The added mass forces in insect flapping wings.

PubMed

Liu, Longgui; Sun, Mao

2018-01-21

The added mass forces of three-dimensional (3D) flapping wings of some representative insects, and the accuracy of the often used simple two-dimensional (2D) method, are studied. The added mass force of a flapping wing is calculated by both 3D and 2D methods, and the total aerodynamic force of the wing is calculated by the CFD method. Our findings are as following. The added mass force has a significant contribution to the total aerodynamic force of the flapping wings during and near the stroke reversals, and the shorter the stroke amplitude is, the larger the added mass force becomes. Thus the added mass force could not be neglected when using the simple models to estimate the aerodynamics force, especially for insects with relatively small stroke amplitudes. The accuracy of the often used simple 2D method is reasonably good: when the aspect ratio of the wing is greater than about 3.3, error in the added mass force calculation due to the 2D assumption is less than 9%; even when the aspect ratio is 2.8 (approximately the smallest for an insect), the error is no more than 13%. Copyright © 2017 Elsevier Ltd. All rights reserved.

A simple model for cell type recognition using 2D-correlation analysis of FTIR images from breast cancer tissue

NASA Astrophysics Data System (ADS)

Ali, Mohamed H.; Rakib, Fazle; Al-Saad, Khalid; Al-Saady, Rafif; Lyng, Fiona M.; Goormaghtigh, Erik

2018-07-01

Breast cancer is the second most common cancer after lung cancer. So far, in clinical practice, most cancer parameters originating from histopathology rely on the visualization by a pathologist of microscopic structures observed in stained tissue sections, including immunohistochemistry markers. Fourier transform infrared spectroscopy (FTIR) spectroscopy provides a biochemical fingerprint of a biopsy sample and, together with advanced data analysis techniques, can accurately classify cell types. Yet, one of the challenges when dealing with FTIR imaging is the slow recording of the data. One cm2 tissue section requires several hours of image recording. We show in the present paper that 2D covariance analysis singles out only a few wavenumbers where both variance and covariance are large. Simple models could be built using 4 wavenumbers to identify the 4 main cell types present in breast cancer tissue sections. Decision trees provide particularly simple models to reach discrimination between the 4 cell types. The robustness of these simple decision-tree models were challenged with FTIR spectral data obtained using different recording conditions. One test set was recorded by transflection on tissue sections in the presence of paraffin while the training set was obtained on dewaxed tissue sections by transmission. Furthermore, the test set was collected with a different brand of FTIR microscope and a different pixel size. Despite the different recording conditions, separating extracellular matrix (ECM) from carcinoma spectra was 100% successful, underlying the robustness of this univariate model and the utility of covariance analysis for revealing efficient wavenumbers. We suggest that 2D covariance maps using the full spectral range could be most useful to select the interesting wavenumbers and achieve very fast data acquisition on quantum cascade laser infrared imaging microscopes.

A simple 2D biofilm model yields a variety of morphological features.

PubMed

Hermanowicz, S W

2001-01-01

A two-dimensional biofilm model was developed based on the concept of cellular automata. Three simple, generic processes were included in the model: cell growth, internal and external mass transport and cell detachment (erosion). The model generated a diverse range of biofilm morphologies (from dense layers to open, mushroom-like forms) similar to those observed in real biofilm systems. Bulk nutrient concentration and external mass transfer resistance had a large influence on the biofilm structure.

Modeling 2D and 3D diffusion.

PubMed

Saxton, Michael J

2007-01-01

Modeling obstructed diffusion is essential to the understanding of diffusion-mediated processes in the crowded cellular environment. Simple Monte Carlo techniques for modeling obstructed random walks are explained and related to Brownian dynamics and more complicated Monte Carlo methods. Random number generation is reviewed in the context of random walk simulations. Programming techniques and event-driven algorithms are discussed as ways to speed simulations.

Simple Common Plane contact algorithm for explicit FE/FD methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vorobiev, O

2006-12-18

Common-plane (CP) algorithm is widely used in Discrete Element Method (DEM) to model contact forces between interacting particles or blocks. A new simple contact algorithm is proposed to model contacts in FE/FD methods which is similar to the CP algorithm. The CP is defined as a plane separating interacting faces of FE/FD mesh instead of blocks or particles used in the original CP method. The new method does not require iterations even for very stiff contacts. It is very robust and easy to implement both in 2D and 3D parallel codes.

Spatial Pattern of Cell Damage in Tissue from Heavy Ions

NASA Technical Reports Server (NTRS)

Ponomarev, Artem L.; Huff, Janice L.; Cucinotta, Francis A.

2007-01-01

A new Monte Carlo algorithm was developed that can model passage of heavy ions in a tissue, and their action on the cellular matrix for 2- or 3-dimensional cases. The build-up of secondaries such as projectile fragments, target fragments, other light fragments, and delta-rays was simulated. Cells were modeled as a cell culture monolayer in one example, where the data were taken directly from microscopy (2-d cell matrix). A simple model of tissue was given as abstract spheres with close approximation to real cell geometries (3-d cell matrix), as well as a realistic model of tissue was proposed based on microscopy images. Image segmentation was used to identify cells in an irradiated cell culture monolayer, or slices of tissue. The cells were then inserted into the model box pixel by pixel. In the case of cell monolayers (2-d), the image size may exceed the modeled box size. Such image was is moved with respect to the box in order to sample as many cells as possible. In the case of the simple tissue (3-d), the tissue box is modeled with periodic boundary conditions, which extrapolate the technique to macroscopic volumes of tissue. For real tissue, specific spatial patterns for cell apoptosis and necrosis are expected. The cell patterns were modeled based on action cross sections for apoptosis and necrosis estimated based on BNL data, and other experimental data.

Simulations of Quantum Dot Growth on Semiconductor Surfaces: Morphological Design of Sensor Concepts

DTIC Science & Technology

2008-12-01

size equalization can be clearly illustrated during the growth process. In this work we develop a fast multiscale 3D kinetic Monte Carlo ( KMC ) QD...model will provide an attractive means for producing predictably ordered nanostructures. MODEL DESCRIPTION The 3D layer-by-layer KMC growth model...Voter, 2001) and KMC simulation experience (Pan et al., 2004; Pan et al., 2006; Meixner et al, 2003) in 2D, we therefore propose the following simple

Testing the Two-Layer Model for Correcting Near Cloud Reflectance Enhancement Using LES SHDOM Simulated Radiances

NASA Technical Reports Server (NTRS)

Wen, Guoyong; Marshak, Alexander; Varnai, Tamas; Levy, Robert

2016-01-01

A transition zone exists between cloudy skies and clear sky; such that, clouds scatter solar radiation into clear-sky regions. From a satellite perspective, it appears that clouds enhance the radiation nearby. We seek a simple method to estimate this enhancement, since it is so computationally expensive to account for all three-dimensional (3-D) scattering processes. In previous studies, we developed a simple two-layer model (2LM) that estimated the radiation scattered via cloud-molecular interactions. Here we have developed a new model to account for cloud-surface interaction (CSI). We test the models by comparing to calculations provided by full 3-D radiative transfer simulations of realistic cloud scenes. For these scenes, the Moderate Resolution Imaging Spectroradiometer (MODIS)-like radiance fields were computed from the Spherical Harmonic Discrete Ordinate Method (SHDOM), based on a large number of cumulus fields simulated by the University of California, Los Angeles (UCLA) large eddy simulation (LES) model. We find that the original 2LM model that estimates cloud-air molecule interactions accounts for 64 of the total reflectance enhancement and the new model (2LM+CSI) that also includes cloud-surface interactions accounts for nearly 80. We discuss the possibility of accounting for cloud-aerosol radiative interactions in 3-D cloud-induced reflectance enhancement, which may explain the remaining 20 of enhancements. Because these are simple models, these corrections can be applied to global satellite observations (e.g., MODIS) and help to reduce biases in aerosol and other clear-sky retrievals.

A Geostationary Earth Orbit Satellite Model Using Easy Java Simulation

ERIC Educational Resources Information Center

Wee, Loo Kang; Goh, Giam Hwee

2013-01-01

We develop an Easy Java Simulation (EJS) model for students to visualize geostationary orbits near Earth, modelled using a Java 3D implementation of the EJS 3D library. The simplified physics model is described and simulated using a simple constant angular velocity equation. We discuss four computer model design ideas: (1) a simple and realistic…

Predicting the Ability of Marine Mammal Populations to Compensate for Behavioral Disturbances

DTIC Science & Technology

2015-09-30

approaches, including simple theoretical models as well as statistical analysis of data rich conditions. Building on models developed for PCoD [2,3], we...conditions is population trajectory most likely to be affected (the central aim of PCoD ). For the revised model presented here, we include a population...averaged condition individuals (here used as a proxy for individual health as defined in PCoD ), and E is the quality of the environment in which the

Profile modifications in laser-driven temperature fronts using flux-limiters and delocalization models

NASA Astrophysics Data System (ADS)

Colombant, Denis; Manheimer, Wallace; Busquet, Michel

2004-11-01

A simple steady-state model using flux-limiters by Day et al [1] showed that temperature profiles could formally be double-valued. Stability of temperature profiles in laser-driven temperature fronts using delocalization models was also discussed by Prasad and Kershaw [2]. We have observed steepening of the front and flattening of the maximum temperature in laser-driven implosions [3]. Following the simple model first proposed in [1], we solve for a two-boundary value steady-state heat flow problem for various non-local heat transport models. For the more complicated models [4,5], we obtain the steady-state solution as the asymptotic limit of the time-dependent solution. Solutions will be shown and compared for these various models. 1.M.Day, B.Merriman, F.Najmabadi and R.W.Conn, Contrib. Plasma Phys. 36, 419 (1996) 2.M.K.Prasad and D.S.Kershaw, Phys. Fluids B3, 3087 (1991) 3.D.Colombant, W.Manheimer and M.Busquet, Bull. Amer. Phys. Soc. 48, 326 (2003) 4.E.M.Epperlein and R.W.Short, Phys. Fluids B3, 3092 (1991) 5.W.Manheimer and D.Colombant, Phys. Plasmas 11, 260 (2004)

Microstructure representations for sound absorbing fibrous media: 3D and 2D multiscale modelling and experiments

NASA Astrophysics Data System (ADS)

Zieliński, Tomasz G.

2017-11-01

The paper proposes and investigates computationally-efficient microstructure representations for sound absorbing fibrous media. Three-dimensional volume elements involving non-trivial periodic arrangements of straight fibres are examined as well as simple two-dimensional cells. It has been found that a simple 2D quasi-representative cell can provide similar predictions as a volume element which is in general much more geometrically accurate for typical fibrous materials. The multiscale modelling allowed to determine the effective speeds and damping of acoustic waves propagating in such media, which brings up a discussion on the correlation between the speed, penetration range and attenuation of sound waves. Original experiments on manufactured copper-wire samples are presented and the microstructure-based calculations of acoustic absorption are compared with the corresponding experimental results. In fact, the comparison suggested the microstructure modifications leading to representations with non-uniformly distributed fibres.

An Inexpensive 2-D and 3-D Model of the Sarcomere as a Teaching Aid

ERIC Educational Resources Information Center

Rios, Vitor Passos; Bonfim, Vanessa Maria Gomes

2013-01-01

To address a common problem of teaching the sliding filament theory (that is, students have difficulty in visualizing how the component proteins of the sarcomere differ, how they organize themselves into a single working unit, and how they function in relation to each other), we have devised a simple model, with inexpensive materials, to be built…

Vehicle Surveillance with a Generic, Adaptive, 3D Vehicle Model.

PubMed

Leotta, Matthew J; Mundy, Joseph L

2011-07-01

In automated surveillance, one is often interested in tracking road vehicles, measuring their shape in 3D world space, and determining vehicle classification. To address these tasks simultaneously, an effective approach is the constrained alignment of a prior model of 3D vehicle shape to images. Previous 3D vehicle models are either generic but overly simple or rigid and overly complex. Rigid models represent exactly one vehicle design, so a large collection is needed. A single generic model can deform to a wide variety of shapes, but those shapes have been far too primitive. This paper uses a generic 3D vehicle model that deforms to match a wide variety of passenger vehicles. It is adjustable in complexity between the two extremes. The model is aligned to images by predicting and matching image intensity edges. Novel algorithms are presented for fitting models to multiple still images and simultaneous tracking while estimating shape in video. Experiments compare the proposed model to simple generic models in accuracy and reliability of 3D shape recovery from images and tracking in video. Standard techniques for classification are also used to compare the models. The proposed model outperforms the existing simple models at each task.

Two dimensional model for coherent synchrotron radiation

NASA Astrophysics Data System (ADS)

Huang, Chengkun; Kwan, Thomas J. T.; Carlsten, Bruce E.

2013-01-01

Understanding coherent synchrotron radiation (CSR) effects in a bunch compressor requires an accurate model accounting for the realistic beam shape and parameters. We extend the well-known 1D CSR analytic model into two dimensions and develop a simple numerical model based on the Liénard-Wiechert formula for the CSR field of a coasting beam. This CSR numerical model includes the 2D spatial dependence of the field in the bending plane and is accurate for arbitrary beam energy. It also removes the singularity in the space charge field calculation present in a 1D model. Good agreement is obtained with 1D CSR analytic result for free electron laser (FEL) related beam parameters but it can also give a more accurate result for low-energy/large spot size beams and off-axis/transient fields. This 2D CSR model can be used for understanding the limitation of various 1D models and for benchmarking fully electromagnetic multidimensional particle-in-cell simulations for self-consistent CSR modeling.

Load partitioning in Ai{sub 2}0{sub 3-}Al composites with three- dimensional periodic architecture.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, M. L.; Rao, R.; Almer, J. D.

2009-05-01

Interpenetrating composites are created by infiltration of liquid aluminum into three-dimensional (3-D) periodic Al{sub 2}O{sub 3} preforms with simple tetragonal symmetry produced by direct-write assembly. Volume-averaged lattice strains in the Al{sub 2}O{sub 3} phase of the composite are measured by synchrotron X-ray diffraction for various uniaxial compression stresses up to -350MPa. Load transfer, found by diffraction to occur from the metal phase to the ceramic phase, is in general agreement with simple rule-of-mixture models and in better agreement with more complex, 3-D finite-element models that account for metal plasticity and details of the geometry of both phases. Spatially resolved diffractionmore » measurements show variations in load transfer at two different positions within the composite.« less

A comprehensive allometric analysis of 2nd digit length to 4th digit length in humans.

PubMed

Lolli, Lorenzo; Batterham, Alan M; Kratochvíl, Lukáš; Flegr, Jaroslav; Weston, Kathryn L; Atkinson, Greg

2017-06-28

It has been widely reported that men have a lower ratio of the 2nd and 4th human finger lengths (2D : 4D). Size-scaling ratios, however, have the seldom-appreciated potential for providing biased estimates. Using an information-theoretic approach, we compared 12 candidate models, with different assumptions and error structures, for scaling untransformed 2D to 4D lengths from 154 men and 262 women. In each hand, the two-parameter power function and the straight line with intercept models, both with normal, homoscedastic error, were superior to the other models and essentially equivalent to each other for normalizing 2D to 4D lengths. The conventional 2D : 4D ratio biased relative 2D length low for the generally bigger hands of men, and vice versa for women, thereby leading to an artefactual indication that mean relative 2D length is lower in men than women. Conversely, use of the more appropriate allometric or linear regression models revealed that mean relative 2D length was, in fact, greater in men than women. We conclude that 2D does not vary in direct proportion to 4D for both men and women, rendering the use of the simple 2D : 4D ratio inappropriate for size-scaling purposes and intergroup comparisons. © 2017 The Author(s).

Effects of 3 dimensional crystal geometry and orientation on 1D and 2D time-scale determinations of magmatic processes using olivine and orthopyroxene

NASA Astrophysics Data System (ADS)

Shea, Thomas; Krimer, Daniel; Costa, Fidel; Hammer, Julia

2014-05-01

One of the achievements in recent years in volcanology is the determination of time-scales of magmatic processes via diffusion in minerals and its addition to the petrologists' and volcanologists' toolbox. The method typically requires one-dimensional modeling of randomly cut crystals from two-dimensional thin sections. Here we address the question whether using 1D (traverse) or 2D (surface) datasets exploited from randomly cut 3D crystals introduces a bias or dispersion in the time-scales estimated, and how this error can be improved or eliminated. Computational simulations were performed using a concentration-dependent, finite-difference solution to the diffusion equation in 3D. The starting numerical models involved simple geometries (spheres, parallelepipeds), Mg/Fe zoning patterns (either normal or reverse), and isotropic diffusion coefficients. Subsequent models progressively incorporated more complexity, 3D olivines possessing representative polyhedral morphologies, diffusion anisotropy along the different crystallographic axes, and more intricate core-rim zoning patterns. Sections and profiles used to compare 1, 2 and 3D diffusion models were selected to be (1) parallel to the crystal axes, (2) randomly oriented but passing through the olivine center, or (3) randomly oriented and sectioned. Results show that time-scales estimated on randomly cut traverses (1D) or surfaces (2D) can be widely distributed around the actual durations of 3D diffusion (~0.2 to 10 times the true diffusion time). The magnitude over- or underestimations of duration are a complex combination of the geometry of the crystal, the zoning pattern, the orientation of the cuts with respect to the crystallographic axes, and the degree of diffusion anisotropy. Errors on estimated time-scales retrieved from such models may thus be significant. Drastic reductions in the uncertainty of calculated diffusion times can be obtained by following some simple guidelines during the course of data collection (i.e. selection of crystals and concentration profiles, acquisition of crystallographic orientation data), thus allowing derivation of robust time-scales.

Galerkin CFD solvers for use in a multi-disciplinary suite for modeling advanced flight vehicles

NASA Astrophysics Data System (ADS)

Moffitt, Nicholas J.

This work extends existing Galerkin CFD solvers for use in a multi-disciplinary suite. The suite is proposed as a means of modeling advanced flight vehicles, which exhibit strong coupling between aerodynamics, structural dynamics, controls, rigid body motion, propulsion, and heat transfer. Such applications include aeroelastics, aeroacoustics, stability and control, and other highly coupled applications. The suite uses NASA STARS for modeling structural dynamics and heat transfer. Aerodynamics, propulsion, and rigid body dynamics are modeled in one of the five CFD solvers below. Euler2D and Euler3D are Galerkin CFD solvers created at OSU by Cowan (2003). These solvers are capable of modeling compressible inviscid aerodynamics with modal elastics and rigid body motion. This work reorganized these solvers to improve efficiency during editing and at run time. Simple and efficient propulsion models were added, including rocket, turbojet, and scramjet engines. Viscous terms were added to the previous solvers to create NS2D and NS3D. The viscous contributions were demonstrated in the inertial and non-inertial frames. Variable viscosity (Sutherland's equation) and heat transfer boundary conditions were added to both solvers but not verified in this work. Two turbulence models were implemented in NS2D and NS3D: Spalart-Allmarus (SA) model of Deck, et al. (2002) and Menter's SST model (1994). A rotation correction term (Shur, et al., 2000) was added to the production of turbulence. Local time stepping and artificial dissipation were adapted to each model. CFDsol is a Taylor-Galerkin solver with an SA turbulence model. This work improved the time accuracy, far field stability, viscous terms, Sutherland?s equation, and SA model with NS3D as a guideline and added the propulsion models from Euler3D to CFDsol. Simple geometries were demonstrated to utilize current meshing and processing capabilities. Air-breathing hypersonic flight vehicles (AHFVs) represent the ultimate application of the suite. The current models are accurate at low supersonic speed and reasonable for engineering approximation at hypersonic speeds. Improvements to extend the models fully into the hypersonic regime are given in the Recommendations section.

Approximate method for calculating convective heat flux on the surface of bodies of simple geometric shapes

NASA Astrophysics Data System (ADS)

Kuzenov, V. V.; Ryzhkov, S. V.

2017-02-01

The paper formulated engineering and physical mathematical model for aerothermodynamics hypersonic flight vehicle (HFV) in laminar and turbulent boundary layers (model designed for an approximate estimate of the convective heat flow in the range of speeds M = 6-28, and height H = 20-80 km). 2D versions of calculations of convective heat flows for bodies of simple geometric forms (individual elements of the design HFV) are presented.

Numerical Simulation of the Perrin-Like Experiments

ERIC Educational Resources Information Center

Mazur, Zygmunt; Grech, Dariusz

2008-01-01

A simple model of the random Brownian walk of a spherical mesoscopic particle in viscous liquids is proposed. The model can be solved analytically and simulated numerically. The analytic solution gives the known Einstein-Smoluchowski diffusion law r[superscript 2] = 2Dt, where the diffusion constant D is expressed by the mass and geometry of a…

Diffusion and chaos from near AdS 2 horizons

DOE PAGES

Blake, Mike; Donos, Aristomenis

2017-02-03

We calculate the thermal diffusivity D =more » $$\\kappa/c_\\rho$$ and butterfy velocity $$\\upsilon_\\beta$$ in holographic models that flow to $$AdS_2$$ x $R^d$ fixed points in the infra-red. We show that both these quantities are governed by the same irrelevant deformation of $$AdS_2$$ and hence establish a simple relationship between them. When this deformation corresponds to a universal dilaton mode of dimension $$\\Delta$$ = 2 then this relationship is always given by D = $$\\upsilon_B^2$$/(2$$\\pi$$T).« less

Some properties of correlations of quantum lattice systems in thermal equilibrium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fröhlich, Jürg, E-mail: juerg@phys.ethz.ch; Ueltschi, Daniel, E-mail: daniel@ueltschi.org

Simple proofs of uniqueness of the thermodynamic limit of KMS states and of the decay of equilibrium correlations are presented for a large class of quantum lattice systems at high temperatures. New quantum correlation inequalities for general Heisenberg models are described. Finally, a simplified derivation of a general result on power-law decay of correlations in 2D quantum lattice systems with continuous symmetries is given, extending results of McBryan and Spencer for the 2D classical XY model.

Voronoi Cell Patterns: theoretical model and application to submonolayer growth

NASA Astrophysics Data System (ADS)

González, Diego Luis; Einstein, T. L.

2012-02-01

We use a simple fragmentation model to describe the statistical behavior of the Voronoi cell patterns generated by a homogeneous and isotropic set of points in 1D and in 2D. In particular, we are interested in the distribution of sizes of these Voronoi cells. Our model is completely defined by two probability distributions in 1D and again in 2D, the probability to add a new point inside an existing cell and the probability that this new point is at a particular position relative to the preexisting point inside this cell. In 1D the first distribution depends on a single parameter while the second distribution is defined through a fragmentation kernel; in 2D both distributions depend on a single parameter. The fragmentation kernel and the control parameters are closely related to the physical properties of the specific system under study. We apply our model to describe the Voronoi cell patterns of island nucleation for critical island sizes i=0,1,2,3. Experimental results for the Voronoi cells of InAs/GaAs quantum dots are also described by our model.

Calculation of density of states for modeling photoemission using method of moments

NASA Astrophysics Data System (ADS)

Finkenstadt, Daniel; Lambrakos, Samuel G.; Jensen, Kevin L.; Shabaev, Andrew; Moody, Nathan A.

2017-09-01

Modeling photoemission using the Moments Approach (akin to Spicer's "Three Step Model") is often presumed to follow simple models for the prediction of two critical properties of photocathodes: the yield or "Quantum Efficiency" (QE), and the intrinsic spreading of the beam or "emittance" ɛnrms. The simple models, however, tend to obscure properties of electrons in materials, the understanding of which is necessary for a proper prediction of a semiconductor or metal's QE and ɛnrms. This structure is characterized by localized resonance features as well as a universal trend at high energy. Presented in this study is a prototype analysis concerning the density of states (DOS) factor D(E) for Copper in bulk to replace the simple three-dimensional form of D(E) = (m/π2 h3)p2mE currently used in the Moments approach. This analysis demonstrates that excited state spectra of atoms, molecules and solids based on density-functional theory can be adapted as useful information for practical applications, as well as providing theoretical interpretation of density-of-states structure, e.g., qualitatively good descriptions of optical transitions in matter, in addition to DFT's utility in providing the optical constants and material parameters also required in the Moments Approach.

Predicting Organic Cation Sorption Coefficients: Accounting for Competition from Sorbed Inorganic Cations Using a Simple Probe Molecule.

PubMed

Jolin, William C; Goyetche, Reaha; Carter, Katherine; Medina, John; Vasudevan, Dharni; MacKay, Allison A

2017-06-06

With the increasing number of emerging contaminants that are cationic at environmentally relevant pH values, there is a need for robust predictive models of organic cation sorption coefficients (K d ). Current predictive models fail to account for the differences in the identity, abundance, and affinity of surface-associated inorganic exchange ions naturally present at negatively charged receptor sites on environmental solids. To better understand how organic cation sorption is influenced by surface-associated inorganic exchange ions, sorption coefficients of 10 organic cations (including eight pharmaceuticals and two simple probe organic amines) were determined for six homoionic forms of the aluminosilicate mineral, montmorillonite. Organic cation sorption coefficients exhibited consistent trends for all compounds across the various homoionic clays with sorption coefficients (K d ) decreasing as follows: K d Na + > K d NH 4 + ≥ K d K + > K d Ca 2+ ≥ K d Mg 2+ > K d Al 3+ . This trend for competition between organic cations and exchangeable inorganic cations is consistent with the inorganic cation selectivity sequence, determined for exchange between inorganic ions. Such consistent trends in competition between organic and inorganic cations suggested that a simple probe cation, such as phenyltrimethylammonium or benzylamine, could capture soil-to-soil variations in native inorganic cation identity and abundance for the prediction of organic cation sorption to soils and soil minerals. Indeed, sorption of two pharmaceutical compounds to 30 soils was better described by phenyltrimethylammonium sorption than by measures of benzylamine sorption, effective cation exchange capacity alone, or a model from the literature (Droge, S., and Goss, K. Environ. Sci. Technol. 2013, 47, 14224). A hybrid approach integrating structural scaling factors derived from this literature model of organic cation sorption, along with phenyltrimethylammonium K d values, allowed for estimation of K d values for more structurally complex organic cations to homoionic montmorillonites and to heteroionic soils (mean absolute error of 0.27 log unit). Accordingly, we concluded that the use of phenyltrimethylammonium as a probe compound was a promising means to account for the identity, affinity, and abundance of natural exchange ions in the prediction of organic cation sorption coefficients for environmental solids.

L3.PHI.CTF.P10.02-rev2 Coupling of Subchannel T/H (CTF) and CRUD Chemistry (MAMBA1D)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salko, Robert K.; Palmtag, Scott; Collins, Benjamin S.

2015-05-15

The purpose of this milestone is to create a preliminary capability for modeling light water reactor (LWR) thermal-hydraulic (T/H) and CRUD growth using the CTF subchannel code and the subgrid version of the MAMBA CRUD chemistry code, MAMBA1D. In part, this is a follow-on to Milestone L3.PHI.VCS.P9.01, which is documented in Report CASL-U-2014-0188-000, titled "Development of CTF Capability for Modeling Reactor Operating Cycles with Crud Growth". As the title suggests, the previous milestone set up a framework for modeling reactor operation cycles with CTF. The framework also facilitated coupling to a CRUD chemistry capability for modeling CRUD growth throughout themore » reactor operating cycle. To demonstrate the capability, a simple CRUD \\surrogate" tool was developed and coupled to CTF; however, it was noted that CRUD growth predictions by the surrogate were not considered realistic. This milestone builds on L3.PHI.VCS.P9.01 by replacing this simple surrogate tool with the more advanced MAMBA1D CRUD chemistry code. Completing this task involves addressing unresolved tasks from Milestone L3.PHI.VCS.P9.01, setting up an interface to MAMBA1D, and extracting new T/H information from CTF that was not previously required in the simple surrogate tool. Speci c challenges encountered during this milestone include (1) treatment of the CRUD erosion model, which requires local turbulent kinetic energy (TKE) (a value that CTF does not calculate) and (2) treatment of the MAMBA1D CRUD chimney boiling model in the CTF rod heat transfer solution. To demonstrate this new T/H, CRUD modeling capability, two sets of simulations were performed: (1) an 18 month cycle simulation of a quarter symmetry model of Watts Bar and (2) a simulation of Assemblies G69 and G70 from Seabrook Cycle 5. The Watts Bar simulation is merely a demonstration of the capability. The simulation of the Seabrook cycle, which had experienced CRUD-related fuel rod failures, had actual CRUD-scrape data to compare with results. As results show, the initial CTF/MAMBA1D-predicted CRUD thicknesses were about half of their expected values, so further investigation will be required for this simulation.« less

Sum rules for quasifree scattering of hadrons

NASA Astrophysics Data System (ADS)

Peterson, R. J.

2018-02-01

The areas d σ /d Ω of fitted quasifree scattering peaks from bound nucleons for continuum hadron-nucleus spectra measuring d2σ /d Ω d ω are converted to sum rules akin to the Coulomb sums familiar from continuum electron scattering spectra from nuclear charge. Hadronic spectra with or without charge exchange of the beam are considered. These sums are compared to the simple expectations of a nonrelativistic Fermi gas, including a Pauli blocking factor. For scattering without charge exchange, the hadronic sums are below this expectation, as also observed with Coulomb sums. For charge exchange spectra, the sums are near or above the simple expectation, with larger uncertainties. The strong role of hadron-nucleon in-medium total cross sections is noted from use of the Glauber model.

Reconstruction of implanted marker trajectories from cone-beam CT projection images using interdimensional correlation modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Hyekyun

Purpose: Cone-beam CT (CBCT) is a widely used imaging modality for image-guided radiotherapy. Most vendors provide CBCT systems that are mounted on a linac gantry. Thus, CBCT can be used to estimate the actual 3-dimensional (3D) position of moving respiratory targets in the thoracic/abdominal region using 2D projection images. The authors have developed a method for estimating the 3D trajectory of respiratory-induced target motion from CBCT projection images using interdimensional correlation modeling. Methods: Because the superior–inferior (SI) motion of a target can be easily analyzed on projection images of a gantry-mounted CBCT system, the authors investigated the interdimensional correlation ofmore » the SI motion with left–right and anterior–posterior (AP) movements while the gantry is rotating. A simple linear model and a state-augmented model were implemented and applied to the interdimensional correlation analysis, and their performance was compared. The parameters of the interdimensional correlation models were determined by least-square estimation of the 2D error between the actual and estimated projected target position. The method was validated using 160 3D tumor trajectories from 46 thoracic/abdominal cancer patients obtained during CyberKnife treatment. The authors’ simulations assumed two application scenarios: (1) retrospective estimation for the purpose of moving tumor setup used just after volumetric matching with CBCT; and (2) on-the-fly estimation for the purpose of real-time target position estimation during gating or tracking delivery, either for full-rotation volumetric-modulated arc therapy (VMAT) in 60 s or a stationary six-field intensity-modulated radiation therapy (IMRT) with a beam delivery time of 20 s. Results: For the retrospective CBCT simulations, the mean 3D root-mean-square error (RMSE) for all 4893 trajectory segments was 0.41 mm (simple linear model) and 0.35 mm (state-augmented model). In the on-the-fly simulations, prior projections over more than 60° appear to be necessary for reliable estimations. The mean 3D RMSE during beam delivery after the simple linear model had established with a prior 90° projection data was 0.42 mm for VMAT and 0.45 mm for IMRT. Conclusions: The proposed method does not require any internal/external correlation or statistical modeling to estimate the target trajectory and can be used for both retrospective image-guided radiotherapy with CBCT projection images and real-time target position monitoring for respiratory gating or tracking.« less

Pairwise domain adaptation module for CNN-based 2-D/3-D registration.

PubMed

Zheng, Jiannan; Miao, Shun; Jane Wang, Z; Liao, Rui

2018-04-01

Accurate two-dimensional to three-dimensional (2-D/3-D) registration of preoperative 3-D data and intraoperative 2-D x-ray images is a key enabler for image-guided therapy. Recent advances in 2-D/3-D registration formulate the problem as a learning-based approach and exploit the modeling power of convolutional neural networks (CNN) to significantly improve the accuracy and efficiency of 2-D/3-D registration. However, for surgery-related applications, collecting a large clinical dataset with accurate annotations for training can be very challenging or impractical. Therefore, deep learning-based 2-D/3-D registration methods are often trained with synthetically generated data, and a performance gap is often observed when testing the trained model on clinical data. We propose a pairwise domain adaptation (PDA) module to adapt the model trained on source domain (i.e., synthetic data) to target domain (i.e., clinical data) by learning domain invariant features with only a few paired real and synthetic data. The PDA module is designed to be flexible for different deep learning-based 2-D/3-D registration frameworks, and it can be plugged into any pretrained CNN model such as a simple Batch-Norm layer. The proposed PDA module has been quantitatively evaluated on two clinical applications using different frameworks of deep networks, demonstrating its significant advantages of generalizability and flexibility for 2-D/3-D medical image registration when a small number of paired real-synthetic data can be obtained.

Total electron scattering cross sections of some important biomolecules at 0.2-6.0 keV energies

NASA Astrophysics Data System (ADS)

Gurung, Meera Devi; Ariyasinghe, W. M.

2017-12-01

The total electron scattering cross sections (TCS) of five nucleic bases (adenine, cytosine, guanine, thymine and uracil), phosphoric acid, three amino acids (glycine, lysine, and L-histidine), D-glucose, alpha-D-glucose, tetrahydropyran (THP), 3-hydroxytetrahydrofuran and furan have been determined in the energy range 0.2-6.0 keV using a simple model based on the effective atomic total electron scattering cross sections (EATCS). The reliability of the model is confirmed by comparing the determined TCS with the predictions of those by existing theoretical models.

A thermal analysis of a spirally wound battery using a simple mathematical model

NASA Technical Reports Server (NTRS)

Evans, T. I.; White, R. E.

1989-01-01

A two-dimensional thermal model for spirally wound batteries has been developed. The governing equation of the model is the energy balance. Convective and insulated boundary conditions are used, and the equations are solved using a finite element code called TOPAZ2D. The finite element mesh is generated using a preprocessor to TOPAZ2D called MAZE. The model is used to estimate temperature profiles within a spirally wound D-size cell. The model is applied to the lithium/thionyl chloride cell because of the thermal management problems that this cell exhibits. Simplified one-dimensional models are presented that can be used to predict best and worst temperature profiles. The two-dimensional model is used to predict the regions of maximum temperature within the spirally wound cell. Normal discharge as well as thermal runaway conditions are investigated.

Modeling the lung: Design and development of tissue engineered macro- and micro-physiologic lung models for research use.

PubMed

Nichols, Joan E; Niles, Jean A; Vega, Stephanie P; Argueta, Lissenya B; Eastaway, Adriene; Cortiella, Joaquin

2014-09-01

Respiratory tract specific cell populations, or tissue engineered in vitro grown human lung, have the potential to be used as research tools to mimic physiology, toxicology, pathology, as well as infectious diseases responses of cells or tissues. Studies related to respiratory tract pathogenesis or drug toxicity testing in the past made use of basic systems where single cell populations were exposed to test agents followed by evaluations of simple cellular responses. Although these simple single-cell-type systems provided good basic information related to cellular responses, much more can be learned from cells grown in fabricated microenvironments which mimic in vivo conditions in specialized microfabricated chambers or by human tissue engineered three-dimensional (3D) models which allow for more natural interactions between cells. Recent advances in microengineering technology, microfluidics, and tissue engineering have provided a new approach to the development of 2D and 3D cell culture models which enable production of more robust human in vitro respiratory tract models. Complex models containing multiple cell phenotypes also provide a more reasonable approximation of what occurs in vivo without the confounding elements in the dynamic in vivo environment. The goal of engineering good 3D human models is the formation of physiologically functional respiratory tissue surrogates which can be used as pathogenesis models or in the case of 2D screening systems for drug therapy evaluation as well as human toxicity testing. We hope that this manuscript will serve as a guide for development of future respiratory tract model systems as well as a review of conventional models. © 2014 by the Society for Experimental Biology and Medicine.

A distributed Clips implementation: dClips

NASA Technical Reports Server (NTRS)

Li, Y. Philip

1993-01-01

A distributed version of the Clips language, dClips, was implemented on top of two existing generic distributed messaging systems to show that: (1) it is easy to create a coarse-grained parallel programming environment out of an existing language if a high level messaging system is used; and (2) the computing model of a parallel programming environment can be changed easily if we change the underlying messaging system. dClips processes were first connected with a simple master-slave model. A client-server model with intercommunicating agents was later implemented. The concept of service broker is being investigated.

Rubber friction and tire dynamics.

PubMed

Persson, B N J

2011-01-12

We propose a simple rubber friction law, which can be used, for example, in models of tire (and vehicle) dynamics. The friction law is tested by comparing numerical results to the full rubber friction theory (Persson 2006 J. Phys.: Condens. Matter 18 7789). Good agreement is found between the two theories. We describe a two-dimensional (2D) tire model which combines the rubber friction model with a simple mass-spring description of the tire body. The tire model is very flexible and can be used to accurately calculate μ-slip curves (and the self-aligning torque) for braking and cornering or combined motion (e.g. braking during cornering). We present numerical results which illustrate the theory. Simulations of anti-blocking system (ABS) braking are performed using two simple control algorithms.

Voronoi cell patterns: Theoretical model and applications

NASA Astrophysics Data System (ADS)

González, Diego Luis; Einstein, T. L.

2011-11-01

We use a simple fragmentation model to describe the statistical behavior of the Voronoi cell patterns generated by a homogeneous and isotropic set of points in 1D and in 2D. In particular, we are interested in the distribution of sizes of these Voronoi cells. Our model is completely defined by two probability distributions in 1D and again in 2D, the probability to add a new point inside an existing cell and the probability that this new point is at a particular position relative to the preexisting point inside this cell. In 1D the first distribution depends on a single parameter while the second distribution is defined through a fragmentation kernel; in 2D both distributions depend on a single parameter. The fragmentation kernel and the control parameters are closely related to the physical properties of the specific system under study. We use our model to describe the Voronoi cell patterns of several systems. Specifically, we study the island nucleation with irreversible attachment, the 1D car-parking problem, the formation of second-level administrative divisions, and the pattern formed by the Paris Métro stations.

A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.

PubMed

Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li

2013-01-21

A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments.

Modeling Intrajunction Dispersion at a Well-Mixed Tidal River Junction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolfram, Phillip J.; Fringer, Oliver B.; Monsen, Nancy E.

In this paper, the relative importance of small-scale, intrajunction flow features such as shear layers, separation zones, and secondary flows on dispersion in a well-mixed tidal river junction is explored. A fully nonlinear, nonhydrostatic, and unstructured three-dimensional (3D) model is used to resolve supertidal dispersion via scalar transport at a well-mixed tidal river junction. Mass transport simulated in the junction is compared against predictions using a simple node-channel model to quantify the effects of small-scale, 3D intrajunction flow features on mixing and dispersion. The effects of three-dimensionality are demonstrated by quantifying the difference between two-dimensional (2D) and 3D model results.more » An intermediate 3D model that does not resolve the secondary circulation or the recirculating flow at the junction is also compared to the 3D model to quantify the relative sensitivity of mixing on intrajunction flow features. Resolution of complex flow features simulated by the full 3D model is not always necessary because mixing is primarily governed by bulk flow splitting due to the confluence–diffluence cycle. Finally, results in 3D are comparable to the 2D case for many flow pathways simulated, suggesting that 2D modeling may be reasonable for nonstratified and predominantly hydrostatic flows through relatively straight junctions, but not necessarily for the full junction network.« less

Modeling Intrajunction Dispersion at a Well-Mixed Tidal River Junction

DOE PAGES

Wolfram, Phillip J.; Fringer, Oliver B.; Monsen, Nancy E.; ...

2016-08-01

In this paper, the relative importance of small-scale, intrajunction flow features such as shear layers, separation zones, and secondary flows on dispersion in a well-mixed tidal river junction is explored. A fully nonlinear, nonhydrostatic, and unstructured three-dimensional (3D) model is used to resolve supertidal dispersion via scalar transport at a well-mixed tidal river junction. Mass transport simulated in the junction is compared against predictions using a simple node-channel model to quantify the effects of small-scale, 3D intrajunction flow features on mixing and dispersion. The effects of three-dimensionality are demonstrated by quantifying the difference between two-dimensional (2D) and 3D model results.more » An intermediate 3D model that does not resolve the secondary circulation or the recirculating flow at the junction is also compared to the 3D model to quantify the relative sensitivity of mixing on intrajunction flow features. Resolution of complex flow features simulated by the full 3D model is not always necessary because mixing is primarily governed by bulk flow splitting due to the confluence–diffluence cycle. Finally, results in 3D are comparable to the 2D case for many flow pathways simulated, suggesting that 2D modeling may be reasonable for nonstratified and predominantly hydrostatic flows through relatively straight junctions, but not necessarily for the full junction network.« less

Hydrogen recycling in graphite at higher fluxes

NASA Astrophysics Data System (ADS)

Larsson, D.; Bergsåker, H.; Hedqvist, A.

Understanding hydrogen recycling is essential for particle control in fusion devices with a graphite wall. At Extrap T2 three different models have been used. A zero-dimensional (0D) recycling model reproduces the density behavior in plasma discharges as well as in helium glow discharge. A more sophisticated one-dimensional (1D) model is used along with a simple mixing model to explain the results in isotopic exchange experiments. Due to high fluxes some changes in the models were needed. In the paper, the three models are discussed and the results are compared with experimental data.

Membrane Interaction of Antimicrobial Peptides Using E. coli Lipid Extract as Model Bacterial Cell Membranes and SFG Spectroscopy

PubMed Central

Soblosky, Lauren; Ramamoorthy, Ayyalusamy; Chen, Zhan

2015-01-01

Supported lipid bilayers are used as a convenient model cell membrane system to study biologically important molecule-lipid interactions in situ. However, the lipid bilayer models are often simple and the acquired results with these models may not provide all pertinent information related to a real cell membrane. In this work, we use sum frequency generation (SFG) vibrational spectroscopy to study molecular-level interactions between the antimicrobial peptides (AMPs) MSI-594, ovispirin-1 G18, magainin 2 and a simple 1,2-dipalmitoyl-d62-sn-glycero-3-phosphoglycerol (dDPPG)-1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) bilayer. We compared such interactions to those between the AMPs and a more complex dDPPG/E. coli polar lipid extract bilayer. We show that to fully understand more complex aspects of peptide-bilayer interaction, such as interaction kinetics, a heterogeneous lipid composition is required, such as the E. coli polar lipid extract. The discrepancy in peptide-bilayer interaction is likely due in part to the difference in bilayer charge between the two systems since highly negative charged lipids can promote more favorable electrostatic interactions between the peptide and lipid bilayer. Results presented in this paper indicate that more complex model bilayers are needed to accurately analyze peptide-cell membrane interactions and demonstrates the importance of using an appropriate lipid composition to study AMP interaction properties. PMID:25707312

SutraPrep, a pre-processor for SUTRA, a model for ground-water flow with solute or energy transport

USGS Publications Warehouse

Provost, Alden M.

2002-01-01

SutraPrep facilitates the creation of three-dimensional (3D) input datasets for the USGS ground-water flow and transport model SUTRA Version 2D3D.1. It is most useful for applications in which the geometry of the 3D model domain and the spatial distribution of physical properties and boundary conditions is relatively simple. SutraPrep can be used to create a SUTRA main input (?.inp?) file, an initial conditions (?.ics?) file, and a 3D plot of the finite-element mesh in Virtual Reality Modeling Language (VRML) format. Input and output are text-based. The code can be run on any platform that has a standard FORTRAN-90 compiler. Executable code is available for Microsoft Windows.

Lithospheric structure of Taiwan from gravity modelling and sequential inversion of seismological and gravity data

NASA Astrophysics Data System (ADS)

Masson, F.; Mouyen, M.; Hwang, C.; Wu, Y.-M.; Ponton, F.; Lehujeur, M.; Dorbath, C.

2012-11-01

Using a Bouguer anomaly map and a dense seismic data set, we have performed two studies in order to improve our knowledge of the deep structure of Taiwan. First, we model the Bouguer anomaly along a profile crossing the island using simple forward modelling. The modelling is 2D, with the hypothesis of cylindrical symmetry. Second we present a joint analysis of gravity anomaly and seismic arrival time data recorded in Taiwan. An initial velocity model has been obtained by local earthquake tomography (LET) of the seismological data. The LET velocity model was used to construct an initial 3D gravity model, using a linear velocity-density relationship (Birch's law). The synthetic Bouguer anomaly calculated for this model has the same shape and wavelength as the observed anomaly. However some characteristics of the anomaly map are not retrieved. To derive a crustal velocity/density model which accounts for both types of observations, we performed a sequential inversion of seismological and gravity data. The variance reduction of the arrival time data for the final sequential model was comparable to the variance reduction obtained by simple LET. Moreover, the sequential model explained about 80% of the observed gravity anomaly. New 3D model of Taiwan lithosphere is presented.

On CD-AFM bias related to probe bending

NASA Astrophysics Data System (ADS)

Ukraintsev, V. A.; Orji, N. G.; Vorburger, T. V.; Dixson, R. G.; Fu, J.; Silver, R. M.

2012-03-01

Critical Dimension AFM (CD-AFM) is a widely used reference metrology. To characterize modern semiconductor devices, very small and flexible probes, often 15 nm to 20 nm in diameter, are now frequently used. Several recent publications have reported on uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements [1,2]. Results obtained in this work suggest that probe bending can be on the order of several nanometers and thus potentially can explain much of the observed CD-AFM probe-to-probe bias variation. We have developed and experimentally tested one-dimensional (1D) and two-dimensional (2D) models to describe the bending of cylindrical probes. An earlier 1D bending model reported by Watanabe et al. [3] was refined. Contributions from several new phenomena were considered, including: probe misalignment, diameter variation near the carbon nanotube tip (CNT) apex, probe bending before snapping, distributed van der Waals-London force, etc. The methodology for extraction of the Hamaker probe-surface interaction energy from experimental probe bending data was developed. To overcome limitations of the 1D model, a new 2D distributed force (DF) model was developed. Comparison of the new model with the 1D single point force (SPF) model revealed about 27 % difference in probe bending bias between the two. A simple linear relation between biases predicted by the 1D SPF and 2D DF models was found. This finding simplifies use of the advanced 2D DF model of probe bending in various CD-AFM applications. New 2D and three-dimensional (3D) CDAFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

Unravelling InSAR observed Antarctic ice-shelf flexure using 2-D elastic and viscoelastic modelling

NASA Astrophysics Data System (ADS)

Wild, Christian T.; Marsh, Oliver J.; Rack, Wolfgang

2018-04-01

Ice-shelf grounding zones link the Antarctic ice-sheets to the ocean. Differential interferometric synthetic aperture radar (DInSAR) is commonly used to monitor grounding-line locations, but also contains information on grounding-zone ice thickness, ice properties and tidal conditions beneath the ice shelf. Here, we combine in-situ data with numerical modelling of ice-shelf flexure to investigate 2-D controls on the tidal bending pattern on the Southern McMurdo Ice Shelf. We validate our results with 9 double-differential TerraSAR-X interferograms. It is necessary to make adjustments to the tidal forcing to directly compare observations with model output and we find that when these adjustments are small (< 1.5 cm) a viscoelastic model matches better, while an elastic model is more robust overall. Within landward embayments, where lateral stresses from surrounding protrusions damp the flexural response, a 2-D model captures behaviour that is missed in simple 1-D models. We conclude that improvements in current tide models are required to allow for the full exploitation of DInSAR in grounding-zone glaciology.

Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates

PubMed Central

Yogurtcu, Osman N.; Johnson, Margaret E.

2015-01-01

The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute to dense systems. PMID:26328828

Review of Software Platforms for Agent Based Models

DTIC Science & Technology

2008-04-01

EINSTein 4.3.2 Battlefield Python (optional, for batch runs) MANA 4.3.3 Battlefield N/A MASON 4.3.4 General Java NetLogo 4.3.5 General Logo-variant...through the use of relatively simple Python scripts. It also has built-in functions for parameter sweeps, and can plot the resulting fitness landscape ac...Nonetheless its ease of use, and support for automatic drawing of agents in 2D or 3D2 makes this a suitable platform for beginner programmers. 2Only in the

Semi-analytical model for a slab one-dimensional photonic crystal

NASA Astrophysics Data System (ADS)

Libman, M.; Kondratyev, N. M.; Gorodetsky, M. L.

2018-02-01

In our work we justify the applicability of a dielectric mirror model to the description of a real photonic crystal. We demonstrate that a simple one-dimensional model of a multilayer mirror can be employed for modeling of a slab waveguide with periodically changing width. It is shown that this width change can be recalculated to the effective refraction index modulation. The applicability of transfer matrix method of reflection properties calculation was demonstrated. Finally, our 1-D model was employed to analyze reflection properties of a 2-D structure - a slab photonic crystal with a number of elliptic holes.

Simple and Inexpensive 3D Printed Filter Fluorometer Designs: User-Friendly Instrument Models for Laboratory Learning and Outreach Activities

ERIC Educational Resources Information Center

Porter, Lon A., Jr.; Chapman, Cole A.; Alaniz, Jacob A.

2017-01-01

In this work, a versatile and user-friendly selection of stereolithography (STL) files and computer-aided design (CAD) models are shared to assist educators and students in the production of simple and inexpensive 3D printed filter fluorometer instruments. These devices are effective resources for supporting active learners in the exploration of…

Emergence of fully gapped s++-wave and nodal d-wave states mediated by orbital and spin fluctuations in a ten-orbital model of KFe2Se2

NASA Astrophysics Data System (ADS)

Saito, Tetsuro; Onari, Seiichiro; Kontani, Hiroshi

2011-04-01

We study the superconducting state in recently discovered high-Tc superconductor KxFe2Se2 based on the ten-orbital Hubbard-Holstein model without hole pockets. When the Coulomb interaction is large, a spin-fluctuation-mediated d-wave state appears due to the nesting between electron pockets. Interestingly, the symmetry of the body-centered tetragonal structure in KxFe2Se2 requires the existence of nodes in the d-wave gap, although a fully gapped d-wave state is realized in the case of a simple tetragonal structure. In the presence of moderate electron-phonon interaction due to Fe-ion optical modes, however, orbital fluctuations give rise to the fully gapped s++-wave state without sign reversal. Therefore, both superconducting states are distinguishable by careful measurements of the gap structure or the impurity effect on Tc.

Simple formula for the surface area of the body and a simple model for anthropometry.

PubMed

Reading, Bruce D; Freeman, Brian

2005-03-01

The body surface area (BSA) of any adult, when derived from the arithmetic mean of the different values calculated from four independent accepted formulae, can be expressed accurately in Systeme International d'Unites (SI) units by the simple equation BSA = 1/6(WH)0.5, where W is body weight in kg, H is body height in m, and BSA is in m2. This formula, which is derived in part by modeling the body as a simple solid of revolution or a prolate spheroid (i.e., a stretched ellipsoid of revolution) gives students, teachers, and clinicians a simple rule for the rapid estimation of surface area using rational units. The formula was tested independently for human subjects by using it to predict body volume and then comparing this prediction against the actual volume measured by Archimedes' principle. Copyright 2005 Wiley-Liss, Inc.

Testing the Two-Layer Model for Correcting Clear Sky Reflectance near Clouds

NASA Technical Reports Server (NTRS)

Wen, Guoyong; Marshak, Alexander; Evans, Frank; Varnai, Tamas; Levy, Rob

2015-01-01

A two-layer model (2LM) was developed in our earlier studies to estimate the clear sky reflectance enhancement due to cloud-molecular radiative interaction at MODIS at 0.47 micrometers. Recently, we extended the model to include cloud-surface and cloud-aerosol radiative interactions. We use the LES/SHDOM simulated 3D true radiation fields to test the 2LM for reflectance enhancement at 0.47 micrometers. We find: The simple model captures the viewing angle dependence of the reflectance enhancement near cloud, suggesting the physics of this model is correct; the cloud-molecular interaction alone accounts for 70 percent of the enhancement; the cloud-surface interaction accounts for 16 percent of the enhancement; the cloud-aerosol interaction accounts for an additional 13 percent of the enhancement. We conclude that the 2LM is simple to apply and unbiased.

Three-dimensional to two-dimensional transition in mode-I fracture microbranching in a perturbed hexagonal close-packed lattice

NASA Astrophysics Data System (ADS)

Heizler, Shay I.; Kessler, David A.

2017-06-01

Mode-I fracture exhibits microbranching in the high velocity regime where the simple straight crack is unstable. For velocities below the instability, classic modeling using linear elasticity is valid. However, showing the existence of the instability and calculating the dynamics postinstability within the linear elastic framework is difficult and controversial. The experimental results give several indications that the microbranching phenomenon is basically a three-dimensional (3D) phenomenon. Nevertheless, the theoretical effort has been focused mostly on two-dimensional (2D) modeling. In this paper we study the microbranching instability using three-dimensional atomistic simulations, exploring the difference between the 2D and the 3D models. We find that the basic 3D fracture pattern shares similar behavior with the 2D case. Nevertheless, we exhibit a clear 3D-2D transition as the crack velocity increases, whereas as long as the microbranches are sufficiently small, the behavior is pure 3D behavior, whereas at large driving, as the size of the microbranches increases, more 2D-like behavior is exhibited. In addition, in 3D simulations, the quantitative features of the microbranches, separating the regimes of steady-state cracks (mirror) and postinstability (mist-hackle) are reproduced clearly, consistent with the experimental findings.

Touch Interaction with 3D Geographical Visualization on Web: Selected Technological and User Issues

NASA Astrophysics Data System (ADS)

Herman, L.; Stachoň, Z.; Stuchlík, R.; Hladík, J.; Kubíček, P.

2016-10-01

The use of both 3D visualization and devices with touch displays is increasing. In this paper, we focused on the Web technologies for 3D visualization of spatial data and its interaction via touch screen gestures. At the first stage, we compared the support of touch interaction in selected JavaScript libraries on different hardware (desktop PCs with touch screens, tablets, and smartphones) and software platforms. Afterward, we realized simple empiric test (within-subject design, 6 participants, 2 simple tasks, LCD touch monitor Acer and digital terrain models as stimuli) focusing on the ability of users to solve simple spatial tasks via touch screens. An in-house testing web tool was developed and used based on JavaScript, PHP, and X3DOM languages and Hammer.js libraries. The correctness of answers, speed of users' performances, used gestures, and a simple gesture metric was recorded and analysed. Preliminary results revealed that the pan gesture is most frequently used by test participants and it is also supported by the majority of 3D libraries. Possible gesture metrics and future developments including the interpersonal differences are discussed in the conclusion.

A zero-equation turbulence model for two-dimensional hybrid Hall thruster simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cappelli, Mark A., E-mail: cap@stanford.edu; Young, Christopher V.; Cha, Eunsun

2015-11-15

We present a model for electron transport across the magnetic field of a Hall thruster and integrate this model into 2-D hybrid particle-in-cell simulations. The model is based on a simple scaling of the turbulent electron energy dissipation rate and the assumption that this dissipation results in Ohmic heating. Implementing the model into 2-D hybrid simulations is straightforward and leverages the existing framework for solving the electron fluid equations. The model recovers the axial variation in the mobility seen in experiments, predicting the generation of a transport barrier which anchors the region of plasma acceleration. The predicted xenon neutral andmore » ion velocities are found to be in good agreement with laser-induced fluorescence measurements.« less

Drop formation, pinch-off dynamics and liquid transfer of simple and complex fluids

NASA Astrophysics Data System (ADS)

Dinic, Jelena; Sharma, Vivek

Liquid transfer and drop formation processes underlying jetting, spraying, coating, and printing - inkjet, screen, roller-coating, gravure, nanoimprint hot embossing, 3D - often involve formation of unstable columnar necks. Capillary-driven thinning of such necks and their pinchoff dynamics are determined by a complex interplay of inertial, viscous and capillary stresses for simple, Newtonian fluids. Micro-structural changes in response to extensional flow field that arises within the thinning neck give rise to additional viscoelastic stresses in complex, non- Newtonian fluids. Using FLOW-3D, we simulate flows realized in prototypical geometries (dripping and liquid bridge stretched between two parallel plates) used for studying pinch-off dynamics and influence of microstructure and viscoelasticity. In contrast with often-used 1D or 2D models, FLOW-3D allows a robust evaluation of the magnitude of the underlying stresses and extensional flow field (both uniformity and magnitude). We find that the simulated radius evolution profiles match the pinch-off dynamics that are experimentally-observed and theoretically-predicted for model Newtonian fluids and complex fluids.

Atmospheric Nitrogen Trifluoride: Optimized emission estimates using 2-D and 3-D Chemical Transport Models from 1973-2008

NASA Astrophysics Data System (ADS)

Ivy, D. J.; Rigby, M. L.; Prinn, R. G.; Muhle, J.; Weiss, R. F.

2009-12-01

We present optimized annual global emissions from 1973-2008 of nitrogen trifluoride (NF3), a powerful greenhouse gas which is not currently regulated by the Kyoto Protocol. In the past few decades, NF3 production has dramatically increased due to its usage in the semiconductor industry. Emissions were estimated through the 'pulse-method' discrete Kalman filter using both a simple, flexible 2-D 12-box model used in the Advanced Global Atmospheric Gases Experiment (AGAGE) network and the Model for Ozone and Related Tracers (MOZART v4.5), a full 3-D atmospheric chemistry model. No official audited reports of industrial NF3 emissions are available, and with limited information on production, a priori emissions were estimated using both a bottom-up and top-down approach with two different spatial patterns based on semiconductor perfluorocarbon (PFC) emissions from the Emission Database for Global Atmospheric Research (EDGAR v3.2) and Semiconductor Industry Association sales information. Both spatial patterns used in the models gave consistent results, showing the robustness of the estimated global emissions. Differences between estimates using the 2-D and 3-D models can be attributed to transport rates and resolution differences. Additionally, new NF3 industry production and market information is presented. Emission estimates from both the 2-D and 3-D models suggest that either the assumed industry release rate of NF3 or industry production information is still underestimated.

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

A charge-based model of Junction Barrier Schottky rectifiers

NASA Astrophysics Data System (ADS)

Latorre-Rey, Alvaro D.; Mudholkar, Mihir; Quddus, Mohammed T.; Salih, Ali

2018-06-01

A new charge-based model of the electric field distribution for Junction Barrier Schottky (JBS) diodes is presented, based on the description of the charge-sharing effect between the vertical Schottky junction and the lateral pn-junctions that constitute the active cell of the device. In our model, the inherently 2-D problem is transformed into a simple but accurate 1-D problem which has a closed analytical solution that captures the reshaping and reduction of the electric field profile responsible for the improved electrical performance of these devices, while preserving physically meaningful expressions that depend on relevant device parameters. The validation of the model is performed by comparing calculated electric field profiles with drift-diffusion simulations of a JBS device showing good agreement. Even though other fully 2-D models already available provide higher accuracy, they lack physical insight making the proposed model an useful tool for device design.

