Coupling of Electrochemistry with Surface Science and Computational Modeling to Understand Nanoparticle Electrocatalysts
For presentation at the 244th ECS Meeting, Gothenburg, Sweden, October 8-12, 2023.
Deng, Xingyi↗
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An Introduction to the E3SM Special Collection: Goals, Science Drivers, Development, and Analysis
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54 ENVIRONMENTAL SCIENCES↗
Learning a general model of single phase flow in complex 3D porous media
Modeling effective transport properties of 3D porous media, such as permeability, at multiple scales is challenging as a result of the combined complexity of the pore structures and fluid physics—in particular, confinement effects which vary across the nanoscale to the microscale. While numerical simulation is possible, the computational cost is prohibitive for realistic domains, which are large and complex. Although machine learning (ML) models have been proposed to circumvent simulation, none so far has simultaneously accounted for heterogeneous 3D structures, fluid confinement effects, and multiple simulation resolutions. By utilizing numerous computer science techniques to improve the scalability of training, we have for the first time developed a general flow model that accounts for the pore-structure and corresponding physical phenomena at scales from Angstrom to the micrometer. Using synthetic computational domains for training, our ML model exhibits strong performance (R 2 = 0.9) when tested on extremely diverse real domains at multiple scales.
36 MATERIALS SCIENCE↗
FleCSI Project
This report discusses the structure of computational science.
99 GENERAL AND MISCELLANEOUS↗
Building a Diverse and Inclusive HPC Community for Mission-Driven Team Science
The U.S. Department of Energy (DOE) has been a long-standing leader in driving advances in science and technology through advanced computing. However, DOE laboratories are currently facing urgent workforce challenges, particularly in terms of underrepresentation from key communities, including people of color, women, persons with disabilities, and first-generation scholars. This paper introduces the work carried out as part of the Exascale Computing Project (ECP) Broadening Participation Initiative, which aims to address workforce challenges through a lens that considers the distinct needs and culture of high-performance computing (HPC). The work focuses on three main efforts: hosting Intro to HPC Bootcamps, expanding the Sustainable Research Pathways (SRP) internship and workforce development program, and establishing an HPC Workforce Development and Retention Action Group. Finally, the paper also highlights various workforce efforts throughout the computational science community and explores opportunities for future work aimed at broadening participation in HPC.
97 MATHEMATICS AND COMPUTING↗
Predictive scale-bridging simulations through active learning
Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh elements. For instance, quantitative predictions of transport in nanoporous media, critical to hydrocarbon extraction from tight shale formations, are impossible without accounting for molecular-level interactions. Similarly, inertial confinement fusion simulations rely on numerical diffusion to simulate molecular effects such as non-local transport and mixing without truly accounting for molecular interactions. With these two disparate applications in mind, we develop a novel capability which uses an active learning approach to optimize the use of local fine-scale simulations for informing coarse-scale hydrodynamics. Our approach addresses three challenges: forecasting continuum coarse-scale trajectory to speculatively execute new fine-scale molecular dynamics calculations, dynamically updating coarse-scale from fine-scale calculations, and quantifying uncertainty in neural network models.
97 MATHEMATICS AND COMPUTING↗
Maximum Kolmogorov-Sinai Entropy Versus Minimum Mixing Time in Markov Chains
We establish a link between the maximization of Kolmogorov Sinai entropy (KSE) and the minimization of the mixing time for general Markov chains. Since the maximisation of KSE is analytical and easier to compute in general than mixing time, this link provides a new faster method to approximate the minimum mixing time dynamics. It could be interesting in computer sciences and statistical physics, for computations that use random walks on graphs that can be represented as Markov chains.
