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At least 487 records · Page 27

Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200 ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10– 30°C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40°C and attains a completely closed conformation at 50°C. We also found that the presence of glycan moieties did not influence the observed protein dynamics. Nevertheless, the closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

ZZ instantons and the non-perturbative dual of $c$ = 1 string theory

We study the effect of ZZ instantons in c = 1 string theory, and demonstrate that they give rise to non-perturbative corrections to scattering amplitudes that do not saturate unitarity within the closed string sector. Beyond the leading non-perturbative order, logarithmic divergences are canceled between worldsheet diagrams of different topologies, due to the Fischler-Susskind-Polchinski mechanism. We propose that the closed string vacuum in c = 1 string theory is non-perturbatively dual to a state of the matrix quantum mechanics in which all scattering states up to a given energy with no incoming flux from the “other side” of the potential are occupied by free fermions. Under such a proposal, we find detailed agreement of non-perturbative corrections to closed string amplitudes in the worldsheet description and in the dual matrix model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The gravitational path integral from an observer’s point of view

One of the fundamental problems in quantum gravity is to describe the experience of a gravitating observer in generic spacetimes. In this paper, we develop a framework for describing non-perturbative physics relative to an observer using the gravitational path integral. We apply our proposal to an observer that lives in a closed universe and one that falls behind a black hole horizon. We find that the Hilbert space that describes the experience of the observer is much larger than the Hilbert space in the absence of an observer. In the case of closed universes, the Hilbert space is not one-dimensional, as calculations in the absence of the observer suggest. Rather, its dimension scales exponentially with ${G}_{N}^{-1}$. Similarly, from an observer’s perspective, the dimension of the Hilbert space in a two-sided black hole is increased. We compute various observables probing the experience of a gravitating observer in this Hilbert space. We find that an observer experiences non-trivial physics in the closed universe in contrast to what it would see in a one-dimensional Hilbert space. In the two-sided black hole setting, our proposal implies that non-perturbative corrections to effective field theory for an infalling observer are suppressed until times exponential in the black hole entropy, resolving a recently-raised puzzle in black hole physics. While the framework that we develop is exemplified in the toy-model of JT gravity, most of our analysis can be extended to higher dimensions and, in particular, to generic spacetimes not admitting a conventional holographic description, such as cosmological universes or black hole interiors.

2D gravity↗

A defect in AdS 3 /CFT 2 duality

AdS 3 string theory in the stringy regime k = (R AdS /ℓ s ) 2 < 1 provides a laboratory for the study of holography in which both sides of AdS/CFT duality are under fairly good control. Worldsheet string theory is solvable, and for closed strings the dual spacetime CFT is a deformation of a symmetric product orbifold. Here we extend this construction to include open strings by adding a probe D-string, described semiclassically by an AdS 2 D-brane in AdS 3 . The dual defect or boundary conformal field theory (BCFT) is again a deformed symmetric product, which now describes the Fock space of long open and closed strings near the AdS boundary, with a boundary deformation implementing the open/closed transition in addition to the symmetric product $\mathbb{Z}$ 2 twist deformation that implements closed string joining/splitting. The construction thus provides an explicit example of an AdS 3 /BCFT 2 duality.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A double copy from twisted (co)homology at genus one

We study the twisted (co)homology of a family of genus-one integrals — the so called Riemann-Wirtinger integrals. These integrals are closely related to one-loop string amplitudes in chiral splitting where one leaves the loop-momentum, modulus and all but one puncture un-integrated. While not actual one-loop string integrals, they share many properties and are simple enough that the associated twisted (co)homologies have been completely characterized [1]. Using intersection numbers — an inner product on the vector space of allowed differential forms — we derive the Gauss-Manin connection for two bases of the twisted cohomology providing an independent check of [2]. We also use the intersection index — an inner product on the vector space of allowed contours — to derive a double-copy formula for the closed-string analogues of Riemann-Wirtinger integrals (one-dimensional integrals over the torus). Similar to the celebrated KLT formula between open- and closed-string tree-level amplitudes, these intersection indices form a genus-one KLT-like kernel defining bilinears in meromorphic Riemann-Wirtinger integrals that are equal to their complex counterparts.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Minimal-Area Metrics on the Swiss Cross and Punctured Torus

