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At least 577 records · Page 32

Towards the ionizing radiation induced bond dissociation mechanism in oxygen, water, guanine and DNA fragmentation: a density functional theory simulation

The radiation-induced damages in bio-molecules are ubiquitous processes in radiotherapy and radio-biology, and critical to space projects. In this study, we present a precise quantification of the fragmentation mechanisms of deoxyribonucleic acid (DNA) and the molecules surrounding DNA such as oxygen and water under non-equilibrium conditions using the first-principle calculations based on density functional theory (DFT). Our results reveal the structural stability of DNA bases and backbone that withstand up to a combined threshold of charge and hydrogen abstraction owing to simultaneously direct and indirect ionization processes. We show the hydrogen contents of the molecules significantly control the stability in the presence of radiation. This study provides comprehensive information on the impact of the direct and indirect induced bond dissociations and DNA damage and introduces a systematic methodology for fine-tuning the input parameters necessary for the large-scale Monte Carlo simulations of radio-biological responses and mitigation of detrimental effects of ionizing radiation.

59 BASIC BIOLOGICAL SCIENCES↗

A Comparison of Bank Control and Direct Force Control for Aerocapture at Uranus

We compare bank angle control and direct force control for aerocapture at Uranus. We utilize the Fully Numerical Predictor-corrector Aerocapture Guidance for both configurations and discuss modifications to the direct force control corrector to handle multiple roots. Using the Genesis flight mechanics simulation, we analyze both nominal and dispersed three-degree-of-freedom trajectories with perfect navigation and control. We present Monte Carlo results and discuss differences between the performance of the two control approaches. We find that increased bank angle rate and acceleration limits do not increase the performance of the bank control configuration. We analyze a variation with tighter angle of attack bounds and find that the tuning and performance of the two configurations converges, because direct force control is less able to modulate drag.

Sergio A Sandoval↗

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or “material voxels” and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies, but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. In conclusion, x-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A theoretical and numerical study of polarimetric scattering and emission from random rough surfaces with anisotropic directional spectrum

In this paper, theoretical and numerical results of the polarimetric scattering and emission from random rough surfaces with anisotropic directional spectrum are presented for the remote sensing of ocean and soil surfaces. The polarimetric scattered field for rough dielectric surfaces is derived to the second order by the small perturbation method (SPM). It is found that the second-order scattered field is coherent in nature, and its coefficients for different polarizations present the lowest-order corrections to the Fresnel reflection coefficients of the surfaces. In addition, the cross-polarized (HV and VH) components of the coherent fields are reciprocal and not zero for surfaces with anisotropic directional spectrum when the azimuth angle of the incident direction is not aligned with the symmetry directions of surfaces. In order to verify the energy conservation condition of the theoretical results, which is important if the theory is to be applied to the passive polarimetry of rough surfaces, a Monte Carlo simulation is performed to numerically calculate the polarimetric reflectivities of one-dimensional random rough surfaces which are generated with a prescribed power-law spectrum in the spectral domain and transformed to the spatial domain by the FFT. The surfaces simulated by this approach are periodic with the period corresponding to the low-wavenumber cutoff. To calculate the scattering from periodic dielectric surfaces, the authors present a new numerical technique which applies the Floquet theorem to reduce the problem to one period and does not require the evaluation of one-dimensional periodic Green's function used in the conventional method of moment formulation. Once the scattering coefficients are obtained, the polarimetric Stokes vectors for the emission from the random surfaces are then calculated according to the Kirchhoff's law and are illustrated as functions of relative azimuth observation and row directions. The second-order SPM is also reduced to this one-dimensional case, and theoretical results for all four Stokes parameters are in excellent agreement with the numerical results obtained from the Monte Carlo simulation. Moreover, the second order coherent fields are found to be necessary for the theoretical evaluation of the third and fourth Stokes parameters. Without that, the reflectivities of random rough surfaces are significantly over-estimated, and the signs of the third and the fourth Stokes parameters are found to be incorrect, if calculated by using the first-order incoherent fields alone.

Yueh, S. H.↗

Partial deconfinement at strong coupling on the lattice

We provide evidence for partial deconfinement — the deconfinement of a SU(M) subgroup of the SU(N) gauge group — by using lattice Monte Carlo simulations. We take matrix models as concrete examples. By appropriately fixing the gauge, we observe that the M × M submatrices deconfine. This gives direct evidence for partial deconfinement at strong coupling. We discuss the applications to QCD and holography.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A radiometric model of an earth radiation budget radiometer optical system with diffuse-specular surfaces

The Earth Radiation Budget Experiment (ERBE) is to fly on NASA's Earth Radiation Budget Satellite (ERBS) and on NOAA F and NOAA G. Large spatial scale earth energy budget data will be derived primarily from measurements made by the ERBE nonscanning instrument (ERBE-NS). A description is given of a mathematical model capable of simulating the radiometric response of any of the ERBE-NS earth viewing channels. The model uses a Monte Carlo method to accurately account for directional distributions of emission and reflection from optical surfaces which are neither strictly diffuse nor strictly specular. The model computes radiation exchange factors among optical system components, and determines the distribution in the optical system of energy from an outside source. Attention is also given to an approach for implementing the model and results obtained from the implementation.

