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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 NTRS2005

Particle Acceleration, Magnetic Field Generation, and Emission in Relativistic Pair Jets

Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created by relativistic pair jets are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic jet propagating through an ambient plasma with and without initial magnetic fields. The growth rates of the Weibel instability depends on the distribution of pair jets. Simulations show that the Weibel instability created in the collisionless shock accelerates particles perpendicular and parallel to the jet propagation direction. The simulation results show that this instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields, which contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Nishikawa, K.-I.↗

NASA NTRS2005

Spreading of thermonuclear flames on the neutron star in SAX J1808.4-3658: an observational tool

We analyse archival Rossi X-Ray Timing Explorer (RXTE) proportional counter array (PCA) data of thermonuclear X-ray bursts from the 2002 outburst of the accreting millisecond pulsar SAX 51808.4-3658. We present evidence of a complex frequency modulation of oscillations during burst rise, and correlations among the time evolution of the oscillation frequency, amplitude, and the inferred burning region area. We discuss these findings in the context of a model, based on thermonuclear flame spreading on the neutron star surface, that can qualitatively explain these features. From our model, we infer that for the 2002 Oct. 15 thermonuclear burst, the ignition likely occurred in the mid-latitudes, the burning region took approx. 0.2 s to nearly encircle the equatorial region of the neutron star, and after that the lower amplitude oscillation originated from the remaining asymmetry of the burning front in the same hemisphere where the burst ignited. We emphasize that studies of the evolution of burst oscillation properties during burst rise can provide a powerful tool to understand thermonuclear flame spreading on neutron star surfaces under extreme physical conditions.

Bhattacharyya, Sudip↗

NASA NTRS2006

3-D RPIC simulations of relativistic jets: Particle acceleration, magnetic field generation, and emission

Nonthermal radiation observed from astrophysical systems containing (relativistic) jets and shocks, e.g., supernova remnants, active galactic nuclei (AGNs), gamma-ray bursts (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Fermi acceleration is the mechanism usually assumed for the acceleration of particles in astrophysical environments. Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets show that acceleration occurs within the downstream jet, rather than by the scattering of particles back and forth across the shock as in Fermi acceleration. Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the .shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants. We will review recent PIC simulations which show particle acceleration in jets.

Nishikawa, K.-I.↗

NASA NTRS2006

Particle Acceleration, Magnetic Field Generation and Emission from Relativistic Jets

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., active galactic nuclei (AGNs), gamma-ray bursts (GRBs), supernova remnants, and Galactic microquasar systems usually have power-law emission spectra. Fermi acceleration is the mechanism usually assumed for the acceleration of particles in astrophysical environments. Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets show that particle acceleration occurs within the downstream jet, rather than by the scattering of particles back and forth across the shock as in Fermi acceleration. Shock acceleration' is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different spectral properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants. We will review recent PIC simulations of relativistic jets and try to make a connection with observations.

Nishikawa, K.-I.↗

NASA NTRS2006

A Computational and Experimental Investigation of Shear Coaxial Jet Atomization

The instability and subsequent atomization of a viscous liquid jet emanated into a high-pressure gaseous surrounding is studied both computationally and experimentally. Liquid water issued into nitrogen gas at elevated pressures is used to simulate the flow conditions in a coaxial shear injector element relevant to liquid propellant rocket engines. The theoretical analysis is based on a simplified mathematical formulation of the continuity and momentum equations in their conservative form. Numerical solutions of the governing equations subject to appropriate initial and boundary conditions are obtained via a robust finite difference scheme. The computations yield real-time evolution and subsequent breakup characteristics of the liquid jet. The experimental investigation utilizes a digital imaging technique to measure resultant drop sizes. Data were collected for liquid Reynolds number between 2,500 and 25,000, aerodynamic Weber number range of 50-500 and ambient gas pressures from 150 to 1200 psia. Comparison of the model predictions and experimental data for drop sizes at gas pressures of 150 and 300 psia reveal satisfactory agreement particularly for lower values of investigated Weber number. The present model is intended as a component of a practical tool to facilitate design and optimization of coaxial shear atomizers.

Ibrahim, Essam A.↗

NASA NTRS2006

3-D RPIC Simulations of Relativistic Jets: Particle Acceleration, Magnetic Field Generation, and Emission

Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets into ambient plasmas show that acceleration occurs in relativistic shocks. The Weibel instability created in shocks is responsible for particle acceleration, and generation and amplification of highly inhomogeneous, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection in relativistic jets. The "jitter" radiation from deflected electrons has different properties than the synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understand the complex time evolution and spectral structure in relativistic jets and gamma-ray bursts. We will present recent PIC simulations which show particle acceleration and magnetic field generation. We will also calculate associated self-consistent emission from relativistic shocks.

