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FutureTense

Protective vaccines and reliable diagnostics are essential tools for controlling viral diseases. However, the efficacy of these tools can be diminished by mutations in viral genomes. The delay between the emergence of new viral strains and the redesign of vaccines and diagnostics allows for continued viral transmission. Is it possible to address this challenge by computationally predicting viral genome sequence evolution? Can we “future-proof” vaccines and diagnostics by targeting both current and anticipated future sequence variants? While predicting viral evolution is still an unsolved, “grand challenge” problem in biology, the large, and rapidly growing, number of SARS-CoV-2 genome sequences provide an opportunity to quantify the ability of machine learning to predict viral genome sequence evolution. Towards this end, we have developed a simple computational model for predicting viral evolution at the level of individual nucleotides. The key metric for quantifying the per-base, prediction accuracy for viral evolution is the Mann-Whitney U statistic (or, equivalently, the area under the receiver operator curve). Since the Mann-Whitney U statistic is not a differentiable function, existing deep leaning packages (like Pytorch and Keras/TensorFlow) are not useful, as they require that the accuracy metric/objective function be analytically differentiable with respect to the model parameters. To overcome this challenge, we have implemented custom software, “FutureTense”, that can train a machine learning model by maximizing the non-differentiable Mann-Whitney U statistic. This software trains a machine learning model by exploring along the direction of the discrete gradient of the Mann-Whitney U statistic in the model parameter space. Parallel computing and genome sequence-specific optimizations are used to accelerate model training. The resulting machine learning model learns the observed high C->U mutation rates in the SARS-CoV-2 genome (which are potentially induced by host defenses) and provides prediction accuracies that are significantly better than one would expect from random chance. While predicting viral evolution is still quite far from a solved problem, the surprising performance of this simple model gives hope that the accuracy of predicting viral genome evolution can be further increased by more sophisticated approaches.

Gans, Jason↗

Pair-instability Supernova Simulations: Progenitor Evolution, Explosion, and Light Curves

In recent years, the viability of the pair-instability supernova (PISN) scenario for explaining superluminous supernovae has all but disappeared except for a few slowly-evolving examples. However, PISNe are not predicted to be superluminous throughout the bulk of their mass range. In fact, it is more likely that the first PISN we see (if we have not seen one already) will not be superluminous. Here, we present hydrodynamic simulations of PISNe for four stellar models with unique envelope properties spanning the PISN mass range. In addition, we compute synthetic light curves (LCs) for comparison with current and future observations. We also investigate, in the context of our most massive model, the prospect of mixing in the supernova ejecta, alleviating discrepancies between current PISN models and the remaining superluminous candidate events. To this end, we present the first published 3D hydrodynamic simulations of PISNe. After achieving convergence between 1D, 2D, and 3D simulations, we examine mixing in the supernova ejecta and its affect on the bolometric LC. We observe slight deviations from spherical symmetry, which increase with the number of dimensions. We find no significant effects on the bolometric LC; however, we conclude that mixing between the silicon and oxygen rich layers caused by the Rayleigh–Taylor instability may affect spectra.

79 ASTRONOMY AND ASTROPHYSICS↗

The future of interaction on the Internet

The federated collection of heterogeneous computers we collectively term the Internet has been the force behind revolutionary change, both in terms of actual practice and imagination of what might be. The raw numbers are staggering: IP registrations are now ten times that of only five years ago; and between 1992 - 1993 the amount of information being transferred tripled. Changes in three key areas: knowledge discovery; intelligent information access; and collaboration on the Internet are discussed.

Maybury, Mark T.↗

Modeling Analog Tile-Based Accelerators Using SST

Analog computing has been widely proposed to improve the energy efficiency of multiple important workloads including neural network operations, and other linear algebra kernels. To properly evaluate analog computing and explore more complex workloads such as systems consisting of multiple analog data paths, system level simulations are required. Moreover, prior work on system architectures for analog computing often rely on custom simulators creating signficant additional design effort and complicating comparisons between different systems. To remedy these issues, this report describes the design and implementation of a flexible tile-based analog accelerator element for the Structural Simulation Toolkit (SST). The element focuses on heavily on the tile controller—an often neglected aspect of prior work—that is sufficiently versatile to simulate a wide range of different tile operations including neural network layers, signal processing kernels, and generic linear algebra operations without major constraints. The tile model also interoperates with existing SST memory and network models to reduce the overall development load and enable future simulation of heterogeneous systems with both conventional digital logic and analog compute tiles. Finally, both the tile and array models are designed to easily support future extensions as new analog operations and applications that can benefit from analog computing are developed.

