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At least 379 records · Page 21

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering

Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.

59 BASIC BIOLOGICAL SCIENCES↗

Parallel sorting algorithm classification: is manual instrumentation necessary?

Understanding parallel algorithms is crucial for accelerating scientific simulations on complex, distributed memory, high-performance computers. Modern algorithm classification approaches learn semantics directly from source code to differentiate between algorithms, however, accessing source code is not always possible. We can learn about parallel algorithms from observing their performance, as programs running the same algorithms and using the same hardware should exhibit similar performance characteristics. We present an approach to learn algorithm classes from parallel performance data directly in order to classify algorithms without access to the source code. We extend previous work to enable classifying parallel sorting algorithms using automatic instrumentation instead of requiring manual region annotations in the source code. In this work, we design and demonstrate a study for classification of parallel sorting algorithms using parallel performance data collected from automatic instrumentation, and evaluate the performance of our new methodology on classification. We leverage Caliper to collect the performance data, Thicket for our exploratory data analysis (EDA), and PyTorch and Scikit-learn to evaluate the effectiveness of random forests, support vector machines (SVMs), decision trees, neural networks, and logistic regressions on parallel performance data. Additionally, we study noise in parallel performance data, whether the removal of noise and pre-processing of the data is necessary to accurately classify parallel sorting algorithms, and determine the effectiveness of features created from performance data. In conclusion, we demonstrate classification accuracy for these five different models of up to 97.7% across four different parallel algorithm classes.

Algorithm Classification↗

A performant energy-conserving particle reweighting method for Particle-in-Cell simulations

A new particle-based reweighting method is developed and demonstrated in the Aleph Particle-in-Cell with Direct Simulation Monte Carlo (PIC-DSMC) program. Novel splitting and merging algorithms ensure that modified particles maintain physically consistent positions and velocities. This method allows a single reweighting simulation to efficiently model plasma evolution over orders of magnitude variation in density, while accurately preserving energy distribution functions (EDFs). Demonstrations on electrostatic sheath and collisional rate dynamics show that reweighting simulations achieve accuracy comparable to fixed weight simulations with substantial computational time savings. This highly performant reweighting method is recommended for modeling plasma applications that require accurate resolution of EDFs or exhibit significant density variations in time or space.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SmartFuse: Reconfigurable Smart Switches to Accelerate Fused Collectives in HPC Applications

Communication switches have sometimes been augmented to process collectives (e.g., the IBM BlueGene project and the Mellanox SHArP switch). In this work, we find that there is a great acceleration opportunity through the further augmentation of switches to accelerate more complex functions that combine communication with computation. We consider three types of such functions. The first is fully-fused collectives built by fusing multiple existing collectives like Allreduce with Alltoall. The second is semi-fused collectives built by combining a collective with another computation. The third we refer to as higher-order collectives built by combining multiple computations and communications, such as to perform matrix-matrix multiply (PGEMM). In this work, we propose a framework called SmartFuse to accelerate fused collective functions. The core of SmartFuse is a reconfigurable smart switch to support these operations. The semi/fully fused collectives are implemented with a CGRAlike architecture, while higher-order collectives are implemented with a more specialized computational unit that can also schedule communication. Supporting our framework is software to evaluate and translate relevant parts of the input program, compile them into a control data flow graph, and then map this graph to the switch hardware. The proposed framework, once deployed, has the strong potential to accelerate existing HPC applications transparently by encapsulation within an MPI implementation. Experimental results show that this approach improves the performance of the PGEMM kernel, MINIFE, and AMG by, on average, 94%, 15%, and 13%, respectively.

