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NASA NTRS2014

RITRACKS: A Software for Simulation of Stochastic Radiation Track Structure, Micro and Nanodosimetry, Radiation Chemistry and DNA Damage for Heavy Ions

The code RITRACKS (Relativistic Ion Tracks) has been developed over the last few years at the NASA Johnson Space Center to simulate the effects of ionizing radiations at the microscopic scale, to understand the effects of space radiation at the biological level. The fundamental part of this code is the stochastic simulation of radiation track structure of heavy ions, an important component of space radiations. The code can calculate many relevant quantities such as the radial dose, voxel dose, and may also be used to calculate the dose in spherical and cylindrical targets of various sizes. Recently, we have incorporated DNA structure and damage simulations at the molecular scale in RITRACKS. The direct effect of radiations is simulated by introducing a slight modification of the existing particle transport algorithms, using the Binary‐Encounter‐Bethe model of ionization cross sections for each molecular orbitals of DNA. The simulation of radiation chemistry is done by a step‐by‐step diffusion‐reaction program based on the Green's functions of the diffusion equation]. This approach is also used to simulate the indirect effect of ionizing radiation on DNA. The software can be installed independently on PC and tablets using the Windows operating system and does not require any coding from the user. It includes a Graphic User Interface (GUI) and a 3D OpenGL visualization interface. The calculations are executed simultaneously (in parallel) on multiple CPUs. The main features of the software will be presented.

Plante, I↗

NASA NTRS2009

Simulating and Detecting Radiation-Induced Errors for Onboard Machine Learning

Spacecraft processors and memory are subjected to high radiation doses and therefore employ radiation-hardened components. However, these components are orders of magnitude more expensive than typical desktop components, and they lag years behind in terms of speed and size. We have integrated algorithm-based fault tolerance (ABFT) methods into onboard data analysis algorithms to detect radiation-induced errors, which ultimately may permit the use of spacecraft memory that need not be fully hardened, reducing cost and increasing capability at the same time. We have also developed a lightweight software radiation simulator, BITFLIPS, that permits evaluation of error detection strategies in a controlled fashion, including the specification of the radiation rate and selective exposure of individual data structures. Using BITFLIPS, we evaluated our error detection methods when using a support vector machine to analyze data collected by the Mars Odyssey spacecraft. We found ABFT error detection for matrix multiplication is very successful, while error detection for Gaussian kernel computation still has room for improvement.

data analysis↗

NASA NTRS2004

Novel Image Processing Interface to Relate DSB Spatial Distribution from Immunofluorescence Foci Experiments to the State-of-the-Art Models of DNA Breakage

A recently developed software (NASARadiationTrackImage) allows a quick and automatic segmentation of foci that indicate spatial localization of specific proteins that are visualized by immunofluorescence. Of interest are the spatial and temporal distribution of foci such as gammaH2AX, a signal of the phosphorylation of a variant of the histone H2A that has been shown to correspond to DSBs, or proteins involved in DSB processing, such as ATM, Rad51, and p53, following exposures of human cells to high charge and energy (HZE) ion irradiation. Experimental data are recorded as sets of two-dimensional images in color with cells and foci of gammaH2AX, ATM, Rad51 or others shown. Different cells, levels of radiation and timing after radiation were recorded. The software allows us to calculate the number of foci per cell, overall intensity of light in foci and their spatial organization. A simple statistical model allows for testing of foci overlap (eclipse). A more complex statistical model previously known as DNAbreak simulates track structure and random chromosome geometry. It has one adjustable parameter corresponding to an average intensity of DSB creation in cubic micrometers of DNA volume per particle track or unit dose. Its limitation is the low-resolution limit both in physical space and DSB's along DNA. It works adequately on the scale of a cell and provides further insights on how the geometry of tracks and DNA affects genomic damage of the cell and subsequent repair. Future developments of the model for the description of the time evolution of DNA damage response proteins, and more robust track structure models will be discussed.

