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At least 1,711 records · Page 95

Evaluation of a concerted vs. sequential oxygen activation mechanism in α-ketoglutarate–dependent nonheme ferrous enzymes

Determining the requirements for efficient oxygen (O 2 ) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)–dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O 2 ) and a sequential mechanism (cofactor binding and reaction with O 2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Interestingly, spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the Fe II ), αKG binding to Fe II -DAOCS results in ~45% five-coordinate sites that selectively react with O 2 relative to the remaining six-coordinate sites. However, this reaction produces an Fe III species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to Fe II -DAOCS produces five-coordinate sites that rapidly react with O 2 to form an Fe IV =O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reaction mechanism for atmospheric pressure plasma treatment of cysteine in solution

Mechanisms for the cold atmospheric plasma (CAP) treatment of cells in solution are needed for more optimum design of plasma devices for wound healing, cancer treatment, and bacterial inactivation. However, the complexity of organic molecules on cell membranes makes understanding mechanisms that result in modifications (i.e. oxidation) of such compounds difficult. As a surrogate to these systems, a reaction mechanism for the oxidation of cysteine in CAP activated water was developed and implemented in a 0-dimensional (plug-flow) global plasma chemistry model with the capability of addressing plasma-liquid interactions. Reaction rate coefficients for organic reactions in water were estimated based on available data in the literature or by analogy to gas-phase reactions. The mechanism was validated by comparison to experimental mass-spectrometry data for COST-jets sustained in He/O 2 , He/H 2 O and He/N 2 /O 2 mixtures treating cysteine in water. Results from the model were used to determine the consequences of changing COST-jet operating parameters, such as distance from the substrate and inlet gas composition, on cysteine oxidation product formation. Results indicate that operating parameters can be adjusted to select for desired cysteine oxidation products, including nitrosylated products.

60 APPLIED LIFE SCIENCES↗

Aging studies on chemical vapor deposition and mechanically exfoliated molybdenum disulfide flakes heated in ambient air

The structural integrity of atomically thin two-dimensional molybdenum disulfide (MoS 2 ) is crucial for high-temperature applications, including nanoelectronics and optoelectronics. This study explores the structural stability and electrical performance, under extended thermal exposure in air, of MoS 2 flakes synthesized via chemical vapor deposition (CVD) and mechanical exfoliation. The MoS 2 flakes, both CVD-grown and mechanically exfoliated, were subjected to heating at 200 °C with a relative humidity of 60(±5)% for a prolonged period and investigated with atomic force microscopy and Raman spectroscopy. This study shows that CVD-grown flakes developed noticeable cracks after prolonged heating, whereas mechanically exfoliated flakes mostly retained their structural integrity. Also, both types of flakes showed a decrease in layer thickness and lateral size over time, with mechanically exfoliated flakes exhibiting a comparatively smaller reduction in substrate coverage area. In addition, MoS 2 -based two-terminal devices were subjected to heating at 150 °C for approximately 1100 h, and their electrical characterization revealed a steady rise in current during constant voltage (5 V) conditions. This study enhances our understanding of MoS 2 stability and provides guidance for improving the reliability of MoS 2 -based devices in high-temperature electronic applications.

2D materials↗

Electronic structure and mechanical properties of crystalline precipitate phases M 23 C 6 (M=Cr, W, Mo, Fe) in Ni-based superalloys

The presence of precipitate phases M 23 C 6 (M=Cr, Fe, Mo, or W) plays a significant role in the mechanical strength of Ni-based superalloys. The crystal structure of these complex carbides consists of 116 atoms in the cubic cell of an fcc lattice. Here we report the investigation of the electronic structure, interatomic bonding and mechanical properties for four binary phases of M 23 C 6 , and M 23 N 6 , and six ternary phases of M1 23–x M2 x C 6 . Based on the results of our comprehensive calculations and the evaluation of a quantum mechanical metric called the total bond order density (TBOD), we conclude that Fe tends to make the intermetallic structure less stable whereas W makes the crystal more compressible. We trace the root of these observations to the size of the metal ions and the complex interatomic bonding between C atoms and the metal d electrons. In addition, we correlate the TBOD with calculated mechanical properties leading to confirmation that Cr 23 C 6 is the most stable precipitate phase with superior overall physical properties. On the other hand, replacing C with N in these crystals does not result in discernable differences in their properties. Furthermore, our detailed investigation sheds much light on the use of carbides precipitates as a stabilization strategy for Ni-based superalloys.