Haghi, Pouya↗

cppTPSA/pyTPSA: a C++/Python package for truncated power series algebra

The truncated power series algebra (TPSA), also referred to as differential algebra (DA), is a well-established and widely used method in particle accelerator physics and astronomy. The most straightforward usage of TPSA/DA is to calculate the Taylor expansion of a given function at a specific point up to order ?. In recent years, as the application of TPSA/TA has been extended to other fields, a reusable implementation of TPSA/DA as a modern C++ library or other high level programming language like Python has become desirable. The cppTPSA package implements TPSA/DA in C++11 and provides developers a convenient library with which to build advanced TPSA/DA-based methods. A Python 3 library, pyTPSA, has also been developed based on the C++ lib.

97 MATHEMATICS AND COMPUTING↗

Annual Site Environmental Report (CY2019)

The primary purpose of this report is to summarize the performance of Ames Laboratory’s environmental programs, present highlights of significant environmental activities, and confirm compliance with environmental regulations and requirements for calendar year 2019. This report is a working requirement of Department of Energy Order 231.1B, Environment, Safety and Health Reporting. It includes descriptions of the Laboratory’s site, mission, the status of its compliance with applicable environmental regulations, its planning and activities to maintain compliance, and a comprehensive review of its environmental protection, surveillance and monitoring activities.

54 ENVIRONMENTAL SCIENCES↗

Fuel Effects on Multimode Engine Operation (Sandia National Laboratories) (DOE VTO Annual Progress Report for FY21)

In total, light-duty vehicles in the United States travel on the order of 3 trillion miles annually, providing tremendous societal and personal benefits. However, the environmental burden is excessive, prompting Co-Optimization of Fuel and Engines (Co-Optima) program efforts to provide the science needed to increase engine efficiency and produce non-fossil fuels with reduced greenhouse gas emissions. Boosted spark-ignition (SI) engines provide high power density by offering high loads and engine speeds, making them light-weight and attractive for light-duty vehicles. Unfortunately, the engine efficiency drops off at lower loads and speeds, where the engine spends most time during typical driving. Multimode SI engines can use a more efficient advanced lean combustion mode at lower loads and speeds, while reverting to boosted SI under high-load conditions. Within Co-Optima, multiple advanced lean combustion modes have been explored; these include stratified-charge SI, pre-chamber lean SI, and advanced compression ignition (ACI) techniques such as spark-assisted compression ignition (SACI). For these combustion modes, focus has been on determining fuel properties that enable higher engine efficiency, clean and stable combustion, and effective exhaust aftertreatment. This report highlights recent efforts funded by the Vehicle Technologies Office at multiple National Laboratories that supported the multimode project in Co-Optima. It also includes a brief summary of biofuel production research funded by the Bioenergy Technologies Office.

33 ADVANCED PROPULSION SYSTEMS↗

Annual Site Environmental Report: 2019 (ASER) for the SLAC National Accelerator Laboratory

To satisfy the requirements of the United States Department of Energy (DOE) SLAC Site Office approved Site Compliance Plan for DOE Order 231.1B, “Environment, Safety and Health Reporting,” the Environment, Safety and Health Division (ES&H) of the SLAC National Accelerator Laboratory prepares an annual report describing its environmental programs and activities. This Annual Site Environmental Report: 2019 summarizes the SLAC National Accelerator Laboratory compliance with standards and requirements, describes the management and monitoring systems in place, and highlights significant accomplishments for the year.

54 ENVIRONMENTAL SCIENCES↗

Plant Engineers Solar Energy Handbook: Southern California Region

Discussed in order after the introduction are solar components and systems (collectors, storage, service hot water systems, space heating with liquid and air systems, space cooling, heat pumps and controls); computer programs for system optimization; local solar and weather data; a description of buildings and plants in Southern California applying solar technology; current Federal and California solar legislation; standards, codes and performance testing information; a listing of manufacturers, distributors, and professional services available in Southern California region; and information access. Finally, solar design check lists for those engineers who wish to design their own systems. The program for the Solar Workshop for the Plant Engineer, March 30, 1978, Los Angeles, California is included.

14 SOLAR ENERGY↗

HighNESS conceptual design report: Volume II. The NNBAR experiment.

