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At least 1,603 records · Page 89

Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications

Lack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability, Workflow, and Unit Operation, effectively streamlining the Design‑Build‑Test‑Learn (DBTL) cycle. This framework enables more modular, flexible, and automated experimental workflows. It improves communication between researchers and systems, supports reproducibility, and facilitates better integration of software tools and artificial intelligence. Our approach lays the foundation for a globally interoperable biofoundry network, advancing collaborative synthetic biology and accelerating innovation in response to scientific and societal challenges.

Kim, Haseong↗

Issues in Bi-Directional Interoperability between BIM and BEM

The state-of-the-art interoperability between Building Information Modeling (BIM) and Building Energy Modeling (BEM) is mainly one-way. BEM software like EnergyPlus takes design input from BIM and simulates the energy consumption of the building. BIM, however, is unable to leverage energy simulation results from BEM smoothly. This lack of bi-directional interoperability between BIM and BEM prevents buildings from seeking more energy-efficient design options and limits BIM applications in optimal generative design. In this research, the authors have conducted the following activities related to two-way interoperability between BIM and BEM: (1) surveyed its current status through literature review, (2) investigated barriers to the bi-directional interoperability, and (3) suggested possible approaches to enable bi-directional interoperability and research outlook in the field. As a result, the authors have identified three main barriers to BIM BEM interoperability, namely, inefficient collaboration, limited scope in information transformation, and lack of BEM to BIM transformation. Future directions are suggested to address these barriers.

building design↗

Investigation of periodically driven systems by x-ray absorption spectroscopy using asynchronous data collection mode

Here, we report the development, testing, and demonstration of a setup for modulation excitation spectroscopy experiments at the Inner Shell Spectroscopy beamline of National Synchrotron Light Source - II. A computer algorithm and dedicated software were developed for asynchronous data processing and analysis. We demonstrate the reconstruction of X-ray absorption spectra for different time points within the modulation pulse using a model system. This setup and the software are intended for a broad range of functional materials which exhibit structural and/or electronic responses to the external stimulation, such as catalysts, energy and battery materials, and electromechanical devices.

36 MATERIALS SCIENCE↗

CSP-Plant Modeling Guidelines and Compliance of the System Advisor Model (SAM)

Accurately modeling risks, costs, and electricity output is essential to the financing and advancement of concentrating solar power projects. To address this need, a group of CSP experts created a guideline document, titled SolarPACES Guideline for Bankable STE Yield Assessment [1]. To make this information more accessible and allow stakeholders to test specific models against the recommendations, the guidelines have been condensed into a spreadsheet-based checklist. The checklist was applied to NREL's System Advisor Model (SAM) software, providing useful feedback to both the checklist group and the SAM development team. This study showed strong agreement between SAM and the guidelines, demonstrated the use of the guidelines in model validation, and resulted in several recommended improvements to SAM.

14 SOLAR ENERGY↗

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-Performance Computing Based EMT Simulation: Power Grid with IBRs

Electromagnetic transient (EMT) simulation of power grids with high-fidelity models of inverter-based resources (IBRs) is time-consuming and difficult to scale. The necessity for high-fidelity models of IBRs that incorporate the dynamics of individual inverters within IBRs has been showcased in recent studies. These studies focused on events with partial power reduction in each IBR during a transmission line fault in the power grid. These types of events have been documented in multiple North American Electric Reliability Council (NERC) reports in the past decade. It is imperative then to find solutions to speed-up EMT simulations and scale the size of the region with IBRs studied in EMT simulations. In this paper, a combination of numerical simulation algorithms with high-performance computing techniques are employed in discretization and linear solvers employed in the proposed RE-INTEGRATE EMT simulation platform for power grid with IBRs. For ease of scalability, modular and object-oriented programming is used as these techniques are implemented. Additionally, automation software is developed to convert legacy software codes to the proposed RE-INTEGRATE EMT simulation platform. Thereafter, this platform is evaluated on multi-core central processing units (CPUs). Finally, scale-up tests are performed to showcase the scalability that is possible.