Luther, M. R.↗

Program Predicts Microstructural Changes In Materials

MCFET computer program, named for combined Monte Carlo Finite Element Technique, implements specialized microstructural-lattice simulation technique. Developed to simulate microstructural evolution in material systems in which modulated phases occur and directionality of modulation influenced by internal and external stresses. Written in FORTRAN.

Gayda, J.↗

A New Model for Simulating the Imbibition of a Wetting-Phase Fluid in a Matrix-Fracture Dual Connectivity System

The imbibition experiment is an effective approach for measuring petrophysical properties of porous media, with many such experiments performed over the past decade. Quite some empirical, analytical, and numerical models have been developed to simulate spontaneous imbibition of the wetting phase fluid into porous media, but limitations still exist. In previous studies, the imbibition process has been considered to give a piston-like displacement or the porous medium modeled as multiply-sized pores linked with bonds; both approaches fail to yield comprehensive results due to their neglect of the presence of irregular fractures or nonuniform flow paths through the matrix. By building a numerical model for simulating laboratory-scale experimental data, we performed imbibition tests on several fractured Barnett Shale samples having fractures either parallel ( P ) or transverse ( T ) to the bedding plane and used MATLAB to build a new numerical model by combining the imbibition process in fractures and the matrix using concepts from percolation theory. The experimental data show that the rocks with P -direction fractures have a more steady increase of imbibition rates than the case of T -direction one. As the shale matrix with low pore connectivity hampers the upward water movement, the imbibition rate of shales with T -direction fractures will decrease suddenly after the bottom layer in contact with water is saturated during the initial period. This wetting phase movement (WPM) model can simulate 3D porous media with 2D fractures. The rate of imbibition by fractured porous media is associated with physical parameters such as porosity and fracture distribution (e.g., the number and angle of fractures). Using Monte Carlo methods, we examined fracture parameters and predicted elapsed time and cumulative water imbibition, for the Barnett Shale samples. The results show that the rate of imbibed water mass is sensitive to the number of fractures directly connected to water source, and the connectivity between two neighboring grid cells is a key parameter for the wetting-front progression. The findings of this study can help to better understand the imbibition process with multiple influencing processes and factors in fractured-matrix rocks. Although the experiments, data simulation, and prediction results are based only on Barnett Shale samples, the model is readily applicable to imbibition tests of other fractured rocks to show the spatial and temporal behavior during a dynamic imbibition process that are not easily captured experimentally.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Pilgrim : A thermal rate constant calculator and a chemical kinetics simulator

Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state theory (TST) or by using VTST. In the current version, Pilgrim can evaluate thermal rates using the canonical version of reaction-path VTST, which requires the calculation of the minimum energy path (MEP) associated with each elementary step or transition structure. Multi-dimensional quantum effects can be incorporated through the small-curvature tunneling (SCT) approximation. These methodologies are available both for reactions involving a single structure of the reactants and the transition state and also for reactions involving flexible molecules with multiple conformations of the reactant and/or of the transition state. For systems with many conformers, the program can evaluate each of the elementary reaction rate constants by multipath canonical VTST or multi-structural VTST. Moreover, the reactant can be unimolecular or bimolecular. Torsional anharmonicity can be incorporated through either the MSTor or the Q2DTor programs. Dual-level calculations are also available in Pilgrim: automatic high-level single-point energies can be used to correct the energy of reactants, transition states, products, and MEP points using the interpolated single-point energies (ISPE) algorithm. When the rate constants of all the chemical processes of interest are known, by means of their calculation using Pilgrim or alternatively through analytical fits to the rate constants as functions of temperature, it is possible to simulate a multistep mechanism under specified laboratory conditions using KMC. Finally, this algorithm allows performing a kinetic simulation to monitor the evolution of each chemical species with time and obtain the product yields.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

