Results for “interface tracking” — Page 23

DOE OSTI2020

A mass-transfer particle-tracking method for simulating transport with discontinuous diffusion coefficients

The problem of a spatially discontinuous diffusion coefficient (D(x)) is one that may be encountered in hydrogeologic systems due to natural geological features or as a consequence of numerical discretization of flow properties. To date, mass-transfer particle-tracking (MTPT) methods, a family of Lagrangian methods in which diffusion is jointly simulated by random walk and diffusive mass transfers, have been unable to solve this problem. This manuscript presents a new mass-transfer (MT) algorithm that enables MTPT methods to accurately solve the problem of discontinuous D(x). To achieve this, we derive a semi-analytical solution to the discontinuous D(x) problem by employing a predictor-corrector approach, and we use this semi-analytical solution as the weighting function in a reformulated MT algorithm. Furthermore, this semi-analytical solution is generalized for cases with multiple 1D interfaces as well as for 2D cases, including a 2 × 2 tiling of 4 subdomains that corresponds to a numerically-generated diffusion field. The solutions generated by this new mass-transfer algorithm closely agree with an analytical 1D solution or, in more complicated cases, trusted numerical results, demonstrating the success of our proposed approach.

42 ENGINEERING↗

DOE OSTI2025

Commercialization of the Transportation-Security, Tracking, and Reporting System (T-STAR)

The Transportation-Security, Tracking, and Reporting System (T-STAR) was developed by the National Nuclear Security Administration, NA-21, Office of Radiological Security (ORS) to provide a transportation security system for detection and tracking during transport of Category 1 and Category 2 radiological material. Few off-the-shelf systems for conveyance tracking offer detection of a cargo compartment breach or a removal of the cargo. Systems that do offer this capability often require permanent installation through modifying of the conveyance itself. This is not sustainable in many countries where ORS is building use, storage, and transport security capacity. The development of T-STAR has moved from fielding robust prototypes deployed in countries ranging from North America, Latin America and Central Asia to a commercially produced product that can now be deployed to provide enhanced security during transit. Each prototype deployment resulted in important lessons learned, which informed the requirements for the final commercial product. T-STAR uses both cellular and Iridium satellite modems to provide redundant communications to provide the configuration, status, and alerts to a server monitoring the shipment, which is accessible using a multilanguage browser-based user interface. A wireless security system employing using Z-wave sensors for intrusion detection located in the conveyance provide low cost but effective solution for a wide range of conveyance types. Additional capabilities include the ability to monitor a vehicles’ CANBUS (Controller Area Network) system, an ethernet port for high throughput sensor information such as video cameras, and the ability to power and use advanced external sensor payloads. These features make the T-STAR a capable and expandable security gateway that can be deployed on a variety of conveyances from box trucks to open trailers. The ability to provide tracking, monitoring, and detection provide a key component in overall best practices designed to protect shipments of radioactive material.

Schultze, Michael [ORNL] (ORCID:0000000283205671)↗

DOE OSTI2025

Announcing the Biomedical Data Translator: Initial Public Release

ABSTRACT The growing availability of biomedical data offers vast potential to improve human health, but the complexity and lack of integration of these datasets often limit their utility. To address this, the Biomedical Data Translator Consortium has developed an open‐source knowledge graph–based system—Translator—designed to integrate, harmonize, and make inferences over diverse biomedical data sources. We announce here Translator's initial public release and provide an overview of its architecture, standards, user interface, and core features. Translator employs a scalable, federated, knowledge graph framework for the integration of clinical, genomic, pharmacological, and other biomedical knowledge sources, enabling query retrieval, inference, and hypothesis generation. Translator's user interface is designed to support the exploration of knowledge relationships and the generation of insights, without requiring deep technical expertise and gradually revealing more detailed evidence, provenance, and confidence information, as needed by a given user. To demonstrate Translator's application and impact, we highlight features of the user interface in the context of three real‐world use cases: suggesting potential therapeutics for patients with rare disease; explaining the mechanism of action of a pipeline drug; and screening and validating drug candidates in a model organism. We discuss strengths and limitations of reasoning within a largely federated system and the need for rich concept modeling and deep provenance tracking. Finally, we outline future directions for enhancing Translator's functionality and expanding its data sources. Translator represents a significant step forward in making complex biomedical knowledge more accessible and actionable, aiming to accelerate translational research and improve patient care.