Ponomarev, A. L.↗

NASA NTRS2011

The Analysis of the Patterns of Radiation-Induced DNA Damage Foci by a Stochastic Monte Carlo Model of DNA Double Strand Breaks Induction by Heavy Ions and Image Segmentation Software

To create a generalized mechanistic model of DNA damage in human cells that will generate analytical and image data corresponding to experimentally observed DNA damage foci and will help to improve the experimental foci yields by simulating spatial foci patterns and resolving problems with quantitative image analysis. Material and Methods: The analysis of patterns of RIFs (radiation-induced foci) produced by low- and high-LET (linear energy transfer) radiation was conducted by using a Monte Carlo model that combines the heavy ion track structure with characteristics of the human genome on the level of chromosomes. The foci patterns were also simulated in the maximum projection plane for flat nuclei. Some data analysis was done with the help of image segmentation software that identifies individual classes of RIFs and colocolized RIFs, which is of importance to some experimental assays that assign DNA damage a dual phosphorescent signal. Results: The model predicts the spatial and genomic distributions of DNA DSBs (double strand breaks) and associated RIFs in a human cell nucleus for a particular dose of either low- or high-LET radiation. We used the model to do analyses for different irradiation scenarios. In the beam-parallel-to-the-disk-of-a-flattened-nucleus scenario we found that the foci appeared to be merged due to their high density, while, in the perpendicular-beam scenario, the foci appeared as one bright spot per hit. The statistics and spatial distribution of regions of densely arranged foci, termed DNA foci chains, were predicted numerically using this model. Another analysis was done to evaluate the number of ion hits per nucleus, which were visible from streaks of closely located foci. In another analysis, our image segmentaiton software determined foci yields directly from images with single-class or colocolized foci. Conclusions: We showed that DSB clustering needs to be taken into account to determine the true DNA damage foci yield, which helps to determine the DSB yield. Using the model analysis, a researcher can refine the DSB yield per nucleus per particle. We showed that purely geometric artifacts, present in the experimental images, can be analytically resolved with the model, and that the quantization of track hits and DSB yields can be provided to the experimentalists who use enumeration of radiation-induced foci in immunofluorescence experiments using proteins that detect DNA damage. An automated image segmentaiton software can prove useful in a faster and more precise object counting for colocolized foci images.

Ponomarev, Artem↗

NASA NTRS2001

Development of a Space Radiation Monte-Carlo Computer Simulation Based on the FLUKE and Root Codes

The radiation environment in space is a complex problem to model. Trying to extrapolate the projections of that environment into all areas of the internal spacecraft geometry is even more daunting. With the support of our CERN colleagues, our research group in Houston is embarking on a project to develop a radiation transport tool that is tailored to the problem of taking the external radiation flux incident on any particular spacecraft and simulating the evolution of that flux through a geometrically accurate model of the spacecraft material. The output will be a prediction of the detailed nature of the resulting internal radiation environment within the spacecraft as well as its secondary albedo. Beyond doing the physics transport of the incident flux, the software tool we are developing will provide a self-contained stand-alone object-oriented analysis and visualization infrastructure. It will also include a graphical user interface and a set of input tools to facilitate the simulation of space missions in terms of nominal radiation models and mission trajectory profiles. The goal of this project is to produce a code that is considerably more accurate and user-friendly than existing Monte-Carlo-based tools for the evaluation of the space radiation environment. Furthermore, the code will be an essential complement to the currently existing analytic codes in the BRYNTRN/HZETRN family for the evaluation of radiation shielding. The code will be directly applicable to the simulation of environments in low earth orbit, on the lunar surface, on planetary surfaces (including the Earth) and in the interplanetary medium such as on a transit to Mars (and even in the interstellar medium). The software will include modules whose underlying physics base can continue to be enhanced and updated for physics content, as future data become available beyond the timeframe of the initial development now foreseen. This future maintenance will be available from the authors of FLUKA as part of their continuing efforts to support the users of the FLUKA code within the particle physics community. In keeping with the spirit of developing an evolving physics code, we are planning as part of this project, to participate in the efforts to validate the core FLUKA physics in ground-based accelerator test runs. The emphasis of these test runs will be the physics of greatest interest in the simulation of the space radiation environment. Such a tool will be of great value to planners, designers and operators of future space missions, as well as for the design of the vehicles and habitats to be used on such missions. It will also be of aid to future experiments of various kinds that may be affected at some level by the ambient radiation environment, or in the analysis of hybrid experiment designs that have been discussed for space-based astronomy and astrophysics. The tool will be of value to the Life Sciences personnel involved in the prediction and measurement of radiation doses experienced by the crewmembers on such missions. In addition, the tool will be of great use to the planners of experiments to measure and evaluate the space radiation environment itself. It can likewise be useful in the analysis of safe havens, hazard migration plans, and NASA's call for new research in composites and to NASA engineers modeling the radiation exposure of electronic circuits. This code will provide an important complimentary check on the predictions of analytic codes such as BRYNTRN/HZETRN that are presently used for many similar applications, and which have shortcomings that are more easily overcome with Monte Carlo type simulations. Finally, it is acknowledged that there are similar efforts based around the use of the GEANT4 Monte-Carlo transport code currently under development at CERN. It is our intention to make our software modular and sufficiently flexible to allow the parallel use of either FLUKA or GEANT4 as the physics transport engine.