Modeling the Elastic Modulus of 2D Woven CVI SiC Composites

NASA Technical Reports Server (NTRS)

Morscher, Gregory N.

2006-01-01

The use of fiber, interphase, CVI SiC minicomposites as structural elements for 2D-woven SiC fiber reinforced chemically vapor infiltrated (CVI) SiC matrix composites is demonstrated to be a viable approach to model the elastic modulus of these composite systems when tensile loaded in an orthogonal direction. The 0deg (loading direction) and 90deg (perpendicular to loading direction) oriented minicomposites as well as the open porosity and excess SiC associated with CVI SiC composites were all modeled as parallel elements using simple Rule of Mixtures techniques. Excellent agreement for a variety of 2D woven Hi-Nicalon(TradeMark) fiber-reinforced and Sylramic-iBN reinforced CVI SiC matrix composites that differed in numbers of plies, constituent content, thickness, density, and number of woven tows in either direction (i.e, balanced weaves versus unbalanced weaves) was achieved. It was found that elastic modulus was not only dependent on constituent content, but also the degree to which 90deg minicomposites carried load. This depended on the degree of interaction between 90deg and 0deg minicomposites which was quantified to some extent by composite density. The relationships developed here for elastic modulus only necessitated the knowledge of the fractional contents of fiber, interphase and CVI SiC as well as the tow size and shape. It was concluded that such relationships are fairly robust for orthogonally loaded 2D woven CVI SiC composite system and can be implemented by ceramic matrix composite component modelers and designers for modeling the local stiffness in simple or complex parts fabricated with variable constituent contents.

Distributed force probe bending model of critical dimension atomic force microscopy bias

NASA Astrophysics Data System (ADS)

Ukraintsev, Vladimir A.; Orji, Ndubuisi G.; Vorburger, Theodore V.; Dixson, Ronald G.; Fu, Joseph; Silver, Rick M.

2013-04-01

Critical dimension atomic force microscopy (CD-AFM) is a widely used reference metrology technique. To characterize modern semiconductor devices, small and flexible probes, often 15 to 20 nm in diameter, are used. Recent studies have reported uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements. To understand the source of these variations, tip-sample interactions between high aspect ratio features and small flexible probes, and their influence on measurement bias, should be carefully studied. Using theoretical and experimental procedures, one-dimensional (1-D) and two-dimensional (2-D) models of cylindrical probe bending relevant to carbon nanotube (CNT) AFM probes were developed and tested. An earlier 1-D bending model was refined, and a new 2-D distributed force (DF) model was developed. Contributions from several factors were considered, including: probe misalignment, CNT tip apex diameter variation, probe bending before snapping, and distributed van der Waals-London force. A method for extracting Hamaker probe-surface interaction energy from experimental probe-bending data was developed. Comparison of the new 2-D model with 1-D single point force (SPF) model revealed a difference of about 28% in probe bending. A simple linear relation between biases predicted by the 1-D SPF and 2-D DF models was found. The results suggest that probe bending can be on the order of several nanometers and can partially explain the observed CD-AFM probe-to-probe variation. New 2-D and three-dimensional CD-AFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

Quantifying seismic anisotropy induced by small-scale chemical heterogeneities

NASA Astrophysics Data System (ADS)

Alder, C.; Bodin, T.; Ricard, Y.; Capdeville, Y.; Debayle, E.; Montagner, J. P.

2017-12-01

Observations of seismic anisotropy are usually used as a proxy for lattice-preferred orientation (LPO) of anisotropic minerals in the Earth's mantle. In this way, seismic anisotropy observed in tomographic models provides important constraints on the geometry of mantle deformation associated with thermal convection and plate tectonics. However, in addition to LPO, small-scale heterogeneities that cannot be resolved by long-period seismic waves may also produce anisotropy. The observed (i.e. apparent) anisotropy is then a combination of an intrinsic and an extrinsic component. Assuming the Earth's mantle exhibits petrological inhomogeneities at all scales, tomographic models built from long-period seismic waves may thus display extrinsic anisotropy. In this paper, we investigate the relation between the amplitude of seismic heterogeneities and the level of induced S-wave radial anisotropy as seen by long-period seismic waves. We generate some simple 1-D and 2-D isotropic models that exhibit a power spectrum of heterogeneities as what is expected for the Earth's mantle, that is, varying as 1/k, with k the wavenumber of these heterogeneities. The 1-D toy models correspond to simple layered media. In the 2-D case, our models depict marble-cake patterns in which an anomaly in shear wave velocity has been advected within convective cells. The long-wavelength equivalents of these models are computed using upscaling relations that link properties of a rapidly varying elastic medium to properties of the effective, that is, apparent, medium as seen by long-period waves. The resulting homogenized media exhibit extrinsic anisotropy and represent what would be observed in tomography. In the 1-D case, we analytically show that the level of anisotropy increases with the square of the amplitude of heterogeneities. This relation is numerically verified for both 1-D and 2-D media. In addition, we predict that 10 per cent of chemical heterogeneities in 2-D marble-cake models can induce more than 3.9 per cent of extrinsic radial S-wave anisotropy. We thus predict that a non-negligible part of the observed anisotropy in tomographic models may be the result of unmapped small-scale heterogeneities in the mantle, mainly in the form of fine layering, and that caution should be taken when interpreting observed anisotropy in terms of LPO and mantle deformation. This effect may be particularly strong in the lithosphere where chemical heterogeneities are assumed to be the strongest.

A three-dimensional cell culture system as an in vitro canine mammary carcinoma model for the expression of connective tissue modulators.

PubMed

Cardoso, T C; Sakamoto, S S; Stockmann, D; Souza, T F B; Ferreira, H L; Gameiro, R; Vieira, F V; Louzada, M J Q; Andrade, A L; Flores, E F

2017-06-01

In this study, derived complex carcinoma (CC) and simple carcinoma (SC) cell lines were established and cultured under two-dimensional (2D) and three-dimensional (3D) conditions. The 3D was performed in six-well AlgiMatrix™ (LifeTechnologies®, Carlsbad, CA, USA) scaffolds, resulting in spheroids sized 50-125 µm for CC and 175-200 µm for SC. Cell viability was demonstrated up to 14 days for both models. Epidermal growth factor receptor (EGFR) was expressed in CC and SC in both systems. However, higher mRNA and protein levels were observed in SC 2D and 3D systems when compared with CC (P < 0.005). The connective tissue modulators, metalloproteinases-1, -2, -9 and -13 (MMPs), relaxin receptors 1 and 2 (RXR1 and RXR2) and E-cadherin (CDH1) were quantitated. All were upregulated similarly when canine mammary tumour (CMT)-derived cell lines were cultured under 3D AlgiMatrix, except CDH1 that was downregulated (P < 0.005). These results are promising towards the used of 3D system to increase a high throughput in vitro canine tumour model. © 2016 John Wiley & Sons Ltd.

Development of an algorithm to predict serum vitamin D levels using a simple questionnaire based on sunlight exposure.

PubMed

Vignali, Edda; Macchia, Enrico; Cetani, Filomena; Reggiardo, Giorgio; Cianferotti, Luisella; Saponaro, Federica; Marcocci, Claudio

2017-01-01

Sun exposure is the main determinant of vitamin D production. The aim of this study was to develop an algorithm to assess individual vitamin D status, independently of serum 25(OHD) measurement, using a simple questionnaire, mostly relying upon sunlight exposure, which might help select subjects requiring serum 25(OHD) measurement. Six hundred and twenty adult subjects living in a mountain village in Southern Italy, located at 954 m above the sea level and at a latitude of 40°50'11″76N, were asked to fill the questionnaire in two different periods of the year: August 2010 and March 2011. Seven predictors were considered: month of investigation, age, sex, BMI, average daily sunlight exposure, beach holidays in the past 12 months, and frequency of going outdoors. The statistical model assumes four classes of serum 25(OHD) concentrations: ≤10, 10-19.9, 20-29.9, and ≥30 ng/ml. The algorithm was developed using a two-step procedure. In Step 1, the linear regression equation was defined in 385 randomly selected subjects. In Step 2, the predictive ability of the regression model was tested in the remaining 235 subjects. Seasonality, daily sunlight exposure and beach holidays in the past 12 months accounted for 27.9, 13.5, and 6.4 % of the explained variance in predicting vitamin D status, respectively. The algorithm performed extremely well: 212 of 235 (90.2 %) subjects were assigned to the correct vitamin D status. In conclusion, our pilot study demonstrates that an algorithm to estimate the vitamin D status can be developed using a simple questionnaire based on sunlight exposure.

Increased Expression of Simple Ganglioside Species GM2 and GM3 Detected by MALDI Imaging Mass Spectrometry in a Combined Rat Model of Aβ Toxicity and Stroke

PubMed Central

Caughlin, Sarah; Hepburn, Jeffrey D.; Park, Dae Hee; Jurcic, Kristina; Yeung, Ken K.-C.; Cechetto, David F.; Whitehead, Shawn N.

2015-01-01

The aging brain is often characterized by the presence of multiple comorbidities resulting in synergistic damaging effects in the brain as demonstrated through the interaction of Alzheimer’s disease (AD) and stroke. Gangliosides, a family of membrane lipids enriched in the central nervous system, may have a mechanistic role in mediating the brain’s response to injury as their expression is altered in a number of disease and injury states. Matrix-Assisted Laser Desorption Ionization (MALDI) Imaging Mass Spectrometry (IMS) was used to study the expression of A-series ganglioside species GD1a, GM1, GM2, and GM3 to determine alteration of their expression profiles in the presence of beta-amyloid (Aβ) toxicity in addition to ischemic injury. To model a stroke, rats received a unilateral striatal injection of endothelin-1 (ET-1) (stroke alone group). To model Aβ toxicity, rats received intracerebralventricular (icv) injections of the toxic 25-35 fragment of the Aβ peptide (Aβ alone group). To model the combination of Aβ toxicity with stroke, rats received both the unilateral ET-1 injection and the bilateral icv injections of Aβ₂₅₋₃₅ (combined Aβ/ET-1 group). By 3 d, a significant increase in the simple ganglioside species GM2 was observed in the ischemic brain region of rats who received a stroke (ET-1), with or without Aβ. By 21 d, GM2 levels only remained elevated in the combined Aβ/ET-1 group. GM3 levels however demonstrated a different pattern of expression. By 3 d GM3 was elevated in the ischemic brain region only in the combined Aβ/ET-1 group. By 21 d, GM3 was elevated in the ischemic brain region in both stroke alone and Aβ/ET-1 groups. Overall, results indicate that the accumulation of simple ganglioside species GM2 and GM3 may be indicative of a mechanism of interaction between AD and stroke. PMID:26086081

Increased Expression of Simple Ganglioside Species GM2 and GM3 Detected by MALDI Imaging Mass Spectrometry in a Combined Rat Model of Aβ Toxicity and Stroke.

PubMed

Caughlin, Sarah; Hepburn, Jeffrey D; Park, Dae Hee; Jurcic, Kristina; Yeung, Ken K-C; Cechetto, David F; Whitehead, Shawn N

2015-01-01

The aging brain is often characterized by the presence of multiple comorbidities resulting in synergistic damaging effects in the brain as demonstrated through the interaction of Alzheimer's disease (AD) and stroke. Gangliosides, a family of membrane lipids enriched in the central nervous system, may have a mechanistic role in mediating the brain's response to injury as their expression is altered in a number of disease and injury states. Matrix-Assisted Laser Desorption Ionization (MALDI) Imaging Mass Spectrometry (IMS) was used to study the expression of A-series ganglioside species GD1a, GM1, GM2, and GM3 to determine alteration of their expression profiles in the presence of beta-amyloid (Aβ) toxicity in addition to ischemic injury. To model a stroke, rats received a unilateral striatal injection of endothelin-1 (ET-1) (stroke alone group). To model Aβ toxicity, rats received intracerebralventricular (i.c.v.) injections of the toxic 25-35 fragment of the Aβ peptide (Aβ alone group). To model the combination of Aβ toxicity with stroke, rats received both the unilateral ET-1 injection and the bilateral icv injections of Aβ25-35 (combined Aβ/ET-1 group). By 3 d, a significant increase in the simple ganglioside species GM2 was observed in the ischemic brain region of rats who received a stroke (ET-1), with or without Aβ. By 21 d, GM2 levels only remained elevated in the combined Aβ/ET-1 group. GM3 levels however demonstrated a different pattern of expression. By 3 d GM3 was elevated in the ischemic brain region only in the combined Aβ/ET-1 group. By 21 d, GM3 was elevated in the ischemic brain region in both stroke alone and Aβ/ET-1 groups. Overall, results indicate that the accumulation of simple ganglioside species GM2 and GM3 may be indicative of a mechanism of interaction between AD and stroke.

Validation of optical codes based on 3D nanostructures

NASA Astrophysics Data System (ADS)

Carnicer, Artur; Javidi, Bahram

2017-05-01

Image information encoding using random phase masks produce speckle-like noise distributions when the sample is propagated in the Fresnel domain. As a result, information cannot be accessed by simple visual inspection. Phase masks can be easily implemented in practice by attaching cello-tape to the plain-text message. Conventional 2D-phase masks can be generalized to 3D by combining glass and diffusers resulting in a more complex, physical unclonable function. In this communication, we model the behavior of a 3D phase mask using a simple approach: light is propagated trough glass using the angular spectrum of plane waves whereas the diffusor is described as a random phase mask and a blurring effect on the amplitude of the propagated wave. Using different designs for the 3D phase mask and multiple samples, we demonstrate that classification is possible using the k-nearest neighbors and random forests machine learning algorithms.

Simple Parametric Model for Airfoil Shape Description

NASA Astrophysics Data System (ADS)

Ziemkiewicz, David

2017-12-01

We show a simple, analytic equation describing a class of two-dimensional shapes well suited for representation of aircraft airfoil profiles. Our goal was to create a description characterized by a small number of parameters with easily understandable meaning, providing a tool to alter the shape with optimization procedures as well as manual tweaks by the designer. The generated shapes are well suited for numerical analysis with 2D flow solving software such as XFOIL.

The magnetisation distribution of the Ising model - a new approach

NASA Astrophysics Data System (ADS)

Hakan Lundow, Per; Rosengren, Anders

2010-03-01

A completely new approach to the Ising model in 1 to 5 dimensions is developed. We employ a generalisation of the binomial coefficients to describe the magnetisation distributions of the Ising model. For the complete graph this distribution is exact. For simple lattices of dimensions d=1 and d=5 the magnetisation distributions are remarkably well-fitted by the generalized binomial distributions. For d=4 we are only slightly less successful, while for d=2,3 we see some deviations (with exceptions!) between the generalized binomial and the Ising distribution. The results speak in favour of the generalized binomial distribution's correctness regarding their general behaviour in comparison to the Ising model. A theoretical analysis of the distribution's moments also lends support their being correct asymptotically, including the logarithmic corrections in d=4. The full extent to which they correctly model the Ising distribution, and for which graph families, is not settled though.

Analysis of bacterial migration. 2: Studies with multiple attractant gradients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strauss, I.; Frymier, P.D.; Hahn, C.M.

1995-02-01

Many motile bacteria exhibit chemotaxis, the ability to bias their random motion toward or away from increasing concentrations of chemical substances which benefit or inhibit their survival, respectively. Since bacteria encounter numerous chemical concentration gradients simultaneously in natural surroundings, it is necessary to know quantitatively how a bacterial population responds in the presence of more than one chemical stimulus to develop predictive mathematical models describing bacterial migration in natural systems. This work evaluates three hypothetical models describing the integration of chemical signals from multiple stimuli: high sensitivity, maximum signal, and simple additivity. An expression for the tumbling probability for individualmore » stimuli is modified according to the proposed models and incorporated into the cell balance equation for a 1-D attractant gradient. Random motility and chemotactic sensitivity coefficients, required input parameters for the model, are measured for single stimulus responses. Theoretical predictions with the three signal integration models are compared to the net chemotactic response of Escherichia coli to co- and antidirectional gradients of D-fucose and [alpha]-methylaspartate in the stopped-flow diffusion chamber assay. Results eliminate the high-sensitivity model and favor the simple additivity over the maximum signal. None of the simple models, however, accurately predict the observed behavior, suggesting a more complex model with more steps in the signal processing mechanism is required to predict responses to multiple stimuli.« less

Membrane interaction of antimicrobial peptides using E. coli lipid extract as model bacterial cell membranes and SFG spectroscopy.

PubMed

Soblosky, Lauren; Ramamoorthy, Ayyalusamy; Chen, Zhan

2015-04-01

Supported lipid bilayers are used as a convenient model cell membrane system to study biologically important molecule-lipid interactions in situ. However, the lipid bilayer models are often simple and the acquired results with these models may not provide all pertinent information related to a real cell membrane. In this work, we use sum frequency generation (SFG) vibrational spectroscopy to study molecular-level interactions between the antimicrobial peptides (AMPs) MSI-594, ovispirin-1 G18, magainin 2 and a simple 1,2-dipalmitoyl-d62-sn-glycero-3-phosphoglycerol (dDPPG)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) bilayer. We compared such interactions to those between the AMPs and a more complex dDPPG/Escherichia coli (E. coli) polar lipid extract bilayer. We show that to fully understand more complex aspects of peptide-bilayer interaction, such as interaction kinetics, a heterogeneous lipid composition is required, such as the E. coli polar lipid extract. The discrepancy in peptide-bilayer interaction is likely due in part to the difference in bilayer charge between the two systems since highly negative charged lipids can promote more favorable electrostatic interactions between the peptide and lipid bilayer. Results presented in this paper indicate that more complex model bilayers are needed to accurately analyze peptide-cell membrane interactions and demonstrates the importance of using an appropriate lipid composition to study AMP interaction properties. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Forecasting Tunisian type 2 diabetes prevalence to 2027: validation of a simple model.

PubMed

Saidi, Olfa; O'Flaherty, Martin; Mansour, Nadia Ben; Aissi, Wafa; Lassoued, Olfa; Capewell, Simon; Critchley, Julia A; Malouche, Dhafer; Romdhane, Habiba Ben

2015-02-07

Most projections of type 2 diabetes (T2D) prevalence are simply based on demographic change (i.e. ageing). We developed a model to predict future trends in T2D prevalence in Tunisia, explicitly taking into account trends in major risk factors (obesity and smoking). This could improve assessment of policy options for prevention and health service planning. The IMPACT T2D model uses a Markov approach to integrate population, obesity and smoking trends to estimate future T2D prevalence. We developed a model for the Tunisian population from 1997 to 2027, and validated the model outputs by comparing with a subsequent T2D prevalence survey conducted in 2005. The model estimated that the prevalence of T2D among Tunisians aged over 25 years was 12.0% in 1997 (95% confidence intervals 9.6%-14.4%), increasing to 15.1% (12.5%-17.4%) in 2005. Between 1997 and 2005, observed prevalence in men increased from 13.5% to 16.1% and in women from 12.9% to 14.1%. The model forecast for a dramatic rise in prevalence by 2027 (26.6% overall, 28.6% in men and 24.7% in women). However, if obesity prevalence declined by 20% in the 10 years from 2013, and if smoking decreased by 20% over 10 years from 2009, a 3.3% reduction in T2D prevalence could be achieved in 2027 (2.5% in men and 4.1% in women). This innovative model provides a reasonably close estimate of T2D prevalence for Tunisia over the 1997-2027 period. Diabetes burden is now a significant public health challenge. Our model predicts that this burden will increase significantly in the next two decades. Tackling obesity, smoking and other T2D risk factors thus needs urgent action. Tunisian decision makers have therefore defined two strategies: obesity reduction and tobacco control. Responses will be evaluated in future population surveys.

The null distribution of the heterogeneity lod score does depend on the assumed genetic model for the trait.

PubMed

Huang, J; Vieland, V J

2001-01-01

It is well known that the asymptotic null distribution of the homogeneity lod score (LOD) does not depend on the genetic model specified in the analysis. When appropriately rescaled, the LOD is asymptotically distributed as 0.5 chi(2)(0) + 0.5 chi(2)(1), regardless of the assumed trait model. However, because locus heterogeneity is a common phenomenon, the heterogeneity lod score (HLOD), rather than the LOD itself, is often used in gene mapping studies. We show here that, in contrast with the LOD, the asymptotic null distribution of the HLOD does depend upon the genetic model assumed in the analysis. In affected sib pair (ASP) data, this distribution can be worked out explicitly as (0.5 - c)chi(2)(0) + 0.5chi(2)(1) + cchi(2)(2), where c depends on the assumed trait model. E.g., for a simple dominant model (HLOD/D), c is a function of the disease allele frequency p: for p = 0.01, c = 0.0006; while for p = 0.1, c = 0.059. For a simple recessive model (HLOD/R), c = 0.098 independently of p. This latter (recessive) distribution turns out to be the same as the asymptotic distribution of the MLS statistic under the possible triangle constraint, which is asymptotically equivalent to the HLOD/R. The null distribution of the HLOD/D is close to that of the LOD, because the weight c on the chi(2)(2) component is small. These results mean that the cutoff value for a test of size alpha will tend to be smaller for the HLOD/D than the HLOD/R. For example, the alpha = 0.0001 cutoff (on the lod scale) for the HLOD/D with p = 0.05 is 3.01, while for the LOD it is 3.00, and for the HLOD/R it is 3.27. For general pedigrees, explicit analytical expression of the null HLOD distribution does not appear possible, but it will still depend on the assumed genetic model. Copyright 2001 S. Karger AG, Basel

Evidence for a Significant Level of Extrinsic Anisotropy Due to Heterogeneities in the Mantle.

NASA Astrophysics Data System (ADS)

Alder, C.; Bodin, T.; Ricard, Y. R.; Capdeville, Y.; Debayle, E.; Montagner, J. P.

2017-12-01

Observations of seismic anisotropy are used as a proxy for lattice-preferred orientation (LPO) of anisotropic minerals in the Earth's mantle. In this way, it provides important constraints on the geometry of mantle deformation. However, in addition to LPO, small-scale heterogeneities that cannot be resolved by long-period seismic waves may also produce anisotropy. The observed (i.e. apparent) anisotropy is then a combination of an intrinsic and an extrinsic component. Assuming the Earth's mantle exhibits petrological inhomogeneities at all scales, tomographic models built from long-period seismic waves may thus display extrinsic anisotropy. Here, we investigate the relation between the amplitude of seismic heterogeneities and the level of induced S-wave radial anisotropy as seen by long-period seismic waves. We generate some simple 1D and 2D isotropic models that exhibit a power spectrum of heterogeneities as what is expected for the Earth's mantle, i.e. varying as 1/k, with k the wavenumber of these heterogeneities. The 1D toy models correspond to simple layered media. In the 2D case, our models depict marble-cake patterns in which an anomaly in S-wave velocity has been advected within convective cells. The long-wavelength equivalents of these models are computed using upscaling relations that link properties of a rapidly varying elastic medium to properties of the effective, i.e. apparent, medium as seen by long-period waves. The resulting homogenized media exhibit extrinsic anisotropy and represent what would be observed in tomography. In the 1D case, we analytically show that the level of anisotropy increases with the square of the amplitude of heterogeneities. This relation is numerically verified for both 1D and 2D media. In addition, we predict that 10 % of chemical heterogeneities in 2D marble-cake models can induce more than 3.9 % of extrinsic radial S-wave anisotropy. We thus predict that a non-negligible part of the observed anisotropy in tomographic models may be the result of unmapped small-scale heterogeneities in the mantle, mainly in the form of fine layering, and that caution should be taken when interpreting observed anisotropy in terms of LPO and mantle deformation. This effect may be particularly strong in the lithosphere where chemical heterogeneities are assumed to be the strongest.

Angular distributions for a model system of nonadiabatic molecular collisions: The quenching of Na*(3p) by H/sub 2/ and D/sub 2/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reiland, W.; Tittes, U.; Hertel, I.V.

Angular distributions for the electronic to vibrational rotational and translational energy (E-VRT) transfer process Na*(3p)+H/sub 2/,D/sub 2/..-->..Na(3s)+H/sub 2/(v',j') with product energy analysis have been measured for the first time. The differential cross sections are forward peaked, constant but small between 35/sup 0/ and 160/sup 0/ and very slightly increasing at 180/sup 0/. The observations can be qualitatively understood by a simple model for the particle motion on the attractive A/sup 2/B/sub 2/ excited-state surface with a hop to the repulsive X/sup 2/A/sub 1/ ground state.

Transferring of speech movements from video to 3D face space.

PubMed

Pei, Yuru; Zha, Hongbin

2007-01-01

We present a novel method for transferring speech animation recorded in low quality videos to high resolution 3D face models. The basic idea is to synthesize the animated faces by an interpolation based on a small set of 3D key face shapes which span a 3D face space. The 3D key shapes are extracted by an unsupervised learning process in 2D video space to form a set of 2D visemes which are then mapped to the 3D face space. The learning process consists of two main phases: 1) Isomap-based nonlinear dimensionality reduction to embed the video speech movements into a low-dimensional manifold and 2) K-means clustering in the low-dimensional space to extract 2D key viseme frames. Our main contribution is that we use the Isomap-based learning method to extract intrinsic geometry of the speech video space and thus to make it possible to define the 3D key viseme shapes. To do so, we need only to capture a limited number of 3D key face models by using a general 3D scanner. Moreover, we also develop a skull movement recovery method based on simple anatomical structures to enhance 3D realism in local mouth movements. Experimental results show that our method can achieve realistic 3D animation effects with a small number of 3D key face models.

2D MHD AND 1D HD MODELS OF A SOLAR FLARE—A COMPREHENSIVE COMPARISON OF THE RESULTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Falewicz, R.; Rudawy, P.; Murawski, K.

Without any doubt, solar flaring loops possess a multithread internal structure that is poorly resolved, and there are no means to observe heating episodes and thermodynamic evolution of the individual threads. These limitations cause fundamental problems in numerical modeling of flaring loops, such as selection of a structure and a number of threads, and an implementation of a proper model of the energy deposition process. A set of one-dimensional (1D) hydrodynamic and two-dimensional (2D) magnetohydrodynamic models of a flaring loop are developed to compare energy redistribution and plasma dynamics in the course of a prototypical solar flare. Basic parameters ofmore » the modeled loop are set according to the progenitor M1.8 flare recorded in AR 10126 on 2002 September 20 between 09:21 UT and 09:50 UT. The nonideal 1D models include thermal conduction and radiative losses of the optically thin plasma as energy-loss mechanisms, while the nonideal 2D models take into account viscosity and thermal conduction as energy-loss mechanisms only. The 2D models have a continuous distribution of the parameters of the plasma across the loop and are powered by varying in time and space along and across the loop heating flux. We show that such 2D models are an extreme borderline case of a multithread internal structure of the flaring loop, with a filling factor equal to 1. Nevertheless, these simple models ensure the general correctness of the obtained results and can be adopted as a correct approximation of the real flaring structures.« less

CaveCAD: a tool for architectural design in immersive virtual environments

NASA Astrophysics Data System (ADS)

Schulze, Jürgen P.; Hughes, Cathleen E.; Zhang, Lelin; Edelstein, Eve; Macagno, Eduardo

2014-02-01

Existing 3D modeling tools were designed to run on desktop computers with monitor, keyboard and mouse. To make 3D modeling possible with mouse and keyboard, many 3D interactions, such as point placement or translations of geometry, had to be mapped to the 2D parameter space of the mouse, possibly supported by mouse buttons or keyboard keys. We hypothesize that had the designers of these existing systems had been able to assume immersive virtual reality systems as their target platforms, they would have been able to design 3D interactions much more intuitively. In collaboration with professional architects, we created a simple, but complete 3D modeling tool for virtual environments from the ground up and use direct 3D interaction wherever possible and adequate. In this publication, we present our approaches for interactions for typical 3D modeling functions, such as geometry creation, modification of existing geometry, and assignment of surface materials. We also discuss preliminary user experiences with this system.

Engineering cancer microenvironments for in vitro 3-D tumor models

PubMed Central

Asghar, Waseem; El Assal, Rami; Shafiee, Hadi; Pitteri, Sharon; Paulmurugan, Ramasamy; Demirci, Utkan

2017-01-01

The natural microenvironment of tumors is composed of extracellular matrix (ECM), blood vasculature, and supporting stromal cells. The physical characteristics of ECM as well as the cellular components play a vital role in controlling cancer cell proliferation, apoptosis, metabolism, and differentiation. To mimic the tumor microenvironment outside the human body for drug testing, two-dimensional (2-D) and murine tumor models are routinely used. Although these conventional approaches are employed in preclinical studies, they still present challenges. For example, murine tumor models are expensive and difficult to adopt for routine drug screening. On the other hand, 2-D in vitro models are simple to perform, but they do not recapitulate natural tumor microenvironment, because they do not capture important three-dimensional (3-D) cell–cell, cell–matrix signaling pathways, and multi-cellular heterogeneous components of the tumor microenvironment such as stromal and immune cells. The three-dimensional (3-D) in vitro tumor models aim to closely mimic cancer microenvironments and have emerged as an alternative to routinely used methods for drug screening. Herein, we review recent advances in 3-D tumor model generation and highlight directions for future applications in drug testing. PMID:28458612

Numerical modelling of CIGS/CdS solar cell

NASA Astrophysics Data System (ADS)

Devi, Nisha; Aziz, Anver; Datta, Shouvik

2018-05-01

In this work, we design and analyze the Cu(In,Ga)Se2 (CIGS) solar cell using simulation software "Solar Cell Capacitance Simulator in One Dimension (SCAPS-1D)". The conventional CIGS solar cell uses various layers, like intrinsic ZnO/Aluminium doped ZnO as transparent oxide, antireflection layer MgF2, and electron back reflection (EBR) layer at CIGS/Mo interface for good power conversion efficiency. We replace this conventional model by a simple model which is easy to fabricate and also reduces the cost of this cell because of use of lesser materials. The new designed model of CIGS solar cell is ITO/CIGS/OVC/CdS/Metal contact, where OVC is ordered vacancy compound. From this simple structure, even at very low illumination we are getting good results. We simulate this CIGS solar cell model by varying various physical parameters of CIGS like thickness, carrier density, band gap and temperature.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Damao; Wang, Zhien; Heymsfield, Andrew J.

Measurement of ice number concentration in clouds is important but still challenging. Stratiform mixed-phase clouds (SMCs) provide a simple scenario for retrieving ice number concentration from remote sensing measurements. The simple ice generation and growth pattern in SMCs offers opportunities to use cloud radar reflectivity (Ze) measurements and other cloud properties to infer ice number concentration quantitatively. To understand the strong temperature dependency of ice habit and growth rate quantitatively, we develop a 1-D ice growth model to calculate the ice diffusional growth along its falling trajectory in SMCs. The radar reflectivity and fall velocity profiles of ice crystals calculatedmore » from the 1-D ice growth model are evaluated with the Atmospheric Radiation Measurements (ARM) Climate Research Facility (ACRF) ground-based high vertical resolution radar measurements. Combining Ze measurements and 1-D ice growth model simulations, we develop a method to retrieve the ice number concentrations in SMCs at given cloud top temperature (CTT) and liquid water path (LWP). The retrieved ice concentrations in SMCs are evaluated with in situ measurements and with a three-dimensional cloud-resolving model simulation with a bin microphysical scheme. These comparisons show that the retrieved ice number concentrations are within an uncertainty of a factor of 2, statistically.« less

Three-dimensional portable document format: a simple way to present 3-dimensional data in an electronic publication.

PubMed

Danz, Jan C; Katsaros, Christos

2011-08-01

Three-dimensional (3D) models of teeth and soft and hard tissues are tessellated surfaces used for diagnosis, treatment planning, appliance fabrication, outcome evaluation, and research. In scientific publications or communications with colleagues, these 3D data are often reduced to 2-dimensional pictures or need special software for visualization. The portable document format (PDF) offers a simple way to interactively display 3D surface data without additional software other than a recent version of Adobe Reader (Adobe, San Jose, Calif). The purposes of this article were to give an example of how 3D data and their analyses can be interactively displayed in 3 dimensions in electronic publications, and to show how they can be exported from any software for diagnostic reports and communications among colleagues. Copyright © 2011 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

X-ray spectroscopy of the super soft source RXJ0925.7-475

NASA Technical Reports Server (NTRS)

Ebisawa, Ken; Asai, Kazumi; Dotani, Tadayasu; Mukai, Koji; Smale, Alan

1996-01-01

The super soft source (SSS) RXJ 0925.7-475 was observed with the Advanced Satellite for Cosmology and Astrophysics (ASCA) solid state spectrometer and its energy spectrum was analyzed. A simple black body model does not fit the data, and several absorption edges of ionized heavy elements are required. Without the addition of absorption edges, the best-fit black body radius and the estimated bolometric luminosity are 6800 (d/1 kpc) km and 1.2 x 10(exp 37) (d/1 kps)(exp 2) erg/s, respectively. The introduction of absorption edges significantly reduces the best-fit radius and luminosity to 140 (d/1 KPS) km and 6 x 10(exp 34) (d/1 kpc)(exp 2) erg/s, respectively. This suggests that the estimation of the emission region size and luminosity of SSS based on the black body model fit to the observed data is not reliable.

No-Enclave Percolation Corresponds to Holes in the Cluster Backbone.

PubMed

Hu, Hao; Ziff, Robert M; Deng, Youjin

2016-10-28

The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ=1.82(1) as found for the NEP model. An argument is given that τ=1+d_{B}/2≈1.822 for backbone holes, where d_{B} is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ=1+d_{f}/2=187/96≈1.948, where d_{f} is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ=1.91(6). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at p_{c}, signifying explosive percolation behavior.

Active earth pressure model tests versus finite element analysis

NASA Astrophysics Data System (ADS)

Pietrzak, Magdalena

2017-06-01

The purpose of the paper is to compare failure mechanisms observed in small scale model tests on granular sample in active state, and simulated by finite element method (FEM) using Plaxis 2D software. Small scale model tests were performed on rectangular granular sample retained by a rigid wall. Deformation of the sample resulted from simple wall translation in the direction `from the soil" (active earth pressure state. Simple Coulomb-Mohr model for soil can be helpful in interpreting experimental findings in case of granular materials. It was found that the general alignment of strain localization pattern (failure mechanism) may belong to macro scale features and be dominated by a test boundary conditions rather than the nature of the granular sample.

Enhancement of orientation gradients during simple shear deformation by application of simple compression

NASA Astrophysics Data System (ADS)

Jahedi, Mohammad; Ardeljan, Milan; Beyerlein, Irene J.; Paydar, Mohammad Hossein; Knezevic, Marko

2015-06-01

We use a multi-scale, polycrystal plasticity micromechanics model to study the development of orientation gradients within crystals deforming by slip. At the largest scale, the model is a full-field crystal plasticity finite element model with explicit 3D grain structures created by DREAM.3D, and at the finest scale, at each integration point, slip is governed by a dislocation density based hardening law. For deformed polycrystals, the model predicts intra-granular misorientation distributions that follow well the scaling law seen experimentally by Hughes et al., Acta Mater. 45(1), 105-112 (1997), independent of strain level and deformation mode. We reveal that the application of a simple compression step prior to simple shearing significantly enhances the development of intra-granular misorientations compared to simple shearing alone for the same amount of total strain. We rationalize that the changes in crystallographic orientation and shape evolution when going from simple compression to simple shearing increase the local heterogeneity in slip, leading to the boost in intra-granular misorientation development. In addition, the analysis finds that simple compression introduces additional crystal orientations that are prone to developing intra-granular misorientations, which also help to increase intra-granular misorientations. Many metal working techniques for refining grain sizes involve a preliminary or concurrent application of compression with severe simple shearing. Our finding reveals that a pre-compression deformation step can, in fact, serve as another processing variable for improving the rate of grain refinement during the simple shearing of polycrystalline metals.

In-to-Out Body Antenna-Independent Path Loss Model for Multilayered Tissues and Heterogeneous Medium

PubMed Central

Kurup, Divya; Vermeeren, Günter; Tanghe, Emmeric; Joseph, Wout; Martens, Luc

2015-01-01

In this paper, we investigate multilayered lossy and heterogeneous media for wireless body area networks (WBAN) to develop a simple, fast and efficient analytical in-to-out body path loss (PL) model at 2.45 GHz and, thus, avoid time-consuming simulations. The PL model is an antenna-independent model and is validated with simulations in layered medium, as well as in a 3D human model using electromagnetic solvers. PMID:25551483

A Secret 3D Model Sharing Scheme with Reversible Data Hiding Based on Space Subdivision

NASA Astrophysics Data System (ADS)

Tsai, Yuan-Yu

2016-03-01

Secret sharing is a highly relevant research field, and its application to 2D images has been thoroughly studied. However, secret sharing schemes have not kept pace with the advances of 3D models. With the rapid development of 3D multimedia techniques, extending the application of secret sharing schemes to 3D models has become necessary. In this study, an innovative secret 3D model sharing scheme for point geometries based on space subdivision is proposed. Each point in the secret point geometry is first encoded into a series of integer values that fall within [0, p - 1], where p is a predefined prime number. The share values are derived by substituting the specified integer values for all coefficients of the sharing polynomial. The surface reconstruction and the sampling concepts are then integrated to derive a cover model with sufficient model complexity for each participant. Finally, each participant has a separate 3D stego model with embedded share values. Experimental results show that the proposed technique supports reversible data hiding and the share values have higher levels of privacy and improved robustness. This technique is simple and has proven to be a feasible secret 3D model sharing scheme.

Too Big to Be Real? No Depleted Core in Holm 15A

NASA Astrophysics Data System (ADS)

Bonfini, Paolo; Dullo, Bililign T.; Graham, Alister W.

2015-07-01

Partially depleted cores, as measured by core-Sérsic model “break radii,” are typically tens to a few hundred parsecs in size. Here we investigate the unusually large ({R}γ \\prime =0.5 = 4.57 kpc) depleted core recently reported for Holm 15A, the brightest cluster galaxy of Abell 85. We model the one-dimensional (1D) light profile, and also the two-dimensional (2D) image (using Galfit-Corsair, a tool for fitting the core-Sérsic model in 2D). We find good agreement between the 1D and 2D analyses, with minor discrepancies attributable to intrinsic ellipticity gradients. We show that a simple Sérsic profile (with a low index n and no depleted core) plus the known outer exponential “halo” provide a good description of the stellar distribution. We caution that while almost every galaxy light profile will have a radius where the negative logarithmic slope of the intensity profile γ \\prime equals 0.5, this alone does not imply the presence of a partially depleted core within this radius.

Dynamic Paper Constructions for Easier Visualization of Molecular Symmetry

ERIC Educational Resources Information Center

Sein, Lawrence T., Jr.

2010-01-01

A system for construction of simple poster-board models is described. The models dynamically demonstrate the symmetry operations of proper rotation, improper rotation, reflection, and inversion for the chemically important point groups D[subscript 3h], D[subscript 4h], D[subscript 5h], D[subscript 6h], T[subscript d], and O[subscript h]. The…

How do generalized jamming transitions affect collective migration in confluent tissues?

NASA Astrophysics Data System (ADS)

Manning, M. Lisa

Recent experiments have demonstrated that tissues involved in embryonic development, lung function, wound healing, and cancer progression are close to fluid-to-solid, or ``jamming'' transitions. Theoretical models for confluent 2D tissues have also been shown to exhibit continuous rigidity transitions. However, in vivobiological systems can differ in significant ways from the simple 2D models. For example, many tissues are three-dimensional, mechanically heterogeneous, and/or composed of mechanosensitive cells interspersed with extracellular matrix. We have extended existing models for confluent tissues to capture these features, and we find interesting predictions for collective cell motion that are ultimately related to an underlying generalized jamming transition. For example, in 2D, we find that heterogeneous mixtures of cells spontaneously self-organize into rigid regions of stiffer cells interspersed with string-like groups of soft cells, reminiscent of cellular streaming seen in cancer. We also find that alignment interactions (of the sort often explored in self-propelled particle models) alter the transition and generate interesting flocked liquid and flocked solid collective migration patterns. Our model predicts that 3D tissues also exhibit a jamming transition governed by cell shape, as well as history-dependent aging, and we are currently exploring whether ECM-like interactions in 3D models might help explain compressional stiffening seen in experiments on human tissue.

Technical report. The application of probability-generating functions to linear-quadratic radiation survival curves.

PubMed

Kendal, W S

2000-04-01

To illustrate how probability-generating functions (PGFs) can be employed to derive a simple probabilistic model for clonogenic survival after exposure to ionizing irradiation. Both repairable and irreparable radiation damage to DNA were assumed to occur by independent (Poisson) processes, at intensities proportional to the irradiation dose. Also, repairable damage was assumed to be either repaired or further (lethally) injured according to a third (Bernoulli) process, with the probability of lethal conversion being directly proportional to dose. Using the algebra of PGFs, these three processes were combined to yield a composite PGF that described the distribution of lethal DNA lesions in irradiated cells. The composite PGF characterized a Poisson distribution with mean, chiD+betaD2, where D was dose and alpha and beta were radiobiological constants. This distribution yielded the conventional linear-quadratic survival equation. To test the composite model, the derived distribution was used to predict the frequencies of multiple chromosomal aberrations in irradiated human lymphocytes. The predictions agreed well with observation. This probabilistic model was consistent with single-hit mechanisms, but it was not consistent with binary misrepair mechanisms. A stochastic model for radiation survival has been constructed from elementary PGFs that exactly yields the linear-quadratic relationship. This approach can be used to investigate other simple probabilistic survival models.

DCO+, DCN, and N2D+ reveal three different deuteration regimes in the disk around the Herbig Ae star HD 163296

NASA Astrophysics Data System (ADS)

Salinas, V. N.; Hogerheijde, M. R.; Mathews, G. S.; Öberg, K. I.; Qi, C.; Williams, J. P.; Wilner, D. J.

2017-10-01

Context. Deuterium fractionation has been used to study the thermal history of prestellar environments. Their formation pathways trace different regions of the disk and may shed light into the physical structure of the disk, including locations of important features for planetary formation. Aims: We aim to constrain the radial extent of the main deuterated species; we are particularly interested in spatially characterizing the high and low temperature pathways for enhancing deuteration of these species. Methods: We observed the disk surrounding the Herbig Ae star HD 163296 using ALMA in Band 6 and obtained resolved spectral imaging data of DCO+ (J = 3 - 2), DCN (J = 3 - 2) and N2D+ (J = 3 - 2) with synthesized beam sizes of 0.̋53 × 0.̋42, 0.̋53 × 0.̋42, and 0.̋50 × 0.̋39, respectively. We adopted a physical model of the disk from the literature and use the 3D radiative transfer code LIME to estimate an excitation temperature profile for our detected lines. We modeled the radial emission profiles of DCO+, DCN, and N2D+, assuming their emission is optically thin, using a parametric model of their abundances and our excitation temperature estimates. Results: DCO+ can be described by a three-region model with constant-abundance rings centered at 70 AU, 150 AU, and 260 AU. The DCN radial profile peaks at about 60 AU and N2D+ is seen in a ring at 160 AU. Simple models of both molecules using constant abundances reproduce the data. Assuming reasonable average excitation temperatures for the whole disk, their disk-averaged column densities (and deuterium fractionation ratios) are 1.6-2.6×1012 cm-2 (0.04-0.07), 2.9-5.2×1012 cm-2 ( 0.02), and 1.6-2.5×1011 cm-2 (0.34-0.45) for DCO+, DCN, and N2D+, respectively. Conclusions: Our simple best-fit models show a correlation between the radial location of the first two rings in DCO+ and the DCN and N2D+ abundance distributions that can be interpreted as the high and low temperature deuteration pathways regimes. The origin of the third DCO+ ring at 260 AU is unknown but may be due to a local decrease of ultraviolet opacity allowing the photodesorption of CO or due to thermal desorption of CO as a consequence of radial drift and settlement of dust grains. The derived Df values agree with previous estimates of 0.05 for DCO+/HCO+ and 0.02 for DCN/HCN in HD 163296, and 0.3-0.5 for N2D+/N2H+ in AS 209, a T Tauri disk. The high N2D+/N2H+ confirms N2D+ as a good candidate for tracing ionization in the cold outer disk. The reduced images (FITS files) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/606/A125

Computational fluid dynamics analysis of space shuttle main propulsion feed line 17-inch disconnect valves

NASA Technical Reports Server (NTRS)

Kandula, Max; Pearce, Daniel

1989-01-01

A steady incompressible three-dimensional (3-D) viscous flow analysis was conducted for the Space Shuttle Main Propulsion External Tank (ET)/Orbiter (ORB) propellant feed line quick separable 17-inch disconnect flapper valves for liquid oxygen (LO2) and liquid hydrogen (LH2). The main objectives of the analysis were to predict and correlate the hydrodynamic stability of the flappers and pressure drop with available water test data. Computational Fluid Dynamics (CFD) computer codes were procured at no cost from the public domain, and were modified and extended to carry out the disconnect flow analysis. The grid generator codes SVTGD3D and INGRID were obtained. NASA Ames Research Center supplied the flow solution code INS3D, and the color graphics code PLOT3D. A driver routine was developed to automate the grid generation process. Components such as pipes, elbows, and flappers can be generated with simple commands, and flapper angles can be varied easily. The flow solver INS3D code was modified to treat interior flappers, and other interfacing routines were developed, which include a turbulence model, a force/moment routine, a time-step routine, and initial and boundary conditions. In particular, an under-relaxation scheme was implemented to enhance the solution stability. Major physical assumptions and simplifications made in the analysis include the neglect of linkages, slightly reduced flapper diameter, and smooth solid surfaces. A grid size of 54 x 21 x 25 was employed for both the LO2 and LH2 units. Mixing length theory applied to turbulent shear flow in pipes formed the basis for the simple turbulence model. Results of the analysis are presented for LO2 and LH2 disconnects.

A 3D Bioprinted Model for the Study of Premalignant Breast Disease

DTIC Science & Technology

2017-05-01

these glands and performed proof-of-principle 3D printing . We have printed simple ductal structures (tubes) and seeded breast epithelial cells. The...performed proof-of-principle 3D printing . We have printed simple ductal structures (tubes) and seeded breast epithelial cells. The next year we will...All of the PN17 reconstruction data from the 5 completed strains has also been sent to the University of Pittsburg for 3D printing . A summary of the

The evaluation of the average energy parameters for spectra of quasimonoenergetic neutrons produced in (p,n)-reactions on solid tritium targets

NASA Astrophysics Data System (ADS)

Sosnin, A. N.; Shorin, V. S.

1989-10-01

Fast neutron cross-section measurements using quasimonoenergetic (p,n) neutron sources require the determination of the average neutron spectrum parameters such as the mean energy < E> and the variance D. In this paper a simple model has been considered for determining the < E>- andD-values. The approach takes into account the actual layout of the solid tritium target and the irradiated sample. It is valid for targets with a thickness of less than 1 mg/cm 2. It has been shown that the first and the second tritium distribution function moments < x> and < x2> are connected by simple analytical expressions with average characteristics of the neutron yield measured above the (p,n) reaction threshold energy. Our results are compared with accurate calculations for Sc-T targets.

Chemotaxis of C. elegans in 3D media: a model for navigation of undulatory microswimmers

NASA Astrophysics Data System (ADS)

Patel, Amar; Bilbao, Alejandro; Rahman, Mizanur; Vanapalli, Siva; Blawzdziewicz, Jerzy

2017-11-01

While the natural environment of C. elegans consists of complex 3D media (e.g., decomposing organic matter and water), most studies of chemotactic behavior of this nematode are limited to 2D. We present a 3D chemotaxis model that combines a realistic geometrical representation of body movements associated with 3D maneuvers, an analysis of mechanical interactions of the nematode body with the surrounding medium to determine nematode trajectories, and a simple memory-function description of chemosensory apparatus that controls the frequency, magnitude, and timing of turning maneuvers. We show that two main chemotaxis strategies of C. elegans moving in 2D, i.e., the biased random walk and gradual turn, are effective also in 3D, provided that 2D turns are supplemented by the roll maneuvers that enable 3D reorientation. Optimal choices of chemosensing and gait-control parameters are discussed; we show that the nematode can maintain efficient chemotaxis in burrowing and swimming by adjusting the undulation frequency alone, without changing the chemotactic component of the body control. Understanding how C. elegans efficiently navigates in 3D media may help in developing self-navigating artificial microswimmers. Supported by NSF Grant No. CBET 1603627.

Optical identification using imperfections in 2D materials

NASA Astrophysics Data System (ADS)

Cao, Yameng; Robson, Alexander J.; Alharbi, Abdullah; Roberts, Jonathan; Woodhead, Christopher S.; Noori, Yasir J.; Bernardo-Gavito, Ramón; Shahrjerdi, Davood; Roedig, Utz; Fal'ko, Vladimir I.; Young, Robert J.

2017-12-01

The ability to uniquely identify an object or device is important for authentication. Imperfections, locked into structures during fabrication, can be used to provide a fingerprint that is challenging to reproduce. In this paper, we propose a simple optical technique to read unique information from nanometer-scale defects in 2D materials. Imperfections created during crystal growth or fabrication lead to spatial variations in the bandgap of 2D materials that can be characterized through photoluminescence measurements. We show a simple setup involving an angle-adjustable transmission filter, simple optics and a CCD camera can capture spatially-dependent photoluminescence to produce complex maps of unique information from 2D monolayers. Atomic force microscopy is used to verify the origin of the optical signature measured, demonstrating that it results from nanometer-scale imperfections. This solution to optical identification with 2D materials could be employed as a robust security measure to prevent counterfeiting.

The transmissibility estimation of influenza with early stage data of small-scale outbreaks in Changsha, China, 2005-2013.

PubMed

Chen, T M; Chen, Q P; Liu, R C; Szot, A; Chen, S L; Zhao, J; Zhou, S S

2017-02-01

Hundreds of small-scale influenza outbreaks in schools are reported in mainland China every year, leading to a heavy disease burden which seriously impacts the operation of affected schools. Knowing the transmissibility of each outbreak in the early stage has become a major concern for public health policy-makers and primary healthcare providers. In this study, we collected all the small-scale outbreaks in Changsha (a large city in south central China with ~7·04 million population) from January 2005 to December 2013. Four simple and popularly used models were employed to calculate the reproduction number (R) of these outbreaks. Given that the duration of a generation interval Tc = 2·7 and the standard deviation (s.d.) σ = 1·1, the mean R estimated by an epidemic model, normal distribution and delta distribution were 2·51 (s.d. = 0·73), 4·11 (s.d. = 2·20) and 5·88 (s.d. = 5·00), respectively. When Tc = 2·9 and σ = 1·4, the mean R estimated by the three models were 2·62 (s.d. = 0·78), 4·72 (s.d. = 2·82) and 6·86 (s.d. = 6·34), respectively. The mean R estimated by gamma distribution was 4·32 (s.d. = 2·47). We found that the values of R in small-scale outbreaks in schools were higher than in large-scale outbreaks in a neighbourhood, city or province. Normal distribution, delta distribution, and gamma distribution models seem to more easily overestimate the R of influenza outbreaks compared to the epidemic model.

Coherent Anomaly Method Calculation on the Cluster Variation Method. II.

NASA Astrophysics Data System (ADS)

Wada, Koh; Watanabe, Naotosi; Uchida, Tetsuya

The critical exponents of the bond percolation model are calculated in the D(= 2,3,…)-dimensional simple cubic lattice on the basis of Suzuki's coherent anomaly method (CAM) by making use of a series of the pair, the square-cactus and the square approximations of the cluster variation method (CVM) in the s-state Potts model. These simple approximations give reasonable values of critical exponents α, β, γ and ν in comparison with ones estimated by other methods. It is also shown that the results of the pair and the square-cactus approximations can be derived as exact results of the bond percolation model on the Bethe and the square-cactus lattice, respectively, in the presence of ghost field without recourse to the s→1 limit of the s-state Potts model.

Computing the Sensitivity Kernels for 2.5-D Seismic Waveform Inversion in Heterogeneous, Anisotropic Media

NASA Astrophysics Data System (ADS)

Zhou, Bing; Greenhalgh, S. A.

2011-10-01

2.5-D modeling and inversion techniques are much closer to reality than the simple and traditional 2-D seismic wave modeling and inversion. The sensitivity kernels required in full waveform seismic tomographic inversion are the Fréchet derivatives of the displacement vector with respect to the independent anisotropic model parameters of the subsurface. They give the sensitivity of the seismograms to changes in the model parameters. This paper applies two methods, called `the perturbation method' and `the matrix method', to derive the sensitivity kernels for 2.5-D seismic waveform inversion. We show that the two methods yield the same explicit expressions for the Fréchet derivatives using a constant-block model parameterization, and are available for both the line-source (2-D) and the point-source (2.5-D) cases. The method involves two Green's function vectors and their gradients, as well as the derivatives of the elastic modulus tensor with respect to the independent model parameters. The two Green's function vectors are the responses of the displacement vector to the two directed unit vectors located at the source and geophone positions, respectively; they can be generally obtained by numerical methods. The gradients of the Green's function vectors may be approximated in the same manner as the differential computations in the forward modeling. The derivatives of the elastic modulus tensor with respect to the independent model parameters can be obtained analytically, dependent on the class of medium anisotropy. Explicit expressions are given for two special cases—isotropic and tilted transversely isotropic (TTI) media. Numerical examples are given for the latter case, which involves five independent elastic moduli (or Thomsen parameters) plus one angle defining the symmetry axis.

Highly selective deuteration of pharmaceutically relevant nitrogen-containing heterocycles: a flow chemistry approach.

PubMed

Ötvös, Sándor B; Mándity, István M; Fülöp, Ferenc

2011-08-01

A simple and efficient flow-based technique is reported for the catalytic deuteration of several model nitrogen-containing heterocyclic compounds which are important building blocks of pharmacologically active materials. A continuous flow reactor was used in combination with on-demand pressure-controlled electrolytic D(2) production. The D(2) source was D(2)O, the consumption of which was very low. The experimental set-up allows the fine-tuning of pressure, temperature, and flow rate so as to determine the optimal conditions for the deuteration reactions. The described procedure lacks most of the drawbacks of the conventional batch deuteration techniques, and additionally is highly selective and reproducible.

Formation, levitation, and stability of prominences in the magnetized solar atmosphere

NASA Technical Reports Server (NTRS)

Drake, J. F.; Mok, Y.; Van Hoven, G.

1993-01-01

The dynamic formation of prominences in the initial magnetothermal equilibrium and their stability to sideward displacements are investigated focusing on the structure of the 2D solar atmosphere in the presence of coronal arcades or loops. A model based on 2D magnetohydrodynamic equations takes into account gravity, compressible flows, heating, radiation, anisotropic thermal conduction, and coupling to a deep chromosphere. It is found that prominences in simple arcades characterized by magnetic field with significant curvature at the apex are unstable to a lateral displacement.

Revising Hydrology of a Land Surface Model

NASA Astrophysics Data System (ADS)

Le Vine, Nataliya; Butler, Adrian; McIntyre, Neil; Jackson, Christopher

2015-04-01

Land Surface Models (LSMs) are key elements in guiding adaptation to the changing water cycle and the starting points to develop a global hyper-resolution model of the terrestrial water, energy and biogeochemical cycles. However, before this potential is realised, there are some fundamental limitations of LSMs related to how meaningfully hydrological fluxes and stores are represented. An important limitation is the simplistic or non-existent representation of the deep subsurface in LSMs; and another is the lack of connection of LSM parameterisations to relevant hydrological information. In this context, the paper uses a case study of the JULES (Joint UK Land Environmental Simulator) LSM applied to the Kennet region in Southern England. The paper explores the assumptions behind JULES hydrology, adapts the model structure and optimises the coupling with the ZOOMQ3D regional groundwater model. The analysis illustrates how three types of information can be used to improve the model's hydrology: a) observations, b) regionalized information, and c) information from an independent physics-based model. It is found that: 1) coupling to the groundwater model allows realistic simulation of streamflows; 2) a simple dynamic lower boundary improves upon JULES' stationary unit gradient condition; 3) a 1D vertical flow in the unsaturated zone is sufficient; however there is benefit in introducing a simple dual soil moisture retention curve; 4) regionalized information can be used to describe soil spatial heterogeneity. It is concluded that relatively simple refinements to the hydrology of JULES and its parameterisation method can provide a substantial step forward in realising its potential as a high-resolution multi-purpose model.

Prediction Models for Dynamic Demand Response

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aman, Saima; Frincu, Marc; Chelmis, Charalampos

2015-11-02

As Smart Grids move closer to dynamic curtailment programs, Demand Response (DR) events will become necessary not only on fixed time intervals and weekdays predetermined by static policies, but also during changing decision periods and weekends to react to real-time demand signals. Unique challenges arise in this context vis-a-vis demand prediction and curtailment estimation and the transformation of such tasks into an automated, efficient dynamic demand response (D 2R) process. While existing work has concentrated on increasing the accuracy of prediction models for DR, there is a lack of studies for prediction models for D 2R, which we address inmore » this paper. Our first contribution is the formal definition of D 2R, and the description of its challenges and requirements. Our second contribution is a feasibility analysis of very-short-term prediction of electricity consumption for D 2R over a diverse, large-scale dataset that includes both small residential customers and large buildings. Our third, and major contribution is a set of insights into the predictability of electricity consumption in the context of D 2R. Specifically, we focus on prediction models that can operate at a very small data granularity (here 15-min intervals), for both weekdays and weekends - all conditions that characterize scenarios for D 2R. We find that short-term time series and simple averaging models used by Independent Service Operators and utilities achieve superior prediction accuracy. We also observe that workdays are more predictable than weekends and holiday. Also, smaller customers have large variation in consumption and are less predictable than larger buildings. Key implications of our findings are that better models are required for small customers and for non-workdays, both of which are critical for D 2R. Also, prediction models require just few days’ worth of data indicating that small amounts of historical training data can be used to make reliable predictions, simplifying the complexity of big data challenge associated with D 2R.« less

Fibre inflation and α-attractors

NASA Astrophysics Data System (ADS)

Kallosh, Renata; Linde, Andrei; Roest, Diederik; Westphal, Alexander; Yamada, Yusuke

2018-02-01

Fibre inflation is a specific string theory construction based on the Large Volume Scenario that produces an inflationary plateau. We outline its relation to α-attractor models for inflation, with the cosmological sector originating from certain string theory corrections leading to α = 2 and α = 1/2. Above a certain field range, the steepening effect of higher-order corrections leads first to the breakdown of single-field slow-roll and after that to the onset of 2-field dynamics: the overall volume of the extra dimensions starts to participate in the effective dynamics. Finally, we propose effective supergravity models of fibre inflation based on an \\overline{D3} uplift term with a nilpotent superfield. Specific moduli dependent \\overline{D3} induced geometries lead to cosmological fibre models but have in addition a de Sitter minimum exit. These supergravity models motivated by fibre inflation are relatively simple, stabilize the axions and disentangle the Hubble parameter from supersymmetry breaking.