36 MATERIALS SCIENCE↗

Emergent quantum mechanics at the boundary of a local classical lattice model

We formulate a model in which quantum mechanics emerges from classical mechanics. Given a local Hamiltonian H acting on n qubits, we define a local classical model with an additional spatial dimension whose boundary dynamics is approximately—but to arbitrary precision—described by Schrödinger's equation and H. The bulk consists of a lattice of classical bits that propagate towards the boundary through a circuit of stochastic matrices. The bits reaching the boundary are governed by a probability distribution whose deviation from the uniform distribution can be interpreted as the quantum-mechanical wave function. Bell nonlocality is achieved because information can move through the bulk much faster than the boundary speed of light. Finally, we analytically estimate how much the model deviates from quantum mechanics, and we validate these estimates using computer simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Self-consistent feedback mechanism for the sudden viscous dissipation of finite-Mach-number compressing turbulence

Previous work [Davidovits and Fisch, Phys. Rev. Lett. 116, 105004 (2016)] demonstrated that the compression of a turbulent field can lead to a sudden viscous dissipation of turbulent kinetic energy (TKE), and that paper suggested this mechanism could potentially be used to design new fast-ignition schemes for inertial confinement fusion (ICF). We expand on previous work here by accounting for finite Mach numbers, rather than relying on a zero-Mach-limit assumption as previously done. The finite-Mach-number formulation is necessary to capture a self-consistent feedback mechanism in which dissipated TKE increases the temperature of the system, which in turn modifies the viscosity and thus the TKE dissipation itself. Direct numerical simulations with a tenth-order accurate Padé scheme were carried out to analyze this self-consistent feedback loop for compressing turbulence. Results show that, for finite Mach numbers, the sudden viscous dissipation of TKE still occurs, for both the solenoidal and dilatational turbulent fields. As the domain is compressed, oscillations in dilatational TKE are encountered due to the highly oscillatory nature of the pressure dilatation. An analysis of the source terms for the internal energy shows that the mechanical-work term dominates the viscous turbulent dissipation. As a result, the effect of the suddenly dissipated TKE on temperature is minimal for the Mach numbers tested. Moreover, an analytical expression is derived that confirms the dissipated TKE does not significantly alter the temperature evolution for low Mach numbers, regardless of compression speed. The self-consistent feedback mechanism is thus quite weak for subsonic turbulence, which could limit its applicability for ICF.

42 ENGINEERING↗

Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

X-ray crystallographic structures of four p53 core-domain variants were determined in order to gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53. To gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53, X-ray crystallographic structures of four p53 core-domain variants were determined. These include an oncogenic mutant, V157F, two single-site suppressor mutants, N235K and N239Y, and the rescued cancer mutant V157F/N235K/N239Y. The V157F mutation substitutes a smaller hydrophobic valine with a larger hydrophobic phenylalanine within strand S4 of the hydrophobic core. The structure of this cancer mutant shows no gross structural changes in the overall fold of the p53 core domain, only minor rearrangements of side chains within the hydrophobic core of the protein. Based on biochemical analysis, these small local perturbations induce instability in the protein, increasing the free energy by 3.6 kcal mol{sup −1} (15.1 kJ mol{sup −1}). Further biochemical evidence shows that each suppressor mutation, N235K or N239Y, acts individually to restore thermodynamic stability to V157F and that both together are more effective than either alone. All rescued mutants were found to have wild-type DNA-binding activity when assessed at a permissive temperature, thus pointing to thermodynamic stability as the critical underlying variable. Interestingly, thermodynamic analysis shows that while N239Y demonstrates stabilization of the wild-type p53 core domain, N235K does not. These observations suggest distinct structural mechanisms of rescue. A new salt bridge between Lys235 and Glu198, found in both the N235K and rescued cancer mutant structures, suggests a rescue mechanism that relies on stabilizing the β-sandwich scaffold. On the other hand, the substitution N239Y creates an advantageous hydrophobic contact between the aromatic ring of this tyrosine and the adjacent Leu137. Surprisingly, the rescued cancer mutant shows much larger structural deviations than the cancer mutant alone when compared with wild-type p53. These suppressor mutations appear to rescue p53 function by creating novel intradomain interactions that stabilize the core domain, allowing compensation for the destabilizing V157F mutation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A prediction of the thermodynamic, thermophysical, and mechanical properties of CrTaO 4 from first principles