Pinsky, L. S.↗

NASA NTRS1998

Design of the Experimental Exposure Conditions to Simulate Ionizing Radiation Effects on Candidate Replacement Materials for the Hubble Space Telescope

In this effort, experimental exposure times for monoenergetic electrons and protons were determined to simulate the space radiation environment effects on Teflon components of the Hubble Space Telescope. Although the energy range of the available laboratory particle accelerators was limited, optimal exposure times for 50 keV, 220 keV, 350 keV, and 500 KeV electrons were calculated that produced a dose-versus-depth profile that approximated the full spectrum profile, and were realizable with existing equipment. For the case of proton exposure, the limited energy range of the laboratory accelerator restricted simulation of the dose to a depth of .5 mil. Also, while optimal exposure times were found for 200 keV, 500 keV and 700 keV protons that simulated the full spectrum dose-versus-depth profile to this depth, they were of such short duration that the existing laboratory could not be controlled to within the required accuracy. In addition to the obvious experimental issues, other areas exist in which the analytical work could be advanced. Improved computer codes for the dose prediction- along with improved methodology for data input and output- would accelerate and make more accurate the calculational aspects. This is particularly true in the case of proton fluxes where a paucity of available predictive software appears to exist. The dated nature of many of the existing Monte Carlo particle/radiation transport codes raises the issue as to whether existing codes are sufficient for this type of analysis. Other areas that would result in greater fidelity of laboratory exposure effects to the space environment is the use of a larger number of monoenergetic particle fluxes and improved optimization algorithms to determine the weighting values.

Smith, L. Montgomery↗

NASA NTRS2000

A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation

DNA double-strand breaks (DSBs) produced by densely ionizing radiation are not located randomly in the genome: recent data indicate DSB clustering along chromosomes. Stochastic DSB clustering at large scales, from > 100 Mbp down to < 0.01 Mbp, is modeled using computer simulations and analytic equations. A random-walk, coarse-grained polymer model for chromatin is combined with a simple track structure model in Monte Carlo software called DNAbreak and is applied to data on alpha-particle irradiation of V-79 cells. The chromatin model neglects molecular details but systematically incorporates an increase in average spatial separation between two DNA loci as the number of base-pairs between the loci increases. Fragment-size distributions obtained using DNAbreak match data on large fragments about as well as distributions previously obtained with a less mechanistic approach. Dose-response relations, linear at small doses of high linear energy transfer (LET) radiation, are obtained. They are found to be non-linear when the dose becomes so large that there is a significant probability of overlapping or close juxtaposition, along one chromosome, for different DSB clusters from different tracks. The non-linearity is more evident for large fragments than for small. The DNAbreak results furnish an example of the RLC (randomly located clusters) analytic formalism, which generalizes the broken-stick fragment-size distribution of the random-breakage model that is often applied to low-LET data.