A key aim of the HighNESS project for the European Spallation Source is to enable cutting-edge particle physics experiments. This volume presents a conceptual design report for the NNBAR experiment. NNBAR would exploit a new cold lower moderator to make the first search in over thirty years for free neutrons converting to anti-neutrons. The observation of such a baryon-number-violating signature would be of fundamental significance and tackle open questions in modern physics, including the origin of the matter-antimatter asymmetry. This report shows the design of the beamline, supermirror focusing system, magnetic and radiation shielding, and anti-neutron detector necessary for the experiment. A range of simulation programs are employed to quantify the performance of the experiment and show how background can be suppressed. For a search with full background suppression, a sensitivity improvement of three orders of magnitude is expected, as compared with the previous search. Civil engineering studies for the NNBAR beamline are also shown, as is a costing model for the experiment.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measuring Young Stars in Space and Time. I. The Photometric Catalog and Extinction Properties of N44

In order to better understand the role of high-mass stellar feedback in regulating star formation in giant molecular clouds, we carried out a Hubble Space Telescope (HST) Treasury Program Measuring Young Stars in Space and Time (MYSST) targeting the star-forming complex N44 in the Large Magellanic Cloud (LMC). Using the F555W and F814W broadband filters of both the ACS and WFC3/UVIS, we built a photometric catalog of 461,684 stars down to m {sub F555W} ≃ 29 mag and m {sub F814W} ≃ 28 mag, corresponding to the magnitude of an unreddened 1 Myr pre-main-sequence star of ≈ 0.09 M {sub ☉} at the LMC distance. In this first paper we describe the observing strategy of MYSST and the data reduction procedure and present the photometric catalog. We identify multiple young stellar populations tracing the gaseous rim of N44's superbubble, together with various contaminants belonging to the LMC field population. We also determine the reddening properties from the slope of the elongated red clump (RC) feature by applying the machine-learning algorithm RANSAC, and we select a set of upper-main-sequence stars as primary probes to build an extinction map, deriving a relatively modest median extinction A {sub F555W} ≃ 0.77 mag. The same procedure applied to the RC provides A {sub F555W} ≃ 0.68 mag.

47 OTHER INSTRUMENTATION↗

Technology Development for Modular, Low-Cost, High-Temperature Recuperators for Supercritical CO 2 Power Cycles (Final Report)

The program’s focus was to evaluate, advance, and demonstrate recuperator design concepts, materials, and fabrication methods that facilitate the commercial availability of compact and low-cost recuperators. Emphasis was placed on recompression closed Brayton cycles having a turbine inlet temperature exceeding 700°C and differential pressures on the order of 200 bar and were scalable to accommodate plant sizes from 10 to 1,000 MWe. The primary objectives of the first budget period, which included conceptual design, preliminary development, and prototype fabrication and testing, were accomplished. A new recuperator design concept, stacked-sheet heat exchanger (SSHX), was realized during the project. The design was taken from paper to hardware and successfully tested. The SSHX prototype recuperator met or exceeded program thermal, hydraulic and performance/cost metrics goals. The first budget period was extended to retire risk in scaling the recuperator from the kWt to MWt thermal capacity scale. The fabrication and design requirements for the budget period one extension were met. Delays associated with the Covid-19 pandemic prevented the fabrication and testing of the industrial scale prototype.

14 SOLAR ENERGY↗

Evaluation of Physical Security Risk for Potential Implementation of FLEX using Dynamic Simulation Methods

