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At least 1,135 records · Page 63

FOXM1-activated SIRT4 inhibits NF-κB signaling and NLRP3 inflammasome to alleviate kidney injury and podocyte pyroptosis in diabetic nephropathy

Highlights: • FOXM1 is downregulated in kidney tissues of patients with DN. • Overexpression of FOXM1 alleviates kidney injury in DN modeled mice. • Overexpression of FOXM1 reduces pyroptosis of HG-treated podocytes. • FOXM1 activates SIRT4 to inhibit the NFκB pathway and the NLRP3 inflammasome. • Downregulation of SIRT4 blocks the protective roles of FOXM1 in podocytes and mice. Forkhead box M1 (FOXM1) has been reported to play a protective role against acute kidney injury by driving tubular regeneration. This study aims to probe the function of FOXM1 in diabetic nephropathy (DN) and the molecules involved. FOXM1 was poorly expressed in DN-diseased kidney tissues. A murine model of DN was established, and podocytes cells (MPC5) were treated with high-glucose (HG) for in vitro studies. FOXM1 overexpression improved kidney function and reduced pathological changes in mice, and it increased the expression of the podocyte marker Nephrin in kidney tissues. In vitro, FOXM1 increased viability and reduced pyroptosis of the HG-treated MPC5 cells, and it elevated the expression of the podocyte marker Nephrin whereas reduced the expression of pyroptosis-related NLRP3 inflammasome and cleaved caspase 1. FOXM1 bound to the promoter of sirtuin 4 (SIRT4) to induce transcriptional activation. Downregulation of SIRT4 blocked the protective roles of FOXM1 both in vivo and in vitro. Phosphorylation of nuclear factor-kappa B (NF-κB) in HG-treated cells was suppressed by FOXM1 but restored after SIRT4 inhibition. In conclusion, this study suggested that FOXM1 transcriptionally activates SIRT4 and inhibits NF-κB signaling and the NLRP3 inflammasome to alleviate kidney injury and podocyte pyroptosis in DN.

60 APPLIED LIFE SCIENCES↗

Single cell RNA sequencing reveals shifts in cell maturity and function of endogenous and infiltrating cell types in response to acute intervertebral disc injury

Intervertebral disc (IVD) degeneration contributes to disabling back pain. Degeneration can be initiated by injury and progressively leads to an irreversible loss of cells and function. IVD function restoration through cell replacement therapies have had limited success due to knowledge gaps in the critical cell populations important for repair. Here, in this study, we used single cell RNA sequencing to identify the transcriptional changes of IVD resident and infiltrating cell populations from Control and Injured coccygeal IVDs extracted from 12-week-old female C57BL/6J mice 7 days post injury. Clustering, gene ontology, and pseudotime trajectory analyses determined transcriptomic divergences with injury, flow cytometry identified they types of infiltrating immune cells, and immunofluorescence was utilized to define mesenchymal stem cell (MSC) localization. We identified 11 distinct clusters that included IVD, immune, vascular cells, and MSCs. Differential gene expression analysis determined that Outer Annulus Fibrosus, Neutrophils, Saa2-High MSCs, Macrophages, and Krt18 + Nucleus Pulposus (NP) cells were the major drivers of transcriptomic differences between Control and Injured cells. Gene ontology revealed that the most upregulated biological pathways were angiogenesis and T cell-related while wound healing and ECM regulation were downregulated. Pseudotime trajectory analyses revealed that IVD injury directed cells towards increased differentiation in all clusters, except for Krt18 + NP cells which remained in a less mature cell state. Saa2-High and Grem1-High MSCs populations shifted towards more differentiated IVD cells profiles with injury and localized distinctly within the IVD. This study revealed novel MSC populations with the potential to be leveraged for future IVD repair studies.

