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DOE OSTI2020

Development of an Encoding Method on an Co-simulation Platform for Mitigating the Impact of Unreliable Communication

This report presents a hardware-in-the-loop (HIL) based modeling approach for simulating impacts of unreliable communication on the performance of centralized volt-var control and for developing an encoding method to mitigate the impacts. First, an asynchronous real-time HIL simulation platform is introduced to enable multi-rate co-simulation of a distribution system with many inverter-based distributed energy resources (DERs). The distribution system is modeled by milliseconds phasor-based models and the DERs are modeled by micro-seconds power electronic models. Communication connections between a centralized volt-var controller (modeled externally to the HIL testbed) and smart inverters are built by implementing Modbus links and the Long Term Evolution network. On this co-simulation platform, an enhanced, augmented Lagrangian multiplier based encoded data recovery (EALM-EDR) algorithm for mitigating the impact of unreliable communication is developed and validated. Simulation results demonstrate the efficacy of using the HIL-based co-simulation platform as a power grid digital twin for developing algorithms that coordinate a large number of heterogeneous control systems through wired and wireless communication links.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Control System of Multi-Port Autonomous Reconfigurable Solar Power Plant (MARS) & HIL Platforms for Design

Multi-port autonomous reconfigurable solar power plant (MARS) provides an attractive alternative to connect photovoltaic (PV) and energy storage systems (ESSs) to high-voltage direct current (HVdc) links and high-voltage alternating current (ac) grids. In this paper, a unique hierarchical control system of MARS is proposed and evaluated. To evaluate the control system and associated algorithms in early-stage research of complex architectures like MARS, it is important to develop unique suitable hardware-in-the-loop (HIL) platforms. In this paper, the HIL platforms for MARS to evaluate the performance of the hierarchical control system and the control algorithms implemented are presented. Further, they help with the design process of control systems. The real-time simulation models and algorithms that are utilized for MARS in the HIL platforms are also discussed in the paper. The HIL experiments of the control system of MARS showcase the capability to provide continuity of operation under faults and frequency support to the power grid during loss of generation. They also showcase the stability of the proposed hierarchical control system of MARS.

14 SOLAR ENERGY↗

DOE OSTI2014

SU-E-J-44: Design a Platform and Phantom Model for Photoacoustic Imaging in Combination with CT

Purpose: Our (long-term) objective is to develop a US manipulator that will provide in situ radiation response and image-guided therapy for bladder cancer based on photoacoustic molecular imaging. Methods: A platform was devised to provide a reproducible positional frame of reference for targeting anatomic structure between MDCT and US scans, in lieu of CBCT, and to fuse photoacoustic molecular imaging. US and photoacoustic scans are taken of a patient while in the CT scanner and IRMT. Through co-registration, based on anatomical positions, we identified a common coordinate system to be used in Eclipse. A bladder phantom was constructed to validate anatomical tracking via US and photoacoustic imaging. We tested the platform using phantom model to demonstrate validity once moved from the CT couch to the linear accelerator couch. Results: This platform interlocks with Varian exact couch index points for reproducibility of positioning. Construction from low Z material and sized appropriately to fit in CT/IMRT gantry. Error in conversion from cylindrical coordinates of the manipulator to X, Y, Z coordinates of the treatment couch was less than 1mm. We measured the bladder size in 3 different directions in both Eclipse from the CT and Acuson from US. The error was less than 2mm in all directions. CT and US images were co-registered in MATLAB. Co-registration of photoacoustic images is still being developed. Conclusion: For Linear Accelerators without on board imaging, MV portal images are not a viable option for the localization of soft tissue anatomy. We believe our manipulator provides an alternative using US imaging, which will be examined in an upcoming clinical trial. We plan to examine the value of hypoxia guided treatment through photoacoustic imaging during this trial.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

