The arctic winter stratosphere: simulated with a 3-D chemistry transport model
NASA Astrophysics Data System (ADS)
van den Broek, Martina Maria Petronella
2004-10-01
During the past two decades, the ozone layer has developed a “hole” each winter and spring above the Antarctic continent. Also in cold Arctic winters substantial stratospheric ozone depletion has been measured, although less than in the Antarctic stratosphere. In the Arctic winter stratosphere, the amount of ozone depletion varies interannually and within one winter, depending on polar vortex stability and temperature. The simulation of transport and chemical conversion of ozone and related species requires a three-dimensional (3D) chemistry transport model (CTM), because of the non-symmetric behaviour of the Arctic polar vortex. This thesis reports on several studies of the Arctic winter stratosphere carried out with such a CTM, using off-line meteorological fields. In Chapter II, chlorine activation and ozone depletion in the Arctic winter stratosphere of 1996-1997 are modelled with the newly developed stratospheric version of our CTM. Comparisons have been made with total O3 columns and ClO concentrations observed by satellites, and with ozone loss rates derived from observations during February and March 1997. ClO concentrations and ozone depletion are somewhat underestimated by the model. Key model parameters have been varied to explain this underestimation. Next to temperature, the formation mechanism of solid and/or liquid PSC particles constitutes the main model uncertainty. The representation of tracer transport is a third uncertain parameter, influencing both ozone and inorganic chlorine. In Chapter III, we have used the CTM with different horizontal resolutions to evaluate this stratospheric transport by simulating the long-lived tracers HF and CH4 during the Arctic winter of 1999/2000. Outside the vortex the model results agree well with the observations, but inside, the model underestimates the observed vertical gradient in HF and CH4. Too strong mixing through the vortex edge could be a cause for these model discrepancies, e.g. associated with the
MT3D was first developed by Chunmiao Zheng in 1990 at S.S. Papadopulos & Associates, Inc. with partial support from the U.S. Environmental Protection Agency (USEPA). Starting in 1990, MT3D was released as a pubic domain code from the USEPA. Commercial versions with enhanced capab...
NASA Astrophysics Data System (ADS)
Utembe, S. R.; Cooke, M. C.; Archibald, A. T.; Shallcross, D. E.; Derwent, R. G.; Jenkin, M. E.
2011-03-01
A secondary organic aerosol (SOA) code, coupled to the reduced Common Representative Intermediates chemical mechanism (CRI v2-R5), has been used in the global 3-D chemistry-transport model, STOCHEM, to simulate the global distribution of organic aerosol (OA) mass loadings. The SOA code represents the gas-to-aerosol partitioning of products formed over several generations of oxidation of a variety of organic precursors emitted from anthropogenic, biogenic and biomass burning sources. The model also includes emissions of primary organic aerosol (POA), based on the AeroCom inventory and the Global Fire Emissions database (GFED). The calculated burdens for POA, 0.89 Tg, and SOA, 0.23 Tg, are well within the range of values that have been reported in previous modelling studies. The calculated SOA annual in-situ production of 22.5 Tg yr -1 also falls within the 8-110 Tg yr -1 range calculated by other models, but is somewhat lower than observationally-constrained top-down estimates which have been reported recently. The oxidation of biogenic precursors is found to account for about 90% of the global SOA burden, and this makes a substantial contribution to the highest annual mean surface OA concentrations (up to 8 μg m -3), which are simulated in tropical forested regions. Comparison of the simulated OA mass loadings with surface observations from a variety of locations indicate a good description of the OA distribution, but with an average underestimation of about a factor of 3. Sustained formation of SOA into the free troposphere is simulated, with important contributions from second and third-generation products of terpene oxidation in the upper troposphere. Comparison of the simulated OA mass loadings with vertical profiles from the ACE-Asia campaign indicates a very good description of the relative variation of OA with altitude, but with consistent underestimation of about a factor of 5. Although the absolute magnitude of the global source strength is underestimated
3D printing in chemistry: past, present and future
NASA Astrophysics Data System (ADS)
Shatford, Ryan; Karanassios, Vassili
2016-05-01
During the last years, 3d printing for rapid prototyping using additive manufacturing has been receiving increased attention in the technical and scientific literature including some Chemistry-related journals. Furthermore, 3D printing technology (defining size and resolution of 3D objects) and properties of printed materials (e.g., strength, resistance to chemical attack, electrical insulation) proved to be important for chemistry-related applications. In this paper these are discussed in detail. In addition, application of 3D printing for development of Micro Plasma Devices (MPDs) is discussed and 2d-profilometry data of a 3D printed surfaces is reported. And, past and present chemistry and bio-related applications of 3D printing are reviewed and possible future directions are postulated.
3D Multigroup Sn Neutron Transport Code
Energy Science and Technology Software Center (ESTSC)
2001-02-14
ATTILA is a 3D multigroup transport code with arbitrary order ansotropic scatter. The transport equation is solved in first order form using a tri-linear discontinuous spatial differencing on an arbitrary tetrahedral mesh. The overall solution technique is source iteration with DSA acceleration of the scattering source. Anisotropic boundary and internal sources may be entered in the form of spherical harmonics moments. Alpha and k eigenvalue problems are allowed, as well as fixed source problems. Forwardmore » and adjoint solutions are available. Reflective, vacumn, and source boundary conditions are available. ATTILA can perform charged particle transport calculations using slowing down (CSD) terms. ATTILA can also be used to peform infra-red steady-state calculations for radiative transfer purposes.« less
3D Multigroup Sn Neutron Transport Code
McGee, John; Wareing, Todd; Pautz, Shawn
2001-02-14
ATTILA is a 3D multigroup transport code with arbitrary order ansotropic scatter. The transport equation is solved in first order form using a tri-linear discontinuous spatial differencing on an arbitrary tetrahedral mesh. The overall solution technique is source iteration with DSA acceleration of the scattering source. Anisotropic boundary and internal sources may be entered in the form of spherical harmonics moments. Alpha and k eigenvalue problems are allowed, as well as fixed source problems. Forward and adjoint solutions are available. Reflective, vacumn, and source boundary conditions are available. ATTILA can perform charged particle transport calculations using slowing down (CSD) terms. ATTILA can also be used to peform infra-red steady-state calculations for radiative transfer purposes.
Quantifying the surface chemistry of 3D matrices in situ
NASA Astrophysics Data System (ADS)
Tzeranis, Dimitrios S.; So, Peter T. C.; Yannas, Ioannis V.
2014-03-01
Despite the major role of the matrix (the insoluble environment around cells) in physiology and pathology, there are very few and limited methods that can quantify the surface chemistry of a 3D matrix such as a biomaterial or tissue ECM. This study describes a novel optical-based methodology that can quantify the surface chemistry (density of adhesion ligands for particular cell adhesion receptors) of a matrix in situ. The methodology utilizes fluorescent analogs (markers) of the receptor of interest and a series of binding assays, where the amount of bound markers on the matrix is quantified via spectral multi-photon imaging. The study provides preliminary results for the quantification of the ligands for the two major collagen-binding integrins (α1β1, α2β1) in porous collagen scaffolds that have been shown to be able to induce maximum regeneration in transected peripheral nerves. The developed methodology opens the way for quantitative descriptions of the insoluble microenvironment of cells in physiology and pathology, and for integrating the matrix in quantitative models of cell signaling. α
Quantum transport through 3D Dirac materials
Salehi, M.; Jafari, S.A.
