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At least 649 records · Page 36

Frameshifting Stimulatory Sequence Induces Large Structural Change of Ribosomal Proteins When Bound to E. coli Ribosomes

Biological macromolecular machines occupy a continuum of structural conformations to perform cellular tasks. Mapping this conformational space provides an insight into its functionality. While the cryo-electron microscopy resolution revolution has expanded our ability to characterize the conformational continuums, there are obstacles in structurally characterizing regions of high flexibility. These technical barriers have impeded characterization of flexible ribosomal proteins when the ribosome is interacting with mRNA stem-loop structures such as a frameshifting stimulatory sequence (FSS). Small-angle neutron/X-ray scattering and electron microscopy were used to study ribosomal samples and compared structural differences between a ribosome that is bound to an FSS stem-loop compared to a ribosome bound to linear mRNA. This comparison shows that a large protein stalk elongates by 22% when the 70S interacts with an mRNA stem-loop. Finally, our results suggest that ribosomal proteins have extensive flexibility and may influence important ribosomal mechanisms, such as those that involve FSS.

36 MATERIALS SCIENCE↗

Phase Change-Driven Negative Activation Energies in Pd/Carbon-Based/Organic Getter Hydrogenation Reactions

In this study, the hydrogenation of 1,4-diphenylbutadiyne (DPB) blended with carbon-supported Pd (DPB–Pd/C) in the form of pellets was investigated by isothermal–isobaric experiments at 1333 Pa of H 2 and in the temperature range of 291–315 K. The extracted kinetics were then used in conjunction with a complementary constant rate of H 2 input experimentation to model the performance of a DPB-catalysis/support system as a function of temperature and H 2 partial pressure. First-principles density functional theory (DFT) calculations were also performed to shed light on the molecular level energetics of DPB and its intermediate states. A seemingly puzzling formation of alternate positive activation energy barrier (higher reaction rate with higher temperature) and negative activation energy barrier (higher reaction rate with lower temperature) zones during the hydrogenation process was discovered. However, this observed phenomenon can be logically explained in terms of the associated phase changes and H 2 transport in the material. This work provides a good illustration of a rarely encountered chemical process with a negative activation energy barrier.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scaling of Transition State Vibrational Frequencies and Application of d -Band Theory to the Brønsted–Evans–Polanyi Relationship on Surfaces

Semiempirical energy relations provide a means of estimating thermodynamic properties. Specifically, linear scaling relationships (LSRs) and Brønsted–Evans–Polanyi (BEP) relationships correlate adsorption energies between adsorbates across surfaces and reaction energies with activation barriers, respectively. Although vibrational scaling relations (VSRs) exist between adsorbates at identical sites, scaling between vibrational frequencies of adsorbed local minima and transition states is lacking. Here, we present density functional theory calculations for AH X (A = C, N, O) diffusions on transition metal surfaces and reveal linear scaling between frequencies of local minima and the transition state between those minima. Using d-band theory and linear muffin tin orbital theory (LMTO), we derive the slopes of these transition state vibrational scaling relations (TSVSRs) and, in so doing, provide a rigorous theory extending the original BEP relations developed for solution chemistry to surface chemistry. Furthermore, with a single reference DFT calculation, we predict the slopes and quantify uncertainty in the predictions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fluorine-Tuned Carbon-Based Nickel Single-Atom Catalysts for Scalable and Highly Efficient CO 2 Electrocatalytic Reduction

