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At least 361 records · Page 20

A novel framework for elastoplastic behaviour of anisotropic solids

A general framework for developing nonlinear hyperelastic/plastic constitutive laws for anisotropic solids experiencing large strains and strain rates has been developed. The proposed framework does not rely on the “a priori” known strain energy function, but instead introduces a physical decomposition of the material element into seven physically independent stress bearing mechanisms, each of which has a constitutive law in terms of internal moments described by a scalar function of a single variable. Furthermore, the model has been encoded into a combined finite-discrete element method and tested against static geomechanical test data. The numerical validation experiments show the model can reproduce plastic anisotropic behavior in both biaxial and uniaxial loading of a geomaterial.

58 GEOSCIENCES↗

Chapter 4: Physically informed deep learning networks for simulating microstructure evolution of 3D polycrystals

As discussed in the previous chapter, high energy diffraction microscopy (HEDM) is used to study the micromechanical evolution of a material during in situ loading. HEDM experiments have been used to verify crystal plasticity (CP) simulations [119, 91, 90, 120], for experimental planning, material design, and to further analyze experimental results. However, Fast Fourier transform-based CP (CP-FFT) or finite element-based CP (CP-FE) methods are often too slow to be used in real-time during an experiment. CP-FFT is faster than CP-FE simulations due to the absence of meshing, but can still take hours to simulate the response of a single volume depending on the size and number of strain steps [127]. Reducing computation time would create a larger exploration space in planning and design, and enable faster analysis of experimental results and real-time feedback during an experiment. This research expands upon previous works to develop a workflow for predicting the full-field evolution of a 3D polycrystal. The workflow is simplified from previous works to predict only orientation and elastic strain tensors (from which stress tensors are calculated). The network is physically informed through loss functions and network architecture for a more robust model. The orientation predictions are informed about the cubic crystal symmetry of the material by incorporating disorientation and misorientation information into the network architecture and loss. The Von Mises stress is used to enforce the correct stress-strain trends in the strain tensor predictions. Additional total strain steps from the elastic and elastoplastic region are included to better capture the stress-strain evolution at smaller total strain steps. Material and hardening parameters are additional inputs into the networks to further inform the network and to study the network’s ability to predict different materials other than those used for training.

36 MATERIALS SCIENCE↗

Fungal community structure and function shifts with atmospheric nitrogen deposition

Fungal decomposition of soil organic matter depends on soil nitrogen (N) availability. This ecosystem process is being jeopardized by changes in N inputs that have resulted from a tripling of atmospheric N deposition in the last century. Soil fungi are impacted by atmospheric N deposition due to higher N availability, as soils are acidified, or as micronutrients become increasingly limiting. Fungal communities that persist with chronic N deposition may be enriched with traits that enable them to tolerate environmental stress, which may trade-off with traits enabling organic matter decomposition. We hypothesized that fungal communities would respond to N deposition by shifting community composition and functional gene abundances toward those that tolerate stress but are weak decomposers. We sampled soils at seven eastern US hardwood forests where ambient N deposition varied from 3.2 to 12.6 kg N ha -1 year -1 , five of which also have experimental plots where atmospheric N deposition was simulated through fertilizer application treatments (25–50 kg N ha -1 year -1 ). Fungal community and functional responses to fertilizer varied across the ambient N deposition gradient. Fungal biomass and richness increased with simulated N deposition at sites with low ambient deposition and decreased at sites with high ambient deposition. Fungal functional genes involved in hydrolysis of organic matter increased with ambient N deposition while genes involved in oxidation of organic matter decreased. One of four genes involved in generalized abiotic stress tolerance increased with ambient N deposition. In summary, we found that the divergent response to simulated N deposition depended on ambient N deposition levels. Fungal biomass, richness, and oxidative enzyme potential were reduced by N deposition where ambient N deposition was high suggesting fungal communities were pushed beyond an environmental stress threshold. Fungal community structure and function responses to N enrichment depended on ambient N deposition at a regional scale.