2015-08-15
Bismuth and its alloys provide a paradigm to realize three dimensional materials whose low-energy effective theory is given by Dirac equation in 3+1 dimensions. We study the quantum transport properties of three dimensional Dirac materials within the framework of Landauer–Büttiker formalism. Charge carriers in normal metal satisfying the Schrödinger equation, can be split into four-component with appropriate matching conditions at the boundary with the three dimensional Dirac material (3DDM). We calculate the conductance and the Fano factor of an interface separating 3DDM from a normal metal, as well as the conductance through a slab of 3DDM. Under certain circumstances the 3DDM appears transparent to electrons hitting the 3DDM. We find that electrons hitting the metal-3DDM interface from metallic side can enter 3DDM in a reversed spin state as soon as their angle of incidence deviates from the direction perpendicular to interface. However the presence of a second interface completely cancels this effect.
Quantum transport through 3D Dirac materials
NASA Astrophysics Data System (ADS)
Salehi, M.; Jafari, S. A.
2015-08-01
Bismuth and its alloys provide a paradigm to realize three dimensional materials whose low-energy effective theory is given by Dirac equation in 3+1 dimensions. We study the quantum transport properties of three dimensional Dirac materials within the framework of Landauer-Büttiker formalism. Charge carriers in normal metal satisfying the Schrödinger equation, can be split into four-component with appropriate matching conditions at the boundary with the three dimensional Dirac material (3DDM). We calculate the conductance and the Fano factor of an interface separating 3DDM from a normal metal, as well as the conductance through a slab of 3DDM. Under certain circumstances the 3DDM appears transparent to electrons hitting the 3DDM. We find that electrons hitting the metal-3DDM interface from metallic side can enter 3DDM in a reversed spin state as soon as their angle of incidence deviates from the direction perpendicular to interface. However the presence of a second interface completely cancels this effect.
3-D UNSTRUCTURED HEXAHEDRAL-MESH Sn TRANSPORT METHODS
J. MOREL; J. MCGHEE; ET AL
2000-11-01
This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). We have developed a method for solving the neutral-particle transport equation on 3-D unstructured hexahedral meshes using a S{sub n} discretization in angle in conjunction with a discontinuous finite-element discretization in space and a multigroup discretization in energy. Previous methods for solving this equation in 3-D have been limited to rectangular meshes. The unstructured-mesh method that we have developed is far more efficient for solving problems with complex 3-D geometric features than rectangular-mesh methods. In spite of having to make several compromises in our spatial discretization technique and our iterative solution technique, our method has been found to be both accurate and efficient for a broad class of problems.
A non-conforming 3D spherical harmonic transport solver
Van Criekingen, S.
2006-07-01
A new 3D transport solver for the time-independent Boltzmann transport equation has been developed. This solver is based on the second-order even-parity form of the transport equation. The angular discretization is performed through the expansion of the angular neutron flux in spherical harmonics (PN method). The novelty of this solver is the use of non-conforming finite elements for the spatial discretization. Such elements lead to a discontinuous flux approximation. This interface continuity requirement relaxation property is shared with mixed-dual formulations such as the ones based on Raviart-Thomas finite elements. Encouraging numerical results are presented. (authors)
Challenges in Lagrangian transport and predictability in 3D flows
NASA Astrophysics Data System (ADS)
Branicki, M.; Wiggins, S.; Kirwan, A. D.; Malek-Madani, R.
2011-12-01
The interplay between the geometrical theory of dynamical systems and the trajectory-based description of aperiodically time-dependent fluid flows has led to significant advances in understanding the role of chaotic transport in geophysical flows at scales dominated by advection. Lagrangian transport analysis utilizing either the time-dependent geometry of intersecting stable and unstable manifolds of the so-called Distinguished Hyperbolic Trajectories (DHT), or ridges of finite-time Lyapunov exponent fields (LCS), provide a much needed and complementary insight into ephemeral mechanisms responsible for the existence of `leaky' transport barriers and 'leaky' mesoscale eddies. However, to date most oceanic applications have been confined to 2D analysis of near surface regions in 'perfect' flows not accounting for model or measurement error, and with the tacit assumption of negligible vertical velocities. I will systematically address issues concerning the regimes of applicability of two-dimensional analysis in 3D aperiodically time-dependent flows, as well as outstanding challenges in fully 3D Lagrangian transport analysis. Even for perfect horizontal velocities, little is known about the vertical extent of stable/unstable manifolds associated with DHTs and/or other special structures relevant to stratified 3D flows. In particular, their sensitivity to errors in the vertical velocities and data assimilation methods has been little studied. Rigorous results regarding the above issues will be illustrated by revealing and mathematically tractable toy models, as well as examples from a detailed study in an eddy-rich region from the Gulf of Mexico and the Mediterranean. New ways of quantifying the uncertainty in Lagrangian predictions will also be presented.
3D Shape and Indirect Appearance by Structured Light Transport.
OToole, Matthew; Mather, John; Kutulakos, Kiriakos N
2016-07-01
We consider the problem of deliberately manipulating the direct and indirect light flowing through a time-varying, general scene in order to simplify its visual analysis. Our approach rests on a crucial link between stereo geometry and light transport: while direct light always obeys the epipolar geometry of a projector-camera pair, indirect light overwhelmingly does not. We show that it is possible to turn this observation into an imaging method that analyzes light transport in real time in the optical domain, prior to acquisition. This yields three key abilities that we demonstrate in an experimental camera prototype: (1) producing a live indirect-only video stream for any scene, regardless of geometric or photometric complexity; (2) capturing images that make existing structured-light shape recovery algorithms robust to indirect transport; and (3) turning them into one-shot methods for dynamic 3D shape capture. PMID:27295455
NASA Technical Reports Server (NTRS)
Bidwell, Colin S.; Pinella, David; Garrison, Peter
1999-01-01
Collection efficiency and ice accretion calculations were made for a commercial transport using the NASA Lewis LEWICE3D ice accretion code, the ICEGRID3D grid code and the CMARC panel code. All of the calculations were made on a Windows 95 based personal computer. The ice accretion calculations were made for the nose, wing, horizontal tail and vertical tail surfaces. Ice shapes typifying those of a 30 minute hold were generated. Collection efficiencies were also generated for the entire aircraft using the newly developed unstructured collection efficiency method. The calculations highlight the flexibility and cost effectiveness of the LEWICE3D, ICEGRID3D, CMARC combination.
Turbulence and transport in a 3D magnetic boundary
NASA Astrophysics Data System (ADS)
Agostini, Matteo; Carraro, Lorella; Ciaccio, Giovanni; de Masi, Gianluca; Rea, Cristina; Scarin, Paolo; Spizzo, Gianluca; Spolaore, Monica; Vianello, Nicola
2014-10-01
In present fusion devices the interaction between 3D magnetic field, edge kinetic properties and turbulence is a crucial issue; not only in intrinsically 3D configurations such as the stellarators, but also in tokamaks, where magnetic perturbations are applied to control ELMs and plasma wall interaction. In the RFX-mod reversed field pinch the spontaneous development at high plasma current of a helical magnetic state displays strong analogies with the aforementioned configurations. At the edge the presence of a stochastic layer and magnetic islands with a well-defined helical symmetry leads to a helical pattern of flow, pressure gradients and turbulent fluctuations: larger fluctuations and shorter correlation lengths are observed near the X-point of the magnetic island, where also a flow slowing-down occurs. Aim of this work is to study the effect of edge turbulence on particle transport in a 3D magnetic boundary, characterizing the properties of the edge blobs along the helical deformation. The magnetic topology also modifies kinetic properties, with higher pressure gradients observed close to the O-point of the island. The measurement of the time evolution of pressure gradient and blob characteristics, can clarify the mutual relation between these two quantities.