DNA/radiation effects↗

NASA NTRS2011

Approximate Simulation of Acute Hypobaric Hypoxia with Normobaric Hypoxia

INTRODUCTION. Some manufacturers of reduced oxygen (O2) breathing devices claim a comparable hypobaric hypoxia (HH) training experience by providing F(sub I) O2 < 0.209 at or near sea level pressure to match the ambient O2 partial pressure (iso-pO2) of the target altitude. METHODS. Literature from investigators and manufacturers indicate that these devices may not properly account for the 47 mmHg of water vapor partial pressure that reduces the inspired partial pressure of O2 (P(sub I) O2). Nor do they account for the complex reality of alveolar gas composition as defined by the Alveolar Gas Equation. In essence, by providing iso-pO2 conditions for normobaric hypoxia (NH) as for HH exposures the devices ignore P(sub A)O2 and P(sub A)CO2 as more direct agents to induce signs and symptoms of hypoxia during acute training exposures. RESULTS. There is not a sufficient integrated physiological understanding of the determinants of P(sub A)O2 and P(sub A)CO2 under acute NH and HH given the same hypoxic pO2 to claim a device that provides isohypoxia. Isohypoxia is defined as the same distribution of hypoxia signs and symptoms under any circumstances of equivalent hypoxic dose, and hypoxic pO2 is an incomplete hypoxic dose. Some devices that claim an equivalent HH experience under NH conditions significantly overestimate the HH condition, especially when simulating altitudes above 10,000 feet (3,048 m). CONCLUSIONS. At best, the claim should be that the devices provide an approximate HH experience since they only duplicate the ambient pO2 at sea level as at altitude (iso-pO2 machines). An approach to reduce the overestimation is to at least provide machines that create the same P(sub I)O2 (iso-P(sub I)O2 machines) conditions at sea level as at the target altitude, a simple software upgrade.

Conkin, J.↗

NASA NTRS2001

Visual assessment of the radiation distribution in the ISS Lab module: visualization in the human body

The US Lab module of the International Space Station (ISS) is a primary working area where the crewmembers are expected to spend majority of their time. Because of the directionality of radiation fields caused by the Earth shadow, trapped radiation pitch angle distribution, and inherent variations in the ISS shielding, a model is needed to account for these local variations in the radiation distribution. We present the calculated radiation dose (rem/yr) values for over 3,000 different points in the working area of the Lab module and estimated radiation dose values for over 25,000 different points in the human body for a given ambient radiation environment. These estimated radiation dose values are presented in a three dimensional animated interactive visualization format. Such interactive animated visualization of the radiation distribution can be generated in near real-time to track changes in the radiation environment during the orbit precession of the ISS.

NASA Center JSC↗

NASA NTRS2007

SPENVIS Implementation of End-of-Life Solar Cell Calculations Using the Displacement Damage Dose Methodology

This paper presents a method for using the SPENVIS on-line computational suite to implement the displacement damage dose (D(sub d)) methodology for calculating end-of-life (EOL) solar cell performance for a specific space mission. This paper builds on our previous work that has validated the D(sub d) methodology against both measured space data [1,2] and calculations performed using the equivalent fluence methodology developed by NASA JPL [3]. For several years, the space solar community has considered general implementation of the D(sub d) method, but no computer program exists to enable this implementation. In a collaborative effort, NRL, NASA and OAI have produced the Solar Array Verification and Analysis Tool (SAVANT) under NASA funding, but this program has not progressed beyond the beta-stage [4]. The SPENVIS suite with the Multi Layered Shielding Simulation Software (MULASSIS) contains all of the necessary components to implement the Dd methodology in a format complementary to that of SAVANT [5]. NRL is currently working with ESA and BIRA to include the Dd method of solar cell EOL calculations as an integral part of SPENVIS. This paper describes how this can be accomplished.

Walters, Robert↗

NASA NTRS2013

Development of the Code RITRACKS

A document discusses the code RITRACKS (Relativistic Ion Tracks), which was developed to simulate heavy ion track structure at the microscopic and nanoscopic scales. It is a Monte-Carlo code that simulates the production of radiolytic species in water, event-by-event, and which may be used to simulate tracks and also to calculate dose in targets and voxels of different sizes. The dose deposited by the radiation can be calculated in nanovolumes (voxels). RITRACKS allows simulation of radiation tracks without the need of extensive knowledge of computer programming or Monte-Carlo simulations. It is installed as a regular application on Windows systems. The main input parameters entered by the user are the type and energy of the ion, the length and size of the irradiated volume, the number of ions impacting the volume, and the number of histories. The simulation can be started after the input parameters are entered in the GUI. The number of each kind of interactions for each track is shown in the result details window. The tracks can be visualized in 3D after the simulation is complete. It is also possible to see the time evolution of the tracks and zoom on specific parts of the tracks. The software RITRACKS can be very useful for radiation scientists to investigate various problems in the fields of radiation physics, radiation chemistry, and radiation biology. For example, it can be used to simulate electron ejection experiments (radiation physics).