Electrocatalytic CO 2 reduction is garnering significant interest due to its potential applications in mitigating CO 2 and producing fuel. However, the scaling up of related catalysis is still hindered by several challenges, including the cost of the catalytic materials, low selectivity, small current densities to maintain desirable selectivity. In this study, Fluorine (F) atoms were introduced into an N-doped carbon-supported single nickel (Ni) atom catalyst via facile polymer-assisted pyrolysis. This method not only maintains the high atom utilization efficiency of Ni in a cost-effective and sustainable manner but also effectively manipulates the electronic structure of the active Ni-N 4 site through F doping. The catalyst has also been further optimized by controlling the F states, including convalent and semi-ionic states, by adjusting the fluorine sources involved. Consequently, this catalyst with unique structure exhibited comparable electrocatalytic performance for CO 2 -to-CO conversion, achieving a Faradaic efficiency (FE) of over 99% across a wide potential range and an exceptional CO evolution rate of 9.5 x 10 4 h -1 at -1.16 V vs reversible hydrogen electrode (RHE). It also delivered a practical current of 400 mA cm -2 while maintaining more than 95% CO FE. Experimental analysis combined with density functional theory (DFT) calculations have also shown that F-doping modifies the electron configuration at the central Ni-N 4 sites. In conclusion, this modification lowers the energy barrier for CO 2 activation, thereby facilitating the production of the crucial *COOH intermediate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Magnetic Blocking in Fluoflavine Radical-Bridged Dilanthanide Complexes

Magnetic exchange coupling is difficult to foster in polynuclear lanthanide (Ln) complexes and poorly understood. While coupling Ln ions through closed-shell ligands is inherently weak due to the contracted 4f orbitals, placing open-shell ligands instead has proven to promote orders of magnitude stronger coupling, giving rise to single-molecule magnets (SMMs) innate to real magnetic memory effect in the case of the anisotropic Ln ions. Notably, the impact of radical bridges with differing oxidation states on magnetic blocking remains unexplored due to lack of Ln SMMs with radicals in two distinct charge states. Herein, the first dilanthanide complexes (Ln = Gd, Dy) containing fluoflavine (flv) bridges, [(Cp* 2 Ln) 2 (μ-flv z )]X, (where X = [Al(OC{CF 3 } 3 ) 4 ] − (z = 1−•), 1-Ln; X = 0 (z = 2−), 2-Ln; X =[K(crypt-222)] + (z = 3−•), 3-Ln) are reported. 1-Ln and 3-Ln, comprising the flv 1−• and flv 3−• radical bridges, were investigated via single-crystal X-ray diffraction (SCXRD), ultraviolet−visible (UV−vis) spectroscopy, Superconducting Quantum Interference Device (SQUID) magnetometry, high-field electron paramagnetic resonance (HF-EPR) spectroscopy and broken-symmetry density functional theory (BS-DFT) calculations. 1-Dy and 3-Dy constitute the first SMMs innate to radicals in two differing oxidation states. 1-Dy exhibits a spin-reversal barrier U eff of 28.36 cm −1 and open magnetic hysteresis loops below 3 K. By contrast, 3-Dy displays a much higher U eff of 143(2) cm −1 and open hysteresis loops until 9.5 K, representing a record for dilanthanide SMMs containing an organic radical bridge. The boost in SMM properties in 3-Dy is attributed to spin-phonon coupling and improved frontier orbital structure. This study paves the way for advanced design strategies of polynuclear Ln SMMs.

Benner, Florian [Michigan State Univ., East Lansin↗

Mechanistic insights into the conversion of polyalcohols over Brønsted acid sites

Multi-layered plastic (MLP) films provide excellent properties for food packaging; however, because of the complicated chemistry of the hydrophobic substrates and tightly laminated hydrophilic layers, it is challenging to recycle the MLP films. The selective conversion of polar functional groups in hydrophilic layers with a minimal destruction of the carbon backbone of constituted polymers is considered a promising approach to improve the recyclability of MLP films. Here, in this study, we combine computational and experimental studies to investigate the acid-catalyzed conversion of functional groups in polyalcohols, through which we report potential reaction pathways involved in the conversion of ethylene vinyl alcohol (EVOH), a common copolymer used in MLP films as an oxygen barrier. Using 2,4-pentanediol as a model compound, we show that its conversion proceeds primarily through the dehydration of a hydroxyl group via either a stepwise or a concerted mechanism to form an unsaturated alcohol that can be further converted into a conjugated diene or a saturated ketone; this secondary reaction determines the product selectivity. The rate determining intermediates and transition states are identified, and the activation barriers are calculated, in agreement with experimentally observed product selectivities. This study thus provides insights for the selective conversion of EVOH.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Separability of H 2 O molecular potential surfaces in hyperspherical coordinates via adiabatic approximation