New Algorithms for Large-scale 3D Radiation Transport
NASA Astrophysics Data System (ADS)
Lentz, Eric J.
2009-05-01
Radiation transport is critical not only for analysis of astrophysical objects but also for the dynamical transport of energy within. Increased fidelity and dimensionality of the other components of such models requires a similar improvement in the radiation transport. Modern astrophysical simulations can be large enough that the values for a single variable for the entire computational domain cannot be stored on a single compute node. The natural solution is to decompose the physical domain into pieces with each node responsible for a single sub-domain. Using localized plus "ghost" zone data works well for problems like explicit hydrodynamics or nuclear reaction networks with modest impact from inter-process communication. Unfortunately, radiation transport is an inherently non-local process that couples the entire model domain together and efficient algorithms are needed to conquer this problem. In this poster, I present the early development of a new parallel, 3-D transport code using ray tracing to formally solve the transport equation across numerically decomposed domains. The algorithm model takes advantage of one-sided communication to develop a scalable, parallel formal solver. Other aspects and future direction of the parallel code development such as scalability and the inclusion of scattering will also be discussed.
Illustrating Concepts in Physical Organic Chemistry with 3D Printed Orbitals
ERIC Educational Resources Information Center
Robertson, Michael J.; Jorgensen, William L.
2015-01-01
Orbital theory provides a powerful tool for rationalizing and understanding many phenomena in chemistry. In most introductory chemistry courses, students are introduced to atomic and molecular orbitals in the form of two-dimensional drawings. In this work, we describe a general method for producing 3D printing files of orbital models that can be…
Transport of 3D space charge dominated beams
NASA Astrophysics Data System (ADS)
Lü, Jian-Qin
2013-10-01
In this paper we present the theoretical analysis and the computer code design for the intense pulsed beam transport. Intense beam dynamics is a very important issue in low-energy high-current accelerators and beam transport systems. This problem affects beam transmission and beam qualities. Therefore, it attracts the attention of the accelerator physicists worldwide. The analysis and calculation for the intense beam dynamics are very complicated, because the state of particle motion is dominated not only by the applied electromagnetic fields, but also by the beam-induced electromagnetic fields (self-fields). Moreover, the self fields are related to the beam dimensions and particle distributions. So, it is very difficult to get the self-consistent solutions of particle motion analytically. For this reason, we combine the Lie algebraic method and the particle in cell (PIC) scheme together to simulate intense 3D beam transport. With the Lie algebraic method we analyze the particle nonlinear trajectories in the applied electromagnetic fields up to third order approximation, and with the PIC algorithm we calculate the space charge effects to the particle motion. Based on the theoretical analysis, we have developed a computer code, which calculates beam transport systems consisting of electrostatic lenses, electrostatic accelerating columns, solenoid lenses, magnetic and electric quadruples, magnetic sextupoles, octopuses and different kinds of electromagnetic analyzers. The optimization calculations and the graphic display for the calculated results are provided by the code.
3-D numerical simulations of volcanic ash transport and deposition
NASA Astrophysics Data System (ADS)
Suzuki, Y. J.; Koyaguchi, T.
2012-12-01
During an explosive volcanic eruption, volcanic gas and pyroclasts are ejected from the volcanic vent. The pyroclasts are carried up within a convective plume, advected by the surrounding wind field, and sediment on the ground depending on their terminal velocity. The fine ash are expected to have atmospheric residence, whereas the coarser particles form fall deposits. Accurate modeling of particle transport and deposition is of critical importance from the viewpoint of disaster prevention. Previously, some particle-tracking models (e.g., PUFF) and advection-diffusion models (e.g., TEPHRA2 and FALL3D) tried to forecast particle concentration in the atmosphere and particle loading at ground level. However, these models assumed source conditions (the grain-size distribution, plume height, and mass release location) based on the simple 1-D model of convective plume. In this study, we aim to develop a new 3-D model which reproduces both of the dynamics of convective plume and the ash transport. The model is designed to describe the injection of eruption cloud and marker particles from a circular vent above a flat surface into the stratified atmosphere. Because the advection is the predominant mechanism of particle transport near the volcano, the diffusive process is not taken into account in this model. The distribution of wind velocity is given as an initial condition. The model of the eruption cloud dynamics is based on the 3-D time-dependent model of Suzuki et al. (2005). We apply a pseudo-gas model to calculate the eruption cloud dynamics: the effect of particle separation on the cloud dynamics is not considered. In order to reproduce the drastic change of eruption cloud density, we change the effective gas constant and heat capacity of the mixture in the equation of state for ideal gases with the mixing ratio between the ejected material and entrained air. In order to calculate the location and movement of ash particles, the present model employs Lagrangian marker
Moving Chemistry Education into 3D: A Tetrahedral Metaphor for Understanding Chemistry
ERIC Educational Resources Information Center
Mahaffy, Peter
2006-01-01
A new conceptual metaphor is proposed to enrich the description of chemistry education and support the many existing efforts to help students make connections with the chemistry found in textbooks. A widely used metaphor for chemistry education takes the shape of a planar triangle that highlights three thinking levels in learning chemistry such as…
ERIC Educational Resources Information Center
Merchant, Zahira; Goetz, Ernest T.; Keeney-Kennicutt, Wendy; Kwok, Oi-man; Cifuentes, Lauren; Davis, Trina J.
2012-01-01
We examined a model of the impact of a 3D desktop virtual reality environment on the learner characteristics (i.e. perceptual and psychological variables) that can enhance chemistry-related learning achievements in an introductory college chemistry class. The relationships between the 3D virtual reality features and the chemistry learning test as…
Exploring 3-D Virtual Reality Technology for Spatial Ability and Chemistry Achievement
ERIC Educational Resources Information Center
Merchant, Z.; Goetz, E. T.; Keeney-Kennicutt, W.; Cifuentes, L.; Kwok, O.; Davis, T. J.
2013-01-01
We investigated the potential of Second Life® (SL), a three-dimensional (3-D) virtual world, to enhance undergraduate students' learning of a vital chemistry concept. A quasi-experimental pre-posttest control group design was used to conduct the study. A total of 387 participants completed three assignment activities either in SL or using…
3D-printed devices for continuous-flow organic chemistry
Dragone, Vincenza; Sans, Victor; Rosnes, Mali H; Kitson, Philip J
2013-01-01
Summary We present a study in which the versatility of 3D-printing is combined with the processing advantages of flow chemistry for the synthesis of organic compounds. Robust and inexpensive 3D-printed reactionware devices are easily connected using standard fittings resulting in complex, custom-made flow systems, including multiple reactors in a series with in-line, real-time analysis using an ATR-IR flow cell. As a proof of concept, we utilized two types of organic reactions, imine syntheses and imine reductions, to show how different reactor configurations and substrates give different products. PMID:23766811
Defining an optimal surface chemistry for pluripotent stem cell culture in 2D and 3D
NASA Astrophysics Data System (ADS)
Zonca, Michael R., Jr.
