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At least 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Poster - 14: Batch Effect Reduction in in-vitro Raman Microscopic Radiosensitivity Study Using Ovarian Cancer Cells

Purpose: To improve classification by reducing batch effect in samples from the ovarian carcinoma cell lines A2780s (parental wild type) and A2780cp (cisplatin cross-radio-resistant), before, right after, and 24 hours after irradiation to 10Gy. Methods: Spectra were acquired with a home built confocal Raman microscope in 3 distinct runs of six samples: unirradiated s&cp (control pair), then 0h and 24h after irradiation. The Raman spectra were noise reduced, then background subtracted with SMIRF algorithm. ∼35 cell spectra were collected from each sample in 1024 channels from 700cm-1 to 1618cm-1. The spectra were analyzed by regularized multiclass LDA. For feature reduction the spectra were grouped into 3 overlapping group pairs: s-cp, 0Gy–10Gy0h and 0Gy10–Gy24h. The three features, the three differences of the mean spectra were mapped to the analysis sub-space by the inverse regularized covariance matrix. The batch effect noticeably confounded the dose and time effect. Results: To remove the batch effect, the 2+2=4D subspace extended by the covariance matrix of the means of the 0Gy control groups was subtracted from the spectra of each sample. Repeating the analysis on the spectra with the control group variability removed, the batch effect was dramatically reduced in the dose and time directions enabling sharp linear discrimination. The cell type classification also improved. Conclusions: We identified a efficient batch effect removal technique crucial to the applicability of Raman microscopy to radiosensitivity studies both on cell cultures and potential clinical diagnostic applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Segregation-induced ordered superstructures at general grain boundaries in a nickel-bismuth alloy

The properties of materials change, sometimes catastrophically, as alloying elements and impurities accumulate preferentially at grain boundaries. Studies of bicrystals show that regular atomic patterns often arise as a result of this solute segregation at high-symmetry boundaries, but it is not known whether superstructures exist at general grain boundaries in polycrystals. In bismuth-doped polycrystalline nickel, we found that ordered, segregation-induced grain boundary superstructures occur at randomly selected general grain boundaries, and that these reconstructions are driven by the orientation of the terminating grain surfaces rather than by lattice matching between grains. This discovery shows that adsorbate-induced superstructures are not limited to special grain boundaries but may exist at a variety of general grain boundaries, and hence they can affect the performance of polycrystalline engineering alloys.

Science & Technology - Other Topics↗
DOE OSTI2017

Comprehensive computational design of ordered peptide macrocycles

Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with l -amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of l - and d -amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.

Hosseinzadeh, Parisa (ORCID:0000000231287433)↗
DOE OSTI2015

Gravitating lepton bag model

The Kerr–Newman (KN) black hole (BH) solution exhibits the external gravitational and electromagnetic field corresponding to that of the Dirac electron. For the large spin/mass ratio, a ≫ m, the BH loses horizons and acquires a naked singular ring creating two-sheeted topology. This space is regularized by the Higgs mechanism of symmetry breaking, leading to an extended particle that has a regular spinning core compatible with the external KN solution. We show that this core has much in common with the known MIT and SLAC bag models, but has the important advantage of being in accordance with the external gravitational and electromagnetic fields of the KN solution. A peculiar two-sheeted structure of Kerr’s gravity provides a framework for the implementation of the Higgs mechanism of symmetry breaking in configuration space in accordance with the concept of the electroweak sector of the Standard Model. Similar to other bag models, the KN bag is flexible and pliant to deformations. For parameters of a spinning electron, the bag takes the shape of a thin rotating disk of the Compton radius, with a ring–string structure and a quark-like singular pole formed at the sharp edge of this disk, indicating that the considered lepton bag forms a single bag–string–quark system.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Vacuum polarization in the field of a multidimensional global monopole

An approximate expression for the Euclidean Green function of a massless scalar field in the spacetime of a multidimensional global monopole has been derived. Expressions for the vacuum expectation values 〈ϕ{sup 2}〉{sub ren} and 〈T{sub 00}〉{sub ren} have been derived by the dimensional regularization method. Comparison with the results obtained by alternative regularization methods is made.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Light-front chiral effective field theory

We propose a general framework to calculate the nonperturbative structure of relativistic bound state systems. The state vector of the bound state is calculated in the covariant formulation of light-front dynamics. In this scheme, the state vector is defined on the light front of general position {omega} {center_dot} x = 0, where {omega} is an arbitrary light-like four-vector. This enables a strict control of any violation of rotational invariance. The state vector is then decomposed in Fock components. Our formalism is applied to the description of the nucleon properties at low energy, in chiral perturbation theory. We also show that the use of a recently proposed regularization scheme, the so-called Taylor-Lagrange regularization scheme, is very adequate in order to treat divergences in this nonperturbative framework.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Substantiation of the Possibility of Predicting Behavior of Solids under Extreme Conditions at Various High-Intensity Impacts