Coherent Anomaly Method Calculation on the Cluster Variation Method. II. Critical Exponents of Bond Percolation Model

NASA Astrophysics Data System (ADS)

Wada, Koh; Watanabe, Naotosi; Uchida, Tetsuya

1991-10-01

The critical exponents of the bond percolation model are calculated in the D(=2, 3, \\cdots)-dimensional simple cubic lattice on the basis of Suzuki’s coherent anomaly method (CAM) by making use of a series of the pair, the square-cactus and the square approximations of the cluster variation method (CVM) in the s-state Potts model. These simple approximations give reasonable values of critical exponents α, β, γ and ν in comparison with ones estimated by other methods. It is also shown that the results of the pair and the square-cactus approximations can be derived as exact results of the bond percolation model on the Bethe and the square-cactus lattice, respectively, in the presence of ghost field without recourse to the s→1 limit of the s-state Potts model.

Transitions between strongly correlated and random steady-states for catalytic CO-oxidation on surfaces at high-pressure

DOE PAGES

Liu, Da -Jiang; Evans, James W.

2015-04-02

We explore simple lattice-gas reaction models for CO-oxidation on 1D and 2D periodic arrays of surface adsorption sites. The models are motivated by studies of CO-oxidation on RuO 2(110) at high-pressures. Although adspecies interactions are neglected, the effective absence of adspecies diffusion results in kinetically-induced spatial correlations. A transition occurs from a random mainly CO-populated steady-state at high CO-partial pressure p CO, to a strongly-correlated near-O-covered steady-state for low p CO as noted. In addition, we identify a second transition to a random near-O-covered steady-state at very low p CO.

Magneto-hydrodynamic modeling of gas discharge switches

NASA Astrophysics Data System (ADS)

Doiphode, P.; Sakthivel, N.; Sarkar, P.; Chaturvedi, S.

2002-12-01

We have performed one-dimensional, time-dependent magneto-hydrodynamic modeling of fast gas-discharge switches. The model has been applied to both high- and low-pressure switches, involving a cylindrical argon-filled cavity. It is assumed that the discharge is initiated in a small channel near the axis of the cylinder. Joule heating in this channel rapidly raises its temperature and pressure. This drives a radial shock wave that heats and ionizes the surrounding low-temperature region, resulting in progressive expansion of the current channel. Our model is able to reproduce this expansion. However, significant difference of detail is observed, as compared with a simple model reported in the literature. In this paper, we present details of our simulations, a comparison with results from the simple model, and a physical interpretation for these differences. This is a first step towards development of a detailed 2-D model for such switches.

A Semimetal Model of the Normal State Susceptibility and Transport Properties of Ba(Fe1-xCox)2As2 Superconductors

NASA Astrophysics Data System (ADS)

Sales, Brian; Sefat, Athena; McGuire, Michael; Mandrus, David

2010-03-01

A simple two-band 3D model of a semimetal is constructed to see which normal state features of the Ba(Fe1-xCox)2As2 superconductors can be qualitatively understood within this framework. The model is able to account in a semiquantitative fashion for the measured magnetic susceptibility, Hall, and Seebeck data, and the low temperature Sommerfeld coefficient for 0

Soft tissue models: easy and inexpensive flexible 3D printing as a help in surgical planning of cardiovascular disorders

NASA Astrophysics Data System (ADS)

Starosolski, Zbigniew; Ezon, David S.; Krishnamurthy, Rajesh; Dodd, Nicholas; Heinle, Jeffrey; Mckenzie, Dean E.; Annapragada, Ananth

2017-03-01

We developed a technology that allows a simple desktop 3D printer with dual extruder to fabricate 3D flexible models of Major AortoPulmonary Collateral Arteries. The study was designed to assess whether the flexible 3D printed models could help during surgical planning phase. Simple FDM 3D printers are inexpensive, versatile in use and easy to maintain, but complications arise when the designed model is complex and has tubular structures with small diameter less than 2mm. The advantages of FDM printers are cost and simplicity of use. We use precisely selected materials to overcome the obstacles listed above. Dual extruder allows to use two different materials while printing, which is especially important in the case of fragile structures like pulmonary vessels and its supporting structures. The latter should not be removed by hand to avoid a truncation of the model. We utilize the water soluble PVA as a supporting structure and Poro-Lay filament for flexible model of AortoPulmonary collateral arteries. Poro-Lay filament is different as compared to all the other flexible ones like polymer-based. Poro-Lay is rigid while printing and this allows printing of structures small in diameter. It achieves flexibility after washing out of printed model with water. It becomes soft in touch and gelatinous. Using both PVA and Poro-Lay gives a huge advantage allowing to wash out the supporting structures and achieve flexibility in one washing operation, saving time and avoiding human error with cleaning the model. We evaluated 6 models for MAPCAS surgical planning study. This approach is also cost-effective - an average cost of materials for print is less than $15; models are printed in facility without any delays. Flexibility of 3D printed models approximate soft tissues properly, mimicking Aortopulmonary collateral arteries. Second utilization models has educational value for both residents and patients' family. Simplification of 3D flexible process could help in other models of soft tissue pathologies like aneurysms, ventricular septal defects and other vascular anomalies.

Holography and quantum states in elliptic de Sitter space

NASA Astrophysics Data System (ADS)

Halpern, Illan F.; Neiman, Yasha

2015-12-01

We outline a program for interpreting the higher-spin dS/CFT model in terms of physics in the causal patch of a dS observer. The proposal is formulated in "elliptic" de Sitter space d{S}_4/{Z}_2 , obtained by identifying antipodal points in dS 4. We discuss recent evidence that the higher-spin model is especially well-suited for this, since the antipodal symmetry of bulk solutions has a simple encoding on the boundary. For context, we test some other (free and interacting) theories for the same property. Next, we analyze the notion of quantum field states in the non-time-orientable d{S}_4/{Z}_2 . We compare the physics seen by different observers, with the outcome depending on whether they share an arrow of time. Finally, we implement the marriage between higher-spin holography and observers in d{S}_4/{Z}_2 , in the limit of free bulk fields. We succeed in deriving an observer's operator algebra and Hamiltonian from the CFT, but not her S-matrix. We speculate on the extension of this to interacting higher-spin theory.

Self-Assembly through Noncovalent Preorganization of Reactants: Explaining the Formation of a Polyfluoroxometalate.

PubMed

Schreiber, Roy E; Avram, Liat; Neumann, Ronny

2018-01-09

High-order elementary reactions in homogeneous solutions involving more than two molecules are statistically improbable and very slow to proceed. They are not generally considered in classical transition-state or collision theories. Yet, rather selective, high-yield product formation is common in self-assembly processes that require many reaction steps. On the basis of recent observations of crystallization as well as reactions in dense phases, it is shown that self-assembly can occur by preorganization of reactants in a noncovalent supramolecular assembly, whereby directing forces can lead to an apparent one-step transformation of multiple reactants. A simple and general kinetic model for multiple reactant transformation in a dense phase that can account for many-bodied transformations was developed. Furthermore, the self-assembly of polyfluoroxometalate anion [H 2 F 6 NaW 18 O 56 ] 7- from simple tungstate Na 2 WO 2 F 4 was demonstrated by using 2D 19 F- 19 F NOESY, 2D 19 F- 19 F COSY NMR spectroscopy, a new 2D 19 F{ 183 W} NMR technique, as well as ESI-MS and diffusion NMR spectroscopy, and the crucial involvement of a supramolecular assembly was found. The deterministic kinetic reaction model explains the reaction in a dense phase and supports the suggested self-assembly mechanism. Reactions in dense phases may be of general importance in understanding other self-assembly reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Failure models for textile composites

NASA Technical Reports Server (NTRS)

Cox, Brian

1995-01-01

The goals of this investigation were to: (1) identify mechanisms of failure and determine how the architecture of reinforcing fibers in 3D woven composites controlled stiffness, strength, strain to failure, work of fracture, notch sensitivity, and fatigue life; and (2) to model composite stiffness, strength, and fatigue life. A total of 11 different angle and orthogonal interlock woven composites were examined. Composite properties depended on the weave architecture, the tow size, and the spatial distributions and strength of geometrical flaws. Simple models were developed for elastic properties, strength, and fatigue life. A more complicated stochastic model, called the 'Binary Model,' was developed for damage tolerance and ultimate failure. These 3D woven composites possessed an extraordinary combination of strength, damage tolerance, and notch insensitivity.

Modeling of the merging of two colliding field reversed configuration plasmoids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Guanqiong; Wang, Xiaoguang; Li, Lulu

2016-06-15

The field reversed configuration (FRC) is one of the candidate plasma targets for the magneto-inertial fusion, and a high temperature FRC can be formed by using the collision-merging technology. Although the merging process and mechanism of FRC are quite complicated, it is thinkable to build a simple model to investigate the macroscopic equilibrium parameters including the density, the temperature and the separatrix volume, which may play an important role in the collision-merging process of FRC. It is quite interesting that the estimates of the related results based on our simple model are in agreement with the simulation results of amore » two-dimensional magneto-hydrodynamic code (MFP-2D), which has being developed by our group since the last couple of years, while these results can qualitatively fit the results of C-2 experiments by Tri-alpha energy company. On the other hand, the simple model can be used to investigate how to increase the density of the merged FRC. It is found that the amplification of the density depends on the poloidal flux-increase factor and the temperature increases with the translation speed of two plasmoids.« less

Automated Generation of 3D Volcanic Gas Plume Models for Geobrowsers

NASA Astrophysics Data System (ADS)

Wright, T. E.; Burton, M.; Pyle, D. M.

2007-12-01

A network of five UV spectrometers on Etna automatically gathers column amounts of SO2 during daylight hours. Near-simultaneous scans from adjacent spectrometers, comprising 210 column amounts in total, are then converted to 2D slices showing the spatial distribution of the gas by tomographic reconstruction. The trajectory of the plume is computed using an automatically-submitted query to NOAA's HYSPLIT Trajectory Model. This also provides local estimates of air temperature, which are used to determine the atmospheric stability and therefore the degree to which the plume is dispersed by turbulence. This information is sufficient to construct an animated sequence of models which show how the plume is advected and diffused over time. These models are automatically generated in the Collada Digital Asset Exchange format and combined into a single file which displays the evolution of the plume in Google Earth. These models are useful for visualising and predicting the shape and distribution of the plume for civil defence, to assist field campaigns and as a means of communicating some of the work of volcano observatories to the public. The Simultaneous Algebraic Reconstruction Technique is used to create the 2D slices. This is a well-known method, based on iteratively updating a forward model (from 2D distribution to column amounts). Because it is based on a forward model, it also provides a simple way to quantify errors.

Strain memory of 2D and 3D rigid inclusion populations in viscous flows - What is clast SPO telling us?

NASA Astrophysics Data System (ADS)

Stahr, Donald W.; Law, Richard D.

2014-11-01

We model the development of shape preferred orientation (SPO) of a large population of two- and three-dimensional (2D and 3D) rigid clasts suspended in a linear viscous matrix deformed by superposed steady and continuously non-steady plane strain flows to investigate the sensitivity of clasts to changing boundary conditions during a single or superposed deformation events. Resultant clast SPOs are compared to one developed by an identical initial population that experienced a steady flow history of constant kinematic vorticity and reached an identical finite strain state, allowing examination of SPO sensitivity to deformation path. Rotation paths of individual triaxial inclusions are complex, even for steady plane strain flow histories. It has been suggested that the 3D nature of the system renders predictions based on 2D models inadequate for applied clast-based kinematic vorticity gauges. We demonstrate that for a large population of clasts, simplification to a 2D model does provide a good approximation to the SPO predicted by full 3D analysis for steady and non-steady plane strain deformation paths. Predictions of shape fabric development from 2D models are not only qualitatively similar to the more complex 3D analysis, but they display the same limitations of techniques based on clast SPO commonly used as a quantitative kinematic vorticity gauge. Our model results from steady, superposed, and non-steady flow histories with a significant pure shearing component at a wide range of finite strain resemble predictions for an identical initial population that experienced a single steady simple shearing deformation. We conclude that individual 2D and 3D clasts respond instantaneously to changes in boundary conditions, however, in aggregate, the SPO of a population of rigid inclusions does not reflect the late-stage kinematics of deformation, nor is it an indicator of the unique 'mean' kinematic vorticity experienced by a deformed rock volume.

B decays in an asymmetric left-right model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frank, Mariana; Hayreter, Alper; Turan, Ismail

2010-08-01

Motivated by recently observed disagreements with the standard model predictions in B decays, we study b{yields}d, s transitions in an asymmetric class of SU(2){sub L}xSU(2){sub R}xU(1){sub B-L} models, with a simple one-parameter structure of the right-handed mixing matrix for the quarks, which obeys the constraints from kaon physics. We use experimental constraints on the branching ratios of b{yields}s{gamma}, b{yields}ce{nu}{sub e}, and B{sub d,s}{sup 0}-B{sub d,s}{sup 0} mixing to restrict the parameters of the model: g{sub R}/g{sub L}, M{sub W{sub 2}}, M{sub H}{sup {+-}}, tan{beta} as well as the elements of the right-handed quark mixing matrix V{sub CKM}{sup R}. We presentmore » a comparison with the more commonly used (manifest) left-right symmetric model. Our analysis exposes the parameters most sensitive to b transitions and reveals a large parameter space where left- and right-handed quarks mix differently, opening the possibility of observing marked differences in behavior between the standard model and the left-right model.« less

Interactive graphic editing tools in bioluminescent imaging simulation

NASA Astrophysics Data System (ADS)

Li, Hui; Tian, Jie; Luo, Jie; Wang, Ge; Cong, Wenxiang

2005-04-01

It is a challenging task to accurately describe complicated biological tissues and bioluminescent sources in bioluminescent imaging simulation. Several graphic editing tools have been developed to efficiently model each part of the bioluminescent simulation environment and to interactively correct or improve the initial models of anatomical structures or bioluminescent sources. There are two major types of graphic editing tools: non-interactive tools and interactive tools. Geometric building blocks (i.e. regular geometric graphics and superquadrics) are applied as non-interactive tools. To a certain extent, complicated anatomical structures and bioluminescent sources can be approximately modeled by combining a sufficient large number of geometric building blocks with Boolean operators. However, those models are too simple to describe the local features and fine changes in 2D/3D irregular contours. Therefore, interactive graphic editing tools have been developed to facilitate the local modifications of any initial surface model. With initial models composed of geometric building blocks, interactive spline mode is applied to conveniently perform dragging and compressing operations on 2D/3D local surface of biological tissues and bioluminescent sources inside the region/volume of interest. Several applications of the interactive graphic editing tools will be presented in this article.

Investigation of unsteadiness in Shock-particle cloud interaction: Fully resolved two-dimensional simulation and one-dimensional modeling

NASA Astrophysics Data System (ADS)

Hosseinzadeh-Nik, Zahra; Regele, Jonathan D.

2015-11-01

Dense compressible particle-laden flow, which has a complex nature, exists in various engineering applications. Shock waves impacting a particle cloud is a canonical problem to investigate this type of flow. It has been demonstrated that large flow unsteadiness is generated inside the particle cloud from the flow induced by the shock passage. It is desirable to develop models for the Reynolds stress to capture the energy contained in vortical structures so that volume-averaged models with point particles can be simulated accurately. However, the previous work used Euler equations, which makes the prediction of vorticity generation and propagation innacurate. In this work, a fully resolved two dimensional (2D) simulation using the compressible Navier-Stokes equations with a volume penalization method to model the particles has been performed with the parallel adaptive wavelet-collocation method. The results still show large unsteadiness inside and downstream of the particle cloud. A 1D model is created for the unclosed terms based upon these 2D results. The 1D model uses a two-phase simple low dissipation AUSM scheme (TSLAU) developed by coupled with the compressible two phase kinetic energy equation.

Ab initio optimization principle for the ground states of translationally invariant strongly correlated quantum lattice models.

PubMed

Ran, Shi-Ju

2016-05-01

In this work, a simple and fundamental numeric scheme dubbed as ab initio optimization principle (AOP) is proposed for the ground states of translational invariant strongly correlated quantum lattice models. The idea is to transform a nondeterministic-polynomial-hard ground-state simulation with infinite degrees of freedom into a single optimization problem of a local function with finite number of physical and ancillary degrees of freedom. This work contributes mainly in the following aspects: (1) AOP provides a simple and efficient scheme to simulate the ground state by solving a local optimization problem. Its solution contains two kinds of boundary states, one of which play the role of the entanglement bath that mimics the interactions between a supercell and the infinite environment, and the other gives the ground state in a tensor network (TN) form. (2) In the sense of TN, a novel decomposition named as tensor ring decomposition (TRD) is proposed to implement AOP. Instead of following the contraction-truncation scheme used by many existing TN-based algorithms, TRD solves the contraction of a uniform TN in an opposite way by encoding the contraction in a set of self-consistent equations that automatically reconstruct the whole TN, making the simulation simple and unified; (3) AOP inherits and develops the ideas of different well-established methods, including the density matrix renormalization group (DMRG), infinite time-evolving block decimation (iTEBD), network contractor dynamics, density matrix embedding theory, etc., providing a unified perspective that is previously missing in this fields. (4) AOP as well as TRD give novel implications to existing TN-based algorithms: A modified iTEBD is suggested and the two-dimensional (2D) AOP is argued to be an intrinsic 2D extension of DMRG that is based on infinite projected entangled pair state. This paper is focused on one-dimensional quantum models to present AOP. The benchmark is given on a transverse Ising chain and 2D classical Ising model, showing the remarkable efficiency and accuracy of the AOP.

Irreparable complex DNA double-strand breaks induce chromosome breakage in organotypic three-dimensional human lung epithelial cell culture

PubMed Central

Asaithamby, Aroumougame; Hu, Burong; Delgado, Oliver; Ding, Liang-Hao; Story, Michael D.; Minna, John D.; Shay, Jerry W.; Chen, David J.

2011-01-01

DNA damage and consequent mutations initiate the multistep carcinogenic process. Differentiated cells have a reduced capacity to repair DNA lesions, but the biological impact of unrepaired DNA lesions in differentiated lung epithelial cells is unclear. Here, we used a novel organotypic human lung three-dimensional (3D) model to investigate the biological significance of unrepaired DNA lesions in differentiated lung epithelial cells. We showed, consistent with existing notions that the kinetics of loss of simple double-strand breaks (DSBs) were significantly reduced in organotypic 3D culture compared to kinetics of repair in two-dimensional (2D) culture. Strikingly, we found that, unlike simple DSBs, a majority of complex DNA lesions were irreparable in organotypic 3D culture. Levels of expression of multiple DNA damage repair pathway genes were significantly reduced in the organotypic 3D culture compared with those in 2D culture providing molecular evidence for the defective DNA damage repair in organotypic culture. Further, when differentiated cells with unrepaired DNA lesions re-entered the cell cycle, they manifested a spectrum of gross-chromosomal aberrations in mitosis. Our data suggest that downregulation of multiple DNA repair pathway genes in differentiated cells renders them vulnerable to DSBs, promoting genome instability that may lead to carcinogenesis. PMID:21421565

Canopy-Forming Seaweeds in Urchin-Dominated Systems in Eastern Canada: Structuring Forces or Simple Prey for Keystone Grazers?

PubMed Central

Blain, Caitlin; Gagnon, Patrick

2014-01-01

Models of benthic community dynamics for the extensively studied, shallow rocky ecosystems in eastern Canada emphasize kelp-urchin interactions. These models may bias the perception of factors and processes that structure communities, for they largely overlook the possible contribution of other seaweeds to ecosystem resilience. We examined the persistence of the annual, acidic (H2SO4), brown seaweed Desmarestia viridis in urchin barrens at two sites in Newfoundland (Canada) throughout an entire growth season (February to October). We also compared changes in epifaunal assemblages in D. viridis and other conspicuous canopy-forming seaweeds, the non-acidic conspecific Desmarestia aculeata and kelp Agarum clathratum. We show that D. viridis can form large canopies within the 2-to-8 m depth range that represent a transient community state termed “Desmarestia bed”. The annual resurgence of Desmarestia beds and continuous occurrence of D. aculeata and A. clathratum, create biological structure for major recruitment pulses in invertebrate and fish assemblages (e.g. from quasi-absent gastropods to >150 000 recruits kg−1 D. viridis). Many of these pulses phase with temperature-driven mass release of acid to the environment and die-off in D. viridis. We demonstrate experimentally that the chemical makeup of D. viridis and A. clathratum helps retard urchin grazing compared to D. aculeata and the highly consumed kelp Alaria esculenta. In light of our findings and related studies, we propose fundamental changes to the study of community shifts in shallow, rocky ecosystems in eastern Canada. In particular, we advocate the need to regard certain canopy-forming seaweeds as structuring forces interfering with top-down processes, rather than simple prey for keystone grazers. We also propose a novel, empirical model of ecological interactions for D. viridis. Overall, our study underscores the importance of studying organisms together with cross-scale environmental variability to better understand the factors and processes that shape marine communities. PMID:24859311

Simple models for the simulation of submarine melt for a Greenland glacial system model

NASA Astrophysics Data System (ADS)

Beckmann, Johanna; Perrette, Mahé; Ganopolski, Andrey

2018-01-01

Two hundred marine-terminating Greenland outlet glaciers deliver more than half of the annually accumulated ice into the ocean and have played an important role in the Greenland ice sheet mass loss observed since the mid-1990s. Submarine melt may play a crucial role in the mass balance and position of the grounding line of these outlet glaciers. As the ocean warms, it is expected that submarine melt will increase, potentially driving outlet glaciers retreat and contributing to sea level rise. Projections of the future contribution of outlet glaciers to sea level rise are hampered by the necessity to use models with extremely high resolution of the order of a few hundred meters. That requirement in not only demanded when modeling outlet glaciers as a stand alone model but also when coupling them with high-resolution 3-D ocean models. In addition, fjord bathymetry data are mostly missing or inaccurate (errors of several hundreds of meters), which questions the benefit of using computationally expensive 3-D models for future predictions. Here we propose an alternative approach built on the use of a computationally efficient simple model of submarine melt based on turbulent plume theory. We show that such a simple model is in reasonable agreement with several available modeling studies. We performed a suite of experiments to analyze sensitivity of these simple models to model parameters and climate characteristics. We found that the computationally cheap plume model demonstrates qualitatively similar behavior as 3-D general circulation models. To match results of the 3-D models in a quantitative manner, a scaling factor of the order of 1 is needed for the plume models. We applied this approach to model submarine melt for six representative Greenland glaciers and found that the application of a line plume can produce submarine melt compatible with observational data. Our results show that the line plume model is more appropriate than the cone plume model for simulating the average submarine melting of real glaciers in Greenland.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Youkhana, Adel H.; Ogoshi, Richard M.; Kiniry, James R.

Biomass is a promising renewable energy option that provides a more environmentally sustainable alternative to fossil resources by reducing the net flux of greenhouse gasses to the atmosphere. Yet, allometric models that allow the prediction of aboveground biomass (AGB), biomass carbon (C) stock non-destructively have not yet been developed for tropical perennial C 4 grasses currently under consideration as potential bioenergy feedstock in Hawaii and other subtropical and tropical locations. The objectives of this study were to develop optimal allometric relationships and site-specific models to predict AGB, biomass C stock of napiergrass, energycane, and sugarcane under cultivation practices for renewablemore » energy and validate these site-specific models against independent data sets generated from sites with widely different environments. Several allometric models were developed for each species from data at a low elevation field on the island of Maui, Hawaii. A simple power model with stalk diameter (D) was best related to AGB and biomass C stock for napiergrass, energycane, and sugarcane, (R 2 = 0.98, 0.96, and 0.97, respectively). The models were then tested against data collected from independent fields across an environmental gradient. For all crops, the models over-predicted AGB in plants with lower stalk D, but AGB was under-predicted in plants with higher stalk D. The models using stalk D were better for biomass prediction compared to dewlap H (Height from the base cut to most recently exposed leaf dewlap) models, which showed weak validation performance. Although stalk D model performed better, however, the mean square error (MSE)-systematic was ranged from 23 to 43 % of MSE for all crops. A strong relationship between model coefficient and rainfall was existed, although these were irrigated systems; suggesting a simple site-specific coefficient modulator for rainfall to reduce systematic errors in water-limited areas. These allometric equations provide a tool for farmers in the tropics to estimate perennial C4 grass biomass and C stock during decision-making for land management and as an environmental sustainability indicator within a renewable energy system.« less

Simple inflationary quintessential model. II. Power law potentials

NASA Astrophysics Data System (ADS)

de Haro, Jaume; Amorós, Jaume; Pan, Supriya

2016-09-01

The present work is a sequel of our previous work [Phys. Rev. D 93, 084018 (2016)] which depicted a simple version of an inflationary quintessential model whose inflationary stage was described by a Higgs-type potential and the quintessential phase was responsible due to an exponential potential. Additionally, the model predicted a nonsingular universe in past which was geodesically past incomplete. Further, it was also found that the model is in agreement with the Planck 2013 data when running is allowed. But, this model provides a theoretical value of the running which is far smaller than the central value of the best fit in ns , r , αs≡d ns/d l n k parameter space where ns, r , αs respectively denote the spectral index, tensor-to-scalar ratio and the running of the spectral index associated with any inflationary model, and consequently to analyze the viability of the model one has to focus in the two-dimensional marginalized confidence level in the allowed domain of the plane (ns,r ) without taking into account the running. Unfortunately, such analysis shows that this model does not pass this test. However, in this sequel we propose a family of models runs by a single parameter α ∈[0 ,1 ] which proposes another "inflationary quintessential model" where the inflation and the quintessence regimes are respectively described by a power law potential and a cosmological constant. The model is also nonsingular although geodesically past incomplete as in the cited model. Moreover, the present one is found to be more simple compared to the previous model and it is in excellent agreement with the observational data. In fact, we note that, unlike the previous model, a large number of the models of this family with α ∈[0 ,1/2 ) match with both Planck 2013 and Planck 2015 data without allowing the running. Thus, the properties in the current family of models compared to its past companion justify its need for a better cosmological model with the successive improvement of the observational data.

A surprisingly complex aqueous chemistry of the simplest amino acid. A pulse radiolysis and theoretical study on H/D kinetic isotope effects in the reaction of glycine anions with hydroxyl radicals.

PubMed

Stefanić, I; Ljubić, I; Bonifacić, M; Sabljić, A; Asmus, K-D; Armstrong, D A

2009-04-07

A pulse radiolysis study was carried out of the reaction rate constants and kinetic isotope effects of hydroxyl-radical-induced H/D abstraction from the most-simple alpha-amino acid glycine in its anionic form in water. The rate constants and yields of three predominantly formed radical products, glycyl (NH2-*CH-CO2-), aminomethyl (NH2-*CH2), and aminyl (*NH-CH2-CO2-) radicals, as well as of their partially or fully deuterated analogs, were found to be of comparable magnitude. The primary, secondary, and primary/secondary H/D kinetic isotope effects on the rate constants were determined with respect to each of the three radicals. The unusual variety of products for such an elementary reaction between two small and simple species indicates a complex mechanism with several reactions taking place simultaneously. Thus, a theoretical modeling of the reaction mechanism and kinetics in the gas- and aqueous phase was performed by using the unrestricted density functional theory with the BB1K functional (employing the polarizable continuum model for the aqueous phase), unrestricted coupled cluster UCCSD(T) method, and improved canonical variational theory. Several hydrogen-bonded prereaction complexes and transition states were detected. In particular, the calculations pointed to a significant mechanistic role of the three-electron two-orbital (sigma/sigma* N therefore O) hemibonded prereaction complexes in the aqueous phase. A good agreement with the experimental rate constants and kinetic isotope effects was achieved by downshifting the calculated reaction barriers by 3 kcal mol(-1) and damping the NH(D) stretching frequency by a factor of 0.86.

Three Dimensional (3D) Printing: A Straightforward, User-Friendly Protocol to Convert Virtual Chemical Models to Real-Life Objects

ERIC Educational Resources Information Center

Rossi, Sergio; Benaglia, Maurizio; Brenna, Davide; Porta, Riccardo; Orlandi, Manuel

2015-01-01

A simple procedure to convert protein data bank files (.pdb) into a stereolithography file (.stl) using VMD software (Virtual Molecular Dynamic) is reported. This tutorial allows generating, with a very simple protocol, three-dimensional customized structures that can be printed by a low-cost 3D-printer, and used for teaching chemical education…

The vertical variability of hyporheic fluxes inferred from riverbed temperature data

NASA Astrophysics Data System (ADS)

Cranswick, Roger H.; Cook, Peter G.; Shanafield, Margaret; Lamontagne, Sebastien

2014-05-01

We present detailed profiles of vertical water flux from the surface to 1.2 m beneath the Haughton River in the tropical northeast of Australia. A 1-D numerical model is used to estimate vertical flux based on raw temperature time series observations from within downwelling, upwelling, neutral, and convergent sections of the hyporheic zone. A Monte Carlo analysis is used to derive error bounds for the fluxes based on temperature measurement error and uncertainty in effective thermal diffusivity. Vertical fluxes ranged from 5.7 m d-1 (downward) to -0.2 m d-1 (upward) with the lowest relative errors for values between 0.3 and 6 m d-1. Our 1-D approach provides a useful alternative to 1-D analytical and other solutions because it does not incorporate errors associated with simplified boundary conditions or assumptions of purely vertical flow, hydraulic parameter values, or hydraulic conditions. To validate the ability of this 1-D approach to represent the vertical fluxes of 2-D flow fields, we compare our model with two simple 2-D flow fields using a commercial numerical model. These comparisons showed that: (1) the 1-D vertical flux was equivalent to the mean vertical component of flux irrespective of a changing horizontal flux; and (2) the subsurface temperature data inherently has a "spatial footprint" when the vertical flux profiles vary spatially. Thus, the mean vertical flux within a 2-D flow field can be estimated accurately without requiring the flow to be purely vertical. The temperature-derived 1-D vertical flux represents the integrated vertical component of flux along the flow path intersecting the observation point. This article was corrected on 6 JUN 2014. See the end of the full text for details.

Positive Psychological Interventions for Patients with Type 2 Diabetes: Rationale, Theoretical Model, and Intervention Development

PubMed Central

Huffman, Jeff C.; DuBois, Christina M.; Millstein, Rachel A.; Celano, Christopher M.; Wexler, Deborah

2015-01-01

Most patients with type 2 diabetes (T2D) have suboptimal adherence to recommended diet, physical activity, and/or medication. Current approaches to improve health behaviors in T2D have been variably effective, and successful interventions are often complex and intensive. It is therefore vital to develop interventions that are simple, well-accepted, and applicable to a wide range of patients who suffer from T2D. One approach may be to boost positive psychological states, such as positive affect or optimism, as these constructs have been prospectively and independently linked to improvements in health behaviors. Positive psychology (PP) interventions, which utilize systematic exercises to increase optimism, well-being, and positive affect, consistently increase positive states and are easily delivered to patients with chronic illnesses. However, to our knowledge, PP interventions have not been formally tested in T2D. In this paper, we review a theoretical model for the use of PP interventions to target health behaviors in T2D, describe the structure and content of a PP intervention for T2D patients, and describe baseline data from a single-arm proof-of-concept (N = 15) intervention study in T2D patients with or without depression. We also discuss how PP interventions could be combined with motivational interviewing (MI) interventions to provide a blended psychological-behavioral approach. PMID:26064980

Critical space-time networks and geometric phase transitions from frustrated edge antiferromagnetism

NASA Astrophysics Data System (ADS)

Trugenberger, Carlo A.

2015-12-01

Recently I proposed a simple dynamical network model for discrete space-time that self-organizes as a graph with Hausdorff dimension dH=4 . The model has a geometric quantum phase transition with disorder parameter (dH-ds) , where ds is the spectral dimension of the dynamical graph. Self-organization in this network model is based on a competition between a ferromagnetic Ising model for vertices and an antiferromagnetic Ising model for edges. In this paper I solve a toy version of this model defined on a bipartite graph in the mean-field approximation. I show that the geometric phase transition corresponds exactly to the antiferromagnetic transition for edges, the dimensional disorder parameter of the former being mapped to the staggered magnetization order parameter of the latter. The model has a critical point with long-range correlations between edges, where a continuum random geometry can be defined, exactly as in Kazakov's famed 2D random lattice Ising model but now in any number of dimensions.

A statistical approach to estimate the 3D size distribution of spheres from 2D size distributions

USGS Publications Warehouse

Kong, M.; Bhattacharya, R.N.; James, C.; Basu, A.

2005-01-01

Size distribution of rigidly embedded spheres in a groundmass is usually determined from measurements of the radii of the two-dimensional (2D) circular cross sections of the spheres in random flat planes of a sample, such as in thin sections or polished slabs. Several methods have been devised to find a simple factor to convert the mean of such 2D size distributions to the actual 3D mean size of the spheres without a consensus. We derive an entirely theoretical solution based on well-established probability laws and not constrained by limitations of absolute size, which indicates that the ratio of the means of measured 2D and estimated 3D grain size distribution should be r/4 (=.785). Actual 2D size distribution of the radii of submicron sized, pure Fe0 globules in lunar agglutinitic glass, determined from backscattered electron images, is tested to fit the gamma size distribution model better than the log-normal model. Numerical analysis of 2D size distributions of Fe0 globules in 9 lunar soils shows that the average mean of 2D/3D ratio is 0.84, which is very close to the theoretical value. These results converge with the ratio 0.8 that Hughes (1978) determined for millimeter-sized chondrules from empirical measurements. We recommend that a factor of 1.273 (reciprocal of 0.785) be used to convert the determined 2D mean size (radius or diameter) of a population of spheres to estimate their actual 3D size. ?? 2005 Geological Society of America.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tokola, Ryan A; Mikkilineni, Aravind K; Boehnen, Chris Bensing

Despite being increasingly easy to acquire, 3D data is rarely used for face-based biometrics applications beyond identification. Recent work in image-based demographic biometrics has enjoyed much success, but these approaches suffer from the well-known limitations of 2D representations, particularly variations in illumination, texture, and pose, as well as a fundamental inability to describe 3D shape. This paper shows that simple 3D shape features in a face-based coordinate system are capable of representing many biometric attributes without problem-specific models or specialized domain knowledge. The same feature vector achieves impressive results for problems as diverse as age estimation, gender classification, and racemore » classification.« less

A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes.

PubMed

Ovchinnikov, Victor; Nam, Kwangho; Karplus, Martin

2016-08-25

A method is developed to obtain simultaneously free energy profiles and diffusion constants from restrained molecular simulations in diffusive systems. The method is based on low-order expansions of the free energy and diffusivity as functions of the reaction coordinate. These expansions lead to simple analytical relationships between simulation statistics and model parameters. The method is tested on 1D and 2D model systems; its accuracy is found to be comparable to or better than that of the existing alternatives, which are briefly discussed. An important aspect of the method is that the free energy is constructed by integrating its derivatives, which can be computed without need for overlapping sampling windows. The implementation of the method in any molecular simulation program that supports external umbrella potentials (e.g., CHARMM) requires modification of only a few lines of code. As a demonstration of its applicability to realistic biomolecular systems, the method is applied to model the α-helix ↔ β-sheet transition in a 16-residue peptide in implicit solvent, with the reaction coordinate provided by the string method. Possible modifications of the method are briefly discussed; they include generalization to multidimensional reaction coordinates [in the spirit of the model of Ermak and McCammon (Ermak, D. L.; McCammon, J. A. J. Chem. Phys. 1978, 69, 1352-1360)], a higher-order expansion of the free energy surface, applicability in nonequilibrium systems, and a simple test for Markovianity. In view of the small overhead of the method relative to standard umbrella sampling, we suggest its routine application in the cases where umbrella potential simulations are appropriate.

Identifying mechanisms for superdiffusive dynamics in cell trajectories

NASA Astrophysics Data System (ADS)

Passucci, Giuseppe; Brasch, Megan; Henderson, James; Manning, M. Lisa

Self-propelled particle (SPP) models have been used to explore features of active matter such as motility-induced phase separation, jamming, and flocking, and are often used to model biological cells. However, many cells exhibit super-diffusive trajectories, where displacements scale faster than t 1 / 2 in all directions, and these are not captured by traditional SPP models. We extract cell trajectories from image stacks of mouse fibroblast cells moving on 2D substrates and find super-diffusive mean-squared displacements in all directions across varying densities. Two SPP model modifications have been proposed to capture super-diffusive dynamics: Levy walks and heterogeneous motility parameters. In mouse fibroblast cells displacement probability distributions collapse when time is rescaled by a power greater than 1/2, which is consistent with Levy walks. We show that a simple SPP model with heterogeneous rotational noise can also generate a similar collapse. Furthermore, a close examination of statistics extracted directly from cell trajectories is consistent with a heterogeneous mobility SPP model and inconsistent with a Levy walk model. Our work demonstrates that a simple set of analyses can distinguish between mechanisms for anomalous diffusion in active matter.

Isotope effect in acetylene C2H2 and C2D2 rotations on Cu(001)

NASA Astrophysics Data System (ADS)

Shchadilova, Yulia E.; Tikhodeev, Sergei G.; Paulsson, Magnus; Ueba, Hiromu

2014-04-01

A comprehensive analysis of the elementary processes behind the scanning tunneling microscope controlled rotation of C2H2 and C2D2, isotopologues of a single acetylene molecule adsorbed on the Cu(001) surface, is given, with a focus on the isotope effects. With the help of density-functional theory we calculate the vibrational modes of C2H2 and C2D2 on Cu(001) and estimate the anharmonic couplings between them, using a simple strings-on-rods model. The probability of the elementary processes, nonlinear and combination band, is estimated using the Keldysh diagram technique. This allows us to clarify the main peculiarities and the isotope effects of the C2H2 and C2D2 on Cu(001) rotation, discovered in the pioneering work [B. C. Stipe et al., Phys. Rev. Lett. 81, 1263 (1998), 10.1103/PhysRevLett.81.1263], which have not been previously understood.

From Heuristic to Mathematical Modeling of Drugs Dissolution Profiles: Application of Artificial Neural Networks and Genetic Programming

PubMed Central

Mendyk, Aleksander; Güres, Sinan; Szlęk, Jakub; Wiśniowska, Barbara; Kleinebudde, Peter

2015-01-01

The purpose of this work was to develop a mathematical model of the drug dissolution (Q) from the solid lipid extrudates based on the empirical approach. Artificial neural networks (ANNs) and genetic programming (GP) tools were used. Sensitivity analysis of ANNs provided reduction of the original input vector. GP allowed creation of the mathematical equation in two major approaches: (1) direct modeling of Q versus extrudate diameter (d) and the time variable (t) and (2) indirect modeling through Weibull equation. ANNs provided also information about minimum achievable generalization error and the way to enhance the original dataset used for adjustment of the equations' parameters. Two inputs were found important for the drug dissolution: d and t. The extrudates length (L) was found not important. Both GP modeling approaches allowed creation of relatively simple equations with their predictive performance comparable to the ANNs (root mean squared error (RMSE) from 2.19 to 2.33). The direct mode of GP modeling of Q versus d and t resulted in the most robust model. The idea of how to combine ANNs and GP in order to escape ANNs' black-box drawback without losing their superior predictive performance was demonstrated. Open Source software was used to deliver the state-of-the-art models and modeling strategies. PMID:26101544

From Heuristic to Mathematical Modeling of Drugs Dissolution Profiles: Application of Artificial Neural Networks and Genetic Programming.

PubMed

Mendyk, Aleksander; Güres, Sinan; Jachowicz, Renata; Szlęk, Jakub; Polak, Sebastian; Wiśniowska, Barbara; Kleinebudde, Peter

2015-01-01

The purpose of this work was to develop a mathematical model of the drug dissolution (Q) from the solid lipid extrudates based on the empirical approach. Artificial neural networks (ANNs) and genetic programming (GP) tools were used. Sensitivity analysis of ANNs provided reduction of the original input vector. GP allowed creation of the mathematical equation in two major approaches: (1) direct modeling of Q versus extrudate diameter (d) and the time variable (t) and (2) indirect modeling through Weibull equation. ANNs provided also information about minimum achievable generalization error and the way to enhance the original dataset used for adjustment of the equations' parameters. Two inputs were found important for the drug dissolution: d and t. The extrudates length (L) was found not important. Both GP modeling approaches allowed creation of relatively simple equations with their predictive performance comparable to the ANNs (root mean squared error (RMSE) from 2.19 to 2.33). The direct mode of GP modeling of Q versus d and t resulted in the most robust model. The idea of how to combine ANNs and GP in order to escape ANNs' black-box drawback without losing their superior predictive performance was demonstrated. Open Source software was used to deliver the state-of-the-art models and modeling strategies.

Micro 3D printing using a digital projector and its application in the study of soft materials mechanics.

PubMed

Lee, Howon; Fang, Nicholas X

2012-11-27

Buckling is a classical topic in mechanics. While buckling has long been studied as one of the major structural failure modes(1), it has recently drawn new attention as a unique mechanism for pattern transformation. Nature is full of such examples where a wealth of exotic patterns are formed through mechanical instability(2-5). Inspired by this elegant mechanism, many studies have demonstrated creation and transformation of patterns using soft materials such as elastomers and hydrogels(6-11). Swelling gels are of particular interest because they can spontaneously trigger mechanical instability to create various patterns without the need of external force(6-10). Recently, we have reported demonstration of full control over buckling pattern of micro-scaled tubular gels using projection micro-stereolithography (PμSL), a three-dimensional (3D) manufacturing technology capable of rapidly converting computer generated 3D models into physical objects at high resolution(12,13). Here we present a simple method to build up a simplified PμSL system using a commercially available digital data projector to study swelling-induced buckling instability for controlled pattern transformation. A simple desktop 3D printer is built using an off-the-shelf digital data projector and simple optical components such as a convex lens and a mirror(14). Cross-sectional images extracted from a 3D solid model is projected on the photosensitive resin surface in sequence, polymerizing liquid resin into a desired 3D solid structure in a layer-by-layer fashion. Even with this simple configuration and easy process, arbitrary 3D objects can be readily fabricated with sub-100 μm resolution. This desktop 3D printer holds potential in the study of soft material mechanics by offering a great opportunity to explore various 3D geometries. We use this system to fabricate tubular shaped hydrogel structure with different dimensions. Fixed on the bottom to the substrate, the tubular gel develops inhomogeneous stress during swelling, which gives rise to buckling instability. Various wavy patterns appear along the circumference of the tube when the gel structures undergo buckling. Experiment shows that circumferential buckling of desired mode can be created in a controlled manner. Pattern transformation of three-dimensionally structured tubular gels has significant implication not only in mechanics and material science, but also in many other emerging fields such as tunable matamaterials.

SIMPL: A Simplified Model-Based Program for the Analysis and Visualization of Groundwater Rebound in Abandoned Mines to Prevent Contamination of Water and Soils by Acid Mine Drainage

PubMed Central

Kim, Sung-Min

2018-01-01

Cessation of dewatering following underground mine closure typically results in groundwater rebound, because mine voids and surrounding strata undergo flooding up to the levels of the decant points, such as shafts and drifts. SIMPL (Simplified groundwater program In Mine workings using the Pipe equation and Lumped parameter model), a simplified lumped parameter model-based program for predicting groundwater levels in abandoned mines, is presented herein. The program comprises a simulation engine module, 3D visualization module, and graphical user interface, which aids data processing, analysis, and visualization of results. The 3D viewer facilitates effective visualization of the predicted groundwater level rebound phenomenon together with a topographic map, mine drift, goaf, and geological properties from borehole data. SIMPL is applied to data from the Dongwon coal mine and Dalsung copper mine in Korea, with strong similarities in simulated and observed results. By considering mine workings and interpond connections, SIMPL can thus be used to effectively analyze and visualize groundwater rebound. In addition, the predictions by SIMPL can be utilized to prevent the surrounding environment (water and soil) from being polluted by acid mine drainage. PMID:29747480

A distance constrained synaptic plasticity model of C. elegans neuronal network

NASA Astrophysics Data System (ADS)

Badhwar, Rahul; Bagler, Ganesh

2017-03-01

Brain research has been driven by enquiry for principles of brain structure organization and its control mechanisms. The neuronal wiring map of C. elegans, the only complete connectome available till date, presents an incredible opportunity to learn basic governing principles that drive structure and function of its neuronal architecture. Despite its apparently simple nervous system, C. elegans is known to possess complex functions. The nervous system forms an important underlying framework which specifies phenotypic features associated to sensation, movement, conditioning and memory. In this study, with the help of graph theoretical models, we investigated the C. elegans neuronal network to identify network features that are critical for its control. The 'driver neurons' are associated with important biological functions such as reproduction, signalling processes and anatomical structural development. We created 1D and 2D network models of C. elegans neuronal system to probe the role of features that confer controllability and small world nature. The simple 1D ring model is critically poised for the number of feed forward motifs, neuronal clustering and characteristic path-length in response to synaptic rewiring, indicating optimal rewiring. Using empirically observed distance constraint in the neuronal network as a guiding principle, we created a distance constrained synaptic plasticity model that simultaneously explains small world nature, saturation of feed forward motifs as well as observed number of driver neurons. The distance constrained model suggests optimum long distance synaptic connections as a key feature specifying control of the network.

A new model to estimate insulin resistance via clinical parameters in adults with type 1 diabetes.

PubMed

Zheng, Xueying; Huang, Bin; Luo, Sihui; Yang, Daizhi; Bao, Wei; Li, Jin; Yao, Bin; Weng, Jianping; Yan, Jinhua

2017-05-01

Insulin resistance (IR) is a risk factor to assess the development of micro- and macro-vascular complications in type 1 diabetes (T1D). However, diabetes management in adults with T1D is limited by the difficulty of lacking simple and reliable methods to estimate insulin resistance. The aim of this study was to develop a new model to estimate IR via clinical parameters in adults with T1D. A total of 36 adults with adulthood onset T1D (n = 20) or childhood onset T1D (n = 16) were recruited by quota sampling. After an overnight insulin infusion to stabilize the blood glucose at 5.6 to 7.8 mmol/L, they underwent a 180-minute euglycemic-hyperinsulinemic clamp. Glucose disposal rate (GDR, mg kg -1  min -1 ) was calculated by data collected from the last 30 minutes during the test. Demographic factors (age, sex, and diabetes duration) and metabolic parameters (blood pressure, glycated hemoglobin A 1c [HbA 1c ], waist to hip ratio [WHR], and lipids) were collected to evaluate insulin resistance. Then, age at diabetes onset and clinical parameters were used to develop a model to estimate lnGDR by stepwise linear regression. From the stepwise process, a best model to estimate insulin resistance was generated, including HbA 1c , diastolic blood pressure, and WHR. Age at diabetes onset did not enter any of the models. We proposed the following new model to estimate IR as in GDR for adults with T1D: lnGDR = 4.964 - 0.121 × HbA 1c (%) - 0.012 × diastolic blood pressure (mmHg) - 1.409 × WHR, (adjusted R 2  = 0.616, P < .01). Insulin resistance in adults living with T1D can be estimated using routinely collected clinical parameters. This simple model provides a potential tool for estimating IR in large-scale epidemiological studies of adults with T1D regardless of age at onset. Copyright © 2016 John Wiley & Sons, Ltd.

Energy levels and exchange interactions of spin clusters

NASA Astrophysics Data System (ADS)

Belorizky, E.

1993-02-01

We first describe a simple method for diagonalizing the isotropic exchange Hamiltonian of a cluster of N spins in the most general case where all the exchange constants are different. The technique, based on the rotation invariance of the system, leads to a considerable reduction of the total matrix. Simple expressions of the magnetization and susceptibility are provided and an example of the determination of the exchange constants of a complex with five Cu^{2+} ions is given. It is also shown that for a large variety of spin configurations occuring in metal complexes, it is possible to diagonalize the dominant isotropic exchange spin hamiltonian in a straightforward way by using recoupling techniques. This allows to solve problems up to a nine spin cluster with spins having different g values. This survey is pursued by the theoretical approach of the magnetic properties of interacting spins on a finite ring with a detailed study of an oligonuclear metal nitroxide complex formed by six Mn^{2+}(S = 5/2) and six free radicals (s = 1/2). The temperature behaviour of the susceptibility is interpreted with a semi-classical model of a cyclic alternate finite chain. Finally we give a procedure for determining the three exchange constants of three spin 1/2 coupled by isotropic exchange constants in the unsolved case where these constants are all dilferent. Nous décrivons d'abord une méthode simple pour diagonaliser l'Hamiltonien d'échange isotrope d'un cluster de N spins dans le cas le plus général où toutes les constantes d'échange sont différentes. La technique, basée sur l'invariance rotationnelle du système, conduit à une réduction considérable de la matrice totale. On donne des expressions simples de l'aimantation et de la susceptibilité et la méthode est appliquée à la détermination des interactions d'échange d'un complexe comprenant cinq ions Cu^{2+}. On montre également que pour une assez grande variété de configurations de spins présentes dans les complexes métalliques, on peut résoudre l'Hamiltonien de spin d'échange isotrope dominant de manière directe par des techniques de recouplage. Ceci permet de traiter des clusters jusqu'à neuf spins, ces derniers pouvant avoir des facteurs g différents. Nous poursuivons cette revue par une étude théorique des propriétés magnétiques de spins en interaction sur un anneau avec une étude détaillée d'un complexe oligonucléaire métal-nitroxyde formé de six ions Mn^{2+}(S = 5/2) et de six radicaux libres (s = 1/2). Le comportement en fonction de la température de la susceptibilité est interprété à l'aide d'un modèle semi-classique de chaine alternée cyclique. Enfin, nous donnons un procédé pour déterminer les trois constantes d'échange d'un système de trois spins 1/2 couplés par échange isotrope dans le cas non résolu où ces trois constantes sont toutes différentes.

A Simple Plasma Retinol Isotope Ratio Method for Estimating β-Carotene Relative Bioefficacy in Humans: Validation with the Use of Model-Based Compartmental Analysis.

PubMed

Ford, Jennifer Lynn; Green, Joanne Balmer; Lietz, Georg; Oxley, Anthony; Green, Michael H

2017-09-01

Background: Provitamin A carotenoids are an important source of dietary vitamin A for many populations. Thus, accurate and simple methods for estimating carotenoid bioefficacy are needed to evaluate the vitamin A value of test solutions and plant sources. β-Carotene bioefficacy is often estimated from the ratio of the areas under plasma isotope response curves after subjects ingest labeled β-carotene and a labeled retinyl acetate reference dose [isotope reference method (IRM)], but to our knowledge, the method has not yet been evaluated for accuracy. Objectives: Our objectives were to develop and test a physiologically based compartmental model that includes both absorptive and postabsorptive β-carotene bioconversion and to use the model to evaluate the accuracy of the IRM and a simple plasma retinol isotope ratio [(RIR), labeled β-carotene-derived retinol/labeled reference-dose-derived retinol in one plasma sample] for estimating relative bioefficacy. Methods: We used model-based compartmental analysis (Simulation, Analysis and Modeling software) to develop and apply a model that provided known values for β-carotene bioefficacy. Theoretical data for 10 subjects were generated by the model and used to determine bioefficacy by RIR and IRM; predictions were compared with known values. We also applied RIR and IRM to previously published data. Results: Plasma RIR accurately predicted β-carotene relative bioefficacy at 14 d or later. IRM also accurately predicted bioefficacy by 14 d, except that, when there was substantial postabsorptive bioconversion, IRM underestimated bioefficacy. Based on our model, 1-d predictions of relative bioefficacy include absorptive plus a portion of early postabsorptive conversion. Conclusion: The plasma RIR is a simple tracer method that accurately predicts β-carotene relative bioefficacy based on analysis of one blood sample obtained at ≥14 d after co-ingestion of labeled β-carotene and retinyl acetate. The method also provides information about the contributions of absorptive and postabsorptive conversion to total bioefficacy if an additional sample is taken at 1 d. © 2017 American Society for Nutrition.

Modeling a surface-mounted Lamb wave emission-reception system: applications to structural health monitoring.

PubMed

Moulin, Emmanuel; Grondel, Sébastien; Assaad, Jamal; Duquenne, Laurent

2008-12-01

The work described in this paper is intended to present a simple and efficient way of modeling a full Lamb wave emission and reception system. The emitter behavior and the Lamb wave generation are predicted using a two-dimensional (2D) hybrid finite element-normal mode expansion model. Then the receiver electrical response is obtained from a finite element computation with prescribed displacements. A numerical correction is applied to the 2D results in order to account for the in-plane radiation divergence caused by the finite length of the emitter. The advantage of this modular approach is that realistic configurations can be simulated without performing cumbersome modeling and time-consuming computations. It also provides insight into the physical interpretation of the results. A good agreement is obtained between predicted and measured signals. The range of application of the method is discussed.

Modeling and numerical analysis of a magneto-inertial fusion concept with the target created through FRC merging

NASA Astrophysics Data System (ADS)

Li, Chenguang; Yang, Xianjun

2016-10-01

The Magnetized Plasma Fusion Reactor concept is proposed as a magneto-inertial fusion approach based on the target plasma created through the collision merging of two oppositely translating field reversed configuration plasmas, which is then compressed by the imploding liner driven by the pulsed-power driver. The target creation process is described by a two-dimensional magnetohydrodynamics model, resulting in the typical target parameters. The implosion process and the fusion reaction are modeled by a simple zero-dimensional model, taking into account the alpha particle heating and the bremsstrahlung radiation loss. The compression on the target can be 2D cylindrical or 2.4D with the additive axial contraction taken into account. The dynamics of the liner compression and fusion burning are simulated and the optimum fusion gain and the associated target parameters are predicted. The scientific breakeven could be achieved at the optimized conditions.

3D abnormal behavior recognition in power generation

NASA Astrophysics Data System (ADS)

Wei, Zhenhua; Li, Xuesen; Su, Jie; Lin, Jie

2011-06-01

So far most research of human behavior recognition focus on simple individual behavior, such as wave, crouch, jump and bend. This paper will focus on abnormal behavior with objects carrying in power generation. Such as using mobile communication device in main control room, taking helmet off during working and lying down in high place. Taking account of the color and shape are fixed, we adopted edge detecting by color tracking to recognize object in worker. This paper introduces a method, which using geometric character of skeleton and its angle to express sequence of three-dimensional human behavior data. Then adopting Semi-join critical step Hidden Markov Model, weighing probability of critical steps' output to reduce the computational complexity. Training model for every behavior, mean while select some skeleton frames from 3D behavior sample to form a critical step set. This set is a bridge linking 2D observation behavior with 3D human joints feature. The 3D reconstruction is not required during the 2D behavior recognition phase. In the beginning of recognition progress, finding the best match for every frame of 2D observed sample in 3D skeleton set. After that, 2D observed skeleton frames sample will be identified as a specifically 3D behavior by behavior-classifier. The effectiveness of the proposed algorithm is demonstrated with experiments in similar power generation environment.

The Phyre2 web portal for protein modelling, prediction and analysis

PubMed Central

Kelley, Lawrence A; Mezulis, Stefans; Yates, Christopher M; Wass, Mark N; Sternberg, Michael JE

2017-01-01

Summary Phyre2 is a suite of tools available on the web to predict and analyse protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a protocol. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyse the effect of amino-acid variants (e.g. nsSNPs) for a user’s protein sequence. Users are guided through results by a simple interface at a level of detail determined by them. This protocol will guide a user from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30mins and 2 hours after submission. PMID:25950237

Projecting 2D gene expression data into 3D and 4D space.

PubMed

Gerth, Victor E; Katsuyama, Kaori; Snyder, Kevin A; Bowes, Jeff B; Kitayama, Atsushi; Ueno, Naoto; Vize, Peter D

2007-04-01

Video games typically generate virtual 3D objects by texture mapping an image onto a 3D polygonal frame. The feeling of movement is then achieved by mathematically simulating camera movement relative to the polygonal frame. We have built customized scripts that adapt video game authoring software to texture mapping images of gene expression data onto b-spline based embryo models. This approach, known as UV mapping, associates two-dimensional (U and V) coordinates within images to the three dimensions (X, Y, and Z) of a b-spline model. B-spline model frameworks were built either from confocal data or de novo extracted from 2D images, once again using video game authoring approaches. This system was then used to build 3D models of 182 genes expressed in developing Xenopus embryos and to implement these in a web-accessible database. Models can be viewed via simple Internet browsers and utilize openGL hardware acceleration via a Shockwave plugin. Not only does this database display static data in a dynamic and scalable manner, the UV mapping system also serves as a method to align different images to a common framework, an approach that may make high-throughput automated comparisons of gene expression patterns possible. Finally, video game systems also have elegant methods for handling movement, allowing biomechanical algorithms to drive the animation of models. With further development, these biomechanical techniques offer practical methods for generating virtual embryos that recapitulate morphogenesis.

Three-dimensional computer simulation of radiostereometric analysis (RSA) in distal radius fractures.

PubMed

Madanat, Rami; Moritz, Niko; Aro, Hannu T

2007-01-01

Physical phantom models have conventionally been used to determine the accuracy and precision of radiostereometric analysis (RSA) in various orthopaedic applications. Using a phantom model of a fracture of the distal radius it has previously been shown that RSA is a highly accurate and precise method for measuring both translation and rotation in three-dimensions (3-D). The main shortcoming of a physical phantom model is its inability to mimic complex 3-D motion. The goal of this study was to create a realistic computer model for preoperative planning of RSA studies and to test the accuracy of RSA in measuring complex movements in fractures of the distal radius using this new model. The 3-D computer model was created from a set of tomographic scans. The simulation of the radiographic imaging was performed using ray-tracing software (POV-Ray). RSA measurements were performed according to standard protocol. Using a two-part fracture model (AO/ASIF type A2), it was found that for simple movements in one axis, translations in the range of 25microm-2mm could be measured with an accuracy of +/-2microm. Rotations ranging from 16 degrees to 2 degrees could be measured with an accuracy of +/-0.015 degrees . Using a three-part fracture model the corresponding values of accuracy were found to be +/-4microm and +/-0.031 degrees for translation and rotation, respectively. For complex 3-D motion in a three-part fracture model (AO/ASIF type C1) the accuracy was +/-6microm for translation and +/-0.120 degrees for rotation. The use of 3-D computer modelling can provide a method for preoperative planning of RSA studies in complex fractures of the distal radius and in other clinical situations in which the RSA method is applicable.