Surface chemistry is critical for growing pluripotent stem cells in an undifferentiated state. There is great potential to engineer the surface chemistry at the nanoscale level to regulate stem cell adhesion. However, the challenge is to identify the optimal surface chemistry of the substrata for ES cell attachment and maintenance. Using a high-throughput polymerization and screening platform, a chemically defined, synthetic polymer grafted coating that supports strong attachment and high expansion capacity of pluripotent stem cells has been discovered using mouse embryonic stem (ES) cells as a model system. This optimal substrate, N-[3-(Dimethylamino)propyl] methacrylamide (DMAPMA) that is grafted on 2D synthetic poly(ether sulfone) (PES) membrane, sustains the self-renewal of ES cells (up to 7 passages). DMAPMA supports cell attachment of ES cells through integrin beta1 in a RGD-independent manner and is similar to another recently reported polymer surface. Next, DMAPMA has been able to be transferred to 3D by grafting to synthetic, polymeric, PES fibrous matrices through both photo-induced and plasma-induced polymerization. These 3D modified fibers exhibited higher cell proliferation and greater expression of pluripotency markers of mouse ES cells than 2D PES membranes. Our results indicated that desirable surfaces in 2D can be scaled to 3D and that both surface chemistry and structural dimension strongly influence the growth and differentiation of pluripotent stem cells. Lastly, the feasibility of incorporating DMAPMA into a widely used natural polymer, alginate, has been tested. Novel adhesive alginate hydrogels have been successfully synthesized by either direct polymerization of DMAPMA and methacrylic acid blended with alginate, or photo-induced DMAPMA polymerization on alginate nanofibrous hydrogels. In particular, DMAPMA-coated alginate hydrogels support strong ES cell attachment, exhibiting a concentration dependency of DMAPMA. This research provides a
3-D PARTICLE TRANSPORT WITHIN THE HUMAN UPPER RESPIRATORY TRACT
In this study trajectories of inhaled particulate matter (PM) were simulated within a three-dimensional (3-D) computer model of the human upper respiratory tract (URT). The airways were described by computer-reconstructed images of a silicone rubber cast of the human head, throat...
NASA Technical Reports Server (NTRS)
Chin, Mian; Ginoux, Paul; Torres, Omar; Zhao, Xue-Peng
2005-01-01
We propose a research project to incorporate a global 3-D model and satellite data into the multi-national Aerosol Characterization Experiment-Asia (ACE-Asia) mission. Our objectives are (1) to understand the physical, chemical, and optical properties of aerosols and the processes that control those properties over the Asian-Pacific region, (2) to investigate the interaction between aerosols and tropospheric chemistry, and (3) to determine the aerosol radiative forcing over the Asia-Pacific region. We will use the Georgia TecWGoddard Global Ozone Chemistry Aerosol Radiation and Transport (GOCART) model to link satellite observations and the ACE-Asia measurements. First, we will use the GOCART model to simulate aerosols and related species, and evaluate the model with satellite and in-situ observations. Second, the model generated aerosol vertical profiles and compositions will be used to validate the satellite products; and the satellite data will be used for during- and post- mission analysis. Third, we will use the model to analyze and interpret both satellite and ACE- Asia field campaign data and investigate the aerosol-chemistry interactions. Finally, we will calculate aerosol radiative forcing over the Asian-Pacific region, and assess the influence of Asian pollution in the global atmosphere. We propose a research project to incorporate a global 3-D model and satellite data into
Stratospheric chemistry and transport
NASA Technical Reports Server (NTRS)
Prather, Michael; Garcia, Maria M.
1990-01-01
A Chemical Tracer Model (CTM) that can use wind field data generated by the General Circulation Model (GCM) is developed to implement chemistry in the three dimensional GCM of the middle atmosphere. Initially, chemical tracers with simple first order losses such as N2O are used. Successive models are to incorporate more complex ozone chemistry.
SOLIDFELIX: a transportable 3D static volume display
NASA Astrophysics Data System (ADS)
Langhans, Knut; Kreft, Alexander; Wörden, Henrik Tom
2009-02-01
Flat 2D screens cannot display complex 3D structures without the usage of different slices of the 3D model. Volumetric displays like the "FELIX 3D-Displays" can solve the problem. They provide space-filling images and are characterized by "multi-viewer" and "all-round view" capabilities without requiring cumbersome goggles. In the past many scientists tried to develop similar 3D displays. Our paper includes an overview from 1912 up to today. During several years of investigations on swept volume displays within the "FELIX 3D-Projekt" we learned about some significant disadvantages of rotating screens, for example hidden zones. For this reason the FELIX-Team started investigations also in the area of static volume displays. Within three years of research on our 3D static volume display at a normal high school in Germany we were able to achieve considerable results despite minor funding resources within this non-commercial group. Core element of our setup is the display volume which consists of a cubic transparent material (crystal, glass, or polymers doped with special ions, mainly from the rare earth group or other fluorescent materials). We focused our investigations on one frequency, two step upconversion (OFTS-UC) and two frequency, two step upconversion (TFTSUC) with IR-Lasers as excitation source. Our main interest was both to find an appropriate material and an appropriate doping for the display volume. Early experiments were carried out with CaF2 and YLiF4 crystals doped with 0.5 mol% Er3+-ions which were excited in order to create a volumetric pixel (voxel). In addition to that the crystals are limited to a very small size which is the reason why we later investigated on heavy metal fluoride glasses which are easier to produce in large sizes. Currently we are using a ZBLAN glass belonging to the mentioned group and making it possible to increase both the display volume and the brightness of the images significantly. Although, our display is currently
Towards a 3D Space Radiation Transport Code
NASA Technical Reports Server (NTRS)
Wilson, J. W.; Tripathl, R. K.; Cicomptta, F. A.; Heinbockel, J. H.; Tweed, J.
2002-01-01
High-speed computational procedures for space radiation shielding have relied on asymptotic expansions in terms of the off-axis scatter and replacement of the general geometry problem by a collection of flat plates. This type of solution was derived for application to human rated systems in which the radius of the shielded volume is large compared to the off-axis diffusion limiting leakage at lateral boundaries. Over the decades these computational codes are relatively complete and lateral diffusion effects are now being added. The analysis for developing a practical full 3D space shielding code is presented.
NASA Astrophysics Data System (ADS)
Monge-Sanz, B. M.; Chipperfield, M. P.; Cariolle, D.; Feng, W.