97 MATHEMATICS AND COMPUTING↗
Multiphysics coupling in the Exascale computing project
Multiphysics coupling presents a significant challenge in terms of both computational accuracy and performance. Achieving high performance on coupled simulations can be particularly challenging in a high-performance computing context. The US Department of Energy Exascale Computing Project has the mission to prepare mission-relevant applications for the delivery of the exascale computers starting in 2023. Many of these applications require multiphysics coupling, and the implementations must be performant on exascale hardware. In this special issue we feature six articles performing advanced multiphysics coupling that span the computational science domains in the Exascale Computing Project.
97 MATHEMATICS AND COMPUTING↗
Laboratory Directed Research and Development Program (FY 2019 Annual Summary of Completed Projects)
Oak Ridge National Laboratory (ORNL) is the US Department of Energy’s (DOE’s) largest multiprogram science, technology, and energy laboratory with distinctive capabilities in neutron science, computing, advanced materials, and nuclear science and technology. Using these capabilities, ORNL conducts basic and applied research and development (R&D) to support DOE’s overarching mission to “ensure America’s security and prosperity by addressing its energy, environmental and nuclear challenges through transformative science and technology solutions.” As a national resource, ORNL also applies its capabilities and skills to specific needs of other federal agencies and customers through the DOE Strategic Partnership Projects (SPP) program. Information about the laboratory and its programs is available at the ORNL website. The Laboratory Directed Research and Development (LDRD) program at ORNL operates under the authority of the DOE Order 413.2C, “Laboratory Directed Research and Development,” which establishes DOE’s requirements for the program while providing the laboratory director broad flexibility for program implementation. The LDRD program funds are obtained through a charge to all laboratory programs. ORNL reports on the program status to DOE each year.
99 GENERAL AND MISCELLANEOUS↗
Laboratory Directed Research and Development Program: FY 2023 Completed Projects Report
Oak Ridge National Laboratory (ORNL) is the US Department of Energy’s (DOE’s) largest multiprogram science, technology, and energy laboratory. It possesses distinctive capabilities in a variety of fields, such as neutron science, computing, advanced materials, and nuclear science and technology. Using these capabilities, ORNL conducts basic and applied research and development (R&D) to support DOE’s overarching mission “to ensure America’s security and prosperity by addressing its energy, environmental and nuclear challenges through transformative science and technology solutions.” As a national resource, ORNL also applies its capabilities and skills to the specific needs of other federal agencies and customers through the DOE Strategic Partnership Projects (SPP) Program. Information about the laboratory and its programs is available on the ORNL website. The Laboratory Directed Research and Development (LDRD) Program at ORNL operates under the authority of the DOE Order 413.2C, Laboratory Directed Research and Development, which establishes DOE’s requirements for the program while providing the laboratory director broad flexibility for program implementation. The LDRD Program funds are obtained through a charge to all laboratory programs. Although it represents a relatively small portion of the overall research budget, the LDRD Program plays an essential role in maintaining the laboratory’s ability to respond to national needs. The program allows ORNL to improve its distinctive capabilities and to enhance its ability to conduct cutting-edge R&D. This report provides an overview of the LDRD Program at ORNL in FY 2023 and contains summaries of all the LDRD research projects that concluded between October 1, 2022, and September 30, 2023.
