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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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At least 1,585 records · Page 88
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DOE OSTI2015

Constraint methods that accelerate free-energy simulations of biomolecules

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann’s law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Effect of finite ion mass on relativistic self-induced transparency of plasma layers with a sharp boundary

We consider the effect of ion mobility on the threshold of relativistic self-induced transparency under irradiation of thin plasma layers by circularly polarised laser radiation. An analytical model of the motion of ions during the removal of electrons from the layer surface by the ponderomotive force of laser radiation is constructed. The model is used to analyse the motion of probe electrons in the resulting electromagnetic field. It is shown that the higher the ion mobility and the longer the laser pulse, the more stable the plasma layer to longitudinal perturbations of a finite value and the higher the threshold of self-induced transparency. These conclusions are verified by one-dimensional numerical simulation of a complete system of kinetic equations for plasma and Maxwell’s equations. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Alma view of G0.253+0.016: Can cloud-cloud collision form the cloud?

We present the results of the sulfur monoxide, SO, line emission observations of G0.253+0.016 with the Atacama Large Millimeter/Submillimeter Array at an angular resolution of 1.''7. The dense and massive molecular cloud of G0.253+0.016 is highly sub-structured, yet it shows no obvious signs of cluster formation. We found three outstanding features of the cloud from the SO emission, namely, shell structure with a radius of 1.3 pc, large velocity gradients of 20 km s{sup –1} pc{sup –1} with the cloud, and cores with large velocity dispersions (30-40 km s{sup –1}) around the shell structure. We suggest that these large-velocity dispersion cores will form high-mass stars in the future. In an attempt to explore the formation scenario of the dense cloud, we compared our results with numerical simulations; therefore, we propose that G0.253+0.016 may have formed due to a cloud-cloud collision process.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

FORMING REALISTIC LATE-TYPE SPIRALS IN A {Lambda}CDM UNIVERSE: THE ERIS SIMULATION

Simulations of the formation of late-type spiral galaxies in a cold dark matter ({Lambda}CDM) universe have traditionally failed to yield realistic candidates. Here we report a new cosmological N-body/smooth particle hydrodynamic simulation of extreme dynamic range in which a close analog of a Milky Way disk galaxy arises naturally. Named 'Eris', the simulation follows the assembly of a galaxy halo of mass M{sub vir} = 7.9 Multiplication-Sign 10{sup 11} M{sub Sun} with a total of N = 18.6 million particles (gas + dark matter + stars) within the final virial radius, and a force resolution of 120 pc. It includes radiative cooling, heating from a cosmic UV field and supernova explosions (blastwave feedback), a star formation recipe based on a high gas density threshold (n{sub SF} = 5 atoms cm{sup -3} rather than the canonical n{sub SF} = 0.1 atoms cm{sup -3}), and neglects any feedback from an active galactic nucleus. Artificial images are generated to correctly compare simulations with observations. At the present epoch, the simulated galaxy has an extended rotationally supported disk with a radial scale length R{sub d} = 2.5 kpc, a gently falling rotation curve with circular velocity at 2.2 disk scale lengths of V{sub 2.2} = 214 km s{sup -1}, an i-band bulge-to-disk ratio B/D = 0.35, and a baryonic mass fraction within the virial radius that is 30% below the cosmic value. The disk is thin, has a typical H I-to-stellar mass ratio, is forming stars in the region of the {Sigma}{sub SFR}-{Sigma}{sub HI} plane occupied by spiral galaxies, and falls on the photometric Tully-Fisher and the stellar-mass-halo-virial-mass relations. Hot (T > 3 Multiplication-Sign 10{sup 5} K) X-ray luminous halo gas makes up only 26% of the universal baryon fraction and follows a 'flattened' density profile {proportional_to}r{sup -1.13} out to r = 100 kpc. Eris appears then to be the first cosmological hydrodynamic simulation in which the galaxy structural properties, the mass budget in the various components, and the scaling relations between mass and luminosity are all consistent with a host of observational constraints. A twin simulation with a low star formation density threshold results in a galaxy with a more massive bulge and a much steeper rotation curve, as in previously published work. A high star formation threshold appears therefore key in obtaining realistic late-type galaxies, as it enables the development of an inhomogeneous interstellar medium where star formation and heating by supernovae occur in a clustered fashion. The resulting outflows at high redshifts reduce the baryonic content of galaxies and preferentially remove low-angular-momentum gas, decreasing the mass of the bulge component. Simulations of even higher resolution that follow the assembly of galaxies with different merger histories shall be used to verify our results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