Cartilage↗

Dynamics and bifurcations of laminar annular swirling and non-swirling jets

This paper presents bifurcation analyses characterising the nonlinear dynamics of fully developed laminar annular jets with respect to the centrebody diameter ${ {d}}$ , Reynolds number ${ {Re}}$ , and swirl ratio ${ {S}}$ . Similar flows appear in numerous applications and feature a vibrant range of topological and dynamical characteristics associated with phenomena including shear layer separation and vortex breakdown. Our results begin by describing the non-monotonic evolution of the axisymmetric jet's steady topology under varying ${ {S}}$ . In accord with earlier reports, the jet progresses through a sequence of wake, breakdown and wall jet regimes in a qualitatively similar manner across a wide span of ${ {d}}$ and ${ {Re}}$ values. In the wake regime, the non-swirling jet bifurcates to a plane-symmetric, but not axisymmetric, steady flow pattern beyond a ${ {d}}$ -dependent critical ${ {Re}}$ value. With further increase in ${ {Re}}$ , the steady non-swirling jet destabilises subsequently via multiple distinct Hopf bifurcations. Introducing ${ {S}}>0$ to the jet also induces unsteadiness by twisting the singly azimuthally periodic ( $|m|=1$ ) asymmetric wake structure and causing it to precess periodically in time about the central axis. Intermediate swirl stabilises this unsteady dynamics and restores the jet's axisymmetry. This stabilising effect is then reversed in the breakdown regime at higher ${ {S}}$ , where a variety of different $|m|=1$ and $|m|=2$ instabilities bifurcate from the steady flow as ${ {S}}$ is increased. Several instances of hysteresis and subcritical behaviour are reported and discussed, including one that manifests precessing vortex core oscillations.

Douglas, Christopher M. (ORCID:0000000259683315)↗

Floquet stability analyses of stratified oscillating boundary layers on adiabatic slopes

The presence of a no-slip, impermeable, adiabatic, sloped boundary in an otherwise quiescent, stably stratified, Boussinesq flow generates baroclinic vorticity within a diffusive boundary layer. Such conditions are typical of the oscillating boundary layers on adiabatic abyssal slopes, sloped lake bathymetry and sloped coastal bathymetry in the absence of high-wavenumber internal waves, mean flows, far-field turbulence on larger scales, and resonant tidal–bathymetric interaction. We investigate the linear stability of the oscillating flow within non-dimensional parameter space typical of the $M_2$ tide and hydraulically smooth, middle-latitude abyssal slopes through Floquet linear stability analysis. The flow dynamics depends on three non-dimensional variables: the Reynolds number for Stokes’ second problem, the Prandtl number, and a frequency ratio that accounts for the resonance conditions ($C$, criticality) of the buoyant restoring force and the tidal forcing. The Floquet analysis results suggest that oscillating laminar boundary layers on adiabatic abyssal slopes are increasingly unstable as Reynolds number, criticality parameter and/or spanwise disturbance wavenumber are increased. We also show that the two-dimensional Floquet linear instability necessarily generates three-dimensional baroclinic vorticity, which suggests that the evolution of the gravitational instabilities may be nonlinear as $t→∞$.

42 ENGINEERING↗

Koopman wavefunctions and Clebsch variables in Vlasov–Maxwell kinetic theory

Motivated by recent discussions on the possible role of quantum computation in plasma simulations, here, we present different approaches to Koopman's Hilbert-space formulation of classical mechanics in the context of Vlasov–Maxwell kinetic theory. The celebrated Koopman–von Neumann construction is provided with two different Hamiltonian structures: one is canonical and recovers the usual Clebsch representation of the Vlasov density, the other is non-canonical and appears to overcome certain issues emerging in the canonical formalism. Furthermore, the canonical structure is restored for a variant of the Koopman–von Neumann construction that carries a different phase dynamics. Going back to van Hove's prequantum theory, the corresponding Koopman–van Hove equation provides an alternative Clebsch representation which is then coupled to the electromagnetic fields. Finally, the role of gauge transformations in the new context is discussed in detail.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Halide Ion Migration in Perovskite Nanocrystals and Nanostructures