The paper is devoted to the data analysis on the amplitude-time regularities of the dynamic failure process of solids under various types of high-intensity impact in the ranges of nonequilibrium states from 3 × 10{sup −10} to 10{sup −5} s and establishing general regularities of behavior of unstudied materials under extreme conditions. We have analyzed the process of dynamic destruction of solids of different nature using the method of magnetic-pulse loading in the microsecond range of nonequilibrium states, as well as the dynamic failure process for a number of metals in the mode of pulsed volume heating under the action of pulsed relativistic electron beams in the nanosecond and subnanosecond range of nonequilibrium states. It has been shown that, upon using different methods of pulsed loading in the dynamic longevity range, the failure time as a function of amplitude of applied load has an exponential form for various solid materials. This indicates the scaling nature of the destruction process. The foregoing determines the possibility of predicting the behavior of unstudied solid bodies in the dynamic range of nonequilibrium states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Topics in theory of generalized parton distributions

Several topics in the theory of generalized parton distributions (GPDs) are reviewed. First, we give a brief overview of the basics of the theory of generalized parton distributions and their relationship with simpler phenomenological functions, viz. form factors, parton densities and distribution amplitudes. Then, we discuss recent developments in building models for GPDs that are based on the formalism of double distributions (DDs). A special attention is given to a careful analysis of the singularity structure of DDs. The DD formalism is applied to construction of a model GPDs with a singular Regge behavior. Within the developed DD-based approach, we discuss the structure of GPD sum rules. It is shown that separation of DDs into the so-called “plus” part and the D -term part may be treated as a renormalization procedure for the GPD sum rules. This approach is compared with an alternative prescription based on analytic regularization.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

NSVZ Relation and the Dimensional Reduction in N = 1 SQED

It is known that factorization of the β-function loop integrals into integrals of double total derivatives is an important ingredient needed for deriving the NSVZ relation by direct perturbative calculations in N=1 SQED regularized by thehigher derivatives. It allows to relate the β-function and the anomalous dimension of the matter superfields defined in terms of the bare coupling constant. In this work we find the analog of this result in the case of using dimensional reduction regularization in the lowest orders. However, we demonstrate that in this case the NSVZ relation is not satisfied for the RG functions defined in terms of the bare coupling constant. Nevertheless, it is possible to impose boundary conditions to the renormalization constants determining the NSVZ scheme in the three-loop order for the RG functions defined in terms of the renormalized coupling constant.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Magnetized Solutions in Minimal Gauged Supergravity

We present new black hole solutions in five-dimensional Einstein–Maxwell–Chern–Simons theory with a negative cosmological constant. They rotate with two equal-magnitude angular momenta and they are electrically charged. In addition they possess a non-vanishing magnetic potential at infinity, where they approach asymptotically a global AdS5 space-time. We investigate some of their properties, and we show that these black holes possess a regular extremal limit, and under some additional conditions, a regular solitonic limit as well.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2011

Nonequilibrium radiative properties in fluctuating plasmas1

A general kinetic model was developed to simulate the radiative properties of nonstationary fluctuating plasmas and characterize the relationship between the nonstationary fluctuation time and the atomic relaxation times. The developed theory is applied to the radiative line emission in the case of instabilities in tokamaks. It is shown by exact time dependent simulations that involve explicitly LSJ-split excited states that the radiation emission in fluctuating plasma can be larger than in the corresponding stationary limits. For regular fluctuations like the sawtooth activity, also the startup phase of sawtooth activity can lead to higher emission compared to the time dependent regular phase. It is demonstrated that the sawtooth crash can be almost exactly followed by resonance line emission like H-like Lyman-alpha and He-like Helium-alpha of, e.g., argon impurity ions, whereas the effective charge state distribution lags seriously behind.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2011

Electron states in single-layer graphene containing short-range defects: The potential separable in the momentum representation

Electron states in single-layer graphene containing short-range defects are studied. A model potential concentrated on a circle and asymmetric with respect to the band number is treated. The study is carried out for the (2 + 1)-dimensional Dirac equation with a potential separable in the angular momentum representation. The characteristic equation derived in the study for bound and resonance states is compared with the equation derived previously for the same system by another method. The momentum representation used in this study provides a means for satisfactorily regularizing the Hadamard-incorrect problem with a singular potential. The method developed here is applied to regularization of the previously derived formulas for the scattering parameters and conductivity in graphene.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Site-Controlled Growth of GaN Nanorods with Inserted InGaN Quantum Wells on μ-Cone Patterned Sapphire Substrates by Plasma-Assisted MBE

We report on a new approach to fabricate regular arrays of GaN nanorods (NRs) with InGaN QWs by plasma-assisted molecular-beam epitaxy (PA MBE) on micro-cone patterned sapphire substrates (μ-CPSSs). A two-stage PA MBE fabrication process of GaN NRs has been developed, starting with a high temperature nucleation layer growth at metal-rich conditions to aggregate selectively GaN nucleus on c-oriented areas of the μ-CPSSs and followed by growth of 1-μm-thick GaN NRs at strongly nitrogen-rich conditions exactly on the cone tips. These results are explained by energetically favorable GaN growth on the (000-) oriented sapphire surface. Both micro-photoluminescence and micro-cathodoluminescence confirm the formation of regular array of optically and spectrally isolated NRs without usage of any nanolithography.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Shape Effect in Layering of Solid Solutions in Small Volume: Bismuth–Antimony Alloy