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.↗

Direct Simulation of Extinction in a Slab of Spherical Particles

The exact multiple sphere superposition method is used to calculate the coherent and incoherent contributions to the ensemble-averaged electric field amplitude and Poynting vector in systems of randomly positioned nonabsorbing spherical particles. The target systems consist of cylindrical volumes, with radius several times larger than length, containing spheres with positional configurations generated by a Monte Carlo sampling method. Spatially dependent values for coherent electric field amplitude, coherent energy flux, and diffuse energy flux, are calculated by averaging of exact local field and flux values over multiple configurations and over spatially independent directions for fixed target geometry, sphere properties, and sphere volume fraction. Our results reveal exponential attenuation of the coherent field and the coherent energy flux inside the particulate layer and thereby further corroborate the general methodology of the microphysical radiative transfer theory. An effective medium model based on plane wave transmission and reflection by a plane layer is used to model the dependence of the coherent electric field on particle packing density. The effective attenuation coefficient of the random medium, computed from the direct simulations, is found to agree closely with effective medium theories and with measurements. In addition, the simulation results reveal the presence of a counter-propagating component to the coherent field, which arises due to the internal reflection of the main coherent field component by the target boundary. The characteristics of the diffuse flux are compared to, and found to be consistent with, a model based on the diffusion approximation of the radiative transfer theory.

spheres↗

Abundance recovery error analysis using simulated AVIRIS data

Measurement noise and imperfect atmospheric correction translate directly into errors in the determination of the surficial abundance of materials from imaging spectrometer data. The effects of errors on abundance recovery were investigated previously using Monte Carlo simulation methods by Sabol et. al. The drawback of the Monte Carlo approach is that thousands of trials are needed to develop good statistics on the probable error in abundance recovery. This computational burden invariably limits the number of scenarios of interest that can practically be investigated. A more efficient approach is based on covariance analysis. The covariance analysis approach expresses errors in abundance as a function of noise in the spectral measurements and provides a closed form result eliminating the need for multiple trials. Monte Carlo simulation and covariance analysis are used to predict confidence limits for abundance recovery for a scenario which is modeled as being derived from Airborne Visible/Infrared Imaging Spectrometer (AVIRIS).

Stoner, William W.↗

Monte Carlo calculations of the extraction of scintillation light from cryogenic $N$-type GaAs

We report the high scintillation luminosity of n-type GaAs at 10 °K is surprising because (1) with a refractive index of 3.5, escape is inhibited by total internal reflection and (2) narrow-beam experiments at 90 °K report infrared absorption coefficients of several per cm. This paper presents Monte Carlo calculations showing that the high luminosity at 10 °K can be explained if (1) the narrow-beam absorption is almost all optical scattering and (2) the absolute absorption coefficient is below 0.1 per cm. Sixteen surface reflector configurations are simulated for a range of internal scattering and absolute absorption coefficients, and these can guide the design of cryogenic scintillating GaAs targets for the direct detection of dark matter. The discussion section presents a possible infrared scattering mechanism based on the metallic nature of n-type GaAs. A supplement file describes (1) the Monte Carlo program steps in detail and (2) how narrow-beam and integrating sphere experiments can measure the cryogenic optical scattering and absolute absorption coefficients.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Ethanol Conversion over La 0.7 Sr 0.3 MnO 3–x (100): Autocatalysis, Adjacent O-Vacancies, Disproportionation, and Dehydrogenation

The mechanism for catalytic conversion of ethanol over La 0.7 Sr 0.3 MnO 3– x (100) surface to acetaldehyde and ethene was investigated. Pre-exposure temperature-programmed reaction (PE-TPR) experiments were performed in which ethanol was introduced to oxidized or reduced surfaces followed by heating. In particular, sequential PE-TPR experiments were conducted to incrementally and gradually reduce the surface. The products and their ratios were investigated as a function of surface reduction. The data show that acetaldehyde and ethene production is catalyzed with hydrogen abstraction and oxygen abstraction reactions occurring by intermediates in vacancies at various temperatures >400 K. Adsorption of acetaldehyde followed by a temperature-programmed reaction does not produce ethene, indicating that acetaldehyde is not an intermediate to ethene and that the hydrogen and oxygen abstraction from ethanol to ethene are decoupled steps. Further evidence for this mechanistic nuance was obtained using isotopically labeled ethanol (CD 3 CH 2 OH), which produces CD 3 CHO and CD 2 CH 2 . Additionally, the ratio of aldehyde production to alkene production increases with reduction, suggesting that aldehyde is produced from a disproportionation reaction between ethoxy species in adjacent O-vacancies, while ethene is produced from a dehydrogenation reaction with ethoxy species in vacancies without requiring adjacent O-vacancies. Counterintuitively, this finding indicates that the more oxygenated product (aldehyde vs ethene) is favored with more vacancies and that the net alcohol conversion is autocatalytic. Density functional theory calculations were able to find the previously unknown disproportionation pathway between ethoxies in adjacent O-vacancies, and kinetic Monte Carlo simulations support this interpretation by reproducing experimental selectivities. The activation energies for these pathways are estimated as 132 ± 10 kJ/mol for the disproportionation reaction (when occurring between ethoxies in adjacent vacancies) and as 148 ± 11 kJ/mol for the direct dehydrogenation reaction of an ethoxy in a vacancy. Based on these results, a mechanism with operative pathways based on elementary steps in O-vacancies is reported.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Anisotropic Cahn-Hilliard free energy and interfacial energies for binary alloys with pairwise interactions

