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RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules ( e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

59 BASIC BIOLOGICAL SCIENCES↗

Best Practices for Nuclear Experiment Data Preservation at Idaho National Laboratory: A Guide for Researchers and Reactor Operators

Preserving experimental data is essential for supporting advancements in nuclear science and ensuring the longevity of Idaho National Laboratory's contributions to reactor technology and safety. This report provides a comprehensive guide to best practices for experimental data management and preservation, focusing on standardized data formats, redundancy in storage, metadata documentation, and alignment with international standards. By following these recommendations, experimentalists and reactor operators can enhance the accessibility, reproducibility, and utility of critical datasets for regulatory review, validation computational methods, and future research.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

CUF-Links: Continuous and Ubiquitous FAIRness Linkages for Reproducible Research

Despite much creative work on methods and tools, reproducibility— the ability to repeat the computational steps used to obtain a research result—remains elusive. One reason for these difficulties is that extant tools for capturing research processes, while powerful, often fail to capture vital connections as research projects grow in extent and complexity. We explain here how these interstitial connections can be preserved via simple methods that integrate easily with current work practices to capture basic information about every data product consumed or produced in a project. By thus extending the scope of findable, accessible, interoperable, and reusable (FAIR) data in both time and space to enable the creation of a continuous chain of Continuous and Ubiquitous FAIRness linkages (CUFlinks) from inputs to outputs, such mechanisms can facilitate capture of the provenance linkages that are essential to reproducible research. Herein we give examples of mechanisms that can facilitate the use of these methods, and review how they have been applied in practice.

97 MATHEMATICS AND COMPUTING↗

Superconductor/Ferromagnet Heterostructures: A Platform for Superconducting Spintronics and Quantum Computation

The interplay between superconductivity and ferromagnetism in the superconductor/ferromagnet (SC/FM) heterostructures generates many interesting physical phenomena, including spin-triplet superconductivity, superconducting order parameter oscillation, and topological superconductivity. The unique physical properties make the SC/FM heterostructure as promising platforms for future superconducting spintronics and quantum computation applications. In this article, important research progress of SC/FM heterostructures from superconducting spintronics to quantum computation is reviewed, and it is organized as follows. First, the progress of spin current carriers in SC/FM heterostructures including Bogoliubov quasiparticles, superconducting vortex, and spin-triplet Cooper pairs which might be used for long-range spin transport is discussed. Then, the π Josephson junctions and their application for constructing π qubits are described. Finally, experimental signatures of Majorana states in the SC/FM heterostructures and the theoretically proposed manipulation are briefly reviewed, which could be useful to realize fault-tolerant topological quantum computing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum computation of silicon electronic band structure

Development of quantum architectures during the last decade has inspired hybrid classical–quantum algorithms in physics and quantum chemistry that promise simulations of fermionic systems beyond the capability of modern classical computers, even before the era of quantum computing fully arrives. Strong research efforts have been recently made to obtain minimal depth quantum circuits which could accurately represent chemical systems. Here, we show that unprecedented methods used in quantum chemistry, designed to simulate molecules on quantum processors, can be extended to calculate properties of periodic solids. In particular, we present minimal depth circuits implementing the variational quantum eigensolver algorithm and successfully use it to compute the band structure of silicon on a quantum machine for the first time. We are convinced that the presented quantum experiments performed on cloud-based platforms will stimulate more intense studies towards scalable electronic structure computation of advanced quantum materials.