Study of Magnetic Damping Effect on Convection and Solidification Under G-Jitter Conditions

NASA Technical Reports Server (NTRS)

Li, Ben Q.; deGroh, H. C., III

1999-01-01

As shown by NASA resources dedicated to measuring residual gravity (SAMS and OARE systems), g-jitter is a critical issue affecting space experiments on solidification processing of materials. This study aims to provide, through extensive numerical simulations and ground based experiments, an assessment of the use of magnetic fields in combination with microgravity to reduce the g-jitter induced convective flows in space processing systems. We have so far completed asymptotic analyses based on the analytical solutions for g-jitter driven flow and magnetic field damping effects for a simple one-dimensional parallel plate configuration, and developed both 2-D and 3-D numerical models for g-jitter driven flows in simple solidification systems with and without presence of an applied magnetic field. Numerical models have been checked with the analytical solutions and have been applied to simulate the convective flows and mass transfer using both synthetic g-jitter functions and the g-jitter data taken from space flight. Some useful findings have been obtained from the analyses and the modeling results. Some key points may be summarized as follows: (1) the amplitude of the oscillating velocity decreases at a rate inversely proportional to the g-jitter frequency and with an increase in the applied magnetic field; (2) the induced flow approximately oscillates at the same frequency as the affecting g-jitter, but out of a phase angle; (3) the phase angle is a complicated function of geometry, applied magnetic field, temperature gradient and frequency; (4) g-jitter driven flows exhibit a complex fluid flow pattern evolving in time; (5) the damping effect is more effective for low frequency flows; and (6) the applied magnetic field helps to reduce the variation of solutal distribution along the solid-liquid interface. Work in progress includes numerical simulations and ground-based measurements. Both 2-D and 3-D numerical simulations are being continued to obtain further information on g-jitter driven flows and magnetic field effects. A physical model for ground-based measurements is completed and some measurements of the oscillating convection are being taken on the physical model. The comparison of the measurements with numerical simulations is in progress. Additional work planned in the project will also involve extending the 2-D numerical model to include the solidification phenomena with the presence of both g-jitter and magnetic fields.

The Simple View of Reading as a Framework for National Literacy Initiatives: A Hierarchical Model of Pupil-Level and Classroom-Level Factors

ERIC Educational Resources Information Center

Savage, Robert; Burgos, Giovani; Wood, Eileen; Piquette, Noella

2015-01-01

The Simple View of Reading (SVR) describes Reading Comprehension as the product of distinct child-level variance in decoding (D) and linguistic comprehension (LC) component abilities. When used as a model for educational policy, distinct classroom-level influences of each of the components of the SVR model have been assumed, but have not yet been…

Exploring gravitational lensing model variations in the Frontier Fields galaxy clusters

NASA Astrophysics Data System (ADS)

Harris James, Nicholas John; Raney, Catie; Brennan, Sean; Keeton, Charles

2018-01-01

Multiple groups have been working on modeling the mass distributions of the six lensing galaxy clusters in the Hubble Space Telescope Frontier Fields data set. The magnification maps produced from these mass models will be important for the future study of the lensed background galaxies, but there exists significant variation in the different groups’ models and magnification maps. We explore the use of two-dimensional histograms as a tool for visualizing these magnification map variations. Using a number of simple, one- or two-halo singular isothermal sphere models, we explore the features that are produced in 2D histogram model comparisons when parameters such as halo mass, ellipticity, and location are allowed to vary. Our analysis demonstrates the potential of 2D histograms as a means of observing the full range of differences between the Frontier Fields groups’ models.This work has been supported by funding from National Science Foundation grants PHY-1560077 and AST-1211385, and from the Space Telescope Science Institute.

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Kurkcuoglu, Zeynep; Koukos, Panagiotis I.; Citro, Nevia; Trellet, Mikael E.; Rodrigues, J. P. G. L. M.; Moreira, Irina S.; Roel-Touris, Jorge; Melquiond, Adrien S. J.; Geng, Cunliang; Schaarschmidt, Jörg; Xue, Li C.; Vangone, Anna; Bonvin, A. M. J. J.

2018-01-01

We present the performance of HADDOCK, our information-driven docking software, in the second edition of the D3R Grand Challenge. In this blind experiment, participants were requested to predict the structures and binding affinities of complexes between the Farnesoid X nuclear receptor and 102 different ligands. The models obtained in Stage1 with HADDOCK and ligand-specific protocol show an average ligand RMSD of 5.1 Å from the crystal structure. Only 6/35 targets were within 2.5 Å RMSD from the reference, which prompted us to investigate the limiting factors and revise our protocol for Stage2. The choice of the receptor conformation appeared to have the strongest influence on the results. Our Stage2 models were of higher quality (13 out of 35 were within 2.5 Å), with an average RMSD of 4.1 Å. The docking protocol was applied to all 102 ligands to generate poses for binding affinity prediction. We developed a modified version of our contact-based binding affinity predictor PRODIGY, using the number of interatomic contacts classified by their type and the intermolecular electrostatic energy. This simple structure-based binding affinity predictor shows a Kendall's Tau correlation of 0.37 in ranking the ligands (7th best out of 77 methods, 5th/25 groups). Those results were obtained from the average prediction over the top10 poses, irrespective of their similarity/correctness, underscoring the robustness of our simple predictor. This results in an enrichment factor of 2.5 compared to a random predictor for ranking ligands within the top 25%, making it a promising approach to identify lead compounds in virtual screening.

A device that operates within a self-assembled 3D DNA crystal

NASA Astrophysics Data System (ADS)

Hao, Yudong; Kristiansen, Martin; Sha, Ruojie; Birktoft, Jens J.; Hernandez, Carina; Mao, Chengde; Seeman, Nadrian C.

2017-08-01

Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

Scaling laws between population and facility densities.

PubMed

Um, Jaegon; Son, Seung-Woo; Lee, Sung-Ik; Jeong, Hawoong; Kim, Beom Jun

2009-08-25

When a new facility like a grocery store, a school, or a fire station is planned, its location should ideally be determined by the necessities of people who live nearby. Empirically, it has been found that there exists a positive correlation between facility and population densities. In the present work, we investigate the ideal relation between the population and the facility densities within the framework of an economic mechanism governing microdynamics. In previous studies based on the global optimization of facility positions in minimizing the overall travel distance between people and facilities, it was shown that the density of facility D and that of population rho should follow a simple power law D approximately rho(2/3). In our empirical analysis, on the other hand, the power-law exponent alpha in D approximately rho(alpha) is not a fixed value but spreads in a broad range depending on facility types. To explain this discrepancy in alpha, we propose a model based on economic mechanisms that mimic the competitive balance between the profit of the facilities and the social opportunity cost for populations. Through our simple, microscopically driven model, we show that commercial facilities driven by the profit of the facilities have alpha = 1, whereas public facilities driven by the social opportunity cost have alpha = 2/3. We simulate this model to find the optimal positions of facilities on a real U.S. map and show that the results are consistent with the empirical data.

Semi-classical approach to compute RABBITT traces in multi-dimensional complex field distributions.

PubMed

Lucchini, M; Ludwig, A; Kasmi, L; Gallmann, L; Keller, U

2015-04-06

We present a semi-classical model to calculate RABBITT (Reconstruction of Attosecond Beating By Interference of Two-photon Transitions) traces in the presence of a reference infrared field with a complex two-dimensional (2D) spatial distribution. The evolution of the electron spectra as a function of the pump-probe delay is evaluated starting from the solution of the classical equation of motion and incorporating the quantum phase acquired by the electron during the interaction with the infrared field. The total response to an attosecond pulse train is then evaluated by a coherent sum of the contributions generated by each individual attosecond pulse in the train. The flexibility of this model makes it possible to calculate spectrograms from non-trivial 2D field distributions. After confirming the validity of the model in a simple 1D case, we extend the discussion to describe the probe-induced phase in photo-emission experiments on an ideal metallic surface.

Geology on a Sand Budget

ERIC Educational Resources Information Center

Kane, Jacqueline

2004-01-01

Earth science teachers know how frustrating it can be to spend hundreds of dollars on three-dimensional (3-D) models of Earth's geologic features, to use the models for only a few class periods. To avoid emptying an already limited science budget, the author states that teachers can use a simple alternative to the expensive 3-D models--sand. She…

The role of extra-foveal processing in 3D imaging

NASA Astrophysics Data System (ADS)

Eckstein, Miguel P.; Lago, Miguel A.; Abbey, Craig K.

2017-03-01

The field of medical image quality has relied on the assumption that metrics of image quality for simple visual detection tasks are a reliable proxy for the more clinically realistic visual search tasks. Rank order of signal detectability across conditions often generalizes from detection to search tasks. Here, we argue that search in 3D images represents a paradigm shift in medical imaging: radiologists typically cannot exhaustively scrutinize all regions of interest with the high acuity fovea requiring detection of signals with extra-foveal areas (visual periphery) of the human retina. We hypothesize that extra-foveal processing can alter the detectability of certain types of signals in medical images with important implications for search in 3D medical images. We compare visual search of two different types of signals in 2D vs. 3D images. We show that a small microcalcification-like signal is more highly detectable than a larger mass-like signal in 2D search, but its detectability largely decreases (relative to the larger signal) in the 3D search task. Utilizing measurements of observer detectability as a function retinal eccentricity and observer eye fixations we can predict the pattern of results in the 2D and 3D search studies. Our findings: 1) suggest that observer performance findings with 2D search might not always generalize to 3D search; 2) motivate the development of a new family of model observers that take into account the inhomogeneous visual processing across the retina (foveated model observers).

Direct Measurements of Oxygen Gradients in Spheroid Culture System Using Electron Parametric Resonance Oximetry

PubMed Central

Langan, Laura M.; Dodd, Nicholas J. F.; Owen, Stewart F.; Purcell, Wendy M.; Jackson, Simon K.; Jha, Awadhesh N.

2016-01-01

Advanced in vitro culture from tissues of different origin includes three-dimensional (3D) organoid micro structures that may mimic conditions in vivo. One example of simple 3D culture is spheroids; ball shaped structures typically used as liver and tumour models. Oxygen is critically important in physiological processes, but is difficult to quantify in 3D culture: and the question arises, how small does a spheroid have to be to have minimal micro-environment formation? This question is of particular importance in the growing field of 3D based models for toxicological assessment. Here, we describe a simple non-invasive approach modified for the quantitative measurement and subsequent evaluation of oxygen gradients in spheroids developed from a non-malignant fish cell line (i.e. RTG-2 cells) using Electron Paramagnetic Resonance (EPR) oximetry. Sonication of the paramagnetic probe Lithium phthalocyanine (LiPc) allows for incorporation of probe particulates into spheroid during its formation. Spectra signal strength after incorporation of probe into spheroid indicated that a volume of 20 μl of probe (stock solution: 0.10 mg/mL) is sufficient to provide a strong spectra across a range of spheroid sizes. The addition of non-toxic probes (that do not produce or consume oxygen) report on oxygen diffusion throughout the spheroid as a function of size. We provide evidence supporting the use of this model over a range of initial cell seeding densities and spheroid sizes with the production of oxygen distribution as a function of these parameters. In our spheroid model, lower cell seeding densities (∼2,500 cells/spheroid) and absolute size (118±32 μm) allow control of factors such as pre-existing stresses (e.g. ∼ 2% normoxic/hypoxic interface) for more accurate measurement of treatment response. The applied methodology provides an elegant, widely applicable approach to directly characterize spheroid (and other organoid) cultures in biomedical and toxicological research. PMID:26900704

Direct Measurements of Oxygen Gradients in Spheroid Culture System Using Electron Parametric Resonance Oximetry.

PubMed

Langan, Laura M; Dodd, Nicholas J F; Owen, Stewart F; Purcell, Wendy M; Jackson, Simon K; Jha, Awadhesh N

2016-01-01

Advanced in vitro culture from tissues of different origin includes three-dimensional (3D) organoid micro structures that may mimic conditions in vivo. One example of simple 3D culture is spheroids; ball shaped structures typically used as liver and tumour models. Oxygen is critically important in physiological processes, but is difficult to quantify in 3D culture: and the question arises, how small does a spheroid have to be to have minimal micro-environment formation? This question is of particular importance in the growing field of 3D based models for toxicological assessment. Here, we describe a simple non-invasive approach modified for the quantitative measurement and subsequent evaluation of oxygen gradients in spheroids developed from a non-malignant fish cell line (i.e. RTG-2 cells) using Electron Paramagnetic Resonance (EPR) oximetry. Sonication of the paramagnetic probe Lithium phthalocyanine (LiPc) allows for incorporation of probe particulates into spheroid during its formation. Spectra signal strength after incorporation of probe into spheroid indicated that a volume of 20 μl of probe (stock solution: 0.10 mg/mL) is sufficient to provide a strong spectra across a range of spheroid sizes. The addition of non-toxic probes (that do not produce or consume oxygen) report on oxygen diffusion throughout the spheroid as a function of size. We provide evidence supporting the use of this model over a range of initial cell seeding densities and spheroid sizes with the production of oxygen distribution as a function of these parameters. In our spheroid model, lower cell seeding densities (∼2,500 cells/spheroid) and absolute size (118±32 μm) allow control of factors such as pre-existing stresses (e.g. ∼ 2% normoxic/hypoxic interface) for more accurate measurement of treatment response. The applied methodology provides an elegant, widely applicable approach to directly characterize spheroid (and other organoid) cultures in biomedical and toxicological research.

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

PubMed

Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

2011-07-01

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

SU-F-T-285: Evaluation of a Patient DVH-Based IMRT QA System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhen, H; Redler, G; Chu, J

2016-06-15

Purpose: To evaluate the clinical performance of a patient DVH-based QA system for prostate VMAT QA. Methods: Mobius3D(M3D) is a QA software with an independent beam model and dose engine. The MobiusFX(MFX) add-on predicts patient dose using treatment machine log files. We commissioned the Mobius beam model in two steps. First, the stock beam model was customized using machine commissioning data, then verified against the TPS with 12 simple phantom plans and 7 clinical 3D plans. Secondly, the Dosimetric Leaf Gap(DLG) in the Mobius model was fine-tuned for VMAT treatment based on ion chamber measurements for 6 clinical VMAT plans.more » Upon successful commissioning, we retrospectively performed IMRT QA for 12 VMAT plans with the Mobius system as well as the ArcCHECK-3DVH system. Selected patient DVH values (PTV D95, D50; Bladder D2cc, Dmean; Rectum D2cc) were compared between TPS, M3D, MFX, and 3DVH. Results: During the first commissioning step, TPS and M3D calculated target Dmean for 3D plans agree within 0.7%±0.7%, with 3D gamma passing rates of 98%±2%. In the second commissioning step, the Mobius DLG was adjusted by 1.2mm from the stock value, reducing the average difference between MFX calculation and ion chamber measurement from 3.2% to 0.1%. In retrospective prostate VMAT QA, 5 of 60 MFX calculated DVH values have a deviation greater than 5% compared to TPS. One large deviation at high dose level was identified as a potential QA failure. This echoes the 3DVH QA result, which identified 2 instances of large DVH deviation on the same structure. For all DVH’s evaluated, M3D and MFX show high level of agreement (0.1%±0.2%), indicating that the observed deviation is likely from beam modelling differences rather than delivery errors. Conclusion: Mobius system provides a viable solution for DVH based VMAT QA, with the capability of separating TPS and delivery errors.« less

A Simple Physical Model for Spall from Nuclear Explosions Based Upon Two-Dimensional Nonlinear Numerical Simulations

DTIC Science & Technology

1990-05-01

forms included (1) analytic distribu- tions of initial velocities which initiate at the same instant across the crack ( t o is con - stant), (2) random...gAH(O,tl) + (19) [jLVgf (Vg)- gMo (vg ,V2 )]AH(t1l,t2) We note that for any distribution d)(v), the high frequency response will be dominated by the 8...body waves from the tension crack model is a narrowband signal. To see this, consider Equation (25). As w-O, P (co) approaches a constant pro

DAVIS: A direct algorithm for velocity-map imaging system

NASA Astrophysics Data System (ADS)

Harrison, G. R.; Vaughan, J. C.; Hidle, B.; Laurent, G. M.

2018-05-01

In this work, we report a direct (non-iterative) algorithm to reconstruct the three-dimensional (3D) momentum-space picture of any charged particles collected with a velocity-map imaging system from the two-dimensional (2D) projected image captured by a position-sensitive detector. The method consists of fitting the measured image with the 2D projection of a model 3D velocity distribution defined by the physics of the light-matter interaction. The meaningful angle-correlated information is first extracted from the raw data by expanding the image with a complete set of Legendre polynomials. Both the particle's angular and energy distributions are then directly retrieved from the expansion coefficients. The algorithm is simple, easy to implement, fast, and explicitly takes into account the pixelization effect in the measurement.

GEO2D - Two-Dimensional Computer Model of a Ground Source Heat Pump System

DOE Data Explorer

James Menart

2013-06-07

This file contains a zipped file that contains many files required to run GEO2D. GEO2D is a computer code for simulating ground source heat pump (GSHP) systems in two-dimensions. GEO2D performs a detailed finite difference simulation of the heat transfer occurring within the working fluid, the tube wall, the grout, and the ground. Both horizontal and vertical wells can be simulated with this program, but it should be noted that the vertical wall is modeled as a single tube. This program also models the heat pump in conjunction with the heat transfer occurring. GEO2D simulates the heat pump and ground loop as a system. Many results are produced by GEO2D as a function of time and position, such as heat transfer rates, temperatures and heat pump performance. On top of this information from an economic comparison between the geothermal system simulated and a comparable air heat pump systems or a comparable gas, oil or propane heating systems with a vapor compression air conditioner. The version of GEO2D in the attached file has been coupled to the DOE heating and cooling load software called ENERGYPLUS. This is a great convenience for the user because heating and cooling loads are an input to GEO2D. GEO2D is a user friendly program that uses a graphical user interface for inputs and outputs. These make entering data simple and they produce many plotted results that are easy to understand. In order to run GEO2D access to MATLAB is required. If this program is not available on your computer you can download the program MCRInstaller.exe, the 64 bit version, from the MATLAB website or from this geothermal depository. This is a free download which will enable you to run GEO2D..

A comparison of numerical and machine-learning modeling of soil water content with limited input data

NASA Astrophysics Data System (ADS)

Karandish, Fatemeh; Šimůnek, Jiří

2016-12-01

Soil water content (SWC) is a key factor in optimizing the usage of water resources in agriculture since it provides information to make an accurate estimation of crop water demand. Methods for predicting SWC that have simple data requirements are needed to achieve an optimal irrigation schedule, especially for various water-saving irrigation strategies that are required to resolve both food and water security issues under conditions of water shortages. Thus, a two-year field investigation was carried out to provide a dataset to compare the effectiveness of HYDRUS-2D, a physically-based numerical model, with various machine-learning models, including Multiple Linear Regressions (MLR), Adaptive Neuro-Fuzzy Inference Systems (ANFIS), and Support Vector Machines (SVM), for simulating time series of SWC data under water stress conditions. SWC was monitored using TDRs during the maize growing seasons of 2010 and 2011. Eight combinations of six, simple, independent parameters, including pan evaporation and average air temperature as atmospheric parameters, cumulative growth degree days (cGDD) and crop coefficient (Kc) as crop factors, and water deficit (WD) and irrigation depth (In) as crop stress factors, were adopted for the estimation of SWCs in the machine-learning models. Having Root Mean Square Errors (RMSE) in the range of 0.54-2.07 mm, HYDRUS-2D ranked first for the SWC estimation, while the ANFIS and SVM models with input datasets of cGDD, Kc, WD and In ranked next with RMSEs ranging from 1.27 to 1.9 mm and mean bias errors of -0.07 to 0.27 mm, respectively. However, the MLR models did not perform well for SWC forecasting, mainly due to non-linear changes of SWCs under the irrigation process. The results demonstrated that despite requiring only simple input data, the ANFIS and SVM models could be favorably used for SWC predictions under water stress conditions, especially when there is a lack of data. However, process-based numerical models are undoubtedly a better choice for predicting SWCs with lower uncertainties when required data are available, and thus for designing water saving strategies for agriculture and for other environmental applications requiring estimates of SWCs.

A simple and accurate rule-based modeling framework for simulation of autocrine/paracrine stimulation of glioblastoma cell motility and proliferation by L1CAM in 2-D culture.

PubMed

Caccavale, Justin; Fiumara, David; Stapf, Michael; Sweitzer, Liedeke; Anderson, Hannah J; Gorky, Jonathan; Dhurjati, Prasad; Galileo, Deni S

2017-12-11

Glioblastoma multiforme (GBM) is a devastating brain cancer for which there is no known cure. Its malignancy is due to rapid cell division along with high motility and invasiveness of cells into the brain tissue. Simple 2-dimensional laboratory assays (e.g., a scratch assay) commonly are used to measure the effects of various experimental perturbations, such as treatment with chemical inhibitors. Several mathematical models have been developed to aid the understanding of the motile behavior and proliferation of GBM cells. However, many are mathematically complicated, look at multiple interdependent phenomena, and/or use modeling software not freely available to the research community. These attributes make the adoption of models and simulations of even simple 2-dimensional cell behavior an uncommon practice by cancer cell biologists. Herein, we developed an accurate, yet simple, rule-based modeling framework to describe the in vitro behavior of GBM cells that are stimulated by the L1CAM protein using freely available NetLogo software. In our model L1CAM is released by cells to act through two cell surface receptors and a point of signaling convergence to increase cell motility and proliferation. A simple graphical interface is provided so that changes can be made easily to several parameters controlling cell behavior, and behavior of the cells is viewed both pictorially and with dedicated graphs. We fully describe the hierarchical rule-based modeling framework, show simulation results under several settings, describe the accuracy compared to experimental data, and discuss the potential usefulness for predicting future experimental outcomes and for use as a teaching tool for cell biology students. It is concluded that this simple modeling framework and its simulations accurately reflect much of the GBM cell motility behavior observed experimentally in vitro in the laboratory. Our framework can be modified easily to suit the needs of investigators interested in other similar intrinsic or extrinsic stimuli that influence cancer or other cell behavior. This modeling framework of a commonly used experimental motility assay (scratch assay) should be useful to both researchers of cell motility and students in a cell biology teaching laboratory.

Two-dimensional model of resonant electron collisions with diatomic molecules and molecular cations

NASA Astrophysics Data System (ADS)

Vana, Martin; Hvizdos, David; Houfek, Karel; Curik, Roman; Greene, Chris H.; Rescigno, Thomas N.; McCurdy, C. William

2016-05-01

A simple model for resonant collisions of electrons with diatomic molecules with one electronic and one nuclear degree of freedom (2D model) which was solved numerically exactly within the time-independent approach was used to probe the local complex potential approximation and nonlocal approximation to nuclear dynamics of these collisions. This model was reformulated in the time-dependent picture and extended to model also electron collisions with molecular cations, especially with H2+.This model enables an assessment of approximate methods, such as the boomerang model or the frame transformation theory. We will present both time-dependent and time-independent results and show how we can use the model to extract deeper insight into the dynamics of the resonant collisions.

Sensitivity studies and a simple ozone perturbation experiment with a truncated two-dimensional model of the stratosphere

NASA Technical Reports Server (NTRS)

Stordal, Frode; Garcia, Rolando R.

1987-01-01

The 1-1/2-D model of Holton (1986), which is actually a highly truncated two-dimensional model, describes latitudinal variations of tracer mixing ratios in terms of their projections onto second-order Legendre polynomials. The present study extends the work of Holton by including tracers with photochemical production in the stratosphere (O3 and NOy). It also includes latitudinal variations in the photochemical sources and sinks, improving slightly the calculated global mean profiles for the long-lived tracers studied by Holton and improving substantially the latitudinal behavior of ozone. Sensitivity tests of the dynamical parameters in the model are performed, showing that the response of the model to changes in vertical residual meridional winds and horizontal diffusion coefficients is similar to that of a full two-dimensional model. A simple ozone perturbation experiment shows the model's ability to reproduce large-scale latitudinal variations in total ozone column depletions as well as ozone changes in the chemically controlled upper stratosphere.

The "universal" behavior of the Breakthrough Curve in 3D aquifer transport and the validity of the First-Order solution

NASA Astrophysics Data System (ADS)

Jankovic, Igor; Maghrebi, Mahdi; Fiori, Aldo; Zarlenga, Antonio; Dagan, Gedeon

2017-04-01

We examine the impact of permeability structures on the Breakthrough Curve (BTC) of solute, at a distance x from the injection plane, under mean uniform flow of mean velocity U. The study is carried out through accurate 3D numerical simulations, rather than the 2D models adopted in most of previous works. All structures share the same univariate distribution of the logconductivity Y = lnK and autocorrelation function ρY , but differ in higher order statistics. The main finding is that the BTC of ergodic plumes for the different examined structures is quite robust, displaying a seemingly "universal" behavior. The result is in variance with similar analyses carried out in the past for 2D permeability structures. The basic parameters (i.e. the geometric mean, the logconductivity variance σY 2 and the horizontal integral scale I) have to be identified from field data (e.g. core analysis, pumping test or other methods). However, prediction requires the knowledge of U, and the results suggest that improvement of the BTC prediction in applications can be achieved by independent estimates of the mean velocity U, e.g. by pumping tests, rather than attempting to characterize the permeability structure beyond its second-order characterization. The BTC prediction made by the Inverse Gaussian (IG) distribution, adopting the macrodispersion coefficient estimated by the First Order approximation αL = σY 2I, is also quite robust, providing a simple and effective solution to be employed in applications. The consequences of the latter result are further explored by modeling the mass distribution that occurred at the MADE-1 natural gradient experiment, for which we show that most of the plume features are adequately captured by the simple First Order approach.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubrovsky, V. G.; Topovsky, A. V.

New exact solutions, nonstationary and stationary, of Veselov-Novikov (VN) equation in the forms of simple nonlinear and linear superpositions of arbitrary number N of exact special solutions u{sup (n)}, n= 1, Horizontal-Ellipsis , N are constructed via Zakharov and Manakov {partial_derivative}-dressing method. Simple nonlinear superpositions are represented up to a constant by the sums of solutions u{sup (n)} and calculated by {partial_derivative}-dressing on nonzero energy level of the first auxiliary linear problem, i.e., 2D stationary Schroedinger equation. It is remarkable that in the zero energy limit simple nonlinear superpositions convert to linear ones in the form of the sums ofmore » special solutions u{sup (n)}. It is shown that the sums u=u{sup (k{sub 1})}+...+u{sup (k{sub m})}, 1 Less-Than-Or-Slanted-Equal-To k{sub 1} < k{sub 2} < Horizontal-Ellipsis < k{sub m} Less-Than-Or-Slanted-Equal-To N of arbitrary subsets of these solutions are also exact solutions of VN equation. The presented exact solutions include as superpositions of special line solitons and also superpositions of plane wave type singular periodic solutions. By construction these exact solutions represent also new exact transparent potentials of 2D stationary Schroedinger equation and can serve as model potentials for electrons in planar structures of modern electronics.« less

@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes.

PubMed

Pons, Jean-Luc; Labesse, Gilles

2009-07-01

@TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein-protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein-ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/

@TOME-2: a new pipeline for comparative modeling of protein–ligand complexes

PubMed Central

Pons, Jean-Luc; Labesse, Gilles

2009-01-01

@TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein–protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein–ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/ PMID:19443448

Self-organization in a simple model of adaptive agents playing 2×2 games with arbitrary payoff matrices

NASA Astrophysics Data System (ADS)

Fort, H.; Viola, S.

2004-03-01

We analyze, both analytically and numerically, the self-organization of a system of “selfish” adaptive agents playing an arbitrary iterated pairwise game (defined by a 2×2 payoff matrix). Examples of possible games to play are the prisoner’s dilemma (PD) game, the chicken game, the hero game, etc. The agents have no memory, use strategies not based on direct reciprocity nor “tags” and are chosen at random, i.e., geographical vicinity is neglected. They can play two possible strategies: cooperate (C) or defect (D). The players measure their success by comparing their utilities with an estimate for the expected benefits and update their strategy following a simple rule. Two versions of the model are studied: (1) the deterministic version (the agents are either in definite states C or D) and (2) the stochastic version (the agents have a probability c of playing C). Using a general master equation we compute the equilibrium states into which the system self-organizes, characterized by their average probability of cooperation ceq. Depending on the payoff matrix, we show that ceq can take five different values. We also consider the mixing of agents using two different payoff matrices and show that any value of ceq can be reached by tuning the proportions of agents using each payoff matrix. In particular, this can be used as a way to simulate the effect of a fraction d of “antisocial” individuals—incapable of realizing any value to cooperation—on the cooperative regime hold by a population of neutral or “normal” agents.

Self-organization in a simple model of adaptive agents playing 2 x 2 games with arbitrary payoff matrices.

PubMed

Fort, H; Viola, S

2004-03-01

We analyze, both analytically and numerically, the self-organization of a system of "selfish" adaptive agents playing an arbitrary iterated pairwise game (defined by a 2 x 2 payoff matrix). Examples of possible games to play are the prisoner's dilemma (PD) game, the chicken game, the hero game, etc. The agents have no memory, use strategies not based on direct reciprocity nor "tags" and are chosen at random, i.e., geographical vicinity is neglected. They can play two possible strategies: cooperate (C) or defect (D). The players measure their success by comparing their utilities with an estimate for the expected benefits and update their strategy following a simple rule. Two versions of the model are studied: (1) the deterministic version (the agents are either in definite states C or D) and (2) the stochastic version (the agents have a probability c of playing C). Using a general master equation we compute the equilibrium states into which the system self-organizes, characterized by their average probability of cooperation c(eq). Depending on the payoff matrix, we show that c(eq) can take five different values. We also consider the mixing of agents using two different payoff matrices and show that any value of c(eq) can be reached by tuning the proportions of agents using each payoff matrix. In particular, this can be used as a way to simulate the effect of a fraction d of "antisocial" individuals--incapable of realizing any value to cooperation--on the cooperative regime hold by a population of neutral or "normal" agents.

Two-dimensional nature of the active Brownian motion of catalytic microswimmers at solid and liquid interfaces

NASA Astrophysics Data System (ADS)

Dietrich, Kilian; Renggli, Damian; Zanini, Michele; Volpe, Giovanni; Buttinoni, Ivo; Isa, Lucio

2017-06-01

Colloidal particles equipped with platinum patches can establish chemical gradients in H2O2-enriched solutions and undergo self-propulsion due to local diffusiophoretic migration. In bulk (3D), this class of active particles swim in the direction of the surface heterogeneities introduced by the patches and consequently reorient with the characteristic rotational diffusion time of the colloids. In this article, we present experimental and numerical evidence that planar 2D confinements defy this simple picture. Instead, the motion of active particles both on solid substrates and at flat liquid-liquid interfaces is captured by a 2D active Brownian motion model, in which rotational and translational motion are constrained in the xy-plane. This leads to an active motion that does not follow the direction of the surface heterogeneities and to timescales of reorientation that do not match the free rotational diffusion times. Furthermore, 2D-confinement at fluid-fluid interfaces gives rise to a unique distribution of swimming velocities: the patchy colloids uptake two main orientations leading to two particle populations with velocities that differ up to one order of magnitude. Our results shed new light on the behavior of active colloids in 2D, which is of interest for modeling and applications where confinements are present.

An approach to 3D model fusion in GIS systems and its application in a future ECDIS

NASA Astrophysics Data System (ADS)

Liu, Tao; Zhao, Depeng; Pan, Mingyang

2016-04-01

Three-dimensional (3D) computer graphics technology is widely used in various areas and causes profound changes. As an information carrier, 3D models are becoming increasingly important. The use of 3D models greatly helps to improve the cartographic expression and design. 3D models are more visually efficient, quicker and easier to understand and they can express more detailed geographical information. However, it is hard to efficiently and precisely fuse 3D models in local systems. The purpose of this study is to propose an automatic and precise approach to fuse 3D models in geographic information systems (GIS). It is the basic premise for subsequent uses of 3D models in local systems, such as attribute searching, spatial analysis, and so on. The basic steps of our research are: (1) pose adjustment by principal component analysis (PCA); (2) silhouette extraction by simple mesh silhouette extraction and silhouette merger; (3) size adjustment; (4) position matching. Finally, we implement the above methods in our system Automotive Intelligent Chart (AIC) 3D Electronic Chart Display and Information Systems (ECDIS). The fusion approach we propose is a common method and each calculation step is carefully designed. This approach solves the problem of cross-platform model fusion. 3D models can be from any source. They may be stored in the local cache or retrieved from Internet, or may be manually created by different tools or automatically generated by different programs. The system can be any kind of 3D GIS system.

Simple Analytic Collisional Rates for non-LTE Vibrational Populations in Astrophysical Environments: the Cases of Circumstellar SiO Masers and Shocked H2

NASA Astrophysics Data System (ADS)

Bieniek, Ronald

2008-05-01

Rates for collisionally induced transitions between molecular vibrational levels are important in modeling a variety of non-LTE processes in astrophysical environments. Two examples are SiO masering in circumstellar envelopes in certain late-type stars [1] and the vibrational populations of molecular hydrogen in shocked interstellar medium [cf 2]. A simple exponential-potential model of molecular collisions leads to a two-parameter analytic expression for state-to-state and thermally averaged rates for collisionally induced vibrational-translational (VT) transitions in diatomic molecules [3,4]. The thermally averaged rates predicted by this formula have been shown to be in excellent numerical agreement with absolute experimental and quantum mechanical rates over large temperature ranges and initial vibrational excitation levels in a variety of species, e.g., OH, O2, N2 [3] and even for the rate of H2(v=1)+H2, which changes by five orders of magnitude in the temperature range 50-2000 K [4]. Analogous analytic rates will be reported for vibrational transitions in SiO due to collisions with H2 and compared to the numerical fit of quantum-mechanical rates calculated by Bieniek and Green [5]. [1] Palov, A.P., Gray, M.D., Field, D., & Balint-Kurti, G.G. 2006, ApJ, 639, 204. [2] Flower, D. 2007, Molecular Collisions in the Interstellar Medium (Cambridge: Cambridge Univ. Press) [3] Bieniek, R.J. & Lipson, S.J. 1996, Chem. Phys. Lett. 263, 276. [4] Bieniek, R.J. 2006, Proc. NASA LAW (Lab. Astrophys. Workshop) 2006, 299; http://www.physics.unlv.edu/labastro/nasalaw2006proceedings.pdf. [5] Bieniek, R.J., & Green, S. 1983, ApJ, 265, L29 and 1983, ApJ, 270, L101.

On the p, q-binomial distribution and the Ising model

NASA Astrophysics Data System (ADS)

Lundow, P. H.; Rosengren, A.

2010-08-01

We employ p, q-binomial coefficients, a generalisation of the binomial coefficients, to describe the magnetisation distributions of the Ising model. For the complete graph this distribution corresponds exactly to the limit case p = q. We apply our investigation to the simple d-dimensional lattices for d = 1, 2, 3, 4, 5 and fit p, q-binomial distributions to our data, some of which are exact but most are sampled. For d = 1 and d = 5, the magnetisation distributions are remarkably well-fitted by p,q-binomial distributions. For d = 4 we are only slightly less successful, while for d = 2, 3 we see some deviations (with exceptions!) between the p, q-binomial and the Ising distribution. However, at certain temperatures near T c the statistical moments of the fitted distribution agree with the moments of the sampled data within the precision of sampling. We begin the paper by giving results of the behaviour of the p, q-distribution and its moment growth exponents given a certain parameterisation of p, q. Since the moment exponents are known for the Ising model (or at least approximately for d = 3) we can predict how p, q should behave and compare this to our measured p, q. The results speak in favour of the p, q-binomial distribution's correctness regarding its general behaviour in comparison to the Ising model. The full extent to which they correctly model the Ising distribution, however, is not settled.

MnO2 nanosheet mediated "DD-A" FRET binary probes for sensitive detection of intracellular mRNA.

PubMed

Ou, Min; Huang, Jin; Yang, Xiaohai; Quan, Ke; Yang, Yanjing; Xie, Nuli; Wang, Kemin

2017-01-01

The donor donor-acceptor (DD-A) FRET model has proven to have a higher FRET efficiency than donor-acceptor acceptor (D-AA), donor-acceptor (D-A), and donor donor-acceptor acceptor (DD-AA) FRET models. The in-tube and in-cell experiments clearly demonstrate that the "DD-A" FRET binary probes can indeed increase the FRET efficiency and provide higher imaging contrast, which is about one order of magnitude higher than the ordinary "D-A" model. Furthermore, MnO 2 nanosheets were employed to deliver these probes into living cells for intracellular TK1 mRNA detection because they can adsorb ssDNA probes, penetrate across the cell membrane and be reduced to Mn 2+ ions by intracellular GSH. The results indicated that the MnO 2 nanosheet mediated "DD-A" FRET binary probes are capable of sensitive and selective sensing gene expression and chemical-stimuli changes in gene expression levels in cancer cells. We believe that the MnO 2 nanosheet mediated "DD-A" FRET binary probes have the potential as a simple but powerful tool for basic research and clinical diagnosis.

Comparison of a vertically-averaged and a vertically-resolved model for hyporheic flow beneath a pool-riffle bedform

NASA Astrophysics Data System (ADS)

Ibrahim, Ahmad; Steffler, Peter; She, Yuntong

2018-02-01

The interaction between surface water and groundwater through the hyporheic zone is recognized to be important as it impacts the water quantity and quality in both flow systems. Three-dimensional (3D) modeling is the most complete representation of a real-world hyporheic zone. However, 3D modeling requires extreme computational power and efforts; the sophistication is often significantly compromised by not being able to obtain the required input data accurately. Simplifications are therefore often needed. The objective of this study was to assess the accuracy of the vertically-averaged approximation compared to a more complete vertically-resolved model of the hyporheic zone. The groundwater flow was modeled by either a simple one-dimensional (1D) Dupuit approach or a two-dimensional (2D) horizontal/vertical model in boundary fitted coordinates, with the latter considered as a reference model. Both groundwater models were coupled with a 1D surface water model via the surface water depth. Applying the two models to an idealized pool-riffle sequence showed that the 1D Dupuit approximation gave comparable results in determining the characteristics of the hyporheic zone to the reference model when the stratum thickness is not very large compared to the surface water depth. Conditions under which the 1D model can provide reliable estimate of the seepage discharge, upwelling/downwelling discharges and locations, the hyporheic flow, and the residence time were determined.

A modeling paradigm for interdisciplinary water resources modeling: Simple Script Wrappers (SSW)

NASA Astrophysics Data System (ADS)

Steward, David R.; Bulatewicz, Tom; Aistrup, Joseph A.; Andresen, Daniel; Bernard, Eric A.; Kulcsar, Laszlo; Peterson, Jeffrey M.; Staggenborg, Scott A.; Welch, Stephen M.

2014-05-01

Holistic understanding of a water resources system requires tools capable of model integration. This team has developed an adaptation of the OpenMI (Open Modelling Interface) that allows easy interactions across the data passed between models. Capabilities have been developed to allow programs written in common languages such as matlab, python and scilab to share their data with other programs and accept other program's data. We call this interface the Simple Script Wrapper (SSW). An implementation of SSW is shown that integrates groundwater, economic, and agricultural models in the High Plains region of Kansas. Output from these models illustrates the interdisciplinary discovery facilitated through use of SSW implemented models. Reference: Bulatewicz, T., A. Allen, J.M. Peterson, S. Staggenborg, S.M. Welch, and D.R. Steward, The Simple Script Wrapper for OpenMI: Enabling interdisciplinary modeling studies, Environmental Modelling & Software, 39, 283-294, 2013. http://dx.doi.org/10.1016/j.envsoft.2012.07.006 http://code.google.com/p/simple-script-wrapper/

Dynamic tracking of prosthetic valve motion and deformation from bi-plane x-ray views: feasibility study

NASA Astrophysics Data System (ADS)

Hatt, Charles R.; Wagner, Martin; Raval, Amish N.; Speidel, Michael A.

2016-03-01

Transcatheter aortic valve replacement (TAVR) requires navigation and deployment of a prosthetic valve within the aortic annulus under fluoroscopic guidance. To support improved device visualization in this procedure, this study investigates the feasibility of frame-by-frame 3D reconstruction of a moving and expanding prosthetic valve structure from simultaneous bi-plane x-ray views. In the proposed method, a dynamic 3D model of the valve is used in a 2D/3D registration framework to obtain a reconstruction of the valve. For each frame, valve model parameters describing position, orientation, expansion state, and deformation are iteratively adjusted until forward projections of the model match both bi-plane views. Simulated bi-plane imaging of a valve at different signal-difference-to-noise ratio (SDNR) levels was performed to test the approach. 20 image sequences with 50 frames of valve deployment were simulated at each SDNR. The simulation achieved a target registration error (TRE) of the estimated valve model of 0.93 +/- 2.6 mm (mean +/- S.D.) for the lowest SDNR of 2. For higher SDNRs (5 to 50) a TRE of 0.04 mm +/- 0.23 mm was achieved. A tabletop phantom study was then conducted using a TAVR valve. The dynamic 3D model was constructed from high resolution CT scans and a simple expansion model. TRE was 1.22 +/- 0.35 mm for expansion states varying from undeployed to fully deployed, and for moderate amounts of inter-frame motion. Results indicate that it is feasible to use bi-plane imaging to recover the 3D structure of deformable catheter devices.

Dynamic tracking of prosthetic valve motion and deformation from bi-plane x-ray views: feasibility study.

PubMed

Hatt, Charles R; Wagner, Martin; Raval, Amish N; Speidel, Michael A

2016-01-01

Transcatheter aortic valve replacement (TAVR) requires navigation and deployment of a prosthetic valve within the aortic annulus under fluoroscopic guidance. To support improved device visualization in this procedure, this study investigates the feasibility of frame-by-frame 3D reconstruction of a moving and expanding prosthetic valve structure from simultaneous bi-plane x-ray views. In the proposed method, a dynamic 3D model of the valve is used in a 2D/3D registration framework to obtain a reconstruction of the valve. For each frame, valve model parameters describing position, orientation, expansion state, and deformation are iteratively adjusted until forward projections of the model match both bi-plane views. Simulated bi-plane imaging of a valve at different signal-difference-to-noise ratio (SDNR) levels was performed to test the approach. 20 image sequences with 50 frames of valve deployment were simulated at each SDNR. The simulation achieved a target registration error (TRE) of the estimated valve model of 0.93 ± 2.6 mm (mean ± S.D.) for the lowest SDNR of 2. For higher SDNRs (5 to 50) a TRE of 0.04 mm ± 0.23 mm was achieved. A tabletop phantom study was then conducted using a TAVR valve. The dynamic 3D model was constructed from high resolution CT scans and a simple expansion model. TRE was 1.22 ± 0.35 mm for expansion states varying from undeployed to fully deployed, and for moderate amounts of inter-frame motion. Results indicate that it is feasible to use bi-plane imaging to recover the 3D structure of deformable catheter devices.

Engineering light outcoupling in 2D materials.

PubMed

Lien, Der-Hsien; Kang, Jeong Seuk; Amani, Matin; Chen, Kevin; Tosun, Mahmut; Wang, Hsin-Ping; Roy, Tania; Eggleston, Michael S; Wu, Ming C; Dubey, Madan; Lee, Si-Chen; He, Jr-Hau; Javey, Ali

2015-02-11

When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells.

Relating renormalizability of D-dimensional higher-order electromagnetic and gravitational models to the classical potential at the origin

NASA Astrophysics Data System (ADS)

Accioly, Antonio; Correia, Gilson; de Brito, Gustavo P.; de Almeida, José; Herdy, Wallace

2017-03-01

Simple prescriptions for computing the D-dimensional classical potential related to electromagnetic and gravitational models, based on the functional generator, are built out. These recipes are employed afterward as a support for probing the premise that renormalizable higher-order systems have a finite classical potential at the origin. It is also shown that the opposite of the conjecture above is not true. In other words, if a higher-order model is renormalizable, it is necessarily endowed with a finite classical potential at the origin, but the reverse of this statement is untrue. The systems used to check the conjecture were D-dimensional fourth-order Lee-Wick electrodynamics, and the D-dimensional fourth- and sixth-order gravity models. A special attention is devoted to New Massive Gravity (NMG) since it was the analysis of this model that inspired our surmise. In particular, we made use of our premise to resolve trivially the issue of the renormalizability of NMG, which was initially considered to be renormalizable, but it was shown some years later to be non-renormalizable. We remark that our analysis is restricted to local models in which the propagator has simple and real poles.

Chiral Dark Sector

NASA Astrophysics Data System (ADS)

Co, Raymond T.; Harigaya, Keisuke; Nomura, Yasunori

2017-03-01

We present a simple and natural dark sector model in which dark matter particles arise as composite states of hidden strong dynamics and their stability is ensured by accidental symmetries. The model has only a few free parameters. In particular, the gauge symmetry of the model forbids the masses of dark quarks, and the confinement scale of the dynamics provides the unique mass scale of the model. The gauge group contains an Abelian symmetry U (1 )D , which couples the dark and standard model sectors through kinetic mixing. This model, despite its simple structure, has rich and distinctive phenomenology. In the case where the dark pion becomes massive due to U (1 )D quantum corrections, direct and indirect detection experiments can probe thermal relic dark matter which is generically a mixture of the dark pion and the dark baryon, and the Large Hadron Collider can discover the U (1 )D gauge boson. Alternatively, if the dark pion stays light due to a specific U (1 )D charge assignment of the dark quarks, then the dark pion constitutes dark radiation. The signal of this radiation is highly correlated with that of dark baryons in dark matter direct detection.

Chiral Dark Sector.

PubMed

Co, Raymond T; Harigaya, Keisuke; Nomura, Yasunori

2017-03-10

We present a simple and natural dark sector model in which dark matter particles arise as composite states of hidden strong dynamics and their stability is ensured by accidental symmetries. The model has only a few free parameters. In particular, the gauge symmetry of the model forbids the masses of dark quarks, and the confinement scale of the dynamics provides the unique mass scale of the model. The gauge group contains an Abelian symmetry U(1)_{D}, which couples the dark and standard model sectors through kinetic mixing. This model, despite its simple structure, has rich and distinctive phenomenology. In the case where the dark pion becomes massive due to U(1)_{D} quantum corrections, direct and indirect detection experiments can probe thermal relic dark matter which is generically a mixture of the dark pion and the dark baryon, and the Large Hadron Collider can discover the U(1)_{D} gauge boson. Alternatively, if the dark pion stays light due to a specific U(1)_{D} charge assignment of the dark quarks, then the dark pion constitutes dark radiation. The signal of this radiation is highly correlated with that of dark baryons in dark matter direct detection.

Electrodiffusion kinetics of ionic transport in a simple membrane channel.

PubMed

Valent, Ivan; Petrovič, Pavol; Neogrády, Pavel; Schreiber, Igor; Marek, Miloš

2013-11-21

We employ numerical techniques for solving time-dependent full Poisson-Nernst-Planck (PNP) equations in 2D to analyze transient behavior of a simple ion channel subject to a sudden electric potential jump across the membrane (voltage clamp). Calculated spatiotemporal profiles of the ionic concentrations and electric potential show that two principal exponential processes can be distinguished in the electrodiffusion kinetics, in agreement with original Planck's predictions. The initial fast process corresponds to the dielectric relaxation, while the steady state is approached in a second slower exponential process attributed to the nonlinear ionic redistribution. Effects of the model parameters such as the channel length, height of the potential step, boundary concentrations, permittivity of the channel interior, and ionic mobilities on electrodiffusion kinetics are studied. Numerical solutions are used to determine spatiotemporal profiles of the electric field, ionic fluxes, and both the conductive and displacement currents. We demonstrate that the displacement current is a significant transient component of the total electric current through the channel. The presented results provide additional information about the classical voltage-clamp problem and offer further physical insights into the mechanism of electrodiffusion. The used numerical approach can be readily extended to multi-ionic models with a more structured domain geometry in 2D or 3D, and it is directly applicable to other systems, such as synthetic nanopores, nanofluidic channels, and nanopipettes.

Analytical results for the statistical distribution related to a memoryless deterministic walk: dimensionality effect and mean-field models.

PubMed

Terçariol, César Augusto Sangaletti; Martinez, Alexandre Souto

2005-08-01

Consider a medium characterized by N points whose coordinates are randomly generated by a uniform distribution along the edges of a unitary d-dimensional hypercube. A walker leaves from each point of this disordered medium and moves according to the deterministic rule to go to the nearest point which has not been visited in the preceding mu steps (deterministic tourist walk). Each trajectory generated by this dynamics has an initial nonperiodic part of t steps (transient) and a final periodic part of p steps (attractor). The neighborhood rank probabilities are parametrized by the normalized incomplete beta function Id= I1/4 [1/2, (d+1) /2] . The joint distribution S(N) (mu,d) (t,p) is relevant, and the marginal distributions previously studied are particular cases. We show that, for the memory-less deterministic tourist walk in the euclidean space, this distribution is Sinfinity(1,d) (t,p) = [Gamma (1+ I(-1)(d)) (t+ I(-1)(d) ) /Gamma(t+p+ I(-1)(d)) ] delta(p,2), where t=0, 1,2, ... infinity, Gamma(z) is the gamma function and delta(i,j) is the Kronecker delta. The mean-field models are the random link models, which correspond to d-->infinity, and the random map model which, even for mu=0 , presents nontrivial cycle distribution [ S(N)(0,rm) (p) proportional to p(-1) ] : S(N)(0,rm) (t,p) =Gamma(N)/ {Gamma[N+1- (t+p) ] N( t+p)}. The fundamental quantities are the number of explored points n(e)=t+p and Id. Although the obtained distributions are simple, they do not follow straightforwardly and they have been validated by numerical experiments.

Allometric Models for Predicting Aboveground Biomass and Carbon Stock of Tropical Perennial C 4 Grasses in Hawaii

DOE PAGES

Youkhana, Adel H.; Ogoshi, Richard M.; Kiniry, James R.; ...

2017-05-02

Biomass is a promising renewable energy option that provides a more environmentally sustainable alternative to fossil resources by reducing the net flux of greenhouse gasses to the atmosphere. Yet, allometric models that allow the prediction of aboveground biomass (AGB), biomass carbon (C) stock non-destructively have not yet been developed for tropical perennial C 4 grasses currently under consideration as potential bioenergy feedstock in Hawaii and other subtropical and tropical locations. The objectives of this study were to develop optimal allometric relationships and site-specific models to predict AGB, biomass C stock of napiergrass, energycane, and sugarcane under cultivation practices for renewablemore » energy and validate these site-specific models against independent data sets generated from sites with widely different environments. Several allometric models were developed for each species from data at a low elevation field on the island of Maui, Hawaii. A simple power model with stalk diameter (D) was best related to AGB and biomass C stock for napiergrass, energycane, and sugarcane, (R 2 = 0.98, 0.96, and 0.97, respectively). The models were then tested against data collected from independent fields across an environmental gradient. For all crops, the models over-predicted AGB in plants with lower stalk D, but AGB was under-predicted in plants with higher stalk D. The models using stalk D were better for biomass prediction compared to dewlap H (Height from the base cut to most recently exposed leaf dewlap) models, which showed weak validation performance. Although stalk D model performed better, however, the mean square error (MSE)-systematic was ranged from 23 to 43 % of MSE for all crops. A strong relationship between model coefficient and rainfall was existed, although these were irrigated systems; suggesting a simple site-specific coefficient modulator for rainfall to reduce systematic errors in water-limited areas. These allometric equations provide a tool for farmers in the tropics to estimate perennial C4 grass biomass and C stock during decision-making for land management and as an environmental sustainability indicator within a renewable energy system.« less

Kinetic electron model for plasma thruster plumes

NASA Astrophysics Data System (ADS)

Merino, Mario; Mauriño, Javier; Ahedo, Eduardo

2018-03-01

A paraxial model of an unmagnetized, collisionless plasma plume expanding into vacuum is presented. Electrons are treated kinetically, relying on the adiabatic invariance of their radial action integral for the integration of Vlasov's equation, whereas ions are treated as a cold species. The quasi-2D plasma density, self-consistent electric potential, and electron pressure, temperature, and heat fluxes are analyzed. In particular, the model yields the collisionless cooling of electrons, which differs from the Boltzmann relation and the simple polytropic laws usually employed in fluid and hybrid PIC/fluid plume codes.

Autophagy in Dictyostelium: Mechanisms, regulation and disease in a simple biomedical model.

PubMed

Mesquita, Ana; Cardenal-Muñoz, Elena; Dominguez, Eunice; Muñoz-Braceras, Sandra; Nuñez-Corcuera, Beatriz; Phillips, Ben A; Tábara, Luis C; Xiong, Qiuhong; Coria, Roberto; Eichinger, Ludwig; Golstein, Pierre; King, Jason S; Soldati, Thierry; Vincent, Olivier; Escalante, Ricardo

2017-01-02

Autophagy is a fast-moving field with an enormous impact on human health and disease. Understanding the complexity of the mechanism and regulation of this process often benefits from the use of simple experimental models such as the social amoeba Dictyostelium discoideum. Since the publication of the first review describing the potential of D. discoideum in autophagy, significant advances have been made that demonstrate both the experimental advantages and interest in using this model. Since our previous review, research in D. discoideum has shed light on the mechanisms that regulate autophagosome formation and contributed significantly to the study of autophagy-related pathologies. Here, we review these advances, as well as the current techniques to monitor autophagy in D. discoideum. The comprehensive bioinformatics search of autophagic proteins that was a substantial part of the previous review has not been revisited here except for those aspects that challenged previous predictions such as the composition of the Atg1 complex. In recent years our understanding of, and ability to investigate, autophagy in D. discoideum has evolved significantly and will surely enable and accelerate future research using this model.

The Smoluchowski limit for a simple mechanical model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calderoni, P.; Duerr, D.

1989-05-01

The authors consider a vertical stick constantly accelerated along the x-axis by a force F and which elastically collides with point particles of the same mass (atoms). The atoms are initially Poisson distributed and are allowed to have four velocities only. It is shown that under suitable scaling of the system the displacement Q(t) of the stick satisfies a nontrivial CLT: Q(t) = vFt + D{sup 1/2}W(t) (Smoluchowski equation), where the values of v and D depend on the fact that one atom may collide several times.

Effects of protein versus simple sugar intake on weight loss in polycystic ovary syndrome (according to the National Institutes of Health criteria).

PubMed

Kasim-Karakas, Sidika E; Almario, Rogelio U; Cunningham, Wendy

2009-07-01

To compare the effects of protein vs. simple sugars on weight loss, body composition, and metabolic and endocrine parameters in polycystic ovary syndrome (PCOS). A 2-month, free-living, randomized, single-blinded study. University PCOS clinic. Thirty-three patients with PCOS. To achieve a final energy reduction of 450 kcal/day, first the daily energy intake was reduced by 700 kcal; then a 240-kcal supplement containing either whey protein or simple sugars was added. Changes in weight, fat mass, fasting glucose and insulin, plasma lipoproteins, and sex steroids. Twenty-four subjects (13 in the simple sugars group and 11 in the protein group) completed the study. The protein group lost more weight (-3.3 +/- 0.8 kg vs. -1.1 +/- 0.6 kg) and more fat mass (-3.1 +/- 0.9 kg vs. -0.5 +/- 0.6 kg) and had larger decreases in serum cholesterol (-33.0 +/- 8.4 mg/dL vs. -2.3 +/- 6.8 mg/dL), high-density lipoprotein cholesterol (-4.5 +/- 1.3 mg/dL vs. -0.4 +/- 1.3 mg/dL), and apoprotein B (-20 +/- 5 mg/dL vs. 3 +/- 5 mg/dL). In patients with PCOS, a hypocaloric diet supplemented with protein reduced body weight, fat mass, serum cholesterol, and apoprotein B more than the diet supplemented with simple sugars.

Molecular-dynamics simulation of mutual diffusion in nonideal liquid mixtures

NASA Astrophysics Data System (ADS)

Rowley, R. L.; Stoker, J. M.; Giles, N. F.

1991-05-01

The mutual-diffusion coefficients, D 12, of n-hexane, n-heptane, and n-octane in chloroform were modeled using equilibrium molecular-dynamics (MD) simulations of simple Lennard-Jones (LJ) fluids. Pure-component LJ parameters were obtained by comparison of simulations to experimental self-diffusion coefficients. While values of “effective” LJ parameters are not expected to simulate accurately diverse thermophysical properties over a wide range of conditions, it was recently shown that effective parameters obtained from pure self-diffusion coefficients can accurately model mutual diffusion in ideal, liquid mixtures. In this work, similar simulations are used to model diffusion in nonideal mixtures. The same combining rules used in the previous study for the cross-interaction parameters were found to be adequate to represent the composition dependence of D 12. The effect of alkane chain length on D 12 is also correctly predicted by the simulations. A commonly used assumption in empirical correlations of D 12, that its kinetic portion is a simple, compositional average of the intradiffusion coefficients, is inconsistent with the simulation results. In fact, the value of the kinetic portion of D 12 was often outside the range of values bracketed by the two intradiffusion coefficients for the nonideal system modeled here.

Survey of the (. cap alpha. ,/sup 2/He) reaction on 1p- and 2s1d-shell nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jahn, R.; Stahel, D.P.; Wozniak, G.J.

A /sup 2/He detection system has been developed and used to investigate the (..cap alpha..,/sup 2/He) reaction at bombarding energies of 55 and 65 MeV on targets of /sup 12/C, /sup 13/C, /sup 14/N, /sup 15/N, /sup 16/O, /sup 18/O, /sup 20/Ne, /sup 22/Ne, /sup 24/Mg, /sup 26/Mg, /sup 28/Si, /sup 29/Si, /sup 32/S, /sup 36/Ar, /sup 38/Ar, and /sup 40/Ca. Preferential population of two-neutron states with dominant (d/sub 5/2/)/sup 2//sub 4/, (d/sub 3/2/f/sub 7/2/)/sub 5/, and (f/sub 7/2/)/sup 2//sub 6/ character was observed. A linear A dependence of the binding energies of the J/sup ..pi../ = 5/sup -/ andmore » 6/sup +/ states was obtained. This systematic behavior is well described by the Bansal-French model, using the parameters a = - 0.30 MeV and b = 2.6 MeV. Simple shell-model calculations for the 2n configurations are in good agreement with the experimental data.« less

Development of a hybrid 3-D hydrological model to simulate hillslopes and the regional unconfined aquifer system in Earth system models

NASA Astrophysics Data System (ADS)

Hazenberg, P.; Broxton, P. D.; Brunke, M.; Gochis, D.; Niu, G. Y.; Pelletier, J. D.; Troch, P. A. A.; Zeng, X.