59 BASIC BIOLOGICAL SCIENCES↗

De novo transcriptome in roots of switchgrass ( Panicum virgatum L. ) reveals gene expression dynamic and act network under alkaline salt stress

Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

59 BASIC BIOLOGICAL SCIENCES↗

Statistical evaluation of microscale stress conditions leading to void nucleation in the weak shock regime

Here, we investigate the heterogeneity of the stress state driven by anisotropic deformation response at the single crystal level through five statistical volume element (SVE) calculations of polycrystalline BCC tantalum. This work focuses on grain boundaries as a prominent material defect type prone to void nucleation based upon experimental observations of predominantly intergranular void nucleation in this material. The SVEs are constructed to be statistically representative of larger volumes of material and are meshed such that mean and standard deviation of grain size and orientation information is reconstructed. The computational meshes feature hexahedral (brick) elements and smooth conformal grain boundaries where significant stress concentration is known to occur, a tail effect of interest in the extreme events process of dynamic ductile damage. An existing micromechanical crystallographic plasticity model shown to capture the single crystal behavior of BCC tantalum well is used to perform the polycrystal calculations. The model includes representation of the non-Schmid effect of non-planar screw dislocation kinetics in tantalum. A three-dimensional stress state time profile predicted by damage modeling of a flyer plate impact experiment is applied as boundary conditions to each SVE. Resulting grain boundary stress state statistics are strongly non-Gaussian. Significant structural evolution is observed within the compressive hold before unloading into tension in the stress profile. Strong angular dependence of grain boundary traction magnitude with shock direction is observed. Non-Schmid effects continue to suggest their influence on propensity of microstructural defect types to nucleate voids. A general void nucleation criterion is proposed using probability theory. The general framework is specified to polycrystalline BCC tantalum in the weak shock regime to include the SVE calculations and literature molecular dynamics calculations of grain boundary void nucleation strength. Probability density functions (PDFs) are used to describe the interaction between the local stress state heterogeneity and the distributed grain boundary void nucleation strength state. A causation entropy maximization procedure removes the requirement for ad hoc selection of a PDF functional form and provides a rigorous procedure for data-based PDF determination. The resulting physically informed PDF describes the spatial appearance frequency of nucleated voids as a function of applied macroscale pressure. Lower length scale physics are thus packaged in a precise and computationally efficient way to provide computational plasticity insight to macroscale dynamic ductile damage models.

36 MATERIALS SCIENCE↗

A tissue‐resolved, network‐based transcriptomic framework for abiotic stress responses in sorghum

Developing climate‐resilient crops requires a detailed understanding of stress‐induced gene expression dynamics, as maladaptive responses can compromise their productivity and survival. Sorghum, a globally important cereal with exceptional tolerance to multiple abiotic stresses, provides a powerful system for investigating these dynamics. However, how stress type, tissue specificity, and temporal progression jointly shape transcriptomic responses in crops remains poorly understood. Here, we present a comparative, time‐resolved transcriptomic atlas of sorghum responses to drought, heat, and salinity stress across shoot and root tissues. Integrative analyses revealed that tissue specificity is the dominant determinant of abiotic stress‐induced gene reprogramming across all three stresses. Building on these global comparisons, we focused on heat stress, as it elicited the most coherent and pronounced transcriptional and regulatory responses, enabling deeper network‐level interrogation. Co‐expression network analysis identified tissue‐specific modules enriched for phytohormone‐responsive genes, while gene regulatory network (GRN) mapping and cistrome analyses uncovered transcription factors (TFs) controlling key hub genes within these modules. Together, this study provides a foundational transcriptomic and network‐based resource for dissecting the regulatory architecture of abiotic stress responses in sorghum and offers prioritized candidates for future functional validation and engineering of climate‐resilient crops.

abiotic stress↗

Biomarkers of oxidative stress, diet and exercise distinguish soldiers selected and non-selected for special forces training