Research & Experimental Medicine↗

DOE OSTI2016

SU-G-BRB-07: Developing a QA Procedure for Gated VMAT SABR Treatments Using 10 MV Beam in Flattening-Filter Free Mode

Purpose: To develop a QA procedure for gated VMAT stereotactic ablative radiotherapy (SABR) treatments. Methods: An interface was constructed to attach the translational stage of a Quasar respiratory motion phantom to a pinpoint ion chamber insert and move the ion chamber inside an ArcCheck diode array. The Quasar phantom controller used a patient specific breathing pattern to translate the ion chamber in a superior-inferior direction inside the ArcCheck. An amplitude-based RPM tracking system was specified to turn the beam on during the exhale phase of the breathing pattern. SABR plans were developed using Eclipse for liver PTVs ranging in size from 3-12 cm in diameter using a 2-arc VMAT technique. Dose was measured in the middle of the penumbra region, where the high dose gradient allowed for sensitive detection of any inaccuracies in gated dose delivery. The overall fidelity of the dose distribution was confirmed using ArcCheck. The sensitivity of the gating QA procedure was investigated with respect to the following four parameters: PTV size, duration of exhale, baseline drift, and gating window size. Results: The difference between the measured dose to a point in the penumbra and the Eclipse calculated dose was under 2% for small residual motions. The QA procedure was independent of PTV size and duration of exhale. Baseline drift and gating window size, however, significantly affected the penumbral dose measurement, with differences of up to 30% compared to Eclipse. Conclusion: This study described a highly sensitive QA procedure for gated VMAT SABR treatments. The QA outcome was dependent on the gating window size and baseline drift. Analysis of additional patient breathing patterns will be required to determine a clinically relevant gating window size and an appropriate tolerance level for this procedure.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. Here, as anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

TH-EF-BRB-02: Feasibility of Optimization for Dynamic Trajectory Radiotherapy

Purpose: Over the last years, volumetric modulated arc therapy (VMAT) has been widely introduced into clinical routine using a coplanar delivery technique. However, VMAT might be improved by including dynamic couch and collimator rotations, leading to dynamic trajectory radiotherapy (DTRT). In this work the feasibility and the potential benefit of DTRT was investigated. Methods: A general framework for the optimization was developed using the Eclipse Scripting Research Application Programming Interface (ESRAPI). Based on contoured target and organs at risk (OARs), the structures are extracted using the ESRAPI. Sampling potential beam directions, regularly distributed on a sphere using a Fibanocci-lattice, the fractional volume-overlap of each OAR and the target is determined and used to establish dynamic gantry-couch movements. Then, for each gantry-couch track the most suitable collimator angle is determined for each control point by optimizing the area between the MLC leaves and the target contour. The resulting dynamic trajectories are used as input to perform the optimization using a research version of the VMAT optimization algorithm and the ESRAPI. The feasibility of this procedure was tested for a clinically motivated head and neck case. Resulting dose distributions for the VMAT plan and for the dynamic trajectory treatment plan were compared based on DVH-parameters. Results: While the DVH for the target is virtually preserved, improvements in maximum dose for the DTRT plan were achieved for all OARs except for the inner-ear, where maximum dose remains the same. The major improvements in maximum dose were 6.5% of the prescribed dose (66 Gy) for the parotid and 5.5% for the myelon and the eye. Conclusion: The result of this work suggests that DTRT has a great potential to reduce dose to OARs with similar target coverage when compared to conventional VMAT treatment plans. This work was supported by Varian Medical Systems. This work was supported by Varian Medical Systems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Modeling Electrodeposition in 3D Porous Architectures for Solid-State Li-Metal Batteries

Li-metal storage in three-dimensional (3D) electrodes is considered a potential dendrite-mitigation strategy. The large surface area and high porosity of these electrodes result in reduced local Li-plating current densities. The porous topology provides a scaffold for Li-deposition and stripping, maintaining both mechanical integrity and Li accessibility. The goal of this study is to understand how characteristics, such as geometry and material properties, affect the current distribution and deposition pattern. To this end, we developed a computational method to track material growth driven by electrodeposition within a complex geometry. This method ensures that the finite-element discretization remains conforming to the moving boundary while preserving an adequate mesh quality, and thus maintains solution accuracy. Using this new computational tool, we analyze the conditions under which porous anode architectures effectively expand the surface area of the charge-transfer interface, and self-regulate current density and dendrite growth.