SU-E-J-04: Integration of Interstitial High Intensity Therapeutic Ultrasound Applicators On a Clinical MRI-Guided High Intensity Focused Ultrasound Treatment Planning Software Platform

Purpose: Interstitial high intensity therapeutic ultrasound (HITU) applicators can be used to ablate tissue percutaneously, allowing for minimally-invasive treatment without ionizing radiation [1,2]. The purpose of this study was to evaluate the feasibility and usability of combining multielement interstitial HITU applicators with a clinical magnetic resonance imaging (MRI)-guided focused ultrasound software platform. Methods: The Sonalleve software platform (Philips Healthcare, Vantaa, Finland) combines anatomical MRI for target selection and multi-planar MRI thermometry to provide real-time temperature information. The MRI-compatible interstitial US applicators (Acoustic MedSystems, Savoy, IL, USA) had 1–4 cylindrical US elements, each 1 cm long with either 180° or 360° of active surface. Each applicator (4 Fr diameter, enclosed within a 13 Fr flexible catheter) was inserted into a tissue-mimicking agar-silica phantom. Degassed water was circulated around the transducers for cooling and coupling. Based on the location of the applicator, a virtual transducer overlay was added to the software to assist targeting and to allow automatic thermometry slice placement. The phantom was sonicated at 7 MHz for 5 minutes with 6–8 W of acoustic power for each element. MR thermometry data were collected during and after sonication. Results: Preliminary testing indicated that the applicator location could be identified in the planning images and the transducer locations predicted within 1 mm accuracy using the overlay. Ablation zones (thermal dose ≥ 240 CEM43) for 2 active, adjacent US elements ranged from 18 mm × 24 mm (width × length) to 25 mm × 25 mm for the 6 W and 8 W sonications, respectively. Conclusion: The combination of interstitial HITU applicators and this software platform holds promise for novel approaches in minimally-invasive MRI-guided therapy, especially when bony structures or air-filled cavities may preclude extracorporeal HIFU.[1] Diederich et al. IEEE UFFFC 46.5 (1999): 1218.[2] Chopra et al. PMB 50.21 (2005): 4957. Funding support was provided by Philips Healthcare and in-kind support from Acoustic MedSystems Inc. Ari Partanen is a paid employee of Philips Healthcare. Goutam Ghoshal and Everette Clif Burdette are paid employees of Acoustic MedSystems Inc.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-EF-BRB-07: Novel Hardware and Software Platform for Intermediate Energy 4π Radiotherapy

Purpose: To develop a robust and efficient platform for the optimization and robotic delivery of highly noncoplanar intensity modulated radiotherapy, which enables significant reduction of normal tissue toxicity and escalation of tumor dose. Methods: An innovative high-output compact 3 MV linac was designed for mounting onto a commercial robotic system in order to access the entire 4π beam solution space without moving the patient couch. The use of intermediate energy X-rays for radiotherapy was evaluated in comparison to clinical plans delivered using 6 MV X-rays and a state-of-the-art delivery system. Monte Carlo simulations of a 3 MV percent depth dose curve were performed for intermediate energy dose calculation. The beam model was used to create a convolution/superposition-based dose calculation engine for 3MV X-rays. The 4π greedy column generation algorithm was used for optimized beam selection and fluence map optimization. Results: A detailed design of the first 3 MV linac capable of producing a competitively high dose rate of >800 cGy/min at 100 cm was completed and verified through extensive simulation. The complete linac head including a multileaf collimator can access most of the 4π solution space including the posterior orientations without changing the couch height. When compared to 6 MV clinical plans, the proposed 3 MV 4π plans demonstrated significantly better dose compactness and normal tissue sparing in brain, prostate, and partial breast treatment plans. Conclusion: We demonstrate the design of a highly versatile radiotherapy machine to natively deliver non-coplanar 4π radiotherapy without the need to move the patient during treatment. This novel platform is efficient and capable of providing dosimetry that is 30–50% more compact than existing therapy platforms. The new system is projected to be cost effective due to improved treatment time and automation. NIH R43CA183390, NIH R01CA188300.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Technical Note: SCUDA: A software platform for cumulative dose assessment