Nishikawa, K.-I.↗

NASA NTRS2007

Cloud Resolving Modeling

One of the most promising methods to test the representation of cloud processes used in climate models is to use observations together with cloud-resolving models (CRMs). CRMs use more sophisticated and realistic representations of cloud microphysical processes, and they can reasonably well resolve the time evolution, structure, and life cycles of clouds and cloud systems (with sizes ranging from about 2-200 km). CRMs also allow for explicit interaction between clouds, outgoing longwave (cooling) and incoming solar (heating) radiation, and ocean and land surface processes. Observations are required to initialize CRMs and to validate their results. This paper provides a brief discussion and review of the main characteristics of CRMs as well as some of their major applications. These include the use of CRMs to improve our understanding of: (1) convective organization, (2) cloud temperature and water vapor budgets, and convective momentum transport, (3) diurnal variation of precipitation processes, (4) radiative-convective quasi-equilibrium states, (5) cloud-chemistry interaction, (6) aerosol-precipitation interaction, and (7) improving moist processes in large-scale models. In addition, current and future developments and applications of CRMs will be presented.

Tao, Wei-Kuo↗

NASA NTRS2007

Experimental Evaluation of an Isolated Synthetic Jet IN Crossflow

The second case for this workshop builds upon the isolated synthetic jet of Case 1 by adding a crossflow, with no streamwise pressure gradient, for the developing jet to interact with. Formally, Case 2 examines the interaction of a single, isolated, synthetic jet and a fully turbulent zero-pressure gradient boundary layer. The resulting flow has many of the characteristics that need to be modeled with fidelity if the results of the calculations are to serve as the basis for research and design with active flow control devices. These include the turbulence in the boundary layer, the time-evolution of the large vortical structure emanating from the jet orifice and its subsequent interaction with and distortion by the boundary layer turbulence, and the effect of the suction cycle on the boundary layer flow. In a synthetic jet, the flow through the orifice and out into the outer flowfield alternates between an exhaust and a suction cycle, driven by the contraction and expansion of a cavity internal to the actuator. In the present experiment, the volume changes in the internal cavity are accomplished by replacing one of the rigid walls of the cavity, the wall opposite the orifice exit, with a deformable wall. This flexible wall is driven by a bottom-mounted moveable piston. The piston is driven electro-mechanically. The synthetic jet issues into the external flow through a circular orifice. In the present experiment, this orifice has a diameter of 0.250 inches (6.35 mm). The flow is conceptually similar to that documented in Schaeffler [1]. To document the flow, several measurement techniques were utilized. The upstream boundary conditions (in-flow conditions), and several key phase-averaged velocity profiles were measured with a 3-component laser-Doppler velocimetry system. Phase-averaged velocity field measurements were made with both stereo digital particle image velocimetry and 2-D digital particle image velocimetry as the primary measurement system. Surface pressure measurements were made utilizing an electronically scanned pressure system.

Schaeffler, Norman W.↗

NASA NTRS2007

The SMM Model as a Boundary Value Problem Using the Discrete Diffusion Equation

A generalized single step stepwise mutation model (SMM) is developed that takes into account an arbitrary initial state to a certain partial difference equation. This is solved in both the approximate continuum limit and the more exact discrete form. A time evolution model is developed for Y DNA or mtDNA that takes into account the reflective boundary modeling minimum microsatellite length and the original difference equation. A comparison is made between the more widely known continuum Gaussian model and a discrete model, which is based on modified Bessel functions of the first kind. A correction is made to the SMM model for the probability that two individuals are related that takes into account a reflecting boundary modeling minimum microsatellite length. This method is generalized to take into account the general n-step model and exact solutions are found. A new model is proposed for the step distribution.

Campbell, Joel↗

NASA NTRS2007

Solar Occultation Satellite Data and Derived Meteorological Products: Sampling Issues and Comparisons with Aura MLS

Derived Meteorological Products (DMPs, including potential temperature (theta), potential vorticity, equivalent latitude (EqL), horizontal winds and tropopause locations) have been produced for the locations and times of measurements by several solar occultation (SO) instruments and the Aura Microwave Limb Sounder (MLS). DMPs are calculated from several meteorological analyses for the Atmospheric Chemistry Experiment-Fourier Transform Spectrometer, Stratospheric Aerosol and Gas Experiment II and III, Halogen Occultation Experiment, and Polar Ozone and Aerosol Measurement II and III SO instruments and MLS. Time-series comparisons of MLS version 1.5 and SO data using DMPs show good qualitative agreement in time evolution of O3, N2O, H20, CO, HNO3, HCl and temperature; quantitative agreement is good in most cases. EqL-coordinate comparisons of MLS version 2.2 and SO data show good quantitative agreement throughout the stratosphere for most of these species, with significant biases for a few species in localized regions. Comparisons in EqL coordinates of MLS and SO data, and of SO data with geographically coincident MLS data provide insight into where and how sampling effects are important in interpretation of the sparse SO data, thus assisting in fully utilizing the SO data in scientific studies and comparisons with other sparse datasets. The DMPs are valuable for scientific studies and to facilitate validation of non-coincident measurements.

