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DOE OSTI2025

CASM Monte Carlo: Calculations of the thermodynamic and kinetic properties of complex multicomponent crystals

Monte Carlo techniques play a central role in statistical mechanics approaches that connect macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo techniques for the study of multicomponent crystalline materials within the Clusters Approach to Statistical Mechanics (CASM) software suite, and demonstrates their use in model systems to calculate free energies and kinetic coefficients, study phase transitions, and construct phase diagrams from first principles. Many crystal structures are complex, with multiple sublattices occupied by differing sets of chemical species, along with the presence of vacancies or interstitial species. This imposes constraints on concentration variables, the form of thermodynamic potentials, and the values of kinetic transport coefficients. The framework used by CASM to formulate thermodynamic potentials and kinetic transport coefficients accounting for arbitrarily complex crystal structures is presented and demonstrated with examples of increasing complexity. Additionally, an overview of the capabilities of the CASM software specific to Monte Carlo methods is given, and a new CASM software package is introduced, casm-flow, which helps automate the setup, submission, management, and analysis of Monte Carlo simulations.

Cluster expansion↗

DOE OSTI2016

A journey from nuclear criticality methods to high energy density radflow experiments

Los Alamos National Laboratory is a nuclear weapons laboratory supporting our nation's defense. In support of this mission is a high energy-density physics program in which we design and execute experiments to study radiationhydrodynamics phenomena and improve the predictive capability of our largescale multi-physics software codes on our big-iron computers. The Radflow project’s main experimental effort now is to understand why we haven't been able to predict opacities on Sandia National Laboratory's Z-machine. We are modeling an increasing fraction of the Z-machine's dynamic hohlraum to find multi-physics explanations for the experimental results. Further, we are building an entirely different opacity platform on Lawrence Livermore National Laboratory's National Ignition Facility (NIF), which is set to get results early 2017. Will the results match our predictions, match the Z-machine, or give us something entirely different? The new platform brings new challenges such as designing hohlraums and spectrometers. The speaker will recount his history, starting with one-dimensional Monte Carlo nuclear criticality methods in graduate school, radiative transfer methods research and software development for his first 16 years at LANL, and, now, radflow technology and experiments. Who knew that the real world was more than just radiation transport? Experiments aren't easy and they are as saturated with politics as a presidential election, but they sure are fun.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2017

A journey from nuclear criticality methods to high energy density radflow experiments

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Characterizing the Impact of Soft Errors Affecting Floating-point ALUs using RTL-level Fault Injection

Strategies to detect, correct, or mitigate the impact of soft errors rely on errors-injection experiments. For efficient evaluation, such experiments typically inject errors in software by sampling errors from a candidate distribution. Most often, these strategies randomly select and flip one bit in the output of an instruction. While single-bit flips might constitute a meaningful model for errors affecting hardware, the appropriateness of this model for software-based errors has not been studied. In this paper, we study the manifestation of errors in the output registers due to errors affecting candidate instructions executed by floating point ALUs. We inject single-bit flips into the RTL descriptions of floating point ALUs and analyze the differences between anticipated and observed outputs when executing floating-point addition, subtraction, multiplication, and division. We choose the operands for these instructions randomly and from operands observed in five benchmarks. We observe a rich distribution of errors in the output and analyze their implications for software-based fault-injection campaigns.

Subasi, Omer↗

DOE OSTI2016

4D-CT scans reveal reduced magnitude of respiratory liver motion achieved by different abdominal compression plate positions in patients with intrahepatic tumors undergoing helical tomotherapy