2010-05-01
A detailed full-chemistry 3-D chemistry and transport model (CTM) is used to evaluate the current stratospheric O3 parameterisation in the European Centre for Medium-Range Weather Forecasts (ECMWF) model and to obtain an alternative version of the ozone scheme implicitly including heterogeneous chemistry. The approach avoids the inaccurate treatment currently given to heterogeneous ozone chemistry in the ECMWF model, as well as the uncertainties of a cold-tracer. The new O3 scheme (COPCAT) is evaluated within the same CTM used to calculate it. It is the first time such a comparison has been possible, providing direct information on the validity of the linear parameterisation approach for stratospheric ozone. Simulated total column and O3 profiles are compared against Total Ozone Mapping Spectrometer (TOMS) and Halogen Occultation Experiment (HALOE) observations. COPCAT successfully simulates polar loss and reproduces a realistic Antarctic O3 hole. The new scheme is comparable to the full-chemistry in many regions for multiannual runs. The parameterisation produces less ozone over the tropics around 10 hPa, compared to full-chemistry and observations, however, this problem can be ameliorated by choosing a different ozone climatology for the scheme. The new scheme is compared to the current ECMWF scheme in the same CTM runs. The Antarctic O3 hole with the current ECMWF scheme is weaker and disappears earlier than with the new COPCAT scheme. Differences between the current ECMWF scheme and COPCAT are difficult to explain due to the different approach used for heterogeneous chemistry and differences in the photochemical models used to calculate the scheme coefficients. Results with the new COPCAT scheme presented here show that heterogeneous and homogeneous ozone chemistry can be included in a consistent way in a linear ozone parameterisation, without any additional tunable parameters, providing a parameterisation scheme in much better agreement with the current
NASA Astrophysics Data System (ADS)
Monge-Sanz, B. M.; Chipperfield, M. P.; Cariolle, D.; Feng, W.
2011-02-01
A detailed full-chemistry 3-D chemistry and transport model (CTM) is used to evaluate the current stratospheric O3 parameterisation in the European Centre for Medium-Range Weather Forecasts (ECMWF) model and to obtain an alternative version of the ozone scheme implicitly including heterogeneous chemistry. The approach avoids the inaccurate treatment currently given to heterogeneous ozone chemistry in the ECMWF model, as well as the uncertainties of a cold-tracer. The new O3 scheme (COPCAT) is evaluated within the same CTM used to calculate it. It is the first time such a comparison has been possible, providing direct information on the validity of the linear parameterisation approach for stratospheric ozone. Simulated total column and O3 profiles are compared against Total Ozone Mapping Spectrometer (TOMS) and Halogen Occultation Experiment (HALOE) observations. COPCAT successfully simulates polar loss and reproduces a realistic Antarctic O3 hole. The new scheme is comparable to the full-chemistry in many regions for multiannual runs. The parameterisation produces less ozone over the tropics around 10 hPa, compared to full-chemistry and observations. However, this problem can be ameliorated by choosing a different ozone climatology for the scheme. The new scheme is compared to the current ECMWF scheme in the same CTM runs. The Antarctic O3 hole with the current ECMWF scheme is weaker and disappears earlier than with the new COPCAT scheme. Differences between the current ECMWF scheme and COPCAT are difficult to explain due to the different approach used for heterogeneous chemistry and differences in the photochemical models used to calculate the scheme coefficients. Results with the new COPCAT scheme presented here show that heterogeneous and homogeneous ozone chemistry can be included in a consistent way in a linear ozone parameterisation, without any additional tunable parameters, providing a parameterisation scheme in better agreement with the current knowledge
3D unstructured-mesh radiation transport codes
Morel, J.
1997-12-31
Three unstructured-mesh radiation transport codes are currently being developed at Los Alamos National Laboratory. The first code is ATTILA, which uses an unstructured tetrahedral mesh in conjunction with standard Sn (discrete-ordinates) angular discretization, standard multigroup energy discretization, and linear-discontinuous spatial differencing. ATTILA solves the standard first-order form of the transport equation using source iteration in conjunction with diffusion-synthetic acceleration of the within-group source iterations. DANTE is designed to run primarily on workstations. The second code is DANTE, which uses a hybrid finite-element mesh consisting of arbitrary combinations of hexahedra, wedges, pyramids, and tetrahedra. DANTE solves several second-order self-adjoint forms of the transport equation including the even-parity equation, the odd-parity equation, and a new equation called the self-adjoint angular flux equation. DANTE also offers three angular discretization options: $S{_}n$ (discrete-ordinates), $P{_}n$ (spherical harmonics), and $SP{_}n$ (simplified spherical harmonics). DANTE is designed to run primarily on massively parallel message-passing machines, such as the ASCI-Blue machines at LANL and LLNL. The third code is PERICLES, which uses the same hybrid finite-element mesh as DANTE, but solves the standard first-order form of the transport equation rather than a second-order self-adjoint form. DANTE uses a standard $S{_}n$ discretization in angle in conjunction with trilinear-discontinuous spatial differencing, and diffusion-synthetic acceleration of the within-group source iterations. PERICLES was initially designed to run on workstations, but a version for massively parallel message-passing machines will be built. The three codes will be described in detail and computational results will be presented.
A killer micro attack on 3D neutron transport
Dorr, M.R.; Ferguson, J.M.
1990-11-01
We describe the deterministic solution of the neutron transport equation and the computation of the effective criticality of three-dimensional assemblies using the BBN TC2000 killer micros. We observe that the performance of our research code PTRAN running on 48 processors of the TC2000 is competitive with the partially vectorizable version running on a single Cray Y/MP processor. This performance scales well with the number of processors on real problems, including those that are not load balanced a priori. To obtain this performance, we explicitly specify and exploit data locality and data dependence using domain decomposition and dynamic job scheduling. 3 refs., 4 figs., 2 tabs.
A killer micro attack on 3D neutron transport
Dorr, M.R.; Ferguson, J.M.
1990-11-16
In this paper, we describe the deterministic solution of the neutron transport equation and the computation of the effective criticality of three-dimensional assemblies using the BBN TC2000 killer micros. We observe that the performance of our research code PTRAN running on 48 processors of the TC2000 is competitive with the partially vectorizable version running on a single Cray Y/MP processor. This performance scales well with the number of processors on real problems, including those that are not load balanced a priori. To obtain this performance, we explicitly specify and exploit data locality and data dependence using domain decomposition and dynamic job scheduling. From the results obtained here, it appears that, at least for this application, a production machine based on the TC2000 architecture with more powerful processors and a commensurate increase in switch speed could yield a significant gain in our design capability. 2 refs., 5 figs., 2 tabs.
Convection and chemistry effects in CVD: A 3-D analysis for silicon deposition
NASA Technical Reports Server (NTRS)
Gokoglu, S. A.; Kuczmarski, M. A.; Tsui, P.; Chait, A.
1989-01-01
The computational fluid dynamics code FLUENT has been adopted to simulate the entire rectangular-channel-like (3-D) geometry of an experimental CVD reactor designed for Si deposition. The code incorporated the effects of both homogeneous (gas phase) and heterogeneous (surface) chemistry with finite reaction rates of important species existing in silane dissociation. The experiments were designed to elucidate the effects of gravitationally-induced buoyancy-driven convection flows on the quality of the grown Si films. This goal is accomplished by contrasting the results obtained from a carrier gas mixture of H2/Ar with the ones obtained from the same molar mixture ratio of H2/He, without any accompanying change in the chemistry. Computationally, these cases are simulated in the terrestrial gravitational field and in the absence of gravity. The numerical results compare favorably with experiments. Powerful computational tools provide invaluable insights into the complex physicochemical phenomena taking place in CVD reactors. Such information is essential for the improved design and optimization of future CVD reactors.
