lattices, which decreases the Li + diffusion barrier and increases the electronic conductivity, as confirmed by density functional theory (DFT) calculation and demonstrated by diverse electrochemical characterizations. The successful Cu 2+ doping significantly reduces the lattice expansion coefficient from 7.26% to 4.61% after Li + insertion along the b-axis of TiNb 2 O 7 , as visualized from in situ and ex situ XRD analysis. The optimal 5% Cu 2+ -doped TiNb 2 O 7 with surface coating of N-doped carbon exhibits significantly enhanced specific capacity and rate and cyclic performances in both half- and full-cell configurations, demonstrating an excellent electrochemical behavior for fast-charging LIB applications.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Electronic band structure and magnetism of CoFeV 0.5 Mn 0.5 Si

Half-metallic Heusler alloys have attracted significant attention due to their potential application in spin-transport-based devices. We have synthesized one such alloy, CoFeV 0.5 Mn 0.5 Si, using arc melting and high-vacuum annealing at 600 °C for 24 hours. First principles calculation indicates that CoFeV 0.5 Mn 0.5 Si shows a nearly half-metallic band structure with a degree of spin polarization of about 93%. In addition, this value can be enhanced by the application of tensile strain. The room temperature x-ray diffraction patterns are indexed with the cubic crystal structure without secondary phases. The annealed sample shows ferromagnetic order with the Curie temperature well above room temperature ( T c = 657 K) and a saturation magnetization of about 92 emu/g. Our results indicate that CoFeV 0.5 Mn 0.5 Si has a potential for room temperature spin-transport-based devices.

36 MATERIALS SCIENCE↗