Manney, Gloria↗

NASA NTRS2007

Particle Acceleration, Magnetic Field Generation, and Associated Emission in Collisionless Relativistic Jets

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., active galactic nuclei (AGNs), gamma-ray bursts (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Recent PIC simulations using injected relativistic electron-ion (electro-positron)jets show that acceleration occurs within the downstream jet. Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Nishikawa, K.-I.↗

NASA NTRS2007

Relativistic Particle-in-Cell Simulation Studies of Prompt and Early Afterglows Observed by GLAST

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., gamma-ray bursts (GRBs), active galactic nuclei (AGNs), and Galactic microquasar systems usually have power-law emission spectra. Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets show that acceleration occurs within the downstream jet. Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The "'jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Mizuno, Y.↗

NASA NTRS2007

Particle Acceleration, Magnetic Field Generation and Associated Emission in Collisionless Relativistic Jets

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., active galactic nuclei (AGNs), gamma-ray bursts (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets show that acceleration occurs within the downstream jet. Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Nishikawa, K. I.↗

NASA NTRS2008

Relativistic Particle-In-Cell Simulation Studies of Prompt and Early Afterglows from GRBs

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., gamma-ray bursts (GRBs), active galactic nuclei (AGNs), and Galactic microquasar systems usually have power-law emission spectra. Recent PIC simulations of relativistic electron-ion (electro-positron) jets injected into a stationary medium show that particle acceleration occurs within the downstream jet. In the collisionless relativistic shock particle acceleration is due to plasma waves and their associated instabilities {e.g., the Weibel (filamentation) instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.-/

Nishikawa, Ken-Ichi↗

NASA NTRS2005

Anvil Glaciation in a Deep Cumulus Updraught over Florida Simulated with the Explicit Microphysics Model. I: Impact of Various Nucleation Processes

Simulations of a cumulonimbus cloud observed in the Cirrus regional Study of Tropical Anvils and Cirrus Layers-Florida Area Cirrus Experiment (CRYSTAL-FACE) with an advanced version of the Explicit Microphysics Model (EMM) are presented. The EMM has size-resolved aerosols and predicts the time evolution of sizes, bulk densities and axial ratios of ice particles. Observations by multiple aircraft in the troposphere provide inputs to the model, including observations of the ice nuclei and of the entire size distribution of condensation nuclei. Homogeneous droplet freezing is found to be the source of almost all of the ice crystals in the anvil updraught of this particular model cloud. Most of the simulated droplets that freeze to form anvil crystals appear to be nucleated by activation of aerosols far above cloud base in the interior of the cloud ("secondary" or "in cloud" droplet nucleation). This is partly because primary droplets formed at cloud base are invariably depleted by accretion before they can reach the anvil base in the updraught, which promotes an increase with height of the average supersaturation in the updraught aloft. More than half of these aerosols, activated far above cloud base, are entrained into the updraught of this model cloud from the lateral environment above about 5 km above mean sea level. This confirms the importance of remote sources of atmospheric aerosol for anvil glaciation. Other nucleation processes impinge indirectly upon the anvil glaciation by modifying the concentration of supercooled droplets in the upper levels of the mixed-phase region. For instance, the warm-rain process produces a massive indirect impact on the anvil crystal concentration, because it determines the mass of precipitation forming in the updraught. It competes with homogeneous freezing as a sink for cloud droplets. The effects from turbulent enhancement of the warm-rain process and from the nucleation processes on the anvil ice properties are assessed.

Phillips, Vaughan T. J.↗

NASA NTRS2008

New Relativistic Particle-In-Cell Simulation Studies of Prompt and Early Afterglows from GRBs

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., gamma-ray bursts (GRBs), active galactic nuclei (AGNs), and Galactic microquasar systems usually have power-law emission spectra. Recent PIC simulations of relativistic electron-ion (electro-positron) jets injected into a stationary medium show that particle acceleration occurs within the downstream jet. In the collisionless relativistic shock particle acceleration is due to plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel (filamentation) instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The 'jitter' radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Nishikawa, Ken-ichi↗

NASA NTRS2008

Radiation from Relativistic Jets

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., gamma-ray bursts (GRBs), active galactic nuclei (AGNs), and Galactic microquasar systems usually have power-law emission spectra. Recent PIC simulations of relativistic electron-ion (electron-positron) jets injected into a stationary medium show that particle acceleration occurs within the downstream jet. In the presence of relativistic jets, instabilities such as the Buneman instability, other two-streaming instability, and the Weibel (filamentation) instability create collisionless shocks, which are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The 'jitter' radiation from deflected electrons in small-scale magnetic fields has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation, a case of diffusive synchrotron radiation, may be important to understand the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Nishikawa, K.-I.↗