99 GENERAL AND MISCELLANEOUS↗
Laboratory Directed Research and Development Program: FY 2024 Completed Projects Report
Oak Ridge National Laboratory (ORNL) is the US Department of Energy’s (DOE’s) largest multiprogram science, technology, and energy laboratory. It possesses distinctive capabilities in a variety of fields, such as neutron science, computing, advanced materials, and nuclear science and technology. Using these capabilities, ORNL conducts basic and applied research and development (R&D) to support DOE’s overarching mission “to ensure America’s security and prosperity by addressing its energy, environmental and nuclear challenges through transformative science and technology solutions.” As a national resource, ORNL also applies its capabilities and skills to the specific needs of other federal agencies and customers through the DOE Strategic Partnership Projects (SPP) Program. Information about the laboratory and its programs is available on the ORNL website. The Laboratory Directed Research and Development (LDRD) Program at ORNL operates under the authority of DOE Order 413.2C, Laboratory Directed Research and Development,3 which establishes DOE’s requirements for the program while providing the laboratory director broad flexibility for program implementation. The LDRD Program funds are obtained through a charge to all laboratory programs. Although it represents a relatively small portion of the overall research budget, the LDRD Program plays an essential role in maintaining the laboratory’s ability to respond to national needs. The program allows ORNL to improve its distinctive capabilities and to enhance its ability to conduct cutting-edge R&D. In accordance with the DOE order, R&D projects funded through the LDRD Program at ORNL support the goals of • maintaining the scientific and technical vitality of the laboratory; • enhancing the laboratory’s ability to address future DOE missions; • fostering creativity and stimulating exploration of forefront areas of science and technology; • serving as a proving ground for new concepts in R&D; and • supporting high-risk, potentially high-value R&D. This report provides an overview of the LDRD Program at ORNL in FY 2024 and contains summaries of all the LDRD research projects that concluded between October 1, 2023, and September 30, 2024.
99 GENERAL AND MISCELLANEOUS↗
Laboratory Directed Research and Development Program: FY 2025 Completed Projects
Oak Ridge National Laboratory (ORNL) is the US Department of Energy’s (DOE’s) largest multiprogram science, technology, and energy laboratory. It possesses distinctive capabilities in a variety of fields, such as neutron science, computing, advanced materials, and nuclear science and technology. Using these capabilities, ORNL conducts basic and applied research and development (R&D) to support DOE’s overarching mission “to ensure America’s security and prosperity by addressing its energy, environmental and nuclear challenges through transformative science and technology solutions.” As a national resource, ORNL also applies its capabilities and skills to the specific needs of other federal agencies and customers through the DOE Strategic Partnership Projects (SPP) Program. Information about the laboratory and its programs is available on the ORNL website. The Laboratory Directed Research and Development (LDRD) Program at ORNL operates under the authority of DOE Order 413.2C, Laboratory Directed Research and Development, which establishes DOE’s requirements for the program while providing the laboratory director broad flexibility for program implementation. The LDRD Program funds are obtained through a charge to all laboratory programs. Although it represents a relatively small portion of the overall research budget, the LDRD Program plays an essential role in maintaining the laboratory’s ability to respond to national needs. The program allows ORNL to improve its distinctive capabilities and enhance its ability to conduct cutting-edge R&D. In accordance with the DOE order, R&D projects funded through the LDRD Program at ORNL support the goals of • maintaining the scientific and technical vitality of the laboratory, • enhancing the laboratory’s ability to address future DOE missions, • fostering creativity and stimulating exploration of forefront areas of science and technology, • serving as a proving ground for new concepts in R&D, and • supporting high-risk, potentially high-value R&D. This report provides an overview of the LDRD Program at ORNL in FY 2025 and contains summaries of all the LDRD research projects that concluded between October 1, 2024, and September 30, 2025.
99 GENERAL AND MISCELLANEOUS↗
Laboratory Directed Research and Development Program: FY 2025 Completed Projects
Oak Ridge National Laboratory (ORNL) is the US Department of Energy’s (DOE’s) largest multiprogram science, technology, and energy laboratory. It possesses distinctive capabilities in a variety of fields, such as neutron science, computing, advanced materials, and nuclear science and technology. Using these capabilities, ORNL conducts basic and applied research and development (R&D) to support DOE’s overarching mission “to ensure America’s security and prosperity by addressing its energy, environmental and nuclear challenges through transformative science and technology solutions.” As a national resource, ORNL also applies its capabilities and skills to the specific needs of other federal agencies and customers through the DOE Strategic Partnership Projects (SPP) Program. Information about the laboratory and its programs is available on the ORNL website.
99 GENERAL AND MISCELLANEOUS↗
CSGL: chemical synthesis graph learning for molecule representation
Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.