Purpose: Accurate tracking of anatomical changes and computation of actually delivered dose to the patient are critical for successful adaptive radiation therapy (ART). Additionally, efficient data management and fast processing are practically important for the adoption in clinic as ART involves a large amount of image and treatment data. The purpose of this study was to develop an accurate and efficient Software platform for CUmulative Dose Assessment (SCUDA) that can be seamlessly integrated into the clinical workflow. Methods: SCUDA consists of deformable image registration (DIR), segmentation, dose computation modules, and a graphical user interface. It is connected to our image PACS and radiotherapy informatics databases from which it automatically queries/retrieves patient images, radiotherapy plan, beam data, and daily treatment information, thus providing an efficient and unified workflow. For accurate registration of the planning CT and daily CBCTs, the authors iteratively correct CBCT intensities by matching local intensity histograms during the DIR process. Contours of the target tumor and critical structures are then propagated from the planning CT to daily CBCTs using the computed deformations. The actual delivered daily dose is computed using the registered CT and patient setup information by a superposition/convolution algorithm, and accumulated using the computed deformation fields. Both DIR and dose computation modules are accelerated by a graphics processing unit. Results: The cumulative dose computation process has been validated on 30 head and neck (HN) cancer cases, showing 3.5 ± 5.0 Gy (mean±STD) absolute mean dose differences between the planned and the actually delivered doses in the parotid glands. On average, DIR, dose computation, and segmentation take 20 s/fraction and 17 min for a 35-fraction treatment including additional computation for dose accumulation. Conclusions: The authors developed a unified software platform that provides accurate and efficient monitoring of anatomical changes and computation of actually delivered dose to the patient, thus realizing an efficient cumulative dose computation workflow. Evaluation on HN cases demonstrated the utility of our platform for monitoring the treatment quality and detecting significant dosimetric variations that are keys to successful ART.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Efficient Parallel Discrete Event Simulation on Cloud/Virtual Machine Platforms

Cloud and Virtual machine (VM) technologies present new challenges with respect to performance and monetary cost in executing parallel discrete event simulation (PDES) applications. Due to the introduction of overall cost as a metric, the traditional use of the highest-end computing configuration is no longer the most obvious choice. Moreover, the unique runtime dynamics and configuration choices of Cloud and VM platforms introduce new design considerations and runtime characteristics specific to PDES over Cloud/VMs. Here, an empirical study is presented to guide an understanding of the dynamics, trends, and trade-offs in executing PDES on Cloud/VM platforms. Performance and cost measures obtained from multiple PDES applications executed on the Amazon EC2 Cloud and on a high-end VM host machine reveal new, counterintuitive VM--PDES dynamics and guidelines. One of the critical aspects uncovered is the fundamental mismatch in hypervisor scheduler policies designed for general cloud workloads versus the virtual time ordering needed for PDES workloads. This insight is supported by experimental data revealing the gross deterioration in PDES performance traceable to VM scheduling policy. To overcome this fundamental problem, the design and implementation of a new deadlock-free scheduler algorithm are presented, optimized specifically for PDES applications on VMs. The scalability of our scheduler has been tested up to 128 VMs multiplexed on 32 cores, showing significant improvement in the runtime relative to the default Cloud/VM scheduler. The observations, algorithmic design, and results are timely for emerging cloud/VM-based installations, highlighting the need for PDES-specific support in high performance discrete event simulations on Cloud/VM platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

PlanetSense: A Real-time Streaming and Spatio-temporal Analytics Platform for Gathering Geo-spatial Intelligence from Open Source Data