The closed string theory minimal-area problem asks for the conformal metric of least area on a Riemann surface with the condition that all non-contractible closed curves have length greater than or equal to an arbitrary constant that can be set to one. Through every point in such a metric there is a geodesic that saturates the length condition, and the saturating geodesics in a given homotopy class form a band. The extremal metric is unknown when bands of geodesics cross, as it happens for surfaces of non-zero genus. Here, we use recently proposed convex programs to numerically find the minimal-area metric on the square torus with a square boundary, for various sizes of the boundary. For large enough boundary the problem is equivalent to the “Swiss cross” challenge posed by Strebel. We find that the metric is positively curved in the two-band region and flat in the single-band regions. For small boundary the metric develops a third band of geodesics wrapping around it, and has both regions of positive and of negative curvature. This surface can be completed to provide the minimal-area metric on a once-punctured torus, representing a closed-string tadpole diagram.

97 MATHEMATICS AND COMPUTING↗

Dimension of Restricted Classes of Interval Orders

Rabinovitch showed in 1978 that the interval orders having a representation consisting of only closed unit intervals have order dimension at most 3. Herein, this article shows that the same dimension bound applies to two other classes of posets: those having a representation consisting of unit intervals (but with a mixture of open and closed intervals allowed) and those having a representation consisting of closed intervals with lengths in {0,1}.

97 MATHEMATICS AND COMPUTING↗

Natively oxidized amino acid residues in the spinach PS I-LHC I supercomplex

Reactive oxygen species (ROS) production is an unavoidable byproduct of electron transport under aerobic conditions. Photosystem II (PS II), the cytochrome b 6 /ƒ complex and Photosystem I (PS I) are all demonstrated sources of ROS. It has been proposed that PS I produces substantial levels of a variety of ROS including O$_{2}^{·-}$, 1 O 2 , H 2 O 2 and, possibly, ∙OH, however, the site(s) of ROS production within PS I has been the subject of significant debate. We hypothesize that amino acid residues close to the sites of ROS generation will be more susceptible to oxidative modification than distant residues. In this study, we have identified oxidized amino acid residues in spinach PS I which was isolated from field-grown spinach. The modified residues were identified by high-resolution tandem mass spectrometry. As expected, many of the modified residues lie on the surface of the complex. However, a well-defined group of oxidized residues, both buried and surface-exposed, lead from the chl a’ of P 700 to the surface of PS I. These residues (PsaB: 609 F, 611 E, 617 M, 619 W, 620 L, and PsaF: 139 L, 142 A, 143 D) may identify a preferred route for ROS, probably 1 O 2 , to egress the complex from the vicinity of P 700 . Additionally, two buried residues located in close proximity to A1B (PsaB: 712 H and 714 S) were modified, which may be consistent with A 1B being a source of O$_{2}^{·-}$. Surprisingly, no oxidatively modified residues were identified in close proximity to the 4Fe-FS clusters F X , F A or F B . These cofactors had been identified as a principal targets for ROS damage in the photosystem. Finally, a large number of residues located in the hydrophobic cores of Lhca1-Lhca4 are oxidatively modified. These appear to be the result of 1 O 2 production by the distal antennae for the photosystem.