CATASTROPHIC QUENCHING IN {alpha}{Omega} DYNAMOS REVISITED

At large magnetic Reynolds numbers, magnetic helicity evolution plays an important role in astrophysical large-scale dynamos. The recognition of this fact led to the development of the dynamical {alpha} quenching formalism, which predicts catastrophically low mean fields in open systems. Here, we show that in oscillatory {alpha}{Omega} dynamos this formalism predicts an unphysical magnetic helicity transfer between scales. An alternative technique is proposed where this artifact is removed by using the evolution equation for the magnetic helicity of the total field in the shearing advective gauge. In the traditional dynamical {alpha} quenching formalism, this can be described by an additional magnetic helicity flux of small-scale fields that does not appear in homogeneous {alpha}{sup 2} dynamos. In {alpha}{Omega} dynamos, the alternative formalism is shown to lead to larger saturation fields than what has been obtained in some earlier models with the traditional formalism. We have compared the predictions of the two formalisms to results of direct numerical simulations, finding that the alternative formulation provides a better fit. This suggests that worries about catastrophic dynamo behavior in the limit of large magnetic Reynolds number are unfounded.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

MAGNETIC WREATHS AND CYCLES IN CONVECTIVE DYNAMOS

Solar-type stars exhibit a rich variety of magnetic activity. Seeking to explore the convective origins of this activity, we have carried out a series of global three-dimensional magnetohydrodynamic simulations with the anelastic spherical harmonic code. Here we report on the dynamo mechanisms achieved as the effects of artificial diffusion are systematically decreased. The simulations are carried out at a nominal rotation rate of three times the solar value (3 {Omega}{sub Sun }), but similar dynamics may also apply to the Sun. Our previous simulations demonstrated that convective dynamos can build persistent toroidal flux structures (magnetic wreaths) in the midst of a turbulent convection zone and that high rotation rates promote the cyclic reversal of these wreaths. Here we demonstrate that magnetic cycles can also be achieved by reducing the diffusion, thus increasing the Reynolds and magnetic Reynolds numbers. In these more turbulent models, diffusive processes no longer play a significant role in the key dynamical balances that establish and maintain the differential rotation and magnetic wreaths. Magnetic reversals are attributed to an imbalance in the poloidal magnetic induction by convective motions that is stabilized at higher diffusion levels. Additionally, the enhanced levels of turbulence lead to greater intermittency in the toroidal magnetic wreaths, promoting the generation of buoyant magnetic loops that rise from the deep interior to the upper regions of our simulated domain. The implications of such turbulence-induced magnetic buoyancy for solar and stellar flux emergence are also discussed.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

A NEW MODEL FOR MIXING BY DOUBLE-DIFFUSIVE CONVECTION (SEMI-CONVECTION). II. THE TRANSPORT OF HEAT AND COMPOSITION THROUGH LAYERS

Regions of stellar and planetary interiors that are unstable according to the Schwarzschild criterion, but stable according to the Ledoux criterion, are subject to a form of oscillatory double-diffusive (ODD) convection often called ''semi-convection''. In this series of papers, we use an extensive suite of three-dimensional (3D) numerical simulations to quantify the transport of heat and composition by ODD convection, and ultimately propose a new 1D prescription that can be used in stellar and planetary structure and evolution models. The first paper in this series demonstrated that under certain conditions ODD convection spontaneously transitions from an initial homogeneous state of weak wave-breaking turbulence into a staircase of fully convective layers, which results in a substantial increase in the transport of heat and composition. Here, we present simulations of ODD convection in this layered regime, we describe the dynamical behavior of the layers, and we derive empirical scaling laws for the transport through layered convection.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