The requirements for United States nuclear power plants to maintain a large onsite physical security force contribute to their large operational costs. The cost of maintaining the current physical security posture is approximately 10% of the overall operation and maintenance budget for commercial nuclear power plants. The goal of the Light Water Reactor Sustainability Program Physical Security Pathway is to develop tools, methods, and technologies and provide the technical basis for an optimized physical security posture. This pathway will analyze and minimize the conservatisms built into current security postures in order to reduce security costs while still ensuring adequate security and operational safety. The research performed at Idaho National Laboratory within this pathway has successfully developed a dynamic force-on-force (FOF) modeling framework using various computer simulation tools and integrated them with the dynamic assessment Event Modeling Risk Assessment using Linked Diagrams (EMRALD) tool. This document provides an overview of lessons learned in applying a dynamic computational framework that links results from a commercially available FOF simulation tool, a commercially available thermal-hydraulic tool, and EMRALD to an operating commercial nuclear power plant. This process of including plant procedures and multiple analysis results is being called Modeling and Analysis for Safety Security using Dynamic EMRALD Framework. Previous reports described how a user could integrate their plant-specific FOF models with the dynamic simulation tool EMRALD, model operator actions, integrate with probabilistic risk assessment tools, such as Computer Aided Fault Tree Analysis System or Systems Analysis Programs for Hands-on Integrated Reliability Evaluations, and with thermal-hydraulic tools, such as RELAP-5. Previous reports applied various combinations of available simulations codes with EMRALD using generic plant models to demonstrate how to perform the analysis. This report documents the results of applying the dynamic computational framework to an actual nuclear facility using their security scenarios and timelines. The purpose of this study was to verify that results achieved using generic models are similar to actual plant results and to refine our guidance of the use of the framework. Such an assessment enables further analysis, such as what-if scenarios and staff-reduction evaluation, thereby optimizing physical security at plants. NOTE: The work performed in this report is based on a generic EMRALD model with actual plant data used for the analysis. However, only the generic model and general results of the analysis are in the report. No plant’s sensitive information is discussed in this report. The discussion shows examples of insights that can be obtained from the MASS-DEF methodology.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Domain-decomposition nonlinear manifold reduced order model

This software combines nonlinear-manifold reduced order models (NM-ROMs) with domain decomposition (DD) techniques. NM-ROMs, which utilize a shallow, sparse autoencoder trained with full order model (FOM) snapshot data, approximate the FOM state on a nonlinear manifold. These models offer advantages over linear-subspace ROMs (LS-ROMs) particularly in scenarios with slowly decaying Kolmogorov n-width. However, the training of NM-ROMs involves a number of parameters that scale with the size of the FOM, and storing high-dimensional FOM snapshots can significantly increase the cost of ROM training for extreme-scale problems. To mitigate these costs, the software employs DD to partition the FOM into smaller subdomains, computes NM-ROMs for each, and then integrates these to form a global NM-ROM. This strategy offers multiple benefits: it enables parallel training of subdomain NM-ROMs, reduces the number of parameters needed, decreases the dimensional requirements of subdomain FOM training data, and allows for customization to the unique characteristics of each FOM subdomain. The use of a shallow, sparse autoencoder architecture in each subdomain NM-ROM facilitates the application of hyper-reduction (HR), simplifying the nonlinear complexities and enhancing computational speed. This software marks the inaugural application of NM-ROM combined with HR to a DD problem. It features an algebraic DD reformulation of the FOM, training of NM-ROMs with HR for each subdomain, and employs a sequential quadratic programming (SQP) solver for the evaluation of the coupled global NMROM. The effectiveness of the DD NM-ROM with HR is numerically demonstrated on the 2D steady-state Burgers' equation, showing an order of magnitude improvement in accuracy over the DD LS-ROM with HR.

Diaz, AlejandroN↗

PS3: The Pheno-Synthesis software suite for integration and analysis of multi-scale, multi-platform phenological data