3D electrode architectures↗

DOE OSTI2026

Intelligent Experiments through Real-Time AI: Fast Data Processing and Autonomous Detector Control for High-Energy Nuclear Experiments

The aim of this project is to develop software and hardware for fast real-time data processing and autonomous detector control and calibration for the sPHENIX and the future EIC experiments. Below summarizes Georgia Tech team efforts in the past year: 1. We developed a real-time clustering algorithm and FPGA-based pipeline architecture for processing fired pixel data from ALPIDE sensors in sPHENIX experiments. Our Columnar Clustering Co-Design introduces a hardware-aware, stream-friendly approach that segments pixel data by column pairs using a Column Pair Clustering (CPC) strategy, followed by Cluster Stitching to merge adjacent subclusters. Implemented in Vitis HLS, the pipeline comprises five stages—read-in, subclustering, stitching, analysis, and write-out—connected by tagged HLS streams with custom end-of-event signaling for robust synchronization. We designed a pipelined dataflow model optimized for throughput, low latency, and minimal buffering, enabling scalable clustering across events of arbitrary size. Our system maintains spatial precision via center-of-mass and shape key extraction and efficiently handles edge cases such as fragmented or nested clusters. Compared against DBSCAN in both software and hardware, our approach demonstrates competitive performance under FPGA constraints. 2. We also conducted a comprehensive algorithm-to-hardware co-design of connected component analysis tailored for sPHENIX experiments, focusing on real-time, low-latency processing using FPGAs and High-Level Synthesis (HLS). Starting from a Python-based particle tracking pipeline, the team translated the core logic—graph traversal via DFS and Union-Find—into an HLS-compatible C++ model, replacing dynamic memory and recursion with static arrays and pipelined control flow. The final design includes a fully streamed and dataflow-compatible Union-Find kernel optimized across five iterations, incorporating loop pipelining, array partitioning, AXI/FIFO interface tuning, and function flattening. Experimental results show up to 14.8× speedup over the CPU baseline, reducing per-graph latency to 1.58 μs and demonstrating strong resource efficiency with only ~7k LUTs and zero BRAM usage. The design maintains functional correctness against the Python reference using a Python-based C-simulation framework and Mean Squared Error metrics. This work validates the potential of HLS-driven FPGA designs for edge-level HEP data acquisition, laying a scalable foundation for future integration with real-time detector pipelines and multi-graph processing systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

The Accelerator Neutrino Neutron InteractionExperiment: Design, Construction and Preparationfor First Physics

This thesis covers work performed for the Accelerator Neutrino Neutron Interaction Experiment (ANNIE) between 2015 and 2020. ANNIE is a beamline neutrino experiment located at the Fermi National Accelerator Laboratory in Chicago. Its primary physics goals are the measurement of neutrino interaction cross-sections on oxygen, and a measurement of the multiplicity of final state neutrons from these interactions, both as functions of final state kinematics. In order to achieve these goals ANNIE will be pioneering the use of Large Area Picosecond Photodetectors and the use of gadolinium doping to enhance neutron visibility in a water Cherenkov detector. Over the time period of this thesis the ANNIE detector was constructed, an initial 'Phase I' background run was completed, the detector was decommissioned and then substantially upgraded in preparation for the main 'Phase II' physics run. At the time of writing ANNIE is being re-commissioned, with Phase II data taking anticipated to begin in 2021. During this time I spent 21/2 years on-site contributing to almost all aspects of hardware work, while performing software development for the simulation and analysis frameworks. As my first software task I developed Monte Carlo simulations of the detector response, based on the WCSim framework. While thismore » framework provided a starting point for the tank simulation significant modifications were required to implement the complete ANNIE detector system. This included a rewrite of the geometry, along with modifications to the photosensor definitions, hit collections, digitization, triggering, input and output interfaces, etc. To take advantage of improved modelling of neutrons in Geant4.10 the physics lists were also reimplemented in the new version format. As part of this work I determined performance metrics based on the output files, calculating kinematic acceptance, detector efficiency and expected event rates. My contributions on reconstruction focused primarily on the MRD, for which I implemented two track reconstruction algorithms, specialised for high and low energy muons. The high energy algorithm achieves >90% efficiency for tracks with at least 8 hits, and is robust against dead paddles and unrelated hits. The low energy algorithm performs a search in combination with tank information to provide sensitivity down to a single MRD hit. Early data handling work for the Phase I background run included writing the code for handling TDC hits and performing studies on neutron detection without the requirement of multi-hit coincidence. As the collaboration moved to a new framework for the Phase II analysis I performed a substantial amount of work to develop the codebase, implementing tools to perform tasks such as file IO, data parsing, waveform processing, event building, timestamp alignment, time clustering, hit residual calculation, event visualisation etc. I helped develop the python API for integrating multi-language tools, and ported the framework into a Singularity container to provide a self-contained environment that…« less