The metabolomic profiles of Soldiers entering the U.S. Special Forces Assessment and Selection course (SFAS) have not been evaluated. To compare pre-SFAS blood metabolomes of Soldiers selected during SFAS versus those not selected, and explore the relationships between the metabolome, physical performance, and diet quality. Fasted blood samples and food frequency questionnaires were collected from 761 Soldiers prior to entering SFAS to assess metabolomic profiles and diet quality, respectively. Physical performance was assessed throughout SFAS. Between-group differences (False Discovery Rate < 0.05) in 108 metabolites were detected. Selected candidates had higher levels of compounds within xenobiotic, pentose phosphate, and corticosteroid metabolic pathways, while non-selected candidates had higher levels of compounds potentially indicative of oxidative stress (i.e., sphingomyelins, acylcarnitines, glutathione, amino acids). Multiple compounds higher in non-selected versus selected candidates included: 1-carboxyethylphenylalanine; 4-hydroxy-nonenal-glutathione; α-hydroxyisocaproate; hexanoylcarnitine; sphingomyelin and were associated with lower diet quality and worse physical performance. Candidates selected during SFAS had higher pre-SFAS levels of circulating metabolites that were associated with resistance to oxidative stress, higher physical performance and higher diet quality. In contrast, non-selected candidates had higher levels of metabolites potentially indicating elevated oxidative stress. These findings indicate that Soldiers who were selected for continued Special Forces training enter the SFAS course with metabolites associated with healthier diets and better physical performance. Additionally, the non-selected candidates had higher levels of metabolites that may indicate elevated oxidative stress, which could result from poor nutrition, non-functional overreaching/overtraining, or incomplete recovery from previous physical activity.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of fine-scale B2 precipitation on dynamic compression and wear properties in hypo-eutectic Al0.5CoCrFeNi high-entropy alloy

The near equiatomic high-entropy alloys based on Al, Co, Cr, Fe, Ni have provided a novel microstructural template for alloy design. The face-centered cubic (FCC) matrix strengthened by body-centered cubic (BCC) based ordered B2 precipitates can be used to develop a new generation of precipitation strengthened alloys. The present study focuses on an Al0.5CoCrFeNi hypo-eutectic alloy consisting of an as-solidified FCC+B2 microstructure. Guided by solution thermodynamic modeling, this alloy has been isothermally aged for solid-state precipitation of a high fraction of fine-scale intragranular B2 particles. The dynamic compressive strength, hardness, and sliding wear response of the alloy as a function of B2 phase fraction is examined. The flow stress at 0.02% true strain increased from ~ 670 MPa to ~1350 (102%) MPa, the ultimate compressive strength increased from ~1160 MPa to 1500 MPa (20%), and the wear resistance increased more than 5 times with progressively increasing phase fraction of B2 precipitates.

Gwalani, Bharat↗

Mesoscale Modeling Approach for Quantifying Microstructure-Aware Micromechanical Responses in Metal Hydrides

Metal hydrides can undergo significant volume changes upon hydrogen uptake and release, which induce a mechanical response that depends not only on the evolving hydrogen composition but also on the microstructure. We present a comprehensive mesoscale modeling framework based on microelasticity theory to quantify the micromechanical responses of metal hydrides, specifically focusing on a hydrogenating polycrystalline MgH 2x particle within a host material as a model micromechanical system. Utilizing digitally generated realistic microstructures and density-functional-theory-derived parameters, we analyzed highly nonuniform local stress profiles in the polycrystalline hydrides under the clamping force exerted by the host during hydrogenation. Our framework also allows us to predict the corresponding strain energy accumulation and mechanical hot spots formation in the hydrides, highlighting their roles in thermodynamic destabilization and mechanical failure, respectively. Through extensive parametric simulations, we further quantified the influence of interface type, crystallinity, grain size, loading ratio, and host stiffness, providing practical guidance for optimizing microstructural design and host material selection. This proposed approach is broadly applicable to micromechanical systems with complex microstructural features involving chemical reaction- and/or phase-transformation-induced deformation.

36 MATERIALS SCIENCE↗

A cytosolic glyoxylate shunt complements the canonical photorespiratory pathway in Arabidopsis

Photorespiration functions in part to support photosynthetic performance, especially under stress such as high light, yet the underlying mechanisms are poorly understood. To identify modulators of photorespiration under high light, we have isolated genetic suppressors of the photorespiratory mutant hpr1 (hydroxypyruvate reductase 1) from Arabidopsis. A suppressor that partially rescues hpr1 is mapped to GLYR1, which encodes the cytosolic glyoxylate reductase 1 that converts glyoxylate to glycolate. Independent glyr1 mutants also partially rescue hpr1 and another photorespiratory mutant, catalase 2. Our genetic, transcriptomic and metabolic profiling analyses together reveal a connection between cytosolic glyoxylate and a non-canonical photorespiratory route mediated by HPR2, which we name the photorespiratory glyoxylate shunt. This shunt complements the canonical photorespiratory pathway and is especially critical when high photorespiratory fluxes are required and when the major photorespiratory pathway is deficient. Our findings support the metabolic flexibility of photorespiration and may help to improve crop performance under stress.