Marthi, Phani Ratna Vanamali [ORNL] (ORCID:0000000↗

Dedicated short range communications used as fail-safe in autonomous navigation

Here in this paper, we have analyzed scenarios for leader-follower vehicle convoys that have the potential to be unsafe, hazardous, or even fatal in order to provide insight on dangerous driving conditions for autonomous vehicle platoons. These scenarios were created in a simulation software called Prescan, and are made to reflect the behavior of the vehicle dynamics and sensor characteristics of a real-world vehicle convoy that is currently being tested at the American Center for Mobility (ACM) and sponsored by the Department of Energy (DOE), National Renewable Energy Laboratory (NREL), the U.S. Army Combat Capabilities Development Command - Ground Vehicle Systems Center (U.S. Army CC-DEVCOM) and the Michigan Department of Transportation (MDOT). The follower vehicle in this study is tested under multiple scenarios, equipped with a Dedicated Short Range vehicle-to-vehicle communication system (DSRC), a radar-based adaptive cruise control system (ACC) and a precision global positioning system (GPS).

42 ENGINEERING↗

WE-AB-BRA-08: Results of a Multi-Institutional Study for the Evaluation of Deformable Image Registration Algorithms for Structure Delineation Via Computational Phantoms

Purpose: To investigate the accuracy of various algorithms for deformable image registration (DIR), to propagate regions of interest (ROIs) in computational phantoms based on patient images using different commercial systems. This work is part of an Italian multi-institutional study to test on common datasets the accuracy, reproducibility and safety of DIR applications in Adaptive Radiotherapy. Methods: Eleven institutions with three available commercial solutions provided data to assess the agreement of DIR-propagated ROIs with automatically drown ROIs considered as ground-truth for the comparison. The DIR algorithms were tested on real patient data from three different anatomical districts: head and neck, thorax and pelvis. For every dataset two specific Deformation Vector Fields (DVFs) provided by ImSimQA software were applied to the reference data set. Three different commercial software were used in this study: RayStation, Velocity and Mirada. The DIR-mapped ROIs were then compared with the reference ROIs using the Jaccard Conformity Index (JCI). Results: More than 600 DIR-mapped ROIs were analyzed. Putting together all JCI data of all institutions for the first DVF, the mean JCI was 0.87 ± 0.7 (1 SD) while for the second DVF JCI was 0.8 ± 0.13 (1 SD). Several considerations on different structures are available from collected data: the standard deviation among different institutions on specific structure raise as the larger is the applied DVF. The higher value is 10% for bladder. Conclusion: Although the complexity of deformation of human body is very difficult to model, this work illustrates some clinical scenarios with well-known DVFs provided by specific software. CI parameter gives the inter-user variability and may put in evidence the need of improving the working protocol in order to reduce the inter-institution JCI variability.

60 APPLIED LIFE SCIENCES↗

SU-F-I-53: Coded Aperture Coherent Scatter Spectral Imaging of the Breast: A Monte Carlo Evaluation of Absorbed Dose

Purpose: Coherent scatter based imaging has shown improved contrast and molecular specificity over conventional digital mammography however the biological risks have not been quantified due to a lack of accurate information on absorbed dose. This study intends to characterize the dose distribution and average glandular dose from coded aperture coherent scatter spectral imaging of the breast. The dose deposited in the breast from this new diagnostic imaging modality has not yet been quantitatively evaluated. Here, various digitized anthropomorphic phantoms are tested in a Monte Carlo simulation to evaluate the absorbed dose distribution and average glandular dose using clinically feasible scan protocols. Methods: Geant4 Monte Carlo radiation transport simulation software is used to replicate the coded aperture coherent scatter spectral imaging system. Energy sensitive, photon counting detectors are used to characterize the x-ray beam spectra for various imaging protocols. This input spectra is cross-validated with the results from XSPECT, a commercially available application that yields x-ray tube specific spectra for the operating parameters employed. XSPECT is also used to determine the appropriate number of photons emitted per mAs of tube current at a given kVp tube potential. With the implementation of the XCAT digital anthropomorphic breast phantom library, a variety of breast sizes with differing anatomical structure are evaluated. Simulations were performed with and without compression of the breast for dose comparison. Results: Through the Monte Carlo evaluation of a diverse population of breast types imaged under real-world scan conditions, a clinically relevant average glandular dose for this new imaging modality is extrapolated. Conclusion: With access to the physical coherent scatter imaging system used in the simulation, the results of this Monte Carlo study may be used to directly influence the future development of the modality to keep breast dose to a minimum while still maintaining clinically viable image quality.