Purpose: While abdominal compression (AC) can be used to reduce respiratory liver motion in patients receiving helical tomotherapy for hepatocellular carcinoma, the nature and extent of this effect is not well described. The purpose of this study was to evaluate the changes in magnitude of three-dimensional liver motion with abdominal compression using four-dimensional (4D) computed tomography (CT) images of several plate positions. Methods: From January 2012 to October 2015, 72 patients with intrahepatic carcinoma and divided into four groups underwent 4D-CT scans to assess respiratory liver motion. Of the 72 patients, 19 underwent abdominal compression of the cephalic area between the subxiphoid and umbilicus (group A), 16 underwent abdominal compression of the caudal region between the subxiphoid area and the umbilicus (group B), 11 patients underwent abdominal compression of the caudal umbilicus (group C), and 26 patients remained free breathing (group D). 4D-CT images were sorted into ten-image series, according to the respiratory phase from the end inspiration to the end expiration, and then transferred to treatment planning software. All liver contours were drawn by a single physician and confirmed by a second physician. Liver relative coordinates were automatically generated to calculate the liver respiratory motion in different axial directions to compile the 10 ten contours into a single composite image. Differences in respiratory liver motion were assessed with a one-way analysis of variance test of significance. Results: The average respiratory liver motion in the Y axial direction was 4.53 ± 1.16, 7.56 ± 1.30, 9.95 ± 2.32, and 9.53 ± 2.62 mm in groups A, B, C, and D, respectively, with a significant change among the four groups (p < 0.001). Abdominal compression was most effective in group A (compression plate on the subxiphoid area), with liver displacement being 2.53 ± 0.93, 4.53 ± 1.16, and 2.14 ± 0.92 mm on the X-, Y-, and Z-axes, respectively. There was no significant difference in respiratory liver motion between group C (displacement: 3.23 ± 1.47, 9.95 ± 2.32, and 2.92 ± 1.10 mm on the X-, Y-, and Z-axes, respectively) and group D (displacement: 3.35 ± 1.55, 9.53 ± 2.62, and 3.35 ± 1.73 mm on the X-, Y-, and Z-axes, respectively). Abdominal compression was least effective in group C (compression on caudal umbilicus), with liver motion in this group similar to that of free-breathing patients (group D). Conclusions: 4D-CT scans revealed significant liver motion control via abdominal compression of the subxiphoid area; however, this control of liver motion was not observed with compression of the caudal umbilicus. The authors, therefore, recommend compression of the subxiphoid area in patients undergoing external radiotherapy for intrahepatic carcinoma.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Experimental Characterization of OpenMP Offloading Memory Operations and Unified Shared Memory Support

The OpenMP specification recently introduced support for unified shared memory, allowing implementation to leverage underlying system software to provide a simpler GPU offloading model where explicit mapping of variables is optional. Support for this feature is becoming more available in different OpenMP implementations on several hardware platforms. A deeper understanding of the different implementation’s execution profile and performance is crucial for applications as they consider the performance portability implications of adopting a unified memory offloading programming style. This work introduces a benchmark tool to characterize unified memory support in several OepnMP compilers and runtimes, with emphasis on identifying discrepancies between different OpenMP implementations as to how they various memory allocation strategies interact with unified shared memory. The benchmark tool is used to characterize OpenMP compilers on three leading High Performance Computing platforms supporting different CPU and device architectures. The benchmark tool is used to assess the impact of enabling unified shared memory on the performance of memory-bound code, highlighting implementation differences that should be accounted for when applications consider performance portability across platforms and compilers.

Elwasif, Wael↗

DOE OSTI2015

Physics-based multiscale coupling for full core nuclear reactor simulation

Numerical simulation of nuclear reactors is a key technology in the quest for improvements in efficiency, safety, and reliability of both existing and future reactor designs. Historically, simulation of an entire reactor was accomplished by linking together multiple existing codes that each simulated a subset of the relevant multiphysics phenomena. Recent advances in the MOOSE (Multiphysics Object Oriented Simulation Environment) framework have enabled a new approach: multiple domain-specific applications, all built on the same software framework, are efficiently linked to create a cohesive application. This is accomplished with a flexible coupling capability that allows for a variety of different data exchanges to occur simultaneously on high performance parallel computational hardware. Examples based on the KAIST-3A benchmark core, as well as a simplified Westinghouse AP-1000 configuration, demonstrate the power of this new framework for tackling—in a coupled, multiscale manner—crucial reactor phenomena such as CRUD-induced power shift and fuel shuffle. 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2017

Precision analysis of the photomultiplier response to ultra low signals

Here, a new computational model for the description of the photon detector response functions measured in conditions of low light is presented, together with examples of the observed photomultiplier signal amplitude distributions, successfully described using the parameterized model equation. In extension to the previously known approximations, the new model describes the underlying discrete statistical behavior of the photoelectron cascade multiplication processes in photon detectors with complex non-uniform gain structure of the first dynode. Important features of the model include the ability to represent the true single-photoelectron spectra from different photomultipliers with a variety of parameterized shapes, reflecting the variability in the design and in the individual parameters of the detectors. The new software tool is available for evaluation of the detectors’ performance, response, and efficiency parameters that may be used in various applications including the ultra low background experiments such as the searches for Dark Matter and rare decays, underground neutrino studies, optimizing operations of the Cherenkov light detectors, help in the detector selection procedures, and in the experiment simulations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2019