OS3D/GIMRT software for modeling multicomponent-multidimensional reactive transport
CI Steefel; SB Yabusaki
2000-05-17
OS3D/GIMRT is a numerical software package for simulating multicomponent reactive transport in porous media. The package consists of two principal components: (1) the code OS3D (Operator Splitting 3-Dimensional Reactive Transport) which simulates reactive transport by either splitting the reaction and transport steps in time, i.e., the classic time or operator splitting approach, or by iterating sequentially between reactions and transport, and (2) the code GIMRT (Global Implicit Multicomponent Reactive Transport) which treats up to two dimensional reactive transport with a one step or global implicit approach. Although the two codes do not yet have totally identical capabilities, they can be run from the same input file, allowing comparisons to be made between the two approaches in many cases. The advantages and disadvantages of the two approaches are discussed more fully below, but in general OS3D is designed for simulation of transient concentration fronts, particularly under high Peclet number transport conditions, because of its use of a total variation diminishing or TVD transport algorithm. GIMRT is suited for simulating water-rock alteration over long periods of time where the aqueous concentration field is at or close to a quasi-stationary state and the numerical transport errors are less important. Where water-rock interaction occurs over geological periods of time, GIMRT may be preferable to OS3D because of its ability to take larger time steps.
How do hydrodynamic instabilities affect 3D transport in geophysical vortices?
NASA Astrophysics Data System (ADS)
Wang, Peng; Özgökmen, Tamay M.
2015-03-01
Three-dimensional (3D) transport within geophysical vortices (e.g. ocean eddies) is important in understanding processes at a variety of scales, ranging from plankton production to climate variability. 3D transport can be affected by hydrodynamic instabilities of geophysical vortices; however, how the instabilities affecting 3D transport is not clear. Focusing on barotropic, inertial and 3D instabilities, we investigate the joint impacts of instabilities on 3D transport by using analytical methods and direct numerical simulations. We discover for the first time that material can be exchanged through 3D pathways which link a family of vortices generated by the instabilities in a single, initially unstable vortex. We also show that instabilities can increase the magnitude of vertical velocity, mixing rate and vertical material exchange. Besides, we find that instabilities can cause the kinetic energy wavenumber spectrum to have a power-law regime different than the classic regimes of k - 5 / 3 and k-3, and propose a new energy spectrum to interpret the non-classic regime.
Predicting longshore gradients in longshore transport: the CERC formula compared to Delft3D
List, Jeffrey H.; Hanes, Daniel M.; Ruggiero, Peter
2007-01-01
The prediction of longshore transport gradients is critical for forecasting shoreline change. We employ simple test cases consisting of shoreface pits at varying distances from the shoreline to compare the longshore transport gradients predicted by the CERC formula against results derived from the process-based model Delft3D. Results show that while in some cases the two approaches give very similar results, in many cases the results diverge greatly. Although neither approach is validated with field data here, the Delft3D-based transport gradients provide much more consistent predictions of erosional and accretionary zones as the pit location varies across the shoreface.
Pore-scale intermittent velocity structure underpinning anomalous transport through 3-D porous media
NASA Astrophysics Data System (ADS)
Kang, Peter K.; Anna, Pietro; Nunes, Joao P.; Bijeljic, Branko; Blunt, Martin J.; Juanes, Ruben
2014-09-01
We study the nature of non-Fickian particle transport in 3-D porous media by simulating fluid flow in the intricate pore space of real rock. We solve the full Navier-Stokes equations at the same resolution as the 3-D micro-CT (computed tomography) image of the rock sample and simulate particle transport along the streamlines of the velocity field. We find that transport at the pore scale is markedly anomalous: longitudinal spreading is superdiffusive, while transverse spreading is subdiffusive. We demonstrate that this anomalous behavior originates from the intermittent structure of the velocity field at the pore scale, which in turn emanates from the interplay between velocity heterogeneity and velocity correlation. Finally, we propose a continuous time random walk model that honors this intermittent structure at the pore scale and captures the anomalous 3-D transport behavior at the macroscale.
Moving from Batch to Field Using the RT3D Reactive Transport Modeling System
NASA Astrophysics Data System (ADS)
Clement, T. P.; Gautam, T. R.
2002-12-01
The public domain reactive transport code RT3D (Clement, 1997) is a general-purpose numerical code for solving coupled, multi-species reactive transport in saturated groundwater systems. The code uses MODFLOW to simulate flow and several modules of MT3DMS to simulate the advection and dispersion processes. RT3D employs the operator-split strategy which allows the code solve the coupled reactive transport problem in a modular fashion. The coupling between reaction and transport is defined through a separate module where the reaction equations are specified. The code supports a versatile user-defined reaction option that allows users to define their own reaction system through a Fortran-90 subroutine, known as the RT3D-reaction package. Further a utility code, known as BATCHRXN, allows the users to independently test and debug their reaction package. To analyze a new reaction system at a batch scale, users should first run BATCHRXN to test the ability of their reaction package to model the batch data. After testing, the reaction package can simply be ported to the RT3D environment to study the model response under 1-, 2-, or 3-dimensional transport conditions. This paper presents example problems that demonstrate the methods for moving from batch to field-scale simulations using BATCHRXN and RT3D codes. The first example describes a simple first-order reaction system for simulating the sequential degradation of Tetrachloroethene (PCE) and its daughter products. The second example uses a relatively complex reaction system for describing the multiple degradation pathways of Tetrachloroethane (PCA) and its daughter products. References 1) Clement, T.P, RT3D - A modular computer code for simulating reactive multi-species transport in 3-Dimensional groundwater aquifers, Battelle Pacific Northwest National Laboratory Research Report, PNNL-SA-28967, September, 1997. Available at: http://bioprocess.pnl.gov/rt3d.htm.
An implicit dispersive transport algorithm for the US Geological Survey MOC3D solute-transport model
Kipp, K.L., Jr.; Konikow, L.F.; Hornberger, G.Z.
1998-01-01
This report documents an extension to the U.S. Geological Survey MOC3D transport model that incorporates an implicit-in-time difference approximation for the dispersive transport equation, including source/sink terms. The original MOC3D transport model (Version 1) uses the method of characteristics to solve the transport equation on the basis of the velocity field. The original MOC3D solution algorithm incorporates particle tracking to represent advective processes and an explicit finite-difference formulation to calculate dispersive fluxes. The new implicit procedure eliminates several stability criteria required for the previous explicit formulation. This allows much larger transport time increments to be used in dispersion-dominated problems. The decoupling of advective and dispersive transport in MOC3D, however, is unchanged. With the implicit extension, the MOC3D model is upgraded to Version 2. A description of the numerical method of the implicit dispersion calculation, the data-input requirements and output options, and the results of simulator testing and evaluation are presented. Version 2 of MOC3D was evaluated for the same set of problems used for verification of Version 1. These test results indicate that the implicit calculation of Version 2 matches the accuracy of Version 1, yet is more efficient than the explicit calculation for transport problems that are characterized by a grid Peclet number less than about 1.0.
Bailey, Ryan T.; Morway, Eric D.; Niswonger, Richard G.; Gates, Timothy K.