The optical and electronic properties of metal halide perovskites provide insight into the operation of solar cells as well as their long-term operational stability. Halide mobility in perovskite films is an important factor influencing solar cell performance. One can visualize halide ion migration through halide exchange between two nanocrystal suspensions or between physically paired films of two different metal halide perovskites. The ability to tune band gap by varying halide ratios (Cl:Br or Br:I) allows the synthesis of mixed halide perovskites with tailored absorption and emission across the entire visible spectrum. Interestingly, mixed halide (e.g., MAPb(Br 0.5 I 0.5 ) 3 ) films undergo phase segregation to form Br-rich and I-rich sites under steady state illumination. Upon halting illumination, segregated phases mix to restore original mixed halide compositions. Introducing multiple cations (Cs, formamidinium) at the A site or alloying with Cl greatly suppresses halide mobilities. Long-term irradiation of MAPb(Br 0.5 I 0.5 ) 3 films also cause expulsion of iodide leaving behind Br-rich phases. Hole trapping at I-rich sites in MAPb(Br 0.5 I 0.5 ) 3 is considered to be an important step in inducing halide mobility in photoirradiated films. Finally, this Account focuses on halide ion migration in nanocrystals and nanostructured films driven by entropy of mixing in dark and phase segregation under light irradiation.

14 SOLAR ENERGY↗

Redox Mechanisms and Migration Tendencies in Earth-Abundant 0.7Li 2 MnO 3 ·0.3LiFeO 2 Cathodes: Coupling Spin-Resolved X-ray Absorption Near Edge and X-ray Absorption Fine Structure Spectroscopies

We report the use of iron 1s3p resonant X-ray emission processes to conduct spin-selective, high-energy resolution fluorescence detected X-ray absorption near-edge spectroscopy (HERFD-XANES) on an iron-containing, lithium- and manganese-rich, fully earth-abundant cathode material, Li 1.3 Mn 0.5 Fe 0.2 O 2 (0.7Li 2 MnO 3 ·0.3LiFeO 2 ). Coupling this technique with conventional Mn K-edge XANES and detailed extended X-ray absorption fine structure (EXAFS) analysis from both the Mn and Fe vantage points, we gain fundamental insights into the redox processes and migration tendencies of transition metals in this cathode material at the bulk level. We show that during the first charge, Fe 3+ undergoes oxidation to form Fe 4+ prior to the activation plateau. Toward the end of activation, a significant fraction of the iron is present as tetrahedral Fe 3+ . This observation reveals that iron migration from octahedral to tetrahedral sites and iron reduction are initiated during activation. Upon first discharge from the activated state, a continuous and overlapping reduction of both Fe and Mn is observed, with Fe largely restored back as an octahedrally coordinated Fe 3+ . The manganese local environment gradually changes to a distorted cooperative Jahn–Teller Mn 3+ structure during discharge, with the clear presence of two Mn–O as well as two Mn–Mn correlation distances at 2.0 V. The significant reduction of manganese in the very first discharge is distinctly different from that seen in typical nickel-based lithium-manganese-rich materials but is similar to that observed for pure Li 2 MnO 3 . In conclusion, these findings shed light on key structure–property correlations in the cathode material and point to a causative relationship between the redox mechanisms as well as structural changes endured by the material and relatively poor performance during extended electrochemical cycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intercalation-Induced Amorphization Boosts Aqueous Magnesium-Ion Storage

The design of aqueous battery cathode materials that can store divalent ions with high capacity and satisfactory reversibility is of great technical importance and challenge. Here, we report that divalent Mg 2+ storage is facilitated by an intercalation-induced amorphization of vanadate electrode materials. Electrokinetic analyses and in situ synchrotron X-ray diffraction and absorption spectroscopy collectively demonstrate that vanadate layered materials (Li–V 3 O 8 ) undergo a structural transformation to amorphization induced by Mg 2+ intercalation, and a reversible restoration of crystalline structure upon Mg 2+ deintercalation. Debye scattering simulations suggest that intercalation-induced turbostratic disorder, especially random rotations, translational shifts, oscillatory motions, or varied interlayer spacing of adjacent V–O molecular layers, could be responsible for the observed amorphization. The highly distorted local structure, in turn, facilitates Mg 2+ intercalation across the vanadate electrode materials, responsible for nearly 3/7 of the total Mg 2+ ions intercalated. The study presented reveals an intriguing relationship between ion transport and the reversible amorphization-to-crystallization dynamics it induces, opening a paradigm for designing advanced aqueous battery electrodes.