Highly Efficient Single-Pot Scarless Golden Gate Assembly

We report that Golden Gate assembly is one of the most widely used DNA assembly methods due to its robustness and modularity. However, despite its popularity, the need for BsaI-free parts, the introduction of scars between junctions, as well as the lack of a comprehensive study on the linkers hinders its more widespread use. Here, we first developed a novel sequencing scheme to test the efficiency and specificity of 96 linkers of 4-bp length and experimentally verified these linkers and their effects on Golden Gate assembly efficiency and specificity. We then used this sequencing data to generate 200 distinct linker sets that can be used by the community to perform efficient Golden Gate assemblies of different sizes and complexity. We also present a single-pot scarless Golden Gate assembly and BsaI removal scheme and its accompanying assembly design software to perform point mutations and Golden Gate assembly. Finally, this assembly scheme enables scarless assembly without compromising efficiency by choosing optimized linkers near assembly junctions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Theoretical and numerical predictions of hypervelocity impact-generated plasma

The hypervelocity impact generated plasmas (HVIGP) in thermodynamic non-equilibrium state were theoretically analyzed, and a physical model was presented to explore the relationship between plasma ionization degree and internal energy of the system by a group of equations including a chemical reaction equilibrium equation, a chemical reaction rate equation, and an energy conservation equation. A series of AUTODYN 3D (a widely used software in dynamic numerical simulations and developed by Century Dynamic Inc.) numerical simulations of the impacts of hypervelocity Al projectile on its targets at different incident angles were performed. The internal energy and the material density obtained from the numerical simulations were then used to calculate the ionization degree and the electron temperature. Based on a self-developed 2D smooth particle hydrodynamic (SPH) code and the theoretical model, the plasmas generated by 6 hypervelocity impacts were directly simulated and their total charges were calculated. The numerical results are in good agreements with the experimental results as well as the empirical formulas, demonstrating that the theoretical model is justified by the AUTODYN 3D and self-developed 2D SPH simulations and applicable to predict HVIGPs. The study is of significance for astrophysical and cosmonautic researches and safety.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2019

Effect of Carbon Dioxide Recirculation and Pressure on Efficiency of the TIPS and ENEL Oxy-Coal Power Cycles

This paper presents the results of thermal efficiency of two coal based oxy-combustion thermodynamic cycles that are modeled using aspen plus. The objective of the present study is to perform a parametric analysis, investigating the effect of different recirculation ratios at different pressures on the efficiencies of the cycle named for the company, ENEL, and the thermo energy power system, TIPS, cycles using aspen plus® software. Variables include the flue gas recycle flow rate, the combustor temperature, and the operational pressure. Five recirculation ratios were investigated, ranging from 20% to 75%. It was determined that as the amount of recycled gas into the combustor increased, the thermal efficiency increased for both the TIPS and ENEL cycles. Here, the highest thermal efficiency for TIPS is 37% and for ENEL is 38%, both occurring at a 75% recirculation ratio. After investigation, since combustion temperature and specific heat capacity decreases at higher recirculation ratios, the mass flow rate was the dominant factor that contributes to the increase in thermal efficiency of the cycle. At each recirculation ratio, the effect of pressure is also determined. For ENEL, the increase in cycle efficiency is 10% over the pressure range of 1–12 bar at a recirculation ratio of 20%, while the increase in cycle efficiency is only 1.5% at a higher recirculation ratio of 75%. For TIPS, the cycle efficiency increases by 4% at the recirculation ratio of 20% and increases by 3% at the recirculation ratio of 75% for a pressure range of 50–80 bar.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2015

SU-F-BRA-07: Dosimetric Verification of the Valencia Skin Applicator Using Gafchromic EBT3 Film

