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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

The response of tissue-equivalent proportional counters to heavy ions

The paper presents a theoretical model for the response of a tissue-equivalent proportional counter (TEPC) irradiated with charged particles. Heavy ions and iron ions in particular constitute a significant part of radiation in space. TEPCs are used for all space shuttle and International Space Station (ISS) missions to estimate the dose and radiation quality (in terms of lineal energy) inside spacecraft. The response of the tissue-equivalent proportional counters shows distortions at the wall/cavity interface. In this paper, we present microdosimetric investigation using Monte Carlo track structure calculations to simulate the response of a TEPC to charged particles of various LET (1 MeV protons, 2.4 MeV alpha particles, 46 MeV/nucleon 20Ne, 55 MeV/nucleon 20Ne, 45 MeV/nucleon 40Ar, and 1.05 GeV/nucleon 56Fe). Data are presented for energy lost and energy absorbed in the counter cavity and wall. The model calculations are in good agreement with the results of Rademacher et al. (Radiat. Res. 149, 387-389, 1998), including the study of the interface between the wall and the sensitive region of the counter. It is shown that the anomalous response observed at large event sizes in the experiment is due to an enhanced entry of secondary electrons from the wall into the gas cavity.

NASA Discipline Radiation Health↗
DOE OSTI2025

Toward Drilling the Perfect Geothermal Well: An International Research Coordination Network for Geothermal Drilling Optimization Supported by Deep Machine Learning and Cloud Based Data Aggregation

The EDGE project, supported by the U.S. Department of Energy Geothermal Technologies Office under award DE-EE0008793, established a data-driven framework for improving the efficiency, cost-effectiveness, and reliability of geothermal well drilling. The project focused on developing scalable data infrastructure, advanced machine learning and probabilistic models, and integrated analytics tools to support continuous drilling optimization. A central objective was to reduce geothermal drilling costs by up to seventy percent while minimizing the risk of well failure through predictive diagnostics and adaptive planning. Over the project period, a comprehensive data repository was designed and deployed, incorporating records from over one hundred geothermal wells across varied geological settings. This repository supported both structured and unstructured data and adhered to FAIR data principles, enabling provenance tracking, quality control, and standardized metadata. The project introduced automated ingestion pipelines and a cloud-hosted platform that facilitated access to raw, processed, and derived datasets. This infrastructure served as the foundation for model development and analysis. Machine learning workflows were developed to predict key drilling metrics including rate of penetration, non-productive time, and total drilling costs. Self-organizing maps and dimensionality reduction methods were used to uncover operational patterns and outliers, while supervised learning algorithms such as random forests and deep neural networks were applied to forecast performance outcomes. The models were validated on heterogeneous datasets from both U.S. and Icelandic fields, demonstrating variable but significant predictive accuracy. The results indicated that finer temporal resolution, inclusion of lithological data, and consistency in operational annotations could substantially improve model performance. The project also implemented process mining techniques to reconstruct state-transition models from drilling event logs. These models enabled the identification of deviations from optimal workflows and provided insights into recurring failure modes. Analysis of non-productive time highlighted the impact of equipment failures, geological challenges, and human factors, offering opportunities for targeted mitigation strategies. The EDGE Dashboard was developed as a web-based expert system integrating data visualization, model outputs, and user-driven queries. It provided an accessible interface for operators to explore historical data, evaluate predicted outcomes, and compare drilling scenarios. Initial feedback from project partners suggested that the dashboard could serve as a foundation for more advanced advisory and optimization tools. Overall, the EDGE project demonstrated the feasibility and value of applying modern data science techniques to geothermal drilling. It delivered a set of interoperable tools and models that can support more efficient, lower-risk well development. The findings point toward a viable path for transitioning from advisory analytics to semi-autonomous drilling systems, contingent on continued collaboration, expanded datasets, and field validation. The project results have immediate relevance for drilling operations, data management practices, and future geothermal R&D efforts aimed at achieving reliable, cost-competitive geothermal energy at scale.