2015-12-01

The terrestrial hydrological system, including surface and subsurface water, is an essential component of the Earth's climate system. Over the past few decades, land surface modelers have built one-dimensional (1D) models resolving the vertical flow of water through the soil column for use in Earth system models (ESMs). These models generally have a relatively coarse model grid size (~25-100 km) and only account for sub-grid lateral hydrological variations using simple parameterization schemes. At the same time, hydrologists have developed detailed high-resolution (~0.1-10 km grid size) three dimensional (3D) models and showed the importance of accounting for the vertical and lateral redistribution of surface and subsurface water on soil moisture, the surface energy balance and ecosystem dynamics on these smaller scales. However, computational constraints have limited the implementation of the high-resolution models for continental and global scale applications. The current work presents a hybrid-3D hydrological approach is presented, where the 1D vertical soil column model (available in many ESMs) is coupled with a high-resolution lateral flow model (h2D) to simulate subsurface flow and overland flow. H2D accounts for both local-scale hillslope and regional-scale unconfined aquifer responses (i.e. riparian zone and wetlands). This approach was shown to give comparable results as those obtained by an explicit 3D Richards model for the subsurface, but improves runtime efficiency considerably. The h3D approach is implemented for the Delaware river basin, where Noah-MP land surface model (LSM) is used to calculated vertical energy and water exchanges with the atmosphere using a 10km grid resolution. Noah-MP was coupled within the WRF-Hydro infrastructure with the lateral 1km grid resolution h2D model, for which the average depth-to-bedrock, hillslope width function and soil parameters were estimated from digital datasets. The ability of this h3D approach to simulate the hydrological dynamics of the Delaware River basin will be assessed by comparing the model results (both hydrological performance and numerical efficiency) with the standard setup of the NOAH-MP model and a high-resolution (1km) version of NOAH-MP, which also explicitly accounts for lateral subsurface and overland flow.

Circuit models and three-dimensional electromagnetic simulations of a 1-MA linear transformer driver stage

NASA Astrophysics Data System (ADS)

Rose, D. V.; Miller, C. L.; Welch, D. R.; Clark, R. E.; Madrid, E. A.; Mostrom, C. B.; Stygar, W. A.; Lechien, K. R.; Mazarakis, M. A.; Langston, W. L.; Porter, J. L.; Woodworth, J. R.

2010-09-01

A 3D fully electromagnetic (EM) model of the principal pulsed-power components of a high-current linear transformer driver (LTD) has been developed. LTD systems are a relatively new modular and compact pulsed-power technology based on high-energy density capacitors and low-inductance switches located within a linear-induction cavity. We model 1-MA, 100-kV, 100-ns rise-time LTD cavities [A. A. Kim , Phys. Rev. ST Accel. Beams 12, 050402 (2009)PRABFM1098-440210.1103/PhysRevSTAB.12.050402] which can be used to drive z-pinch and material dynamics experiments. The model simulates the generation and propagation of electromagnetic power from individual capacitors and triggered gas switches to a radially symmetric output line. Multiple cavities, combined to provide voltage addition, drive a water-filled coaxial transmission line. A 3D fully EM model of a single 1-MA 100-kV LTD cavity driving a simple resistive load is presented and compared to electrical measurements. A new model of the current loss through the ferromagnetic cores is developed for use both in circuit representations of an LTD cavity and in the 3D EM simulations. Good agreement between the measured core current, a simple circuit model, and the 3D simulation model is obtained. A 3D EM model of an idealized ten-cavity LTD accelerator is also developed. The model results demonstrate efficient voltage addition when driving a matched impedance load, in good agreement with an idealized circuit model.

A class of simple bouncing and late-time accelerating cosmologies in f(R) gravity

NASA Astrophysics Data System (ADS)

Kuiroukidis, A.

We consider the field equations for a flat FRW cosmological model, given by Eq. (??), in an a priori generic f(R) gravity model and cast them into a, completely normalized and dimensionless, system of ODEs for the scale factor and the function f(R), with respect to the scalar curvature R. It is shown that under reasonable assumptions, namely for power-law functional form for the f(R) gravity model, one can produce simple analytical and numerical solutions describing bouncing cosmological models where in addition there are late-time accelerating. The power-law form for the f(R) gravity model is typically considered in the literature as the most concrete, reasonable, practical and viable assumption [see S. D. Odintsov and V. K. Oikonomou, Phys. Rev. D 90 (2014) 124083, arXiv:1410.8183 [gr-qc

5D Modelling: An Efficient Approach for Creating Spatiotemporal Predictive 3D Maps of Large-Scale Cultural Resources

NASA Astrophysics Data System (ADS)

Doulamis, A.; Doulamis, N.; Ioannidis, C.; Chrysouli, C.; Grammalidis, N.; Dimitropoulos, K.; Potsiou, C.; Stathopoulou, E.-K.; Ioannides, M.

2015-08-01

Outdoor large-scale cultural sites are mostly sensitive to environmental, natural and human made factors, implying an imminent need for a spatio-temporal assessment to identify regions of potential cultural interest (material degradation, structuring, conservation). On the other hand, in Cultural Heritage research quite different actors are involved (archaeologists, curators, conservators, simple users) each of diverse needs. All these statements advocate that a 5D modelling (3D geometry plus time plus levels of details) is ideally required for preservation and assessment of outdoor large scale cultural sites, which is currently implemented as a simple aggregation of 3D digital models at different time and levels of details. The main bottleneck of such an approach is its complexity, making 5D modelling impossible to be validated in real life conditions. In this paper, a cost effective and affordable framework for 5D modelling is proposed based on a spatial-temporal dependent aggregation of 3D digital models, by incorporating a predictive assessment procedure to indicate which regions (surfaces) of an object should be reconstructed at higher levels of details at next time instances and which at lower ones. In this way, dynamic change history maps are created, indicating spatial probabilities of regions needed further 3D modelling at forthcoming instances. Using these maps, predictive assessment can be made, that is, to localize surfaces within the objects where a high accuracy reconstruction process needs to be activated at the forthcoming time instances. The proposed 5D Digital Cultural Heritage Model (5D-DCHM) is implemented using open interoperable standards based on the CityGML framework, which also allows the description of additional semantic metadata information. Visualization aspects are also supported to allow easy manipulation, interaction and representation of the 5D-DCHM geometry and the respective semantic information. The open source 3DCityDB incorporating a PostgreSQL geo-database is used to manage and manipulate 3D data and their semantics.

SURVIAC Bulletin: RPG Encounter Modeling, Vol 27, Issue 1, 2012

DTIC Science & Technology

2012-01-01

return a probability of hit ( PHIT ) for the scenario. In the model, PHIT depends on the presented area of the targeted system and a set of errors infl...simplifying assumptions, is data-driven, and uses simple yet proven methodologies to determine PHIT . Th e inputs to THREAT describe the target, the RPG, and...Point on 2-D Representation of a CH-47 Th e determination of PHIT by THREAT is performed using one of two possible methodologies. Th e fi rst is a

Exploring the piezoelectric performance of PZT particulate-epoxy composites loaded in shear

NASA Astrophysics Data System (ADS)

Van Loock, F.; Deutz, D. B.; van der Zwaag, S.; Groen, W. A.

2016-08-01

The active and passive piezoelectric response of lead zirconium titanate (PZT)-epoxy particulate composites loaded in shear is studied using analytical models, a finite element model and by experiments. The response is compared to that of the same composites when loaded in simple tension. Analogously to bulk PZT, particulate PZT-polymer composites loaded in shear show higher piezoelectric charge coefficient (d 15) and energy density figure of merit (FOM15) values compared to simple tension (d 33) and (FOM33). This outcome demonstrates the as-yet barely explored potential of piezoelectric particulate composites for optimal strain energy harvesting when activated in shear.

Measurement and modeling of CO2 mass transfer in brine at reservoir conditions

NASA Astrophysics Data System (ADS)

Shi, Z.; Wen, B.; Hesse, M. A.; Tsotsis, T. T.; Jessen, K.

2018-03-01

In this work, we combine measurements and modeling to investigate the application of pressure-decay experiments towards delineation and interpretation of CO2 solubility, uptake and mass transfer in water/brine systems at elevated pressures of relevance to CO2 storage operations in saline aquifers. Accurate measurements and modeling of mass transfer in this context are crucial to an improved understanding of the longer-term fate of CO2 that is injected into the subsurface for storage purposes. Pressure-decay experiments are presented for CO2/water and CO2/brine systems with and without the presence of unconsolidated porous media. We demonstrate, via high-resolution numerical calculations in 2-D, that natural convection will complicate the interpretation of the experimental observations if the particle size is not sufficiently small. In such settings, we demonstrate that simple 1-D interpretations can result in an overestimation of the uptake (diffusivity) by two orders of magnitude. Furthermore, we demonstrate that high-resolution numerical calculations agree well with the experimental observations for settings where natural convection contributes substantially to the overall mass transfer process.

Falling Magnets and Electromagnetic Braking

NASA Astrophysics Data System (ADS)

Culbreath, Christopher; Palffy-Muhoray, Peter

2009-03-01

The slow fall of a rare earth magnet through a copper pipe is a striking example of electromagnetic braking; this remarkable phenomenon has been the subject of a number of scientific paper s [1, 2]. In a pipe having radius R and wall thickness D, the terminal velocity of the falling magnet is proportional to (R̂4)/D. It is interesting to ask what happens in the limit as D becomes very large. We report our experimental observations and theoretical predictions of the dependence of the terminal velocity on pipe radius R for large D. [1] Y. Levin, F.L. da Silveira, and F.B. Rizzato, ``Electromagnetic braking: A simple quantitative model''. American Journal of Physics, 74(9): p. 815-817 (2006). [2] J.A. Pelesko, M. Cesky, and S. Huertas, Lenz's law and dimensional analysis. American Journal of Physics, 3(1): p. 37-39. 2005.

2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching.

PubMed

Matsumoto, Atsushi; Miyazaki, Naoyuki; Takagi, Junichi; Iwasaki, Kenji

2017-03-23

In this study, we develop an approach termed "2D hybrid analysis" for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.

Dynamic self-assembly of charged colloidal strings and walls in simple fluid flows.

PubMed

Abe, Yu; Zhang, Bo; Gordillo, Leonardo; Karim, Alireza Mohammad; Francis, Lorraine F; Cheng, Xiang

2017-02-22

Colloidal particles can self-assemble into various ordered structures in fluid flows that have potential applications in biomedicine, materials synthesis and encryption. These dynamic processes are also of fundamental interest for probing the general principles of self-assembly under non-equilibrium conditions. Here, we report a simple microfluidic experiment, where charged colloidal particles self-assemble into flow-aligned 1D strings with regular particle spacing near a solid boundary. Using high-speed confocal microscopy, we systematically investigate the influence of flow rates, electrostatics and particle polydispersity on the observed string structures. By studying the detailed dynamics of stable flow-driven particle pairs, we quantitatively characterize interparticle interactions. Based on the results, we construct a simple model that explains the intriguing non-equilibrium self-assembly process. Our study shows that the colloidal strings arise from a delicate balance between attractive hydrodynamic coupling and repulsive electrostatic interaction between particles. Finally, we demonstrate that, with the assistance of transverse electric fields, a similar mechanism also leads to the formation of 2D colloidal walls.

Object detection in natural backgrounds predicted by discrimination performance and models

NASA Technical Reports Server (NTRS)

Rohaly, A. M.; Ahumada, A. J. Jr; Watson, A. B.

1997-01-01

Many models of visual performance predict image discriminability, the visibility of the difference between a pair of images. We compared the ability of three image discrimination models to predict the detectability of objects embedded in natural backgrounds. The three models were: a multiple channel Cortex transform model with within-channel masking; a single channel contrast sensitivity filter model; and a digital image difference metric. Each model used a Minkowski distance metric (generalized vector magnitude) to summate absolute differences between the background and object plus background images. For each model, this summation was implemented with three different exponents: 2, 4 and infinity. In addition, each combination of model and summation exponent was implemented with and without a simple contrast gain factor. The model outputs were compared to measures of object detectability obtained from 19 observers. Among the models without the contrast gain factor, the multiple channel model with a summation exponent of 4 performed best, predicting the pattern of observer d's with an RMS error of 2.3 dB. The contrast gain factor improved the predictions of all three models for all three exponents. With the factor, the best exponent was 4 for all three models, and their prediction errors were near 1 dB. These results demonstrate that image discrimination models can predict the relative detectability of objects in natural scenes.

Sensorimotor Model of Obstacle Avoidance in Echolocating Bats

PubMed Central

Vanderelst, Dieter; Holderied, Marc W.; Peremans, Herbert

2015-01-01

Bat echolocation is an ability consisting of many subtasks such as navigation, prey detection and object recognition. Understanding the echolocation capabilities of bats comes down to isolating the minimal set of acoustic cues needed to complete each task. For some tasks, the minimal cues have already been identified. However, while a number of possible cues have been suggested, little is known about the minimal cues supporting obstacle avoidance in echolocating bats. In this paper, we propose that the Interaural Intensity Difference (IID) and travel time of the first millisecond of the echo train are sufficient cues for obstacle avoidance. We describe a simple control algorithm based on the use of these cues in combination with alternating ear positions modeled after the constant frequency bat Rhinolophus rouxii. Using spatial simulations (2D and 3D), we show that simple phonotaxis can steer a bat clear from obstacles without performing a reconstruction of the 3D layout of the scene. As such, this paper presents the first computationally explicit explanation for obstacle avoidance validated in complex simulated environments. Based on additional simulations modelling the FM bat Phyllostomus discolor, we conjecture that the proposed cues can be exploited by constant frequency (CF) bats and frequency modulated (FM) bats alike. We hypothesize that using a low level yet robust cue for obstacle avoidance allows bats to comply with the hard real-time constraints of this basic behaviour. PMID:26502063

What do Cells Really Look Like? An Inquiry into Students' Difficulties in Visualising a 3-D Biological Cell and Lessons for Pedagogy

NASA Astrophysics Data System (ADS)

Vijapurkar, Jyotsna; Kawalkar, Aisha; Nambiar, Priya

2014-04-01

In our explorations of students' concepts in an inquiry science classroom with grade 6 students from urban schools in India, we uncovered a variety of problems in their understanding of biological cells as structural and functional units of living organisms. In particular, we found not only that they visualised the cell as a two-dimensional (2-D) structure, instead of a closed three-dimensional (3-D) functional unit, but that they had a strong resistance to changing their 2-D conception to a 3-D one. Based on analyses of students' oral as well as written descriptions of cells in the classroom, and of models they made of the cell, we were able to identify the causes of students' difficulties in correctly visualising the cell. These insights helped us design a pedagogy involving guided discussions and activities that challenges students' 2-D conceptions of the cell. The activities entail very simple, low-cost, easily doable techniques to help students visualise the cell and to understand that it would not be able to function if its structure were 2-D. We also present the results of our investigations of conceptions of grade 7 students and biology undergraduates, revealing that the incorrect 2-D mental model can persist right up to the college level if it is not explicitly addressed. The classroom interactions described in this study illustrate how students' ideas can be probed and addressed in the classroom using pedagogical action research.

Almost but not quite 2D, Non-linear Bayesian Inversion of CSEM Data

NASA Astrophysics Data System (ADS)

Ray, A.; Key, K.; Bodin, T.

2013-12-01

The geophysical inverse problem can be elegantly stated in a Bayesian framework where a probability distribution can be viewed as a statement of information regarding a random variable. After all, the goal of geophysical inversion is to provide information on the random variables of interest - physical properties of the earth's subsurface. However, though it may be simple to postulate, a practical difficulty of fully non-linear Bayesian inversion is the computer time required to adequately sample the model space and extract the information we seek. As a consequence, in geophysical problems where evaluation of a full 2D/3D forward model is computationally expensive, such as marine controlled source electromagnetic (CSEM) mapping of the resistivity of seafloor oil and gas reservoirs, Bayesian studies have largely been conducted with 1D forward models. While the 1D approximation is indeed appropriate for exploration targets with planar geometry and geological stratification, it only provides a limited, site-specific idea of uncertainty in resistivity with depth. In this work, we extend our fully non-linear 1D Bayesian inversion to a 2D model framework, without requiring the usual regularization of model resistivities in the horizontal or vertical directions used to stabilize quasi-2D inversions. In our approach, we use the reversible jump Markov-chain Monte-Carlo (RJ-MCMC) or trans-dimensional method and parameterize the subsurface in a 2D plane with Voronoi cells. The method is trans-dimensional in that the number of cells required to parameterize the subsurface is variable, and the cells dynamically move around and multiply or combine as demanded by the data being inverted. This approach allows us to expand our uncertainty analysis of resistivity at depth to more than a single site location, allowing for interactions between model resistivities at different horizontal locations along a traverse over an exploration target. While the model is parameterized in 2D, we efficiently evaluate the forward response using 1D profiles extracted from the model at the common-midpoints of the EM source-receiver pairs. Since the 1D approximation is locally valid at different midpoint locations, the computation time is far lower than is required by a full 2D or 3D simulation. We have applied this method to both synthetic and real CSEM survey data from the Scarborough gas field on the Northwest shelf of Australia, resulting in a spatially variable quantification of resistivity and its uncertainty in 2D. This Bayesian approach results in a large database of 2D models that comprise a posterior probability distribution, which we can subset to test various hypotheses about the range of model structures compatible with the data. For example, we can subset the model distributions to examine the hypothesis that a resistive reservoir extends overs a certain spatial extent. Depending on how this conditions other parts of the model space, light can be shed on the geological viability of the hypothesis. Since tackling spatially variable uncertainty and trade-offs in 2D and 3D is a challenging research problem, the insights gained from this work may prove valuable for subsequent full 2D and 3D Bayesian inversions.

Convective Dynamics and Disequilibrium Chemistry in the Atmospheres of Giant Planets and Brown Dwarfs

NASA Astrophysics Data System (ADS)

Bordwell, Baylee; Brown, Benjamin P.; Oishi, Jeffrey S.

2018-02-01

Disequilibrium chemical processes significantly affect the spectra of substellar objects. To study these effects, dynamical disequilibrium has been parameterized using the quench and eddy diffusion approximations, but little work has been done to explore how these approximations perform under realistic planetary conditions in different dynamical regimes. As a first step toward addressing this problem, we study the localized, small-scale convective dynamics of planetary atmospheres by direct numerical simulation of fully compressible hydrodynamics with reactive tracers using the Dedalus code. Using polytropically stratified, plane-parallel atmospheres in 2D and 3D, we explore the quenching behavior of different abstract chemical species as a function of the dynamical conditions of the atmosphere as parameterized by the Rayleigh number. We find that in both 2D and 3D, chemical species quench deeper than would be predicted based on simple mixing-length arguments. Instead, it is necessary to employ length scales based on the chemical equilibrium profile of the reacting species in order to predict quench points and perform chemical kinetics modeling in 1D. Based on the results of our simulations, we provide a new length scale, derived from the chemical scale height, that can be used to perform these calculations. This length scale is simple to calculate from known chemical data and makes reasonable predictions for our dynamical simulations.

Methodology and consistency of slant and vertical assessments for ionospheric electron content models

NASA Astrophysics Data System (ADS)

Hernández-Pajares, Manuel; Roma-Dollase, David; Krankowski, Andrzej; García-Rigo, Alberto; Orús-Pérez, Raül

2017-12-01

A summary of the main concepts on global ionospheric map(s) [hereinafter GIM(s)] of vertical total electron content (VTEC), with special emphasis on their assessment, is presented in this paper. It is based on the experience accumulated during almost two decades of collaborative work in the context of the international global navigation satellite systems (GNSS) service (IGS) ionosphere working group. A representative comparison of the two main assessments of ionospheric electron content models (VTEC-altimeter and difference of Slant TEC, based on independent global positioning system data GPS, dSTEC-GPS) is performed. It is based on 26 GPS receivers worldwide distributed and mostly placed on islands, from the last quarter of 2010 to the end of 2016. The consistency between dSTEC-GPS and VTEC-altimeter assessments for one of the most accurate IGS GIMs (the tomographic-kriging GIM `UQRG' computed by UPC) is shown. Typical error RMS values of 2 TECU for VTEC-altimeter and 0.5 TECU for dSTEC-GPS assessments are found. And, as expected by following a simple random model, there is a significant correlation between both RMS and specially relative errors, mainly evident when large enough number of observations per pass is considered. The authors expect that this manuscript will be useful for new analysis contributor centres and in general for the scientific and technical community interested in simple and truly external ways of validating electron content models of the ionosphere.

Systematic construction of spin liquids on the square lattice from tensor networks with SU(2) symmetry

NASA Astrophysics Data System (ADS)

Mambrini, Matthieu; Orús, Román; Poilblanc, Didier

2016-11-01

We elaborate a simple classification scheme of all rank-5 SU(2) spin rotational symmetric tensors according to (i) the onsite physical spin S , (ii) the local Hilbert space V⊗4 of the four virtual (composite) spins attached to each site, and (iii) the irreducible representations of the C4 v point group of the square lattice. We apply our scheme to draw a complete list of all SU(2)-symmetric translationally and rotationally invariant projected entangled pair states (PEPS) with bond dimension D ≤6 . All known SU(2)-symmetric PEPS on the square lattice are recovered and simple generalizations are provided in some cases. More generally, to each of our symmetry class can be associated a (D -1 )-dimensional manifold of spin liquids (potentially) preserving lattice symmetries and defined in terms of D -independent tensors of a given bond dimension D . In addition, generic (low-dimensional) families of PEPS explicitly breaking either (i) particular point-group lattice symmetries (lattice nematics) or (ii) time-reversal symmetry (chiral spin liquids) or (iii) SU(2) spin rotation symmetry down to U(1 ) (spin nematics or Néel antiferromagnets) can also be constructed. We apply this framework to search for new topological chiral spin liquids characterized by well-defined chiral edge modes, as revealed by their entanglement spectrum. In particular, we show how the symmetrization of a double-layer PEPS leads to a chiral topological state with a gapless edge described by a SU (2) 2 Wess-Zumino-Witten model.

BEYOND MIXING-LENGTH THEORY: A STEP TOWARD 321D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnett, W. David; Meakin, Casey; Viallet, Maxime

2015-08-10

We examine the physical basis for algorithms to replace mixing-length theory (MLT) in stellar evolutionary computations. Our 321D procedure is based on numerical solutions of the Navier–Stokes equations. These implicit large eddy simulations (ILES) are three-dimensional (3D), time-dependent, and turbulent, including the Kolmogorov cascade. We use the Reynolds-averaged Navier–Stokes (RANS) formulation to make concise the 3D simulation data, and use the 3D simulations to give closure for the RANS equations. We further analyze this data set with a simple analytical model, which is non-local and time-dependent, and which contains both MLT and the Lorenz convective roll as particular subsets ofmore » solutions. A characteristic length (the damping length) again emerges in the simulations; it is determined by an observed balance between (1) the large-scale driving, and (2) small-scale damping. The nature of mixing and convective boundaries is analyzed, including dynamic, thermal and compositional effects, and compared to a simple model. We find that (1) braking regions (boundary layers in which mixing occurs) automatically appear beyond the edges of convection as defined by the Schwarzschild criterion, (2) dynamic (non-local) terms imply a non-zero turbulent kinetic energy flux (unlike MLT), (3) the effects of composition gradients on flow can be comparable to thermal effects, and (4) convective boundaries in neutrino-cooled stages differ in nature from those in photon-cooled stages (different Péclet numbers). The algorithms are based upon ILES solutions to the Navier–Stokes equations, so that, unlike MLT, they do not require any calibration to astronomical systems in order to predict stellar properties. Implications for solar abundances, helioseismology, asteroseismology, nucleosynthesis yields, supernova progenitors and core collapse are indicated.« less

Beyond Mixing-length Theory: A Step Toward 321D

NASA Astrophysics Data System (ADS)

Arnett, W. David; Meakin, Casey; Viallet, Maxime; Campbell, Simon W.; Lattanzio, John C.; Mocák, Miroslav

2015-08-01

We examine the physical basis for algorithms to replace mixing-length theory (MLT) in stellar evolutionary computations. Our 321D procedure is based on numerical solutions of the Navier-Stokes equations. These implicit large eddy simulations (ILES) are three-dimensional (3D), time-dependent, and turbulent, including the Kolmogorov cascade. We use the Reynolds-averaged Navier-Stokes (RANS) formulation to make concise the 3D simulation data, and use the 3D simulations to give closure for the RANS equations. We further analyze this data set with a simple analytical model, which is non-local and time-dependent, and which contains both MLT and the Lorenz convective roll as particular subsets of solutions. A characteristic length (the damping length) again emerges in the simulations; it is determined by an observed balance between (1) the large-scale driving, and (2) small-scale damping. The nature of mixing and convective boundaries is analyzed, including dynamic, thermal and compositional effects, and compared to a simple model. We find that (1) braking regions (boundary layers in which mixing occurs) automatically appear beyond the edges of convection as defined by the Schwarzschild criterion, (2) dynamic (non-local) terms imply a non-zero turbulent kinetic energy flux (unlike MLT), (3) the effects of composition gradients on flow can be comparable to thermal effects, and (4) convective boundaries in neutrino-cooled stages differ in nature from those in photon-cooled stages (different Péclet numbers). The algorithms are based upon ILES solutions to the Navier-Stokes equations, so that, unlike MLT, they do not require any calibration to astronomical systems in order to predict stellar properties. Implications for solar abundances, helioseismology, asteroseismology, nucleosynthesis yields, supernova progenitors and core collapse are indicated.

Conservation of cardiac L-type Ca2+ channels and their regulation in Drosophila: A novel genetically-pliable channelopathic model.

PubMed

Limpitikul, Worawan B; Viswanathan, Meera C; O'Rourke, Brian; Yue, David T; Cammarato, Anthony

2018-04-21

Dysregulation of L-type Ca 2+ channels (LTCCs) underlies numerous cardiac pathologies. Understanding their modulation with high fidelity relies on investigating LTCCs in their native environment with intact interacting proteins. Such studies benefit from genetic manipulation of endogenous channels in cardiomyocytes, which often proves cumbersome in mammalian models. Drosophila melanogaster, however, offers a potentially efficient alternative as it possesses a relatively simple heart, is genetically pliable, and expresses well-conserved genes. Fluorescence in situ hybridization confirmed an abundance of Ca-α1D and Ca-α1T mRNA in fly myocardium, which encode subunits that specify hetero-oligomeric channels homologous to mammalian LTCCs and T-type Ca 2+ channels, respectively. Cardiac-specific knockdown of Ca-α1D via interfering RNA abolished cardiac contraction, suggesting Ca-α1D (i.e. A1D) represents the primary functioning Ca 2+ channel in Drosophila hearts. Moreover, we successfully isolated viable single cardiomyocytes and recorded Ca 2+ currents via patch clamping, a feat never before accomplished with the fly model. The profile of Ca 2+ currents recorded in individual cells when Ca 2+ channels were hypomorphic, absent, or under selective LTCC blockage by nifedipine, additionally confirmed the predominance of A1D current across all activation voltages. T-type current, activated at more negative voltages, was also detected. Lastly, A1D channels displayed Ca 2+ -dependent inactivation, a critical negative feedback mechanism of LTCCs, and the current through them was augmented by forskolin, an activator of the protein kinase A pathway. In sum, the Drosophila heart possesses a conserved compendium of Ca 2+ channels, suggesting that the fly may serve as a robust and effective platform for studying cardiac channelopathies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Collective cell behavior on basement membranes floating in space

NASA Astrophysics Data System (ADS)

Ellison, Sarah; Bhattacharjee, Tapomoy; Morley, Cameron; Sawyer, W.; Angelini, Thomas

The basement membrane is an essential part of the polarity of endothelial and epithelial tissues. In tissue culture and organ-on-chip devices, monolayer polarity can be established by coating flat surfaces with extracellular matrix proteins and tuning the trans-substrate permeability. In epithelial 3D culture, spheroids spontaneously establish inside-out polarity, morphing into hollow shell-like structures called acini, generating their own basement membrane on the inner radius of the shell. However, 3D culture approaches generally lack the high degree of control provided by the 2D culture plate or organ-on-chip devices, making it difficult to create more faithful in vitro tissue models with complex surface curvature and morphology. Here we present a method for 3D printing complex basement membranes covered in cells. We 3D print collagen-I and Matrigel into a 3D growth medium made from jammed microgels. This soft, yielding material allows extracellular matrix to be formed as complex surfaces and shapes, floating in space. We then distribute MCF10A epithelial cells across the polymerized surface. We envision employing this strategy to study 3D collective cell behavior in numerous model tissue layers, beyond this simple epithelial model.

The Role of Wakes in Modelling Tidal Current Turbines

NASA Astrophysics Data System (ADS)

Conley, Daniel; Roc, Thomas; Greaves, Deborah

2010-05-01

The eventual proper development of arrays of Tidal Current Turbines (TCT) will require a balance which maximizes power extraction while minimizing environmental impacts. Idealized analytical analogues and simple 2-D models are useful tools for investigating questions of a general nature but do not represent a practical tool for application to realistic cases. Some form of 3-D numerical simulations will be required for such applications and the current project is designed to develop a numerical decision-making tool for use in planning large scale TCT projects. The project is predicated on the use of an existing regional ocean modelling framework (the Regional Ocean Modelling System - ROMS) which is modified to enable the user to account for the effects of TCTs. In such a framework where mixing processes are highly parametrized, the fidelity of the quantitative results is critically dependent on the parameter values utilized. In light of the early stage of TCT development and the lack of field scale measurements, the calibration of such a model is problematic. In the absence of explicit calibration data sets, the device wake structure has been identified as an efficient feature for model calibration. This presentation will discuss efforts to design an appropriate calibration scheme which focuses on wake decay and the motivation for this approach, techniques applied, validation results from simple test cases and limitations shall be presented.

The distinct roles of the nucleus and nucleus-cytoskeleton connections in three-dimensional cell migration

PubMed Central

Khatau, Shyam B.; Bloom, Ryan J.; Bajpai, Saumendra; Razafsky, David; Zang, Shu; Giri, Anjil; Wu, Pei-Hsun; Marchand, Jorge; Celedon, Alfredo; Hale, Christopher M.; Sun, Sean X.; Hodzic, Didier; Wirtz, Denis

2012-01-01

Cells often migrate in vivo in an extracellular matrix that is intrinsically three-dimensional (3D) and the role of actin filament architecture in 3D cell migration is less well understood. Here we show that, while recently identified linkers of nucleoskeleton to cytoskeleton (LINC) complexes play a minimal role in conventional 2D migration, they play a critical role in regulating the organization of a subset of actin filament bundles – the perinuclear actin cap - connected to the nucleus through Nesprin2giant and Nesprin3 in cells in 3D collagen I matrix. Actin cap fibers prolong the nucleus and mediate the formation of pseudopodial protrusions, which drive matrix traction and 3D cell migration. Disruption of LINC complexes disorganizes the actin cap, which impairs 3D cell migration. A simple mechanical model explains why LINC complexes and the perinuclear actin cap are essential in 3D migration by providing mechanical support to the formation of pseudopodial protrusions. PMID:22761994

Size of graphene sheets determines the structural and mechanical properties of 3D graphene foams

NASA Astrophysics Data System (ADS)

Shen, Zhiqiang; Ye, Huilin; Zhou, Chi; Kröger, Martin; Li, Ying

2018-03-01

Graphene is recognized as an emerging 2D nanomaterial for many applications. Assembly of graphene sheets into 3D structures is an attractive way to enable their macroscopic applications and to preserve the exceptional mechanical and physical properties of their constituents. In this study, we develop a coarse-grained (CG) model for 3D graphene foams (GFs) based on the CG model for a 2D graphene sheet by Ruiz et al (2015 Carbon 82 103-15). We find that the size of graphene sheets plays an important role in both the structural and mechanical properties of 3D GFs. When their size is smaller than 10 nm, the graphene sheets can easily stack together under the influence of van der Waals interactions (vdW). These stacks behave like building blocks and are tightly packed together within 3D GFs, leading to high density, small pore radii, and a large Young’s modulus. However, if the sheet sizes exceed 10 nm, they are staggered together with a significant amount of deformation (bending). Therefore, the density of 3D GFs has been dramatically reduced due to the loosely packed graphene sheets, accompanied by large pore radii and a small Young’s modulus. Under uniaxial compression, rubber-like stress-strain curves are observed for all 3D GFs. This material characteristic is dominated by the vdW interactions between different graphene layers and slightly affected by the out-of-plane deformation of the graphene sheets. We find a simple scaling law E˜ {ρ }4.2 between the density ρ and Young’s modulus E for a model of 3D GFs. The simulation results reveal structure-property relations of 3D GFs, which can be applied to guide the design of 3D graphene assemblies with exceptional properties.

3D pancreatic carcinoma spheroids induce a matrix-rich, chemoresistant phenotype offering a better model for drug testing.

PubMed

Longati, Paola; Jia, Xiaohui; Eimer, Johannes; Wagman, Annika; Witt, Michael-Robin; Rehnmark, Stefan; Verbeke, Caroline; Toftgård, Rune; Löhr, Matthias; Heuchel, Rainer L

2013-02-27

Pancreatic ductal adenocarcinoma (PDAC) is the fourth most common cause of cancer related death. It is lethal in nearly all patients, due to an almost complete chemoresistance. Most if not all drugs that pass preclinical tests successfully, fail miserably in the patient. This raises the question whether traditional 2D cell culture is the correct tool for drug screening. The objective of this study is to develop a simple, high-throughput 3D model of human PDAC cell lines, and to explore mechanisms underlying the transition from 2D to 3D that might be responsible for chemoresistance. Several established human PDAC and a KPC mouse cell lines were tested, whereby Panc-1 was studied in more detail. 3D spheroid formation was facilitated with methylcellulose. Spheroids were studied morphologically, electron microscopically and by qRT-PCR for selected matrix genes, related factors and miRNA. Metabolic studies were performed, and a panel of novel drugs was tested against gemcitabine. Comparing 3D to 2D cell culture, matrix proteins were significantly increased as were lumican, SNED1, DARP32, and miR-146a. Cell metabolism in 3D was shifted towards glycolysis. All drugs tested were less effective in 3D, except for allicin, MT100 and AX, which demonstrated effect. We developed a high-throughput 3D cell culture drug screening system for pancreatic cancer, which displays a strongly increased chemoresistance. Features associated to the 3D cell model are increased expression of matrix proteins and miRNA as well as stromal markers such as PPP1R1B and SNED1. This is supporting the concept of cell adhesion mediated drug resistance.

3D pancreatic carcinoma spheroids induce a matrix-rich, chemoresistant phenotype offering a better model for drug testing

PubMed Central

2013-01-01

Background Pancreatic ductal adenocarcinoma (PDAC) is the fourth most common cause of cancer related death. It is lethal in nearly all patients, due to an almost complete chemoresistance. Most if not all drugs that pass preclinical tests successfully, fail miserably in the patient. This raises the question whether traditional 2D cell culture is the correct tool for drug screening. The objective of this study is to develop a simple, high-throughput 3D model of human PDAC cell lines, and to explore mechanisms underlying the transition from 2D to 3D that might be responsible for chemoresistance. Methods Several established human PDAC and a KPC mouse cell lines were tested, whereby Panc-1 was studied in more detail. 3D spheroid formation was facilitated with methylcellulose. Spheroids were studied morphologically, electron microscopically and by qRT-PCR for selected matrix genes, related factors and miRNA. Metabolic studies were performed, and a panel of novel drugs was tested against gemcitabine. Results Comparing 3D to 2D cell culture, matrix proteins were significantly increased as were lumican, SNED1, DARP32, and miR-146a. Cell metabolism in 3D was shifted towards glycolysis. All drugs tested were less effective in 3D, except for allicin, MT100 and AX, which demonstrated effect. Conclusions We developed a high-throughput 3D cell culture drug screening system for pancreatic cancer, which displays a strongly increased chemoresistance. Features associated to the 3D cell model are increased expression of matrix proteins and miRNA as well as stromal markers such as PPP1R1B and SNED1. This is supporting the concept of cell adhesion mediated drug resistance. PMID:23446043

Convective Propagation Characteristics Using a Simple Representation of Convective Organization

NASA Astrophysics Data System (ADS)

Neale, R. B.; Mapes, B. E.

2016-12-01

Observed equatorial wave propagation is intimately linked to convective organization and it's coupling to features of the larger-scale flow. In this talk we a use simple 4 level model to accommodate vertical modes of a mass flux convection scheme (shallow, mid-level and deep). Two paradigms of convection are used to represent convective processes. One that has only both random (unorganized) diagnosed fluctuations of convective properties and one with organized fluctuations of convective properties that are amplified by previously existing convection and has an explicit moistening impact on the local convecting environment We show a series of model simulations in single-column, 2D and 3D configurations, where the role of convective organization in wave propagation is shown to be fundamental. For the optimal choice of parameters linking organization to local atmospheric state, a broad array of convective wave propagation emerges. Interestingly the key characteristics of propagating modes are the low-level moistening followed by deep convection followed by mature 'large-scale' heating. This organization structure appears to hold firm across timescales from 5-day wave disturbances to MJO-like wave propagation.

Fitting of Hadron Mass Spectra and Contributions to Perturbation Theory of Conformal Quantum Field Theory

NASA Astrophysics Data System (ADS)

Luna Acosta, German Aurelio

The masses of observed hadrons are fitted according to the kinematic predictions of Conformal Relativity. The hypothesis gives a remarkably good fit. The isospin SU(2) gauge invariant Lagrangian L(,(pi)NN)(x,(lamda)) is used in the calculation of d(sigma)/d(OMEGA) to 2nd-order Feynman graphs for simplified models of (pi)N(--->)(pi)N. The resulting infinite mass sums over the nucleon (Conformal) families are done via the Generalized-Sommerfeld-Watson Transform Theorem. Even though the models are too simple to be realistic, they indicate that if (DELTA)-internal lines were to be included, 2nd-order Feynman graphs may reproduce the experimental data qualitatively. The energy -dependence of the propagator and couplings in Conformal QFT is different from that of ordinary QFT. Suggestions for further work are made in the areas of ultra-violet divergences and OPEC calculations.

Two-Dimensional Dirac Fermions Protected by Space-Time Inversion Symmetry in Black Phosphorus

NASA Astrophysics Data System (ADS)

Kim, Jimin; Baik, Seung Su; Jung, Sung Won; Sohn, Yeongsup; Ryu, Sae Hee; Choi, Hyoung Joon; Yang, Bohm-Jung; Kim, Keun Su

2017-12-01

We report the realization of novel symmetry-protected Dirac fermions in a surface-doped two-dimensional (2D) semiconductor, black phosphorus. The widely tunable band gap of black phosphorus by the surface Stark effect is employed to achieve a surprisingly large band inversion up to ˜0.6 eV . High-resolution angle-resolved photoemission spectra directly reveal the pair creation of Dirac points and their movement along the axis of the glide-mirror symmetry. Unlike graphene, the Dirac point of black phosphorus is stable, as protected by space-time inversion symmetry, even in the presence of spin-orbit coupling. Our results establish black phosphorus in the inverted regime as a simple model system of 2D symmetry-protected (topological) Dirac semimetals, offering an unprecedented opportunity for the discovery of 2D Weyl semimetals.

A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy

DOE PAGES

Solares, Santiago D.

2015-11-26

This study introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretationmore » of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tappingmode imaging, for both of which the force curves exhibit the expected features. Lastly, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.« less

A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy.

PubMed

Solares, Santiago D

2015-01-01

This paper introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tapping-mode imaging, for both of which the force curves exhibit the expected features. Finally, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.

Describing Site Amplification for Surface Waves in Realistic Basins

NASA Astrophysics Data System (ADS)

Bowden, D. C.; Tsai, V. C.

2017-12-01

Standard characterizations of site-specific site response assume a vertically-incident shear wave; given a 1D velocity profile, amplification and resonances can be calculated based on conservation of energy. A similar approach can be applied to surface waves, resulting in an estimate of amplification relative to a hard rock site that is different in terms of both amount of amplification and frequency. This prediction of surface-wave site amplification has been well validated through simple simulations, and in this presentation we explore the extent to which a 1D profile can explain observed amplifications in more realistic scenarios. Comparisons of various simple 2D and 3D simulations, for example, allow us to explore the effect of different basin shapes and the relative importance of effects such as focusing, conversion of wave-types and lateral surface wave resonances. Additionally, the 1D estimates for vertically-incident shear waves and for surface waves are compared to spectral ratios of historic events in deep sedimentary basins to demonstrate the appropriateness of the two different predictions. This difference in amplification responses between the wave types implies that a single measurement of site response, whether analytically calculated from 1D models or empirically observed, is insufficient for regions where surface waves play a strong role.

The Structure and Dark Halo Core Properties of Dwarf Spheroidal Galaxies

NASA Astrophysics Data System (ADS)

Burkert, A.

2015-08-01

The structure and dark matter halo core properties of dwarf spheroidal galaxies (dSphs) are investigated. A double-isothermal (DIS) model of an isothermal, non-self-gravitating stellar system embedded in an isothermal dark halo core provides an excellent fit to the various observed stellar surface density distributions. The stellar core scale length a* is sensitive to the central dark matter density ρ0,d. The maximum stellar radius traces the dark halo core radius {r}c,d. The concentration c* of the stellar system, determined by a King profile fit, depends on the ratio of the stellar-to-dark-matter velocity dispersion {σ }*/{σ }d. Simple empirical relationships are derived that allow us to calculate the dark halo core parameters ρ0,d, {r}c,d, and σd given the observable stellar quantities σ*, a*, and c*. The DIS model is applied to the Milky Way’s dSphs. All dSphs closely follow the same universal dark halo scaling relations {ρ }0,d× {r}c,d={75}-45+85 M⊙ pc-2 that characterize the cores of more massive galaxies over a large range in masses. The dark halo core mass is a strong function of core radius, {M}c,d˜ {r}c,d2. Inside a fixed radius of ˜400 pc the total dark matter mass is, however, roughly constant with {M}d=2.6+/- 1.4× {10}7 M⊙, although outliers are expected. The dark halo core densities of the Galaxy’s dSphs are very high, with {ρ }0,d ≈ 0.2 M⊙ pc-3. dSphs should therefore be tidally undisturbed. Evidence for tidal effects might then provide a serious challenge for the CDM scenario.

A generalized crystal-cutting method for modeling arbitrarily oriented crystals in 3D periodic simulation cells with applications to crystal-crystal interfaces

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew P.; Mathew, Nithin; Jiang, Shan; Sewell, Thomas D.

2016-10-01

A Generalized Crystal-Cutting Method (GCCM) is developed that automates construction of three-dimensionally periodic simulation cells containing arbitrarily oriented single crystals and thin films, two-dimensionally (2D) infinite crystal-crystal homophase and heterophase interfaces, and nanostructures with intrinsic N-fold interfaces. The GCCM is based on a simple mathematical formalism that facilitates easy definition of constraints on cut crystal geometries. The method preserves the translational symmetry of all Bravais lattices and thus can be applied to any crystal described by such a lattice including complicated, low-symmetry molecular crystals. Implementations are presented with carefully articulated combinations of loop searches and constraints that drastically reduce computational complexity compared to simple loop searches. Orthorhombic representations of monoclinic and triclinic crystals found using the GCCM overcome some limitations in standard distributions of popular molecular dynamics software packages. Stability of grain boundaries in β-HMX was investigated using molecular dynamics and molecular statics simulations with 2D infinite crystal-crystal homophase interfaces created using the GCCM. The order of stabilities for the four grain boundaries studied is predicted to correlate with the relative prominence of particular crystal faces in lab-grown β-HMX crystals. We demonstrate how nanostructures can be constructed through simple constraints applied in the GCCM framework. Example GCCM constructions are shown that are relevant to some current problems in materials science, including shock sensitivity of explosives, layered electronic devices, and pharmaceuticals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eken, T; Mayeda, K; Hofstetter, A

A recently developed coda magnitude methodology was applied to selected broadband stations in Turkey for the purpose of testing the coda method in a large, laterally complex region. As found in other, albeit smaller regions, coda envelope amplitude measurements are significantly less variable than distance-corrected direct wave measurements (i.e., L{sub g} and surface waves) by roughly a factor 3-to-4. Despite strong lateral crustal heterogeneity in Turkey, we found that the region could be adequately modeled assuming a simple 1-D, radially symmetric path correction for 10 narrow frequency bands ranging between 0.02 to 2.0 Hz. For higher frequencies however, 2-D pathmore » corrections will be necessary and will be the subject of a future study. After calibrating the stations ISP, ISKB, and MALT for local and regional distances, single-station moment-magnitude estimates (M{sub w}) derived from the coda spectra were in excellent agreement with those determined from multi-station waveform modeling inversions of long-period data, exhibiting a data standard deviation of 0.17. Though the calibration was validated using large events, the results of the calibration will extend M{sub w} estimates to significantly smaller events which could not otherwise be waveform modeled due to poor signal-to-noise ratio at long periods and sparse station coverage. The successful application of the method is remarkable considering the significant lateral complexity in Turkey and the simple assumptions used in the coda method.« less

Biofilm development in fixed bed biofilm reactors: experiments and simple models for engineering design purposes.

PubMed

Szilágyi, N; Kovács, R; Kenyeres, I; Csikor, Zs

2013-01-01

Biofilm development in a fixed bed biofilm reactor system performing municipal wastewater treatment was monitored aiming at accumulating colonization and maximum biofilm mass data usable in engineering practice for process design purposes. Initially a 6 month experimental period was selected for investigations where the biofilm formation and the performance of the reactors were monitored. The results were analyzed by two methods: for simple, steady-state process design purposes the maximum biofilm mass on carriers versus influent load and a time constant of the biofilm growth were determined, whereas for design approaches using dynamic models a simple biofilm mass prediction model including attachment and detachment mechanisms was selected and fitted to the experimental data. According to a detailed statistical analysis, the collected data have not allowed us to determine both the time constant of biofilm growth and the maximum biofilm mass on carriers at the same time. The observed maximum biofilm mass could be determined with a reasonable error and ranged between 438 gTS/m(2) carrier surface and 843 gTS/m(2), depending on influent load, and hydrodynamic conditions. The parallel analysis of the attachment-detachment model showed that the experimental data set allowed us to determine the attachment rate coefficient which was in the range of 0.05-0.4 m d(-1) depending on influent load and hydrodynamic conditions.

Anatomy of triply-periodic network assemblies: characterizing skeletal and inter-domain surface geometry of block copolymer gyroids.

PubMed

Prasad, Ishan; Jinnai, Hiroshi; Ho, Rong-Ming; Thomas, Edwin L; Grason, Gregory M

2018-05-09

Triply-periodic networks (TPNs), like the well-known gyroid and diamond network phases, abound in soft matter assemblies, from block copolymers (BCPs), lyotropic liquid crystals and surfactants to functional architectures in biology. While TPNs are, in reality, volume-filling patterns of spatially-varying molecular composition, physical and structural models most often reduce their structure to lower-dimensional geometric objects: the 2D interfaces between chemical domains; and the 1D skeletons that thread through inter-connected, tubular domains. These lower-dimensional structures provide a useful basis of comparison to idealized geometries based on triply-periodic minimal, or constant-mean curvature surfaces, and shed important light on the spatially heterogeneous packing of molecular constituents that form the networks. Here, we propose a simple, efficient and flexible method to extract a 1D skeleton from 3D volume composition data of self-assembled networks. We apply this method to both self-consistent field theory predictions as well as experimental electron microtomography reconstructions of the double-gyroid phase of an ABA triblock copolymer. We further demonstrate how the analysis of 1D skeleton, 2D inter-domain surfaces, and combinations therefore, provide physical and structural insight into TPNs, across multiple length scales. Specifically, we propose and compare simple measures of network chirality as well as domain thickness, and analyze their spatial and statistical distributions in both ideal (theoretical) and non-ideal (experimental) double gyroid assemblies.

Sensor fusion V; Proceedings of the Meeting, Boston, MA, Nov. 15-17, 1992

NASA Technical Reports Server (NTRS)

Schenker, Paul S. (Editor)

1992-01-01

Topics addressed include 3D object perception, human-machine interface in multisensor systems, sensor fusion architecture, fusion of multiple and distributed sensors, interface and decision models for sensor fusion, computational networks, simple sensing for complex action, multisensor-based control, and metrology and calibration of multisensor systems. Particular attention is given to controlling 3D objects by sketching 2D views, the graphical simulation and animation environment for flexible structure robots, designing robotic systems from sensorimotor modules, cylindrical object reconstruction from a sequence of images, an accurate estimation of surface properties by integrating information using Bayesian networks, an adaptive fusion model for a distributed detection system, multiple concurrent object descriptions in support of autonomous navigation, robot control with multiple sensors and heuristic knowledge, and optical array detectors for image sensors calibration. (No individual items are abstracted in this volume)

Methods for estimating 2D cloud size distributions from 1D observations

DOE PAGES

Romps, David M.; Vogelmann, Andrew M.

2017-08-04

The two-dimensional (2D) size distribution of clouds in the horizontal plane plays a central role in the calculation of cloud cover, cloud radiative forcing, convective entrainment rates, and the likelihood of precipitation. Here, a simple method is proposed for calculating the area-weighted mean cloud size and for approximating the 2D size distribution from the 1D cloud chord lengths measured by aircraft and vertically pointing lidar and radar. This simple method (which is exact for square clouds) compares favorably against the inverse Abel transform (which is exact for circular clouds) in the context of theoretical size distributions. Both methods also performmore » well when used to predict the size distribution of real clouds from a Landsat scene. When applied to a large number of Landsat scenes, the simple method is able to accurately estimate the mean cloud size. Finally, as a demonstration, the methods are applied to aircraft measurements of shallow cumuli during the RACORO campaign, which then allow for an estimate of the true area-weighted mean cloud size.« less

Methods for estimating 2D cloud size distributions from 1D observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romps, David M.; Vogelmann, Andrew M.

The two-dimensional (2D) size distribution of clouds in the horizontal plane plays a central role in the calculation of cloud cover, cloud radiative forcing, convective entrainment rates, and the likelihood of precipitation. Here, a simple method is proposed for calculating the area-weighted mean cloud size and for approximating the 2D size distribution from the 1D cloud chord lengths measured by aircraft and vertically pointing lidar and radar. This simple method (which is exact for square clouds) compares favorably against the inverse Abel transform (which is exact for circular clouds) in the context of theoretical size distributions. Both methods also performmore » well when used to predict the size distribution of real clouds from a Landsat scene. When applied to a large number of Landsat scenes, the simple method is able to accurately estimate the mean cloud size. Finally, as a demonstration, the methods are applied to aircraft measurements of shallow cumuli during the RACORO campaign, which then allow for an estimate of the true area-weighted mean cloud size.« less

Dynamic origins of fermionic D -terms

NASA Astrophysics Data System (ADS)

Hudson, Jonathan; Schweitzer, Peter

2018-03-01

The D -term is defined through matrix elements of the energy-momentum tensor, similarly to mass and spin, yet this important particle property is experimentally not known any fermion. In this work we show that the D -term of a spin 1/2 fermion is of dynamical origin: it vanishes for a free fermion. This is in pronounced contrast to the bosonic case where already a free spin-0 boson has a non-zero intrinsic D -term. We illustrate in two simple models how interactions generate the D -term of a fermion with an internal structure, the nucleon. All known matter is composed of elementary fermions. This indicates the importance to study this interesting particle property in more detail, which will provide novel insights especially on the structure of the nucleon.

3D-printed gelatin scaffolds of differing pore geometry modulate hepatocyte function and gene expression.

PubMed

Lewis, Phillip L; Green, Richard M; Shah, Ramille N

2018-03-15

Three dimensional (3D) printing is highly amenable to the fabrication of tissue-engineered organs of a repetitive microstructure such as the liver. The creation of uniform and geometrically repetitive tissue scaffolds can also allow for the control over cellular aggregation and nutrient diffusion. However, the effect of differing geometries, while controlling for pore size, has yet to be investigated in the context of hepatocyte function. In this study, we show the ability to precisely control pore geometry of 3D-printed gelatin scaffolds. An undifferentiated hepatocyte cell line (HUH7) demonstrated high viability and proliferation when seeded on 3D-printed scaffolds of two different geometries. However, hepatocyte specific functions (albumin secretion, CYP activity, and bile transport) increases in more interconnected 3D-printed gelatin cultures compared to a less interconnected geometry and to 2D controls. Additionally, we also illustrate the disparity between gene expression and protein function in simple 2D culture modes, and that recreation of a physiologically mimetic 3D environment is necessary to induce both expression and function of cultured hepatocytes. Three dimensional (3D) printing provides tissue engineers the ability spatially pattern cells and materials in precise geometries, however the biological effects of scaffold geometry on soft tissues such as the liver have not been rigorously investigated. In this manuscript, we describe a method to 3D print gelatin into well-defined repetitive geometries that show clear differences in biological effects on seeded hepatocytes. We show that a relatively simple and widely used biomaterial, such as gelatin, can significantly modulate biological processes when fabricated into specific 3D geometries. Furthermore, this study expands upon past research into hepatocyte aggregation by demonstrating how it can be manipulated to enhance protein function, and how function and expression may not precisely correlate in 2D models. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Fragmentation modeling of a resin bonded sand

NASA Astrophysics Data System (ADS)

Hilth, William; Ryckelynck, David

2017-06-01

Cemented sands exhibit a complex mechanical behavior that can lead to sophisticated models, with numerous parameters without real physical meaning. However, using a rather simple generalized critical state bonded soil model has proven to be a relevant compromise between an easy calibration and good results. The constitutive model formulation considers a non-associated elasto-plastic formulation within the critical state framework. The calibration procedure, using standard laboratory tests, is complemented by the study of an uniaxial compression test observed by tomography. Using finite elements simulations, this test is simulated considering a non-homogeneous 3D media. The tomography of compression sample gives access to 3D displacement fields by using image correlation techniques. Unfortunately these fields have missing experimental data because of the low resolution of correlations for low displacement magnitudes. We propose a recovery method that reconstructs 3D full displacement fields and 2D boundary displacement fields. These fields are mandatory for the calibration of the constitutive parameters by using 3D finite element simulations. The proposed recovery technique is based on a singular value decomposition of available experimental data. This calibration protocol enables an accurate prediction of the fragmentation of the specimen.

Two-dimensional simple proportional feedback control of a chaotic reaction system

NASA Astrophysics Data System (ADS)

Mukherjee, Ankur; Searson, Dominic P.; Willis, Mark J.; Scott, Stephen K.

2008-04-01

The simple proportional feedback (SPF) control algorithm may, in principle, be used to attain periodic oscillations in dynamic systems exhibiting low-dimensional chaos. However, if implemented within a discrete control framework with sampling frequency limitations, controller performance may deteriorate. This phenomenon is illustrated using simulations of a chaotic autocatalytic reaction system. A two-dimensional (2D) SPF controller that explicitly takes into account some of the problems caused by limited sampling rates is then derived by introducing suitable modifications to the original SPF method. Using simulations, the performance of the 2D-SPF controller is compared to that of a conventional SPF control law when implemented as a sampled data controller. Two versions of the 2D-SPF controller are described: linear (L2D-SPF) and quadratic (Q2D-SPF). The performance of both the L2D-SPF and Q2D-SPF controllers is shown to be superior to the SPF when controller sampling frequencies are decreased. Furthermore, it is demonstrated that the Q2D-SPF controller provides better fixed point stabilization compared to both the L2D-SPF and the conventional SPF when concentration measurements are corrupted by noise.

Enhancing flood hazard estimation methods on alluvial fans using an integrated hydraulic, geological and geomorphological approach

NASA Astrophysics Data System (ADS)

Mollaei, Zeinab; Davary, Kamran; Majid Hasheminia, Seyed; Faridhosseini, Alireza; Pourmohamad, Yavar

2018-04-01

Due to the uncertainty concerning the location of flow paths on active alluvial fans, alluvial fan floods could be more dangerous than riverine floods. The United States Federal Emergency Management Agency (FEMA) used a simple stochastic model named FAN for this purpose, which has been practiced for many years. In the last decade, this model has been criticized as a consequence of development of more complex computer models. This study was conducted on three alluvial fans located in northeast and southeast Iran using a combination of the FAN model, the hydraulic portion of the FLO-2D model, and geomorphological information. Initial stages included three steps: (a) identifying the alluvial fans' landforms, (b) determining the active and inactive areas of alluvial fans, and (c) delineating 100-year flood within these selected areas. This information was used as an input in the mentioned three approaches of the (i) FLO-2D model, (ii) geomorphological method, and (iii) FAN model. Thereafter, the results of each model were obtained and geographical information system (GIS) layers were created and overlaid. Afterwards, using a scoring system, the results were evaluated and compared. The goal of this research was to introduce a simple but effective solution to estimate the flood hazards. It was concluded that the integrated method proposed in this study is superior at projecting alluvial fan flood hazards with minimum required input data, simplicity, and affordability, which are considered the primary goals of such comprehensive studies. These advantages are more highlighted in underdeveloped and developing countries, which may well lack detailed data and financially cannot support such costly projects. Furthermore, such a highly cost-effective method could be greatly advantageous and pragmatic for developed countries.

Functional Two-Dimensional Coordination Polymeric Layer as a Charge Barrier in Li-S Batteries.

PubMed

Huang, Jing-Kai; Li, Mengliu; Wan, Yi; Dey, Sukumar; Ostwal, Mayur; Zhang, Daliang; Yang, Chih-Wen; Su, Chun-Jen; Jeng, U-Ser; Ming, Jun; Amassian, Aram; Lai, Zhiping; Han, Yu; Li, Sean; Li, Lain-Jong

2018-01-23

Ultrathin two-dimensional (2D) polymeric layers are capable of separating gases and molecules based on the reported size exclusion mechanism. What is equally important but missing today is an exploration of the 2D layers with charge functionality, which enables applications using the charge exclusion principle. This work demonstrates a simple and scalable method of synthesizing a free-standing 2D coordination polymer Zn 2 (benzimidazolate) 2 (OH) 2 at the air-water interface. The hydroxyl (-OH) groups are stoichiometrically coordinated and implement electrostatic charges in the 2D structures, providing powerful functionality as a charge barrier. Electrochemical performance of the Li-S battery shows that the Zn 2 (benzimidazolate) 2 (OH) 2 coordination polymer layers efficiently mitigate the polysulfide shuttling effects and largely enhance the battery capacity and cycle performance. The synthesis of the proposed coordination polymeric layers is simple, scalable, cost saving, and promising for practical use in batteries.

Easy way to determine quantitative spatial resolution distribution for a general inverse problem

NASA Astrophysics Data System (ADS)

An, M.; Feng, M.

2013-12-01

The spatial resolution computation of a solution was nontrivial and more difficult than solving an inverse problem. Most geophysical studies, except for tomographic studies, almost uniformly neglect the calculation of a practical spatial resolution. In seismic tomography studies, a qualitative resolution length can be indicatively given via visual inspection of the restoration of a synthetic structure (e.g., checkerboard tests). An effective strategy for obtaining quantitative resolution length is to calculate Backus-Gilbert resolution kernels (also referred to as a resolution matrix) by matrix operation. However, not all resolution matrices can provide resolution length information, and the computation of resolution matrix is often a difficult problem for very large inverse problems. A new class of resolution matrices, called the statistical resolution matrices (An, 2012, GJI), can be directly determined via a simple one-parameter nonlinear inversion performed based on limited pairs of random synthetic models and their inverse solutions. The total procedure were restricted to forward/inversion processes used in the real inverse problem and were independent of the degree of inverse skill used in the solution inversion. Spatial resolution lengths can be directly given during the inversion. Tests on 1D/2D/3D model inversion demonstrated that this simple method can be at least valid for a general linear inverse problem.

