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All sources NASA NTRS DOE OSTI

DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Micromagnetic Modeling of a Magnetically Unstable Zone and Its Geological Significances

Abstract Recent micromagnetic simulations have found that particles in the transitional zone between the single domain (SD) and single vortex (SV) zone are prone to thermal and external magnetic field instabilities that could adversely affect the accuracy of interpretations of paleomagnetic recordings. In this study, we attempt to evaluate the internal magnetization characteristics of these magnetically unstable (MU) particles and the influence on paleomagnetic observations by simulating the magnetic behavior of 68–104 nm truncated octahedral magnetite particles using the MERRILL modeling software. We found that: (a) The size region of the “MU zone” for grains of truncated octahedron shape is different from cubic octahedrons and spheres, indicating that the zone may be controlled by the geometry and shape of particles; (b) The MU zone has a range of 79–97 nm region, which is dominated by a hard‐axis aligned single vortex (HSV); and (c) MU particles are unstable as a function of temperature and have low coercive fields. Finally, the numerical fitting of hysteresis parameters for experimental data suggests that the influence of such MU particles in samples should not be ignored, especially for samples with fine‐grained magnetic minerals as the primary magnetic recording carriers. This research has extended our understanding of the behavior of the “MU zone” and its significance on paleomagnetic records.

Wang, Yuqin↗

DOE OSTI2021

dCache: Inter-disciplinary storage system

The dCache project provides open-source software deployed internationally to satisfy ever more demanding storage requirements. Its multifaceted approach provides an integrated way of supporting different use-cases with the same storage, from high throughput data ingest, data sharing over wide area networks, efficient access from HPC clusters and long term data persistence on a tertiary storage. Though it was originally developed for the HEP experiments, today it is used by various scientific communities, including astrophysics, biomed, life science, which have their specific requirements. In this paper we describe some of the new requirements as well as demonstrate how dCache developers are addressing them.

Mkrtchyan, Tigran↗

DOE OSTI2021

SINGLE: Atomic-resolution structure identification of nanocrystals by graphene liquid cell EM

Analysis of the three-dimensional (3D) structures of nanocrystals with solution-phase transmission electron microscopy is beginning to reveal their unique physiochemical properties. We developed a “one-particle Brownian 3D reconstruction method” based on imaging of ensembles of colloidal nanocrystals using graphene liquid cell electron microscopy. Projection images of differently rotated nanocrystals are acquired using a direct electron detector with high temporal (<2.5 ms) resolution and analyzed to obtain an ensemble of 3D reconstructions. Here, we introduce computational methods required for successful atomic-resolution 3D reconstruction: (i) tracking of the individual particles throughout the time series, (ii) subtraction of the interfering background of the graphene liquid cell, (iii) identification and rejection of low-quality images, and (iv) tailored strategies for 2D/3D alignment and averaging that differ from those used in biological cryo–electron microscopy. Our developments are made available through the open-source software package SINGLE.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

sCO2 heat exchanger control software

SAND2022-6992 O The sCO2 Heat Exchanger Control Software was written for control and operation of high temperature, high pressure supercritical CO2 systems designed for use as heat exchangers. The software was written using the basic LabVIEW package with LabVIEW modules added to it. The software controls valves and actuators, displays data from pressure transducers and thermocouples, and is able to record data at different storage rates. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Garcia Maldonado, Luis↗

DOE OSTI2017

PIMAL: Phantom wIth Moving Arms and Legs Version 4.1.0

Computational phantoms with articulated arms and legs have been developed to enable radiation dose estimation for male and female receptors in different postures. Using a user-friendly graphical user interface (GUI), the PIMAL (Phantom wIth Moving Arms and Legs) software can be employed to adjust the posture of a phantom, generate a corresponding input file for the Monte Carlo N-Particle (MCNP®) radiation transport code, and perform the radiation transport simulations for the dose calculations in MCNP®. The MCNP® code can be run natively from the PIMAL interface or externally in the MCNP® command prompt via the generated MCNP® PIMAL input file.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2020

FLOP for FLAG Output Plotting

The Los Alamos hydrodynamics code, FLAG, is capable of dumping many types of output for many different variables in an array of formats. While some outputs are best viewed in a multidimensional engineering analysis visualization software, others are best viewed as 1-D “this versus that” curves. During development of a FLAG model, it is frequently required to quickly assess a model’s performance by reviewing such curves, and doing so may involve writing scripts repeatedly, adapting them each time to a specific model’s parameters. This report describes an application developed specifically to improve user efficiency in reviewing 1-D curve dumps from FLAG.