15 GEOTHERMAL ENERGY↗
NASA NTRS2002

CATS-based Air Traffic Controller Agents

This report describes intelligent agents that function as air traffic controllers. Each agent controls traffic in a single sector in real time; agents controlling traffic in adjoining sectors can coordinate to manage an arrival flow across a given meter fix. The purpose of this research is threefold. First, it seeks to study the design of agents for controlling complex systems. In particular, it investigates agent planning and reactive control functionality in a dynamic environment in which a variety perceptual and decision making skills play a central role. It examines how heuristic rules can be applied to model planning and decision making skills, rather than attempting to apply optimization methods. Thus, the research attempts to develop intelligent agents that provide an approximation of human air traffic controller behavior that, while not based on an explicit cognitive model, does produce task performance consistent with the way human air traffic controllers operate. Second, this research sought to extend previous research on using the Crew Activity Tracking System (CATS) as the basis for intelligent agents. The agents use a high-level model of air traffic controller activities to structure the control task. To execute an activity in the CATS model, according to the current task context, the agents reference a 'skill library' and 'control rules' that in turn execute the pattern recognition, planning, and decision-making required to perform the activity. Applying the skills enables the agents to modify their representation of the current control situation (i.e., the 'flick' or 'picture'). The updated representation supports the next activity in a cycle of action that, taken as a whole, simulates air traffic controller behavior. A third, practical motivation for this research is to use intelligent agents to support evaluation of new air traffic control (ATC) methods to support new Air Traffic Management (ATM) concepts. Current approaches that use large, human-in-the-loop simulations are unquestionably valuable for this purpose, but pose considerable logistical, fiscal, and experimental control problems. First, data analysis is extremely complicated, owing simply to the large number of participants and data sources in such simulations. In addition, experienced human air traffic controllers working adjacent sectors tend to flexibly adapt to the evolving control problem - potentially shifting to other strategies than those under investigation. In addition, their performance is tightly coupled to the control interface, which in the development phase may support some concepts and supporting strategies better than others. A simple shift in strategy by one controller can change the character of a particular traffic scenario dramatically, which makes experimental comparison of ATC performance under different traffic scenarios difficult. Training a given team of controllers on operations under a new ATM concept for a sufficient period of time could avert such difficulties, but instituting an adequate training program is expensive and logistically difficult.

Callantine, Todd J.↗
DOE OSTI2012

Zgoubi Users' Guide

The computer code zgoubi calculates trajectories of charged particles in magnetic and electric fields. At the origin specially adapted to the definition and adjustment of beam lines and magnetic spectrometers, it has so evolved that it allows the study of systems including complex sequences of optical elements such as dipoles, quadrupoles, arbitrary multipoles, FFAG magnets and other magnetic or electric devices, and is able as well to handle periodic structures. Compared to other codes, it presents several peculiarities, as follows - a non-exhaustive list : • a numerical method for integrating the Lorentz equation, based on Taylor series, which optimizes computing time and provides high accuracy and strong symplecticity, • spin tracking, using the same numerical method as for the Lorentz equation, • account of stochastic photon emission, and its effects on particle dynamics, • calculation of the synchrotron radiation electric field and spectra in arbitrary magnetic fields, from the ray-tracing outcomes, • the possibility of using a mesh, which allows ray-tracing from simulated or measured (1-D, 2-D or 3-D) electric and magnetic field maps, • a number Monte Carlo procedures : unlimited number of trajectories, in-flight decay, stochastic radiation, etc., • built-in fitting procedures allowing arbitrary variables and a large variety of constraints, easily expandable, • multi-turn tracking in circular accelerators including features proper to machine parameter calculation and survey, • simulation of time-varying power supplies, and • simulation of arbitrary radio-frequency programs. The initial version of zgoubi was dedicated to ray-tracing in magnetic elements, beam lines, spectrometers. It was perfected for the purpose of studying, and operating, the four spectrometers SPES I, II, III, IV at the Laboratoire National SATURNE (CEA-Saclay, France), and, later, SPEG at GANIL (Caen, France). Developments regarding spin tracking and ray-tracing in combined electric and magnetic fields were implemented, in the late 1980s and early 1990s respectively. In the mid-1990s, the computation of synchrotron radiation electromagnetic impulse and spectra was introduced, for the purpose of synchrotron radiation diagnostic R&D at LEP, and further applied to the design of the SR diagnostics installations at LHC in the early 2000s. In the mean time, several new optical elements were added, such as electro-magnetic and other electrostatic lenses. Used since several years for special studies in periodic machines (e.g., SATURNE at Saclay, COSY at Julich, LEP and LHC at CERN), zgoubi has also undergone extensive developments regarding storage ring related features. Many developments have been accomplished since the early 2000s in the frame of a number of project design and beam dynamics studies, as the neutrino factory, lepton and hadron colliders, spin studies at AGS and RHIC, etc. As a consequence the list of optical elements and the compendium of numerical methods, so-called “Glossary of Keywords” list, pp. 7 and 169, has stretched with new simulation and computing procedures, ranging from fitting (FIT2 procedure ; additional constraints) to overlapping magnetic field capabilities (DIPOLES, FFAG), spin manipulation (SPINR), optical elements (BEAMBEAM), radiation damping tools (SRLOSS) and many others (FAISTORE, MAP2D-E, OPTICS, PICKUPS, TWISS, etc.). The graphic interface to zgoubi (zpop, Part D) has undergone extensive developments, making it a convenient companion tool to the use of zgoubi.