59 BASIC BIOLOGICAL SCIENCES↗

Prediction of annual soil respiration from its flux at mean annual temperature

Accurately scaling soil respiration (SR, the soil-to-atmosphere flow of CO2) across time and space is important to constrain and understand ecosystem to global scale SR, a major terrestrial carbon flux to the atmosphere. Year-round SR measurements are however expensive and sometimes impossible to perform. Bahn et al. (2010) developed an approach to estimate annual SR (SRannual) from the flux measured at mean soil temperature (SRMAST), but the robustness of this approach needs to be evaluated in diverse ecosystem types and climatic conditions globally. We used a global soil respiration database (SRDB-V4, with 823 SR observations worldwide) to test the capability of SRMAST to predict SRannual. SRMAST estimated using a variety of methods all showed clear relationships with annual SRannual. Two single-rate methods (i.e., using the single SR rate most close to mean annual soil temperature, or the single SR rate most close to mean annual air temperature) showed the most pronounced divergence from the true SRannual, but errors significantly decreased when using multiple SR rates within 1 ? of the mean annual soil temperature to estimate SRMAST. SRannual was most closely correlated with SRMAST estimated via a Q10 relationship, but this method has a potential autocorrelation issue that we explore and discuss. Air temperature data are much more widely available than is soil temperature, and we found that SR at mean annual air temperature (SRMAAT) can be used to predict SRannual as well. This study builds on Bahn et al. (2010) to demonstrate that SR measured at both annual mean soil and air temperature can be used to predict annual SR, with well-quantified errors. This capability could be used to reduce SR measurement frequency required for estimating SRannual and greatly decrease cost, factors that are generally important but especially in lower-income countries and cold, inaccessible regions.

Soil respiration, temperature, modeling↗

The effect of relative humidity on eddy covariance latent heat flux measurements and its implication for partitioning into transpiration and evaporation

While the eddy covariance (EC) technique is a well-established method for measuring water fluxes (i.e., evaporation or 'evapotranspiration’, ET), the measurement is susceptible to many uncertainties. One such issue is the potential underestimation of ET when relative humidity (RH) is high (> 70%), due to low-pass filtering with some EC systems. Yet, this underestimation for different types of EC systems (e.g. open-path or closed-path sensors) has not been characterized for synthesis datasets such as the widely used FLUXNET2015 dataset. Here, we assess the RH-associated underestimation of latent heat fluxes (LE, or ET) from different EC systems for 163 sites in the FLUXNET2015 dataset. We found that the LE underestimation is most apparent during hours when RH is higher than 70%, predominantly observed at sites using closed-path EC systems, but the extent of the LE underestimation is highly site-specific. We then propose a machine learning based method to correct for this underestimation, and compare it to two energy balance closure based LE correction approaches (Bowen ratio correction, BRC, and attributing all errors to LE). Our correction increases LE by 189% for closed-path sites at high RH (> 90%), while BRC increases LE by around 30% for all RH conditions. Additionally, we assess the influence of these corrections on ET-based transpiration (T) estimates using two different ET partitioning methods. Results show opposite responses (increasing vs. slightly decreasing T-to-ET ratios, T/ET) between the two methods when comparing T based on corrected and uncorrected LE. Overall, our results demonstrate the existence of a high RH bias in water fluxes in the FLUXNET2015 dataset and suggest that this bias is a pronounced source of uncertainty in ET measurements to be considered when estimating ecosystem T/ET and WUE.

54 ENVIRONMENTAL SCIENCES↗

Prediction of α $IIb$ $β$ 3 integrin structures along its minimum free energy activation pathway

The adhesion protein integrin is a transmembrane heterodimer that plays a pivotal role in cellular processes such as cell signaling and cell migration. To execute its function, integrin undergoes extensive conformational changes from a bent-closed to an extended-open state. Resolving the structures across these changes remains a challenge with both experimental and computational methods, but it is crucial for understanding the activation mechanism of integrin. We address this challenge for the platelet integrin α IIb β 3 by employing finite temperature string method with structures of the images along the initial guess path generated by a multiscale data-driven framework. The full-length all-atom structures along the resulting minimum free energy path between the inactive bent-closed and active extended-open states of α IIb β 3 integrin are consistent with a variety of experimentally resolved structures. Changes in these predicted structures along the path show that the extension and separation of the α and β subunits from the bent-closed to the extended-open state require correlated movements between the subdomain pairs in α IIb β 3 . Furthermore, these results provide new insights into integrin activation mechanism, and the predicted structures have potential applications in guiding the design of integrin-targeting therapeutics.