Geospatial intelligence has traditionally relied on the use of archived and unvarying data for planning and exploration purposes. In consequence, the tools and methods that are architected to provide insight and generate projections only rely on such datasets. Albeit, if this approach has proven effective in several cases, such as land use identification and route mapping, it has severely restricted the ability of researchers to inculcate current information in their work. This approach is inadequate in scenarios requiring real-time information to act and to adjust in ever changing dynamic environments, such as evacuation and rescue missions. In this work, we propose PlanetSense, a platform for geospatial intelligence that is built to harness the existing power of archived data and add to that, the dynamics of real-time streams, seamlessly integrated with sophisticated data mining algorithms and analytics tools for generating operational intelligence on the fly. The platform has four main components – i) GeoData Cloud – a data architecture for storing and managing disparate datasets; ii) Mechanism to harvest real-time streaming data; iii) Data analytics framework; iv) Presentation and visualization through web interface and RESTful services. Using two case studies, we underpin the necessity of our platform in modeling ambient population and building occupancy at scale.

big data architecture↗

DOE OSTI2023

A2E2G (Atmosphere to Electrons to the Grid platform) [SWR-23-22]

A2E2G is a platform that integrates 1) forecasting tools to account for weather uncertainty, with 2) aerodynamic wind plant models to account for wake dynamics and wind plant operation, and 3) economic models to advise on operation for a wind power plant that offers grid services in addition to energy. The A2E2G platform can be used as a high-level controller for a wind plant for market participation and real-time wind plant control. The A2E2g platform is a holistic Python tool with modules that can be run to 1) advise on market participation and 2) control and operate a wind power plant in real time. The A2E2g framework assumes two stages: the first stage is in day-ahead and the second stage is in real-time. Managing uncertainty is key in the first stage and managing variability is key in the second stage. The different components have models written and developed in the Python programming language. The code is assembled into a Python package and can be easily downloaded and installed from the A2E2g repository (https://github.com/NREL/a2e2g).

Sinner, Michael↗

DOE OSTI2024

Regional-scale fault-to-structure earthquake simulations with the EQSIM framework: Workflow maturation and computational performance on GPU-accelerated exascale platforms

Continuous advancements in scientific and engineering understanding of earthquake phenomena, combined with the associated development of representative physics-based models, is providing a foundation for high-performance, fault-to-structure earthquake simulations. However, regional-scale applications of high-performance models have been challenged by the computational requirements at the resolutions required for engineering risk assessments. The EarthQuake SIMulation (EQSIM) framework, a software application development under the US Department of Energy (DOE) Exascale Computing Project, is focused on overcoming the existing computational barriers and enabling routine regional-scale simulations at resolutions relevant to a breadth of engineered systems. This multidisciplinary software development—drawing upon expertise in geophysics, engineering, applied math and computer science—is preparing the advanced computational workflow necessary to fully exploit the DOE’s exaflop computer platforms coming online in the 2023 to 2024 timeframe. Achievement of the computational performance required for high-resolution regional models containing upward of hundreds of billions to trillions of model grid points requires numerical efficiency in every phase of a regional simulation. This includes run time start-up and regional model generation, effective distribution of the computational workload across thousands of computer nodes, efficient coupling of regional geophysics and local engineering models, and application-tailored highly efficient transfer, storage, and interrogation of very large volumes of simulation data. This article summarizes the most recent advancements and refinements incorporated in the workflow design for the EQSIM integrated fault-to-structure framework, which are based on extensive numerical testing across multiple graphics processing unit (GPU)-accelerated platforms, and demonstrates the computational performance achieved on the world’s first exaflop computer platform through representative regional-scale earthquake simulations for the San Francisco Bay Area in California, USA.