Plante, Ianik↗

NASA NTRS2010

Permissible Exposure Level for Lunar Dusts: Gaps are Closing

Space faring nations plan to return human explorers to the moon within the next decade. Experience during the Apollo flights suggests that lunar dust will invariably get into the habitat where the finest portion (less than 5 micrometers) could be inhaled by the crew before it is cleared from the atmosphere. NASA is developing a database from which a 6-month, episodic exposure standard for lunar dust can be set. Three kinds of moon dust were prepared from a parent sample of Apollo 14 regolith #14003,96. Our goal was to prepare each type of dust sample with a mean diameter less than 2 m, which is suitable for instillation into the lungs of rats. The three samples were prepared as follows: separation from the parent sample using a fluidized bed, grinding using a jet mill grinder, or grinding with a ball-mill grinder. Grinding simulated restoration of surface activation of dust expected to occur at the surface of the moon on native lunar dust. We used two grinding methods because they seemed to produce different modes of activation. The effects of grinding were preserved by maintaining the dust in ultra-pure nitrogen until immediately before it was placed in suspension for administration to rats. The dust was suspended in physiological saline with 10% Survanta, a lung surfactant. Rats were given intratrachael instillations of the dust suspension at three doses. In addition to the three moon dusts (A, C and E), we instilled the same amount of a negative control (TiO2, B) and a highly-toxic, positive control (quartz, D). These additional mineral dusts were selected because they have well-established and very different permissible exposure levels (PELs). Our goal was to determine where lunar dusts fit between these extremes, and then estimate a PEL for each lunar dust. We evaluated many indices of toxicity to the lung. The figure shows the changes in lactate dehydrogenase (LDH), a marker of cell death, for the five dusts. Benchmark dose software (Version 2.1.2) from the Environmental Protection Agency was used to estimate the 10% effect levels (BMD(sub 10)) using five models. The best-fitting model was used to estimate the optimal BMD(sub 10) (table)

James, John T.↗

NASA NTRS2001

Radiation breakage of DNA: a model based on random-walk chromatin structure

Monte Carlo computer software, called DNAbreak, has recently been developed to analyze observed non-random clustering of DNA double strand breaks in chromatin after exposure to densely ionizing radiation. The software models coarse-grained configurations of chromatin and radiation tracks, small-scale details being suppressed in order to obtain statistical results for larger scales, up to the size of a whole chromosome. We here give an analytic counterpart of the numerical model, useful for benchmarks, for elucidating the numerical results, for analyzing the assumptions of a more general but less mechanistic "randomly-located-clusters" formalism, and, potentially, for speeding up the calculations. The equations characterize multi-track DNA fragment-size distributions in terms of one-track action; an important step in extrapolating high-dose laboratory results to the much lower doses of main interest in environmental or occupational risk estimation. The approach can utilize the experimental information on DNA fragment-size distributions to draw inferences about large-scale chromatin geometry during cell-cycle interphase.