60 APPLIED LIFE SCIENCES↗

KiT-RT: An Extendable Framework for Radiative Transfer and Therapy

Here, in this article, we present Kinetic Transport Solver for Radiation Therapy (KiT-RT), an open-source C++-based framework for solving kinetic equations in therapy applications available at https://github.com/CSMMLab/KiT-RT . This software framework aims to provide a collection of classical deterministic solvers for unstructured meshes that allow for easy extendability. Therefore, KiT-RT is a convenient base to test new numerical methods in various applications and compare them against conventional solvers. The implementation includes spherical harmonics, minimal entropy, neural minimal entropy, and discrete ordinates methods. Solution characteristics and efficiency are presented through several test cases ranging from radiation transport to electron radiation therapy. Due to the variety of included numerical methods and easy extendability, the presented open-source code is attractive for both developers, who want a basis to build their numerical solvers, and users or application engineers, who want to gain experimental insights without directly interfering with the codebase.

97 MATHEMATICS AND COMPUTING↗

Kohn-Sham Solver (KSSOLV) v2.0

KSSOLV is a MATLAB toolbox for solving Kohn-Sham density functional theory based electronic structure eigenvalue problems. It uses an object oriented features of MATLAB to represent atom, molecules, wavefunctions and Hamiltonians and their operations. It is designed to make it easier for users to prototype and test new algorithms for solving the Kohn-Sham problem. KSSOLV2.0 contains significant improvement over the original KSSOLV described in a paper published in ACM Transaction on Mathematical Software (attached). In addition to performing ground state calculation for small molecules, it can also perform geometry optimization for both molecules and solids. It uses standard pseudopotentials and implements local density approximation, generalized gradient approximation and hybrid functionals. Future releases will also include time-dependent DFT and post DFT calculations such as the GW quasi-particle energy calculation and Bethe-Salpeter equation solver for optical absorption.

Yang, Chao↗

SolarPlus-Optimizer v0.1

With the falling costs of solar arrays and battery storage and reduced reliability of the grid due to natural disasters, small-scale local generation and storage resources are beginning to proliferate. However, very few software options exist for integrated control of building loads, batteries and other distributed energy resources. The available software solutions on the market can force customers to adopt one particular ecosystem of products, thus limiting consumer choice, and are often incapable of operating independently of the grid during blackouts. In this software package, we present the "Solar+ Optimizer" (SPO), a control platform that provides demand flexibility, resiliency and reduced utility bills, built using open-source software. SPO employs Model Predictive Control (MPC) to produce real time optimal control strategies for the building loads and the distributed energy resources on site. SPO is designed to be vendor-agnostic, protocol-independent and resilient to loss of wide-area network connectivity. The software was evaluated in a real convenience store in northern California with on-site solar generation, battery storage and control of HVAC and commercial refrigeration loads. Preliminary tests showed price responsiveness of the building and cost savings of more than 10% in energy costs alone.