Light stress↗

Exploring Future Storage Options for ATLAS at the BNL/SDCC facility

The ATLAS experiment is expected to deliver an unprecedented amount of scientific data in the High Luminosity(HL-LHC) era. As the demand for disk storage capacity in ATLAS continues to rise steadily, the BNL Scientific Data and Computing Center (SDCC) faces challenges in terms of cost implications for maintaining multiple disk copies and adapting to the coming ATLAS storage requirements. To address these challenges, the SDCC Storage team has undertaken a thorough analysis of the ATLAS experiment's requirements, matching them to suitable storage options and strategies, and has explored alternatives to enhance or replace the current storage solution. This paper aims to present the main challenges encountered while supporting big data experiments such as ATLAS. We describe the experiment's specific requirements and priorities, particularly focusing on the critical storage system characteristics of the high-luminosity run and how the key storage components provided by the Storage team work together: the dCache disk storage system; its archival back-end, HPSS; and its OS-level backend Storage. Specifically, we investigate a novel approach to integrate Lustre and XRootD. In this setup, Lustre serves as backend storage and XRootD acts as an access layer frontend, supporting various grid access protocols. Additionally, we also describe the validation and commissioning tests, including the performance comparison between dCache and XRootd. Furthermore, we provide a performance and cost analysis comparing OpenZFS and LINUX MD RAID, evaluate different storage software stacks, and showcase stress tests conducted to validate Third Party Copy (TPC) functionality.

99 GENERAL AND MISCELLANEOUS↗

The revised elastic field of an edge dislocation

We modify the traditional linear-elastic field of an edge dislocation. The modifications stem from symmetry and energy requirements imposed in terms of embedded (deformed) coordinates. These requirements are satisfied if a line force is added to the dislocation field. The modification to the stress field is expressed by coefficients that are a function only of Poisson’s ratio. Qualitatively, the field of the dislocation is increased in the glide direction and decreased in the climb direction. There are small changes to the field of a screw dislocation that do not entail the addition of a line force. Effects of nonlinearity, anisotropic elasticity, and image forces are briefly considered.

Hirth, J. P.↗

Radial–axial transport coordination enhances sugar translocation in the phloem vasculature of plants

Abstract Understanding mass transport of photosynthates in the phloem of plants is necessary for predicting plant carbon allocation, productivity, and responses to water and thermal stress. Several hypotheses about optimization of phloem structure and function and limitations of phloem transport under drought have been proposed and tested with models and anatomical data. However, the true impact of radial water exchange of phloem conduits with their surroundings on mass transport of photosynthates has not been addressed. Here, the physics of the Munch mechanism of sugar transport is re-evaluated to include local variations in viscosity resulting from the radial water exchange in two dimensions (axial and radial) using transient flow simulations. Model results show an increase in radial water exchange due to a decrease in sap viscosity leading to increased sugar front speed and axial mass transport across a wide range of phloem conduit lengths. This increase is around 40% for active loaders (e.g. crops) and around 20% for passive loaders (e.g. trees). Thus, sugar transport operates more efficiently than predicted by previous models that ignore these two effects. A faster front speed leads to higher phloem resiliency under drought because more sugar can be transported with a smaller pressure gradient.

58 GEOSCIENCES↗

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗

Late-life restoration of mitochondrial function reverses cardiac dysfunction in old mice

Diastolic dysfunction is a prominent feature of cardiac aging in both mice and humans. We show here that 8-week treatment of old mice with the mitochondrial targeted peptide SS-31 (elamipretide) can substantially reverse this deficit. SS-31 normalized the increase in proton leak and reduced mitochondrial ROS in cardiomyocytes from old mice, accompanied by reduced protein oxidation and a shift towards a more reduced protein thiol redox state in old hearts. Improved diastolic function was concordant with increased phosphorylation of cMyBP-C Ser282 but was independent of titin isoform shift. Late-life viral expression of mitochondrial-targeted catalase (mCAT) produced similar functional benefits in old mice and SS-31 did not improve cardiac function of old mCAT mice, implicating normalizing mitochondrial oxidative stress as an overlapping mechanism. These results demonstrate that pre-existing cardiac aging phenotypes can be reversed by targeting mitochondrial dysfunction and implicate mitochondrial energetics and redox signaling as therapeutic targets for cardiac aging.