43 PARTICLE ACCELERATORS↗

DOE OSTI2017

CUSP-SHAPED STRUCTURE OF A JET OBSERVED BY IRIS AND SDO

On 2014 August 29, the trigger and evolution of a cusp-shaped jet were captured in detail at 1330 Å by the Interface Region Imaging Spectrograph . At first, two neighboring mini-prominences arose in turn from the low solar atmosphere and collided with a loop-like system over them. The collisions between the loop-like system and the mini-prominences lead to the blowout, and then a cusp-shaped jet formed with a spire and an arch-base. In the spire, many brightening blobs originating from the junction between the spire and the arch-base moved upward in a rotating manner and then in a straight line in the late phase of the jet. In the arch-base, dark and bright material simultaneously tracked in a fan-like structure, and the majority of the material moved along the fan's threads. At the later phase of the jet's evolution, bidirectional flows emptied the arch-base, while downflows emptied the spire, thus making the jet entirely vanish. The extremely detailed observations in this study shed new light on how magnetic reconnection alters the inner topological structure of a jet and provides a beneficial complement for understanding current jet models.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Grid Forming Fast Frequency Response for PMSG-Based Wind Turbines

Electric power systems are undergoing a rapid transition from fuel-based generation using synchronous generators to renewable generation interfaced by power electronics. In this context, a key challenge is using renewable generation with limited controllability to contribute to power system stability. In this work, we investigate grid-forming control of permanent magnet synchronous generator (PMSG) wind turbines. The proposed control and curtailment strategy supports the entire spectrum of standard functions of grid-following (e.g. maximum power point tracking (MPPT) and grid-forming control (e.g., primary frequency control) without explicit mode switching. A detailed case study is used to compare the performance of the proposed control at operating points corresponding to MPPT and frequency control with standard grid-forming and grid-following controls. Further, the results demonstrate that (i) the proposed energy balancing grid forming control is self-synchronizing in MPPT mode, (ii) the (limited) energy storage and controllability of wind turbines can be adequately utilized to provide grid support, and (ii) the proposed control exhibits good performance under variable wind speeds and does not result in a significant increase of wind turbine fatigue loads.

17 WIND ENERGY↗

DOE OSTI2013

DIVA V1.0

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface, submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. Once a design has been submitted to the queue, a small number of dedicated staff evaluate the design for feasibility and provide feedback to the responsible researcher if the design is either unreasonable (e.g., encompasses a combinatorial library of a billion constructs) or small design changes could significantly facilitate the downstream implementation process. The dedicated staff then use DNA assembly design automation software to optimize the DNA construction process for the design, leveraging existing parts from the DNA repository where possible and ordering synthetic DNA where necessary. SynTrack software manages the physical locations and availability of the various requisite reagents and process inputs (e.g., DNA templates). Once all requisite process inputs are available, the design progresses from "waiting for reagents" to "in progress" in the design queue. Human-readable and machine-parseable DNA construction protocols output by the DNA assembly design automation software are then executed by the dedicated staff exploiting lab automation devices wherever possible. Since the all employed DNA construction methods are sequence-agnostic, standardized (utilize the same enzymatic master mixes and reaction conditions), completely independent DNA construction tasks can be aggregated into the same multi-well plates and pursued in parallel. The resulting sets of cloned constructs can then be screened by high-throughput next-gen sequencing platforms for sequence correctness. A combination of long read-length (e.g., PacBio) and paired-end read platforms (e.g., Illumina) would be exploited depending the particular task at hand (e.g., PacBio might be sufficient to screen a set of pooled constructs with significant gene divergence). Post sequence verification, designs for which at least one correct clone was identified will progress to a "complete" status, while designs for which no correct clones wereidentified will progress to a "failure" status. Depending on the failure mode (e.g., no transformants), and how many prior attempts/variations of assembly protocol have been already made for a given design, subsequent attempts may be made or the design can progress to a "permanent failure" state. All success and failure rate information will be captured during the process, including at which stage a given clonal construction procedure failed (e.g., no PCR product) and what the exact failure was (e.g. assembly piece 2 missing). This success/failure rate data can be leveraged to refine the DNA assembly design process.