43 PARTICLE ACCELERATORS↗
DOE OSTI2012

Provenance-Enabling DOE Visualization Applications

VisTrails, Inc.’s goal main charter has been to develop provenance management solutions for software tools. As the use of computation increases, keeping track of computational processes and the data they consume and derive is essential for many applications. Provenance (also referred to as audit trail, lineage, and pedigree) captures information about the steps used to generate a given data product. Such information provides important documentation that is key to preserving the data, to determining the data’s quality and authorship, and to reproducing as well as validating the results. Given the growing complexity of the computational processes and the volume of data they manipulate, manual approaches to maintaining provenance are both tedious and error-prone. At VisTrails, Inc., we have implemented infrastructure that can be used to provenance-enable existing tools. We have developed a series of plugins for specific applications, including ParaView and VisIt, which enable these applications to capture provenance. While developing these plugins, we identified general patterns across different applications, and these were used to inform the design of a general framework: the VisTrails Provenance Software Development Kit (SDK). The SDK encapsulates a set of core functionality including methods for capture, navigation, analysis and re-use of provenance. It allows application or plugin developers to more effectively provide provenance support: they can use the core functionality and write code only to handle application specific components. The SDK includes features that can be used in any application, for example, a refined interface for browsing the intermediate and final results captured. While the application-specific plugins were written in Python, the SDK was written from scratch in C++. This has led not only to substantial gains in performance but also the ability to integrate the SDK with applications written in other languages, including Java. To ensure that the SDK supported all of the functionality in the application-specific plugins, we have rewritten some of the existing plugins using the SDK. The SDK can be downloaded from www.vistrals.com/sdk.html.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Deliver Signal Phase and Timing (SPAT) for Energy Optimization of Vehicle Cohort Via Cloud-Computing and LTE Communications

Predictive Signal Phase and Timing (SPAT) message set is one fundamental building block for vehicle-to-infrastructure (V2I) applications such as Eco-Approach and Departure (EAD) at traffic signal controlled urban intersections. Among the two complementary communication methods namely short-range sidelink (PC5) and long-range cellular radio link (Uu), this paper documents the work with long-range link: the complete data chain includes connecting to the traffic signals via existing backhaul communication network, collecting the raw signal phase state data, predicting the signal state changes and delivering the SPAT data via a geofenced service to requests over HTTP protocols. An Application Programming Interface (API) library is developed to support various cellular data transmission reduction and latency improvement techniques. An emulation-based algorithm is applied to predict the traffic signal state changes to provide adequate prediction horizon (e.g., at minimum 2 minutes) for the cohort energy optimization. In fact, the same connectivity and SPAT delivery methodology has been applied to traffic signalized intersections nationwide in the United States upon public agency approvals for access to their firewalled traffic control network and signal control systems or directly to individual controllers. This methodology proves its effectiveness and potential for rapid growth of such SPAT deliveries at mass production scale without needing infrastructure hardware retrofit or excessive communication means. To support the energy optimization of light and heavy-duty vehicle cohorts of mixed automation and propulsion systems (EV, ICE and hybrid), the connection and SPAT deliveries at two sites were completed, including public roads in Washtenaw County, Michigan and closed track test sites at American Center for Mobility (ACM) in Ypsilanti, Michigan. However, only closed test track results at ACM will be presented in this paper. A neuroevolution based optimizer is developed and implemented to control the speed of a vehicle cohort with different propulsion systems and automation levels. Closed track tests showed significant energy savings of the cohort operation.