36 MATERIALS SCIENCE↗

Prepare Ground States of Highly Frustrated Magnetic Clusters on Quantum Computers

Solving challenging problems in physical, chemical, and materials sciences is one of the most promising applications of quantum utility that can be realized on current noisy hardware, considering (i) the direct map (encoding) from the quantum particles and their interactions to the qubits and their entangling gates and (ii) the rapidly improved quantum hardware and advanced error-mitigation techniques. Understanding quantum spin liquid in frustrated magnetic materials is a longstanding challenge in condensed matter physics and the nature of the ground-state phases is highly debated among researchers. Using IBM quantum computers with superconducting qubits, we implemented a variational quantum eigensolver (VQE) algorithm to prepare the ground states of two 12-site cluster approximations of these highly frustrated magnetic materials. The interaction graphs of the two corresponding Hamiltonians are (a) the six-pointed star graph (a unit cell of the kagome lattice) and (b) the cuboctahedral graph (the kagome on a sphere). These are also two instances of Quantum Max Cut problem. With the VQE based on the Hamiltonian variational ansatz acting on a valence bond solid initial trial state, we prepared the ground states and obtained the exact ground energy on simulator and high accuracy on noisy hardware. The deep ansatz necessary to reach the ground state of the cuboctahedral graph indicates that it is a hard instance of Quantum Max Cut.

Wang, Yan↗

Biomanufacturing and Scale-Up: Pathways to Biochemicals, Biofuels, and Biomaterials

Advancing the bioeconomy requires the development of large-scale microbial bioprocesses capable of converting waste carbon streams into biofuels, biochemicals, and biomaterials at industrially relevant scales. While biomanufacturing has been successfully demonstrated at the laboratory scale for a wide range of chemicals, only a few have reached industrial-scale production. This is partly due to the inherent complexity of microbial systems, which rely on living cells with intricate metabolic pathways that are highly sensitive to environmental changes, making large-scale production difficult to optimize and predict. As a result, scaling-up bioprocesses remains a high-stakes challenge that requires deeper exploration. This involves integrating feedstock and microbial selection, upstream and downstream processes, and computational modelling, among other research efforts. Bulk and specialty chemicals derived from biological processes also face competition from fossil-based production routes, which have been refined through decades of technological advancements. While biologically derived molecules may offer more environmentally friendly production pathways than traditional chemical manufacturing, their widespread adoption depends on achieving cost parity-or superiority-relative to fossil-based methods. This emphasizes the importance of holistic research, including techno-economic analyses and life cycle assessments, to ensure both economic viability and environmental sustainability. This editorial and special issue explores state-of-the-art strategies for converting waste carbon sources into valuable products. It discusses how enzymes, single microbes (e.g., extremophiles), and microbiomes (e.g., through division of labor) can be integrated with upstream and downstream process innovations-such as consolidated bioprocessing and in situ product recovery-to improve the efficiency and scalability of biomanufacturing. The editorial further highlights the role of computational modelling in understanding, predicting, and controlling bioprocess performance across scales, and concludes by emphasizing the importance of techno-economic modelling to identify technologies that can move to market.

09 BIOMASS FUELS↗

Solving key challenges in collider physics with foundation models

Foundation models are neural networks that are capable of simultaneously solving many problems. Large language foundation models like ChatGPT have revolutionized many aspects of daily life, but their impact for science is not yet clear. In this paper, we use a new foundation model for hadronic jets to solve three key challenges in collider physics. In particular, we show how experiments can (1) save significant computing power when developing reconstruction algorithms, (2) perform a complete uncertainty quantification for high-dimensional measurements, and (3) search for new physics with model agnostic methods using low-level inputs. In each case, there are significant computational or methodological challenges with current methods that limit the science potential of deep learning algorithms. By solving each problem, we take jet foundation models beyond proof-of-principle studies and into the toolkit of practitioners.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

AdditiveFOAM: A Continuum Multiphysics Code for Additive Manufacturing

AdditiveFOAM is a computational framework that simulates transport phenomena in Additive Manufacturing (AM) processes. It is built on OpenFOAM (Weller et al., 1998), the leading free, open-source software package for computational fluid dynamics (CFD). OpenFOAM offers an extensible platform for solving complex multiphysics problems using state-of-the-art finite volume methods. AdditiveFOAM leverages these capabilities to develop specialized tools aimed at addressing challenges in AM processing. Metal additive manufacturing, also known as metal 3D printing, is an advanced manufacturing technique that creates physical parts from a three-dimensional (3D) digital model by melting metal powder or wire feedstock. A significant area of research in metal AM focuses on process planning to mitigate anomalous features during printing that are deleterious to part performance (e.g., porosity and cracking), as well as controlling localized microstructure and material properties. Given the high costs and substantial time requirements associated with experimental methods for qualifying new materials and processes, there is a compelling incentive for researchers to utilize advanced computational simulations. In this context, AdditiveFOAM offers a simulation framework to better understand undesirable features in printing, thereby enhancing process planning and reducing the reliance on labor-intensive experimental campaigns.