2013-01-01
A numerical model was developed that is capable of simulating multispecies reactive solute transport in variably saturated porous media. This model consists of a modified version of the reactive transport model RT3D (Reactive Transport in 3 Dimensions) that is linked to the Unsaturated-Zone Flow (UZF1) package and MODFLOW. Referred to as UZF-RT3D, the model is tested against published analytical benchmarks as well as other published contaminant transport models, including HYDRUS-1D, VS2DT, and SUTRA, and the coupled flow and transport modeling system of CATHY and TRAN3D. Comparisons in one-dimensional, two-dimensional, and three-dimensional variably saturated systems are explored. While several test cases are included to verify the correct implementation of variably saturated transport in UZF-RT3D, other cases are included to demonstrate the usefulness of the code in terms of model run-time and handling the reaction kinetics of multiple interacting species in variably saturated subsurface systems. As UZF1 relies on a kinematic-wave approximation for unsaturated flow that neglects the diffusive terms in Richards equation, UZF-RT3D can be used for large-scale aquifer systems for which the UZF1 formulation is reasonable, that is, capillary-pressure gradients can be neglected and soil parameters can be treated as homogeneous. Decreased model run-time and the ability to include site-specific chemical species and chemical reactions make UZF-RT3D an attractive model for efficient simulation of multispecies reactive transport in variably saturated large-scale subsurface systems.
Bailey, Ryan T; Morway, Eric D; Niswonger, Richard G; Gates, Timothy K
2013-01-01
A numerical model was developed that is capable of simulating multispecies reactive solute transport in variably saturated porous media. This model consists of a modified version of the reactive transport model RT3D (Reactive Transport in 3 Dimensions) that is linked to the Unsaturated-Zone Flow (UZF1) package and MODFLOW. Referred to as UZF-RT3D, the model is tested against published analytical benchmarks as well as other published contaminant transport models, including HYDRUS-1D, VS2DT, and SUTRA, and the coupled flow and transport modeling system of CATHY and TRAN3D. Comparisons in one-dimensional, two-dimensional, and three-dimensional variably saturated systems are explored. While several test cases are included to verify the correct implementation of variably saturated transport in UZF-RT3D, other cases are included to demonstrate the usefulness of the code in terms of model run-time and handling the reaction kinetics of multiple interacting species in variably saturated subsurface systems. As UZF1 relies on a kinematic-wave approximation for unsaturated flow that neglects the diffusive terms in Richards equation, UZF-RT3D can be used for large-scale aquifer systems for which the UZF1 formulation is reasonable, that is, capillary-pressure gradients can be neglected and soil parameters can be treated as homogeneous. Decreased model run-time and the ability to include site-specific chemical species and chemical reactions make UZF-RT3D an attractive model for efficient simulation of multispecies reactive transport in variably saturated large-scale subsurface systems. PMID:23131109
Reactive Transport from Path3D: A Stream Tube Approach for Heterogeneous Aquifers
NASA Astrophysics Data System (ADS)
LI, L.
2001-05-01
Path3D (Zheng, 1991) is a popular computer program run in series with MODFLOW. Remediation engineers and hydrogeologist use it to track contaminant paths and to estimate solute travel time at heterogeneous sites. In order to predict fate and transport of multiple species at heterogeneous sites, numerical modeling packages, such as MT3D (Zheng,1990) or RT3D (Clement 1997) are often employed. These packages also are based on pre-processing with MODFLOW. However, for complex cases with aquifer heterogeneity, MT3D and RT3D often require very long computer run times. This paper addresses a new, stream-tube, approach that is both highly efficient and accurate to predict multi-species reactive transport at heterogeneous sites with steady flow. Our application of the stream tube approach is different from other stream tube approaches that apply the advection-dispersion-reaction equation in each stream tube (such as Ginn, 2000, Yabusaki, 1998, Charbeneau, 2000). In this work, the authors make use of properties of a linear system,working with decoupled reaction and sorption processes and mixing processes described by residence time distributions (RTDs). RTDs are abstracted from Path3D particle-tracking results and additional temporal and spatial dispersion (not caused by aquifer heterogeneity) is ignored. Reactions, including first order reactions and linear, reversible sorption, are applied through analytical transfer functions (called kinetic response functions). Convolution can then be applied to determine contaminant concentrations at monitoring points, using the RTDs determined from Path3D, kinetic transfer functions (expressed analytically), and expected trends of the source concentration. We are currently testing the approach and noting significant computational advantages for problems in three-dimensions, with first order reaction pathways and different retardation factors. We will demonstrate the method with several examples and compare the performance with MT3D and
Heterogeneous Chemistry in Global Chemistry Transport Models
NASA Astrophysics Data System (ADS)
Stadtler, Scarlet; Simpson, David; Schultz, Martin; Bott, Andreas
2016-04-01
The impact of six tropospheric heterogeneous reactions on ozone and nitrogen species was studied using two chemical transport models EMEP MSC-W and ECHAM6-HAMMOZ. Since heterogeneous reactions depend on reactant concentrations (in this study these are N_2O_5, NO_3, NO_2, O_3, HNO_3, HO_2) and aerosol surface area S_a, the modeled surface area of both models was compared to a satellite product retrieving the surface area. This comparison shows a good agreement in global pattern and especially the capability of both models to capture the extreme aerosol loadings in East Asia. Further, the impact of the heterogeneous reactions was evaluated by the simulation of a reference run containing all heterogeneous reactions and several sensitivity runs. One reaction was turned off in each sensitivity run to compare it with the reference run. As previously shown, the analysis of the sensitivity runs shows that the globally most important heterogeneous reaction is the one of N_2O_5. Nevertheless, NO_2, NO_3, HNO3 and HO2 heterogeneous reactions gain relevance particular in East China due to presence of high NOx concentrations and high Sa in the same region. The heterogeneous reaction of O3 itself on dust is compared to the other heterogeneous reactions of minor relevance. Evaluation of the models with northern hemispheric ozone surface observations yields a better agreement of the models with observations when the heterogeneous reactions are incorporated. Impacts of emission changes on the importance of the heterogeneous chemistry will be discussed.
2D/1D approximations to the 3D neutron transport equation. I: Theory
Kelley, B. W.; Larsen, E. W.
2013-07-01
A new class of '2D/1D' approximations is proposed for the 3D linear Boltzmann equation. These approximate equations preserve the exact transport physics in the radial directions x and y and diffusion physics in the axial direction z. Thus, the 2D/1D equations are more accurate approximations of the 3D Boltzmann equation than the conventional 3D diffusion equation. The 2D/1D equations can be systematically discretized, to yield accurate simulation methods for 3D reactor core problems. The resulting solutions will be more accurate than 3D diffusion solutions, and less expensive to generate than standard 3D transport solutions. In this paper, we (i) show that the simplest 2D/1D equation has certain desirable properties, (ii) systematically discretize this equation, and (iii) derive a stable iteration scheme for solving the discrete system of equations. In a companion paper [1], we give numerical results that confirm the theoretical predictions of accuracy and iterative stability. (authors)
The Transient 3-D Transport Coupled Code TORT-TD/ATTICA3D for High-Fidelity Pebble-Bed HTGR Analyses
NASA Astrophysics Data System (ADS)
Seubert, Armin; Sureda, Antonio; Lapins, Janis; Bader, Johannes; Laurien, Eckart
2012-01-01
This article describes the 3D discrete ordinates-based coupled code system TORT-TD/ATTICA3D that aims at steady state and transient analyses of pebble-bed high-temperature gas cooled reactors. In view of increasing computing power, the application of time-dependent neutron transport methods becomes feasible for best estimate evaluations of safety margins. The calculation capabilities of TORT-TD/ATTICA3D are presented along with the coupling approach, with focus on the time-dependent neutron transport features of TORT-TD. Results obtained for the OECD/NEA/NSC PBMR-400 benchmark demonstrate the transient capabilities of TORT-TD/ATTICA3D.