99 GENERAL AND MISCELLANEOUS↗
NASA NTRS2016

Assessing Dual Sensor Enhanced Flight Vision Systems to Enable Equivalent Visual Operations

Flight deck-based vision system technologies, such as Synthetic Vision (SV) and Enhanced Flight Vision Systems (EFVS), may serve as a revolutionary crew/vehicle interface enabling technologies to meet the challenges of the Next Generation Air Transportation System Equivalent Visual Operations (EVO) concept - that is, the ability to achieve the safety of current-day Visual Flight Rules (VFR) operations and maintain the operational tempos of VFR irrespective of the weather and visibility conditions. One significant challenge lies in the definition of required equipage on the aircraft and on the airport to enable the EVO concept objective. A motion-base simulator experiment was conducted to evaluate the operational feasibility, pilot workload and pilot acceptability of conducting straight-in instrument approaches with published vertical guidance to landing, touchdown, and rollout to a safe taxi speed in visibility as low as 300 ft runway visual range by use of onboard vision system technologies on a Head-Up Display (HUD) without need or reliance on natural vision. Twelve crews evaluated two methods of combining dual sensor (millimeter wave radar and forward looking infrared) EFVS imagery on pilot-flying and pilot-monitoring HUDs as they made approaches to runways with and without touchdown zone and centerline lights. In addition, the impact of adding SV to the dual sensor EFVS imagery on crew flight performance, workload, and situation awareness during extremely low visibility approach and landing operations was assessed. Results indicate that all EFVS concepts flown resulted in excellent approach path tracking and touchdown performance without any workload penalty. Adding SV imagery to EFVS concepts provided situation awareness improvements but no discernible improvements in flight path maintenance.

Kramer, Lynda J.↗
DOE OSTI2020

Impact of thermodynamic fluctuations and pattern size on the nucleation behavior during area selective deposition

In this work, the authors explore the impact that thermodynamic fluctuations have on the spontaneous appearance of defects during area selective deposition on patterned surfaces that are fully covered by adsorbates under local thermodynamic equilibrium, such as self-assembled monolayers. By using a simple lattice gas model for the adsorbed monolayer, the authors were able to track the spontaneous formation of defects in the monolayer as a function of the pattern width. The results indicate that, for pattern widths of the order of tens of nanometers, roughening effects at the pattern edge can be the leading source for the spontaneous appearance of nucleation defects. This leads to an enhancement of the density of defects that can be up to three orders of magnitude higher than those expected in uniform (not patterned) surfaces. The model also predicts a density of defects that is inversely proportional to the pattern width. Finally, if the dynamic nucleation of defects during area selective deposition is driven by thermodynamic fluctuations, the model predicts that the nucleation rate should be proportional to the total precursor fluency and independent of purge times. Moreover, a tight confinement of the monolayer through a high quality smooth interface in the patterned substrate and strong cohesive interactions between adsorbates should each contribute to a reduction of the overall defect density.