Prakash, AnandKrishnan↗

GrayQb TM Single-Faced Version 2 (SF2) Open Environment Test Report (Rev. 1)

This report details the design upgrades incorporated into the new version of the GrayQb TM SF2 device and the characterization testing of this upgraded device. Results from controlled characterization testing in the Savannah River National Laboratory (SRNL) R&D Engineering Imaging and Radiation Lab (IRL) and the Savannah River Site (SRS) Health Physics Instrument Calibration Laboratory (HPICL) is presented, as well as results from the open environment field testing performed in the E-Area Low Level Waste Storage Area. Resultant images presented in this report were generated using the SRNL developed Radiation Analyzer (RAzer TM ) software program which overlays the radiation contour images onto the visual image of the location being surveyed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Innovations in optimization and control of accelerators using methods of differential geometry and genetic algorithms (Final Report)

Online tuning of particle accelerators is necessary in order to achieve optimal machine performance. However, it is also a major challenge due to the large parameter space which must be searched and the fact that many of the desir- able objectives compete with one another, and so will not reach their optimal values simultaneously. In order to mitigate these issues, we have explored using dimension-reduction techniques to reduce the size of the parameter space which must be searched and multi-objective genetic algorithms to obtain the sets of tuning parameters which provide pareto-optimal values for the objectives. These methods have enabled us to obtain improved values of the vertical emittance at the Cornell Electron Storage Ring (CESR), and to do so with greater control of orbit errors. Algorithmic tuning is a multidisciplinary endeavour, requiring expertise in beam dynamics, diagnostics, control systems and computer science, and thus a key practical problem is to formulate a common language in which experts with different specialties can communicate. We developed a solution to this problem in the form of a generic accelerator software interface that allows for rapid prototyping of optimization and control algorithms. Our interface is built on the Experimental Physics and Industrial Control Systems (EPICS) and makes possible testing control code in simulation before deployment on real accelerators, as well as deployment of third-party optimization code.

43 PARTICLE ACCELERATORS↗

Best Paper Award: Gathering Threat Intelligence Through Computer Network Deception

Presented at the 2016 IEEE International Symposium on Technologies for Homeland Security (HST), this LDRD-funded research received a Best Paper award, the highest award presented at the conference. The research focused on developing, implementing, and testing a novel computer network operations architecture that enables proactive defense by managing and monitoring enterprise resource allocations and network flows. The architecture leverages three emerging concepts: software-defined networks, cloud computing, and deception, to enable the detection and identification of anomalous access and intrusions to adjust to the dynamic nature of the adversary and to provide a mechanism to discover and react to the adversary’s attacks in a methodical and proactive manner. Additionally, the work allows network defenders to gather information on an adversary’s tools, tactics and procedures, providing insight into the “what, why, and how” of the adversary’s operations. A summary of the work presented at IEEE can be found at http://tiny.sandia.gov/8d8lu.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Solar+ Optimizer: A Model Predictive Control Optimization Platform for Grid Responsive Building Microgrids

With the falling costs of solar arrays and battery storage and reduced reliability of the grid due to natural disasters, small-scale local generation and storage resources are beginning to proliferate. However, very few software options exist for integrated control of building loads, batteries and other distributed energy resources. The available software solutions on the market can force customers to adopt one particular ecosystem of products, thus limiting consumer choice, and are often incapable of operating independently of the grid during blackouts. In this paper, we present the “Solar+ Optimizer” (SPO), a control platform that provides demand flexibility, resiliency and reduced utility bills, built using open-source software. SPO employs Model Predictive Control (MPC) to produce real time optimal control strategies for the building loads and the distributed energy resources on site. SPO is designed to be vendor-agnostic, protocol-independent and resilient to loss of wide-area network connectivity. The software was evaluated in a real convenience store in northern California with on-site solar generation, battery storage and control of HVAC and commercial refrigeration loads. Preliminary tests showed price responsiveness of the building and cost savings of more than 10% in energy costs alone.

14 SOLAR ENERGY↗

Evaluation of the accuracy of 3DVH software estimates of dose to virtual ion chamber and film in composite IMRT QA