Dasetty, Siva [University of Chicago, IL (United S↗

Upcycling Mixed Spent Ni-Lean Cathodes into Ni-Rich Polycrystalline Cathodes

Sustainable battery recycling is vital for conserving resources and reducing environmental impacts. Current open- and closed-loop recycling strategies often focus on recovering individual components, making the reuse of mixed cathode materials a complex challenge. Meanwhile, the research on upcycling has been limited to using pristine cathode feedstocks and virgin materials for synthesis. Here, to address this issue, we present an upcycling approach for spent Ni-lean mixed cathode materials that integrate an upcycling hydrometallurgical recycling process with traditional hydrometallurgical methods. This strategy achieves a utilization of 92.31 mol % of recycled materials, enabling the regeneration of Ni-rich cathode materials while significantly reducing the reliance on virgin resources. The regenerated 83Ni cathode materials demonstrate physical properties comparable to those produced from virgin materials. Electrochemical evaluations using single-layer pouch cells show that both recycled and virgin cathodes exhibit initial specific capacity close to 201.1 mAh/g and maintain approximately 88 % capacity retention after 500 cycles. Additionally, 2Ah cells confirmed these findings, delivering 85 % capacity retention after about 900 cycles. Techno-economic analysis demonstrates notable environmental benefits, including reductions in greenhouse gas emissions and energy consumption, achieving 232.75 MJ/kg of product, which is 8.6 % lower than traditional methods and comparable to direct upcycling. Furthermore, the upcycling hydrometallurgical recycling process generates the highest profit, proving its economic viability. This scalable and versatile process is adaptable to varying transition metal compositions, facilitating a closed-loop recycling system that bridges mixed spent cathodes with next-generation cathode materials, and offers a sustainable solution for managing waste battery materials.

Hydrometallurgical recycling↗

Isotopic dependence of the frequency of optical vibrations in molybdenum monohydride

We show that it is currently known that three hydrides – PdH x , MoH x , and TiH x – exhibit an inverse isotope effect in superconductivity. Namely, the phase with a heavier hydrogen isotope, deuterium, has a higher critical temperature. Hydrides and deuterides of palladium have intensively been studied both experimentally and theoretically, but the origin of the isotope effect has not been established with certainty. The commonly accepted explanation is that the effect is likely to be due to the strong anharmonicity of the optical hydrogen vibrations, which was considered to be responsible for the large deviation of the ratio of the fundamental optical frequencies ω H /ω D = 1.51 from the harmonic value $\sqrt{2}$ ≈ 1.41. In the present paper, powder samples of MoH 1.1(1) and MoD 1.07(3) were synthesized under a hydrogen / deuterium pressure of several gigapascals and studied by inelastic neutron scattering (INS) at ambient pressure and T = 10 K. The INS study demonstrated that optical vibrations of H atoms in MoH 1.1 and D atoms in MoD 1.07 are harmonic and the ratio of fundamental optical frequencies ω H /ω D = 1.44 is close to the harmonic value $\sqrt{2}$ ≈ 1.41. This shows that anharmonicity is not a necessary condition for the presence of the inverse isotope effect. The MoD 1.07 sample was additionally studied by neutron diffraction (ND) at ambient pressure and T = 100 K. In agreement with previous ND results for MoH 1.2 , the ND study of MoD 1.07 showed that deuterium atoms occupied almost all octahedral interstitial sites in its hexagonal close-packed metal lattice and formed a NiAs-type crystal structure with the composition close to MoD. The overstoichiometric composition MoD 1.07 of the deuteride is likely to result from a small fraction D/Mo ~ 0.07 of deuterium atoms partially occupying the tetrahedral interstices.