97 MATHEMATICS AND COMPUTING↗

A Design Tool for Liquid Rocket Engine Injectors

A practical design tool for the analysis of flowfields near the injector face has been developed and used to analyze the Fastrac engine. The objective was to produce a computational design tool which was detailed enough to predict the interactive effects of injector element impingement angles and points and the momenta of the individual orifice flows. To obtain a model which could be used to simulate a significant number of individual orifices, a homogeneous computational fluid dynamics model was developed. To describe liquid and vapor sub- and super-critical flows, the model included thermal and caloric equations of state which were valid over a wide range of pressures and temperatures. A homogeneous model was constructed such that the local state of the flow was determined directly, i.e. the quality of the flow was calculated. Such a model does not identify drops or their distribution, but it does allow the flow along the injector face and into the acoustic cavity to be predicted. It also allows the film coolant flow to be accurately described. The initial evaluation of the injector code was made by simulating cold flow from an unlike injector element and from a like-on-like overlapping fan (LOL) injector element. The predicted mass flux distributions of these injector elements compared well to cold flow test results. These are the same cold flow tests which serve as the data base for the JANNAF performance prediction codes. The flux distributions 1 inch downstream of the injector face are very similar; the differences were somewhat larger at further distances from the faceplate. Since the cold flow testing did not achieve good mass balances when integrations across the entire fan were made, the CFD simulation appears to be reasonable alternative to future cold flow testing. To simulate the Fastrac, an RP-1/LOX combustion model must be chosen. This submodel must be relatively simple to accomplish three-dimensional, multiphase flow simulations. Single RP-1 pyrolysis and partial oxidation steps were chosen and the combustion was completed with the wet CO mechanism. Soot was also formed with a single global reaction. To validate the combustion submodel, global data from gas generator tests and from subscale motor test were used to predict qualitatively correct mean molecular weights, temperature, and soot levels. Because such tests do not provide general kinetics rates, the methodology is not necessarily appropriate for other than rocket type flows conditions. Soot predictions were made so that radiation heating to the motor walls can be made. These initial studies of the Fastrac were for a small region close to the injector face and chamber wall which included a segment of the acoustic cavity. The region analyzed includes 11 individual orifice holes to represent the LOL elements and the H2 film coolant holes. Typical results of this simulation are shown in Figure 1. At this point the only available test data to verify the predictions are temperatures measured in the acoustic cavity. These temperatures are in reasonable agreement at about 2000R (1111 K). Future work is expected to include improving the computational efficiency or the CFD model and/or using more computer capacity than the single Pentium PC with which these simulations were made.

Farmer, Richard C.↗

Understanding the use of message passing interface in exascale proxy applications

The Exascale Computing Project (ECP) focuses on the development of future exascale-capable applications. Most ECP applications use the message passing interface (MPI) as their parallel programming model with mini-apps serving as proxies. This paper explores the explicit usage of MPI in such ECP proxy applications. We empirically analyze 14 proxy applications from the ECP Proxy Apps Suite. We use the MPI profiling interface (PMPI) to collect MPI usage patterns in ECP proxy apps. Our analysis shows that a small subset of features from MPI is commonly used in the proxies of exascale-capable applications, even when they reference third-party libraries. Overall, this study is intended to provide a better understanding of the use of MPI in current exascale applications. The findings can help focus software investments made for exascale systems in the MPI middleware including optimization, fault-tolerance, tuning, and hardware-offload.

97 MATHEMATICS AND COMPUTING↗

Quantum materials for energy-efficient neuromorphic computing: Opportunities and challenges

Neuromorphic computing approaches become increasingly important as we address future needs for efficiently processing massive amounts of data. The unique attributes of quantum materials can help address these needs by enabling new energy-efficient device concepts that implement neuromorphic ideas at the hardware level. In particular, strong correlations give rise to highly non-linear responses, such as conductive phase transitions that can be harnessed for short- and long-term plasticity. Similarly, magnetization dynamics are strongly non-linear and can be utilized for data classification. This Perspective discusses select examples of these approaches and provides an outlook on the current opportunities and challenges for assembling quantum-material-based devices for neuromorphic functionalities into larger emergent complex network systems.