An adiabatic scheme for separation of the three-dimensional (3D) nuclear dynamics on the ground electronic Born-Oppenheimer potential energy surface of an H 2 O molecule in hyperspherical coordinates is presented. It is found that the three vibrational modes are weakly coupled and the 3D vibrational wave function can be approximated as a product of three separable functions: one represented by the hyperradius and two by the two hyperangles individually. Additionally, this framework is then used for investigation of the formation and the role of a saddlelike barrier arising in the two hyperspherical angles that is to moderate the OH + H dissociation process. In order to test the validity of the framework, vibrational states with energies up to 19 500 cm -1 are constructed under the assumptions of adiabaticity and separability and compared to full three-dimensional high-precision numerical calculations yielding remarkable correspondence. As a result we present a simple construction scheme for separated molecular vibration states as the first step towards theoretical investigation of laser-driven molecular dynamics of triatomic molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗

Tunneling magnetoresistance in MgO tunnel junctions with Fe-based leads in empirically corrected density functional theory

The minority-spin Fe/MgO interface states are at the Fermi level in density functional theory (DFT), but experimental evidence and GW calculations place them slightly higher in energy. This small shift can strongly influence tunneling magnetoresistance (TMR) in junctions with a thin MgO barrier and its dependence on the concentration of Co in the electrodes. Here, in this study, an empirical potential correction to DFT is introduced to shift the interface states up to match the tunnel spectroscopy data. With this shift, TMR in Fe/MgO/Fe junctions exceeds 800% and 3000% at 3 and 4 monolayers (ML) of MgO, respectively. We further consider the effect of alloying of the Fe electrodes with up to 30% Co or 10% V, treating them in the coherent potential approximation (CPA). Alloying with Co broadens the interface states and brings a large incoherent minority-spin spectral weight to the Fermi level. Alloying with V brings the minority-spin resonant states close to the Fermi level. However, in both cases the minority-spin spectral weight at the Fermi level resides primarily at the periphery of the Brillouin zone, which is favorable for spin filtering. Using convolutions of k II -resolved barrier densities of states calculated in CPA, it is found that TMR is strongly reduced by alloying with Co or V but still remains above 500% at 4 ML of MgO up to 30% of Co or 5% V. At 5 ML, the TMR increases above 1000% in all systems considered. However, while TMR declines sharply with increasing bias up to 0.2 eV in the tunnel junctions with pure Fe leads, it remains almost constant up to 0.5 eV if leads are alloyed with Co.

74 ATOMIC AND MOLECULAR PHYSICS↗

Data Science Enabled Enabled Discovery of Superconductors (Final Progress Report)

This Final Technical Report describes efforts by 4 PIs at the University of Florida (Peter Hirschfeld, Richard Hennig, Greg Stewart and James Hamlin), over the period September 2019-August 2023, to use data science and machine learning techniques to discover new conventional superconductors. The PIs constructed a discovery loop with two theorists and two experimentalists to: develop algorithms to machine learn descriptors correlating strongly with the critical temperature Tc (PI's Peter Hirschfeld, UF Physics and Richard Hennig, UF Materials Science and En), synthesize and measure properties of promising materials, and feed back the knowledge gained into the prediction algorithm. This work was motivated by the theoretical prediction and experimental discovery of high-pressure, high-pressure hydride superconductors, and to find ways to recreate the high critical temperatures in these systems at ambient pressure. Highlights from the grant include: 1) a new equation for Tc in terms of moments of the electron-phonon spectral function, improving on the so-called Allen-Dynes equation (1975); 2) study of the metastable A15 superconductor Nb3Si, formed under explosive compression at ~1000GPa to determine the kinetic barrier to the ground state structure; 3) the development of ultra-fast machine-learned atomic potentials for molecular dynamics, and 4) the discovery of superconductivity at 19K in WB2 arising from metastable defect structures in the crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Localized basis set for plutonium