It is reported that the self-forming CrTaO 4 oxide scale can protect refractory high-entropy alloys from oxidation, superior to Cr 2 O 3 . In this paper, the phase stability, mechanical, and thermal properties of three polymorphous phases of CrTaO 4 are systematically investigated from first-principles density functional theory calculations. The mechanical properties predicted using the strain–energy methods indicated that all three phases are mechanically stable. The temperature dependence of elastic constants and polycrystalline moduli of three phases demonstrated the thermal softening as temperature increase. The Helmholtz-free energies as a function of volume and temperature are derived from phonon dispersions within the quasi-harmonic approximation at six strained volumes. The calculated apparent bulk coefficients of thermal expansion of these three phases are evaluated, the highest value approximately 13.4× 10 –6 K –1 within a temperature range of 500–2000 K for the rutile I4 1 md phase. The lattice thermal conductivity calculated by the Debye–Callaway model suggested that the rutile type I4 1 md phase has the lowest value of approximately 2.1 W/m/K at 1800 K. The other two phases, C2/m and P2/c, exhibit higher values due to relatively lower Grüneisen parameters and larger phonon velocities. The melting point of CrTaO 4 is predicted to be between 1975 and 2449 K using ab initio molecular dynamics simulations. Finally, this work provides a comprehensive theoretical understanding of the thermodynamic, mechanical, and thermal properties for the new material CrTaO 4 and serves as an example of a viable computational design strategy for improved oxidation resistance of refractory alloys at high temperatures.

36 MATERIALS SCIENCE↗

Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo

The initial free expansion of the embryo within a seed is at some point inhibited by its contact with the testa, resulting in its formation of folds and borders. Although less obvious, mechanical forces appear to trigger and accelerate seed maturation. However, the mechanistic basis for this effect remains unclear. Manipulation of the mechanical constraints affecting either the in vivo or in vitro growth of oilseed rape embryos was combined with analytical approaches, including magnetic resonance imaging and computer graphic reconstruction, immunolabelling, flow cytometry, transcriptomic, proteomic, lipidomic and metabolomic profiling. Our data implied that, in vivo, the imposition of mechanical restraints impeded the expansion of testa and endosperm, resulting in the embryo's deformation. An acceleration in embryonic development was implied by the cessation of cell proliferation and the stimulation of lipid and protein storage, characteristic of embryo maturation. The underlying molecular signature included elements of cell cycle control, reactive oxygen species metabolism and transcriptional reprogramming, along with allosteric control of glycolytic flux. Constricting the space allowed for the expansion of in vitro grown embryos induced a similar response. The conclusion is that the imposition of mechanical constraints over the growth of the developing oilseed rape embryo provides an important trigger for its maturation.