Enhancement of the spontaneous emission in subwavelength quasi-two-dimensional waveguides and resonators

NASA Astrophysics Data System (ADS)

Tokman, Mikhail; Long, Zhongqu; AlMutairi, Sultan; Wang, Yongrui; Belkin, Mikhail; Belyanin, Alexey

2018-04-01

We consider a quantum-electrodynamic problem of the spontaneous emission from a two-dimensional (2D) emitter, such as a quantum well or a 2D semiconductor, placed in a quasi-2D waveguide or cavity with subwavelength confinement in one direction. We apply the Heisenberg-Langevin approach, which includes dissipation and fluctuations in the electron ensemble and in the electromagnetic field of a cavity on equal footing. The Langevin noise operators that we introduce do not depend on any particular model of dissipative reservoir and can be applied to any dissipation mechanism. Moreover, our approach is applicable to nonequilibrium electron systems, e.g., in the presence of pumping, beyond the applicability of the standard fluctuation-dissipation theorem. We derive analytic results for simple but practically important geometries: strip lines and rectangular cavities. Our results show that a significant enhancement of the spontaneous emission, by a factor of order 100 or higher, is possible for quantum wells and other 2D emitters in a subwavelength cavity.

Ultrafast state detection and 2D ion crystals in a Paul trap

NASA Astrophysics Data System (ADS)

Ip, Michael; Ransford, Anthony; Campbell, Wesley

2016-05-01

Projective readout of quantum information stored in atomic qubits typically uses state-dependent CW laser-induced fluorescence. This method requires an often sophisticated imaging system to spatially filter out the background CW laser light. We present an alternative approach that instead uses simple pulse sequences from a mode-locked laser to affect the same state-dependent excitations in less than 1 ns. The resulting atomic fluorescence occurs in the dark, allowing the placement of non-imaging detectors right next to the atom to improve the qubit state detection efficiency and speed. We also study 2D Coulomb crystals of atomic ions in an oblate Paul trap. We find that crystals with hundreds of ions can be held in the trap, potentially offering an alternative to the use of Penning traps for the quantum simulation of 2D lattice spin models. We discuss the classical physics of these crystals and the metastable states that are supported in 2D. This work is supported by the US Army Research Office.

Coupled Photochemical and Condensation Model for the Venus Atmosphere

NASA Astrophysics Data System (ADS)

Bierson, Carver; Zhang, Xi; Mendonca, Joao; Liang, Mao-Chang

2017-10-01

Ground based and Venus Express observations have provided a wealth of information on the vertical and latitudinal distribution of many chemical species in the Venus atmosphere [1,2]. Previous 1D models have focused on the chemistry of either the lower [3] or middle atmosphere [4,5]. Photochemical models focusing on the sulfur gas chemistry have also been independent from models of the sulfuric acid haze and cloud formation [6,7]. In recent years sulfur-bearing particles have become important candidates for the observed SO2 inversion above 80 km [5]. To test this hypothesis it is import to create a self-consistent model that includes photochemistry, transport, and cloud condensation.In this work we extend the domain of the 1D chemistry model of Zhang et al. (2012) [5] to encompass the region between the surface to 110 km. This model includes a simple sulfuric acid condensation scheme with gravitational settling. It simultaneously solves for the chemistry and condensation allowing for self-consistent cloud formation. We compare the resulting chemical distributions to observations at all altitudes. We have also validated our model cloud mass against pioneer Venus observations [8]. This updated full atmosphere chemistry model is also being applied in our 2D solver (altitude and altitude). With this 2D model we can model how the latitudinal distribution of chemical species depends on the meridional circulation. This allows us to use the existing chemical observations to place constraints on Venus GCMs [9-11].References: [1] Arney et al., JGR:Planets, 2014 [2] Vandaele et al., Icarus 2017 (pt. 1 & 2) [3] Krasnopolsky, Icarus, 2007 [4] Krasnopolsky, Icarus, 2012 [5] Zhang et al., Icarus 2012 [6] Gao et al., Icarus, 2014 [7] Krasnopolsky, Icarus, 2015 [8] Knollenberg and Hunten, JGR:Space Physics, 1980 [9] Lee et al., JGR:Planets, 2007 [10] Lebonnois et al., Towards Understanding the Climate of Venus, 2013 [11] Mendoncca and Read, Planetary and Space Science, 2016

Capillary-Force-Assisted Clean-Stamp Transfer of Two-Dimensional Materials.

PubMed

Ma, Xuezhi; Liu, Qiushi; Xu, Da; Zhu, Yangzhi; Kim, Sanggon; Cui, Yongtao; Zhong, Lanlan; Liu, Ming

2017-11-08

A simple and clean method of transferring two-dimensional (2D) materials plays a critical role in the fabrication of 2D electronics, particularly the heterostructure devices based on the artificial vertical stacking of various 2D crystals. Currently, clean transfer techniques rely on sacrificial layers or bulky crystal flakes (e.g., hexagonal boron nitride) to pick up the 2D materials. Here, we develop a capillary-force-assisted clean-stamp technique that uses a thin layer of evaporative liquid (e.g., water) as an instant glue to increase the adhesion energy between 2D crystals and polydimethylsiloxane (PDMS) for the pick-up step. After the liquid evaporates, the adhesion energy decreases, and the 2D crystal can be released. The thin liquid layer is condensed to the PDMS surface from its vapor phase, which ensures the low contamination level on the 2D materials and largely remains their chemical and electrical properties. Using this method, we prepared graphene-based transistors with low charge-neutral concentration (3 × 10 10 cm -2 ) and high carrier mobility (up to 48 820 cm 2 V -1 s -1 at room temperature) and heterostructure optoelectronics with high operation speed. Finally, a capillary-force model is developed to explain the experiment.

geomIO: A tool for geodynamicists to turn 2D cross-sections into 3D geometries

NASA Astrophysics Data System (ADS)

Baumann, Tobias; Bauville, Arthur

2016-04-01

In numerical deformation models, material properties are usually defined on elements (e.g., in body-fitted finite elements), or on a set of Lagrangian markers (Eulerian, ALE or mesh-free methods). In any case, geometrical constraints are needed to assign different material properties to the model domain. Whereas simple geometries such as spheres, layers or cuboids can easily be programmed, it quickly gets complex and time-consuming to create more complicated geometries for numerical model setups, especially in three dimensions. geomIO (geometry I/O, http://geomio.bitbucket.org/) is a MATLAB-based library that has two main functionalities. First, it can be used to create 3D volumes based on series of 2D vector drawings similar to a CAD program; and second, it uses these 3D volumes to assign material properties to the numerical model domain. The drawings can conveniently be created using the open-source vector graphics software Inkscape. Adobe Illustrator is also partially supported. The drawings represent a series of cross-sections in the 3D model domain, for example, cross-sectional interpretations of seismic tomography. geomIO is then used to read the drawings and to create 3D volumes by interpolating between the cross-sections. In the second part, the volumes are used to assign material phases to markers inside the volumes. Multiple volumes can be created at the same time and, depending on the order of assignment, unions or intersections can be built to assign additional material phases. geomIO also offers the possibility to create 3D temperature structures for geodynamic models based on depth dependent parameterisations, for example the half space cooling model. In particular, this can be applied to geometries of subducting slabs of arbitrary shape. Yet, geomIO is held very general, and can be used for a variety of applications. We present examples of setup generation from pictures of micro-scale tectonics and lithospheric scale setups of 3D present-day model geometries.

Comparison of collimated blue-light generation in 85Rb atoms via the D1 and D2 lines

NASA Astrophysics Data System (ADS)

Prajapati, Nikunj; Akulshin, Alexander M.; Novikova, Irina

2018-05-01

We experimentally studied the characteristics of the collimated blue light (CBL) produced in ${}^{85}$Rb vapor by two resonant laser fields exciting atoms into the $5D_{3/2}$ state, using either the $5P_{1/2}$ or the $5P_{3/2}$ intermediate state. We compared the CBL output at different values of frequency detunings, powers, and polarizations of the pump lasers in these two cases, and confirmed the observed trends using a simple theoretical model. We also demonstrated that the addition of the repump laser, preventing the accumulation of atomic population in the uncoupled hyperfine ground state, resulted in nearly an order of magnitude increase in CBL power output. Overall, we found that the $5S_{1/2} - 5P_{1/2} - 5D_{3/2}$ excitation pathway results in stronger CBL generation, as we detected up to $4.25~\\mu$W using two pumps of the same linear polarization. The optimum CBL output for the $5S_{1/2} - 5P_{3/2} - 5D_{3/2}$ excitation pathway required the two pump lasers to have the same circular polarization, but resulted only in a maximum CBL power of $450$~nW.

Correlations in the three-dimensional Lyman-alpha forest contaminated by high column density absorbers

NASA Astrophysics Data System (ADS)

Rogers, Keir K.; Bird, Simeon; Peiris, Hiranya V.; Pontzen, Andrew; Font-Ribera, Andreu; Leistedt, Boris

2018-05-01

Correlations measured in three dimensions in the Lyman-alpha forest are contaminated by the presence of the damping wings of high column density (HCD) absorbing systems of neutral hydrogen (H I; having column densities N(H I) > 1.6 × 10^{17} atoms cm^{-2}), which extend significantly beyond the redshift-space location of the absorber. We measure this effect as a function of the column density of the HCD absorbers and redshift by measuring three-dimensional (3D) flux power spectra in cosmological hydrodynamical simulations from the Illustris project. Survey pipelines exclude regions containing the largest damping wings. We find that, even after this procedure, there is a scale-dependent correction to the 3D Lyman-alpha forest flux power spectrum from residual contamination. We model this residual using a simple physical model of the HCD absorbers as linearly biased tracers of the matter density distribution, convolved with their Voigt profiles and integrated over the column density distribution function. We recommend the use of this model over existing models used in data analysis, which approximate the damping wings as top-hats and so miss shape information in the extended wings. The simple `linear Voigt model' is statistically consistent with our simulation results for a mock residual contamination up to small scales (|k| < 1 h Mpc^{-1}). It does not account for the effect of the highest column density absorbers on the smallest scales (e.g. |k| > 0.4 h Mpc^{-1} for small damped Lyman-alpha absorbers; HCD absorbers with N(H I) ˜ 10^{21} atoms cm^{-2}). However, these systems are in any case preferentially removed from survey data. Our model is appropriate for an accurate analysis of the baryon acoustic oscillations feature. It is additionally essential for reconstructing the full shape of the 3D flux power spectrum.

Architecture with GIDEON, A Program for Design in Structural DNA Nanotechnology

PubMed Central

Birac, Jeffrey J.; Sherman, William B.; Kopatsch, Jens; Constantinou, Pamela E.; Seeman, Nadrian C.

2012-01-01

We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON – a Graphical Integrated Development Environment for OligoNucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without energetic considerations, can be used to explain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction mis-alignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software. PMID:16630733

Structure and Reversibility of 2D von Neumann Cellular Automata Over Triangular Lattice

NASA Astrophysics Data System (ADS)

Uguz, Selman; Redjepov, Shovkat; Acar, Ecem; Akin, Hasan

2017-06-01

Even though the fundamental main structure of cellular automata (CA) is a discrete special model, the global behaviors at many iterative times and on big scales could be a close, nearly a continuous, model system. CA theory is a very rich and useful phenomena of dynamical model that focuses on the local information being relayed to the neighboring cells to produce CA global behaviors. The mathematical points of the basic model imply the computable values of the mathematical structure of CA. After modeling the CA structure, an important problem is to be able to move forwards and backwards on CA to understand their behaviors in more elegant ways. A possible case is when CA is to be a reversible one. In this paper, we investigate the structure and the reversibility of two-dimensional (2D) finite, linear, triangular von Neumann CA with null boundary case. It is considered on ternary field ℤ3 (i.e. 3-state). We obtain their transition rule matrices for each special case. For given special triangular information (transition) rule matrices, we prove which triangular linear 2D von Neumann CAs are reversible or not. It is known that the reversibility cases of 2D CA are generally a much challenged problem. In the present study, the reversibility problem of 2D triangular, linear von Neumann CA with null boundary is resolved completely over ternary field. As far as we know, there is no structure and reversibility study of von Neumann 2D linear CA on triangular lattice in the literature. Due to the main CA structures being sufficiently simple to investigate in mathematical ways, and also very complex to obtain in chaotic systems, it is believed that the present construction can be applied to many areas related to these CA using any other transition rules.

Foot shape modeling.

PubMed

Luximon, Ameersing; Goonetilleke, Ravindra S

2004-01-01

This study is an attempt to show how a "standard" foot can be parameterized using foot length, foot width, foot height, and a measure of foot curvature so that foot shape can be predicted using these simple anthropometric measures. The prediction model was generated using 40 Hong Kong Chinese men, and the model was validated using a different group of 25 Hong Kong Chinese men. The results show that each individual foot shape may be predicted to a mean accuracy of 2.1 mm for the left foot and 2.4 mm for the right foot. Application of this research includes the potential design and development of custom footwear without the necessity of expensive 3-D scanning of feet.

A three-dimensional FEM-DEM technique for predicting the evolution of fracture in geomaterials and concrete

NASA Astrophysics Data System (ADS)

Zárate, Francisco; Cornejo, Alejandro; Oñate, Eugenio

2018-07-01

This paper extends to three dimensions (3D), the computational technique developed by the authors in 2D for predicting the onset and evolution of fracture in a finite element mesh in a simple manner based on combining the finite element method and the discrete element method (DEM) approach (Zárate and Oñate in Comput Part Mech 2(3):301-314, 2015). Once a crack is detected at an element edge, discrete elements are generated at the adjacent element vertexes and a simple DEM mechanism is considered in order to follow the evolution of the crack. The combination of the DEM with simple four-noded linear tetrahedron elements correctly captures the onset of fracture and its evolution, as shown in several 3D examples of application.

Theoretical study on some plasma parameters and thermophysical properties of various gas mixtures in gas-discharge lasers

NASA Astrophysics Data System (ADS)

Temelkov, K. A.; Slaveeva, S. I.; Fedchenko, Yu I.; Chernogorova, T. P.

2018-03-01

Using the well-known Wassiljewa equation and a new simple method, the thermal conductivities of various 2- and 3-component gas mixtures were calculated and compared under gas-discharge conditions optimal for two prospective lasers excited in a nanosecond pulsed longitudinal discharge. By solving the non-stationary heat-conduction equation for electrons, a 2D numerical model was also developed for determination of the radial and temporal dependences of the electron temperature Te (r, t).

Presurgical Planning for Supratentorial Lesions with Free Slicer Software and Sina App.

PubMed

Chen, Ji-Gang; Han, Kai-Wei; Zhang, Dan-Feng; Li, Zhen-Xing; Li, Yi-Ming; Hou, Li-Jun

2017-10-01

Neuronavigation systems are used widely in the localization of intracranial lesions with satisfactory accuracy. However, they are expensive and difficult to learn. Therefore, a simple and practical augmented reality (AR) system using mobile devices might be an alternative technique. We introduce a mobile AR system for the localization of supratentorial lesions. Its practicability and accuracy were examined by clinical application in patients and comparison with a standard neuronavigation system. A 3-dimensional (3D) model including lesions was created with 3D Slicer. A 2-dimensional image of this 3D model was obtained and overlapped on the patient's head with the Sina app. Registration was conducted with the assistance of anatomical landmarks and fiducial markers. The center of lesion projected on scalp was identified with our mobile AR system and standard neuronavigation system, respectively. The difference in distance between the centers identified by these 2 systems was measured. Our mobile AR system was simple and accurate in the localization of supratentorial lesions with a mean distance difference of 4.4 ± 1.1 mm. Registration added on an average of 141.7 ± 39 seconds to operation time. There was no statistically significant difference for the required time among 3 registrations (P = 0.646). The mobile AR system presents an alternative technology for image-guided neurosurgery and proves to be practical and reliable. The technique contributes to optimal presurgical planning for supratentorial lesions, especially in the absence of a neuronavigation system. Copyright © 2017 Elsevier Inc. All rights reserved.

Meridional distribution of molecular hydrogen and its deuterium content in the atmosphere

NASA Astrophysics Data System (ADS)

Rice, Andrew; Quay, Paul; Stutsman, Johnny; Gammon, Richard; Price, Heather; Jaeglé, Lyatt

2010-06-01

The atmospheric molecular hydrogen concentration and its deuterium abundance were measured in remote air samples collected onboard six Pacific Ocean ship transects between 37°N and 77°S during years 2001 through 2005. The data reveal a year-round interhemispheric gradient in H2 concentration and isotopic composition with the extratropical Northern Hemisphere lower in H2 concentration by 17 ± 11 ppb and δD of H2 by 16 ± 12‰ than the Southern Hemisphere (95% confidence). On the basis of these snapshots, the interhemispheric gradient in δD was observed to be smallest in September through November, a time that experiences the largest gradient in concentration, and the largest in April, a time that has a small gradient in concentration. A simple hemispheric box model of the atmosphere indicates that, while the hemispheric asymmetry in soil sink of H2 is primarily responsible for the observed interhemispheric gradient in H2 concentration, the hemispheric difference in the δD of the H2 sources and sinks are equally responsible for the observed interhemispheric gradient in δD. Both the inverse correlation between interhemispheric H2 and δD gradients and their seasonal changes point to the importance of the H2 produced by photochemical sources. Comparisons with a three-dimensional chemical transport model shows reasonable agreement with mean behavior in both variables and provides an accounting for H2 sources and sinks within ±15% without a dramatic change in the H2 budget. Anomalous H2 concentrations and δD in tropics and low-latitude regions observed during the November-December 2001 meridional H2 and δD snapshot is thought to be a result of H2 emissions from biomass burning, possibly from continental Africa.

Rapid and Efficient Filtration-Based Procedure for Separation and Safe Analysis of CBRN Mixed Samples

PubMed Central

Bentahir, Mostafa; Laduron, Frederic; Irenge, Leonid; Ambroise, Jérôme; Gala, Jean-Luc

2014-01-01

Separating CBRN mixed samples that contain both chemical and biological warfare agents (CB mixed sample) in liquid and solid matrices remains a very challenging issue. Parameters were set up to assess the performance of a simple filtration-based method first optimized on separate C- and B-agents, and then assessed on a model of CB mixed sample. In this model, MS2 bacteriophage, Autographa californica nuclear polyhedrosis baculovirus (AcNPV), Bacillus atrophaeus and Bacillus subtilis spores were used as biological agent simulants whereas ethyl methylphosphonic acid (EMPA) and pinacolyl methylphophonic acid (PMPA) were used as VX and soman (GD) nerve agent surrogates, respectively. Nanoseparation centrifugal devices with various pore size cut-off (30 kD up to 0.45 µm) and three RNA extraction methods (Invisorb, EZ1 and Nuclisens) were compared. RNA (MS2) and DNA (AcNPV) quantification was carried out by means of specific and sensitive quantitative real-time PCRs (qPCR). Liquid chromatography coupled to time-of-flight mass spectrometry (LC/TOFMS) methods was used for quantifying EMPA and PMPA. Culture methods and qPCR demonstrated that membranes with a 30 kD cut-off retain more than 99.99% of biological agents (MS2, AcNPV, Bacillus Atrophaeus and Bacillus subtilis spores) tested separately. A rapid and reliable separation of CB mixed sample models (MS2/PEG-400 and MS2/EMPA/PMPA) contained in simple liquid or complex matrices such as sand and soil was also successfully achieved on a 30 kD filter with more than 99.99% retention of MS2 on the filter membrane, and up to 99% of PEG-400, EMPA and PMPA recovery in the filtrate. The whole separation process turnaround-time (TAT) was less than 10 minutes. The filtration method appears to be rapid, versatile and extremely efficient. The separation method developed in this work constitutes therefore a useful model for further evaluating and comparing additional separation alternative procedures for a safe handling and preparation of CB mixed samples. PMID:24505375

Homogenization Issues in the Combustion of Heterogeneous Solid Propellants

NASA Technical Reports Server (NTRS)

Chen, M.; Buckmaster, J.; Jackson, T. L.; Massa, L.

2002-01-01

We examine random packs of discs or spheres, models for ammonium-perchlorate-in-binder propellants, and discuss their average properties. An analytical strategy is described for calculating the mean or effective heat conduction coefficient in terms of the heat conduction coefficients of the individual components, and the results are verified by comparison with those of direct numerical simulations (dns) for both 2-D (disc) and 3-D (sphere) packs across which a temperature difference is applied. Similarly, when the surface regression speed of each component is related to the surface temperature via a simple Arrhenius law, an analytical strategy is developed for calculating an effective Arrhenius law for the combination, and these results are verified using dns in which a uniform heat flux is applied to the pack surface, causing it to regress. These results are needed for homogenization strategies necessary for fully integrated 2-D or 3-D simulations of heterogeneous propellant combustion.

Atherosclerotic plaque delamination: Experiments and 2D finite element model to simulate plaque peeling in two strains of transgenic mice.

PubMed

Merei, Bilal; Badel, Pierre; Davis, Lindsey; Sutton, Michael A; Avril, Stéphane; Lessner, Susan M

2017-03-01

Finite element analyses using cohesive zone models (CZM) can be used to predict the fracture of atherosclerotic plaques but this requires setting appropriate values of the model parameters. In this study, material parameters of a CZM were identified for the first time on two groups of mice (ApoE -/- and ApoE -/- Col8 -/- ) using the measured force-displacement curves acquired during delamination tests. To this end, a 2D finite-element model of each plaque was solved using an explicit integration scheme. Each constituent of the plaque was modeled with a neo-Hookean strain energy density function and a CZM was used for the interface. The model parameters were calibrated by minimizing the quadratic deviation between the experimental force displacement curves and the model predictions. The elastic parameter of the plaque and the CZM interfacial parameter were successfully identified for a cohort of 11 mice. The results revealed that only the elastic parameter was significantly different between the two groups, ApoE -/- Col8 -/- plaques being less stiff than ApoE -/- plaques. Finally, this study demonstrated that a simple 2D finite element model with cohesive elements can reproduce fairly well the plaque peeling global response. Future work will focus on understanding the main biological determinants of regional and inter-individual variations of the material parameters used in the model. Copyright © 2016 Elsevier Ltd. All rights reserved.

3D spherical-cap fitting procedure for (truncated) sessile nano- and micro-droplets & -bubbles.

PubMed

Tan, Huanshu; Peng, Shuhua; Sun, Chao; Zhang, Xuehua; Lohse, Detlef

2016-11-01

In the study of nanobubbles, nanodroplets or nanolenses immobilised on a substrate, a cross-section of a spherical cap is widely applied to extract geometrical information from atomic force microscopy (AFM) topographic images. In this paper, we have developed a comprehensive 3D spherical-cap fitting procedure (3D-SCFP) to extract morphologic characteristics of complete or truncated spherical caps from AFM images. Our procedure integrates several advanced digital image analysis techniques to construct a 3D spherical-cap model, from which the geometrical parameters of the nanostructures are extracted automatically by a simple algorithm. The procedure takes into account all valid data points in the construction of the 3D spherical-cap model to achieve high fidelity in morphology analysis. We compare our 3D fitting procedure with the commonly used 2D cross-sectional profile fitting method to determine the contact angle of a complete spherical cap and a truncated spherical cap. The results from 3D-SCFP are consistent and accurate, while 2D fitting is unavoidably arbitrary in the selection of the cross-section and has a much lower number of data points on which the fitting can be based, which in addition is biased to the top of the spherical cap. We expect that the developed 3D spherical-cap fitting procedure will find many applications in imaging analysis.

PCTDSE: A parallel Cartesian-grid-based TDSE solver for modeling laser-atom interactions

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Zeng, Jiaolong; Yuan, Jianmin

2017-01-01

We present a parallel Cartesian-grid-based time-dependent Schrödinger equation (TDSE) solver for modeling laser-atom interactions. It can simulate the single-electron dynamics of atoms in arbitrary time-dependent vector potentials. We use a split-operator method combined with fast Fourier transforms (FFT), on a three-dimensional (3D) Cartesian grid. Parallelization is realized using a 2D decomposition strategy based on the Message Passing Interface (MPI) library, which results in a good parallel scaling on modern supercomputers. We give simple applications for the hydrogen atom using the benchmark problems coming from the references and obtain repeatable results. The extensions to other laser-atom systems are straightforward with minimal modifications of the source code.

Modeling reactive transport processes in fractured rock using the time domain random walk approach within a dual-porosity framework

NASA Astrophysics Data System (ADS)

Roubinet, D.; Russian, A.; Dentz, M.; Gouze, P.

2017-12-01

Characterizing and modeling hydrodynamic reactive transport in fractured rock are critical challenges for various research fields and applications including environmental remediation, geological storage, and energy production. To this end, we consider a recently developed time domain random walk (TDRW) approach, which is adapted to reproduce anomalous transport behaviors and capture heterogeneous structural and physical properties. This method is also very well suited to optimize numerical simulations by memory-shared massive parallelization and provide numerical results at various scales. So far, the TDRW approach has been applied for modeling advective-diffusive transport with mass transfer between mobile and immobile regions and simple (theoretical) reactions in heterogeneous porous media represented as single continuum domains. We extend this approach to dual-continuum representations considering a highly permeable fracture network embedded into a poorly permeable rock matrix with heterogeneous geochemical reactions occurring in both geological structures. The resulting numerical model enables us to extend the range of the modeled heterogeneity scales with an accurate representation of solute transport processes and no assumption on the Fickianity of these processes. The proposed model is compared to existing particle-based methods that are usually used to model reactive transport in fractured rocks assuming a homogeneous surrounding matrix, and is used to evaluate the impact of the matrix heterogeneity on the apparent reaction rates for different 2D and 3D simple-to-complex fracture network configurations.

Validation of a method for in vivo 3D dose reconstruction for IMRT and VMAT treatments using on-treatment EPID images and a model-based forward-calculation algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Uytven, Eric, E-mail: eric.vanuytven@cancercare.mb.ca; Van Beek, Timothy; McCowan, Peter M.

2015-12-15

Purpose: Radiation treatments are trending toward delivering higher doses per fraction under stereotactic radiosurgery and hypofractionated treatment regimens. There is a need for accurate 3D in vivo patient dose verification using electronic portal imaging device (EPID) measurements. This work presents a model-based technique to compute full three-dimensional patient dose reconstructed from on-treatment EPID portal images (i.e., transmission images). Methods: EPID dose is converted to incident fluence entering the patient using a series of steps which include converting measured EPID dose to fluence at the detector plane and then back-projecting the primary source component of the EPID fluence upstream of themore » patient. Incident fluence is then recombined with predicted extra-focal fluence and used to calculate 3D patient dose via a collapsed-cone convolution method. This method is implemented in an iterative manner, although in practice it provides accurate results in a single iteration. The robustness of the dose reconstruction technique is demonstrated with several simple slab phantom and nine anthropomorphic phantom cases. Prostate, head and neck, and lung treatments are all included as well as a range of delivery techniques including VMAT and dynamic intensity modulated radiation therapy (IMRT). Results: Results indicate that the patient dose reconstruction algorithm compares well with treatment planning system computed doses for controlled test situations. For simple phantom and square field tests, agreement was excellent with a 2%/2 mm 3D chi pass rate ≥98.9%. On anthropomorphic phantoms, the 2%/2 mm 3D chi pass rates ranged from 79.9% to 99.9% in the planning target volume (PTV) region and 96.5% to 100% in the low dose region (>20% of prescription, excluding PTV and skin build-up region). Conclusions: An algorithm to reconstruct delivered patient 3D doses from EPID exit dosimetry measurements was presented. The method was applied to phantom and patient data sets, as well as for dynamic IMRT and VMAT delivery techniques. Results indicate that the EPID dose reconstruction algorithm presented in this work is suitable for clinical implementation.« less

Alternate methodologies to experimentally investigate shock initiation properties of explosives

NASA Astrophysics Data System (ADS)

Svingala, Forrest R.; Lee, Richard J.; Sutherland, Gerrit T.; Benjamin, Richard; Boyle, Vincent; Sickels, William; Thompson, Ronnie; Samuels, Phillip J.; Wrobel, Erik; Cornell, Rodger

2017-01-01

Reactive flow models are desired for new explosive formulations early in the development stage. Traditionally, these models are parameterized by carefully-controlled 1-D shock experiments, including gas-gun testing with embedded gauges and wedge testing with explosive plane wave lenses (PWL). These experiments are easy to interpret due to their 1-D nature, but are expensive to perform and cannot be performed at all explosive test facilities. This work investigates alternative methods to probe shock-initiation behavior of new explosives using widely-available pentolite gap test donors and simple time-of-arrival type diagnostics. These experiments can be performed at a low cost at most explosives testing facilities. This allows experimental data to parameterize reactive flow models to be collected much earlier in the development of an explosive formulation. However, the fundamentally 2-D nature of these tests may increase the modeling burden in parameterizing these models and reduce general applicability. Several variations of the so-called modified gap test were investigated and evaluated for suitability as an alternative to established 1-D gas gun and PWL techniques. At least partial agreement with 1-D test methods was observed for the explosives tested, and future work is planned to scope the applicability and limitations of these experimental techniques.

Silencing ROR1 and ROR2 inhibits invasion and adhesion in an organotypic model of ovarian cancer metastasis

PubMed Central

Henry, Claire; Hacker, Neville; Ford, Caroline

2017-01-01

OBJECTIVE Elevated expression of the ROR1 and ROR2 Wnt receptors has been noted in both the tumour and stromal compartments of ovarian cancer patient tissue samples. In vitro studies have suggested these receptors play a role in ovarian cancer metastasis. However, these previous studies have utilised simple 2D in vitro models to investigate cancer cell growth and migration, which does not allow investigation of stromal involvement in Wnt driven metastasis. AIM To investigate targeting ROR1 and ROR2 using a primary co-culture 3D model of epithelial ovarian cancer dissemination to the omentum. METHODS Primary fibroblasts (NOF) and mesothelial (HPMC) cells were isolated from fresh samples of omentum collected from women with benign or non-metastatic conditions and cultured with collagen to produce a organotypic 3D model. Stable shRNA knockdown of ROR1, ROR2 and double ROR1/ROR2 in OVCAR4 cells were plated onto the 3D model to measure adhesion, or using a transwell to measure invasion. Gene expression changes in primary cells upon OVCAR4 interaction was evaluated using indirect transwell co-culture. RESULTS Double knockdown of ROR1 and ROR2 strongly inhibited cell adhesion (p<0.05) and invasion (P<0.05) to the omentum model. ROR2 was up regulated in primary fibroblasts when cultured with OVCAR4 (P=0.05) and ectopic overexpression of ROR2 in NOFs inhibited cell proliferation (P<0.01) but increased cell migration. CONCLUSION The combination of ROR1 and ROR2 signalling influences ovarian cancer dissemination to the omentum, however ROR2 may also play a role in stromal activation during metastasis. Therefore, targeting both ROR1 and ROR2 may be a powerful approach to treating ovarian cancer. PMID:29348860

Testing a 1-D Analytical Salt Intrusion Model and the Predictive Equation in Malaysian Estuaries

NASA Astrophysics Data System (ADS)

Gisen, Jacqueline Isabella; Savenije, Hubert H. G.

2013-04-01

Little is known about the salt intrusion behaviour in Malaysian estuaries. Study on this topic sometimes requires large amounts of data especially if a 2-D or 3-D numerical models are used for analysis. In poor data environments, 1-D analytical models are more appropriate. For this reason, a fully analytical 1-D salt intrusion model, based on the theory of Savenije in 2005, was tested in three Malaysian estuaries (Bernam, Selangor and Muar) because it is simple and requires minimal data. In order to achieve that, site surveys were conducted in these estuaries during the dry season (June-August) at spring tide by moving boat technique. Data of cross-sections, water levels and salinity were collected, and then analysed with the salt intrusion model. This paper demonstrates a good fit between the simulated and observed salinity distribution for all three estuaries. Additionally, the calibrated Van der Burgh's coefficient K, Dispersion coefficient D0, and salt intrusion length L, for the estuaries also displayed a reasonable correlations with those calculated from the predictive equations. This indicates that not only is the salt intrusion model valid for the case studies in Malaysia but also the predictive model. Furthermore, the results from this study describe the current state of the estuaries with which the Malaysian water authority in Malaysia can make decisions on limiting water abstraction or dredging. Keywords: salt intrusion, Malaysian estuaries, discharge, predictive model, dispersion

Spin Imbalanced Quasi-Two-Dimensional Fermi Gases

NASA Astrophysics Data System (ADS)

Ong, Willie C.

Spin-imbalanced Fermi gases serve as a testbed for fundamental notions and are efficient table-top emulators of a variety of quantum matter ranging from neutron stars, the quark-gluon plasma, to high critical temperature superconductors. A macroscopic quantum phenomenon which occurs in spin-imbalanced Fermi gases is that of phase separation; in three dimensions, a spin-balanced, fully-paired superfluid core is surrounded by an imbalanced normal-fluid shell, followed by a fully polarized shell. In one dimension, the behavior is reversed; a balanced phase appears outside a spin-imbalanced core. This thesis details the first density profile measurements and studies on spin-imbalanced quasi-2D Fermi gases, accomplished with high-resolution, rapid sequential spin-imaging. The measured cloud radii and central densities are in disagreement with mean-field Bardeen-Cooper-Schrieffer theory for a 2D system. Data for normal-fluid mixtures are well fit by a simple 2D polaron model of the free energy. Not predicted by the model is an observed phase transition to a spin-balanced central core above a critical polarisation.

Simulation of elution profiles in liquid chromatography - II: Investigation of injection volume overload under gradient elution conditions applied to second dimension separations in two-dimensional liquid chromatography.

PubMed

Stoll, Dwight R; Sajulga, Ray W; Voigt, Bryan N; Larson, Eli J; Jeong, Lena N; Rutan, Sarah C

2017-11-10

An important research direction in the continued development of two-dimensional liquid chromatography (2D-LC) is to improve the detection sensitivity of the method. This is especially important in applications where injection of large volumes of effluent from the first dimension ( 1 D) column into the second dimension ( 2 D) column leads to severe 2 D peak broadening and peak shape distortion. For example, this is common when coupling two reversed-phase columns and the organic solvent content of the 1 D mobile phase overwhelms the 2 D column with each injection of 1 D effluent, leading to low resolution in the second dimension. In a previous study we validated a simulation approach based on the Craig distribution model and adapted from the work of Czok and Guiochon [1] that enabled accurate simulation of simple isocratic and gradient separations with very small injection volumes, and isocratic separations with mismatched injection and mobile phase solvents [2]. In the present study we have extended this simulation approach to simulate separations relevant to 2D-LC. Specifically, we have focused on simulating 2 D separations where gradient elution conditions are used, there is mismatch between the sample solvent and the starting point in the gradient elution program, injection volumes approach or even exceed the dead volume of the 2 D column, and the extent of sample loop filling is varied. To validate this simulation we have compared results from simulations and experiments for 101 different conditions, including variation in injection volume (0.4-80μL), loop filling level (25-100%), and degree of mismatch between sample organic solvent and the starting point in the gradient elution program (-20 to +20% ACN). We find that that the simulation is accurate enough (median errors in retention time and peak width of -1.0 and -4.9%, without corrections for extra-column dispersion) to be useful in guiding optimization of 2D-LC separations. However, this requires that real injection profiles obtained from 2D-LC interface valves are used to simulate the introduction of samples into the 2 D column. These profiles are highly asymmetric - simulation using simple rectangular pulses leads to peak widths that are far too narrow under many conditions. We believe the simulation approach developed here will be useful for addressing practical questions in the development of 2D-LC methods. Copyright © 2017 Elsevier B.V. All rights reserved.

A Model for S&T Information Provision to Small R&D Systems in Developing Countries with Case Studies in Ethiopia and Tanzania. Stockholm Papers in Library and Information Science.

ERIC Educational Resources Information Center

Winkel, Annette; Schwarz, Stephan

By carefully considering the special characteristics of two small African scientific and technical (S&T) information systems for research and development (R&D), this report defines a simple and straightforward model which can be easily implemented in similar situations with a minimum of external support. The model is designed to build up a…

The Barrett-Crane model: asymptotic measure factor

NASA Astrophysics Data System (ADS)

Kamiński, Wojciech; Steinhaus, Sebastian

2014-04-01

The original spin foam model construction for 4D gravity by Barrett and Crane suffers from a few troubling issues. In the simple examples of the vertex amplitude they can be summarized as the existence of contributions to the asymptotics from non-geometric configurations. Even restricted to geometric contributions the amplitude is not completely worked out. While the phase is known to be the Regge action, the so-called measure factor has remained mysterious for a decade. In the toy model case of the 6j symbol this measure factor has a nice geometric interpretation of V-1/2 leading to speculations that a similar interpretation should be possible also in the 4D case. In this paper we provide the first geometric interpretation of the geometric part of the asymptotic for the spin foam consisting of two glued 4-simplices (decomposition of the 4-sphere) in the Barrett-Crane model in the large internal spin regime.

Modeling Soft Tissue Damage and Failure Using a Combined Particle/Continuum Approach.

PubMed

Rausch, M K; Karniadakis, G E; Humphrey, J D

2017-02-01

Biological soft tissues experience damage and failure as a result of injury, disease, or simply age; examples include torn ligaments and arterial dissections. Given the complexity of tissue geometry and material behavior, computational models are often essential for studying both damage and failure. Yet, because of the need to account for discontinuous phenomena such as crazing, tearing, and rupturing, continuum methods are limited. Therefore, we model soft tissue damage and failure using a particle/continuum approach. Specifically, we combine continuum damage theory with Smoothed Particle Hydrodynamics (SPH). Because SPH is a meshless particle method, and particle connectivity is determined solely through a neighbor list, discontinuities can be readily modeled by modifying this list. We show, for the first time, that an anisotropic hyperelastic constitutive model commonly employed for modeling soft tissue can be conveniently implemented within a SPH framework and that SPH results show excellent agreement with analytical solutions for uniaxial and biaxial extension as well as finite element solutions for clamped uniaxial extension in 2D and 3D. We further develop a simple algorithm that automatically detects damaged particles and disconnects the spatial domain along rupture lines in 2D and rupture surfaces in 3D. We demonstrate the utility of this approach by simulating damage and failure under clamped uniaxial extension and in a peeling experiment of virtual soft tissue samples. In conclusion, SPH in combination with continuum damage theory may provide an accurate and efficient framework for modeling damage and failure in soft tissues.

Modeling Soft Tissue Damage and Failure Using a Combined Particle/Continuum Approach

PubMed Central

Rausch, M. K.; Karniadakis, G. E.; Humphrey, J. D.

2016-01-01

Biological soft tissues experience damage and failure as a result of injury, disease, or simply age; examples include torn ligaments and arterial dissections. Given the complexity of tissue geometry and material behavior, computational models are often essential for studying both damage and failure. Yet, because of the need to account for discontinuous phenomena such as crazing, tearing, and rupturing, continuum methods are limited. Therefore, we model soft tissue damage and failure using a particle/continuum approach. Specifically, we combine continuum damage theory with Smoothed Particle Hydrodynamics (SPH). Because SPH is a meshless particle method, and particle connectivity is determined solely through a neighbor list, discontinuities can be readily modeled by modifying this list. We show, for the first time, that an anisotropic hyperelastic constitutive model commonly employed for modeling soft tissue can be conveniently implemented within a SPH framework and that SPH results show excellent agreement with analytical solutions for uniaxial and biaxial extension as well as finite element solutions for clamped uniaxial extension in 2D and 3D. We further develop a simple algorithm that automatically detects damaged particles and disconnects the spatial domain along rupture lines in 2D and rupture surfaces in 3D. We demonstrate the utility of this approach by simulating damage and failure under clamped uniaxial extension and in a peeling experiment of virtual soft tissue samples. In conclusion, SPH in combination with continuum damage theory may provide an accurate and efficient framework for modeling damage and failure in soft tissues. PMID:27538848

3D reconstruction of SEM images by use of optical photogrammetry software.

PubMed

Eulitz, Mona; Reiss, Gebhard

2015-08-01

Reconstruction of the three-dimensional (3D) surface of an object to be examined is widely used for structure analysis in science and many biological questions require information about their true 3D structure. For Scanning Electron Microscopy (SEM) there has been no efficient non-destructive solution for reconstruction of the surface morphology to date. The well-known method of recording stereo pair images generates a 3D stereoscope reconstruction of a section, but not of the complete sample surface. We present a simple and non-destructive method of 3D surface reconstruction from SEM samples based on the principles of optical close range photogrammetry. In optical close range photogrammetry a series of overlapping photos is used to generate a 3D model of the surface of an object. We adapted this method to the special SEM requirements. Instead of moving a detector around the object, the object itself was rotated. A series of overlapping photos was stitched and converted into a 3D model using the software commonly used for optical photogrammetry. A rabbit kidney glomerulus was used to demonstrate the workflow of this adaption. The reconstruction produced a realistic and high-resolution 3D mesh model of the glomerular surface. The study showed that SEM micrographs are suitable for 3D reconstruction by optical photogrammetry. This new approach is a simple and useful method of 3D surface reconstruction and suitable for various applications in research and teaching. Copyright © 2015 Elsevier Inc. All rights reserved.

Modeling the phase behavior of H2S+n-alkane binary mixtures using the SAFT-VR+D approach.

PubMed

dos Ramos, M Carolina; Goff, Kimberly D; Zhao, Honggang; McCabe, Clare

2008-08-07

A statistical associating fluid theory for potential of variable range has been recently developed to model dipolar fluids (SAFT-VR+D) [Zhao and McCabe, J. Chem. Phys. 2006, 125, 104504]. The SAFT-VR+D equation explicitly accounts for dipolar interactions and their effect on the thermodynamics and structure of a fluid by using the generalized mean spherical approximation (GMSA) to describe a reference fluid of dipolar square-well segments. In this work, we apply the SAFT-VR+D approach to real mixtures of dipolar fluids. In particular, we examine the high-pressure phase diagram of hydrogen sulfide+n-alkane binary mixtures. Hydrogen sulfide is modeled as an associating spherical molecule with four off-center sites to mimic hydrogen bonding and an embedded dipole moment (micro) to describe the polarity of H2S. The n-alkane molecules are modeled as spherical segments tangentially bonded together to form chains of length m, as in the original SAFT-VR approach. By using simple Lorentz-Berthelot combining rules, the theoretical predictions from the SAFT-VR+D equation are found to be in excellent overall agreement with experimental data. In particular, the theory is able to accurately describe the different types of phase behavior observed for these mixtures as the molecular weight of the alkane is varied: type III phase behavior, according to the scheme of classification by Scott and Konynenburg, for the H2S+methane system, type IIA (with the presence of azeotropy) for the H2S+ethane and+propane mixtures; and type I phase behavior for mixtures of H2S and longer n-alkanes up to n-decane. The theory is also able to predict in a qualitative manner the solubility of hydrogen sulfide in heavy n-alkanes.

Shape coexistence and evolution in 98Sr

NASA Astrophysics Data System (ADS)

Park, J.; Garnsworthy, A. B.; Krücken, R.; Andreoiu, C.; Ball, G. C.; Bender, P. C.; Chester, A.; Close, A.; Finlay, P.; Garrett, P. E.; Glister, J.; Hackman, G.; Hadinia, B.; Leach, K. G.; Rand, E. T.; Sjue, S.; Starosta, K.; Svensson, C. E.; Tardiff, E.

2016-01-01

Shape coexistence between the strongly deformed ground state and the weakly deformed 02+ state in 98Sr has been a major topic of interest due to the energy difference of 215 keV, which is the smallest in all even-even nuclei. The electric monopole transition strength ρ2(E 0 ) is an important quantity that can relate the deformation difference and the shape mixing between the two 0+ states, which are admixtures of the vibrational (S) and the rotational (D) states in a simple mixing model. In a β -decay spectroscopy experiment, the experimental ρ2(E 0 ) was measured. A value of 0.053(5) is consistent with the previous measurement and was combined with known electric quadrupole transition strengths B (E 2 ) in calculations of a two-state mixing model. Based on a systematic study on neighboring Kr, Zr, and Mo isotopes, the mixing of the 0+ and 2+ states in 98Sr was determined to be 8.6% and 1.3%, respectively, corresponding to deformation parameters βD=0.38 (1 ) and βS=-0.23 (2 ) . These parameters reproduce experimental transition strengths well except for the 41+→21+ transition, which suggests a smaller D-band deformation for J ≥4 .

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle.

PubMed

Xue, Song; Wang, Ruiying; Yang, Fangping; Terns, Rebecca M; Terns, Michael P; Zhang, Xinxin; Maxwell, E Stuart; Li, Hong

2010-09-24

Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs. Copyright © 2010 Elsevier Inc. All rights reserved.

A simple inertial model for Neptune's zonal circulation

NASA Technical Reports Server (NTRS)

Allison, Michael; Lumetta, James T.

1990-01-01

Voyager imaging observations of zonal cloud-tracked winds on Neptune revealed a strongly subrotational equatorial jet with a speed approaching 500 m/s and generally decreasing retrograde motion toward the poles. The wind data are interpreted with a speculative but revealingly simple model based on steady gradient flow balance and an assumed global homogenization of potential vorticity for shallow layer motion. The prescribed model flow profile relates the equatorial velocity to the mid-latitude shear, in reasonable agreement with the available data, and implies a global horizontal deformation scale L(D) of about 3000 km.

A review on principles, theory and practices of 2D-QSAR.

PubMed

Roy, Kunal; Das, Rudra Narayan

2014-01-01

The central axiom of science purports the explanation of every natural phenomenon using all possible logics coming from pure as well as mixed scientific background. The quantitative structure-activity relationship (QSAR) analysis is a study correlating the behavioral manifestation of compounds with their structures employing the interdisciplinary knowledge of chemistry, mathematics, biology as well as physics. Several studies have attempted to mathematically correlate the chemistry and property (physicochemical/ biological/toxicological) of molecules using various computationally or experimentally derived quantitative parameters termed as descriptors. The dimensionality of the descriptors depends on the type of algorithm employed and defines the nature of QSAR analysis. The most interesting feature of predictive QSAR models is that the behavior of any new or even hypothesized molecule can be predicted by the use of the mathematical equations. The phrase "2D-QSAR" signifies development of QSAR models using 2D-descriptors. Such predictor variables are the most widely practised ones because of their simple and direct mathematical algorithmic nature involving no time consuming energy computations and having reproducible operability. 2D-descriptors have a deluge of contributions in extracting chemical attributes and they are also capable of representing the 3D molecular features to some extent; although in no case they should be considered as the ultimate one, since they often suffer from the problems of intercorrelation, insufficient chemical information as well as lack of interpretation. However, by following rational approaches, novel 2D-descriptors may be developed to obviate various existing problems giving potential 2D-QSAR equations, thereby solving the innumerable chemical mysteries still unexplored.

First-Pass Angiography in Mice Using FDG-PET: A Simple Method of Deriving the Cardiovascular Transit Time Without the Need of Region-of-Interest Drawing.

PubMed

Wu, Hsiao-Ming; Kreissl, Michael C; Schelbert, Heinrich R; Ladno, Waldemar; Prins, Mayumi; Shoghi-Jadid, Kooresh; Chatziioannou, Arion; Phelps, Michael E; Huang, Sung-Cheng

2005-10-01

In this study, we developed a simple and robust semi-automatic method to measure the right ventricle to left ventricle (RV-to-LV) transit time (TT) in mice using 2-[ 18 F]fluoro-2-deoxy-D-glucose (FDG) positron emission tomography (PET). The accuracy of the method was first evaluated using a 4-D digital dynamic mouse phantom. The RV-to-LV TTs of twenty-nine mouse studies were measured using the new method and compared to those obtained from the conventional ROI-drawing method. The results showed that the new method correctly separated different structures (e.g., RV, lung, and LV) in the PET images and generated corresponding time activity curve (TAC) of each structure. The RV-to-LV TTs obtained from the new method and ROI method were not statistically different (P = 0.20; r = 0.76). We expect that this fast and robust method is applicable to the pathophysiology of cardiovascular diseases using small animal models such as rats and mice.

3D Printing of Plant Golgi Stacks from Their Electron Tomographic Models.

PubMed

Mai, Keith Ka Ki; Kang, Madison J; Kang, Byung-Ho

2017-01-01

Three-dimensional (3D) printing is an effective tool for preparing tangible 3D models from computer visualizations to assist in scientific research and education. With the recent popularization of 3D printing processes, it is now possible for individual laboratories to convert their scientific data into a physical form suitable for presentation or teaching purposes. Electron tomography is an electron microscopy method by which 3D structures of subcellular organelles or macromolecular complexes are determined at nanometer-level resolutions. Electron tomography analyses have revealed the convoluted membrane architectures of Golgi stacks, chloroplasts, and mitochondria. But the intricacy of their 3D organizations is difficult to grasp from tomographic models illustrated on computer screens. Despite the rapid development of 3D printing technologies, production of organelle models based on experimental data with 3D printing has rarely been documented. In this chapter, we present a simple guide to creating 3D prints of electron tomographic models of plant Golgi stacks using the two most accessible 3D printing technologies.

3D-Lab: a collaborative web-based platform for molecular modeling.

PubMed

Grebner, Christoph; Norrby, Magnus; Enström, Jonatan; Nilsson, Ingemar; Hogner, Anders; Henriksson, Jonas; Westin, Johan; Faramarzi, Farzad; Werner, Philip; Boström, Jonas

2016-09-01

The use of 3D information has shown impact in numerous applications in drug design. However, it is often under-utilized and traditionally limited to specialists. We want to change that, and present an approach making 3D information and molecular modeling accessible and easy-to-use 'for the people'. A user-friendly and collaborative web-based platform (3D-Lab) for 3D modeling, including a blazingly fast virtual screening capability, was developed. 3D-Lab provides an interface to automatic molecular modeling, like conformer generation, ligand alignments, molecular dockings and simple quantum chemistry protocols. 3D-Lab is designed to be modular, and to facilitate sharing of 3D-information to promote interactions between drug designers. Recent enhancements to our open-source virtual reality tool Molecular Rift are described. The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.

CONVERTING ISOTOPE RATIOS TO DIET COMPOSITION - THE USE OF MIXING MODELS

EPA Science Inventory

Investigations of wildlife foraging ecology with stable isotope analysis are increasing. Converting isotope values to proportions of different foods in a consumer's diet requires the use of mixing models. Simple mixing models based on mass balance equations have been used for d...

CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm: 2D and 3D Ising, Potts, and XY models

NASA Astrophysics Data System (ADS)

Komura, Yukihiro; Okabe, Yutaka

2014-03-01

We present sample CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm. We deal with the classical spin models; the Ising model, the q-state Potts model, and the classical XY model. As for the lattice, both the 2D (square) lattice and the 3D (simple cubic) lattice are treated. We already reported the idea of the GPU implementation for 2D models (Komura and Okabe, 2012). We here explain the details of sample programs, and discuss the performance of the present GPU implementation for the 3D Ising and XY models. We also show the calculated results of the moment ratio for these models, and discuss phase transitions. Catalogue identifier: AERM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERM_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5632 No. of bytes in distributed program, including test data, etc.: 14688 Distribution format: tar.gz Programming language: C, CUDA. Computer: System with an NVIDIA CUDA enabled GPU. Operating system: System with an NVIDIA CUDA enabled GPU. Classification: 23. External routines: NVIDIA CUDA Toolkit 3.0 or newer Nature of problem: Monte Carlo simulation of classical spin systems. Ising, q-state Potts model, and the classical XY model are treated for both two-dimensional and three-dimensional lattices. Solution method: GPU-based Swendsen-Wang multi-cluster spin flip Monte Carlo method. The CUDA implementation for the cluster-labeling is based on the work by Hawick et al. [1] and that by Kalentev et al. [2]. Restrictions: The system size is limited depending on the memory of a GPU. Running time: For the parameters used in the sample programs, it takes about a minute for each program. Of course, it depends on the system size, the number of Monte Carlo steps, etc. References: [1] K.A. Hawick, A. Leist, and D. P. Playne, Parallel Computing 36 (2010) 655-678 [2] O. Kalentev, A. Rai, S. Kemnitzb, and R. Schneider, J. Parallel Distrib. Comput. 71 (2011) 615-620

Matrix-Assisted Three-Dimensional Printing of Cellulose Nanofibers for Paper Microfluidics.

PubMed

Shin, Sungchul; Hyun, Jinho

2017-08-09

A cellulose nanofiber (CNF), one of the most attractive green bioresources, was adopted for construction of microfluidic devices using matrix-assisted three-dimensional (3D) printing. CNF hydrogels can support structures printed using CAD design in a 3D hydrogel environment with the appropriate combination of rheological properties between the CNF hydrogel and ink materials. Amazingly, the structure printed freely in the bulky CNF hydrogels was able to retain its highly resolved 3D features in an ultrathin two-dimensional (2D) paper using a simple drying process. The dimensional change in the CNF hydrogels from 3D to 2D resulted from simple dehydration of the CNFs and provided transparent, stackable paper-based 3D channel devices. As a proof of principle, the rheological properties of the CNF hydrogels, the 3D structure of the ink, the formation of channels by evacuation of the ink, and the highly localized selectivity of the devices are described.

Hydrodynamics of metachronal paddling in crustaceans

NASA Astrophysics Data System (ADS)

Santhanakrishnan, A.; Lai, H. K.; Samaee, M.; Lewis, T. J.; Guy, R. D.

2016-02-01

Long-tailed crustaceans such as crayfish and krill swim by rhythmically paddling a set of four to five limbs (swimmerets) originating from their abdomen. Despite variations in limb size and stroke frequency, movements of ipsilateral limbs always maintain a tail-to-head metachronal rhythm with an approximate quarter-period inter-limb phase difference. Relatively few studies have examined the fluid dynamics of metachronal limb stroke for the range of Reynolds numbers at which crustaceans operate. The objective of this study is to investigate metachronal paddling as a function of Reynolds number (Re) for quantifying hydrodynamic scalability of this swimming mechanism, including the effect of hinges on paddles as seen in crustacean swimmerets. Our approach included experiments on a scaled physical model and computational fluid dynamics (CFD) simulations using the immersed boundary (IB) method. The scaled robotic model of metachronal paddling consisted of a rectangular aquarium tank fitted above with four stepper motors coupled to a four-bar linkage that actuated four acrylic paddles immersed in water-glycerin fluid medium. 2D particle image velocimetry (PIV) was used for quantitative flow visualization in the experiments. The swimmerets were modeled in CFD simulations as rigid 1D rods in a 2D fluid. The inter-limb phase difference was varied from 0% (synchronous paddling) through 50% across Re range of O(10-1000). Two types of experimental limb models were tested, including a simple flat plate and a `split-paddle' structure with two flat plates connected halfway with hinges. Our results show that the natural tail-to-head metachronal rhythm with an approximate quarter-period phase difference is the most effective and efficient rhythm across a wide range of Reynolds numbers. Limb models with hinges generated increased horizontal flow compared to the simple flat plate paddles, suggesting that asymmetry between power and return stroke is important to augment thrust.

What is Neptune's D/H ratio really telling us about its water abundance?

NASA Astrophysics Data System (ADS)

Ali-Dib, Mohamad; Lakhlani, Gunjan

2018-05-01

We investigate the deep-water abundance of Neptune using a simple two-component (core + envelope) toy model. The free parameters of the model are the total mass of heavy elements in the planet (Z), the mass fraction of Z in the envelope (fenv), and the D/H ratio of the accreted building blocks (D/Hbuild).We systematically search the allowed parameter space on a grid and constrain it using Neptune's bulk carbon abundance, D/H ratio, and interior structure models. Assuming solar C/O ratio and cometary D/H for the accreted building blocks are forming the planet, we can fit all of the constraints if less than ˜15 per cent of Z is in the envelope (f_{env}^{median} ˜ 7 per cent), and the rest is locked in a solid core. This model predicts a maximum bulk oxygen abundance in Neptune of 65× solar value. If we assume a C/O of 0.17, corresponding to clathrate-hydrates building blocks, we predict a maximum oxygen abundance of 200× solar value with a median value of ˜140. Thus, both cases lead to oxygen abundance significantly lower than the preferred value of Cavalié et al. (˜540× solar), inferred from model-dependent deep CO observations. Such high-water abundances are excluded by our simple but robust model. We attribute this discrepancy to our imperfect understanding of either the interior structure of Neptune or the chemistry of the primordial protosolar nebula.

Comparison of rigorous and simple vibrational models for the CO2 gasdynamic laser

NASA Technical Reports Server (NTRS)

Monson, D. J.

1977-01-01

The accuracy of a simple vibrational model for computing the gain in a CO2 gasdynamic laser is assessed by comparing results computed from it with results computed from a rigorous vibrational model. The simple model is that of Anderson et al. (1971), in which the vibrational kinetics are modeled by grouping the nonequilibrium vibrational degrees of freedom into two modes, to each of which there corresponds an equation describing vibrational relaxation. The two models agree fairly well in the computed gain at low temperatures, but the simple model predicts too high a gain at the higher temperatures of current interest. The sources of error contributing to the overestimation given by the simple model are determined by examining the simplified relaxation equations.

Endoperoxide polyketides from a Chinese Plakortis simplex: further evidence of the impact of stereochemistry on antimalarial activity of simple 1,2-dioxanes.

PubMed

Chianese, Giuseppina; Persico, Marco; Yang, Fan; Lin, Hou-Wen; Guo, Yue-Wei; Basilico, Nicoletta; Parapini, Silvia; Taramelli, Donatella; Taglialatela-Scafati, Orazio; Fattorusso, Caterina

2014-09-01

Chemical investigation of the organic extract obtained from the sponge Plakortis simplex collected in the South China Sea afforded five new polyketide endoperoxides (2 and 4-7), along with two known analogues (1 and 3). The stereostructures of these metabolites have been deduced on the basis of spectroscopic analysis and chemical conversion. The isolated endoperoxide derivatives have been tested for their in vitro antimalarial activity against Plasmodium falciparum strains, showing IC50 values in the low micromolar range. The structure-activity relationships were analyzed by means of a detailed computational investigation and rationalized in the light of the mechanism of action proposed for this class of simple antimalarials. The relative orientation of the atoms involved in the putative radical generation and transfer reaction was demonstrated to have a great impact on the antimalarial activity. The resulting 3D pharmacophoric model can be a useful guide to design simple and effective antimalarial lead compounds belonging to the class of 1,2-dioxanes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Kinematic analysis of asymmetric folds in competent layers using mathematical modelling

NASA Astrophysics Data System (ADS)

Aller, J.; Bobillo-Ares, N. C.; Bastida, F.; Lisle, R. J.; Menéndez, C. O.