Purpose: A novel patient-specific intensity modulated radiation therapy (IMRT) QA system, 3DVH software and mapcheck 2, purports to be able to use diode array-measured beam doses and the patient's DICOM RT plan, structure set, and dose files to predict the delivered 3D dose distribution in the patient for comparison to the treatment planning system (TPS) calculated doses. In this study, the composite dose to an ion chamber and film in phantom predicted by the 3DVH and mapcheck 2 system is compared to the actual measured chamber and film doses. If validated in this context, then 3DVH can be used to perform an equivalent dose analysis as that obtained with film dosimetry and ion chamber-based composite IMRT QA. This is important for those losing their ability to perform film dosimetry for true composite IMRT QA and provides a measure of confidence in the accuracy of 3DVH 3D dose calculations which may replace phantom-based IMRT QA. Methods: The dosimetric results from 15 consecutive patient-specific IMRT QA tests performed by composite field irradiation of ion chamber and EDR2 film in a solid water phantom were compared to the predicted doses for those virtual detectors based on the calculated 3D dose by the 3DVH software using mapcheck 2 measured doses of each beam within each plan. For each of the 15 cases, immediately after performing the ion chamber plus film measurements, the mapcheck 2 was used to measure the dose for each beam of the plan. The dose to the volume of the virtual ion chamber and the dose distribution in the plane of the virtual film calculated by the 3DVH software was extracted. The ratio of the measured to 3DVH or eclipse-predicted ion chamber doses was calculated. The same plane in the phantom measured using film and calculated with eclipse was exported from 3DVH and the 2D gamma metric was used to compare the relationship between the film doses and the eclipse or 3DVH predicted planar doses. Also, the 3D gamma value was calculated in the 3DVH software which compares the eclipse dose to the 3DVH predicted dose distribution. For the 2D and 3D gamma metrics, 2% dose and 2 mm distance to agreement (DTA) were used. In addition, a simple dose difference was performed using either a 2% or 3% dose difference tolerance. Results: The mean ratio {+-} standard deviation of the measured vs 3DVH or vs eclipse-predicted dose to the ion chamber was 1.013 {+-} 0.015 and 1.003 {+-} 0.012, respectively. For 3DVH vs eclipse, the mean percentage of pixels failing the 3D gamma metric was 1.2% {+-} 1.4% while the failure rate for the 2D gamma metric was 1.1% {+-} 0.9%. When either 3DVH or eclipse was compared to EDR2 film, the gamma failure rate was 2.3% {+-} 2.0% and 1.6% {+-} 1.7%, respectively. Mean dose difference failures were 9%-27% {+-} 5%-15% for 2 or 3% dose difference tolerances, depending on the combination of systems tested. No statistically significant differences were found for any of the planar dosimetric comparisons. Conclusions: 3DVH + mapcheck 2 predicts the same absolute dose, the percent of pixels failing the gamma metric, and the percent of pixels failing 2% or 3% dose difference tolerance tests as one would have obtained had one made measurements in solid water phantom using an ion chamber and coronal film instead of a diode array. This is also a necessary although not sufficient condition for validation of the accuracy of 3DVH predictions of the 3D dose using beam-by-beam measurements.

61 RADIATION PROTECTION AND DOSIMETRY↗

The Cementitious Barriers Partnership (CBP) Software Toolbox Capabilities in Assessing the Degradation of Cementitious Barriers - 13487

The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste and Nuclear Materials Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to 100 years and longer for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox has produced tangible benefits to the DOE Performance Assessment (PA) community. A review of prior DOE PAs has provided a list of potential opportunities for improving cementitious barrier performance predictions through the use of the CBP software tools. These opportunities include: 1) impact of atmospheric exposure to concrete and grout before closure, such as accelerated slag and Tc-99 oxidation, 2) prediction of changes in K{sub d}/mobility as a function of time that result from changing pH and redox conditions, 3) concrete degradation from rebar corrosion due to carbonation, 4) early age cracking from drying and/or thermal shrinkage and 5) degradation due to sulfate attack. The CBP has already had opportunity to provide near-term, tangible support to ongoing DOE-EM PAs such as the Savannah River Saltstone Disposal Facility (SDF) by providing a sulfate attack analysis that predicts the extent and damage that sulfate ingress will have on the concrete vaults over extended time (i.e., > 1000 years). This analysis is one of the many technical opportunities in cementitious barrier performance that can be addressed by the DOE-EM sponsored CBP software tools. Modification of the existing tools can provide many opportunities to bring defense in depth in prediction of the performance of cementitious barriers over time. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