Purpose: The Valencia applicators have recently been introduced for HDR treatment of small and shallow superficial skin lesions (< 20 mm diameter and 3-mm depth). Per AAPM TG 56, any HDR applicator internal dimensions must be verified prior to clinical use. However radiographic and tomographic imaging to validate the Valencia applicators is impractical due to the Tungsten alloy housing and flattening filter. In this study, we propose to use EBT3 film to indirectly confirm the physical integrity of the Valencia applicators. Methods: Treatment plans were created using the Oncentra MasterPlan TPS v4.5 for the H2 (20-mm dia.) and H3 (30-mm dia.) Valencia Applicators. A virtual CT phantom (2-mm slice thickness) was created with one source position in water. The published effective depth method was used for each applicator to delivery 500 cGy to a 3-mm depth using the TG-43 formalism. Film measurements (n=3) at 3-mm depth and vertical plane in solid water were performed for each applicator to verify the prescribed dose calculated by the TPS. Percent depth dose curves and off-axis profiles (phantom surface and 3-mm depth) were measured and compared to published data. Films were analyzed using an in-house written program and RIT113 v6 software. Film calibration was performed per TG-55 protocol using the Ir-192 source with NIST-traceable calibration. Results: The prescription absolute dose difference was 1% for the Valencia H2 applicator and 4% for the Valencia H3 applicator. The measured percent depth dose curves and off-axis dose profiles measured for the H2 and H2 Valencia applicators are in excellent agreement with the Granero et al. Monte Carlo results{sup 1}. Conclusion: Gafchromic EBT3 film can be used to indirectly verify the internal components of special HDR skin applicators constructed from high Z materials.{sup 1}Granero et al. “Design and evaluation of a HDR skin applicator with flattening filter”, Med. Phys. 35(2), 495–503, 2008.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Backscatter dose effects for high atomic number materials being irradiated in the presence of a magnetic field: A Monte Carlo study for the MRI linac

Purpose: To quantify and explain the backscatter dose effects for clinically relevant high atomic number materials being irradiated in the presence of a 1.5 T transverse magnetic field. Methods: Interface effects were investigated using Monte Carlo simulation techniques. We used GPUMCD (v5.1) and GEANT4 (v10.1) for this purpose. GPUMCD is a commercial software written for the Elekta AB, MRI linac. Dose was scored using GPUMCD in cubic voxels of side 1 and 0.5 mm, in two different virtual phantoms of dimensions 20 × 20 × 20 cm and 5 × 5 × 13.3 cm, respectively. A photon beam was generated from a point 143.5 cm away from the isocenter with energy distribution sampled from a histogram representing the true Elekta, MRI linac photon spectrum. A slab of variable thickness and position containing either bone, aluminum, titanium, stainless steel, or one of the two different dental filling materials was inserted as an inhomogeneity in the 20 × 20 × 20 cm phantom. The 5 × 5 × 13.3 cm phantom was used as a clinical test case in order to explain the dose perturbation effects for a head and neck cancer patient. The back scatter dose factor (BSDF) was defined as the ratio of the doses at a given depth with and without the presence of the inhomogeneity. Backscattered electron fluence was calculated at the inhomogeneity interface using GEANT4. A 1.5 T magnetic field was applied perpendicular to the direction of the beam in both phantoms, identical to the geometry in the Elekta MRI linac. Results: With the application of a 1.5 T magnetic field, all the BSDF’s were reduced by 12%–47%, compared to the no magnetic field case. The corresponding backscattered electron fluence at the interface was also reduced by 45%–64%. The reduction in the BSDF at the interface, due to the application of the magnetic field, is manifested in a different manner for each material. In the case of bone, the dose drops at the interface contrary to the expected increase when no magnetic field is applied. In the case of aluminum, the dose at the interface is the same with and without the presence of the aluminum. For all of the other materials the dose increases at the interface. Conclusions: The reduction in dose at the interface, in the presence of the magnetic field, is directly related to the reduction in backscattered electron fluence. This reduction occurs due to two different reasons. First, the electron spectrum hitting the interface is changed when the magnetic field is turned on, which results in changes in the electron scattering probability. Second, some electrons that have curved trajectories due to the presence of the magnetic field are absorbed by the higher density side of the interface and no longer contribute to the backscattered electron fluence.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Open Source Software Prevalence Ingest Tool