Phenology is the study of recurring plant and animal life-cycle stages which can be observed across spatial and temporal scales that span orders of magnitude (e.g., organisms to landscapes). The variety of scales at which phenological processes operate is reflected in the range of methods for collecting phenologically relevant data, and the programs focused on these collections. Consideration of the scale at which phenological observations are made, and the platform used for observation, is critical for the interpretation of phenological data and the application of these data to both research questions and land management objectives. However, there is currently little capacity to facilitate access, integration and analysis of cross-scale, multi-platform phenological data. This paper reports on a new suite of software and analysis tools – the “Pheno-Synthesis Software Suite,” or PS3 – to facilitate integration and analysis of phenological and ancillary data, enabling investigation and interpretation of phenological processes at scales ranging from organisms to landscapes and from days to decades. We use PS3 to investigate phenological processes in a semi-aride, mixed shrub-grass ecosystem, and find that the apparent importance of seasonal precipitation to vegetation activity (i.e., “greenness”) is affected by the scale and platform of observation. We end by describing potential applications of PS3 to phenological modeling and forecasting, understanding patterns and drivers of phenological activity in real-world ecosystems, and supporting agricultural and natural resource management and decision-making.

54 ENVIRONMENTAL SCIENCES↗

Highly Bright and Photostable Two-Dimensional Nanomaterials Assembled from Sequence-Defined Peptoids

Free-standing two-dimensional (2D) organic nanomaterials are highly attractive for biological applications because of their unique structural properties and high biocompatibility. Herein, we designed and synthesized a new class of highly bright and photostable membrane-mimetic 2D nanosheets from sequence-defined peptoids. These nanosheets exhibited the high quantum yield and photostability as a result of the precise placement and ordering of dansyl dye molecules within crystalline nanosheets. We further showed the use of these nanosheets as biocompatible and programmable probes for live cell imaging and cell labeling. Furthermore, by programing these nanosheets with different surface charges, we achieved the enhanced lysosome escape of these nanosheets, showing their great potential as nanocarriers for the efficient intracellular delivery of macromolecular drugs.

2D nanomaterials↗

Interfacing electron and neutrino quasielastic scattering cross sections with the spectral function in GENIE

Progress in neutrino-nucleus cross section models is being driven by the need for highly accurate predictions for the neutrino oscillation community. These sophisticated models are being developed within a microscopic description of the nucleus with the goal of encompassing all reaction modes relevant for the accelerator neutrino program. The disconnect between these microscopic models and the event generators that will be used in the next generation of experiments represents a critical obstacle that must be overcome in order to precisely measure the neutrino oscillation parameters. To this end we have developed a hadron tensor interface for lepton-nucleus quasielastic (QE) scattering within the GENIE event generator as a proof of principle, with the broader goal of creating an efficient pipeline for incorporating advanced theoretical models in event generators. As a demonstration of this interface we have implemented the spectral function model into GENIE by connecting theorist provided fortran code through the hadron tensor interface. The spectral function model offers a more complete description of the nuclear ground state, as well as the ability to provide quantifiable theoretical uncertainties. Finally, we validate this implementation and compare its predictions against data and against QE models already available in GENIE.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Development and Evaluation of Distributed Energy Resource Device Models: Electric Vehicles, Electric Water Heaters, and Commercial Refrigeration Systems

In order to validate distributed energy resource (DER) models operated with grid services in the GMLC 1.4.2 team’s February (GMLC 2019a) and July (GMLC 2019b) reports, a test and measurement program using actual DER devices was conducted by national laboratories for three devices: (1) electric vehicles (EVs), (2) water heaters, and (3) commercial refrigeration. Test procedures were developed and carried out to identify the mathematical models and their parameters that describe the operational function, characterize the physics, and obey transient response of the devices. This report focuses on the experimental results obtained to develop and verify simulations of three specific EV models. This section summarizes elements of the mathematical model and shows the necessity data collected from the EVs while charging and discharging (driving). In the course of the study, we found it necessary to make some modifications to the model to deal with observed transient behavior. Section 1.2 details the model assumptions and equations, Section 1.3 provides details of the EVs tested, Section 1.4 outlines the test procedures developed for the projects, and Section 1.5 presents the experimental results obtained for the three different EVs tested and how these results compare to the models running the same test profiles.

24 POWER TRANSMISSION AND DISTRIBUTION↗