42 ENGINEERING↗

DOE OSTI2022

National Ignition Facility. Facility and Infrastructure Systems Maintenance Plan

Ensuring the reliability of the NIF, including its support systems, laser systems, target diagnostic systems, and utilities, is essential to the availability of the NIF in its support of NNSA missions. NIF is a key capability in the DOE Stockpile Stewardship Program and supports high energy physics experiments for nuclear weapons, energy, and astrophysics applications. High system reliability provides opportunities for shots and scientific discoveries with opportunities to enhance and upgrade capabilities. This Maintenance Plan (MP) identifies the policies and procedures used to perform and support asset management of the NIF Facility and Infrastructure Systems (FInS), NIF Lasers & Alignment (LASE), NIF Target Experimental Operations (TOPS), NIF Target Area Science and Engineering (TASE), and NIF&PS Control Systems (NCS). The FInS systems include the facility, HVAC, contamination control, beampath, and Line Replaceable Units (LRUs) as well as utilities which create the beampath environments, such as vacuum, argon, or clean dry air. The LASE systems are Programmatic systems which include laser diagnostics, alignment, power conditioning, pulsed power, and input laser systems. The TOPS and TASE systems are also Programmatic systems which include target and diagnostic delivery systems and positioners, many different insertable and fixed target diagnostics, and cryogenic and target gas fill systems. Finally, the NCS systems include both software and hardware for industrial and shot operation control systems. Policies governing administrative and operational practices related to maintenance of FInS, LASE, TOPS, TASE, and NCS systems are described in this plan. In addition, the plan provides processes and procedures for managing, tracking, and documenting the work. This document, the NIF Operations Management Plan, NIF-5020544 (Ref. 1), and NIF Shot Operations Plan, NIF-5018506 (Ref. 2), together satisfy the requirements of the Conduct of Operations. Duties, responsibilities, and reporting requirements of the various positions associated with FInS, LASE, and TOPS maintenance are detailed in this plan. The FInS systems include both Real Property systems with asset management requirements specified in DOE Order 430.1C (Ref. 3) and Programmatic systems. In addition, for FInS, there is a list of the System Level Maintenance Plans (SLMPs) in NIF-1007419198 (Ref. 4) which provide the system descriptions and maintenance plan and schedule. In addition, the list includes the Reliability Centered Maintenance (RCM) and Experience Centered Maintenance (ECM) evaluations that have been performed for applicable FInS systems as well as reliability criticality per Section 3.5. The -AM version of the NIF Maintenance Plan focuses on the reliability program for FInS, LASE, TOPS, TASE, and NCS within the context of the overall NIF Reliability, Availability, and Maintainability (RAM) program and incorporates changes since the -AL version from August 2011 and has been updated to be fully consistent with the updates to Ref. 1. It also includes asset management considerations, updates to the Work Order (WO) process within the NIF Computerized Maintenance Management System (CMMS) which is EAM infor® System Maintenance and Reliability Tracking (SMaRT) (Ref. 5), and updates to metrics and key performance indicators (KPIs).

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

Chemical Reactivity Through Adaptive Quantum Mechanics/Many-Body Representations: Theoretical Development, Software Implementation, and Applications (Final Report)

The main objective of this research project was the development and application of a new theoretical/computational framework to model chemical transformations and electronic excitations in fluid mixtures across different phases. Our theoretical/computational framework combines our data-driven many-body (DD-MB) potentials representing molecular interactions with adaptive schemes for modeling chemical reactions in solution. The combination of these two components resulted in an adaptive quantum mechanics/many-body (adQM/MB) method that largely suppresses discontinuities between QM and MM regions, which affect existing QM/MM methods, and thus provides an accurate representation of both quantum mechanical and environmental effects through a rigorous description of mutual polarization between QM and MM regions. The implementation of our DD-MB potentials and adQM/MB method in popular software enabled computer simulations of solvation phenomena, reactive processes, and electronic excitations in fluid mixtures with chemical and spectroscopic accuracy, representing a major step toward realistic computer simulations of a wide range of molecular systems relevant to the DOE mission.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Computational tools and algorithms for ion mobility spectrometry-mass spectrometry

Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

TDEP: Temperature Dependent Effective Potentials

The Temperature Dependent Effective Potential (TDEP) method is a versatile and efficient approach to include temperature in ab initio materials simulations based on phonon theory. TDEP can be used to describe thermodynamic properties in classical and quantum ensembles, and several response properties ranging from thermal transport to Neutron and Raman spectroscopy. A stable and fast reference implementation is given in the software package of the same name described here. The underlying theoretical framework and foundation is briefly sketched with an emphasis on discerning the conceptual difference between bare and effective phonon theory, in both self-consistent and non-self-consistent formulations. References to numerous applications and more in-depth discussions of the theory are given.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Multi–LDAP Dynamic User Management Tool Utilizing Oracle Application Express and PL/SQL