The implementation of optimal strictly localized atomic orbitals basis for plutonium (Pu) using norm-conserving pseudopotential density-functional theory (DFT) is presented. The basis set was applied to the α, β, γ, δ, δ', and ε phases of Pu, δ-Pu surface, and δ-PuGa alloys. The computed properties of the Pu phases and δ-Pu surface were in good agreement with both available experimental data and prior DFT calculations based on plane-wave methodologies. Results for the δ-PuGa alloys were also in good agreement with experimental data. Finally, the reliability of the basis set was further demonstrated by using ab initio molecular dynamics to model the diffusion coefficient and activation barrier for atomic diffusion in a δ-PuGa alloy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Linking low and high temperature NO oxidation mechanisms over Brønsted acidic chabazite to dynamic changes of the active site

The oxidation of NO over Brønsted acid sites in chabazite (CHA) zeolites shows an atypical temperature dependence; at low temperature the apparent activation energy is negative, but it becomes positive as the temperature exceeds a transition temperature. To explain this behavior we used density functional theory and statistical mechanics to investigate high and low temperature mechanisms for this reaction and propose a dynamic active site change in response to temperature variation. Our simulations show that the apparent activation barrier in the low temperature regime is more negative over Brønsted acidic CHA as compared to the siliceous zeolite framework. This effect is attributed to further enthalpic stabilization of the transition states by physical interaction with the H-CHA Brønsted acid sites. At elevated temperature, our calculations support both the existence and the significant catalytic role of NO+ in providing a modified active site. The temperature dependent transformation of the active site from H-CHA to NO-CHA sites may occur via two plausible ion-exchange mechanisms that define a transition temperature for the reaction. This transition temperature can be tuned by incorporating different trivalent metal atoms (B, Al, Ga or In) within the CHA framework. We found the lowest transition temperature for H-[In] CHA and H-[Ga]CHA. Here, the ability to control the dynamic response of the active site and the associated switch between low and high temperature mechanism with negative and positive apparent activation energy, respectively, is of fundamental interest for the design of zeolite catalysts operating in the presence of NO.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neuroimmune Responses to Space Radiation

One of the main health risks in human deep space exploration is central nervous system (CNS) damage by ionizing radiation due to exposure to galactic cosmic rays (GCRs). In animal models, irradiation with simulated GCRs or their components has been shown to cause neurodegeneration and neuroinflammation associated with cognitive and behavioral dysfunction. The extent of CNS damage is partially mediated by the blood-brain barrier (BBB), which regulates the interaction between CNS and systemic responses to stressors in the rest of the body. The main cellular regulators of BBB permeability are astrocytes, which also modulate neuronal death, neuroinflammation and oxidative stress. However, studies on BBB and astrocyte functions in regulating CNS responses to ionizing radiation have been limited, especially in human tissue/organ analogs. Therefore, we developed a high-throughput 3D organ-on-a-chip system to study human CNS and BBB impairments caused by deep space radiation. We investigated both immediate and delayed CNS responses to major GCR components: 600MeV/n 56Fe ions. We observed ionizing radiation-mediated dose-dependent increases in BBB permeability that was exacerbated by astrocyte presence and accompanied by altered cytokine expression including interleukin-1 receptor alpha downregulation, and increased oxidative stress. In particular, 600MeV/n 56Fe particle irradiation selectively increased damage and blood-brain barrier permeability only in models that contained astrocytes in addition to endothelial cells, indicating astrocytes as a particularly radiosensitive component of the CNS that could therefore be a suitable a target for neuroprotection. Future studies will compare human and mouse CNS model responses to simulated GCRs and evaluate the induction of an anti-inflammatory phenotype in astrocytes as a potential countermeasure. Furthermore, in our lab we have been exploring the individual variability, genomic associations and secreted biomarkers of responses to space radiation, which could eventually be combined to address personalized CNS health risk and develop individual countermeasures. Ultimately, we aim to expand upon these results to uncover novel cellular and mechanistic targets for countermeasure development to mitigate human CNS damage in deep space exploration.

