Results for “toolkit” — Page 97

DOE OSTI2021

Developing Advanced Genetic and Synthetic Biology Tools for Improved Algae Productivity

Under the UCSD-led Productivity Enhanced Algae and ToolKits (PEAK) project we sought to develop tools to enable the production of valuable co-products, as well as strategies to decrease the cost of cultivation, with an intended outcome of enabling the economic production of algae-based biofuel. We have developed new genetic tools and high throughput selection methods for eukaryotic green algae and used them to express a high value recombinant protein; a growth factor known as Osteopontin (OPN). Recombinant OPN protein expression levels were improved through a newly developed rapid breeding and mutagenesis strain improvement method to generate a robust strain capable of growing in outdoors raceway conditions in brackish water that tolerated high pH and large temperature swings. We further applied the new genetic tools to express recombinant protein in a recently bioprospected strain with even more robust growth characteristics. In response to the COVID-19 pandemic we used our improved workflow to rapidly express, purify, and characterize a recombinant SARS-CoV-2 spike protein Receptor Binding Domain (RBD) and demonstrate that it functionally interacts with its cognate human host receptor ACE2. The newly identified extremophile strain Chlamydomonas sp (402), both mating type (mt+) and mating type (mt-), have been deposited in the Chlamydomonas Resource Center (https://www.chlamycollection.org/), making them available world-wide with no restrictions. In addition, all of genetic tools are also deposited at this site and are also available world-wide with no restrictions.

09 BIOMASS FUELS↗

DOE OSTI2021

mystic : software for autonomous discovery and design under uncertainty

Throughout the diverse range of science and engineering applications, there is a growing desire to develop computational methods that can reliably predict the behavior of complex systems. Specifically, there is a strategic need for tools that can robustly forecast the behavior of complex physical systems, where data may be high-dimensional, noisy, or sparse, and models of the system may be time-dependent or include uncertainty. We use mystic to build tools that leverage statistical learning, physics-informed learning, and active learning in the efficient generation of reliably predictive surrogates for complex physical systems. mystic is a robust, proven, open-source optimization and uncertainty quantification toolkit with over a decade of use in the design and optimization of neutron instrumentation, solar-powered drones, and gasguns, and in iterative tuning of models for Raman spectroscopy and elastoplastic materials strength. Recent developments have focused on automated learning of statistically robust surrogates under uncertainty, with applications in materials in extreme environments, nanostructures, materials simulations and strength models, and the failure of shielding under particle radiation. In 2020, McKerns demonstrated active learning of optimally robust surrogates with respect to new simulated data for molecular dynamics simulations of materials mixing in warm dense matter, and is currently applying active learning to the automated steering of particle accelerator beams and the optimal design and control of quantum optical sensor instrumentation.

42 ENGINEERING↗

DOE OSTI2021

Energy Systems Process Modeling, Analysis, and Experiment Design [Slides]

This presentation is to be used in Feynman Center outreach discussions. It describes public information about some Los Alamos interests and activities in modeling and analysis in energy systems including carbon capture and direct air capture. In particular this addresses the CCSI2 project’s open-source toolkit and ongoing partnerships, as well as summarizing the published Feynman Center capability snapshot on direct air capture.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

VTK-m User's' Guide (V.1.7)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction. VTK-m simplifies the development of parallel scientific visualization algorithms by providing a framework of supporting functionality that allows developers to focus on visualization operations. Consider the listings in Figure 1.1 that compares the size of the implementation for the Marching Cubes algorithm in VTK-m with the equivalent reference implementation in the CUDA software development kit. Because VTK-m internally manages the parallel distribution of work and data, the VTK-m implementation is shorter and easier to maintain. Additionally, VTK-m provides data abstractions not provided by other libraries that make code written in VTK-m more versatile.This book includes contributions from the VTK-m community including the VTK-m development team and the user community.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Data Fusion to Enhance Quality Control and Analysis with Instruments at the Marine and Coastal Research Laboratory

Deploying environmental monitoring instruments in the marine environment can be challenging, facing challenges around device survivability, biofouling and corrosion, and consistent data collection. This project explores the use of data fusion – the process of integrating multiple data sources to produce more consistent, accurate, and useful information – to build a consistent long-term monitoring system at the Marine and Coastal Research Laboratory (MCRL) in Sequim, Washington. Unused instruments that had been acquired from past projects were inventoried and deployments planned on the MCRL pier and floating dock. A total of 8 instruments were deployed including a tide gauge, hydrophone, acoustic Doppler current profiler (ADCP), photosynthetically active radiation (PAR) sensors, meteorological station, and three water quality sensors. Deployments were planned to be well-protected around the pier structure and a maintenance schedule was created for cleaning and recalibration. An automated data pipeline was created to aggregate data on edge computers that push data to Amazon Web Services (AWS) cloud storage every 15 minutes, performing automated quality control and data transformations using the Time Series Data Analytical Toolkit (TSDAT). Continued efforts are underway to maintain this system into the future, take a data-driven approach to maintenance scheduling, improve the reliability of the system, and share the data with a variety of end-users.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