The OSSP Ingest Tool accepts user-input organizational information, ingests IT/OT asset lists in Excel format, and ingests the associated CycloneDX SBOM's. It then performs analytics demonstrating the ability to answer the follow research questions: o RQ1. Ability to identify all OSS services running on, and all OSS components present within, an OT device o RQ1a: Ability to differentiate multiple versions of the same OSS component within each OT device. o RQ1b: Ability to differentiate running from not-running OSS components. o RQ1c: Ability to differentiate based on the originator of the component, because a supplier may have modified it after retrieval from the upstream software source. o RQ2. Ability to correlate the identity of a single OSS component across multiple OT devices, mitigating common name variations such as differences in capitalization, '-' vs '_', and so on. o RQ3. Ability to perform subset analysis of OSS components across multiple OT devices o RQ3a: Ability to perform subset analysis across OSS libraries, generating density & distribution graphs to identify commonly-used libraries and outliers. o RQ3b: Ability to perform subset analysis of a single OSS library, generating density & distribution by CI sector, by device type, by device make/model, and/or by firmware version. o RQ3c: Ability to perform subset analysis by grouping OSS libraries according to programming language, then overlay with RQ4b. o RQ3d: Ability to perform subset analysis by OSS upstream source, providing insight into degree of modifications performed by suppliers. o RQ4. Ability to identify dependencies (transitive and direct) of each differentiated OSS library within each OT device, and enable RQ1,2,3 iteratively for dependencies. o RQ1. Ability to identify all OSS services running on, and all OSS components present within, an OT device o RQ1a: Ability to differentiate multiple versions of the same OSS component within each OT device. o RQ1b: Ability Page

Kapadia, Shayna [Lawrence Livermore National Labor↗

DOE OSTI2025

Hydrogen Diffusion Through Stainless Steel

SAND2025-14430O Hydrogen Diffusion Through Stainless Steel is a tool that employs a finite difference method algorithm to solve Fick's law and other mass transport models pertinent to the diffusion of hydrogen through stainless steel. Additionally, the software uses particle swarm optimization to determine physical parameters based on experimental data. 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.

Mason, Tyler [Sandia National Lab. (SNL-CA), Liver↗

DOE OSTI2019

Data from Highly Efficient Single-Pot Scarless Golden Gate Assembly

Golden Gate assembly is one of the most widely used DNA assembly methods due to its robustness and modularity. However, despite its popularity, the need for BsaI-free parts, the introduction of scars between junctions, as well as the lack of a comprehensive study on the linkers hinders its more widespread use. Here, we first developed a novel sequencing scheme to test the efficiency and specificity of 96 linkers of 4-bp length and experimentally verified these linkers and their effects on Golden Gate assembly efficiency and specificity. We then used this sequencing data to generate 200 distinct linker sets that can be used by the community to perform efficient Golden Gate assemblies of different sizes and complexity. We also present a single-pot scarless Golden Gate assembly and BsaI removal scheme and its accompanying assembly design software to perform point mutations and Golden Gate assembly. This assembly scheme enables scarless assembly without compromising efficiency by choosing optimized linkers near assembly junctions.

Conversion↗

DOE OSTI2021

AmeriFlux FLUXNET-1F CA-ER1 Elora Research Station

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site CA-ER1 Elora Research Station. This is the FLUXNET version of the carbon flux data for the site CA-ER1 Elora Research Station produced by applying the standard ONEFlux (1F) software. Site Description - This is an agricultural site that typically grows corn. It is part of a larger research project on N2O fluxes from different fertilizer treatments. The site is relatively flat and homogenous. The site has been managed as agricultural land since the 1960’s and records exist of the previously-grown crops.

Wagner-Riddle, Claudia↗

DOE OSTI2025

Hydropower Biological Evaluation Toolset (HBET) Version 3.0: User Guide

The Hydropower Biological Evaluation Tools (HBET) software package, developed by Pacific Northwest National Laboratory (PNNL), is designed to assemble, organize, and process data collected by Sensor Fish and live fish. HBET enable users to characterize the hydraulic conditions of hydropower structures and estimate fish injury and mortality rates from various stressors. Future updates of the software may support other technologies, such as bead tracking in physical models and computational fluid dynamics. The HBET program can be customized to analyze different hydraulic applications, including turbines, spillways, weirs, pumped storage, and other user-defined functions, and therefore, help researchers, turbine designers, hydropower operators, and regulators better evaluate hydropower structures regarding their environmental sustainability and cost-effectiveness. Added content to the user guide about the new feature for predicting absolute injury rates.

13 HYDRO ENERGY↗