2010-08-01

Mathematical 2D modelling of asymmetric folds is carried out by applying a combination of different kinematic folding mechanisms: tangential longitudinal strain, flexural flow and homogeneous deformation. The main source of fold asymmetry is discovered to be due to the superimposition of a general homogeneous deformation on buckle folds that typically produces a migration of the hinge point. Forward modelling is performed mathematically using the software 'FoldModeler', by the superimposition of simple shear or a combination of simple shear and irrotational strain on initial buckle folds. The resulting folds are Ramsay class 1C folds, comparable to those formed by symmetric flattening, but with different length of limbs and layer thickness asymmetry. Inverse modelling is made by fitting the natural fold to a computer-simulated fold. A problem of this modelling is the search for the most appropriate homogeneous deformation to be superimposed on the initial fold. A comparative analysis of the irrotational and rotational deformations is made in order to find the deformation which best simulates the shapes and attitudes of natural folds. Modelling of recumbent folds suggests that optimal conditions for their development are: a) buckling in a simple shear regime with a sub-horizontal shear direction and layering gently dipping towards this direction; b) kinematic amplification due to superimposition of a combination of simple shear and irrotational strain with a sub-vertical maximum shortening direction for the latter component. The modelling shows that the amount of homogeneous strain necessary for the development of recumbent folds is much less when an irrotational strain component is superimposed at this stage that when the superimposed strain is only simple shear. In nature, the amount of the irrotational strain component probably increases during the development of the fold as a consequence of the increasing influence of the gravity due to the tectonic superimposition of rocks.

A Summary of the Naval Postgraduate School Research Program.

DTIC Science & Technology

1981-04-01

1467-1489. K. M. Lau," Climatic Feedback Mechanisms in the Tropical Pacific,"Ocean Modeling , 28. K. M. Lau,"Oscillation in a Simple Equatorial...and 74 R. H. Shudde Support J. K. Arima Research in Officer Manpower and 75 P. R. Milch Personnel Planning R. A. Weitzman D. R. Barr C3 Technology...Procedures D. P. Gaver Modeling and Influence of Informa- 83 tion on the Progress of Conflict or Combat by Mathematical and Compu- tational Methods D. P. Gaver

Simulations of 4D edge transport and dynamics using the TEMPEST gyro-kinetic code

NASA Astrophysics Data System (ADS)

Rognlien, T. D.; Cohen, B. I.; Cohen, R. H.; Dorr, M. R.; Hittinger, J. A. F.; Kerbel, G. D.; Nevins, W. M.; Xiong, Z.; Xu, X. Q.

2006-10-01

Simulation results are presented for tokamak edge plasmas with a focus on the 4D (2r,2v) option of the TEMPEST continuum gyro-kinetic code. A detailed description of a variety of kinetic simulations is reported, including neoclassical radial transport from Coulomb collisions, electric field generation, dynamic response to perturbations by geodesic acoustic modes, and parallel transport on open magnetic-field lines. Comparison is made between the characteristics of the plasma solutions on closed and open magnetic-field line regions separated by a magnetic separatrix, and simple physical models are used to qualitatively explain the differences observed in mean flow and electric-field generation. The status of extending the simulations to 5D turbulence will be summarized. The code structure used in this ongoing project is also briefly described, together with future plans.

Comparison of Damage Path Predictions for Composite Laminates by Explicit and Standard Finite Element Analysis Tools

NASA Technical Reports Server (NTRS)

Bogert, Philip B.; Satyanarayana, Arunkumar; Chunchu, Prasad B.

2006-01-01

Splitting, ultimate failure load and the damage path in center notched composite specimens subjected to in-plane tension loading are predicted using progressive failure analysis methodology. A 2-D Hashin-Rotem failure criterion is used in determining intra-laminar fiber and matrix failures. This progressive failure methodology has been implemented in the Abaqus/Explicit and Abaqus/Standard finite element codes through user written subroutines "VUMAT" and "USDFLD" respectively. A 2-D finite element model is used for predicting the intra-laminar damages. Analysis results obtained from the Abaqus/Explicit and Abaqus/Standard code show good agreement with experimental results. The importance of modeling delamination in progressive failure analysis methodology is recognized for future studies. The use of an explicit integration dynamics code for simple specimen geometry and static loading establishes a foundation for future analyses where complex loading and nonlinear dynamic interactions of damage and structure will necessitate it.

Analysis of Maneuvering Targets with Complex Motions by Two-Dimensional Product Modified Lv's Distribution for Quadratic Frequency Modulation Signals.

PubMed

Jing, Fulong; Jiao, Shuhong; Hou, Changbo; Si, Weijian; Wang, Yu

2017-06-21

For targets with complex motion, such as ships fluctuating with oceanic waves and high maneuvering airplanes, azimuth echo signals can be modeled as multicomponent quadratic frequency modulation (QFM) signals after migration compensation and phase adjustment. For the QFM signal model, the chirp rate (CR) and the quadratic chirp rate (QCR) are two important physical quantities, which need to be estimated. For multicomponent QFM signals, the cross terms create a challenge for detection, which needs to be addressed. In this paper, by employing a novel multi-scale parametric symmetric self-correlation function (PSSF) and modified scaled Fourier transform (mSFT), an effective parameter estimation algorithm is proposed-referred to as the Two-Dimensional product modified Lv's distribution (2D-PMLVD)-for QFM signals. The 2D-PMLVD is simple and can be easily implemented by using fast Fourier transform (FFT) and complex multiplication. These measures are analyzed in the paper, including the principle, the cross term, anti-noise performance, and computational complexity. Compared to the other three representative methods, the 2D-PMLVD can achieve better anti-noise performance. The 2D-PMLVD, which is free of searching and has no identifiability problems, is more suitable for multicomponent situations. Through several simulations and analyses, the effectiveness of the proposed estimation algorithm is verified.

A simple all-time model for the birth, big bang, and death of the universe

NASA Astrophysics Data System (ADS)

Fischer, Arthur E.

We model the standard ΛCDM model of the universe by the spatially flat FLRW line element dsΛCDM2 = -c2dt2 + 8πGρm,0 Λc22/3 sinh 1 23Λct4/3dσ Euclid2 which we extend for all time t ∈ (-∞,∞). Although there is a cosmological singularity at the big bang t = 0, since the spatial part of the metric collapses to zero, nevertheless, this line element is defined for all time t ∈ (-∞,∞), is C∞ for all t≠0, is C1 differentiable at t = 0, and is non-degenerate and solves Friedmann’s equation for all t≠0. Thus, we can use this extended line element to model the universe from its past-asymptotic initial state dS4- at t = -∞, through the big bang at t = 0, and onward to its future-asymptotic final state dS4+ at t = ∞. Since in this model the universe existed before the big bang, we conclude that (1) the universe was not created de novo at the big bang and (2) cosmological singularities such as black holes or the big bang itself need not be an end to spacetime. Our model shows that the universe was asymptotically created de novo out of nothing at t = -∞ from an unstable vacuum negative half de Sitter dsdS4-2 initial state and then dies asymptotically at t = ∞ as the stable positive half de Sitter dsdS4+2 final state. Since the de Sitter states are vacuum matter states, our model shows that the universe was created from nothing at t = -∞ and dies at t = ∞ to nothing.

Energy Conservation and Conversion in NIMROD Computations of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Maddox, J. A.; Sovinec, C. R.

2017-10-01

Previous work modeling magnetic relaxation during non-inductive start-up at the Pegasus spherical tokamak indicates an order of magnitude gap between measured experimental temperature and simulated temperature in NIMROD. Potential causes of the plasma temperature gap include: insufficient transport modeling, too low modeled injector power input, and numerical loss of energy, as energy is not algorithmically conserved in NIMROD simulations. Simple 2D nonlinear MHD simulations explore numerical energy conservation discrepancies in NIMROD because understanding numerical loss of energy is fundamental to addressing the physical problems of the other potential causes of energy loss. Evolution of these configurations induces magnetic reconnection, which transfers magnetic energy to heat and kinetic energy. The kinetic energy is eventually damped so, magnetic energy loss must correspond to an increase in internal energy. Results in the 2D geometries indicate that numerical energy loss during reconnection depends on the temporal resolution of the dynamics. Work support from U.S. Department of Energy through a subcontract from the Plasma Science and Innovation Center.

A simple methodology to produce flood risk maps consistent with FEMA's base flood elevation maps: Implementation and validation over the entire contiguous United States

NASA Astrophysics Data System (ADS)

Goteti, G.; Kaheil, Y. H.; Katz, B. G.; Li, S.; Lohmann, D.

2011-12-01

In the United States, government agencies as well as the National Flood Insurance Program (NFIP) use flood inundation maps associated with the 100-year return period (base flood elevation, BFE), produced by the Federal Emergency Management Agency (FEMA), as the basis for flood insurance. A credibility check of the flood risk hydraulic models, often employed by insurance companies, is their ability to reasonably reproduce FEMA's BFE maps. We present results from the implementation of a flood modeling methodology aimed towards reproducing FEMA's BFE maps at a very fine spatial resolution using a computationally parsimonious, yet robust, hydraulic model. The hydraulic model used in this study has two components: one for simulating flooding of the river channel and adjacent floodplain, and the other for simulating flooding in the remainder of the catchment. The first component is based on a 1-D wave propagation model, while the second component is based on a 2-D diffusive wave model. The 1-D component captures the flooding from large-scale river transport (including upstream effects), while the 2-D component captures the flooding from local rainfall. The study domain consists of the contiguous United States, hydrologically subdivided into catchments averaging about 500 km2 in area, at a spatial resolution of 30 meters. Using historical daily precipitation data from the Climate Prediction Center (CPC), the precipitation associated with the 100-year return period event was computed for each catchment and was input to the hydraulic model. Flood extent from the FEMA BFE maps is reasonably replicated by the 1-D component of the model (riverine flooding). FEMA's BFE maps only represent the riverine flooding component and are unavailable for many regions of the USA. However, this modeling methodology (1-D and 2-D components together) covers the entire contiguous USA. This study is part of a larger modeling effort from Risk Management Solutions° (RMS) to estimate flood risk associated with extreme precipitation events in the USA. Towards this greater objective, state-of-the-art models of flood hazard and stochastic precipitation are being implemented over the contiguous United States. Results from the successful implementation of the modeling methodology will be presented.

Analysis of Subthreshold Current Reset Noise in Image Sensors.

PubMed

Teranishi, Nobukazu

2016-05-10

To discuss the reset noise generated by slow subthreshold currents in image sensors, intuitive and simple analytical forms are derived, in spite of the subthreshold current nonlinearity. These solutions characterize the time evolution of the reset noise during the reset operation. With soft reset, the reset noise tends to m k T / 2 C P D when t → ∞ , in full agreement with previously published results. In this equation, C P D is the photodiode (PD) capacitance and m is a constant. The noise has an asymptotic time dependence of t - 1 , even though the asymptotic time dependence of the average (deterministic) PD voltage is as slow as log t . The flush reset method is effective because the hard reset part eliminates image lag, and the soft reset part reduces the noise to soft reset level. The feedback reset with reverse taper control method shows both a fast convergence and a good reset noise reduction. When the feedback amplifier gain, A, is larger, even small value of capacitance, C P , between the input and output of the feedback amplifier will drastically decrease the reset noise. If the feedback is sufficiently fast, the reset noise limit when t → ∞ , becomes m k T ( C P D + C P 1 ) 2 2 q 2 A ( C P D + ( 1 + A ) C P ) in terms of the number of electron in the PD. According to this simple model, if CPD = 10 fF, CP/CPD = 0.01, and A = 2700 are assumed, deep sub-electron rms reset noise is possible.

Rabbit Calvarial Defect Model for Customized 3D-Printed Bone Grafts.

PubMed

Lee, Kang-Gon; Lee, Kang-Sik; Kang, Yu-Jeoung; Hwang, Jong-Hyun; Lee, Se-Hwan; Park, Sang-Hyug; Park, Yongdoo; Cho, Young-Sam; Lee, Bu-Kyu

2018-05-01

Bone graft materials are commonly used to regenerate various bone defects, but their application is often limited because of the complex defect shape in various clinical conditions. Hence, customized bone grafts using three-dimensional (3D) printing techniques have been developed. However, conventional simple bone defect models are limited for evaluating the benefits and manufacturing accuracy of 3D-printed customized bone grafts. Thus, the aim of the present study was to develop a complex-shaped bone defect model. We designed an 8-shaped bony defect that consists of two simple circles attached to the rabbit calvarium. To determine the critical-sized defect (CSD) of the 8-shaped defects, 5.6- and 7-mm-diameter trephine burs were tested, and the 7-mm-diameter bur could successfully create a CSD, which was easily reproducible on the rabbit calvarium. The rate of new bone formation was 28.65% ± 8.63% at 16 weeks following creation of the defect. To confirm its efficacy for clinical use, the 8-shaped defect was created on a rabbit calvarium and 3D computed tomography (CT) was performed. A stereolithography file was produced using the CT data, and a 3D-printed polycaprolactone graft was fabricated. Using our 8-shaped defect model, we were able to modify the tolerances of the bone graft and calvarial defect to fabricate a more precise bone graft. Customized characteristics of the bone graft were then used to improve the accuracy of the bone graft. In addition, we confirmed the fitting ability of the 3D-printed graft during implantation of the graft. Our 8-shaped defect model on the rabbit calvarium using a 7.0-mm trephine bur may be a useful CSD model for evaluating 3D-printed graft materials.

Effect of strong elastic contrasts on the propagation of seismic wave in hard-rock environments

NASA Astrophysics Data System (ADS)

Saleh, R.; Zheng, L.; Liu, Q.; Milkereit, B.

2013-12-01

Understanding the propagation of seismic waves in a presence of strong elastic contrasts, such as topography, tunnels and ore-bodies is still a challenge. Safety in mining is a major concern and seismic monitoring is the main tool here. For engineering purposes, amplitudes (peak particle velocity/acceleration) and travel times of seismic events (mostly blasts or microseismic events) are critical parameters that have to be determined at various locations in a mine. These parameters are useful in preparing risk maps or to better understand the process of spatial and temporal stress distributions in a mine. Simple constant velocity models used for monitoring studies in mining, cannot explain the observed complexities in scattered seismic waves. In hard-rock environments modeling of elastic seismic wavefield require detailed 3D petrophysical, infrastructure and topographical data to simulate the propagation of seismic wave with a frequencies up to few kilohertz. With the development of efficient numerical techniques, and parallel computation facilities, a solution for such a problem is achievable. In this study, the effects of strong elastic contrasts such as ore-bodies, rough topography and tunnels will be illustrated using 3D modeling method. The main tools here are finite difference code (SOFI3D)[1] that has been benchmarked for engineering studies, and spectral element code (SPECFEM) [2], which was, developed for global seismology problems. The modeling results show locally enhanced peak particle velocity due to presence of strong elastic contrast and topography in models. [1] Bohlen, T. Parallel 3-D viscoelastic finite difference seismic modeling. Computers & Geosciences 28 (2002) 887-899 [2] Komatitsch, D., and J. Tromp, Introduction to the spectral-element method for 3-D seismic wave propagation, Geophys. J. Int., 139, 806-822, 1999.

A simple method for isocapnic hyperventilation evaluated in a lung model.

PubMed

Hallén, K; Stenqvist, O; Ricksten, S-E; Lindgren, S

2016-05-01

Isocapnic hyperventilation (IHV) has the potential to increase the elimination rate of anaesthetic gases and has been shown to shorten time to wake-up and post-operative recovery time after inhalation anaesthesia. In this bench test, we describe a technique to achieve isocapnia during hyperventilation (HV) by adding carbon dioxide (CO2) directly to the breathing circuit of a standard anaesthesia apparatus with standard monitoring equipment. Into a mechanical lung model, carbon dioxide was added to simulate a CO2 production (V(CO2)) of 175, 200 and 225 ml/min. Dead space (V(D)) volume could be set at 44, 92 and 134 ml. From baseline ventilation (BLV), HV was achieved by doubling the minute ventilation and fresh gas flow for each level of V(CO2), and dead space. During HV, CO2 was delivered (D(CO2)) by a precision flow meter via a mixing box to the inspiratory limb of the anaesthesia circuit to achieve isocapnia. During HV, the alveolar ventilation increased by 113 ± 6%. Tidal volume increased by 20 ± 0.1% during IHV irrespective of V(D) and V(CO2) level. D(CO2) varied between 147 ± 8 and 325 ± 13 ml/min. Low V(CO2) and large V(D) demanded a greater D(CO2) administration to achieve isocapnia. The FICO2 level during IHV varied between 2.3% and 3.3%. It is possible to maintain isocapnia during HV by delivering carbon dioxide through a standard anaesthesia circuit equipped with modern monitoring capacities. From alveolar ventilation, CO2 production and dead space, the amount of carbon dioxide that is needed to achieve IHV can be estimated. © 2015 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

A simple synthesis of 2-keto-3-deoxy-D-erythro-hexonic acid isopropyl ester, a key sugar for the bacterial population living under metallic stress.

PubMed

Grison, Claire M; Renard, Brice-Loïc; Grison, Claude

2014-02-01

2-Keto-3-deoxy-D-erythro-hexonic acid (KDG) is the key intermediate metabolite of the Entner Doudoroff (ED) pathway. A simple, efficient and stereoselective synthesis of KDG isopropyl ester is described in five steps from 2,3-O-isopropylidene-D-threitol with an overall yield of 47%. KDG isopropyl ester is studied as an attractive marker of a functional Entner Doudoroff pathway. KDG isopropyl ester is used to promote growth of ammonium producing bacterial strains, showing interesting features in the remediation of heavy-metal polluted soils. Copyright © 2013 Elsevier Inc. All rights reserved.

Density profile of strongly correlated spherical Yukawa plasmas

NASA Astrophysics Data System (ADS)

Bonitz, M.; Henning, C.; Ludwig, P.; Golubnychiy, V.; Baumgartner, H.; Piel, A.; Block, D.

2006-10-01

Recently the discovery of 3D-dust crystals [1] excited intensive experimental and theoretical activities [2-4]. Details of the shell structure of these crystals has been very well explained theoretically by a simple model involving an isotropic Yukawa-type pair repulsion and an external harmonic confinement potential [4]. On the other hand, it has remained an open question how the average radial density profile, looks like. We show that screening has a dramatic effect on the density profile, which we derive analytically for the ground state. Interestingly, the result applies not only to a continuous plasma distribution but also to simulation data for the Coulomb crystals exhibiting the above mentioned shell structure. Furthermore, excellent agreement between the continuum model and shell models is found [5]. [1] O. Arp, D. Block, A. Piel, and A. Melzer, Phys. Rev. Lett. 93, 165004 (2004). [2] H. Totsuji, C. Totsuji, T. Ogawa, and K. Tsuruta, Phys. Rev. E 71, 045401 (2005) [3] P. Ludwig, S. Kosse, and M. Bonitz, Phys. Rev. E 71, 046403 (2005) [4] M. Bonitz, D. Block, O. Arp, V. Golubnychiy, H. Baumgartner, P. Ludwig, A. Piel, and A. Filinov, Phys. Rev. Lett. 96, 075001 (2006) [5] C. Henning, M. Bonitz, A. Piel, P. Ludwig, H. Baumgartner, V. Golubnichiy, and D. Block, submitted to Phys. Rev. E

Dynamic PET simulator via tomographic emission projection for kinetic modeling and parametric image studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Häggström, Ida, E-mail: haeggsti@mskcc.org; Beattie, Bradley J.; Schmidtlein, C. Ross

2016-06-15

Purpose: To develop and evaluate a fast and simple tool called dPETSTEP (Dynamic PET Simulator of Tracers via Emission Projection), for dynamic PET simulations as an alternative to Monte Carlo (MC), useful for educational purposes and evaluation of the effects of the clinical environment, postprocessing choices, etc., on dynamic and parametric images. Methods: The tool was developed in MATLAB using both new and previously reported modules of PETSTEP (PET Simulator of Tracers via Emission Projection). Time activity curves are generated for each voxel of the input parametric image, whereby effects of imaging system blurring, counting noise, scatters, randoms, and attenuationmore » are simulated for each frame. Each frame is then reconstructed into images according to the user specified method, settings, and corrections. Reconstructed images were compared to MC data, and simple Gaussian noised time activity curves (GAUSS). Results: dPETSTEP was 8000 times faster than MC. Dynamic images from dPETSTEP had a root mean square error that was within 4% on average of that of MC images, whereas the GAUSS images were within 11%. The average bias in dPETSTEP and MC images was the same, while GAUSS differed by 3% points. Noise profiles in dPETSTEP images conformed well to MC images, confirmed visually by scatter plot histograms, and statistically by tumor region of interest histogram comparisons that showed no significant differences (p < 0.01). Compared to GAUSS, dPETSTEP images and noise properties agreed better with MC. Conclusions: The authors have developed a fast and easy one-stop solution for simulations of dynamic PET and parametric images, and demonstrated that it generates both images and subsequent parametric images with very similar noise properties to those of MC images, in a fraction of the time. They believe dPETSTEP to be very useful for generating fast, simple, and realistic results, however since it uses simple scatter and random models it may not be suitable for studies investigating these phenomena. dPETSTEP can be downloaded free of cost from https://github.com/CRossSchmidtlein/dPETSTEP.« less

Effects of non-local electron transport in one-dimensional and two-dimensional simulations of shock-ignited inertial confinement fusion targets

NASA Astrophysics Data System (ADS)

Marocchino, A.; Atzeni, S.; Schiavi, A.

2014-01-01

In some regions of a laser driven inertial fusion target, the electron mean-free path can become comparable to or even longer than the electron temperature gradient scale-length. This can be particularly important in shock-ignited (SI) targets, where the laser-spike heated corona reaches temperatures of several keV. In this case, thermal conduction cannot be described by a simple local conductivity model and a Fick's law. Fluid codes usually employ flux-limited conduction models, which preserve causality, but lose important features of the thermal flow. A more accurate thermal flow modeling requires convolution-like non-local operators. In order to improve the simulation of SI targets, the non-local electron transport operator proposed by Schurtz-Nicolaï-Busquet [G. P. Schurtz et al., Phys. Plasmas 7, 4238 (2000)] has been implemented in the DUED fluid code. Both one-dimensional (1D) and two-dimensional (2D) simulations of SI targets have been performed. 1D simulations of the ablation phase highlight that while the shock profile and timing might be mocked up with a flux-limiter; the electron temperature profiles exhibit a relatively different behavior with no major effects on the final gain. The spike, instead, can only roughly be reproduced with a fixed flux-limiter value. 1D target gain is however unaffected, provided some minor tuning of laser pulses. 2D simulations show that the use of a non-local thermal conduction model does not affect the robustness to mispositioning of targets driven by quasi-uniform laser irradiation. 2D simulations performed with only two final polar intense spikes yield encouraging results and support further studies.

Edge-to-center plasma density ratios in two-dimensional plasma discharges

NASA Astrophysics Data System (ADS)

Lucken, R.; Croes, V.; Lafleur, T.; Raimbault, J.-L.; Bourdon, A.; Chabert, P.

2018-03-01

Edge-to-center plasma density ratios—so-called h factors—are important parameters for global models of plasma discharges as they are used to calculate the plasma losses at the reactor walls. There are well-established theories for h factors in the one-dimensional (1D) case. The purpose of this paper is to establish h factors in two-dimensional (2D) systems, with guidance from a 2D particle-in-cell (PIC) simulation. We derive analytical solutions of a 2D fluid theory that includes the effect of ion inertia, but assumes a constant (independent of space) ion collision frequency (using an average ion velocity) across the discharge. Predicted h factors from this 2D fluid theory have the same order of magnitude and the same trends as the PIC simulations when the average ion velocity used in the collision frequency is set equal to the ion thermal velocity. The best agreement is obtained when the average ion velocity varies with pressure (but remains independent of space), going from half the Bohm velocity at low pressure, to the thermal velocity at high pressure. The analysis also shows that a simple correction of the widely-used 1D heuristic formula may be proposed to accurately incorporate 2D effects.

Chern-Simons gauge theory on orbifolds: Open strings from three dimensions

NASA Astrophysics Data System (ADS)

Hořava, Petr

1996-12-01

Chern-Simons gauge theory is formulated on three-dimensional Z2 orbifolds. The locus of singular points on a given orbifold is equivalent to a link of Wilson lines. This allows one to reduce any correlation function on orbifolds to a sum of more complicated correlation functions in the simpler theory on manifolds. Chern-Simons theory on manifolds is known to be related to two-dimensional (2D) conformal field theory (CFT) on closed-string surfaces; here it is shown that the theory on orbifolds is related to 2D CFT of unoriented closed- and open-string models, i.e. to worldsheet orbifold models. In particular, the boundary components of the worldsheet correspond to the components of the singular locus in the 3D orbifold. This correspondence leads to a simple identification of the open-string spectra, including their Chan-Paton degeneration, in terms of fusing Wilson lines in the corresponding Chern-Simons theory. The correspondence is studied in detail, and some exactly solvable examples are presented. Some of these examples indicate that it is natural to think of the orbifold group Z2 as a part of the gauge group of the Chern-Simons theory, thus generalizing the standard definition of gauge theories.

TAD-free analysis of architectural proteins and insulators.

PubMed

Mourad, Raphaël; Cuvier, Olivier

2018-03-16

The three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression and DNA replication regulations. The mechanisms by which molecular drivers functionally organize the 3D genome, such as topologically associating domains (TADs), remain to be explored. Current approaches consist in assessing the enrichments or influences of proteins at TAD borders. Here, we propose a TAD-free model to directly estimate the blocking effects of architectural proteins, insulators and DNA motifs on long-range contacts, making the model intuitive and biologically meaningful. In addition, the model allows analyzing the whole Hi-C information content (2D information) instead of only focusing on TAD borders (1D information). The model outperforms multiple logistic regression at TAD borders in terms of parameter estimation accuracy and is validated by enhancer-blocking assays. In Drosophila, the results support the insulating role of simple sequence repeats and suggest that the blocking effects depend on the number of repeats. Motif analysis uncovered the roles of the transcriptional factors pannier and tramtrack in blocking long-range contacts. In human, the results suggest that the blocking effects of the well-known architectural proteins CTCF, cohesin and ZNF143 depend on the distance between loci, where each protein may participate at different scales of the 3D chromatin organization.

Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media.

PubMed

Bourg, Ian C; Sposito, Garrison

2010-03-15

In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations, which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer "compartments." We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D(interlayer) of water tracers and representative cations (Na(+), Cs(+), Sr(2+)) in Na-smectite interlayers. We find that a remarkably simple expression relates D(interlayer) to the pore-scale parameter δ(nanopore) ≤ 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: δ(nanopore) = D(interlayer)/D(0), where D(0) is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracers H(2)0, Na(+), Sr(2+), and Cs(+) in compacted Na-smectite-rich materials.

Generalized Feature Extraction for Wrist Pulse Analysis: From 1-D Time Series to 2-D Matrix.

PubMed

Dimin Wang; Zhang, David; Guangming Lu

2017-07-01

Traditional Chinese pulse diagnosis, known as an empirical science, depends on the subjective experience. Inconsistent diagnostic results may be obtained among different practitioners. A scientific way of studying the pulse should be to analyze the objectified wrist pulse waveforms. In recent years, many pulse acquisition platforms have been developed with the advances in sensor and computer technology. And the pulse diagnosis using pattern recognition theories is also increasingly attracting attentions. Though many literatures on pulse feature extraction have been published, they just handle the pulse signals as simple 1-D time series and ignore the information within the class. This paper presents a generalized method of pulse feature extraction, extending the feature dimension from 1-D time series to 2-D matrix. The conventional wrist pulse features correspond to a particular case of the generalized models. The proposed method is validated through pattern classification on actual pulse records. Both quantitative and qualitative results relative to the 1-D pulse features are given through diabetes diagnosis. The experimental results show that the generalized 2-D matrix feature is effective in extracting both the periodic and nonperiodic information. And it is practical for wrist pulse analysis.

The use of high field/frequency EPR in studies of radical and metal sites in proteins and small inorganic models

NASA Astrophysics Data System (ADS)

Andersson, K. Kristoffer; Barra, Anne-Laure

2002-04-01

Low temperature electron paramagnetic resonance (EPR) spectroscopy with frequencies between 95 and 345 GHz and magnetic fields up to 12 T have been used to study radicals and metal sites in proteins and small inorganic model complexes. We have studied radicals, Fe, Cu and Mn containing proteins. For S=1/2 systems, the high frequency method can resolve the g-value anisotropy. It was used in mouse ribonucleotide reductase (RNR) to show the presence of a hydrogen bond to the tyrosyl radical oxygen. At 285 GHz the type 2 Cu(II) signal in the complex enzyme laccase is clearly resolved from the Hg(II) containing laccase peroxide adduct. For simple metal sites, the systems over S=1/2 can be described by the spin Hamiltonian: HS= BgS+ D[ Sz2- S( S+1)/3+ E/ D ( Sx2- Sy2)]. From the high frequency EPR the D-value can be determined directly by, (I) shifts of geff for half-integer spin systems with large D-values as observed at 345 GHz on an Fe(II)NOEDTA complex, which is best described as S=3/2 system with D=11.5 cm -1, E=0.1 cm -1 and gx= gy= gz=2.0; (II) measuring the outermost signal, for systems with small D values, distant of (2 S-1)*∣ D∣ from the center of the spectrum as observed in S=5/2 Fe(III)EDTA. In Mn(II) substituted mouse RNR R2 protein the weakly interacting Mn(II) at X-band could be observed as decoupled Mn(II) at 285 GHz.

Semi-relativistic quark-antiquark potential models

NASA Astrophysics Data System (ADS)

Basdevant, J. L.; Boukraa, S.

We study the qualitative and quantitative properties of the spectrum of a two-body hamiltonian with relativistic kinematics. We show that this kinematics leads in a natural way to the observed features of light flavour (u, d, s) spectroscopy. After having established the basic properties of the operator √ p2 + m2 + V(r) in the cases of linear or logarithmic potentials, we show that, to first approximation, all q1 q2 meson states can be reproduced with a very simple universal flavour-independent potential whose parameters are directly related to basic physical quantities : the Regge slopes of light flavours and the quasi-logarithmic coupling strength of heavy quarks. We can derive equivalent effective non-relativistic hamiltonians which justify the successes of NR approaches. The main difficulties encountered, in particular in incorporating spin effects, appear to be due to the fact that, in phenomenological potential models, chiral symmetry and the ensuing Goldstone nature of the pion cannot be implemented in a natural way. Hence, such an approach can take its full predictive power only if it is based on a deeper field-theoretic level. Devant le succès spectaculaire des modèles potentiels pour la spectroscopie des états formés de quarks lourds (cc, bb, etc.), il est tentant d'essayer d'étendre de tels modèles aux états comprenant des quarks légers, u, d et s. En particulier, la spectroscopie des états mésoniques « lourds » est phénoménologiquement dominée par l'existence d'un potentiel confinant universel, quasi logarithmique entre 0,1 fm et 1 fm, tandis que celle des états légers se décrit de façon simple par des trajectoires de Regge linéaires qui ont une pente universelle. 11 est donc légitime de se demander s'il s'agit là de deux secteurs disjoints du monde hadronique, ou bien s'il existe une certaine unité dans la spectroscopie mésonique au plan phénoménologique. Cependant, en présence de quarks légers, voire de masse nulle, les modèles non relativistes traditionnellement utilisés sont sujets à des critiques évidentes. 11 est donc naturel de mettre à l'épreuve des modèles semi-relativistes, c'est-à-dire des hamiltoniens à cinématique relativiste, qui constituent l'extension la plus simple des modèles non relativistes. Nous étudions ici les propriétés qualitatives et quantitatives des spectres d'hamiltoniens de ce type. Nous montrons que l'usage de la cinématique relativiste rend compte de façon naturelle des caractéristiques principales de la spectroscopie des saveurs légères (u, d, s). Après avoir établi les propriétés essentielles de l'opérateur (p2 + m2)1/2 + V(r) dans le cas du potentiel linéaire et du potentiel logarithmique, nous montrons qu'en première approximation tous les états q1 q2 peuvent être obtenus avec un potentiel universel, indépendant de la saveur, extrêmement simple. Les paramètres de ce potentiel sont directement reliés à des grandeurs physiques de base : la pente universelle des trajectoires de Regge des états légers d'une part, la constante de couplage du potentiel logarithmique des états lourds de l'autre. Nous obtenons des hamiltoniens effectifs non relativistes équivalents qui justifient en un certain sens le succès des approches non relativistes. Les principales difficultés que l'on rencontre, en particulier lorsqu'on tente d'incorporer les corrections de structure fine et hyperfine, semblent provenir de ce que la symétrie chirale, et sa conséquence que le méson soit pratiquement un boson de Goldstone, ne peut être incorporée de façon simple et naturelle dans un modèle hamiltonien. En conséquence, une pareille approche ne peut prendre sa pleine puissance prédictive (avec un nombre restreint de paramètres) que si elle est fondée sur des bases plus profondes déduites d'une théorie des champs.

FRACTAL DIMENSION OF SPIN-GLASSES INTERFACES IN DIMENSION d = 2 AND d = 3 VIA STRONG DISORDER RENORMALIZATION AT ZERO TEMPERATURE

NASA Astrophysics Data System (ADS)

Monthus, Cécile

2015-09-01

For Gaussian Spin-Glasses in low dimensions, we introduce a simple Strong Disorder renormalization at zero temperature in order to construct ground states for Periodic and Anti-Periodic boundary conditions. The numerical study in dimensions d = 2 (up to sizes 20482) and d = 3 (up to sizes 1283) yields that Domain Walls are fractal of dimensions ds(d = 2) ≃ 1.27 and ds(d = 3) ≃ 2.55, respectively.

The influence of resolution of meteorology, biogeochemical models and fossil fuel emissions on forward and inverse modelling of CO2 exchange over Europe using the network of tall towers.

NASA Astrophysics Data System (ADS)

Vermeulen, A.; Verheggen, B.; Pieterse, G.; Haszpra, L.

2007-12-01

Tall towers allow us to observe the integrated influence of carbon exchange processes from large areas on the concentrations of CO2. The signal received shows a large variability at diurnal and synoptic timescales. The question remains how high resolutions and how accurate transport models need to be, in order to discriminate the relevant source terms from the atmospheric signal. We will examine the influence of the resolution of (ECMWF) meteorological fields, antropogenic and biogenic fluxes when going from resolutions of 2° to 0.2° lat-lon, using a simple Lagrangian 2D transport model. Model results will be compared to other Eulerian model results and observations at the CHIOTTO/CarboEurope tall tower network in Europe. Biogenic fluxes taken into account are from the FACEM model (Pieterse et al, 2006). Results show that the relative influence of the different CO2 exchange processes is very different at each tower and that higher model resolution clearly pays off in better model performance.

Magnetic and Electronic Properties of h-BN Nanosheets with Nonmetal Atoms Adsorbed: an Ab Initio Study

NASA Astrophysics Data System (ADS)

Luo, M.; Yin, H. H.; Chu, J. H.

2018-04-01

The magnetic properties of the h-BN monolayer with nonmetal atoms are studied by ab initio methods. Different dopants (C, Cl, F, and O) and doping sites are considered. Magnetic behavior is observed in the two-dimensional (2D) BN system with C, Cl, and O atoms. On the other hand, the O adsorbed system shows a more stable formed structure among above three magnetic materials, we study the ferromagnetic (FM) interaction in 2D-BN system with two O adatoms. Interestingly, as the O-O distance increases, the interaction between two O adatoms prefers to a long-range FM coupling. This phenomenon could be well described by a simple Heisenberg model.

Accurate calculation and modeling of the adiabatic connection in density functional theory

NASA Astrophysics Data System (ADS)

Teale, A. M.; Coriani, S.; Helgaker, T.

2010-04-01

Using a recently implemented technique for the calculation of the adiabatic connection (AC) of density functional theory (DFT) based on Lieb maximization with respect to the external potential, the AC is studied for atoms and molecules containing up to ten electrons: the helium isoelectronic series, the hydrogen molecule, the beryllium isoelectronic series, the neon atom, and the water molecule. The calculation of AC curves by Lieb maximization at various levels of electronic-structure theory is discussed. For each system, the AC curve is calculated using Hartree-Fock (HF) theory, second-order Møller-Plesset (MP2) theory, coupled-cluster singles-and-doubles (CCSD) theory, and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, expanding the molecular orbitals and the effective external potential in large Gaussian basis sets. The HF AC curve includes a small correlation-energy contribution in the context of DFT, arising from orbital relaxation as the electron-electron interaction is switched on under the constraint that the wave function is always a single determinant. The MP2 and CCSD AC curves recover the bulk of the dynamical correlation energy and their shapes can be understood in terms of a simple energy model constructed from a consideration of the doubles-energy expression at different interaction strengths. Differentiation of this energy expression with respect to the interaction strength leads to a simple two-parameter doubles model (AC-D) for the AC integrand (and hence the correlation energy of DFT) as a function of the interaction strength. The structure of the triples-energy contribution is considered in a similar fashion, leading to a quadratic model for the triples correction to the AC curve (AC-T). From a consideration of the structure of a two-level configuration-interaction (CI) energy expression of the hydrogen molecule, a simple two-parameter CI model (AC-CI) is proposed to account for the effects of static correlation on the AC. When parametrized in terms of the same input data, the AC-CI model offers improved performance over the corresponding AC-D model, which is shown to be the lowest-order contribution to the AC-CI model. The utility of the accurately calculated AC curves for the analysis of standard density functionals is demonstrated for the BLYP exchange-correlation functional and the interaction-strength-interpolation (ISI) model AC integrand. From the results of this analysis, we investigate the performance of our proposed two-parameter AC-D and AC-CI models when a simple density functional for the AC at infinite interaction strength is employed in place of information at the fully interacting point. The resulting two-parameter correlation functionals offer a qualitatively correct behavior of the AC integrand with much improved accuracy over previous attempts. The AC integrands in the present work are recommended as a basis for further work, generating functionals that avoid spurious error cancellations between exchange and correlation energies and give good accuracy for the range of densities and types of correlation contained in the systems studied here.

Quenched Large Deviations for Simple Random Walks on Percolation Clusters Including Long-Range Correlations

NASA Astrophysics Data System (ADS)

Berger, Noam; Mukherjee, Chiranjib; Okamura, Kazuki

2018-03-01

We prove a quenched large deviation principle (LDP) for a simple random walk on a supercritical percolation cluster (SRWPC) on {Z^d} ({d ≥ 2}). The models under interest include classical Bernoulli bond and site percolation as well as models that exhibit long range correlations, like the random cluster model, the random interlacement and the vacant set of random interlacements (for {d ≥ 3}) and the level sets of the Gaussian free field ({d≥ 3}). Inspired by the methods developed by Kosygina et al. (Commun Pure Appl Math 59:1489-1521, 2006) for proving quenched LDP for elliptic diffusions with a random drift, and by Yilmaz (Commun Pure Appl Math 62(8):1033-1075, 2009) and Rosenbluth (Quenched large deviations for multidimensional random walks in a random environment: a variational formula. Ph.D. thesis, NYU, arXiv:0804.1444v1) for similar results regarding elliptic random walks in random environment, we take the point of view of the moving particle and prove a large deviation principle for the quenched distribution of the pair empirical measures of the environment Markov chain in the non-elliptic case of SRWPC. Via a contraction principle, this reduces easily to a quenched LDP for the distribution of the mean velocity of the random walk and both rate functions admit explicit variational formulas. The main difficulty in our set up lies in the inherent non-ellipticity as well as the lack of translation-invariance stemming from conditioning on the fact that the origin belongs to the infinite cluster. We develop a unifying approach for proving quenched large deviations for SRWPC based on exploiting coercivity properties of the relative entropies in the context of convex variational analysis, combined with input from ergodic theory and invoking geometric properties of the supercritical percolation cluster.

Quenched Large Deviations for Simple Random Walks on Percolation Clusters Including Long-Range Correlations

NASA Astrophysics Data System (ADS)

Berger, Noam; Mukherjee, Chiranjib; Okamura, Kazuki

2017-12-01

We prove a quenched large deviation principle (LDP) for a simple random walk on a supercritical percolation cluster (SRWPC) on {Z^d} ({d ≥ 2} ). The models under interest include classical Bernoulli bond and site percolation as well as models that exhibit long range correlations, like the random cluster model, the random interlacement and the vacant set of random interlacements (for {d ≥ 3} ) and the level sets of the Gaussian free field ({d≥ 3} ). Inspired by the methods developed by Kosygina et al. (Commun Pure Appl Math 59:1489-1521, 2006) for proving quenched LDP for elliptic diffusions with a random drift, and by Yilmaz (Commun Pure Appl Math 62(8):1033-1075, 2009) and Rosenbluth (Quenched large deviations for multidimensional random walks in a random environment: a variational formula. Ph.D. thesis, NYU, arXiv:0804.1444v1) for similar results regarding elliptic random walks in random environment, we take the point of view of the moving particle and prove a large deviation principle for the quenched distribution of the pair empirical measures of the environment Markov chain in the non-elliptic case of SRWPC. Via a contraction principle, this reduces easily to a quenched LDP for the distribution of the mean velocity of the random walk and both rate functions admit explicit variational formulas. The main difficulty in our set up lies in the inherent non-ellipticity as well as the lack of translation-invariance stemming from conditioning on the fact that the origin belongs to the infinite cluster. We develop a unifying approach for proving quenched large deviations for SRWPC based on exploiting coercivity properties of the relative entropies in the context of convex variational analysis, combined with input from ergodic theory and invoking geometric properties of the supercritical percolation cluster.

Remote sensing of solar radiation absorbed and reflected by vegetated land surfaces

NASA Technical Reports Server (NTRS)

Myneni, Ranga B.; Asrar, Ghassem; Tanre, Didier; Choudhury, Bhaskar J.

1992-01-01

1D and 3D radiative-transfer models have been used to investigate the problem of remotely sensed determination of vegetated land surface-absorbed and reflected solar radiation. Calculations were conducted for various illumination conditions to determine surface albedo, soil- and canopy-absorbed photosynthetically active and nonactive radiation, and normalized difference vegetation index. Simple predictive models are developed on the basis of the relationships among these parameters.

ADPAC v1.0: User's Manual

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Heidegger, Nathan J.; Delaney, Robert A.

1999-01-01

The overall objective of this study was to evaluate the effects of turbulence models in a 3-D numerical analysis on the wake prediction capability. The current version of the computer code resulting from this study is referred to as ADPAC v7 (Advanced Ducted Propfan Analysis Codes -Version 7). This report is intended to serve as a computer program user's manual for the ADPAC code used and modified under Task 15 of NASA Contract NAS3-27394. The ADPAC program is based on a flexible multiple-block and discretization scheme permitting coupled 2-D/3-D mesh block solutions with application to a wide variety of geometries. Aerodynamic calculations are based on a four-stage Runge-Kutta time-marching finite volume solution technique with added numerical dissipation. Steady flow predictions are accelerated by a multigrid procedure. Turbulence models now available in the ADPAC code are: a simple mixing-length model, the algebraic Baldwin-Lomax model with user defined coefficients, the one-equation Spalart-Allmaras model, and a two-equation k-R model. The consolidated ADPAC code is capable of executing in either a serial or parallel computing mode from a single source code.

U (1 ) -symmetric infinite projected entangled-pair states study of the spin-1/2 square J1-J2 Heisenberg model

NASA Astrophysics Data System (ADS)

Haghshenas, R.; Sheng, D. N.

2018-05-01

We develop an improved variant of U (1 ) -symmetric infinite projected entangled-pair states (iPEPS) ansatz to investigate the ground-state phase diagram of the spin-1 /2 square J1-J2 Heisenberg model. In order to improve the accuracy of the ansatz, we discuss a simple strategy to select automatically relevant symmetric sectors and also introduce an optimization method to treat second-neighbor interactions more efficiently. We show that variational ground-state energies of the model obtained by the U (1 ) -symmetric iPEPS ansatz (for a fixed bond dimension D ) set a better upper bound, improving previous tensor-network-based results. By studying the finite-D scaling of the magnetically order parameter, we find a Néel phase for J2/J1<0.53 . For 0.53

Receptor Surface Models in the Classroom: Introducing Molecular Modeling to Students in a 3-D World

ERIC Educational Resources Information Center

Geldenhuys, Werner J.; Hayes, Michael; Van der Schyf, Cornelis J.; Allen, David D.; Malan, Sarel F.

2007-01-01

A simple, novel and generally applicable method to demonstrate structure-activity associations of a group of biologically interesting compounds in relation to receptor binding is described. This method is useful for undergraduates and graduate students in medicinal chemistry and computer modeling programs.

Hemodynamics model of fluid–solid interaction in internal carotid artery aneurysms

PubMed Central

Fu-Yu, Wang; Lei, Liu; Xiao-Jun, Zhang; Hai-Yue, Ju

2010-01-01

The objective of this study is to present a relatively simple method to reconstruct cerebral aneurysms as 3D numerical grids. The method accurately duplicates the geometry to provide computer simulations of the blood flow. Initial images were obtained by using CT angiography and 3D digital subtraction angiography in DICOM format. The image was processed by using MIMICS software, and the 3D fluid model (blood flow) and 3D solid model (wall) were generated. The subsequent output was exported to the ANSYS workbench software to generate the volumetric mesh for further hemodynamic study. The fluid model was defined and simulated in CFX software while the solid model was calculated in ANSYS software. The force data calculated firstly in the CFX software were transferred to the ANSYS software, and after receiving the force data, total mesh displacement data were calculated in the ANSYS software. Then, the mesh displacement data were transferred back to the CFX software. The data exchange was processed in workbench software. The results of simulation could be visualized in CFX-post. Two examples of grid reconstruction and blood flow simulation for patients with internal carotid artery aneurysms were presented. The wall shear stress, wall total pressure, and von Mises stress could be visualized. This method seems to be relatively simple and suitable for direct use by neurosurgeons or neuroradiologists, and maybe a practical tool for planning treatment and follow-up of patients after neurosurgical or endovascular interventions with 3D angiography. PMID:20812022

Hemodynamics model of fluid-solid interaction in internal carotid artery aneurysms.

PubMed

Bai-Nan, Xu; Fu-Yu, Wang; Lei, Liu; Xiao-Jun, Zhang; Hai-Yue, Ju

2011-01-01

The objective of this study is to present a relatively simple method to reconstruct cerebral aneurysms as 3D numerical grids. The method accurately duplicates the geometry to provide computer simulations of the blood flow. Initial images were obtained by using CT angiography and 3D digital subtraction angiography in DICOM format. The image was processed by using MIMICS software, and the 3D fluid model (blood flow) and 3D solid model (wall) were generated. The subsequent output was exported to the ANSYS workbench software to generate the volumetric mesh for further hemodynamic study. The fluid model was defined and simulated in CFX software while the solid model was calculated in ANSYS software. The force data calculated firstly in the CFX software were transferred to the ANSYS software, and after receiving the force data, total mesh displacement data were calculated in the ANSYS software. Then, the mesh displacement data were transferred back to the CFX software. The data exchange was processed in workbench software. The results of simulation could be visualized in CFX-post. Two examples of grid reconstruction and blood flow simulation for patients with internal carotid artery aneurysms were presented. The wall shear stress, wall total pressure, and von Mises stress could be visualized. This method seems to be relatively simple and suitable for direct use by neurosurgeons or neuroradiologists, and maybe a practical tool for planning treatment and follow-up of patients after neurosurgical or endovascular interventions with 3D angiography.

Some Progress in Large-Eddy Simulation using the 3-D Vortex Particle Method

NASA Technical Reports Server (NTRS)

Winckelmans, G. S.

1995-01-01

This two-month visit at CTR was devoted to investigating possibilities in LES modeling in the context of the 3-D vortex particle method (=vortex element method, VEM) for unbounded flows. A dedicated code was developed for that purpose. Although O(N(sup 2)) and thus slow, it offers the advantage that it can easily be modified to try out many ideas on problems involving up to N approx. 10(exp 4) particles. Energy spectrums (which require O(N(sup 2)) operations per wavenumber) are also computed. Progress was realized in the following areas: particle redistribution schemes, relaxation schemes to maintain the solenoidal condition on the particle vorticity field, simple LES models and their VEM extension, possible new avenues in LES. Model problems that involve strong interaction between vortex tubes were computed, together with diagnostics: total vorticity, linear and angular impulse, energy and energy spectrum, enstrophy. More work is needed, however, especially regarding relaxation schemes and further validation and development of LES models for VEM. Finally, what works well will eventually have to be incorporated into the fast parallel tree code.

Many-body effects in nonlinear optical responses of 2D layered semiconductors

DOE PAGES

Aivazian, Grant; Yu, Hongyi; Wu, Sanfeng; ...

2017-01-05

We performed ultrafast degenerate pump-probe spectroscopy on monolayer WSe2 near its exciton resonance. The observed differential reflectance signals exhibit signatures of strong many-body interactions including the exciton-exciton interaction and free carrier induced band gap renormalization. The exciton-exciton interaction results in a resonance blue shift which lasts for the exciton lifetime (several ps), while the band gap renormalization manifests as a resonance red shift with several tens ps lifetime. Our model based on the many-body interactions for the nonlinear optical susceptibility ts well the experimental observations. The power dependence of the spectra shows that with the increase of pump power, themore » exciton population increases linearly and then saturates, while the free carrier density increases superlinearly, implying that exciton Auger recombination could be the origin of these free carriers. Our model demonstrates a simple but efficient method for quantitatively analyzing the spectra, and indicates the important role of Coulomb interactions in nonlinear optical responses of such 2D materials.« less

Many-body effects in nonlinear optical responses of 2D layered semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aivazian, Grant; Yu, Hongyi; Wu, Sanfeng

We performed ultrafast degenerate pump-probe spectroscopy on monolayer WSe2 near its exciton resonance. The observed differential reflectance signals exhibit signatures of strong many-body interactions including the exciton-exciton interaction and free carrier induced band gap renormalization. The exciton-exciton interaction results in a resonance blue shift which lasts for the exciton lifetime (several ps), while the band gap renormalization manifests as a resonance red shift with several tens ps lifetime. Our model based on the many-body interactions for the nonlinear optical susceptibility ts well the experimental observations. The power dependence of the spectra shows that with the increase of pump power, themore » exciton population increases linearly and then saturates, while the free carrier density increases superlinearly, implying that exciton Auger recombination could be the origin of these free carriers. Our model demonstrates a simple but efficient method for quantitatively analyzing the spectra, and indicates the important role of Coulomb interactions in nonlinear optical responses of such 2D materials.« less

Entanglement of two blocks of spins in the critical Ising model

NASA Astrophysics Data System (ADS)

Facchi, P.; Florio, G.; Invernizzi, C.; Pascazio, S.

2008-11-01

We compute the entropy of entanglement of two blocks of L spins at a distance d in the ground state of an Ising chain in an external transverse magnetic field. We numerically study the von Neumann entropy for different values of the transverse field. At the critical point we obtain analytical results for blocks of size L=1 and 2. In the general case, the critical entropy is shown to be additive when d→∞ . Finally, based on simple arguments, we derive an expression for the entropy at the critical point as a function of both L and d . This formula is in excellent agreement with numerical results.

Design and verification of a simple 3D dynamic model of speed skating which mimics observed forces and motions.

PubMed

van der Kruk, E; Veeger, H E J; van der Helm, F C T; Schwab, A L

2017-11-07

Advice about the optimal coordination pattern for an individual speed skater, could be addressed by simulation and optimization of a biomechanical speed skating model. But before getting to this optimization approach one needs a model that can reasonably match observed behaviour. Therefore, the objective of this study is to present a verified three dimensional inverse skater model with minimal complexity, which models the speed skating motion on the straights. The model simulates the upper body transverse translation of the skater together with the forces exerted by the skates on the ice. The input of the model is the changing distance between the upper body and the skate, referred to as the leg extension (Euclidean distance in 3D space). Verification shows that the model mimics the observed forces and motions well. The model is most accurate for the position and velocity estimation (respectively 1.2% and 2.9% maximum residuals) and least accurate for the force estimations (underestimation of 4.5-10%). The model can be used to further investigate variables in the skating motion. For this, the input of the model, the leg extension, can be optimized to obtain a maximal forward velocity of the upper body. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

An Universal and Easy-to-Use Model for the Pressure of Arbitrary-Shape 3D Multifunctional Integumentary Cardiac Membranes.

PubMed

Su, Yewang; Liu, Zhuangjian; Xu, Lizhi

2016-04-20

Recently developed concepts for 3D, organ-mounted electronics for cardiac applications require a universal and easy-to-use mechanical model to calculate the average pressure associated with operation of the device, which is crucial for evaluation of design efficacy and optimization. This work proposes a simple, accurate, easy-to-use, and universal model to quantify the average pressure for arbitrary-shape organs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fish gotta swim, Birds gotta fly, I gotta do Feynmann Graphs 'til I die: A continuum Theory of Flocking

NASA Astrophysics Data System (ADS)

Toner, John; Tu, Yu-Hai

2002-05-01

We have developed a new continuum dynamical model for the collective motion of large "flocks" of biological organisms (e.g., flocks of birds, schools of fish, herds of wildebeest, hordes of bacteria, slime molds, etc.) . This model does for flocks what the Navier-Stokes equation does for fluids. The model predicts that, unlike simple fluids, flocks show huge fluctuation effects in spatial dimensions d < 4 that radically change their behavior. In d=2, it is only these effects that make it possible for the flock to move coherently at all. This explains why a million wildebeest can march together across the Serengeti plain, despite the fact that a million physicists gathered on the same plane could NOT all POINT in the same direction. Detailed quantitative predictions of this theory agree beautifully with computer simulations of flock motion.

Models of SOL transport and their relation to scaling of the divertor heat flux width in DIII-D

DOE PAGES

Makowski, M. A.; Lasnier, C. J.; Leonard, A. W.; ...

2014-10-06

Strong support for the critical pressure gradient model for the heat flux width has been obtained, in that the measured separatrix pressure gradient lies below and scales similarly to the pressure gradient limit obtained from the ideal, infinite-n stability codes, BALOO and 2DX, in all cases that have been examined. Predictions of a heuristic drift model for the heat flux width are also in qualitative agreement with the measurements. We obtained these results by using an improved high rep-rate and higher edge spatial resolution Thomson scattering system on DIII-D to measure the upstream electron temperature and density profiles. In ordermore » to compare theory and experiment, profiles of density, temperature, and pressure for both electrons and ions are needed as well values of these quantitities at the separatrix. We also developed a simple method to identify a proxy for the separatrix.« less

Swimming Performance of Toy Robotic Fish

NASA Astrophysics Data System (ADS)

Petelina, Nina; Mendelson, Leah; Techet, Alexandra

2015-11-01

HEXBUG AquaBotsTM are a commercially available small robot fish that come in a variety of ``species''. These models have varying caudal fin shapes and randomly-varied modes of swimming including forward locomotion, diving, and turning. In this study, we assess the repeatability and performance of the HEXBUG swimming behaviors and discuss the use of these toys to develop experimental techniques and analysis methods to study live fish swimming. In order to determine whether these simple, affordable model fish can be a valid representation for live fish movement, two models, an angelfish and a shark, were studied using 2D Particle Image Velocimetry (PIV) and 3D Synthetic Aperture PIV. In a series of experiments, the robotic fish were either allowed to swim freely or towed in one direction at a constant speed. The resultant measurements of the caudal fin wake are compared to data from previous studies of a real fish and simplified flapping propulsors.

Classical and quantum aspects of Yang-Baxter Wess-Zumino models

NASA Astrophysics Data System (ADS)

Demulder, Saskia; Driezen, Sibylle; Sevrin, Alexander; Thompson, Daniel C.

2018-03-01

We investigate the integrable Yang-Baxter deformation of the 2d Principal Chiral Model with a Wess-Zumino term. For arbitrary groups, the one-loop β-functions are calculated and display a surprising connection between classical and quantum physics: the classical integrability condition is necessary to prevent new couplings being generated by renormalisation. We show these theories admit an elegant realisation of Poisson-Lie T-duality acting as a simple inversion of coupling constants. The self-dual point corresponds to the Wess-Zumino-Witten model and is the IR fixed point under RG. We address the possibility of having supersymmetric extensions of these models showing that extended supersymmetry is not possible in general.

Two-dimensional straightness measurement based on optical knife-edge sensing

NASA Astrophysics Data System (ADS)

Wang, Chen; Zhong, Fenghe; Ellis, Jonathan D.

2017-09-01

Straightness error is a parasitic translation along a perpendicular direction to the primary displacement axis of a linear stage. The parasitic translations could be coupled into other primary displacement directions of a multi-axis platform. Hence, its measurement and compensation are critical in precision multi-axis metrology, calibration, and manufacturing. This paper presents a two-dimensional (2D) straightness measurement configuration based on 2D optical knife-edge sensing, which is simple, light-weight, compact, and easy to align. It applies a 2D optical knife-edge to manipulate the diffraction pattern sensed by a quadrant photodetector, whose output voltages could derive 2D straightness errors after a calibration process. This paper analyzes the physical model of the configuration and performs simulations and experiments to study the system sensitivity, measurement nonlinearity, and error sources. The results demonstrate that the proposed configuration has higher sensitivity and insensitive to beam's vibration, compared with the conventional configurations without using the knife-edge, and could achieve ±0.25 μ m within a ±40 μ m measurement range along a 40 mm primary axial motion.

Spin-orbit interaction of light on the surface of atomically thin crystals

NASA Astrophysics Data System (ADS)

Zhou, Junxiao; Chen, Shizhen; Zhang, Wenshuai; Luo, Hailu; Wen, Shuangchun

2017-09-01

Two-dimensional (2D) atomic crystals have extraordinary electronic and photonic properties and hold great promise in the applications of photonic and optoelectronics. Here, we review some of our works about the spin-orbit interaction of light on the surface of 2D atomic crystals. First, we propose a general model to describe the spin-orbit interaction of light of the 2D free standing atomic crystal, and find that it is not necessary to involve the effective refractive index to describe the spin-orbit interaction. By developing the quantum weak measurements, we detect the spin-orbit interaction of light in 2D atomic crystals, which can act as a simple method for defining the layer numbers of graphene. Moreover, we find the transverse spin-dependent splitting in the photonic spin Hall effect exhibits a quantized behavior. Furthermore, the spin-orbit interaction of light for the case of air-topological insulator interface can be routed by adjusting the strength of the axion coupling. These basic finding may enhance the comprehension of the spin-orbit interaction, and find the important application in optoelectronic.

[Biomass allometric equations of nine common tree species in an evergreen broadleaved forest of subtropical China].