NEAMS-Multiphysics Technical Assistance in FY21

The Multiphysics Object Oriented Simulation Environment (MOOSE) [1] is a massively parallel finite-element/volume package for multiphysics simulation in science and engineering. The package focuses on providing rapid-development capabilities for engineering applications by leveraging well-built features from libMesh [2] and the Portable Extensible Toolkit for Scientific Computation (PETSc) [3]. Fiscal year 2021 (FY-21) was the first year with funding dedicated to supporting MOOSE-derived applications relevant to the Nuclear Engineering Advanced Modeling and Simulation (NEAMS) program. In this report we outline the work done to support NEAMS applications such as BISON, Griffin, Pronghorn, and System Analysis Module (SAM).

42 ENGINEERING↗

DOE OSTI2021

ERAS: Enabling the Integration of Real-World Intellectual Properties (IPs) in Architectural Simulators

Sandia National Laboratories is investigating scalable architectural simulation capabilities with a focus on simulating and evaluating highly scalable supercomputers for high performance computing applications. There is a growing demand for RTL model integration to provide the capability to simulate customized node architectures and heterogeneous systems. This report describes the first steps integrating the ESSENTial Signal Simulation Enabled by Netlist Transforms (ESSENT) tool with the Structural Simulation Toolkit (SST). ESSENT can emit C++ models from models written in FIRRTL to automatically generate components. The integration workflow will automatically generate the SST component and necessary interfaces to ’plug’ the ESSENT model into the SST framework.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

SIERRA/Aero Theory Manual (V.5.2)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

SIERRA/Aero User Manual (V.5.2)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

DOE OSTI2022

SIERRA/Aero Theory Manual (V.5.4)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

SIERRA/Aero User Manual (V.5.4)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Capability: Selective Endotoxin Uptake

Researchers at Los Alamos National Lab are developing a new capability to selectively absorb lipopolysaccharide, also known as endotoxin. Current sepsis treatment technologies generally target the bacteria causing the infection, but do not mitigate the host response that causes sickness. This disruptive capability could enable the removal of endotoxin from patient blood adding a much needed tool to the toolkit of sepsis treatments. We are seeking a CRADA partner with the desire to develop sepsis treatments and collaborate on the next steps.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

SIERRA/Aero Theory Manual (V.5.6)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

DOE OSTI2022

SIERRA/Aero User Manual (V.5.6)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

DOE OSTI2021

REopt ® Lite Overview - Resilience Analysis: Clear Sky Tampa Bay [Slides]

Through the Solar Energy Innovation Network (SEIN), the Clear Sky Tampa Bay team, led by the Tampa Bay Regional Planning Council (TBRPC), developed a toolkit to help local governments prioritize sites for solar photovoltaics (PV) and battery energy storage in the context of resilience and emergency management. At a high level, the Clear Sky Tampa Bay process involves: (1) Identifying sites based on community resilience needs and priorities ("Where do we need a resilient energy solution?"); (2) Screening and prioritizing sites for solar PV and storage suitability based on site conditions and other factors; and (3) Using REopt Lite to screen down-selected facilities to prioritize sites based on resilience project economics. This slide deck focuses on Step 3 above, and provides a general overview of REopt Lite and suggestions and examples tailored to the Clear Sky Tampa Bay team about how to use REopt Lite for additional analysis.

14 SOLAR ENERGY↗

DOE OSTI2022

Recommendations for Radiological Data Assessment Implementation

Since thorough verification, validation, and data quality assessment (DQA) processes may delay incident commanders and elected and appointed officials from making key decisions, the U.S. Department of Homeland Security (DHS) National Urban Security Technology Laboratory (NUSTL) tasked Pacific Northwest National Laboratory (PNNL) to develop tools and guidance for the federal, state, local, tribal, and territorial (FSLTT) responders using research, discussions with select FSLTT responders, and the experiences of subject matter experts in incident response. This report provides NUSTL with recommendations on best practices for verification, validation, and data quality assessment for the data collected by responders during a radiological or nuclear event. The purpose of this report is to inform the development of a DQA toolkit aimed at the needs of data assessors during the response to a radiological incident.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2022

SIERRA/Aero User Manual - Version 5.8

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.

42 ENGINEERING↗

DOE OSTI2022

SIERRA/Aero Theory Manual - Version 5.8

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