36 MATERIALS SCIENCE↗

Mechanisms of Polyethylene Terephthalate Pellet Fragmentation into Nanoplastics and Assimilable Carbons by Wastewater Comamonas

Comamonadaceae bacteria are enriched on poly(ethylene terephthalate) (PET) microplastics in wastewaters and urban rivers, but the PET-degrading mechanisms remain unclear. Here, we investigated these mechanisms with Comamonas testosteroniKF-1, a wastewater isolate, by combining microscopy, spectroscopy, proteomics, protein modeling, and genetic engineering. Compared to minor dents on PET films, scanning electron microscopy revealed significant fragmentation of PET pellets, resulting in a 3.5-fold increase in the abundance of small nanoparticles (<100 nm) during 30-day cultivation. Infrared spectroscopy captured primarily hydrolytic cleavage in the fragmented pellet particles. Solution analysis further demonstrated double hydrolysis of a PET oligomer, bis(2-hydroxyethyl) terephthalate, to the bioavailable monomer terephthalate. Supplementation with acetate, a common wastewater co-substrate, promoted cell growth and PET fragmentation. Of the multiple hydrolases encoded in the genome, intracellular proteomics detected only one, which was found in both acetate-only and PET-only conditions. Homology modeling of this hydrolase structure illustrated substrate binding analogous to reported PET hydrolases, despite dissimilar sequences. Mutants lacking this hydrolase gene were incapable of PET oligomer hydrolysis and had a 21% decrease in PET fragmentation; re-insertion of the gene restored both functions. Thus, we have identified constitutive production of a key PET-degrading hydrolase in wastewater Comamonas, which could be exploited for plastic bioconversion.

54 ENVIRONMENTAL SCIENCES↗

High-Field Magnetoelectric and Spin-Phonon Coupling in Multiferroic (NH 4 ) 2 [FeCl 5 ·(H 2 O)]

We combine high field polarization, magneto-infrared spectroscopy, and lattice dynamics calculations with prior magnetization to explore the properties of (NH 4 ) 2 [FeCl 5 ·(H 2 O)]-a type II molecular multiferroic in which the mixing between charge, structure, and magnetism is controlled by intermolecular hydrogen and halogen bonds. Electric polarization is sensitive to the series of field-induced spin reorientations, increasing linearly with the field and reaching a maximum before collapsing to zero across the quasi-collinear to collinear-sinusoidal reorientation due to the restoration of inversion symmetry. Magnetoelectric coupling is on the order of 1.2 ps/m for the P∥c, H∥c configuration between 5 and 25 T at 1.5 K. In this range, the coupling takes place via an orbital hybridization mechanism. Other forms of mixing are active in (NH 4 ) 2 [FeCl 5 ·(H 2 O)] as well. Magneto-infrared spectroscopy reveals that all of the vibrational modes below 600 cm –1 are sensitive to the field-induced transition to the fully saturated magnetic state at 30 T. We analyze these local lattice distortions and use frequency shifts to extract spin-phonon coupling constants for the Fe–O stretch, Fe–OH 2 rock, and NH 4 + libration. Inspection also reveals subtle symmetry breaking of the ammonium counterions across the ferroelectric transition. Here, the coexistence of such varied mixing processes in a platform with intermolecular hydrogen- and halogen-bonding opens the door to greater understanding of multiferroics and magnetoelectrics governed by through-space interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation

Molecular conformer generation (MCG) is an important task in cheminformatics and drug discovery. The ability to efficiently generate low-energy 3D structures can avoid expensive quantum mechanical simulations, leading to accelerated virtual screenings and enhanced structural exploration. Several generative models have been developed for MCG, but many struggle to consistently produce high-quality conformers for meaningful downstream applications. To address these issues, we introduce CoarsenConf, which coarse-grains molecular graphs based on torsional angles and integrates them into an SE(3)-equivariant hierarchical variational autoencoder. Through equivariant coarse-graining, we aggregate the fine-grained atomic coordinates of subgraphs connected via rotatable bonds, creating a variable-length coarse-grained latent representation. Our model uses a novel aggregated attention mechanism to restore fine-grained coordinates from the coarse-grained latent representation, enabling efficient generation of accurate conformers. Furthermore, we evaluate the chemical and biochemical quality of our generated conformers on multiple downstream applications, including property prediction and large-scale oracle-based protein docking. Overall, CoarsenConf generates more accurate conformer ensembles compared to prior generative models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Significance of Energy Conservation in Coupled-Trajectory Approaches to Nonadiabatic Dynamics