Coleman, John [Oak Ridge National Laboratory (ORNL↗

High-Temperature Gas-Cooled Reactor Research Survey and Overview: Preliminary Data Platform Construction for the Nuclear Energy University Program

Since the U.S. Department of Energy Office of Nuclear Energy initiated the Nuclear Energy University Program (NEUP) in 2009, there are 29 NEUP projects focusing on high-temperature gas-cooled reactor (HTGR) research up to July 2022. The resultant research product, either experimental or computational, were published as final NEUP reports, journal articles and conference proceedings. However, these federally funded products have been scattered and sometimes cannot be easily accessed. To improve access to this valuable HTGR validation data and optimize the return on the significant investment made by the Department of Energy, the Advanced Reactor Technologies (ART) Gas-Cooled Reactor (GCR) program started a survey of completed and ongoing HTGR NEUP projects to develop a public-access database specific for HTGRs applications that can be used to retrieve computational fluid dynamics and system code validation data. This effort will help guide future NEUP-funded research, define new state of the ART Phenomena Identification and Ranking Table (PIRT), and promote the usage of this data in the codes validation matrices. This report provides an overview of the NEUP-funded HTGR-related research projects from Fiscal Year (FY) 2009–2021 and identifies validation knowledge gaps still existing in HTGR thermal-fluid research. A preliminary data platform has been developed for the 29 NEUP projects investigating HTGR thermal hydraulics, including their final reports as well as the available scientific publications. As an ultimate goal for this work, the ART-GCR program will create a central database at Idaho National Laboratory to identify, organize, and store these datasets generated by experimental investigations or computational models, experimental facility descriptions, and publicly-available academic products from the HTGR-related NEUP projects and provide future guidance for the storage and transmission of important project documentations for later NEUP projects as well.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

ERF: Energy Research and Forecasting Model

High performance computing (HPC) architectures have undergone rapid development in recent years. As a result, established software suites face an ever increasing challenge to remain performant on and portable across modern systems. Many of the widely adopted atmospheric modeling codes cannot fully (or in some cases, at all) leverage the acceleration provided by General-Purpose Graphics Processing Units, leaving users of those codes constrained to increasingly limited HPC resources. Energy Research and Forecasting (ERF) is a regional atmospheric modeling code that leverages the latest HPC architectures, whether composed of only Central Processing Units (CPUs) or incorporating GPUs. ERF contains many of the standard discretizations and basic features needed to model general atmospheric dynamics. The modular design of ERF provides a flexible platform for exploring different physics parameterizations and numerical strategies. ERF is built on a state-of-the-art, well-supported, software framework (AMReX) that provides a performance portable interface and ensures ERF's long-term sustainability on next generation computing systems. This paper details the numerical methodology of ERF, presents results for a series of verification/validation cases, and documents ERF's performance on current HPC systems. The roughly 5× speed up of ERF (using GPUs) over Weather Research and Forecasting (CPUs only) for a 3D squall line test case highlights the significance of leveraging GPU acceleration.