The original Cahn-Hilliard derivation of the contribution of compositional inhomogeneity to the free energy of a binary alloy with pairwise interactions is extended to include higher-order inhomogeneity terms. For alloys on a cubic lattice, the coefficient of the first inhomogeneity is a second-rank tensor and reduces to a scalar, but it is shown that the second order and the third order inhomogeneity terms are weighted by fourth-rank and sixth-rank tensors, thus resulting in anisotropic contributions. Furthermore, each interaction shell generates a unique set of inhomogeneity coefficients that is determined by the set of vectors connecting an atom to its neighbors on that shell. These coefficients are calculated for fcc and bcc alloys with interactions up fourth nearest neighbors. Phase field simulations based on these extended Cahn-Hilliard free energies are performed to measure interface free energies along specific crystallographic directions as a function of temperature, and to obtain the equilibrium shape of precipitates. Interface free energies, and the resulting anisotropies, are compared to those obtained by discrete models and Monte Carlo simulations.

36 MATERIALS SCIENCE↗

Direct evaluation of the phase diagrams of dense multicomponent plasmas by integration of the Clapeyron equations

Accurate phase diagrams of multicomponent plasmas are required for the modeling of dense stellar plasmas, such as those found in the cores of white dwarf stars and the crusts of neutron stars. Those phase diagrams have been computed using a variety of standard techniques, which suffer from physical and computational limitations. Here we present an efficient and accurate method that overcomes the drawbacks of previously used approaches. In particular, finite-size effects are avoided as each phase is calculated separately; the plasma electrons and volume changes are explicitly taken into account; and arbitrary analytic fits to simulation data as well as particle insertions are avoided. Furthermore, no simulations at “uninteresting” state conditions, i.e., away from the phase coexistence curves, are required, which improves the efficiency of the technique. The method consists of an adaptation of the so-called Gibbs-Duhem integration approach to electron-ion plasmas, where the coexistence curve is determined by direct numerical integration of its underlying Clapeyron equation. The thermodynamics properties of the coexisting phases are evaluated separately using Monte Carlo simulations in the isobaric semigrand canonical ensemble (NPT Δ μ ). We describe this Monte Carlo-based Clapeyron integration method, including its basic physical and numerical principles, our extension to electron-ion plasmas, and our numerical implementation. We illustrate its applicability and benefits with the calculation of the melting curve of dense carbon-oxygen plasmas under conditions relevant for the cores of white dwarf stars and provide analytic fits to implement this new melting curve in white dwarf models. While this work focuses on the liquid-solid phase boundary of dense two-component plasmas, a wider range of physical systems and phase boundaries are within the scope of the Clapeyron integration method, which had until now only been applied to simple model systems of neutral particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Simulation and analyses of the aeroassist flight experiment attitude update method

A method which will be used to update the alignment of the Aeroassist Flight Experiment's Inertial Measuring Unit is simulated and analyzed. This method, the Star Line Maneuver, uses measurements from the Space Shuttle Orbiter star trackers along with an extended Kalman filter to estimate a correction to the attitude quaternion maintained by an Inertial Measuring Unit in the Orbiter's payload bay. This quaternion is corrupted by on-orbit bending of the Orbiter payload bay with respect to the Orbiter navigation base, which is incorporated into the payload quaternion when it is initialized via a direct transfer of the Orbiter attitude state. The method of updating this quaternion is examined through verification of baseline cases and Monte Carlo analysis using a simplified simulation, The simulation uses nominal state dynamics and measurement models from the Kalman filter as its real world models, and is programmed on Microvax minicomputer using Matlab, and interactive matrix analysis tool. Results are presented which confirm and augment previous performance studies, thereby enhancing confidence in the Star Line Maneuver design methodology.

Carpenter, J. R.↗

Improving Detector Systematic Uncertainties Through Data-Driven Machine Learning

Detector simulation in liquid argon time projection chambers (LArTPCs) is a constant challenge. In particular the modeling of electrons response on wires is highly nontrivial. However, new machine learning techniques exist which can be leveraged to ameliorate these concerns. We present a novel methodology to attempt to learn from cosmic muon data in the ICARUS detector how reconstructed wire signals are influenced by features of the hits such as location, particle direction, angle relative to the wire plane, etc. A model can then be generated which can apply the learned mapping to Monte Carlo events to create a more data-like simulation sample. By creating such a sample we expect to reduce the systematic uncertainties at ICARUS due to our detector modeling.

Hausner, Harry [Fermilab] (ORCID:0000000188932280)↗