59 BASIC BIOLOGICAL SCIENCES↗

Kink band and shear band localization in anisotropic perfectly plastic solids

Shear-driven strain localization has been observed in a wide variety of materials and may take the form of shear bands or kink bands. Based on observations of kink bands in plastically anisotropic metallic nanolaminates and single crystal metals, here we posit that, for the specific case of isochoric deformation, the kinematics of kink band formation are indistinguishable from those of plane strain shear band formation. The only distinction between shear bands and kink bands in these systems would then be that kink bands ‘lock up’ at a particular value of material rotation while shear bands may progress to arbitrarily high strains. In order to investigate whether strong material anisotropy is sufficient to arrest shear localization at a geometry that matches the classic kink band geometry, we model the development of a band of simple shear within an anisotropic perfectly plastic material. The resulting analytical model provides the stress state needed to maintain the kinematics of simple shear as a function of material anisotropy, deformation band orientation, and shear strain (or equivalently, material rotation). It is found that plastic anisotropy can promote either kink band or shear band formation depending on the loading orientation. When the deviatoric stress is positive parallel to the plane of anisotropy, shear localization may progress without bound and a shear band is produced. When the deviatoric stress is negative parallel to the plane of anisotropy, shear localization is arrested after a certain material rotation, resulting in a kink band. Examination of the requisite applied stress state during kink band formation provides an explanation for the experimentally-observed ‘lock up’ geometry. Solutions for the band boundary inclination angle are obtained and used to provide bounds on permissible band angles for both shear bands and kink bands.

36 MATERIALS SCIENCE↗

A Novel Design for Improving the Control on the Stainless-Steel Vessel Welding Process for Superconducting Magnets

Stainless steel vessels see widespread use in superconducting magnets for particle accelerator applications. Their function varies in different magnet designs: they always provide the necessary liquid helium containment, but in some cases are also used to provide azimuthal prestress and can also be welded to the magnet end plate to provide additional longitudinal stiffness. A magnet designed with the bladder and key technology does not rely on the structural role of the vessel. They are structurally supported using azimuthally prestressed aluminum shells, and the longitudinal constraint by rods. In this case, the magnet designer would generally like to minimize the interaction between the magnet and the stainless-steel vessel and to minimize the coil stress variation due to the vessel. The stress state in the vessel and in the coil is a function of the circumferential interference, defined as the vessel azimuthal length minus the magnet circumference. The vessel and the magnet azimuthal length machining tolerances are relatively large resulting in significant stress variations in the superconducting coils. Here in this paper we introduce an interference-control shim, which can significantly limit the stress variation of the coils for a given variation of the interference. The effectiveness of the interference-control shim is evaluated numerically on the MQXF, the low-β quadrupole for the High Luminosity LHC.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A Novel Design for Improving the Control on the Stainless-Steel Vessel Welding Process for Superconducting Magnets

Stainless steel vessels see widespread use in superconducting magnets for particle accelerator applications. Their function varies in different magnet designs: they always provide the necessary liquid helium containment, but in some cases are also used to provide azimuthal prestress and can also be welded to the magnet end plate to provide additional longitudinal stiffness. A magnet designed with the bladder and key technology does not rely on the structural role of the vessel. They are structurally supported using azimuthally prestressed aluminum shells, and the longitudinal constraint by rods. In this case, the magnet designer would generally like to minimize the interaction between the magnet and the stainless-steel vessel and to minimize the coil stress variation due to the vessel. The stress state in the vessel and in the coil is a function of the circumferential interference, defined as the vessel azimuthal length minus the magnet circumference. The vessel and the magnet azimuthal length machining tolerances are relatively large resulting in significant stress variations in the superconducting coils. In this paper we introduce an interference control shim, which can significantly limit the stress variation of the coils for a given variation of the interference. The effectiveness of the interference-control shim is evaluated numerically on the MQXF, the low-β quadrupole for the High Luminosity LHC.

43 PARTICLE ACCELERATORS↗