36 MATERIALS SCIENCE↗
NASA NTRS2021

Modular Composite Damage Detection System (MCDDS)

The 2020 CIF funded Modular Composite Damage Detection System (MCDDS) aims to advance the technology of damage detection in composites in the areas of thin, flexible damage detection panel construction, encapsulation techniques in composite matrixes, innovative integration and interfacing techniques with flexible embedded sensory panels, repair methods of composite materials, and improved packaging of the MCDDS. Custom thin, flexible polyimide printed circuit boards (PCBs) were designed and procured for fabrication of test specimens. A custom interface PCB was designed and fabricated to monitor the newly developed damage detection test specimens. Test specimens were fabricated using the novel flexible circuitry that were either fully or partially encapsulated. The fully encapsulated specimens were used to demonstrate embedded damage detection concepts and the partially encapsulated specimens were used to demonstrate surface-mounted (laminate) damage detection concepts. The new composite damage detection test specimens were tested and evaluated to determine if the novel damage detection sensory panels could withstand low-cycle threshold fatigue loading per a modified version of American Society for Testing and Materials (ASTM) D 7264 for up to 50 cycles without void formation. The data for multiple sensory panels indicates that the newly fabricated sensory panels are robust and do indeed withstand three-point bend flexural loading for more than 50 cycles. Additionally, testing was performed to determine if damage could be detected in damage detection test specimens subjected to failure using a 3-point bend test per a modified version of ASTM D 7264. Again, multiple sensory panels (both fully and partially encapsulated) showed the ability to detect damage to specimens subjected to failure per a modified version of ASTM D 7264. Additionally, a novel concept for tracking and monitoring of cracking (and potentially delamination) in composites was designed and developed that utilizes painted-on conductors.

Christopher Forney↗
NASA NTRS2016

Experimenting Galileo on Board the International Space Station

The SCaN Testbed is an advanced integrated communications system and laboratory facility installed on the International Space Station (ISS) in 2012. The testbed incorporates a set of new generation of Software Defined Radio (SDR) technologies intended to allow researchers to develop, test, and demonstrate new communications, networking, and navigation capabilities in the actual environment of space. Qascom, in cooperation with ESA and NASA, is designing a Software Defined Radio GalileoGPS Receiver capable to provide accurate positioning and timing to be installed on the ISS SCaN Testbed. The GalileoGPS waveform will be operated in the JPL SDR that is constituted by several hardware components that can be used for experimentations in L-Band and S-Band. The JPL SDR includes an L-Band Dorne Margolin antenna mounted onto a choke ring. The antenna is connected to a radio front end capable to provide one bit samples for the three GNSS frequencies (L1, L2 and L5) at 38 MHz, exploiting the subharmonic sampling. The baseband processing is then performed by an ATMEL AT697 processor (100 MIPS) and two Virtex 2 FPGAs. The JPL SDR supports the STRS (Space Telecommunications Radio System) that provides common waveform software interfaces, methods of instantiation, operation, and testing among different compliant hardware and software products. The standard foresees the development of applications that are modular, portable, reconfigurable, and reusable. The developed waveform uses the STRS infrastructure-provided application program interfaces (APIs) and services to load, verify, execute, change parameters, terminate, or unload an application. The project is divided in three main phases. 1)Design and Development of the GalileoGPS waveform for the SCaN Testbed starting from Qascom existing GNSS SDR receiver. The baseline design is limited to the implementation of the single frequency Galileo and GPS L1E1 receiver even if as part of the activity it will be to assess the feasibility of a dual frequency implementation (L1E1+L5E5a) in the same SDR platform.2)Qualification and test the GalileoGPS waveform using ground systems available at the NASA Glenn Research Center. Experimenters can have access to two SCaN Testbed ground based systems for development and verification: the Experimenter Development System (EDS) that is intended to provide initial opportunity for software testing and basic functional validation and the Ground Integration Unit (GIU) that is a high fidelity version of the SCaN Testbed flight system and is therefore used for more controlled final development testing and verification testing.3)Perform in-orbit validation and experimentation: The experimentation phase will consists on the collection of raw measurements (pseudorange, Carrier phase, CN0) in space, assessment on the quality of the measurements and the receiver performances in terms of signal acquisition, tracking, etc. Finally computation of positioning in space (Position, Velocity and time) and assessment of its performance.(Complete abstract in attached document).