A Center for Infrastructure Security Analysis (CISA) client system required support of multiple Lightweight Directory Access Protocol (LDAP) directories for multiple, varied user communities. The LDAP directories were all based upon different technologies, i.e., Microsoft Active Directory (AD), Microsoft Active Directory Lightweight Directory Services (ADLDS), and Oracle Internet Directory (OID), depending on system setup, security requirements, and legacy software. Research revealed that PL/SQL provided the capability to execute dynamic PL/SQL and SQL blocks. The dynamic capabilities were utilized along with several configuration tables to provide an object-oriented, polymorphic-like behavior. This architecture was chosen so that a top-level application programming interface (API) could be defined for all calls, no matter what type of LDAP was being manipulated, as each LDAP type has slightly different attributes and requirements. The dynamic nature of the user management system allowed for easy setup and utilization of any new LDAP directories, minimizing the time and effort expended on system changes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Hardware Aware Mitigation of Timing Side-Channel Vulnerabilities in Critical Infrastructure Software

Program runtime/timing attacks exploit variations in a program’s execution times to extract sensitive information from the program (e.g. encryption keys, sensitive variable data, intellectual property). State-of-the-art solutions to runtime sidechannel attacks attempt to balance the execution time of the sensitive code for different control flow paths to eliminate the timing leakage. However, during the mitigation process, most techniques do not consider the underlying hardware/device on which the target program is supposed to run on. This can lead to over-fixing (unnecessary extra operations), under-fixing (not solving the imbalance properly), and even failures. We propose DISARM, a joint hardware-software methodology (unlike any existing solution) for mitigating runtime side-channel vulnerabilities that utilizes timing values from real embedded devices to generate targeted software fixes. We implement DISARM to support C/C++/Java source codes and validate it across 22 standard benchmarks. DISARM outperforms state-of-the-art solutions such as PENDULUM and DifFuzzAR in terms of execution time overhead (up to −46%), code size overhead (up to −10%), and correctness (no failures) on five different embedded/edge devices.

Suha, Tasneem [University of Maine]↗

DOE OSTI2018

Methodology for Building Granular Testing in Multicomponent Scientific Software

Computational science and engineering communities develop complex application software with multiple mathematical models that need to interact with one another. Partly due to complexity of verifying scientific software, and partly because of the way incentives work in science, there has been insufficient testing of these codes. With a spotlight on the results produced with scientific software, and increasing awareness of software testing and verification as a critical contributor to the reliability of these results, testing is gaining more attention by the developing teams. However, many science teams struggle to find a good solution for themselves due either to lack of training or lack of resources within the team. In this experience paper, we describe test development methodologies utilized in two different scenarios: one explains a methodology for building granular tests where none existed before, while the second demonstrates a methodology for selecting test cases that build confidence in the software through a process similar to scaffolding. The common insight from both the experiences is that testing should be a part of software design from the beginning for better software and scientific productivity.