58 GEOSCIENCES↗

DOE OSTI2023

A microCT-based platform to quantify drug targeting

Abstract Background Heterotopic ossification (HO) is a frequent and debilitating complication of traumatic musculoskeletal injuries and orthopedic procedures. Prophylactic dosing of botulinum toxin type A (BTxA) holds potential as a novel treatment option if accurately distributed throughout soft-tissue volumes where protection is clinically desired. We developed a high-resolution, microcomputed tomography (microCT)-based imaging strategy to assess drug distribution and validated this platform by quantifying distribution achieved via a prototype delivery system versus a single-bolus injection. Methods We injected an iodine-containing contrast agent (iodixanol 320 mg I/mL) into dissected rabbit musculature followed by microCT imaging and analysis. To contrast the performance of distributed versus bolus injections, a three-dimensional (3D) 64-cm 3 -printed soft-tissue holder was developed. A centered 2-cm 3 volume of interest (VOI) was targeted with a single-bolus injection or an equal volume distributed injection delivered via a 3D-printed prototype. VOI drug coverage was quantified as a percentage of the VOI volume that was < 1.0 mm from the injected fluid. Results The microCT-based approach enabled high-resolution quantification of injection distribution within soft tissue. The distributed dosing prototype provided significantly greater tissue coverage of the targeted VOI (72 ± 3%, mean ± standard deviation) when compared to an equal volume bolus dose (43 ± 5%, p = 0.031) while also enhancing the precision of injection targeting. Conclusions A microCT-based imaging technique precisely quantifies drug distribution within a soft-tissue VOI, providing a path to overcome a barrier for clinical translation of prophylactic inhibition of HO by BTxA. Relevance statement This platform will facilitate rapid optimization of injection parameters for clinical devices used to effectively and safely inhibit the formation of heterotopic ossification. Key points • MicroCT provides high-resolution quantification of soft-tissue drug distribution. • Distributed dosing is required to maximize soft-tissue drug coverage. • Imaging platform will enable rapid screening of 3D-printed drug distribution prototypes. Graphical Abstract

Ausk, Brandon J. (ORCID:0000000335338303)↗

DOE OSTI2022

Toward an integrated platform for characterizing laser-driven, isochorically heated plasmas with 1 µm spatial resolution

Warm dense matter is a region of phase space that is of high interest to multiple scientific communities ranging from astrophysics to inertial confinement fusion. Further understanding of the conditions and properties of this complex state of matter necessitates experimental benchmarking of the current theoretical models. We discuss the development of an x-ray radiography platform designed to measure warm dense matter transport properties at large laser facilities such as the OMEGA Laser Facility. Our platform, Fresnel Diffractive Radiography, allows for high spatial resolution imaging of isochorically heated targets, resulting in notable diffractive effects at sharp density gradients that are influenced by transport properties such as thermal conductivity. We discuss initial results, highlighting the capabilities of the platform in measuring diffractive features with micron-level spatial resolution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Characterization of suspended membrane waveguides towards a photonic atom trap integrated platform

We demonstrate an optical waveguide device, capable of supporting the high, in-vacuum, optical power necessary for trapping a single atom or a cold atom ensemble with evanescent fields. Our photonic integrated platform, with suspended membrane waveguides, successfully manages optical powers of 6 mW (500 μ m span) to nearly 30 mW (125 μ m span) over an un-tethered waveguide span. This platform is compatible with laser cooling and magneto-optical traps (MOTs) in the vicinity of the suspended waveguide, called the membrane MOT and the needle MOT, a key ingredient for efficient trap loading. We evaluate two novel designs that explore critical thermal management features that enable this large power handling. This work represents a significant step toward an integrated platform for coupling neutral atom quantum systems to photonic and electronic integrated circuits on silicon.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Platform-agnostic waveguide integration of high-speed photodetectors with evaporated tellurium thin films

Many attractive photonics platforms still lack integrated photodetectors due to inherent material incompatibilities and lack of process scalability, preventing their widespread deployment. Here, we address the problem of scalably integrating photodetectors in a photonics-platform-independent manner. Using a thermal evaporation and deposition technique developed for nanoelectronics, we show that tellurium, a quasi-2D semi-conductive element, can be evaporated at low temperatures directly onto photonic chips to form air-stable, high-speed, ultrawide-band photodetectors. We demonstrate detection from visible (520 nm) to short-wave infrared (2.4 µm), a bandwidth of more than 40 GHz, and platform-independent scalable integration with photonic structures in silicon, silicon nitride, and lithium niobate.