GPS↗
NASA NTRS2016

Experimenting Galileo on Board the International Space Station

The SCaN Testbed is an advanced integrated communications system and laboratory facility installed on the International Space Station (ISS) in 2012. The testbed incorporates a set of new generation of Software Defined Radio (SDR) technologies intended to allow researchers to develop, test, and demonstrate new communications, networking, and navigation capabilities in the actual environment of space. Qascom, in cooperation with ESA and NASA, is designing a Software Defined Radio GalileoGPS Receiver capable to provide accurate positioning and timing to be installed on the ISS SCaN Testbed. The GalileoGPS waveform will be operated in the JPL SDR that is constituted by several hardware components that can be used for experimentations in L-Band and S-Band. The JPL SDR includes an L-Band Dorne Margolin antenna mounted onto a choke ring. The antenna is connected to a radio front end capable to provide one bit samples for the three GNSS frequencies (L1, L2 and L5) at 38 MHz, exploiting the subharmonic sampling. The baseband processing is then performed by an ATMEL AT697 processor (100 MIPS) and two Virtex 2 FPGAs. The JPL SDR supports the STRS (Space Telecommunications Radio System) that provides common waveform software interfaces, methods of instantiation, operation, and testing among different compliant hardware and software products. The standard foresees the development of applications that are modular, portable, reconfigurable, and reusable. The developed waveform uses the STRS infrastructure-provided application program interfaces (APIs) and services to load, verify, execute, change parameters, terminate, or unload an application. The project is divided in three main phases. 1)Design and Development of the GalileoGPS waveform for the SCaN Testbed starting from Qascom existing GNSS SDR receiver. The baseline design is limited to the implementation of the single frequency Galileo and GPS L1E1 receiver even if as part of the activity it will be to assess the feasibility of a dual frequency implementation (L1E1+L5E5a) in the same SDR platform.2)Qualification and test the GalileoGPS waveform using ground systems available at the NASA Glenn Research Center. Experimenters can have access to two SCaN Testbed ground based systems for development and verification: the Experimenter Development System (EDS) that is intended to provide initial opportunity for software testing and basic functional validation and the Ground Integration Unit (GIU) that is a high fidelity version of the SCaN Testbed flight system and is therefore used for more controlled final development testing and verification testing.3)Perform in-orbit validation and experimentation: The experimentation phase will consists on the collection of raw measurements (pseudorange, Carrier phase, CN0) in space, assessment on the quality of the measurements and the receiver performances in terms of signal acquisition, tracking, etc. Finally computation of positioning in space (Position, Velocity and time) and assessment of its performance.(Complete abstract in attached document).

Galileo↗
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↗
DOE OSTI2016

WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio

Purpose: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. Methods: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit. TOPAS-nBio is an extension to TOPAS which utilizes the physics processes in Geant4-DNA to model biological damage from very low energy secondary electrons. Specialized cell, organelle and molecular geometries were designed for the toolkit. Results: TOPAS-nBio gives the user the capability of simulating biological geometries, ranging from the micron-scale (e.g. cells and organelles) to complex nano-scale geometries (e.g. DNA and proteins). The user interacts with TOPAS-nBio through easy-to-use input parameter files. For example, in a simple cell simulation the user can specify the cell type and size as well as the type, number and size of included organelles. For more detailed nuclear simulations, the user can specify chromosome territories containing chromatin fiber loops, the later comprised of nucleosomes on a double helix. The chromatin fibers can be arranged in simple rigid geometries or within factual globules, mimicking realistic chromosome territories. TOPAS-nBio also provides users with the capability of reading protein data bank 3D structural files to simulate radiation damage to proteins or nucleic acids e.g. histones or RNA. TOPAS-nBio has been validated by comparing results to other track structure simulation software and published experimental measurements. Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, giving users without advanced programming skills the ability to design and run complex simulations.

60 APPLIED LIFE SCIENCES↗
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 OSTI2016

Asymmetric collapse by dissolution or melting in a uniform flow

An advection-diffusion-limited dissolution model of an object being eroded by a two-dimensional potential flow is presented. By taking advantage of the conformal invariance of the model, a numerical method is introduced that tracks the evolution of the object boundary in terms of a time-dependent Laurent series. Simulations of a variety of dissolving objects are shown, which shrink and collapse to a single point in finite time. The simulations reveal a surprising exact relationship, whereby the collapse point is the root of a non-Analytic function given in terms of the flow velocity and the Laurent series coefficients describing the initial shape. This result is subsequently derived using residue calculus. The structure of the non-Analytic function is examined for three different test cases, and a practical approach to determine the collapse point using a generalized Newton-Raphson root-finding algorithm is outlined. These examples also illustrate the possibility that the model breaks down in finite time prior to complete collapse, due to a topological singularity, as the dissolving boundary overlaps itself rather than breaking up into multiple domains (analogous to droplet pinch-off in fluid mechanics). In conclusion, the model raises fundamental mathematical questions about broken symmetries in finite-Time singularities of both continuous and stochastic dynamical systems.