17 WIND ENERGY↗

Denial of Service Attack Detection via Differential Analysis of Generalized Entropy Progressions

Denial-of-Service (DoS) attacks are one the most common and consequential cyber attacks in computer networks. While existing research offers a plethora of detection methods, the issue of achieving scalability, a low false positive rate, and high detection accuracy remains open. In this work, we address this problem by developing a differential method based on generalized entropy progression. In this method, named as DoDGE, we continuously fit the line of best fit to the entropy progression of destination addresses and check if the derivative, that is, the slope of this line is less than the negative of the dynamically computed standard deviation of the derivatives. Furthermore, to distinguish from flash events, we leverage the symmetry that when a flash event occurs, the derivative of the entropy progression of source addresses is positive. With this design, we omit the usage of the thresholds and the results with five real-world network traffic datasets confirm that DoDGE outperforms threshold-based DoS attack detection by two orders of magnitude in terms of false positives on average. When compared to ten machine learning (ML) models, DoDGE achieves a balanced accuracy of 99%, while the average balanced accuracy for the ML models is 52%. Moreover, the results show that DoDGE successfully differentiates between a flash event and a DoS attack. Furthermore, since the main computation cost of DoDGE is the entropy computation, which is linear in the volume of the unit-time network flow, uses integer only operations, and works on a small fraction of the total flow, it is lightweight and scalable.

Cybersecurity, wireless communication↗

Livewire Data Platform-A Solution for Energy Efficient Mobility Systems (EEMS) Data Sharing

This presentation is an overview of progress made on the Livewire Data Platform since June 2021. Livewire is a publicly accessible platform for sharing energy efficiency and mobility research data funded by DOE's Vehicle Technologies Office. Core services and platform capabilities of Livewire include: Free, secure data storage; Access management that allows data owners to control who sees their data; Data collection and preservation; Quality characterization; Detailed access and download metrics; and Increased visibility of projects and data.

energy efficiency mobility↗

A general framework for quantifying uncertainty at scale

Abstract In many fields of science, comprehensive and realistic computational models are available nowadays. Often, the respective numerical calculations call for the use of powerful supercomputers, and therefore only a limited number of cases can be investigated explicitly. This prevents straightforward approaches to important tasks like uncertainty quantification and sensitivity analysis. This challenge can be overcome via our recently developed sensitivity-driven dimension-adaptive sparse grid interpolation strategy. The method exploits, via adaptivity, the structure of the underlying model (such as lower intrinsic dimensionality and anisotropic coupling of the uncertain inputs) to enable efficient and accurate uncertainty quantification and sensitivity analysis at scale. Here, we demonstrate the efficiency of this adaptive approach in the context of fusion research, in a realistic, computationally expensive scenario of turbulent transport in a magnetic confinement tokamak device with eight uncertain parameters, reducing the effort by at least two orders of magnitude. In addition, we show that this refinement method intrinsically provides an accurate surrogate model that is nine orders of magnitude cheaper than the high-fidelity model.

Farcaş, Ionuţ-Gabriel (ORCID:0000000238841580)↗

High-Strength, High-Ductility, High Entropy Alloys with High-Efficiency Native Oxide Solar Absorbers for Concentrating Solar Power Systems

This EPSCoR Project has been investigating the synergy between the excellent high-temperature mechanical behavior of FeMnNiAlCr high entropy alloys (HEA) and the high solar absorptance of their native oxides for high efficiency concentrated solar thermal power (CSP) systems working at >700°C. While HEAs have attracted substantial interest in recent years, most investigations have focused on their applications as structural materials rather than functional materials. This EPSCoR project discovered that FeMnNiAlCr HEAs can potentially be applied synergistically as both a structural and functional material for high-efficiency concentrating solar thermal power (CSP) systems working at >700°C. The HEA itself would be used in high-temperature tubing to carry molten salts or supercritical CO 2 , while its surface oxide would act as a high-efficiency solar thermal absorber. With Fe and Mn being the major components in these HEAs (adding up to ~70 at.% of the alloy), these materials are much more cost-effective than the Ni-based superalloys currently being investigated for high-temperature CSP systems. Through this research, these Fe-Mn based HEAs have demonstrated yield strengths 2-3x greater than that of stainless steel at 700°C and a creep lifetime >800 h at 700ºC under a typical CSP tubing mechanical load of 35 MPa. Their Mn-rich surface oxides maintain a high optical-to-thermal conversion efficiency of ~87% under 1000x solar concentration ratio for 20 simulated day-night thermal cycles between 750ºC and room temperature. In preliminary corrosion studies, these HEAs have sustained immersion in unpurified bromide molten salts for 14 days at 750°C with <2% weight loss, in contrast to 70% weight loss from a 316 stainless steel reference. The simultaneous achievement of promising mechanical, optical, and thermochemical properties in this FeMnNiAlCr system opens the door to new applications of HEAs in solar energy harvesting. Partnerships with Ames Laboratory and Oak Ridge National Laboratory (ORNL) also advanced our understanding of the fundamental structure-property relationships through atomic scale material characterization and first-principles computational modeling. The key research results in this project can potentially be extended to other HEAs and their native oxides. In terms of applications, the proposed FeMnNiAlCr HEA/native oxide system could potentially exceed the mechanical and the optical performance of existing tubing and solar coating materials under EERE’s CSP program at lower cost, which also aligns well with the EPSCoR Science and Technology strategies of New Hampshire in boosting the deployment of renewable energy.