59 BASIC BIOLOGICAL SCIENCES↗

A Simple, Scalable Large Deformation Solid Mechanics Implementation in the MOOSE Framework

This article describes a large deformation solid mechanics solver implemented as part of the freely available and open source MOOSE finite element simulation framework. The article documents the choices made in developing the solid mechanics framework and describes novel formulations for the gradient operator and constitutive modeling framework made to simplify implementations of different coordinate systems, stabilized gradient operators, and different constitutive model inputs and outputs. In the process, the article describes a new formulation that casts objective integration of the Cauchy stress as a linear transformation of the small stress rate. Finally, the article presents key implementation details and examines the parallel efficiency of the solid mechanics solver implemented in MOOSE. The implementation retains a good weak scaling efficiency beyond 1,000 parallel processes. The article includes a discussion of the factors limiting the parallel efficiency of implicit, large deformation solid mechanics codes on current high-performance computers, with the main current limitation being the scalability of the algebraic multigrid methods used to solve the linearized equilibrium equations.

Applied computing → Computer-aided design↗

Electrochemical-Mechanical Coupling Strongly Affects the Performance of Nanopore, Thin-Film, and Solid-State Batteries

Here, the present study focuses on the electrochemical-mechanical (ECM) coupling effects of a thin-film, solid-state battery with only stiff, ceramic materials, in contrast to prior investigations that focus on individual active material particles or aggregations of particles. We model the impacts of ECM couplings including stress-transport and stress-equilibrium potential on the full-cell performance and potential mechanical failure modes of a thin-film battery conformally deposited in a nanopore scaffold, which is an experimentally achievable device. Model results indicate electrode volume changes due to lithium insertion or removal, along with mechanical boundary conditions, result in stress gradients that alter the lithium-ion flux, reduce lithium concentration gradients, and improve cell rate capability. However, the high stress levels in the cell can also lead to mechanics-related failure such as the separation of cell layers. For the parameter set in this work, stress-transport coupling has a much greater influence on rate capability than stress-potential coupling. Optimization of thin-film batteries to harness the benefits of ECM coupling effects requires leveraging geometric design and material selection. The current work underscores the need for further theoretical and experimental investigation into ECM coupling effects in thin-film batteries to enhance their understanding and design optimization.

25 ENERGY STORAGE↗

Toward an understanding of the increase in enzymatic hydrolysis by mechanical refining

Mechanical refining is a low-capital and well-established technology used in pulp and paper industry to improve fiber bonding for product strength. Refining can also be applied in a biorefinery context to overcome the recalcitrance of pretreated biomass by opening up the biomass structure and modifying substrate properties (e.g., morphology, particle size, porosity, crystallinity), which increases enzyme accessibility to substrate and improves carbohydrate conversion. Although several characterization methods have been used to identify the changes in substrate properties, there is no systematic approach to evaluate the extent of fiber cell wall disruption and what physical properties can explain the improvement in enzymatic digestibility when pretreated lignocellulosic biomass is mechanically refined. This is because the fiber cell wall is complex across multiple scales, including the molecular scale, nano- and meso-scale (microfibril), and microscale (tissue level). A combination of advanced characterization tools is used in this study to better understand the effect of mechanical refining on the meso-scale microfibril assembly and the relationship between those meso-scale modifications and enzymatic hydrolysis. Enzymatic conversion of autohydrolysis sugarcane bagasse was improved from 69.6 to 77.2% (11% relative increase) after applying mechanical refining and an increase in enzymatic digestibility is observed with an increase in refining intensity. Based on a combination of advanced characterizations employed in this study, it was found that the refining action caused fiber size reduction, internal delamination, and increase in pores and swellability. A higher level of delamination and higher increase in porosity, analyzed by TEM and DSC, were clearly demonstrated, which explain the faster digestibility rate during the first 72 h of enzymatic hydrolysis for disc-refined samples when compared to the PFI-refined samples. Additionally, an increased inter-fibrillar distance between cellulose microfibrils at the nano-meso-scale was also revealed by SFG analysis, while no evidence was found for a change in crystalline structure by XRD and solid-state NMR analysis.