A NUMERICAL METHOD FOR STUDYING SUPER-EDDINGTON MASS TRANSFER IN DOUBLE WHITE DWARF BINARIES

We present a numerical method for the study of double white dwarf (DWD) binary systems at the onset of super-Eddington mass transfer. We incorporate the physics of ideal inviscid hydrodynamical flow, Newtonian self-gravity, and radiation transport on a three-dimensional uniformly rotating cylindrical Eulerian grid. Care has been taken to conserve the key physical quantities such as angular momentum and energy. Our new method conserves total energy to a higher degree of accuracy than other codes that are presently being used to model mass transfer in DWD systems. We present the results of verification tests and simulate the first 20 + orbits of a binary system of mass ratio q 0.7 at the onset of dynamically unstable direct impact mass transfer. The mass transfer rate quickly exceeds the critical Eddington limit by many orders of magnitude, and thus we are unable to model a trans-Eddington phase. It appears that radiation pressure does not significantly affect the accretion flow in the highly super-Eddington regime. An optically thick common envelope forms around the binary within a few orbits. Although this envelope quickly exceeds the spatial domain of the computational grid, the fraction of the common envelope that exceeds zero gravitational binding energy is extremely small, suggesting that radiation-driven mass loss is insignificant in this regime. It remains to be seen whether simulations that capture the trans-Eddington phase of such flows will lead to the same conclusion or show that substantial material gets expelled.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

On the soft limit of the large scale structure power spectrum: UV dependence

We derive a non-perturbative equation for the large scale structure power spectrum of long-wavelength modes. Thereby, we use an operator product expansion together with relations between the three-point function and power spectrum in the soft limit. The resulting equation encodes the coupling to ultraviolet (UV) modes in two time-dependent coefficients, which may be obtained from response functions to (anisotropic) parameters, such as spatial curvature, in a modified cosmology. We argue that both depend weakly on fluctuations deep in the UV. As a byproduct, this implies that the renormalized leading order coefficient(s) in the effective field theory (EFT) of large scale structures receive most of their contribution from modes close to the non-linear scale. Consequently, the UV dependence found in explicit computations within standard perturbation theory stems mostly from counter-term(s). We confront a simplified version of our non-perturbative equation against existent numerical simulations, and find good agreement within the expected uncertainties. Our approach can in principle be used to precisely infer the relevance of the leading order EFT coefficient(s) using small volume simulations in an 'anisotropic separate universe' framework. Our results suggest that the importance of these coefficient(s) is a ∼ 10% effect, and plausibly smaller.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

Nonequilibrium and local detection of the normal fraction of a trapped two-dimensional Bose gas

We propose a method to measure the normal fraction of a two-dimensional Bose gas, a quantity that generally differs from the noncondensed fraction. The idea is based on applying a spatially oscillating artificial gauge field to the atoms. The response of the atoms to the gauge field can be read out either mechanically from the deposited energy into the cloud or optically from the macroscopic optical properties of the atomic gas. The local nature of the proposed scheme allows one to reconstruct the spatial profile of the superfluid component; furthermore, the proposed method does not require having established thermal equilibrium in the gas in the presence of the gauge field. The theoretical description of the system is based on a generalization of the Dum-Olshanii theory of artificial gauge fields to the interacting many-body context. The efficiency of the proposed measurement scheme is assessed by means of classical field numerical simulations. An explicit atomic level scheme minimizing disturbing effects such as spontaneous emission and light shifts is proposed for {sup 87}Rb atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2012

Optimized generation of high resolution breast anthropomorphic software phantoms

Purpose: The authors present an efficient method for generating anthropomorphic software breast phantoms with high spatial resolution. Employing the same region growing principles as in their previous algorithm for breast anatomy simulation, the present method has been optimized for computational complexity to allow for fast generation of the large number of phantoms required in virtual clinical trials of breast imaging. Methods: The new breast anatomy simulation method performs a direct calculation of the Cooper's ligaments (i.e., the borders between simulated adipose compartments). The calculation corresponds to quadratic decision boundaries of a maximum a posteriori classifier. The method is multiscale due to the use of octree-based recursive partitioning of the phantom volume. The method also provides user-control of the thickness of the simulated Cooper's ligaments and skin. Results: Using the proposed method, the authors have generated phantoms with voxel size in the range of (25-1000 {mu}m){sup 3}/voxel. The power regression of the simulation time as a function of the reciprocal voxel size yielded a log-log slope of 1.95 (compared to a slope of 4.53 of our previous region growing algorithm). Conclusions: A new algorithm for computer simulation of breast anatomy has been proposed that allows for fast generation of high resolution anthropomorphic software phantoms.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Rapid Monte Carlo simulation of detector DQE(f)