36 MATERIALS SCIENCE↗

Neutron vibrational spectroscopic evidence for short H∙∙∙H contacts in the RNiInH 1.4; 1.6 (R = Ce, La) metal hydride

Intermetallic metal hydrides are critical materials for hydrogen storage applications, however, metal hydrides with greater storage capacities are still needed. Within metal hydrides, the volumetric storage capacities are limited by the number of hydrogen-accommodating interstitial sites which can be simultaneously occupied given a minimum hydride nearest-neighbor distance of ~2.1 A, according to the Switendick-Westlake criterion. To date, violations of this criterion are rare. Perhaps the most well studied compounds violating this criterion are the RNiInHx compounds (R = Ce, La, Nd). Previous neutron diffraction studies on the deuterated species revealed the presence of Ni-D∙∙∙D-Ni-D∙∙∙D-Ni chains with anomalously close D∙∙∙D contacts of ~1.6 A. Yet there are no neutron vibrational spectroscopic investigations reported for these atypical hydrides. Here we use neutron vibrational spectroscopy (NVS) measurements to probe the hydrogen dynamics in LaNiInHx (x = 0.67, 1.6) and CeNiInH 1.4 . For x > 0.67, the presence of close H...H contacts yields two related features in the vibrational spectrum centered near ~90 meV corresponding to the oscillations of paired H atoms simultaneously occupying neighboring R 3 Ni tetrahedra. Notably, these features are energetically distinct from comparable vibrational motions for "unpaired" H atoms when x = 0.67. To compare, we also present powder neutron diffraction and NVS measurements for the newly characterized, chemically similar Sn compounds CeNiSnH, CeNiSnH 2 , and CeNiSnD 2 . These compounds also contain R 3 Ni tetrahedra, however, the H-occupied tetrahedra are well separated from each other with the closest H∙∙∙H distances exceeding 2.1 A, and the Switendick-Westlake criterion is not violated. Consequently, the spectral signature of the close H∙∙∙H contacts is absent in these hydrides.

08 HYDROGEN↗

Identification and quantification of distinct active sites in Hf-Beta zeolites for transfer hydrogenation catalysis

Despite the significant progress made in characterizing different framework heteroatom sites that exist in Lewis acidic zeolites with probe molecule adsorption and spectroscopy, methods to reliably quantify site counts remain indefinite and have been primarily limited to Sn and Ti Lewis acid sites. Here, methods to quantify framework Lewis acidic Hf 4+ sites in zeolite Beta (Hf-Beta) with two Lewis base titrants (pyridine, deuterated acetonitrile) were developed using infrared (IR) spectroscopy. Lewis acid site counts for Hf-Beta zeolites were validated by measuring integrated molar extinction coefficients (IMECs; ε, cm μmol –1 ) on Sn-Beta zeolites using identical Lewis base titrants to benchmark site counts with established literature procedures to quantify Lewis acid sites in Beta zeolites from IR spectra. Highlighting the importance of benchmarking active site counts against well-established experimental protocols, IMECs of CD 3 CN bound to open (ε(Sn; 2316 cm –1 ): 1.80 ± 0.25) and closed (ε(Sn; 2308 cm –1 ): 3.76 ± 0.33) Sn sites were ~1.8x larger than those previously reported while total Lewis acid site counts agreed with those measured by pyridine (ε(Sn; 1451 cm –1 ): 1.58 ± 0.16) on six different Sn-Beta zeolites. IMECs measured for IR peaks reflecting pyridine bound to Lewis acidic Hf sites (ε(Hf; 1448 cm –1 ): 1.54 ± 0.21) and CD 3 CN bound to open (ε(Hf; 2313 cm –1 ): 2.40 ± 0.22) and closed (ε(Hf; 2307 cm –1 ): 3.55 ± 0.41) Hf sites, gave similar counts for the total number of Lewis acidic sites across six Hf-Beta zeolites (Si/Hf = 100–413). Consistent with previous reports with Sn-Beta catalysts where open Sn sites are responsible for catalytic turnover, apparent first and zero-order MPVO rate constants (0.01–1 M cyclohexanone in 2-butanol; per total Hf, 373 K) correlated with the total number of open Hf sites, per total Hf, but not with the total number of closed Hf sites or total Lewis acid site counts. Measured initial MPVO rates (0.1 M cyclohexanone in 2-butanol, per open Hf, 373 K) were ~25x higher on hydrophobic Hf-Beta-F than on hydrophilic Hf-Beta-OH zeolites. Overall, the apparent first-order MPVO rate constants (2-butanol solvent, per open Hf, 373 K) were ~6x higher on Hf-Beta-F than on Hf-Beta-OH zeolites. The characterization methods reported here enable normalization of MPVO turnover rates on Sn- and Hf-Beta zeolites by their number of open sites. Finally, this enables performing quantitative rate comparisons across Lewis acid zeolites of varying active site identity, solvation, and pore topology used in liquid-phase catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Methane generation from low-maturity coals and shale source rocks at low temperatures (80–120 °C) over 14–38 months