The regularities of the effect of the shape of interphase boundaries in small volume systems on the separation of solutions with an upper critical solution temperature (UCST) are described by the example of Bi–Sb alloy particles with a core–shell configuration. The change in the shape of interphase boundaries is simulated in general by introducing a parameter corresponding to the degree of deviation of the shape of the boundaries from the spherical one. An analysis of the extrema of the Gibbs function revealed regularities in the effect of the shape of the core and shell phases on phase equilibria, the thermodynamic stability of heterogeneous states, and the phase separation diagram. The deviation of the shape of the interphase boundaries from the spherical shape changes the UCST and the mutual solubility of the components. The deformation of the shell of a core–shell particle increases the thermodynamic stability of the heterogeneous state, which contributes to the separation of the solution. The deformation of the core lowers the thermodynamic stability of the heterogeneous state and expands the range of metastable states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Reinforced Concrete Fracture Diagnostics under Conditions of Bending by Parameters of the Electric Response to an Impact Action

Regularities of changes in the stress-strain state of reinforced concrete in the process of testing for four-point bending have been studied. The change in characteristics of the electric response to an impact action in the process of a sequential increase in the external load has been analyzed. Regularities in the relation between parameters of the electric response to the impact action and stages of the stress-strain state of reinforced beams in the process of bending have been revealed. Criteria of determining stages of reinforced beam destruction by parameters of the electric response are proposed.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Discrete models of fluids: spatial averaging, closure and model reduction

We consider semidiscrete ODE models of single-phase fluids and two-fluid mixtures. In the presence of multiple fine-scale heterogeneities, the size of these ODE systems can be very large. Spatial averaging is then a useful tool for reducing computational complexity of the problem. The averages satisfy exact balance equations of mass, momentum, and energy. These equations do not form a satisfactory continuum model because evaluation of stress and heat flux requires solving the underlying ODEs. To produce continuum equations that can be simulated without resolving microscale dynamics, we recently proposed a closure method based on the use of regularized deconvolution. Here we continue the investigation of deconvolution closure with the long term objective of developing consistent computational upscaling for multiphase particle methods. The structure of the fine-scale particle solvers is reminiscent of molecular dynamics. For this reason we use nonlinear averaging introduced for atomistic systems by Noll, Hardy, and Murdoch-Bedeaux. We also consider a simpler linear averaging originally developed in large eddy simulation of turbulence. We present several simple but representative examples of spatially averaged ODEs, where the closure error can be analyzed. Based on this analysis we suggest a general strategy for reducing the relative error of approximate closure. For problems with periodic highly oscillatory material parameters we propose a spectral boosting technique that augments the standard deconvolution and helps to correctly account for dispersion effects. We also conduct several numerical experiments, one of which is a complete mesoscale simulation of a stratified two-fluid flow in a channel. In this simulation, the operation count per coarse time step scales sublinearly with the number of particles.

Multiscale modeling, discrete models, fluid flow↗
DOE OSTI2015

Kullback--Leibler Approximation for Probability Measures on Infinite Dimensional Spaces

In a variety of applications it is important to extract information from a probability measure μ on an infinite dimensional space. Examples include the Bayesian approach to inverse problems and (possibly conditioned) continuous time Markov processes. It may then be of interest to find a measure ν, from within a simple class of measures, which approximates μ. Here, this problem is studied in the case where the Kullback–Leibler divergence is employed to measure the quality of the approximation. A calculus of variations viewpoint is adopted, and the particular case where ν is chosen from the set of Gaussian measures is studied in detail. Basic existence and uniqueness theorems are established, together with properties of minimizing sequences. Furthermore, parameterization of the class of Gaussians through the mean and inverse covariance is introduced, the need for regularization is explained, and a regularized minimization is studied in detail. The calculus of variations framework resulting from this work provides the appropriate underpinning for computational algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Avoiding Communication in Primal and Dual Block Coordinate Descent Methods

Primal and dual block coordinate descent methods are iterative methods for solving regularized and unregularized optimization problems. Distributed-memory parallel implementations of these methods have become popular in analyzing large machine learning datasets. However, existing implementations communicate at every iteration, which, on modern data center and supercomputing architectures, often dominates the cost of floating-point computation. Recent results on communication-avoiding Krylov subspace methods suggest that large speedups are possible by re-organizing iterative algorithms to avoid communication. We show how applying similar algorithmic transformations can lead to primal and dual block coordinate descent methods that only communicate every $s$ iterations---where $s$ is a tuning parameter---instead of every iteration for the regularized least-squares problem. We show that the communication-avoiding variants reduce the number of synchronizations by a factor of $s$ on distributed-memory parallel machines without altering the convergence rate and attain strong scaling speedups of up to $6.1\times$ over the “standard algorithm" on a Cray XC30 supercomputer.

97 MATHEMATICS AND COMPUTING↗