Purpose: Performance optimization of indirect x-ray detectors requires proper characterization of both ionizing (gamma) and optical photon transport in a heterogeneous medium. As the tool of choice for modeling detector physics, Monte Carlo methods have failed to gain traction as a design utility, due mostly to excessive simulation times and a lack of convenient simulation packages. The most important figure-of-merit in assessing detector performance is the detective quantum efficiency (DQE), for which most of the computational burden has traditionally been associated with the determination of the noise power spectrum (NPS) from an ensemble of flood images, each conventionally having 10{sup 7} − 10{sup 9} detected gamma photons. In this work, the authors show that the idealized conditions inherent in a numerical simulation allow for a dramatic reduction in the number of gamma and optical photons required to accurately predict the NPS. Methods: The authors derived an expression for the mean squared error (MSE) of a simulated NPS when computed using the International Electrotechnical Commission-recommended technique based on taking the 2D Fourier transform of flood images. It is shown that the MSE is inversely proportional to the number of flood images, and is independent of the input fluence provided that the input fluence is above a minimal value that avoids biasing the estimate. The authors then propose to further lower the input fluence so that each event creates a point-spread function rather than a flood field. The authors use this finding as the foundation for a novel algorithm in which the characteristic MTF(f), NPS(f), and DQE(f) curves are simultaneously generated from the results of a single run. The authors also investigate lowering the number of optical photons used in a scintillator simulation to further increase efficiency. Simulation results are compared with measurements performed on a Varian AS1000 portal imager, and with a previously published simulation performed using clinical fluence levels. Results: On the order of only 10–100 gamma photons per flood image were required to be detected to avoid biasing the NPS estimate. This allowed for a factor of 10{sup 7} reduction in fluence compared to clinical levels with no loss of accuracy. An optimal signal-to-noise ratio (SNR) was achieved by increasing the number of flood images from a typical value of 100 up to 500, thereby illustrating the importance of flood image quantity over the number of gammas per flood. For the point-spread ensemble technique, an additional 2× reduction in the number of incident gammas was realized. As a result, when modeling gamma transport in a thick pixelated array, the simulation time was reduced from 2.5 × 10{sup 6} CPU min if using clinical fluence levels to 3.1 CPU min if using optimized fluence levels while also producing a higher SNR. The AS1000 DQE(f) simulation entailing both optical and radiative transport matched experimental results to within 11%, and required 14.5 min to complete on a single CPU. Conclusions: The authors demonstrate the feasibility of accurately modeling x-ray detector DQE(f) with completion times on the order of several minutes using a single CPU. Convenience of simulation can be achieved using GEANT4 which offers both gamma and optical photon transport capabilities.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2014

SU-E-J-38: Comparison of 6MV Photon Dose in a Perpendicular and Parallel Magnetic Field

Purpose: Integrating a linac with an MRI system would allow for real time tumour tracking however the patient will be irradiated in the presence of a magnetic field. The present study experimentally investigates the magnetic field effects on entrance, exit, and interface dose for both transverse and parallel magnetic fields. Methods: Polystyrene was used to construct a set of phantoms for Gafchromic film measurements. One phantom had an adjustable air gap and four other phantoms had one surface at various angles. The linac-MR prototype consisting of a biplanar permanent magnet coupled to a linac was used for the transverse magnetic field measurements. A couple of solenoid electromagnets, stacked on top of each other and irradiated along their bore, were used for the parallel field measurements. Results: All doses are relative to no magnetic field. The transverse magnetic field reduced the entrance dose for all surface angles by strongly deflecting the contaminant electrons. The exit dose in a transverse magnetic field was found to be significantly higher. The entrance dose with a parallel magnetic field present is higher due to the contaminant electrons being concentrated within the beam area. The air gap phantom measurements, done in a transverse magnetic field, show a significant increase of the dose at the proximal side of the air gap and a decrease at the distal side. The measurements, done in the parallel magnetic field, show the concentration of secondary electrons in the air gap. Conclusion: The radiation dose measurements of a 6MV beam in a parallel and transverse magnetic field presented here are currently being replicated using Monte Carlo simulations. This verified Monte Carlo system could provide the dose calculation basis for future linac-MR systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Experimental depth dose curves of a 67.5 MeV proton beam for benchmarking and validation of Monte Carlo simulation