test building, granular testing, Earth system mode↗

DOE OSTI2023

Implementation of a High-Fidelity Interface Resolving Method in Nek5000

The development and utilization of computational fluid dynamics (CFD) models for large, high-temperature electric melters in the Waste Treatment and Immobilization Plant (WTP) in eastern Washington State have proven to be valuable for various purposes. These models allow for a better understanding of the physio-chemical processes occurring within the melter vessels and can contribute to improving operational efficiency, throughput, and addressing operational issues related to vitrification. The CFD models employed for these melter vessels incorporate multiphase fluid flow and heat transfer simulations in different regions, including the plenum, cold cap, and molten glass regions. As the tank waste and glass formers are introduced into the melter, a reacting batch layer known as the cold cap forms on top of the molten glass. To enhance the melt rate, forced convection bubblers located at the bottom of the melters generate convection currents that help homogenize the molten glass and provide heat to the cold cap. As the bubbles rise through the highly viscous glass, they adopt a spherical-cap shape [1]. Meanwhile, the conversion of the batch to glass generates significant amounts of gases (such as water vapor, carbon dioxide, sulfur dioxide, and NOx) due to thermal decomposition [2]. These gases become trapped between the cold cap and molten glass, forming a foam layer [3]. For modeling multiphase flow in CFD and heat transfer simulations of waste glass melters at different scales, efforts are underway to augment the capabilities of the Nek5000 [4] and NekRS [5] open-source codes [6]. Nek5000/NekRS is a scalable and efficient spectral element code that has been successfully applied to a wide range of fluid dynamics problems. By leveraging the Nek5000/NekRS software, it becomes possible to model the melter systems more affordably and with lower computational requirements compared to currently utilized commercial CFD software. The specific objectives of this ongoing effort include: 1. Implementation of a level set method in Nek5000/NekRS: The level set method is a numerical technique commonly employed in CFD simulations to track and represent the interface between different phases or materials accurately. By incorporating this method into Nek5000/NekRS, the ability to simulate multiphase flows in waste glass melters at a high level of fidelity can be achieved. 2. Demonstration of capability for air bubbling through molten glass: As part of the development process, a specific case of air bubbling through molten glass will be simulated using the augmented Nek5000/NekRS code. This demonstration aims to showcase the ability of the software to accurately capture and analyze the complex phenomena involved in the multiphase flow within waste glass melters. By achieving these objectives, the improved Nek5000/NekRS code will offer a powerful computational tool for simulating and analyzing waste glass melter systems, enabling better understanding, optimization, and troubleshooting of these vitrification processes. The ability to accurately model and simulate multiphase flows has broad relevance across many industries and scientific domains, and the improved functionality can contribute to advancements in various fields beyond waste glass melter simulations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2026

DISARM: Target Electronic Device Informed Mitigation of Software Runtime Side-Channel Vulnerabilities

Program runtime/timing attacks exploit variations in a program’s execution times to extract sensitive information from the program (e.g. encryption keys, sensitive variable data, intellectual property). State-of-the-art solutions to runtime side-channel attacks attempt to balance the execution time of the sensitive code for different control flow paths to eliminate the timing leakage. However, during the mitigation process, most techniques do not consider the underlying hardware/device on which the target program is supposed to run on. This can lead to over-fixing (unnecessary extra operations), under-fixing (not solving the imbalance properly), and even failures. Here, we propose DISARM, a joint hardware-software methodology (unlike any existing solution) for mitigating runtime side-channel vulnerabilities that utilizes timing values from real embedded devices to generate targeted software fixes. We implement DISARM to support C/C++/Java source codes and validate it across 22 standard benchmarks. DISARM outperforms state-of-the-art solutions such as PENDULUM and DifFuzzaR in terms of execution time overhead, code size overhead, and correctness on five different embedded/edge devices.

Timing/runtime side-channel↗

DOE OSTI2023

Energy Northwest — Advanced Grid Interactive Load Efficiency (AGILE) : A Techno-economic Assessment

The Advanced Grid Interactive Load Efficiency project team, led by Energy Northwest, was awarded funding as part of the fourth round of the Clean Energy Fund program to investigate, co-create, and complete a preliminary design for grid-interactive efficient buildings (GEBs) for a number of schools served by Grays Harbor PUD. The project team has evaluated different combinations of systems at selected school buildings and the potential to respond to grid and customer needs, and develop a preliminary system technical design, including specifying desired GEB technology options, determining communication and electrical interface requirements, assessing control software sensor requirements, and interfacing with building management systems. PNNL led the techno-economic assessment efforts, leveraging its advanced modeling and analytical methods and tools developed for building-to-grid integration. This report documents the economic assessment for different GEB design options, encompassing an in-depth examination of use cases and value propositions, assumptions and inputs, models, methods, case studies, as well as key findings.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Formally Verified ZTA Requirements for OT/ICS Environments with Isabelle/HOL

The clean energy transformation includes the integration of distributed energy resources with the power grid, which has led to a substantial increase in the complexity of power grids infrastructure and the underlying operational technology environment. Power grids infrastructure represents an operational technology environment that has become a system of systems, integrating heterogeneous devices which are both software-and hardware-intensive; as a result, there are increasing demands to exploit advances in the commodity of software-hardware infrastructures to improve energy systems requirements such as cybersecurity and resilience. In such a setting, system requirements at different levels mix, which leads to vulnerabilities and undesirable outcomes. The use of formal methods to characterize and prove system requirements removes ambiguity, increases automation, and provides high levels of assurance and reliability. In this paper, we contribute a methodology and a framework for the system-level verification of zero trust architecture requirements in operational technology environments. We define a formal specification for the core functionalities of operational technology environments, the corresponding invariants, and security proofs. Of particular note is our modular approach for the formal verification of asynchronous interactions in operational technology environments. The formal specification and the proofs have been mechanized using the interactive theorem proving environment Isabelle/HOL.

formal methods↗