Biochemistry & Molecular Biology↗
Analyzing Stochastic Computer Models: A Review with Opportunities
In modern science, computer models are often used to understand complex phenomena and a thriving statistical community has grown around analyzing them. This review aims to bring a spotlight to the growing prevalence of stochastic computer models-providing a catalogue of statistical methods for practitioners, an introductory view for statisticians (whether familiar with deterministic computer models or not), and an emphasis on open questions of relevance to practitioners and statisticians. Gaussian process surrogate models take center stage in this review, and these, along with several extensions needed for stochastic settings, are explained. The basic issues of designing a stochastic computer experiment and calibrating a stochastic computer model are prominent in the discussion. Instructive examples, with data and code, are used to describe the implementation of, and results from, various methods.
agent based model↗
LLNL Response to the DOE ASCR RFI, "Stewardship of Software for Scientific and High-Performance Computing"
For decades, Lawrence Livermore National Laboratory (LLNL) has been engaged in significant research, development, and support for software to enable scientific computing and, particularly, the use of high performance computing (HPC) in the NNSA mission space. In particular, the move in the mid-1990’s to simulation as a leading component of stockpile stewardship through the ASCI and the successor ASC programs, as well as the need for reliable data acquisition and control software for the National Ignition Facility, have been important drivers in building expertise in production-quality software development at LLNL. LLNL has also been a leader in the DOE SciDAC FASTMath Institute and the DOE Exascale Computing Project (ECP), both of which have striven to make scientific computing software – in particular, the enabling technologies underpinning simulation capabilities – more widely adopted and sustainable. As such, we believe that our experience can inform the broader goal of software stewardship for scientific and high-performance computing. LLNL strongly supports the formation of a new DOE ASCR program element in software stewardship and sustainment. Historically, DOE ASCR has funded applied mathematics and computer science research that has led to the development of important new capabilities and algorithms that are expressed as artifacts in research software. Such frameworks, libraries, and tools have seldom been directly funded to address the important issues of code maintenance, documentation, robustness, and community building. Software engineering and support have typically been done on the side in support of the ASCR-driven research products. DOE funding priorities have been slow to recognize that good software engineering, the kind that ensures research investments have more adoption and longevity, requires significant resources. Based upon our experiences, we have prepared this response to highlight the concerns and issues we believe to be important as DOE ASCR considers its role in scientific software stewardship. We believe that role is important and will require a significant investment of new funding to legitimately support the technologies past and future DOE ASCR investments have and will produce to facilitate their uptake and adoption in the broader scientific computing community. Following a summary of our involvement in scientific software development, the remainder our response is organized around the nine topics specifically identified in the RFI.
97 MATHEMATICS AND COMPUTING↗
The in-silico lab-on-a-chip: petascale and high-throughput simulations of microfluidics at cell resolution
We present simulations of blood and cancer cell separation in complex microfluidic channels with subcellular resolution, demonstrating unprecedented time to solution, performing at 65.5% of the available 39.4 PetaInstructions/s in the 18, 688 nodes of the Titan supercomputer. These simulations outperform by one to three orders of magnitude the current state of the art in terms of numbers of simulated cells and computational elements. The computational setup emulates the conditions and the geometric complexity of microfluidic experiments and our results reproduce the experimental findings. These simulations provide sub-micron resolution while accessing time scales relevant to engineering designs. We demonstrate an improvement of up to 45X over competing state-of-the-art solvers, thus establishing the frontiers of simulations by particle based methods. Our simulations redefine the role of computational science for the development of microfluidics –- a technology that is becoming as important to medicine as integrated circuits have been to computers.
Computer Science↗
Software Build and Delivery Systems
This presentation deals with the hierarchy of software build and delivery systems. One of the goals is to maximize the success rate of new users and developers when first trying your software. First impressions are important. Early successes are important. This also reduces critical documentation costs. This is a presentation focused on computer science and goes into detail about code documentation.
97 MATHEMATICS AND COMPUTING↗