42 ENGINEERING↗

DOE OSTI2013

Single-Cell Measurements of IgE-Mediated FcεRI Signaling Using an Integrated Microfluidic Platform

Heterogeneity in responses of cells to a stimulus, such as a pathogen or allergen, can potentially play an important role in deciding the fate of the responding cell population and the overall systemic response. Measuring heterogeneous responses requires tools capable of interrogating individual cells. Cell signaling studies commonly do not have single-cell resolution because of the limitations of techniques used such as Westerns, ELISAs, mass spectrometry, and DNA microarrays. Microfluidics devices are increasingly being used to overcome these limitations. In this paper, we report on a microfluidic platform for cell signaling analysis that combines two orthogonal single-cell measurement technologies: on-chip flow cytometry and optical imaging. The device seamlessly integrates cell culture, stimulation, and preparation with downstream measurements permitting hands-free, automated analysis to minimize experimental variability. The platform was used to interrogate IgE receptor (FcεRI) signaling, which is responsible for triggering allergic reactions, in RBL-2H3 cells. Following on-chip crosslinking of IgE-FcεRI complexes by multivalent antigen, we monitored signaling events including protein phosphorylation, calcium mobilization and the release of inflammatory mediators. The results demonstrate the ability of our platform to produce quantitative measurements on a cell-by-cell basis from just a few hundred cells. Finally, model-based analysis of the Syk phosphorylation data suggests that heterogeneity in Syk phosphorylation can be attributed to protein copy number variations, with the level of Syk phosphorylation being particularly sensitive to the copy number of Lyn.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

The Livewire Data Platform

The Livewire Data Platform makes it easy to search and share transportation and mobility-related data. The Livewire Data Platform supports the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy’s Energy Efficient Mobility Systems (EEMS) Program goal of providing an affordable, efficient, safe, and accessible transportation future where mobility is decoupled from energy consumption. The Livewire Data Platform will function as a repository for all EEMS data and will support the following objectives: (1) EEMS partners with relevant data can catalog, document, and share project datasets via file-based sharing or Application Programming Interface (API) and can provides access management and usage auditing for those resources. (2) EEMS partners can securely search, discover and access shared datasets, their metadata, and available API’s. (3) External partners and researchers can discover EEMS capabilities and collaborate with EEMS partners.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2019

Checkpointing Strategies for Shared High-Performance Computing Platforms

Input/output (I/O) from various sources often contend for scarcely available bandwidth. For example, checkpoint/restart (CR) protocols can help to ensure application progress in failure-prone environments. However, CR I/O alongside an application's normal, requisite I/O can increase I/O contention and might negatively impact performance. In this work, we consider different aspects (system-level scheduling policies and hardware) that optimize the overall performance of concurrently executing CR-based applications that share I/O resources. We provide a theoretical model and derive a set of necessary constraints to minimize the global waste on a given platform. Our results demonstrate that Young/Daly's optimal checkpoint interval, despite providing a sensible metric for a single, undisturbed application, is not sufficient to optimally address resource contention at scale. We show that by combining optimal checkpointing periods with contention-aware system-level I/O scheduling strategies, we can significantly improve overall application performance and maximize the platform throughput. Finally, we evaluate how specialized hardware, namely burst buffers, may help to mitigate the I/O contention problem. Altogether, these results provide critical analysis and direct guidance on how to design efficient, CR ready, large -scale platforms without a large investment in the I/O subsystem.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

Year 2 Final Report - Protein Function Prediction Platform (v.0.5)

Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.

59 BASIC BIOLOGICAL SCIENCES↗