36 MATERIALS SCIENCE↗

Adaptive Management of Computing and Network Resources for Spacecraft Systems

It is likely that NASA's future spacecraft systems will consist of distributed processes which will handle dynamically varying workloads in response to perceived scientific events, the spacecraft environment, spacecraft anomalies and user commands. Since all situations and possible uses of sensors cannot be anticipated during pre-deployment phases, an approach for dynamically adapting the allocation of distributed computational and communication resources is needed. To address this, we are evolving the DeSiDeRaTa adaptive resource management approach to enable reconfigurable ground and space information systems. The DeSiDeRaTa approach embodies a set of middleware mechanisms for adapting resource allocations, and a framework for reasoning about the real-time performance of distributed application systems. The framework and middleware will be extended to accommodate (1) the dynamic aspects of intra-constellation network topologies, and (2) the complete real-time path from the instrument to the user. We are developing a ground-based testbed that will enable NASA to perform early evaluation of adaptive resource management techniques without the expense of first deploying them in space. The benefits of the proposed effort are numerous, including the ability to use sensors in new ways not anticipated at design time; the production of information technology that ties the sensor web together; the accommodation of greater numbers of missions with fewer resources; and the opportunity to leverage the DeSiDeRaTa project's expertise, infrastructure and models for adaptive resource management for distributed real-time systems.

Pfarr, Barbara↗

Variational quantum algorithms

Applications such as simulating complicated quantum systems or solving large-scale linear algebra problems are very challenging for classical computers, owing to the extremely high computational cost. Quantum computers promise a solution, although fault-tolerant quantum computers will probably not be available in the near future. Current quantum devices have serious constraints, including limited numbers of qubits and noise processes that limit circuit depth. Variational quantum algorithms (VQAs), which use a classical optimizer to train a parameterized quantum circuit, have emerged as a leading strategy to address these constraints. VQAs have now been proposed for essentially all applications that researchers have envisaged for quantum computers, and they appear to be the best hope for obtaining quantum advantage. Nevertheless, challenges remain, including the trainability, accuracy and efficiency of VQAs. Here we overview the field of VQAs, discuss strategies to overcome their challenges and finally, we highlight the exciting prospects for using them to obtain quantum advantage.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An Immersed Boundary method with divergence-free velocity interpolation and force spreading

The Immersed Boundary (IB) method is a mathematical framework for constructing robust numerical methods to study fluid–structure interaction in problems involving an elastic structure immersed in a viscous fluid. The IB formulation uses an Eulerian representation of the fluid and a Lagrangian representation of the structure. The Lagrangian and Eulerian frames are coupled by integral transforms with delta function kernels. The discretized IB equations use approximations to these transforms with regularized delta function kernels to interpolate the fluid velocity to the structure, and to spread structural forces to the fluid. It is well-known that the conventional IB method can suffer from poor volume conservation since the interpolated Lagrangian velocity field is not generally divergence-free, and so this can cause spurious volume changes. In practice, the lack of volume conservation is especially pronounced for cases where there are large pressure differences across thin structural boundaries. The aim of this paper is to greatly reduce the volume error of the IB method by introducing velocity-interpolation and force-spreading schemes with the properties that the interpolated velocity field in which the structure moves is at least $\mathscr{C}$ 1 and satisfies a continuous divergence-free condition, and that the force-spreading operator is the adjoint of the velocity-interpolation operator. We confirm through numerical experiments in two and three spatial dimensions that this new IB method is able to achieve substantial improvement in volume conservation compared to other existing IB methods, at the expense of a modest increase in the computational cost. Further, the new method provides smoother Lagrangian forces (tractions) than traditional IB methods. Finally, the method presented here is restricted to periodic computational domains. Its generalization to non-periodic domains is important future work.

97 MATHEMATICS AND COMPUTING↗

Distributed management of scientific projects - An analysis of two computer-conferencing experiments at NASA

Between August 1975 and March 1976, two NASA projects with geographically separated participants used a computer-conferencing system developed by the Institute for the Future for portions of their work. Monthly usage statistics for the system were collected in order to examine the group and individual participation figures for all conferences. The conference transcripts were analysed to derive observations about the use of the medium. In addition to the results of these analyses, the attitudes of users and the major components of the costs of computer conferencing are discussed.