Chromatin/radiation effects↗

NASA NTRS2011

NASA Tech Briefs, August 2011

Topics covered include: Miniature, Variable-Speed Control Moment Gyroscope; NBL Pistol Grip Tool for Underwater Training of Astronauts; HEXPANDO Expanding Head for Fastener-Retention Hexagonal Wrench; Diagonal-Axes Stage for Pointing an Optical Communications Transceiver; Improvements in Speed and Functionality of a 670-GHz Imaging Radar; IONAC-Lite; Large Ka-Band Slot Array for Digital Beam-Forming Applications; Development of a 150-GHz MMIC Module Prototype for Large-Scale CMB Radiation; Coupling Between Waveguide-Fed Slot Arrays; PCB-Based Break-Out Box; Multiple-Beam Detection of Fast Transient Radio Sources; Router Agent Technology for Policy-Based Network Management; Remote Asynchronous Message Service Gateway; Automatic Tie Pointer for In-Situ Pointing Correction; Jitter Correction; MSLICE Sequencing; EOS MLS Level 2 Data Processing Software Version 3; DspaceOgre 3D Graphics Visualization Tool; Metallization for Yb14MnSb11-Based Thermoelectric Materials; Solvent/Non-Solvent Sintering To Make Microsphere Scaffolds; Enhanced Fuel-Optimal Trajectory-Generation Algorithm for Planetary Pinpoint Landing; Self-Cleaning Coatings and Materials for Decontaminating Field-Deployable Land and Water-Based Optical Systems; Separation of Single-Walled Carbon Nanotubes with DEP-FFF; Li Anode Technology for Improved Performance; Post-Fragmentation Whole Genome Amplification-Based Method; Microwave Tissue Soldering for Immediate Wound Closure; Principles, Techniques, and Applications of Tissue Microfluidics; Robotic Scaffolds for Tissue Engineering and Organ Growth; Stress-Driven Selection of Novel Phenotypes; Method for Accurately Calibrating a Spectrometer Using Broadband Light; Catalytic Microtube Rocket Igniter; Stage Cylindrical Immersive Display; Vacuum Camera Cooler; Atomic Oxygen Fluence Monitor; Thermal Management Tools for Propulsion System Trade Studies and Analysis; Introduction to Physical Intelligence; Technique for Solving Electrically Small to Large Structures for Broadband Applications; Accelerated Adaptive MGS Phase Retrieval; Large Eddy Simulation Study for Fluid Disintegration and Mixing; Tropospheric Correction for InSAR Using Interpolated ECMWF Data and GPS Zenith Total Delay; Technique for Calculating Solution Derivatives With Respect to Geometry Parameters in a CFD Code; Acute Radiation Risk and BRYNTRN Organ Dose Projection Graphical User Interface; Probabilistic Path Planning of Montgolfier Balloons in Strong, Uncertain Wind Fields; Flight Simulation of ARES in the Mars Environment; Low-Outgassing Photogrammetry Targets for Use in Outer Space; Planning the FUSE Mission Using the SOVA Algorithm; Monitoring Spacecraft Telemetry Via Optical or RF Link; and Robust Thermal Control of Propulsion Lines for Space Missions.

Source record↗

NASA NTRS2013

Galactic Cosmic Ray Event-Based Risk Model (GERM) Code

This software describes the transport and energy deposition of the passage of galactic cosmic rays in astronaut tissues during space travel, or heavy ion beams in patients in cancer therapy. Space radiation risk is a probability distribution, and time-dependent biological events must be accounted for physical description of space radiation transport in tissues and cells. A stochastic model can calculate the probability density directly without unverified assumptions about shape of probability density function. The prior art of transport codes calculates the average flux and dose of particles behind spacecraft and tissue shielding. Because of the signaling times for activation and relaxation in the cell and tissue, transport code must describe temporal and microspatial density of functions to correlate DNA and oxidative damage with non-targeted effects of signals, bystander, etc. These are absolutely ignored or impossible in the prior art. The GERM code provides scientists data interpretation of experiments; modeling of beam line, shielding of target samples, and sample holders; and estimation of basic physical and biological outputs of their experiments. For mono-energetic ion beams, basic physical and biological properties are calculated for a selected ion type, such as kinetic energy, mass, charge number, absorbed dose, or fluence. Evaluated quantities are linear energy transfer (LET), range (R), absorption and fragmentation cross-sections, and the probability of nuclear interactions after 1 or 5 cm of water equivalent material. In addition, a set of biophysical properties is evaluated, such as the Poisson distribution for a specified cellular area, cell survival curves, and DNA damage yields per cell. Also, the GERM code calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle in a selected material. The GERM code makes the numerical estimates of basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at the NASA Space Radiation Laboratory (NSRL) for the purpose of simulating space radiation biological effects. In the first option, properties of monoenergetic beams are treated. In the second option, the transport of beams in different materials is treated. Similar biophysical properties as in the first option are evaluated for the primary ion and its secondary particles. Additional properties related to the nuclear fragmentation of the beam are evaluated. The GERM code is a computationally efficient Monte-Carlo heavy-ion-beam model. It includes accurate models of LET, range, residual energy, and straggling, and the quantum multiple scattering fragmentation (QMSGRG) nuclear database.

Cucinotta, Francis A.↗