42 ENGINEERING↗
NASA NTRS2010

Situational Awareness from a Low-Cost Camera System

A method gathers scene information from a low-cost camera system. Existing surveillance systems using sufficient cameras for continuous coverage of a large field necessarily generate enormous amounts of raw data. Digitizing and channeling that data to a central computer and processing it in real time is difficult when using low-cost, commercially available components. A newly developed system is located on a combined power and data wire to form a string-of-lights camera system. Each camera is accessible through this network interface using standard TCP/IP networking protocols. The cameras more closely resemble cell-phone cameras than traditional security camera systems. Processing capabilities are built directly onto the camera backplane, which helps maintain a low cost. The low power requirements of each camera allow the creation of a single imaging system comprising over 100 cameras. Each camera has built-in processing capabilities to detect events and cooperatively share this information with neighboring cameras. The location of the event is reported to the host computer in Cartesian coordinates computed from data correlation across multiple cameras. In this way, events in the field of view can present low-bandwidth information to the host rather than high-bandwidth bitmap data constantly being generated by the cameras. This approach offers greater flexibility than conventional systems, without compromising performance through using many small, low-cost cameras with overlapping fields of view. This means significant increased viewing without ignoring surveillance areas, which can occur when pan, tilt, and zoom cameras look away. Additionally, due to the sharing of a single cable for power and data, the installation costs are lower. The technology is targeted toward 3D scene extraction and automatic target tracking for military and commercial applications. Security systems and environmental/ vehicular monitoring systems are also potential applications.

Freudinger, Lawrence C.↗
DOE OSTI2015

SU-E-T-258: Development of a New Patient Set-Up Monitoring System Using Force Sensing Resistor (FSR) Sensor for the Radiation Therapy

Purpose: The purpose of this work is to develop a new patient set-up monitoring system using force sensing resistor (FSR) sensors that can confirm pressure of contact surface and evaluate its feasibility. Methods: In this study, we focused on develop the patient set-up monitoring system to compensate for the limitation of existing optical based monitoring system, so the developed system can inform motion in the radiation therapy. The set-up monitoring system was designed consisting of sensor units (FSR sensor), signal conditioning devices (USB cable/interface electronics), a control PC, and a developed analysis software. The sensor unit was made by attaching FSR sensor and dispersing pressure sponge to prevent error which is caused by concentrating specific point. Measured signal from the FSR sensor was sampled to arduino mega 2560 microcontroller, transferred to control PC by using serial communication. The measured data went through normalization process. The normalized data was displayed through the developed graphic user interface (GUI) software. The software was designed to display a single sensor unit intensity (maximum 16 sensors) and display 2D pressure distribution (using 16 sensors) according to the purpose. Results: Changes of pressure value according to motion was confirmed by the developed set-up monitoring system. Very small movement such as little physical change in appearance can be confirmed using a single unit and using 2D pressure distribution. Also, the set-up monitoring system can observe in real time. Conclusion: In this study, we developed the new set-up monitoring system using FSR sensor. Especially, we expect that the new set-up monitoring system is suitable for motion monitoring of blind area that is hard to confirm existing optical system and compensate existing optical based monitoring system. As a further study, an integrated system will be constructed through correlation of existing optical monitoring system. This work was supported by the Industrial R&D program of MOTIE/KEIT. [10048997, Development of the core technology for integrated therapy devices based on real-time MRI guided tumor tracking] and the Mid-career Researcher Program (2014R1A2A1A10050270) through the National Research Foundation of Korea funded by the Ministry of Science, ICT&Future Planning.

60 APPLIED LIFE SCIENCES↗