space radiation↗

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Estimation of micro-Hall-Petch coefficients for prismatic slip system in Mg-4Al as a function of grain boundary parameters

Grain size strengthening, referred to as the Hall-Petch effect, is a common strategy to improve the yield strength of magnesium (Mg) alloys. Several experimental studies have reported that the Hall-Petch slope strongly depends on the texture of the alloy. This effect arises from altering grain boundaries (GBs) resistance to different slip systems to transfer across adjacent grains. The grain boundary barrier strength of certain grain boundaries to basal slip, referred to as basal micro-Hall-Petch, was investigated in the previous work. Here in this study, the micro-Hall-Petch coefficient values for the prismatic slip $(k^{prismatic}_{μ})$ in Mg-4Al and their correlation with the grain boundary parameters were investigated. An experimental method was developed to initiate the prismatic slip band at low-stress levels. High-resolution electron backscatter diffraction (HR-EBSD) was used to measure the residual stress tensor, from which the resolved shear stress ahead of blocked prismatic slip bands was computed for seven different grain boundaries. $(k^{prismatic}_{μ})$ values for each individual GB were calculated by coupling the stress profile information with a continuum dislocation pile-up model. The $(k^{prismatic}_{μ})$ values vary from 0.138 MPa.m 1/2 to 0.685 MPa. m 1/2 which are almost three times larger than the calculated values for the basal micro-Hall-Petch. The $(k^{prismatic}_{μ})$ values were correlated with the GB parameters, and a functional relationship depending on the two most effective angles, the angle between the traces of the slip planes on the GB plane ($\phi$) and the angle between incoming and outgoing slip directions (κ), was proposed to estimate the Hall-Petch barrier for prismatic slip system. The work provides coefficients that can be supplied as input to crystal plasticity models to couple the effect of texture and grain size effectively.

36 MATERIALS SCIENCE↗

The Value of Watching How Materials Grow: A Multimodal Case Study on Halide Perovskites

Material synthesis is one of the most important aspects in humankinds’ endeavor to discover and create new materials for energy applications. One strategy to tailor materials with desired functions in a rational way is by knowing how functions relate to structure, synthetic variables, arrangement of atoms and molecules, and how functions evolve during synthesis. In order to accelerate materials synthesis, discovery, and optimization by 10 times it is the right time now to integrate computational tools, synthesis, and characterization. One particular barrier to realizing this concept is the understanding of when and how phases form in real time during synthesis, which is challenging to asses by existing theoretical frameworks. In addition, transient or metastable phases with positive free energy above the lowest-free energy ground state can be revealed by such real time (in situ) measurements. Metastable materials are ubiquitous in condensed matter and can show superior properties compared to their equilibrium form. This work discusses the value of emerging multimodal in situ characterizations exemplified on hybrid halide perovskites. Finally, the ways in which the implementation of in situ measurements can advance the materials science synthesis field as well as their role to enable close-loop feedback control and autonomous synthesis are discussed.