14 SOLAR ENERGY↗

AI for Science: Report on the Department of Energy (DOE) Town Halls on Artificial Intelligence (AI) for Science

The report documents the DOE Town Halls held during 2019 at Argonne National Laboratory, Oak Ridge National Laboratory, Lawrence Berkeley National Laboratory, and in Washington, DC. From July to October 2019, the Argonne, Oak Ridge, and Berkeley National Laboratories hosted a series of four town hall meetings attended by more than 1,000 U.S. scientists and engineers. The goal of the town hall series was to examine scientific opportunities in the areas of artificial intelligence (AI), Big Data, and high-performance computing (HPC) in the next decade, and to capture the big ideas, grand challenges, and next steps to realizing these opportunities. In this report and in the Department of Energy (DOE) laboratory community, we use the term “AI for Science” to broadly represent the next generation of methods and scientific opportunities in computing, including the development and application of AI methods (e.g., machine learning, deep learning, statistical methods, data analytics, automated control, and related areas) to build models from data and to use these models alone or in conjunction with simulation and scalable computing to advance scientific research. The AI for Science town hall discussions focused on capturing the transformational uses of AI that employ HPC and/or data analysis, leveraging data sets from HPC simulations or instruments and user facilities, and addressing scientific challenges unique to DOE user facilities and the agency’s wide-ranging fundamental and applied science enterprise.

36 MATERIALS SCIENCE↗

A hybrid finite volume method and smoothed particle hydrodynamics approach for efficient and accurate blast simulations

Modeling strong shock waves in fluids remains a persistent challenge in computational physics. Essential to research efforts in industry and defense, numerous methods have been devised to improve the accuracy and efficiency of shock simulations. A novel, hybrid Finite Volume Method (FVM)-Smoothed Particle Hydrodynamics (SPH) approach is capable of further improving efficiency and retaining accuracy by exploiting the favorable characteristics of each respective method. This hybrid approach is presented for shock capturing in compressible fluids. The Python framework Pyro2 is employed to simulate a coarse FVM mesh, while the Python framework PySPH is utilized to model the fluid in regions with high gradients through SPH particles. The performance of the hybrid FVM-SPH scheme, compared to the individual FVM and SPH methods, is assessed in 1 kt and 10 kt blast simulations. Our results indicate that the hybrid approach offers higher computational efficiency than SPH while preserving its accuracy and characteristics. The hybrid approach had a relative speedup of 11.3x and 22.3x over the FVM and SPH approaches for the 1 kt simulation and a relative speedup of 14.7x and 20.9x over the FVM and SPH approaches for the 10 kt simulation. The hybrid SPH algorithm enables future compressible fluid simulations with more extensive capabilities than grid-based methods alone, presenting potential applications in modeling fluid-structure interactions and solid deformation and fracturing in blast simulations.