This study contributes long-term (14 to 38 months) experimental evidence for geocatalytically mediated methanogenesis in immature to early mature shale and coal source rocks at temperatures from 80 to 120 °C. Borosilicate glass tubes with pre-outgassed coal and shale source rock chips and water were sealed under vacuum, sterilized, heated isothermally, and finally opened in connection with a vacuum line where headspace gases methane (CH 4 ) and carbon dioxide (CO 2 ) were collected. The possibility of admitting pre-existing CH 4 from closed pores into product gases during heating experiments was evaluated by comparative ball milling of original and heated rock chips, followed by quantitation of released gases with a novel closed-circuit laser-based SARAD RTM2200 gas detector system with sub-µmol sensitivity. The yields of produced CH 4 from individual source rocks were corrected by subtracting the amounts of pre-existing CH 4 from formerly closed pores in original source rocks that had leaked during long-term heating. Different shales and coals express contrasting propensities to geocatalytically generate CH 4 and CO 2 , with CH 4 yields ranging from 0.1 to 5.5 µmol g-1 total organic carbon (TOC). CH 4 yields from two petrographically different samples of Springfield Coal with comparable thermal maturity suggest that liptinite expresses a far higher propensity for methanogenesis, but liberates less CO 2 than vitrinite. Shale from the Second White Specks Formation generated approximately 10 times more CH 4 than New Albany Shale per g of TOC, further suggesting complex controls on CH 4 generation during catalytic methanogenesis. Higher temperature can enhance the activities of catalytic methanogenesis. Here, the extrapolation of laboratory-based reaction rates to natural conditions in organic-rich buried sediments suggests that geocatalytic methanogenesis can be fast enough in some source rocks to generate economically sizeable gas plays from immature to early mature source rocks over geologic time.

03 NATURAL GAS↗

Hydrodynamics and Load Shedding Behavior of a Variable-Geometry Oscillating Surge Wave Energy Converter (OSWEC)

In order to improve their long-term viability, wave energy converters (WECs) need to be able to shed loads when a threshold wave condition is exceeded. As shown by Tom et al. (2016) [1], provision of adjustable flaps within the body of an oscillating surge wave energy converter (OSWEC) allows wave energy to pass through the device. A control system may then be able to open and close the flaps when waves approaching the device exceed preset thresholds. The variable-geometry OSWEC (VG-OSWEC) concept studied in this paper is a bottom-hinged, rectangular wave paddle with five flaps of elliptical cross-section embedded into the face of the paddle. System ID tests were conducted on this VG-OSWEC device at a 1:14 scale in a wave basin. Free decay tests showed that the damping was distinctly nonlinear when the flaps were fully open, and the natural frequency increased by 40% when compared with the flaps in a fully closed configuration. Tests with regular wave conditions were used to develop the response amplitude operator for the rotational motion about the hinge. These response amplitude operator results when compared with numerical simulations run using WEC-Sim/WAMIT and ANSYS AQWA, show strong agreement with the flap open and closed conditions. The regular-wave condition measurements also show that the wave excitation moment about the hinge was reduced by up to 60% when the flaps were fully open. The experiments serve to demonstrate the potential of the variable geometry design to shed loads and survive harsh ocean environments.

load shedding↗