Practical methods for simulating photo-induced dynamics of molecules often rely on a trajectory-description of the nuclear dynamics, incorporating approximate electron-nuclear feedback. Through approximating electron–nuclear correlation terms in the exact factorization approach, trajectory-based methods have been derived and successfully applied to the dynamics of a variety of light-induced molecular processes, capturing quantum (de)coherence effects rigorously. These terms account for the coupling among the trajectories, recovering the nonlocal nature of quantum nuclear dynamics that is completely overlooked in traditional independent-trajectory algorithms. Nevertheless, some of the approximations introduced in the derivation of some of these methods do not conserve the total energy. We analyze energy conservation in the coupled trajectory mixed quantum-classical (CTMQC) algorithm and explore the performance of a modified algorithm, CTMQC-E, where some of the terms are redefined to restore energy conservation. Here, a set of molecular models is used as a test, namely, 2-cis-penta-2,4-dienimium cation, bis(methylene) adamantyl radical cation, butatriene cation, uracil radical cation, and neutral pyrazine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Localized Active Space Method with Unitary Selective Coupled Cluster

Here, we introduce a hybrid quantum-classical algorithm, the localized active space unitary selective coupled cluster singles and doubles (LAS-USCCSD) method. Derived from the localized active space unitary coupled cluster (LAS-UCCSD) method, LAS-USCCSD first performs a classical LASSCF calculation, then selectively identifies the most important parameters (cluster amplitudes used to build the multireference UCC ansatz) for restoring interfragment interaction energy using this reduced set of parameters with the variational quantum eigensolver method. We benchmark LAS-USCCSD against LAS-UCCSD by calculating the total energies of (H 2 ) 2 , (H 2 ) 4 , and trans-butadiene, and the magnetic coupling constant for a bimetallic compound [Cr 2 (OH) 3 (NH 3 ) 6 ] 3+ . For these systems, we find that LAS-USCCSD reduces the number of required parameters and thus the circuit depth by at least 1 order of magnitude, an aspect which is important for the practical implementation of multireference hybrid quantum-classical algorithms like LAS-UCCSD on near-term quantum computers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Local Spin Density Approximation Strongly Improved by a Better-Informed Local Scaling of Its Self-Interaction Correction

The Perdew−Zunger self-interaction correction (PZSIC) makes density functional approximations (DFAs) exact for all one-electron densities. However, it overcorrects in manyelectron regions, introducing errors for the uniform-density limit, where uncorrected DFAs are exact. The locally scaled PZSIC (LSIC), based on the iso-orbital indicator zσ [which distinguishes single-orbital and slowly varying density regions and is used with the local spin density approximation (LSDA)], restores the uniform-density limit and significantly improves results for many properties, including chemical reaction barrier heights, atomization energies, and ionization potentials. Yet, LSIC performs poorly for weakly bonded systems, leaving many unbound, due to limitations of its iso-orbital indicator. To correct this, in this work we propose a new local scaling, LSIC-α, based on the iso-orbital indicator ασ (which additionally identifies regions of overlapping density tails). A two-parameter scaling function of ασ is fitted to a subset of the nonbonded appropriate norms for the SCAN and r2SCAN meta- GGAs, and tested on many properties of main-group atoms, molecules, and molecular complexes. LSIC-α greatly improves the interaction energies of weakly bonded systems in the S22 data set while retaining LSIC’s accuracy for other properties. This work shows that the errors of LSDA (and presumably of higher-level DFAs) can be largely but not entirely repaired by a proper “do no harm” self-interaction correction.