Myers, Conner↗

2020 Exascale Computing Project Annual Meeting (Executive Summary Report)

The Exascale Computing Project (ECP) delivers specific applications, software products, and outcomes on DOE computing facilities. Integration across these elements for specific hardware technologies for exascale system instantiations is fundamental to ECP success. The outcome of the ECP is the delivery of a capable exascale computing ecosystem to provide breakthrough solutions addressing our most critical challenges in scientific discovery, energy assurance, economic competitiveness, and national security. This outcome is not a matter of ensuring more powerful computing systems. The ECP is designed to create more valuable and rapid insights from a wide variety of applications (“capable”), which requires a much higher level of inherent efficacy in all methods, software tools, and ECP-enabled computing technologies to be acquired by DOE laboratories (“ecosystem”). The ECP annual meeting provides a unique opportunity for the core technical expertise in the United States focused on achieving this next plateau of computational science and computing performance to engage in direct discussions on project execution. Face-to-face gatherings in technical communities like this are common and needed for the exchange of scientific ideas and technical performance. The ECP annual meeting stands apart from other technical conferences and meetings in the computing community as it is uniquely and solely focused on the execution of the ECP and the integration of technical activities leading to the creation of the exascale computing ecosystem for the future. The direct interaction of key critical technical staff, who are leaders in their respective fields, and the resulting give-and-take between software, applications, and hardware and the technical co-design therein, is unique and essential to the effective execution of the ECP. The first annual meeting was held in Knoxville, Tennessee, January 31 – February 2, 2017 and brought together, for the first time, a diverse collection of researchers from 16 DOE national laboratories as well as university computer and computational science researchers to discuss shared problems and joint solutions for the development of a capable exascale computing ecosystem. These interactions resulted in focused technical plans and an energized community centered on advances for ECP. The second annual meeting was held in Knoxville, Tennessee, February 5–9, 2018. It included 643 individual thought leaders and performers in application development, software research and deployment, and hardware research and integrators, all of whom are part of the multifaceted, billion dollar HPC community. This meeting provided a platform to discuss and disseminate numerous examples where researchers with common goals and synergistic solutions came together for the first time to deliver tangible results. Additionally, at the 2018 meeting, ECP researchers had the opportunity to digest all US HPC vendor R&D product roadmaps pointing to exascale – not only to learn how their research can play a role, but, more importantly, to influence those roadmaps to ensure successful delivery on DOE applications that will contribute to (if not solve) problems of national interest in national security, science, energy, and health, as well as growing security threats. The third annual meeting was held in Houston, Texas, January 14–17, 2019. With a 19% increase in the number of registrations (768 people), and the change in location, the third annual meeting was considered the most impactful of the three at the time. The new website provided a better platform for the dissemination of the content, the new venue as a meeting hotel instead of a conference center facilitated interactions and discussions after event hours, and the addition of an award-winning mobile event conference app (Whova) transformed dramatically the attendee experience at the event. This fourth annual meeting was held in Houston, Texas, February 3-7, 2020. This meeting had an increase in the number of attendees for a total of 824 people registered (782 attendees) and included numerous enhancements based on feedback and lessons learned from previous meetings, some of which are listed here: Improved quality of the sessions, their material and the whole program.; Had more industry participation and addition of external collaborators from overseas.; Published the full agenda earlier to better accommodate attendance and travel plans based on schedule.; Centralized all sessions in one venue.; Provided additional hotels and room blocks for the attendees.; Improved communication with the audience (links, material, directions, notifications, etc.) to go paperless.; Enhanced side meeting scheduling, management and user experience.; Made available additional space and tables for impromptu meetings and side discussions.; Improved IT and A/V solutions for speakers. In addition, our final survey captured the following points as opportunities for improvement in future meetings: consider a different meeting location that is more pedestrian friendly, reduce talks during working meals to allow more collaboration and informal time, adapt the agenda to acknowledge attendees from different timezones, consider recording some of the tutorials and/or sessions to share broadly with the HPC community, have a larger poster room, provide additional power strips, and improve the WiFi.

97 MATHEMATICS AND COMPUTING↗