Vallee, J.↗

Computational structures technology and UVA Center for CST

Rapid advances in computer hardware have had a profound effect on various engineering and mechanics disciplines, including the materials, structures, and dynamics disciplines. A new technology, computational structures technology (CST), has recently emerged as an insightful blend between material modeling, structural and dynamic analysis and synthesis on the one hand, and other disciplines such as computer science, numerical analysis, and approximation theory, on the other hand. CST is an outgrowth of finite element methods developed over the last three decades. The focus of this presentation is on some aspects of CST which can impact future airframes and propulsion systems, as well as on the newly established University of Virginia (UVA) Center for CST. The background and goals for CST are described along with the motivations for developing CST, and a brief discussion is made on computational material modeling. We look at the future in terms of technical needs, computing environment, and research directions. The newly established UVA Center for CST is described. One of the research projects of the Center is described, and a brief summary of the presentation is given.

Noor, Ahmed K.↗

Introduction and Highlights of the Workshop

Four generations of CAD/CAM systems can be identified, corresponding to changes in both modeling functionality and software architecture. The systems evolved from 2D and wireframes to solid modeling, to parametric/variational modelers to the current simulation-embedded systems. Recent developments have enabled design engineers to perform many of the complex analysis tasks, typically performed by analysis experts. Some of the characteristics of the current and emerging CAD/CAM/CAE systems are described in subsequent presentations. The focus of the workshop is on the potential of CAD/CAM/CAE systems for use in simulating the entire mission and life-cycle of future aerospace systems, and the needed development to realize this potential. First, the major features of the emerging computing, communication and networking environment are outlined; second, the characteristics and design drivers of future aerospace systems are identified; third, the concept of intelligent synthesis environment being planned by NASA, the UVA ACT Center and JPL is presented; and fourth, the objectives and format of the workshop are outlined.

Noor, Ahmed K.↗

High entropy alloys as catalysts: A focused review

A brief literature review of recent experimental and computational efforts on the use of high entropy alloys (HEAs) as catalysts is presented, while also sharing some perspectives and future insights. To fully broach the vast compositional possibilities of HEA materials, integrating computational modeling with high-throughput experimental synthesis and validation is necessary to accelerate their design and development. Once identified, specific HEAs can be a class of materials for the next generation of catalysts when addressing global challenges related to energy independence, commodity chemical production, environmental remediation, abating emissions, and modernized domestic supply chain resilience.

42 - ENGINEERING↗

Analysis of physical-chemical processes governing SSME internal fluid flows

In order to aid the development of current and future SSME type engines, it is necessary to improve the understanding of basic issues related with physical-chemical processes of SSME internal flows. Accomplishments under each of the following specific objectives are described herein: (1) supplying a state-of-the-art CFD code and graphics package; (2) demonstrating code usage on SSME-related problems to NASA MSFC personnel; and (3) performance computations and analysis of problems relevant to current and future SSME's.

Singhal, A. K.↗

Optimization of a Parallel Ocean General Circulation Model

Global climate modeling is one of the grand chalenges of computational science, and ocean modeling plays an important role in both understanding the current climatic conditions and predicting the future climate change.

Optimization Ocean Modeling Parallel Computations↗

Four-Stage Multi-Physics Simulations to Assist Temperature Sensor Design for Industrial-Scale Coal-Fired Boiler

The growth of renewable energy sources presents a pressing challenge to the operation and maintenance of existing fossil fuel power plants, given that fossil fuel remains the predominant fuel source, responsible for over 60% of electricity generation in the United States. One of the main concerns within these fossil fuel power plants is the unpredictable failure of boiler tubes, resulting in emergency maintenance with significant economic and societal consequences. A reliable high-temperature sensor is necessary for in situ monitoring of boiler tubes and the safety of fossil fuel power plants. In this study, a comprehensive four-stage multi-physics computational framework is developed to assist the design, optimization installation, and operation of the high-temperature stainless-steel and quartz coaxial cable sensor (SSQ-CCS) for coal-fired boiler applications. With the consideration of various operation conditions, we predict the distributions of flue gas temperatures within coal-fired boilers, the temperature correlation between the boiler tube and SSQ-CCS, and the safety of SSQ-CCS. With the simulation-guided sensor installation plan, the newly designed SSQ-CCSs have been employed for field testing for more than 430 days. The computational framework developed in this work can guide the future operation of coal-fired plants and other power plants for the safety prediction of boiler operations.

42 ENGINEERING↗

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