09 BIOMASS FUELS↗

Stable Small Animal Mechanical Ventilation for Dynamic Lung Imaging to Support Computational Fluid Dynamics Models

Pulmonary computational fluid dynamics models require 3D images to be acquired over multiple points in the dynamic breathing cycle, with no breath holds or changes in ventilatory mechanics. With small animals, these requirements result in long imaging times ({approx}90 minutes), over which lung mechanics, such as compliance, can gradually change if not carefully monitored and controlled. These changes, caused by derecruitment of parenchymal tissue, are manifested as an upward drift in peak inspiratory pressure or by changes in the pressure waveform and/or lung volume over the course of the experiment. We demonstrate highly repeatable mechanical ventilation in anesthetized rats over a long duration for pulmonary CT imaging throughout the dynamic breathing cycle. We describe significant updates to a basic commercial ventilator that was acquired for these experiments. Key to achieving consistent results was the implementation of periodic deep breaths, or sighs, of extended duration to maintain lung recruitment. In addition, continuous monitoring of breath-to-breath pressure and volume waveforms and long-term trends in peak inspiratory pressure and flow provide diagnostics of changes in breathing mechanics.

59 BASIC BIOLOGICAL SCIENCES↗

Design and Evaluation of a Ring Tension Test Grip for Remote Mechanical Testing of Irradiated Tubular Specimens

Here, the ring tension test (RTT) is a mechanical testing method for determining bulk mechanical behavior in the circumferential or hoop direction for tubular materials. The test is especially useful for testing materials with anisotropic mechanical properties, such as zirconium alloys, which are commonly used as nuclear fuel cladding. Anisotropy requires direction-specific testing to determine the hoop strength. Historically, several RTT methods and grips have been used, each method has its strengths and weaknesses, and, in all cases, the measured strength is subject to uncertainty due to variations of the testing geometry and experimental tolerances. Recent analysis has shown that grips with a hemicylindrical mandrel configuration are recommended as the most robust configuration. The two strictest aspects to be controlled are the ability to determine gage region orientation and closely matching the size of the mandrels to the test specimen. This last requirement is particularly challenging when the dimensions of the specimen vary because of environmental effects such as dimensional changes due to irradiation. This paper presents a new RTT grip designed to incorporate this mandrel shape, hold the gage at the desired orientation, be suitable for remote operation in a hot-cell environment, and be adaptable for different sizes or variations in the specimen size. The general description and the unique design features of the test specimen and grips are given in detail. The performance of the grips in mechanical testing, including in a remote hot-cell environment, is also provided.

42 ENGINEERING↗

Micro-architected material design for mechanical response

Rapid advances in additive manufacturing (AM) have enabled the creation of micro-architected materials—also known as mechanical metamaterials—with unprecedented control over fine-scale geometries and arrangements of multiple material constituents. These “materials” can achieve unique and extraordinary effective mechanical properties through their complex architectures rather than composition alone. A key challenge is to design for these bespoke effective mechanical responses within the constraints of available AM techniques (i.e., given a set of desired effective properties), identify a (often nonunique) micro-architecture and selection of material constituents that achieves them. Two main strategies have emerged. Gradient-based methods use sensitivity analysis to iteratively refine candidate designs, while data-driven methods learn micro-architecture-constituent relationships from existing examples to propose new designs. This article reviews these design approaches for micro-architected materials with tailored mechanical responses that can be fabricated by AM as well as their applications.

Spadaccini, Christopher M [Lawrence Livermore Nati↗

Coupled Geomechanical Modeling to Assess Cap Rock Integrity and Mechanical Fault Stability: Application to Farnsworth Field Unit Project