Approximation↗

Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors

SARS-CoV-2 propagation under nirmatrelvir and ensitrelvir pressure selects for main protease (MPro) drug-resistant mutations E166V (DRM2), L50F/E166V (DRM3), E166A/L167F (DRM4), and L50F/E166A/L167F (DRM5). DRM2-DRM5 undergoes N-terminal autoprocessing to produce mature MPro with dimer dissociation constants (K dimer ) 2–3 times larger than that of the wildtype. Co-selection of L50F restores catalytic activity of DRM2 and DRM4 from ~10 to 30%, relative to that of the wild-type enzyme, without altering K dimer . Binding affinities and thermodynamic profiles that parallel the drug selection pressure, exhibiting significant decreases in affinity through entropy/enthalpy compensation, were compared with GC373. Reorganization of the active sites due to mutations observed in the inhibitor-free DRM3 and DRM4 structures as compared to MPro WT may account for the reduced binding affinities, although DRM2 and DRM3 complexes with ensitrelvir are almost identical to MPro WT -ensitrelvir. In conclusion, chemical reactivity changes of the mutant active sites due to differences in electrostatic and protein dynamics effects likely contribute to losses in binding affinities.

60 APPLIED LIFE SCIENCES↗

State Preparation of Antisymmetrized Geminal Power on a Quantum Computer without Number Projection

The antisymmetrized geminal power (AGP) is equivalent to the number projected Bardeen–Cooper–Schrieffer (PBCS) wave function. It is also an elementary symmetric polynomial (ESP) state. We generalize previous research on deterministically implementing the Dicke state to a state preparation algorithm for an ESP state, or equivalently AGP, on a quantum computer. Our method is deterministic and has polynomial cost, and it does not rely on number symmetry breaking and restoration. We also show that our circuit is equivalent to a disentangled unitary paired coupled cluster operator and a layer of unitary Jastrow operator acting on a single Slater determinant. Here, the method presented herein highlights the ability of disentangled unitary coupled cluster to capture nontrivial entanglement properties that are hardly accessible with traditional Hartree–Fock based electronic structure methods.

97 MATHEMATICS AND COMPUTING↗

Ion Dissociation Dynamics in an Aqueous Premelting Layer

Using molecular dynamics simulations and methods of importance sampling, we study the thermodynamics and dynamics of sodium chloride in the aqueous premelting layer formed spontaneously at the interface between ice and its vapor. We uncover a hierarchy of time scales that characterize the relaxation dynamics of this system, spanning the picoseconds of ionic motion to the tens or hundreds of nanoseconds associated with fluctuations of the liquid-crystal interface in their presence. We find that ions distort both local interfaces, incurring restoring forces that result in the ions preferentially residing in the middle of the layer. While ion pair dissociation is thermodynamically favorable, these structural and dynamic effects cause its rate to vary by over an order of magnitude through the layer, with a maximum rate significantly depressed from the corresponding bulk value. The solvation environment of ions in the premelting layer is distinct from that in a bulk liquid, being dominated by slow reorganization of water molecules and a water structure intermediate between ice and its melt.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Light Induced Processes in CsPbBr 3 –Au Hybrid Nanocrystals: Electron Transfer and Expulsion of Au

Semiconductor–metal heterostructures such as CsPbBr 3 –Au are useful in photocatalysis. When Au nanoparticles are deposited on the CsPbBr 3 nanocrystal surface, they efficiently quench the photoluminescence of the semiconductor. This process has been studied by femtosecond transient absorption spectroscopy measurements, which indicate that electron transfer to the Au nanoparticles occurs from both hot and relaxed electrons in the conduction band of CsPbBr 3 . The electron transfer rate constant is much larger for the hot electrons compared to the relaxed electrons. Under steady state photoirradiation of CsPbBr 3 –Au heterostructure, the photogenerated electrons from the excited CsPbBr 3 nanocrystals continue to charge the Au nanoparticles. After sufficient irradiation, the gold nanoparticles dissociate from the CsPbBr 3 surface and aggregate into larger size gold nanoparticles. The expulsion of gold nanoparticles restores the original luminescence behavior of CsPbBr 3 nanocrystals. The spectroscopic and morphological studies provide insight into the expulsion of gold nanoparticles in photoirradiated CsPbBr 3 –Au heterostructures.

14 SOLAR ENERGY↗