36 MATERIALS SCIENCE↗

Electronic Structure Distortions in Chromium Chelates Impair Redox Kinetics in Flow Batteries

Aminopolycarboxylate chelates are emerging as a promising class of electrolyte materials for aqueous redox flow batteries, offering tunable redox potentials, solubility, and pH stability through careful selection of ligands and transition metal ions. Despite their potential, the impact of molecular structure modifications on the electronic and electrochemical properties of these chelates remains underexplored. Here, in this study, we examine how introducing a hydroxyl group, often employed for its solubilizing properties, to the backbone of CrPDTA, a reference chelate material, significantly changes the thermodynamics and kinetics of the chelate's redox process. We correlate changes in molecular and electronic structures to different electrochemical responses resulting from the hydroxyl addition and show that the introduction of this functional group leads to a distortion in the octahedral coordination of chromium. Furthermore, increased anisotropic spin density and nonintegral oxidation state changes in the Cr metal center result in a larger barrier for electron transfer in CrPDTA‐OH. It is demonstrated that preserving a hexacoordinate chelate structure across a broad pH range is crucial for efficient flow battery application and it is emphasized that ligand modifications must avoid distorting the octahedral coordination of the transition metal.

25 ENERGY STORAGE↗

Gas-Phase Complexes of Americium and Lanthanides with a Bis-triazinyl Pyridine: Reactivity and Bonding of Archetypes for F-Element Separations

Bis-triazinyl pyridines (BTPs) exhibit solution selectivity for trivalent americium over lanthanides (Ln), the origins of which remain uncertain. Here in this paper, electrospray ionization was used to generate gas-phase complexes [ML 3 ] 3+ , where M = La, Lu, or Am and L is EtBTP 2,6-bis(5,6-diethyl-1,2,4-triazin-3-yl)-pyridine. Collision-induced dissociation (CID) of [ML 3 ] 3+ in the presence of H 2 O yielded a protonated ligand [L(H)] + and hydroxide [ML 2 (OH)] 2+ or hydrate [ML(L–H)(H 2 O)] 2+ , where (L–H) - is a deprotonated ligand. Although solution affinities indicate stronger binding of BTPs toward Am 3+ versus Ln 3+ , the observed CID process is contrastingly more facile for M = Am versus Ln. To understand the disparity, density functional theory was employed to compute potential energy surfaces for two possible CID processes, for M = La and Am. In accordance with the CID results, both the rate determining transition state barrier and the net energy are lower for [AmL 3 ] 3+ versus [LaL 3 ] 3+ and for both product isomers, [ML 2 (OH)] 2+ and [ML(L–H)(H 2 O)] 2+ . More facile removal of a ligand from [AmL 3 ] 3+ by CID does not necessarily contradict stronger Am 3+ –L binding, as inferred from solution behavior. In particular, the formation of new bonds in the products can distort kinetics and thermodynamics expected for simple bond cleavage reactions. In addition to correctly predicting the seemingly anomalous CID behavior, the computational results indicate greater participation of Am 5f versus La 4f orbitals in metal–ligand bonding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mesh-like structure integrated core-shell-shell nanocomposites for enhanced stability and performance in carbon capture

Carbon capture is essential for mitigating climate change, yet most sorbents struggle to combine high capacity with chemical stability. Here we report core-shell-shell (CSS) nanocomposites that integrate adsorption efficiency with exceptional robustness. The design couples a metal-organic framework (MOF) core, which enriches local CO 2 concentration, with a polyamine shell that is reorganized into a porous, ordered network through entanglement with an outer covalent organic framework (COF) shell. This hierarchical architecture enables dual amine functionalization via sequential “click” and Schiff-base reactions, achieving a CO 2 uptake of 3.4 mmol g −1 at 1 bar. The COF outer layer also acts as a protective barrier, suppressing humidity interference and doubling cycling stability under simulated flue gas. Remarkably, the nanocomposites maintain structural integrity after one week in strongly acidic (3 M HNO 3 ) or basic (NaOH, pH=14) environments, underscoring their chemical resilience. By uniting high capacity, cycling durability, and environmental tolerance, this CSS strategy offers a versatile platform for next-generation carbon capture materials.

Yang, Sizhuo [Lawrence Berkeley National Laborator↗