PubMed

Zuo, Shu-di; Ren, Yin; Weng, Xian; Ding, Hong-feng; Luo, Yun-jian

2015-02-01

Biomass allometric equation (BAE) considered as a simple and reliable method in the estimation of forest biomass and carbon was used widely. In China, numerous studies focused on the BAEs for coniferous forest and pure broadleaved forest, and generalized BAEs were frequently used to estimate the biomass and carbon of mixed broadleaved forest, although they could induce large uncertainty in the estimates. In this study, we developed the species-specific and generalized BAEs using biomass measurement for 9 common broadleaved trees (Castanopsis fargesii, C. lamontii, C. tibetana, Lithocarpus glaber, Sloanea sinensis, Daphniphyllum oldhami, Alniphyllum fortunei, Manglietia yuyuanensis, and Engelhardtia fenzlii) of subtropical evergreen broadleaved forest, and compared differences in species-specific and generalized BAEs. The results showed that D (diameter at breast height) was a better independent variable in estimating the biomass of branch, leaf, root, aboveground section and total tree than a combined variable (D2 H) of D and H (tree height) , but D2H was better than D in estimating stem biomass. R2 (coefficient of determination) values of BAEs for 6 species decreased when adding H as the second independent variable into D- only BAEs, where R2 value for S. sinensis decreased by 5.6%. Compared with generalized D- and D2H-based BAEs, standard errors of estimate (SEE) of BAEs for 8 tree species decreased, and similar decreasing trend was observed for different components, where SEEs of the branch decreased by 13.0% and 20.3%. Therefore, the biomass carbon storage and its dynamic estimates were influenced largely by tree species and model types. In order to improve the accuracy of the estimates of biomass and carbon, we should consider the differences in tree species and model types.

Experimental study of fusion neutron and proton yields produced by petawatt-laser-irradiated D₂-³He or CD₄-³He clustering gases.

PubMed

Bang, W; Barbui, M; Bonasera, A; Quevedo, H J; Dyer, G; Bernstein, A C; Hagel, K; Schmidt, K; Gaul, E; Donovan, M E; Consoli, F; De Angelis, R; Andreoli, P; Barbarino, M; Kimura, S; Mazzocco, M; Natowitz, J B; Ditmire, T

2013-09-01

We report on experiments in which the Texas Petawatt laser irradiated a mixture of deuterium or deuterated methane clusters and helium-3 gas, generating three types of nuclear fusion reactions: D(d,^{3}He)n, D(d,t)p, and ^{3}He(d,p)^{4}He. We measured the yields of fusion neutrons and protons from these reactions and found them to agree with yields based on a simple cylindrical plasma model using known cross sections and measured plasma parameters. Within our measurement errors, the fusion products were isotropically distributed. Plasma temperatures, important for the cross sections, were determined by two independent methods: (1) deuterium ion time of flight and (2) utilizing the ratio of neutron yield to proton yield from D(d,^{3}He)n and ^{3}He(d,p)^{4}He reactions, respectively. This experiment produced the highest ion temperature ever achieved with laser-irradiated deuterium clusters.

3D modeling and characterization of a calorimetric flow rate sensor for sweat rate sensing applications

NASA Astrophysics Data System (ADS)

Iftekhar, Ahmed Tashfin; Ho, Jenny Che-Ting; Mellinger, Axel; Kaya, Tolga

2017-03-01

Sweat-based physiological monitoring has been intensively explored in the last decade with the hopes of developing real-time hydration monitoring devices. Although the content of sweat (electrolytes, lactate, urea, etc.) provides significant information about the physiology, it is also very important to know the rate of sweat at the time of sweat content measurements because the sweat rate is known to alter the concentrations of sweat compounds. We developed a calorimetric based flow rate sensor using PolydimethylSiloxane that is suitable for sweat rate applications. Our simple approach on using temperature-based flow rate detection can easily be adapted to multiple sweat collection and analysis devices. Moreover, we have developed a 3D finite element analysis model of the device using COMSOL Multiphysics™ and verified the flow rate measurements. The experiment investigated flow rate values from 0.3 μl/min up to 2.1 ml/min, which covers the human sweat rate range (0.5 μl/min-10 μl/min). The 3D model simulations and analytical model calculations covered an even wider range in order to understand the main physical mechanisms of the device. With a verified 3D model, different environmental heat conditions could be further studied to shed light on the physiology of the sweat rate.

Development of an EMC3-EIRENE Synthetic Imaging Diagnostic

NASA Astrophysics Data System (ADS)

Meyer, William; Allen, Steve; Samuell, Cameron; Lore, Jeremy

2017-10-01

2D and 3D flow measurements are critical for validating numerical codes such as EMC3-EIRENE. Toroidal symmetry assumptions preclude tomographic reconstruction of 3D flows from single camera views. In addition, the resolution of the grids utilized in numerical code models can easily surpass the resolution of physical camera diagnostic geometries. For these reasons we have developed a Synthetic Imaging Diagnostic capability for forward projection comparisons of EMC3-EIRENE model solutions with the line integrated images from the Doppler Coherence Imaging diagnostic on DIII-D. The forward projection matrix is 2.8 Mpixel by 6.4 Mcells for the non-axisymmetric case we present. For flow comparisons, both simple line integral, and field aligned component matrices must be calculated. The calculation of these matrices is a massive embarrassingly parallel problem and performed with a custom dispatcher that allows processing platforms to join mid-problem as they become available, or drop out if resources are needed for higher priority tasks. The matrices are handled using standard sparse matrix techniques. Prepared by LLNL under Contract DE-AC52-07NA27344. This material is based upon work supported by the U.S. DOE, Office of Science, Office of Fusion Energy Sciences. LLNL-ABS-734800.

Development of FWIGPR, an open-source package for full-waveform inversion of common-offset GPR data

NASA Astrophysics Data System (ADS)

Jazayeri, S.; Kruse, S.

2017-12-01

We introduce a package for full-waveform inversion (FWI) of Ground Penetrating Radar (GPR) data based on a combination of open-source programs. The FWI requires a good starting model, based on direct knowledge of field conditions or on traditional ray-based inversion methods. With a good starting model, the FWI can improve resolution of selected subsurface features. The package will be made available for general use in educational and research activities. The FWIGPR package consists of four main components: 3D to 2D data conversion, source wavelet estimation, forward modeling, and inversion. (These four components additionally require the development, by the user, of a good starting model.) A major challenge with GPR data is the unknown form of the waveform emitted by the transmitter held close to the ground surface. We apply a blind deconvolution method to estimate the source wavelet, based on a sparsity assumption about the reflectivity series of the subsurface model (Gholami and Sacchi 2012). The estimated wavelet is deconvolved from the data and the sparsest reflectivity series with fewest reflectors. The gprMax code (www.gprmax.com) is used as the forward modeling tool and the PEST parameter estimation package (www.pesthomepage.com) for the inversion. To reduce computation time, the field data are converted to an effective 2D equivalent, and the gprMax code can be run in 2D mode. In the first step, the user must create a good starting model of the data, presumably using ray-based methods. This estimated model will be introduced to the FWI process as an initial model. Next, the 3D data is converted to 2D, then the user estimates the source wavelet that best fits the observed data by sparsity assumption of the earth's response. Last, PEST runs gprMax with the initial model and calculates the misfit between the synthetic and observed data, and using an iterative algorithm calling gprMax several times ineach iteration, finds successive models that better fit the data. To gauge whether the iterative process has arrived at a local or global minima, the process can be repeated with a range of starting models. Tests have shown that this package can successfully improve estimates of selected subsurface model parameters for simple synthetic and real data. Ongoing research will focus on FWI of more complex scenarios.

Coupled two-dimensional edge plasma and neutral gas modeling of tokamak scrape-off-layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maingi, Rajesh

1992-08-01

The objective of this study is to devise a detailed description of the tokamak scrape-off-layer (SOL), which includes the best available models of both the plasma and neutral species and the strong coupling between the two in many SOL regimes. A good estimate of both particle flux and heat flux profiles at the limiter/divertor target plates is desired. Peak heat flux is one of the limiting factors in determining the survival probability of plasma-facing-components at high power levels. Plate particle flux affects the neutral flux to the pump, which determines the particle exhaust rate. A technique which couples a two-dimensionalmore » (2-D) plasma and a 2-D neutral transport code has been developed (coupled code technique), but this procedure requires large amounts of computer time. Relevant physics has been added to an existing two-neutral-species model which takes the SOL plasma/neutral coupling into account in a simple manner (molecular physics model), and this model is compared with the coupled code technique mentioned above. The molecular physics model is benchmarked against experimental data from a divertor tokamak (DIII-D), and a similar model (single-species model) is benchmarked against data from a pump-limiter tokamak (Tore Supra). The models are then used to examine two key issues: free-streaming-limits (ion energy conduction and momentum flux) and the effects of the non-orthogonal geometry of magnetic flux surfaces and target plates on edge plasma parameter profiles.« less

Insects traversing grass-like vertical compliant beams

NASA Astrophysics Data System (ADS)

Li, Chen; Fearing, Ronald; Full, Robert

2014-03-01

Small running animals encounter many challenging terrains. These terrains can be filled with 3D, multi-component obstacles. Here, we study cockroaches (Blaberus discoidalis) moving through grass-like vertical compliant beams during escape. We created an apparatus to control and vary geometric parameters and mechanical properties of model grass including height, width, thickness, lateral and fore-aft spacings, angle, number of layers, stiffness, and damping. We observed a suite of novel locomotor behaviors not previously described on simpler 2D ground. When model grass height was >2 × body length and lateral spacing was <0.5 × body width, the animal primarily (probability P = 50%) rolled its body onto its side to rapidly (time t = 2.1 s) maneuver through the gaps between model grass. We developed a simple energy minimization model, and found that body roll reduces the energy barriers that the animal must overcome during traversal. We hypothesized that the animal's ellipsoidal body shape facilitated traversal. To test our hypothesis, we modified body shape by adding either a rectangular or an oval plate onto its dorsal surface, and found that P dropped by an order of magnitude and t more than doubled. Upon removal of either plate, both P and t recovered. Locomotor kinematics and geometry effectively coupled to terrain properties enables negotiation of 3D, multi-component obstacles, and provides inspiration for small robots to navigate such terrain with minimal sensing and control.

A SIMPLE ASSAY FOR 2,4-DICHLOROPHENOXYACETIC ACID USING COATED TEST-STRIPS

EPA Science Inventory

Immunoassay test strips utilizing ascending chromatography has been devised for the detection of 2.4-dichlorophenoxyacetic acid (2,4-D). This test requires no instrumentation, inexpensive reagents and relies on the application of antibodies to 2,4-D adsorbed onto colloidal gol...

Stochastic model for gene transcription on Drosophila melanogaster embryos

NASA Astrophysics Data System (ADS)

Prata, Guilherme N.; Hornos, José Eduardo M.; Ramos, Alexandre F.

2016-02-01

We examine immunostaining experimental data for the formation of stripe 2 of even-skipped (eve) transcripts on D. melanogaster embryos. An estimate of the factor converting immunofluorescence intensity units into molecular numbers is given. The analysis of the eve dynamics at the region of stripe 2 suggests that the promoter site of the gene has two distinct regimes: an earlier phase when it is predominantly activated until a critical time when it becomes mainly repressed. That suggests proposing a stochastic binary model for gene transcription on D. melanogaster embryos. Our model has two random variables: the transcripts number and the state of the source of mRNAs given as active or repressed. We are able to reproduce available experimental data for the average number of transcripts. An analysis of the random fluctuations on the number of eves and their consequences on the spatial precision of stripe 2 is presented. We show that the position of the anterior or posterior borders fluctuate around their average position by ˜1 % of the embryo length, which is similar to what is found experimentally. The fitting of data by such a simple model suggests that it can be useful to understand the functions of randomness during developmental processes.

A detailed comparison of optimality and simplicity in perceptual decision-making

PubMed Central

Shen, Shan; Ma, Wei Ji

2017-01-01

Two prominent ideas in the study of decision-making have been that organisms behave near-optimally, and that they use simple heuristic rules. These principles might be operating in different types of tasks, but this possibility cannot be fully investigated without a direct, rigorous comparison within a single task. Such a comparison was lacking in most previous studies, because a) the optimal decision rule was simple; b) no simple suboptimal rules were considered; c) it was unclear what was optimal, or d) a simple rule could closely approximate the optimal rule. Here, we used a perceptual decision-making task in which the optimal decision rule is well-defined and complex, and makes qualitatively distinct predictions from many simple suboptimal rules. We find that all simple rules tested fail to describe human behavior, that the optimal rule accounts well for the data, and that several complex suboptimal rules are indistinguishable from the optimal one. Moreover, we found evidence that the optimal model is close to the true model: first, the better the trial-to-trial predictions of a suboptimal model agree with those of the optimal model, the better that suboptimal model fits; second, our estimate of the Kullback-Leibler divergence between the optimal model and the true model is not significantly different from zero. When observers receive no feedback, the optimal model still describes behavior best, suggesting that sensory uncertainty is implicitly represented and taken into account. Beyond the task and models studied here, our results have implications for best practices of model comparison. PMID:27177259

Final-state effect on x-ray photoelectron spectrum of nominally d1 and n -doped d0 transition-metal oxides

NASA Astrophysics Data System (ADS)

Lin, Chungwei; Posadas, Agham; Hadamek, Tobias; Demkov, Alexander A.

2015-07-01

We investigate the x-ray photoelectron spectroscopy (XPS) of nominally d1 and n -doped d0 transition-metal oxides including NbO2,SrVO3, and LaTiO3 (nominally d1), as well as n -doped SrTiO3 (nominally d0). In the case of single phase d1 oxides, we find that the XPS spectra (specifically photoelectrons from Nb 3 d , V 2 p , Ti 2 p core levels) all display at least two, and sometimes three distinct components, which can be consistently identified as d0,d1, and d2 oxidation states (with decreasing order in binding energy). Electron doping increases the d2 component but decreases the d0 component, whereas hole doping reverses this trend; a single d1 peak is never observed, and the d0 peak is always present even in phase-pure samples. In the case of n -doped SrTiO3, the d1 component appears as a weak shoulder with respect to the main d0 peak. We argue that these multiple peaks should be understood as being due to the final-state effect and are intrinsic to the materials. Their presence does not necessarily imply the existence of spatially localized ions of different oxidation states nor of separate phases. A simple model is provided to illustrate this interpretation, and several experiments are discussed accordingly. The key parameter to determine the relative importance between the initial-state and final-state effects is also pointed out.

Onset and saturation of backward stimulated Raman scattering of laser in trapping regime in three spatial dimensions

NASA Astrophysics Data System (ADS)

Yin, L.; Albright, B. J.; Rose, H. A.; Bowers, K. J.; Bergen, B.; Montgomery, D. S.; Kline, J. L.; Fernández, J. C.

2009-11-01

A suite of three-dimensional (3D) VPIC [K. J. Bowers et al., Phys. Plasmas 15, 055703 (2008)] particle-in-cell simulations of backward stimulated Raman scattering (SRS) in inertial confinement fusion hohlraum plasma has been performed on the heterogeneous multicore supercomputer, Roadrunner, presently the world's most powerful supercomputer. These calculations reveal the complex nonlinear behavior of SRS and point to a new era of "at scale" 3D modeling of SRS in solitary and multiple laser speckles. The physics governing nonlinear saturation of SRS in a laser speckle in 3D is consistent with that of prior two-dimensional (2D) studies [L. Yin et al., Phys. Rev. Lett. 99, 265004 (2007)], but with important differences arising from enhanced diffraction and side loss in 3D compared with 2D. In addition to wave front bowing of electron plasma waves (EPWs) due to trapped electron nonlinear frequency shift and amplitude-dependent damping, we find for the first time that EPW self-focusing, which evolved from trapped particle modulational instability [H. A. Rose and L. Yin, Phys. Plasmas 15, 042311 (2008)], also exhibits loss of angular coherence by formation of a filament necklace, a process not available in 2D. These processes in 2D and 3D increase the side-loss rate of trapped electrons, increase wave damping, decrease source coherence for backscattered light, and fundamentally limit how much backscatter can occur from a laser speckle. For both SRS onset and saturation, the nonlinear trapping induced physics is not captured in linear gain modeling of SRS. A simple metric is described for using single-speckle reflectivities obtained from VPIC simulations to infer the total reflectivity from the population of laser speckles of amplitude sufficient for significant trapping-induced nonlinearity to arise.

SU-F-T-142: An Analytical Model to Correct the Aperture Scattered Dose in Clinical Proton Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, B; Liu, S; Zhang, T

2016-06-15

Purpose: Apertures or collimators are used to laterally shape proton beams in double scattering (DS) delivery and to sharpen the penumbra in pencil beam (PB) delivery. However, aperture-scattered dose is not included in the current dose calculations of treatment planning system (TPS). The purpose of this study is to provide a method to correct the aperture-scattered dose based on an analytical model. Methods: A DS beam with a non-divergent aperture was delivered using a single-room proton machine. Dose profiles were measured with an ion-chamber scanning in water and a 2-D ion chamber matrix with solid-water buildup at various depths. Themore » measured doses were considered as the sum of the non-contaminated dose and the aperture-scattered dose. The non-contaminated dose was calculated by TPS and subtracted from the measured dose. Aperture scattered-dose was modeled as a 1D Gaussian distribution. For 2-D fields, to calculate the scatter-dose from all the edges of aperture, a sum of weighted distance was used in the model based on the distance from calculation point to aperture edge. The gamma index was calculated between the measured and calculated dose with and without scatter correction. Results: For a beam with range of 23 cm and aperture size of 20 cm, the contribution of the scatter horn was ∼8% of the total dose at 4 cm depth and diminished to 0 at 15 cm depth. The amplitude of scatter-dose decreased linearly with the depth increase. The 1D gamma index (2%/2 mm) between the calculated and measured profiles increased from 63% to 98% for 4 cm depth and from 83% to 98% at 13 cm depth. The 2D gamma index (2%/2 mm) at 4 cm depth has improved from 78% to 94%. Conclusion: Using the simple analytical method the discrepancy between the measured and calculated dose has significantly improved.« less

Modelling of Tc migration in an un-oxidized fractured drill core from Äspö, Sweden

NASA Astrophysics Data System (ADS)

Huber, F. M.; Totskiy, Y.; Montoya Garcia, V.; Enzmann, F.; Trumm, M.; Wenka, A.; Geckeis, H.; Schaefer, T.

2015-12-01

The radionuclide retention of redox sensitive radionuclides (e.g. Pu, Np, U, Tc) in crystalline host rock greatly depends on the rock matrix and the rock redox capacity. Preservation of drill cores concerning oxidation is therefore of paramount importance to reliably predict the near-natural radionuclide retention properties. Here, experimental results of HTO and Tc laboratory migration experiments in a naturally single fractured Äspö un-oxidized drill core are modelled using two different 2D models. Both models employ geometrical information obtained by μ-computed tomography (μCT) scanning of the drill core. The models differ in geometrical complexity meaning the first model (PPM-MD) consists of a simple parallel plate with a porous matrix adjacent to the fracture whereas the second model (MPM) uses the mid-plane of the 3D fracture only (no porous matrix). Simulation results show that for higher flow rates (Peclet number > 1), the MPM satisfactorily describes the HTO breakthrough curves (BTC) whereas the PPM-MD model nicely reproduces the HTO BTC for small Pe numbers (<1). These findings clearly highlight the influence of fracture geometry/flow field complexity on solute transport for Pe numbers > 1 and the dominating effect of matrix diffusion for Peclet numbers < 1. Retention of Tc is modelled using a simple Kd-approach in case of the PPM-MD and including 1st order sorptive reduction/desorption kinetics in case of the MPM. Batch determined sorptive reduction/desorption kinetic rates and Kd values for Tc on non-oxidized Äspö diorite are used in the model and compared to best fit values. By this approach, the transferability of kinetic data concerning sorptive reduction determined in static batch experiments to dynamic transport experiments is examined.

Stretchable surfaces with programmable 3D texture morphing for synthetic camouflaging skins

NASA Astrophysics Data System (ADS)

Pikul, J. H.; Li, S.; Bai, H.; Hanlon, R. T.; Cohen, I.; Shepherd, R. F.

2017-10-01

Technologies that use stretchable materials are increasingly important, yet we are unable to control how they stretch with much more sophistication than inflating balloons. Nature, however, demonstrates remarkable control of stretchable surfaces; for example, cephalopods can project hierarchical structures from their skin in milliseconds for a wide range of textural camouflage. Inspired by cephalopod muscular morphology, we developed synthetic tissue groupings that allowed programmable transformation of two-dimensional (2D) stretchable surfaces into target 3D shapes. The synthetic tissue groupings consisted of elastomeric membranes embedded with inextensible textile mesh that inflated to within 10% of their target shapes by using a simple fabrication method and modeling approach. These stretchable surfaces transform from flat sheets to 3D textures that imitate natural stone and plant shapes and camouflage into their background environments.

Generation of multicellular tumor spheroids by the hanging-drop method.

PubMed

Timmins, Nicholas E; Nielsen, Lars K

2007-01-01

Owing to their in vivo-like characteristics, three-dimensional (3D) multicellular tumor spheroid (MCTS) cultures are gaining increasing popularity as an in vitro model of tumors. A straightforward and simple approach to the cultivation of these MCTS is the hanging-drop method. Cells are suspended in droplets of medium, where they develop into coherent 3D aggregates and are readily accessed for analysis. In addition to being simple, the method eliminates surface interactions with an underlying substratum (e.g., polystyrene plastic or agarose), requires only a low number of starting cells, and is highly reproducible. This method has also been applied to the co-cultivation of mixed cell populations, including the co-cultivation of endothelial cells and tumor cells as a model of early tumor angiogenesis.

Divergence correction schemes in finite difference method for 3D tensor CSAMT in axial anisotropic media

NASA Astrophysics Data System (ADS)

Wang, Kunpeng; Tan, Handong; Zhang, Zhiyong; Li, Zhiqiang; Cao, Meng

2017-05-01

Resistivity anisotropy and full-tensor controlled-source audio-frequency magnetotellurics (CSAMT) have gradually become hot research topics. However, much of the current anisotropy research for tensor CSAMT only focuses on the one-dimensional (1D) solution. As the subsurface is rarely 1D, it is necessary to study three-dimensional (3D) model response. The staggered-grid finite difference method is an effective simulation method for 3D electromagnetic forward modelling. Previous studies have suggested using the divergence correction to constrain the iterative process when using a staggered-grid finite difference model so as to accelerate the 3D forward speed and enhance the computational accuracy. However, the traditional divergence correction method was developed assuming an isotropic medium. This paper improves the traditional isotropic divergence correction method and derivation process to meet the tensor CSAMT requirements for anisotropy using the volume integral of the divergence equation. This method is more intuitive, enabling a simple derivation of a discrete equation and then calculation of coefficients related to the anisotropic divergence correction equation. We validate the result of our 3D computational results by comparing them to the results computed using an anisotropic, controlled-source 2.5D program. The 3D resistivity anisotropy model allows us to evaluate the consequences of using the divergence correction at different frequencies and for two orthogonal finite length sources. Our results show that the divergence correction plays an important role in 3D tensor CSAMT resistivity anisotropy research and offers a solid foundation for inversion of CSAMT data collected over an anisotropic body.

Post-test analysis of dryout test 7B' of the W-1 Sodium Loop Safety Facility Experiment with the SABRE-2P code. [LMFBR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rose, S.D.; Dearing, J.F.

An understanding of conditions that may cause sodium boiling and boiling propagation that may lead to dryout and fuel failure is crucial in liquid-metal fast-breeder reactor safety. In this study, the SABRE-2P subchannel analysis code has been used to analyze the ultimate transient of the in-core W-1 Sodium Loop Safety Facility experiment. This code has a 3-D simple nondynamic boiling model which is able to predict the flow instability which caused dryout. In other analyses dryout has been predicted for out-of-core test bundles and so this study provides additional confirmation of the model.

Communication: Diverse nanoscale cluster dynamics: Diffusion of 2D epitaxial clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lai, King C.; Evans, James W.; Liu, Da -Jiang

The dynamics of nanoscale clusters can be distinct from macroscale behavior described by continuum formalisms. For diffusion of 2D clusters of N atoms in homoepitaxial systems mediated by edge atom hopping, macroscale theory predicts simple monotonic size scaling of the diffusion coefficient, D N ~ N –β, with β = 3/2. However, modeling for nanoclusters on metal(100) surfaces reveals that slow nucleation-mediated diffusion displaying weak size scaling β < 1 occurs for “perfect” sizes N p = L 2 and L(L+1) for integer L = 3,4,… (with unique square or near-square ground state shapes), and also for N p+3, Nmore » p+4,…. In contrast, fast facile nucleation-free diffusion displaying strong size scaling β ≈ 2.5 occurs for sizes N p+1 and N p+2. D N versus N oscillates strongly between the slowest branch (for N p+3) and the fastest branch (for N p+1). All branches merge for N = O(10 2), but macroscale behavior is only achieved for much larger N = O(10 3). Here, this analysis reveals the unprecedented diversity of behavior on the nanoscale.« less

Communication: Diverse nanoscale cluster dynamics: Diffusion of 2D epitaxial clusters

DOE PAGES

Lai, King C.; Evans, James W.; Liu, Da -Jiang

2017-11-27

The dynamics of nanoscale clusters can be distinct from macroscale behavior described by continuum formalisms. For diffusion of 2D clusters of N atoms in homoepitaxial systems mediated by edge atom hopping, macroscale theory predicts simple monotonic size scaling of the diffusion coefficient, D N ~ N –β, with β = 3/2. However, modeling for nanoclusters on metal(100) surfaces reveals that slow nucleation-mediated diffusion displaying weak size scaling β < 1 occurs for “perfect” sizes N p = L 2 and L(L+1) for integer L = 3,4,… (with unique square or near-square ground state shapes), and also for N p+3, Nmore » p+4,…. In contrast, fast facile nucleation-free diffusion displaying strong size scaling β ≈ 2.5 occurs for sizes N p+1 and N p+2. D N versus N oscillates strongly between the slowest branch (for N p+3) and the fastest branch (for N p+1). All branches merge for N = O(10 2), but macroscale behavior is only achieved for much larger N = O(10 3). Here, this analysis reveals the unprecedented diversity of behavior on the nanoscale.« less

Prediction of insufficient serum vitamin D status in older women: a validated model.

PubMed

Merlijn, T; Swart, K M A; Lips, P; Heymans, M W; Sohl, E; Van Schoor, N M; Netelenbos, C J; Elders, P J M

2018-05-28

We developed an externally validated simple prediction model to predict serum 25(OH)D levels < 30, < 40, < 50 and 60 nmol/L in older women with risk factors for fractures. The benefit of the model reduces when a higher 25(OH)D threshold is chosen. Vitamin D deficiency is associated with increased fracture risk in older persons. General supplementation of all older women with vitamin D could cause medicalization and costs. We developed a clinical model to identify insufficient serum 25-hydroxyvitamin D (25(OH)D) status in older women at risk for fractures. In a sample of 2689 women ≥ 65 years selected from general practices, with at least one risk factor for fractures, a questionnaire was administered and serum 25(OH)D was measured. Multivariable logistic regression models with backward selection were developed to select predictors for insufficient serum 25(OH)D status, using separate thresholds 30, 40, 50 and 60 nmol/L. Internal and external model validations were performed. Predictors in the models were as follows: age, BMI, vitamin D supplementation, multivitamin supplementation, calcium supplementation, daily use of margarine, fatty fish ≥ 2×/week, ≥ 1 hours/day outdoors in summer, season of blood sampling, the use of a walking aid and smoking. The AUC was 0.77 for the model using a 30 nmol/L threshold and decreased in the models with higher thresholds to 0.72 for 60 nmol/L. We demonstrate that the model can help to distinguish patients with or without insufficient serum 25(OH)D levels at thresholds of 30 and 40 nmol/L, but not when a threshold of 50 nmol/L is demanded. This externally validated model can predict the presence of vitamin D insufficiency in women at risk for fractures. The potential clinical benefit of this tool is highly dependent of the chosen 25(OH)D threshold and decreases when a higher threshold is used.

Interactive locomotion: Investigation and modeling of physically-paired humans while walking

PubMed Central

Le Goff, Camille G.; Ijspeert, Auke Jan

2017-01-01

In spite of extensive studies on human walking, less research has been conducted on human walking gait adaptation during interaction with another human. In this paper, we study a particular case of interactive locomotion where two humans carry a rigid object together. Experimental data from two persons walking together, one in front of the other, while carrying a stretcher-like object is presented, and the adaptation of their walking gaits and coordination of the foot-fall patterns are analyzed. It is observed that in more than 70% of the experiments the subjects synchronize their walking gaits; it is shown that these walking gaits can be associated to quadrupedal gaits. Moreover, in order to understand the extent by which the passive dynamics can explain this synchronization behaviour, a simple 2D model, made of two-coupled spring-loaded inverted pendulums, is developed, and a comparison between the experiments and simulations with this model is presented, showing that with this simple model we are able to reproduce some aspects of human walking behaviour when paired with another human. PMID:28877161

Application of Organophosphonic Acids by One-Step Supercritical CO2 on 1D and 2D Semiconductors: Toward Enhanced Electrical and Sensing Performances.

PubMed

Bhartia, Bhavesh; Bacher, Nadav; Jayaraman, Sundaramurthy; Khatib, Salam; Song, Jing; Guo, Shifeng; Troadec, Cedric; Puniredd, Sreenivasa Reddy; Srinivasan, Madapusi Palavedu; Haick, Hossam

2015-07-15

Formation of dense monolayers with proven atmospheric stability using simple fabrication conditions remains a major challenge for potential applications such as (bio)sensors, solar cells, surfaces for growth of biological cells, and molecular, organic, and plastic electronics. Here, we demonstrate a single-step modification of organophosphonic acids (OPA) on 1D and 2D structures using supercritical carbon dioxide (SCCO2) as a processing medium, with high stability and significantly shorter processing times than those obtained by the conventional physisorption-chemisorption method (2.5 h vs 48-60 h).The advantages of this approach in terms of stability and atmospheric resistivity are demonstrated on various 2D materials, such as indium-tin-oxide (ITO) and 2D Si surfaces. The advantage of the reported approach on electronic and sensing devices is demonstrated by Si nanowire field effect transistors (SiNW FETs), which have shown a few orders of magnitude higher electrical and sensing performances, compared with devices obtained by conventional approaches. The compatibility of the reported approach with various materials and its simple implementation with a single reactor makes it easily scalable for various applications.

Minimal Unified Resolution to R_{K^{(*)}} and R(D^{(*)}) Anomalies with Lepton Mixing.

PubMed

Choudhury, Debajyoti; Kundu, Anirban; Mandal, Rusa; Sinha, Rahul

2017-10-13

It is a challenging task to explain, in terms of a simple and compelling new physics scenario, the intriguing discrepancies between the standard model expectations and the data for the neutral-current observables R_{K} and R_{K^{*}}, as well as the charged-current observables R(D) and R(D^{*}). We show that this can be achieved in an effective theory with only two unknown parameters. In addition, this class of models predicts some interesting signatures in the context of both B decays as well as high-energy collisions.

Localized solutions of Lugiato-Lefever equations with focused pump.

PubMed

Cardoso, Wesley B; Salasnich, Luca; Malomed, Boris A

2017-12-04

Lugiato-Lefever (LL) equations in one and two dimensions (1D and 2D) accurately describe the dynamics of optical fields in pumped lossy cavities with the intrinsic Kerr nonlinearity. The external pump is usually assumed to be uniform, but it can be made tightly focused too-in particular, for building small pixels. We obtain solutions of the LL equations, with both the focusing and defocusing intrinsic nonlinearity, for 1D and 2D confined modes supported by the localized pump. In the 1D setting, we first develop a simple perturbation theory, based in the sech ansatz, in the case of weak pump and loss. Then, a family of exact analytical solutions for spatially confined modes is produced for the pump focused in the form of a delta-function, with a nonlinear loss (two-photon absorption) added to the LL model. Numerical findings demonstrate that these exact solutions are stable, both dynamically and structurally (the latter means that stable numerical solutions close to the exact ones are found when a specific condition, necessary for the existence of the analytical solution, does not hold). In 2D, vast families of stable confined modes are produced by means of a variational approximation and full numerical simulations.

Correction tool for Active Shape Model based lumbar muscle segmentation.

PubMed

Valenzuela, Waldo; Ferguson, Stephen J; Ignasiak, Dominika; Diserens, Gaelle; Vermathen, Peter; Boesch, Chris; Reyes, Mauricio

2015-08-01

In the clinical environment, accuracy and speed of the image segmentation process plays a key role in the analysis of pathological regions. Despite advances in anatomic image segmentation, time-effective correction tools are commonly needed to improve segmentation results. Therefore, these tools must provide faster corrections with a low number of interactions, and a user-independent solution. In this work we present a new interactive correction method for correcting the image segmentation. Given an initial segmentation and the original image, our tool provides a 2D/3D environment, that enables 3D shape correction through simple 2D interactions. Our scheme is based on direct manipulation of free form deformation adapted to a 2D environment. This approach enables an intuitive and natural correction of 3D segmentation results. The developed method has been implemented into a software tool and has been evaluated for the task of lumbar muscle segmentation from Magnetic Resonance Images. Experimental results show that full segmentation correction could be performed within an average correction time of 6±4 minutes and an average of 68±37 number of interactions, while maintaining the quality of the final segmentation result within an average Dice coefficient of 0.92±0.03.

Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lambros, Maria Polikandritou, E-mail: mlambros@westernu.edu; Parsa, Cyrus; Mulamalla, HariChandana

2011-02-04

Research highlights: {yields} We irradiated a 3-D human oral cell culture of keratinocytes and fibroblasts with 12 and 2 Gy. {yields} 6 h after irradiation the histopathology and apoptosis of the 3-D culture were evaluated. Microarrays were used to assess the gene expression in the irradiated 3-D tissue. {yields} 12 Gy induced significant histopathologic changes and cellular apoptosis. {yields} 12 Gy significantly affected genes of the NF-kB pathway, inflammatory cytokines and DAMPs. -- Abstract: Mucositis is a debilitating adverse effect of chemotherapy and radiation treatment. It is important to develop a simple and reliable in vitro model, which can routinelymore » be used to screen new drugs for prevention and treatment of mucositis. Furthermore, identifying cell and molecular stresses especially in the initiation phase of mucositis in this model will help towards this end. We evaluated a three-dimensional (3-D) human oral cell culture that consisted of oral keratinocytes and fibroblasts as a model of oral mucositis. The 3-D cell culture model was irradiated with 12 or 2 Gy. Six hours after the irradiation we evaluated microscopic sections of the cell culture for evidence of morphologic changes including apoptosis. We used microarrays to compare the expression of several genes from the irradiated tissue with identical genes from tissue that was not irradiated. We found that irradiation with 12 Gy induced significant histopathologic effects including cellular apoptosis. Irradiation significantly affected the expression of several genes of the NF-kB pathway and several inflammatory cytokines, such as IL-1B, 1L-8, NF-kB1, and FOS compared to tissue that was not irradiated. We identified significant upregulation of several genes that belong to damage-associated molecular patterns (DAMPs) such as HMB1, S100A13, SA10014, and SA10016 in the 3-D tissues that received 12 Gy but not in tissues that received 2 Gy. In conclusion, this model quantifies radiation damage and this is an important first step towards the development 3-D tissue as a screening tool.« less

Efficient exfoliation of layered materials by waste liquor

NASA Astrophysics Data System (ADS)

Ding, Jiheng; Zhao, Hongran; Zheng, Yan; Wang, Qiaolei; Chen, Hao; Dou, Huimin; Yu, Haibin

2018-03-01

Based on their unique material properties, two-dimensional (2D) nanomaterials such as graphene, molybdenum disulfide (MoS2), and boron nitride (BN) have been attracting increased research interest. The potential of 2D materials, in the form of nanoplatelets that are used as new materials, will be important to both nanomaterials and advanced materials. Water is usually considered to be the ideal dispersed medium, and the essential hydrophobicity and limitations to mass production of 2D nanoplatelets have become quite serious obstacles to their usage in various fields. In this paper, pulping black liquor was used as dispersant, with high concentration of lignin to get single- and few-layered nanoplatelets. The whole process required only the high-shear mixing of 2D layered materials and pulping waste liquor. This method was not only simple and efficient but also environmentally friendly and resource-recycling. Moreover, the fabricated single- or few-layered nanoplatelets possessed good solubility in aqueous solution due to their edge functionalization, and could be well dispersed in water at concentrations (10 mg ml-1 for graphene, 6.3 mg ml-1 for MoS2, and 6.0 mg ml-1 for BN) which were much higher than that of other methods. The dispersions of graphene, MoS2, and BN nanosheets were highly stable over several months, which allowed us to easily prepare graphene, MoS2, and BN films through simple vacuum filtration or spraying. These results indicated that pulping black liquor can be used as a material or reagent, and the mass production of 2D material is possible in a simple and fast method.

First Higher-Multipole Model of Gravitational Waves from Spinning and Coalescing Black-Hole Binaries

NASA Astrophysics Data System (ADS)

London, Lionel; Khan, Sebastian; Fauchon-Jones, Edward; García, Cecilio; Hannam, Mark; Husa, Sascha; Jiménez-Forteza, Xisco; Kalaghatgi, Chinmay; Ohme, Frank; Pannarale, Francesco

2018-04-01

Gravitational-wave observations of binary black holes currently rely on theoretical models that predict the dominant multipoles (ℓ=2 ,|m |=2 ) of the radiation during inspiral, merger, and ringdown. We introduce a simple method to include the subdominant multipoles to binary black hole gravitational waveforms, given a frequency-domain model for the dominant multipoles. The amplitude and phase of the original model are appropriately stretched and rescaled using post-Newtonian results (for the inspiral), perturbation theory (for the ringdown), and a smooth transition between the two. No additional tuning to numerical-relativity simulations is required. We apply a variant of this method to the nonprecessing PhenomD model. The result, PhenomHM, constitutes the first higher-multipole model of spinning and coalescing black-hole binaries, and currently includes the (ℓ,|m |)=(2 ,2 ),(3 ,3 ),(4 ,4 ),(2 ,1 ),(3 ,2 ),(4 ,3 ) radiative moments. Comparisons with numerical-relativity waveforms demonstrate that PhenomHM is more accurate than dominant-multipole-only models for all binary configurations, and typically improves the measurement of binary properties.

First Higher-Multipole Model of Gravitational Waves from Spinning and Coalescing Black-Hole Binaries.

PubMed

London, Lionel; Khan, Sebastian; Fauchon-Jones, Edward; García, Cecilio; Hannam, Mark; Husa, Sascha; Jiménez-Forteza, Xisco; Kalaghatgi, Chinmay; Ohme, Frank; Pannarale, Francesco

2018-04-20

Gravitational-wave observations of binary black holes currently rely on theoretical models that predict the dominant multipoles (ℓ=2,|m|=2) of the radiation during inspiral, merger, and ringdown. We introduce a simple method to include the subdominant multipoles to binary black hole gravitational waveforms, given a frequency-domain model for the dominant multipoles. The amplitude and phase of the original model are appropriately stretched and rescaled using post-Newtonian results (for the inspiral), perturbation theory (for the ringdown), and a smooth transition between the two. No additional tuning to numerical-relativity simulations is required. We apply a variant of this method to the nonprecessing PhenomD model. The result, PhenomHM, constitutes the first higher-multipole model of spinning and coalescing black-hole binaries, and currently includes the (ℓ,|m|)=(2,2),(3,3),(4,4),(2,1),(3,2),(4,3) radiative moments. Comparisons with numerical-relativity waveforms demonstrate that PhenomHM is more accurate than dominant-multipole-only models for all binary configurations, and typically improves the measurement of binary properties.

Impact of Basal Hydrology Near Grounding Lines: Results from the MISMIP-3D and MISMIP+ Experiments Using the Community Ice Sheet Model

NASA Astrophysics Data System (ADS)

Leguy, G.; Lipscomb, W. H.; Asay-Davis, X.

2017-12-01

Ice sheets and ice shelves are linked by the transition zone, the region where the grounded ice lifts off the bedrock and begins to float. Adequate resolution of the transition zone is necessary for numerically accurate ice sheet-ice shelf simulations. In previous work we have shown that by using a simple parameterization of the basal hydrology, a smoother transition in basal water pressure between floating and grounded ice improves the numerical accuracy of a one-dimensional vertically integrated fixed-grid model. We used a set of experiments based on the Marine Ice Sheet Model Intercomparison Project (MISMIP) to show that reliable grounding-line dynamics at resolutions 1 km is achievable. In this presentation we use the Community Ice Sheet Model (CISM) to demonstrate how the representation of basal lubrication impacts three-dimensional models using the MISMIP-3D and MISMIP+ experiments. To this end we will compare three different Stokes approximations: the Shallow Shelf Approximation (SSA), a depth-integrated higher-order approximation, and the Blatter-Pattyn model. The results from our one-dimensional model carry over to the 3-D models; a resolution of 1 km (and in some cases 2 km) remains sufficient to accurately simulate grounding-line dynamics.

High-fidelity simulation capability for virtual testing of seismic and acoustic sensors

NASA Astrophysics Data System (ADS)

Wilson, D. Keith; Moran, Mark L.; Ketcham, Stephen A.; Lacombe, James; Anderson, Thomas S.; Symons, Neill P.; Aldridge, David F.; Marlin, David H.; Collier, Sandra L.; Ostashev, Vladimir E.

2005-05-01

This paper describes development and application of a high-fidelity, seismic/acoustic simulation capability for battlefield sensors. The purpose is to provide simulated sensor data so realistic that they cannot be distinguished by experts from actual field data. This emerging capability provides rapid, low-cost trade studies of unattended ground sensor network configurations, data processing and fusion strategies, and signatures emitted by prototype vehicles. There are three essential components to the modeling: (1) detailed mechanical signature models for vehicles and walkers, (2) high-resolution characterization of the subsurface and atmospheric environments, and (3) state-of-the-art seismic/acoustic models for propagating moving-vehicle signatures through realistic, complex environments. With regard to the first of these components, dynamic models of wheeled and tracked vehicles have been developed to generate ground force inputs to seismic propagation models. Vehicle models range from simple, 2D representations to highly detailed, 3D representations of entire linked-track suspension systems. Similarly detailed models of acoustic emissions from vehicle engines are under development. The propagation calculations for both the seismics and acoustics are based on finite-difference, time-domain (FDTD) methodologies capable of handling complex environmental features such as heterogeneous geologies, urban structures, surface vegetation, and dynamic atmospheric turbulence. Any number of dynamic sources and virtual sensors may be incorporated into the FDTD model. The computational demands of 3D FDTD simulation over tactical distances require massively parallel computers. Several example calculations of seismic/acoustic wave propagation through complex atmospheric and terrain environments are shown.

Effect of centrifugal forces on formation of secondary flow structures in a 180-degree curved artery model under pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Callahan, Shannon; Sajjad, Roshan; Bulusu, Kartik V.; Plesniak, Michael W.

2013-11-01

An experimental investigation of secondary flow structures within a 180-degree bent tube model of a curved artery was performed using phase-averaged, two-component, two-dimensional, particle image velocimetry (2C-2D PIV) under pulsatile inflow conditions. Pulsatile waveforms ranging from simple sinusoidal to physiological inflows were supplied. We developed a novel continuous wavelet transform algorithm (PIVlet 1.2) and applied it to vorticity fields for coherent secondary flow structure detection. Regime maps of secondary flow structures revealed new, deceleration-phase-dependent flow morphologies. The temporal instances where streamwise centrifugal forces dominated were associated with large-scale coherent structures, such as deformed Dean-, Lyne- and Wall-type (D-L-W) vortical structures. Magnitudes of streamwise and cross-stream centrifugal forces tend to balance during deceleration phases. Deceleration events were also associated with spatial reorganization and asymmetry in large-scale D-L-W secondary flow structures. Hence, the interaction between streamwise and cross-stream centrifugal forces that affects secondary flow morphologies is explained using a ``residual force'' parameter i.e., the difference in magnitudes of these forces. Supported by the NSF Grant No. CBET- 0828903 and GW Center for Biomimetics and Bioinspired Engineering.

Electronic and magnetic behaviors of B, N, and 3d transition metal substitutions in germanium carbide monolayer

NASA Astrophysics Data System (ADS)

Xu, Zhuo; Li, Yangping; Liu, Zhengtang; Liu, Shengzhong (Frank)

2018-04-01

The structural, electronic, and magnetic behaviors of two-dimensional GeC (2D-GeC) with single vacancy, substitutional B, N, and 3d transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, and Ni) are investigated based on the density functional theory. These impurities are tightly bonded to the surrounding atoms and found energetically more favorable at Ge sub-lattice site. In addition, the electronic band structures and magnetic properties of the doped systems indicate that (i) tunable electronic structures and magnetic moments of 2D-GeC can be obtained depending on different dopant species and sub-lattice sites, (ii) systems such as VC@Sc, VC@Fe, VC@Co, VGe@Fe, and VGe@Co are found to be half-metals, while the other systems all show semiconductor behavior. Simple models of the impurity-vacancy interaction is put forwards to illustrate the origin of the electronic structures and magnetic moments.

Prediction of global and local model quality in CASP8 using the ModFOLD server.

PubMed

McGuffin, Liam J

2009-01-01

The development of effective methods for predicting the quality of three-dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies. Since CASP7, the Quality Assessment (QA) category has existed to gauge the ability of various model quality assessment programs (MQAPs) at predicting the relative quality of individual 3D models. For the CASP8 experiment, automated predictions were submitted in the QA category using two methods from the ModFOLD server-ModFOLD version 1.1 and ModFOLDclust. ModFOLD version 1.1 is a single-model machine learning based method, which was used for automated predictions of global model quality (QMODE1). ModFOLDclust is a simple clustering based method, which was used for automated predictions of both global and local quality (QMODE2). In addition, manual predictions of model quality were made using ModFOLD version 2.0--an experimental method that combines the scores from ModFOLDclust and ModFOLD v1.1. Predictions from the ModFOLDclust method were the most successful of the three in terms of the global model quality, whilst the ModFOLD v1.1 method was comparable in performance to other single-model based methods. In addition, the ModFOLDclust method performed well at predicting the per-residue, or local, model quality scores. Predictions of the per-residue errors in our own 3D models, selected using the ModFOLD v2.0 method, were also the most accurate compared with those from other methods. All of the MQAPs described are publicly accessible via the ModFOLD server at: http://www.reading.ac.uk/bioinf/ModFOLD/. The methods are also freely available to download from: http://www.reading.ac.uk/bioinf/downloads/. Copyright 2009 Wiley-Liss, Inc.

Accounting For Gains And Orientations In Polarimetric SAR

NASA Technical Reports Server (NTRS)

Freeman, Anthony

1992-01-01

Calibration method accounts for characteristics of real radar equipment invalidating standard 2 X 2 complex-amplitude R (receiving) and T (transmitting) matrices. Overall gain in each combination of transmitting and receiving channels assumed different even when only one transmitter and one receiver used. One characterizes departure of polarimetric Synthetic Aperture Radar (SAR) system from simple 2 X 2 model in terms of single parameter used to transform measurements into format compatible with simple 2 X 2 model. Data processed by applicable one of several prior methods based on simple model.

Simple score to predict risk of hepatocellular carcinoma in chronic hepatitis C patients with advanced fibrosis after pegylated interferon and ribavirin therapy.

PubMed

Hu, Ching-Chih; Weng, Cheng-Hao; Chang, Liang-Che; Lin, Chih-Lang; Chen, Yen-Ting; Hu, Ching-Fang; Hua, Man-Chin; Chen, Li-Wei; Chien, Rong-Nan

2018-01-01

Eradication of chronic hepatitis C virus (HCV) after interferon-based therapy and its association with the reduction of risk of hepatocellular carcinoma (HCC) in HCV-infected patients with advanced fibrosis is controversial. The study is aimed to develop a simple scoring model for HCC prediction among advanced fibrotic chronic hepatitis C (CHC) patients after pegylated interferon (pegIFN) and ribavirin (RBV) therapy. We enrolled 271 biopsy-proven CHC patients with advanced fibrosis between 2003 and 2016, and divided them into non-HCC (n=211) and HCC (n=60) groups. The median observation duration was 6.0 years (range: 0.9-12.6 years). The HCC prevalence after pegIFN and RBV therapy in CHC patients with sustained virologic response (SVR) and without SVR was 14.7% and 32.2%, respectively. Multivariate Cox regression showed age ≥59.5 years old at initiation of therapy (HR: 2.542, 95% CI: 1.390-4.650, P =0.002), pretreatment total bilirubin ≥1.1 mg/dL (HR: 2.630, 95% CI: 1.420-4.871, P =0.002), pretreatment platelet counts <146.5 × 10 3 /μL (HR: 2.751, 95% CI: 1.373-5.511, P =0.004), no achievement of SVR (HR: 2.331, 95% CI: 1.277-4.253, P =0.006), and no diabetes at treatment initiation (HR: 3.085, 95% CI: 1.283-7.418, P =0.012) were significant predictors of HCC development. The scoring model consisted of the five categorical predictors and had an optimal cutoff point of 2.5. The area under receiver operating characteristic (AUROC) of the scoring model was 0.774±0.035 ( P <0.001). The sensitivity and specificity of the cutoff value to detect HCC were 81.3% and 57.5%. The 5-year and 10-year cumulative incidence of HCC was 4.9% and 10.0% in patients with simple score ≤2; and 25.9% and 44.6% in patients with simple score ≥3 ( P <0.001). The simple clinical-guided score has high discriminatory power for HCC prediction in advanced fibrotic CHC patients after pegIFN and RBV therapy.

Quantum confinement and dielectric profiles of colloidal nanoplatelets of halide inorganic and hybrid organic-inorganic perovskites

NASA Astrophysics Data System (ADS)

Sapori, Daniel; Kepenekian, Mikaël; Pedesseau, Laurent; Katan, Claudine; Even, Jacky

2016-03-01

Quantum confinement as well as high frequency ε∞ and static εs dielectric profiles are described for nanoplatelets of halide inorganic perovskites CsPbX3 (X = I, Br, Cl) and hybrid organic-inorganic perovskites (HOP) in two-dimensional (2D) and three-dimensional (3D) structures. 3D HOP are currently being sought for their impressive photovoltaic ability. Prior to this sudden popularity, 2D HOP materials were driving intense activity in the field of optoelectronics. Such developments have been enriched by the recent ability to synthesize colloidal nanostructures of controlled sizes of 2D and 3D HOP. This raises the need to achieve a thorough description of the electronic structure and dielectric properties of these systems. In this work, we go beyond the abrupt dielectric interface model and reach the atomic scale description. We examine the influence of the nature of the halogen and of the cation on the band structure and dielectric constants. Similarly, we survey the effect of dimensionality and shape of the perovskite. In agreement with recent experimental results, we show an increase of the band gap and a decrease of ε∞ when the size of a nanoplatelet reduces. By inspecting 2D HOP, we find that it cannot be described as a simple superposition of independent inorganic and organic layers. Finally, the dramatic impact of ionic contributions on the dielectric constant εs is analysed.Quantum confinement as well as high frequency ε∞ and static εs dielectric profiles are described for nanoplatelets of halide inorganic perovskites CsPbX3 (X = I, Br, Cl) and hybrid organic-inorganic perovskites (HOP) in two-dimensional (2D) and three-dimensional (3D) structures. 3D HOP are currently being sought for their impressive photovoltaic ability. Prior to this sudden popularity, 2D HOP materials were driving intense activity in the field of optoelectronics. Such developments have been enriched by the recent ability to synthesize colloidal nanostructures of controlled sizes of 2D and 3D HOP. This raises the need to achieve a thorough description of the electronic structure and dielectric properties of these systems. In this work, we go beyond the abrupt dielectric interface model and reach the atomic scale description. We examine the influence of the nature of the halogen and of the cation on the band structure and dielectric constants. Similarly, we survey the effect of dimensionality and shape of the perovskite. In agreement with recent experimental results, we show an increase of the band gap and a decrease of ε∞ when the size of a nanoplatelet reduces. By inspecting 2D HOP, we find that it cannot be described as a simple superposition of independent inorganic and organic layers. Finally, the dramatic impact of ionic contributions on the dielectric constant εs is analysed. Electronic supplementary information (ESI) available: Complementary results on the electronic structure and dielectric constants of CsPbX3 and CH3NH3PbX3 (X = I, Br, Cl). See DOI: 10.1039/c5nr07175e

A simple numerical model for predicting organic matter decomposition in a fed-batch composting operation.

PubMed

Nakasaki, Kiyohiko; Ohtaki, Akihito

2002-01-01

Using dog food as a model of the organic waste that comprises composting raw material, the degradation pattern of organic materials was examined by continuously measuring the quantity of CO2 evolved during the composting process in both batch and fed-batch operations. A simple numerical model was made on the basis of three suppositions for describing the organic matter decomposition in the batch operation. First, a certain quantity of carbon in the dog food was assumed to be recalcitrant to degradation in the composting reactor within the retention time allowed. Second, it was assumed that the decomposition rate of carbon is proportional to the quantity of easily degradable carbon, that is, the carbon recalcitrant to degradation was subtracted from the total carbon remaining in the dog food. Third, a certain lag time is assumed to occur before the start of active decomposition of organic matter in the dog food; this lag corresponds to the time required for microorganisms to proliferate and become active. It was then ascertained that the decomposition pattern for the organic matter in the dog food during the fed-batch operation could be predicted by the numerical model with the parameters obtained from the batch operation. This numerical model was modified so that the change in dry weight of composting materials could be obtained. The modified model was found suitable for describing the organic matter decomposition pattern in an actual fed-batch composting operation of the garbage obtained from a restaurant, approximately 10 kg d(-1) loading for 60 d.

Regional Seismic Amplitude Modeling and Tomography for Earthquake-Explosion Discrimination

NASA Astrophysics Data System (ADS)

Walter, W. R.; Pasyanos, M. E.; Matzel, E.; Gok, R.; Sweeney, J.; Ford, S. R.; Rodgers, A. J.

2008-12-01

Empirically explosions have been discriminated from natural earthquakes using regional amplitude ratio techniques such as P/S in a variety of frequency bands. We demonstrate that such ratios discriminate nuclear tests from earthquakes using closely located pairs of earthquakes and explosions recorded on common, publicly available stations at test sites around the world (e.g. Nevada, Novaya Zemlya, Semipalatinsk, Lop Nor, India, Pakistan, and North Korea). We are examining if there is any relationship between the observed P/S and the point source variability revealed by longer period full waveform modeling. For example, regional waveform modeling shows strong tectonic release from the May 1998 India test, in contrast with very little tectonic release in the October 2006 North Korea test, but the P/S discrimination behavior appears similar in both events using the limited regional data available. While regional amplitude ratios such as P/S can separate events in close proximity, it is also empirically well known that path effects can greatly distort observed amplitudes and make earthquakes appear very explosion-like. Previously we have shown that the MDAC (Magnitude Distance Amplitude Correction, Walter and Taylor, 2001) technique can account for simple 1-D attenuation and geometrical spreading corrections, as well as magnitude and site effects. However in some regions 1-D path corrections are a poor approximation and we need to develop 2-D path corrections. Here we demonstrate a new 2-D attenuation tomography technique using the MDAC earthquake source model applied to a set of events and stations in both the Middle East and the Yellow Sea Korean Peninsula regions. We believe this new 2-D MDAC tomography has the potential to greatly improve earthquake-explosion discrimination, particularly in tectonically complex regions such as the Middle East.

What makes Stellwagen Bank a whale feeding ground?

NASA Astrophysics Data System (ADS)

Zhai, X.; Flierl, G.; Lermusiaux, P. F. J.; Haley, P. J., Jr.; McCarthy, J. J.

2016-12-01

Stellwagen Bank lies at the Massachusetts Bay's eastern boundary with the Gulf of Maine (GoM) and is encompassed by the Gerry E. Studds Stellwagen Bank National Marine Sanctuary. It is a shoal with primarily sandy bottom and with water depth ranging from 20 meters to 40 meters. All across the Bank these waters are highly productive and support a large and diverse planktonic community and benthic community, a large fish diversity and fish biomass, and it is one of the most active whale feeding grounds in coastal waters of the United States makes. According to previous studies, several factors may contribute to the high biomass over sea banks and sea mounts, such as local enhancement due to high dissolved inorganic nitrogen (DIN = NH4 + NO3) and subsequent retention of productivity, plus the advection and local concentration of food produced elsewhere. In this research, the biological and physical processes which can cause the biomass patterns and accumulations over the Stellwagen Bank and its vicinity are investigated separately and together, using a 3D model which has been built in the MSEAS (Multidisciplinary simulation, estimation, and assimilation system) and a simple 2D cross-bank profile model. The study is focused on figuring out which are the dominant factors and processes that contribute to the abundant food in the Stellwagen Bank ecosystem and are responsible for sustaining the large biomass over the Bank, and how local or regional changes in climate and circulation might affect the food availability in this important whale feeding ground. The 2D model result shows that zooplankton diel migration can significantly affect the biological biomass and DIN concentration over the Bank. Both the 2D and 3D models show that upwelling induced by the Bank topography play an important role in nutrient and biomass enhancement.

Validation of the Two-Layer Model for Correcting Clear Sky Reflectance Near Clouds

NASA Technical Reports Server (NTRS)

Wen, Guoyong; Marshak, Alexander; Evans, K. Frank; Vamal, Tamas

2014-01-01

A two-layer model was developed in our earlier studies to estimate the clear sky reflectance enhancement near clouds. This simple model accounts for the radiative interaction between boundary layer clouds and molecular layer above, the major contribution to the reflectance enhancement near clouds for short wavelengths. We use LES/SHDOM simulated 3D radiation fields to valid the two-layer model for reflectance enhancement at 0.47 micrometer. We find: (a) The simple model captures the viewing angle dependence of the reflectance enhancement near cloud, suggesting the physics of this model is correct; and (b) The magnitude of the 2-layer modeled enhancement agree reasonably well with the "truth" with some expected underestimation. We further extend our model to include cloud-surface interaction using the Poisson model for broken clouds. We found that including cloud-surface interaction improves the correction, though it can introduced some over corrections for large cloud albedo, large cloud optical depth, large cloud fraction, large cloud aspect ratio. This over correction can be reduced by excluding scenes (10 km x 10km) with large cloud fraction for which the Poisson model is not designed for. Further research is underway to account for the contribution of cloud-aerosol radiative interaction to the enhancement.

Evidence for rapid topographic evolution and crater degradation on Mercury from simple crater morphometry

NASA Astrophysics Data System (ADS)

Fassett, Caleb I.; Crowley, Malinda C.; Leight, Clarissa; Dyar, M. Darby; Minton, David A.; Hirabayashi, Masatoshi; Thomson, Bradley J.; Watters, Wesley A.

2017-06-01

Examining the topography of impact craters and their evolution with time is useful for assessing how fast planetary surfaces evolve. Here, new measurements of depth/diameter (d/D) ratios for 204 craters of 2.5 to 5 km in diameter superposed on Mercury's smooth plains are reported. The median d/D is 0.13, much lower than expected for newly formed simple craters ( 0.21). In comparison, lunar craters that postdate the maria are much less modified, and the median crater in the same size range has a d/D ratio that is nearly indistinguishable from the fresh value. This difference in crater degradation is remarkable given that Mercury's smooth plains and the lunar maria likely have ages that are comparable, if not identical. Applying a topographic diffusion model, these results imply that crater degradation is faster by a factor of approximately two on Mercury than on the Moon, suggesting more rapid landform evolution on Mercury at all scales.