Source record↗

DOE OSTI2016

DIVA V2.0

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface, submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. Once a design has been submitted to the queue, a small number of dedicated staff evaluate the design for feasibility and provide feedback to the responsible researcher if the design is either unreasonable (e.g., encompasses a combinatorial library of a billion constructs) or small design changes could significantly facilitate the downstream implementation process. The dedicated staff then use DNA assembly design automation software to optimize the DNA construction process for the design, leveraging existing parts from the DNA repository where possible and ordering synthetic DNA where necessary. SynTrack software manages the physical locations and availability of the various requisite reagents and process inputs (e.g., DNA templates). Once all requisite process inputs are available, the design progresses from "waiting for reagents" to "in progress" in the design queue. Human-readable and machine-parseable DNA construction protocols output by the DNA assembly design automation software are then executed by the dedicated staff exploiting lab automation devices wherever possible. Since the all employed DNA construction methods are sequence-agnostic, standardized (utilize the same enzymatic master mixes and reaction conditions), completely independent DNA construction tasks can be aggregated into the same multi-well plates and pursued in parallel. The resulting sets of cloned constructs can then be screened by high-throughput next-gen sequencing platforms for sequence correctness. A combination of long read-length (e.g., PacBio) and paired-end read platforms (e.g., Illumina) would be exploited depending the particular task at hand (e.g., PacBio might be sufficient to screen a set of pooled constructs with significant gene divergence). Post sequence verification, designs for which at least one correct clone was identified will progress to a "complete" status, while designs for which no correct clones wereidentified will progress to a "failure" status. Depending on the failure mode (e.g., no transformants), and how many prior attempts/variations of assembly protocol have been already made for a given design, subsequent attempts may be made or the design can progress to a "permanent failure" state. All success and failure rate information will be captured during the process, including at which stage a given clonal construction procedure failed (e.g., no PCR product) and what the exact failure was (e.g. assembly piece 2 missing). This success/failure rate data can be leveraged to refine the DNA assembly design process.

CHEN, JOANNA↗

DOE OSTI2021

High-speed synchrotron X-ray phase-contrast imaging for evaluating microscale damage mechanisms and tracking cracking behaviors inside cross-ply GFRCs

In this study, we integrated the high-speed synchrotron X-ray phase-contrast imaging (PCI) with a modified Kolsky compression bar loading platform to visualize the dynamic failure processes of cross-ply glass fiber reinforced composites (GFRCs). Four S-2 glass/SC-15 composite specimens were prepared, having similar thicknesses but different stacking sequences, namely as [0 12 /90 12 ], [90 12 /0 12 ], [0 8 /90 8 /0 8 ], and [90 8 /0 8 /90 8 ]. Three-dimensional synchrotron X-ray computed tomography and scanning electron microscopy (SEM) were employed to examine the microstructures and quantify the fiber volume fractions. Each specimen was notched and subjected to a dynamic three-point flexural loading. The onset of cracking close to the notch tip, crack propagation in 0° or 90° plies and their interface, crack opening, and ultimately failure of the specimen were captured by high-speed synchrotron X-ray PCI. Additional dynamic experiments were performed to determine the average time when the stress wave propagated through the specimen and correlate the X-ray images with the specimen's force-deflection response. Finally, the surface morphology of each specimen after the dynamic loading was imaged by SEM. Comparison between real-time X-ray images and post-fracture SEM images demonstrated the capability of the X-ray method to record damage evolution inside composites. Furthermore, the high spatial and temporal resolutions of the X-ray setup and edge enhancement by PCI enabled the identification of microscale damage features within 1 μs. Two damaging processes were identified, crack growth was quantified, and fracture toughness of the composites was evaluated. The method is deemed useful to reveal microscale damage mechanisms and track cracking behaviors inside cross-ply GFRCs under dynamic loading in real time.