Purpose: To measure depth dose curves for a 67.5 ± 0.1 MeV proton beam for benchmarking and validation of Monte Carlo simulation. Methods: Depth dose curves were measured in 2 beam lines. Protons in the raw beam line traversed a Ta scattering foil, 0.1016 or 0.381 mm thick, a secondary emission monitor comprised of thin Al foils, and a thin Kapton exit window. The beam energy and peak width and the composition and density of material traversed by the beam were known with sufficient accuracy to permit benchmark quality measurements. Diodes for charged particle dosimetry from two different manufacturers were used to scan the depth dose curves with 0.003 mm depth reproducibility in a water tank placed 300 mm from the exit window. Depth in water was determined with an uncertainty of 0.15 mm, including the uncertainty in the water equivalent depth of the sensitive volume of the detector. Parallel-plate chambers were used to verify the accuracy of the shape of the Bragg peak and the peak-to-plateau ratio measured with the diodes. The uncertainty in the measured peak-to-plateau ratio was 4%. Depth dose curves were also measured with a diode for a Bragg curve and treatment beam spread out Bragg peak (SOBP) on the beam line used for eye treatment. The measurements were compared to Monte Carlo simulation done with GEANT4 using TOPAS. Results: The 80% dose at the distal side of the Bragg peak for the thinner foil was at 37.47 ± 0.11 mm (average of measurement with diodes from two different manufacturers), compared to the simulated value of 37.20 mm. The 80% dose for the thicker foil was at 35.08 ± 0.15 mm, compared to the simulated value of 34.90 mm. The measured peak-to-plateau ratio was within one standard deviation experimental uncertainty of the simulated result for the thinnest foil and two standard deviations for the thickest foil. It was necessary to include the collimation in the simulation, which had a more pronounced effect on the peak-to-plateau ratio for the thicker foil. The treatment beam, being unfocussed, had a broader Bragg peak than the raw beam. A 1.3 ± 0.1 MeV FWHM peak width in the energy distribution was used in the simulation to match the Bragg peak width. An additional 1.3–2.24 mm of water in the water column was required over the nominal values to match the measured depth penetration. Conclusions: The proton Bragg curve measured for the 0.1016 mm thick Ta foil provided the most accurate benchmark, having a low contribution of proton scatter from upstream of the water tank. The accuracy was 0.15% in measured beam energy and 0.3% in measured depth penetration at the Bragg peak. The depth of the distal edge of the Bragg peak in the simulation fell short of measurement, suggesting that the mean ionization potential of water is 2–5 eV higher than the 78 eV used in the stopping power calculation for the simulation. The eye treatment beam line depth dose curves provide validation of Monte Carlo simulation of a Bragg curve and SOBP with 4%/2 mm accuracy.

60 APPLIED LIFE SCIENCES↗
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 OSTI2012

Ring-shaped spatial pattern of exciton luminescence formed due to the hot carrier transport in a locally photoexcited electron-hole bilayer

A consistent explanation of the formation of a ring-shaped pattern of exciton luminescence in GaAs/AlGaAs double quantum wells is suggested. The pattern consists of two concentric rings around the laser excitation spot. It is shown that the luminescence rings appear due to the in-layer transport of hot charge carriers at high photoexcitation intensity. Interestingly, one of two causes of this transport might involve self-organized criticality (SOC) that would be the first case of the SOC observation in semiconductor physics. We test this cause in a many-body numerical model by performing extensive molecular dynamics simulations. The results show good agreement with experiments. Moreover, the simulations have enabled us to identify the particular kinetic processes underlying the formation of each of these two luminescence rings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

X-ray optics simulation using Gaussian superposition technique

We present an efficient method to perform x-ray optics simulation with high or partially coherent x-ray sources using Gaussian superposition technique. In a previous paper, we have demonstrated that full characterization of optical systems, diffractive and geometric, is possible by using the Fresnel Gaussian Shape Invariant (FGSI) previously reported in the literature. The complex amplitude distribution in the object plane is represented by a linear superposition of complex Gaussians wavelets and then propagated through the optical system by means of the referred Gaussian invariant. This allows ray tracing through the optical system and at the same time allows calculating with high precision the complex wave-amplitude distribution at any plane of observation. This technique can be applied in a wide spectral range where the Fresnel diffraction integral applies including visible, x-rays, acoustic waves, etc. We describe the technique and include some computer simulations as illustrative examples for x-ray optical component. We show also that this method can be used to study partial or total coherence illumination problem.

47 OTHER INSTRUMENTATION↗