Abstract The SWP project is located in a mature waterflood undergoing conversion to CO2-WAG operations in the Farnsworth, Texas, USA. Anthropogenic CO2 is sourced from a fertilizer and an ethanol plant. This work utilizes Farnsworth’s full-field, history-matched, compositional hydrodynamic coupled geomechanical model for assessing the impact of stress changes observed through the history matched field life. Production and injection induced stress changes, fault stability and caprock integrity investigations are performed to project the potential for fault reactivation and the loss of caprock integrity under shear failure. A static mechanical earth model (MEM) was constructed for use in transient coupled geomechanical model based on the existing Southwest Regional Partnership (SWP) geological model. The static MEM inherits the stratigraphic and structural features of the geologic model and incorporates additional overburden, underburden, and sideburden formations required to impose mechanical boundary conditions. Mechanical properties were distributed in the 3D MEM through integration of geophysical logs and 3-dimensional seismic elastic inversion properties using a combination of Bayesian and stochastic interpolation methods. These data are further enhanced by lab derived strength and failure criteria for the caprock interval. Additionally, interpreted faults and other geological features were included as part of the static structural framework to fully represent subsurface hydraulic and mechanical systems and appropriately integrate heterogeneity. Two-way coupling of hydrodynamic flow and geomechanical simulations incorporates the Kozeny-Carman relationship for updating permeability and is history matched through primary, secondary (waterflooding) and tertiary (CO2 WAG) recovery periods before performing a twenty year forecast. Two-way simulations are performed to understand the effective stress perturbations imposed by field operations: water injection and the more recent implementation of WAG. Evaluation of Mohr circles with liquid production and field pressure charts as well as slip tendency and distance to failure metrics indicate that neither our faults or cap rock are critically stressed. This paper presents the results of the Farnsworth initial attempts to integrate the seismic driven 3D MEM into coupled hydrodynamic geomechanical history match simulation workflow.

02 PETROLEUM↗

Putting a spin on metamaterials: Mechanical incompatibility as magnetic frustration

Mechanical metamaterials present a promising platform for seemingly impossible mechanics. They often require incompatibility of their elementary building blocks, yet a comprehensive understanding of its role remains elusive. Relying on an analogy to ferromagnetic and antiferromagnetic binary spin interactions, we present a general approach to identify and analyze topological mechanical defects for arbitrary building blocks. We underline differences between two- and three-dimensional metamaterials, and show how topological defects can steer stresses and strains in a controlled and non-trivial manner and can inspire the design of materials with hitherto unknown complex mechanical response.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Statistical Mechanics Modeling of Mesoscale Deformation in Metals

The research under this project focused on a theoretical and computational modeling of dislocation dynamics of mesoscale deformation of metal single crystals. Specifically, the work aimed to implement a continuum statistical theory of dislocations to understand strain hardening and cell structure formation under monotonic loading. These aspects of crystal deformation are manifestations of the evolution of the underlying dislocation system under mechanical loading. The project had three research tasks: 1) Investigating the statistical characteristics of dislocation systems in deformed crystals. 2) Formulating kinetic equations of dislocations and coupling these kinetics equations and crystal mechanics. 3) Computational solution of coupled crystal mechanics and dislocation kinetics. Comparison of dislocation dynamics predictions with experimental results in the area of statistical properties of dislocations and their field was also a part of the proposed effort. In the first research task, the dislocation dynamics simulation method was used to investigate the spatial, orientation, velocity, and temporal statistics of dynamical dislocation systems, and on the use of the results from this investigation to complete the kinetic description of dislocations. The second task focused on completing the formulation of a kinetic theory of dislocations that respects the discrete nature of crystallographic slip and the physics of dislocation motion and dislocation interaction in the crystal. Part of this effort also targeted the theoretical basis for establishing the connection between discrete and continuum representation of dislocations and the analysis of discrete dislocation simulation results within the continuum framework. This part of the research enables the enrichment of the kinetic description with information representing the discrete dislocation systems behavior. The third task focused on the development of physics-inspired numerical methods of solution of the coupled dislocation kinetics and crystal mechanics framework. To a large extent, this task has also been successfully started. We have developed a custom finite-element approach with mesh points being a subset of the underlying crystal structure. When used to predict the evolution of the dislocation system, the planar motion of dislocations is naturally captured for all slip systems, thus minimizing numerical errors and providing simple ways to investigate cross slip and dislocation reactions. Preliminary results in this direction show that we are closer than ever in building a predictive framework for dislocation dynamics and mesoscale plasticity based on the first principles of dislocation dynamics. The rest of the report gives and overview of the research performed under this project and highlights the key results and open questions left for future investigations.

36 MATERIALS SCIENCE↗