42 ENGINEERING↗

DOE OSTI2022

Visualizing the Nanoscale Oxygen and Cation Transport Mechanisms during the Early Stages of Oxidation of Fe–Cr–Ni Alloy Using In Situ Atom Probe Tomography

Abstract Understanding the early stages of interactions between oxygen and material surfaces—especially at very high spatial resolutions—is highly beneficial for fields ranging from materials degradation, corrosion, geological sciences, forensics, and catalysis. The ability of in situ atom probe tomography (APT) is demonstrated to track the diffusion of oxygen and metal ions at nanoscale spatial resolution during the early stages of oxidation of a model Fe–Cr–Ni alloy. Using 18 O isotope tracers in these in situ APT experiments and complementary ex situ multimodal microscopy, spectroscopy, and computational simulations allows to precisely analyze the kinetics of oxidation and determine that outward cation diffusion to oxide/air interface is the primary mechanism for intragranular oxide growth in this alloy at 300 °C. This unique in situ isotopic tracer APT approach and the insights gained can be highly beneficial for studying early stages of gas–surface reactions in a broad array of materials.

36 MATERIALS SCIENCE↗

DOE OSTI2014

A fusion nuclear science facility for a fast-track path to DEMO

An accelerated fusion energy development program, a fast-track approach, requires proceeding with a nuclear and materials testing program in parallel with research on burning plasmas, ITER. A Fusion Nuclear Science Facility (FNSF) would address many of the key issues that need to be addressed prior to DEMO, including breeding tritium and completing the fuel cycle, qualifying nuclear materials for high fluence, developing suitable materials for the plasma-boundary interface, and demonstrating power extraction. The Advanced Tokamak (AT) is a strong candidate for an FNSF as a consequence of its mature physics base, capability to address the key issues, and the direct relevance to an attractive target power plant. The standard aspect ratio provides space for a solenoid, assuring robust plasma current initiation,and for an inboard blanket, assuring robust tritium breeding ratio (TBR) >1 for FNSF tritium self-sufficiency and building of inventory needed to start up DEMO. An example design point gives a moderate sized Cu-coil device with R/a = 2.7 m/0.77 κ = 2.3, B T = 5.4 T, I P = 6.6 MA, β N = 2.75, P fus = 127 MW. The modest bootstrap fraction of f BS = 0.55 provides an opportunity to develop steady state with sufficient current drive for adequate control. Lastly, proceeding with a FNSF in parallel with ITER provides a strong basis to begin construction of DEMO upon the achievement of Q ~ 10 in ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

DIVA/DeviceEditor (DIVA) v5.1

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface (DeviceEditor), submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. his success/failure rate data can be leveraged to refine the DNA assembly design process.

Lane, Stephen↗

DOE OSTI2022

DIVA/DeviceEditor (DIVA) v6.0.0

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface (DeviceEditor), submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. Once a design has been submitted to the queue, a small number of dedicated staff evaluate the design for feasibility and provide feedback to the responsible researcher if the design is either unreasonable (e.g., encompasses a combinatorial library of a billion constructs) or small design changes could significantly facilitate the downstream implementation process. The dedicated staff then use DNA assembly design automation software to optimize the DNA construction process for the design, leveraging existing parts from the DNA repository where possible and ordering synthetic DNA where necessary. Once all requisite process inputs are available, the design progresses from "waiting for reagents" to "in progress" in the design queue. Human-readable and machine-parseable DNA construction protocols output by the DNA assembly design automation software are then executed by the dedicated staff exploiting lab automation devices wherever possible. Since the all employed DNA construction methods are sequence-agnostic, standardized (utilize the same enzymatic master mixes and reaction conditions), completely independent DNA construction tasks can be aggregated into the same multi-well plates and pursued in parallel. The resulting sets of cloned constructs can then be screened by high-throughput next-gen sequencing platforms for sequence correctness. A combination of long read-length (e.g., PacBio) and paired-end read platforms (e.g., Illumina) would be exploited depending the particular task at hand (e.g., PacBio might be sufficient to screen a set of pooled constructs with significant gene divergence). Post sequence verification, designs for which at least one correct clone was identified will progress to a "complete" status, while designs for which no correct clones were identified will progress to a "failure" status. Depending on the failure mode (e.g., no transformants), and how many prior attempts/variations of assembly protocol have been already made for a given design, subsequent attempts may be made or the design can progress to a "permanent failure" state. All success and failure rate information will be captured during the process, including at which stage a given clonal construction procedure failed (e.g., no PCR product) and what the exact failure was (e.g. assembly piece 2 missing). This success/failure rate data can be leveraged to refine the DNA assembly design process.

Plahar, Hector↗