How Do Hydrodynamic Instabilities Affect 3D Transport in Geophysical Vortices?
NASA Astrophysics Data System (ADS)
Wang, P.; Ozgokmen, T. M.
2014-12-01
Understanding three-dimensional (3D) transport in ocean eddies is important for processes at a variety of scales, ranging from plankton production to climate variability. It is well known that geophysical vortices are subject to various hydrodynamic instabilities. Yet the influence of these instabilities on 3D material transport in vortex systems is not well investigated. Focusing on barotropic, inertial and 3D instabilities, we analyze these instabilities with normal-mode method, and reproduce their characteristics via highly-resolved numerical simulations using a spectral element Navier-Stokes solver. By comparing the simulation results of stable and unstable vortices, we investigate the joint impacts of instabilities on 3D transport through three major aspects: (i) energy transfer, (ii) overturning transport of the secondary circulation, and (iii) rates of vertical exchange and mixing. It is found that instabilities can enhance local nonlinear interactions and cause the kinetic energy wavenumber spectrum to have slopes between the conventional -5/3 and -3 at inertial ranges. The cascade of a new quantity is proposed to explain these non-conventional slopes. One of our main results is the discovery of material exchange between the central vortex and satellite vortices through 3D pathways, called funnels. These funnels modify the concept of elliptic regions that can trap material when confined to 2D dynamics. Thus, we show that a family of vortices, created by the hydrodynamic instabilities of the initially unstable vortex, can still continue to operate in unity in order to complete the 3D transport in these systems. We also show that flow instabilities can double the magnitude of vertical velocity, increase the rate of vertical exchange by an order of magnitude and enhance mixing rate more than 100%.
The performance of semilocal and hybrid density functionals in 3d transition-metal chemistry
NASA Astrophysics Data System (ADS)
Furche, Filipp; Perdew, John P.
2006-01-01
We investigate the performance of contemporary semilocal and hybrid density functionals for bond energetics, structures, dipole moments, and harmonic frequencies of 3d transition-metal (TM) compounds by comparison with gas-phase experiments. Special attention is given to the nonempirical metageneralized gradient approximation (meta-GGA) of Tao, Perdew, Staroverov, and Scuseria (TPSS) [Phys. Rev. Lett. 91, 146401 (2003)], which has been implemented in TURBOMOLE for the present work. Trends and error patterns for classes of homologous compounds are analyzed, including dimers, monohydrides, mononitrides, monoxides, monofluorides, polyatomic oxides and halogenides, carbonyls, and complexes with organic π ligands such as benzene and cyclopentadienyl. Weakly bound systems such as Ca2, Mn2, and Zn2 are discussed. We propose a reference set of reaction energies for benchmark purposes. Our all-electron results with quadruple zeta valence basis sets validate semilocal density-functional theory as the workhorse of computational TM chemistry. Typical errors in bond energies are substantially larger than in (organic) main group chemistry, however. The Becke-Perdew'86 [Phys. Rev. A 38, 3098 (1988); Phys. Rev. B 33, 8822 (1986)] GGA and the TPSS meta-GGA have the best price/performance ratio, while the TPSS hybrid functional achieves a slightly lower mean absolute error in bond energies. The popular Becke three-parameter hybrid B3LYP underbinds significantly and tends to overestimate bond distances; we give a possible explanation for this. We further show that hybrid mixing does not reduce the width of the error distribution on our reference set. The error of a functional for the s-d transfer energy of a TM atom does not predict its error for TM bond energies and bond lengths. For semilocal functionals, self-interaction error in one- and three-electron bonds appears to be a major source of error in TM reaction energies. Nevertheless, TPSS predicts the correct ground
PHT3D-UZF: A reactive transport model for variably-saturated porous media
Wu, Ming Zhi; Post, Vincent E. A.; Salmon, S. Ursula; Morway, Eric; Prommer, H.
2016-01-01
A modified version of the MODFLOW/MT3DMS-based reactive transport model PHT3D was developed to extend current reactive transport capabilities to the variably-saturated component of the subsurface system and incorporate diffusive reactive transport of gaseous species. Referred to as PHT3D-UZF, this code incorporates flux terms calculated by MODFLOW's unsaturated-zone flow (UZF1) package. A volume-averaged approach similar to the method used in UZF-MT3DMS was adopted. The PHREEQC-based computation of chemical processes within PHT3D-UZF in combination with the analytical solution method of UZF1 allows for comprehensive reactive transport investigations (i.e., biogeochemical transformations) that jointly involve saturated and unsaturated zone processes. Intended for regional-scale applications, UZF1 simulates downward-only flux within the unsaturated zone. The model was tested by comparing simulation results with those of existing numerical models. The comparison was performed for several benchmark problems that cover a range of important hydrological and reactive transport processes. A 2D simulation scenario was defined to illustrate the geochemical evolution following dewatering in a sandy acid sulfate soil environment. Other potential applications include the simulation of biogeochemical processes in variably-saturated systems that track the transport and fate of agricultural pollutants, nutrients, natural and xenobiotic organic compounds and micropollutants such as pharmaceuticals, as well as the evolution of isotope patterns.
PHT3D-UZF: A Reactive Transport Model for Variably-Saturated Porous Media.
Wu, Ming Zhi; Post, Vincent E A; Salmon, S Ursula; Morway, Eric D; Prommer, Henning
2016-01-01
A modified version of the MODFLOW/MT3DMS-based reactive transport model PHT3D was developed to extend current reactive transport capabilities to the variably-saturated component of the subsurface system and incorporate diffusive reactive transport of gaseous species. Referred to as PHT3D-UZF, this code incorporates flux terms calculated by MODFLOW's unsaturated-zone flow (UZF1) package. A volume-averaged approach similar to the method used in UZF-MT3DMS was adopted. The PHREEQC-based computation of chemical processes within PHT3D-UZF in combination with the analytical solution method of UZF1 allows for comprehensive reactive transport investigations (i.e., biogeochemical transformations) that jointly involve saturated and unsaturated zone processes. Intended for regional-scale applications, UZF1 simulates downward-only flux within the unsaturated zone. The model was tested by comparing simulation results with those of existing numerical models. The comparison was performed for several benchmark problems that cover a range of important hydrological and reactive transport processes. A 2D simulation scenario was defined to illustrate the geochemical evolution following dewatering in a sandy acid sulfate soil environment. Other potential applications include the simulation of biogeochemical processes in variably-saturated systems that track the transport and fate of agricultural pollutants, nutrients, natural and xenobiotic organic compounds and micropollutants such as pharmaceuticals, as well as the evolution of isotope patterns. PMID:25628017
NASA Astrophysics Data System (ADS)
Druzgalski, Clara; Mani, Ali
2014-11-01
We have investigated the transport dynamics of an electrokinetic instability that occurs when ions are driven from bulk fluids to ion-selective membranes due to externally applied electric fields. This phenomenon is relevant to a wide range of electrochemical applications including electrodialysis for fresh water production. Using data from our 3D DNS, we show how electroconvective instability, arising from concentration polarization, results in a chaotic flow that significantly alters the net ion transport rate across the membrane surface. The 3D DNS results, which fully resolve the spatiotemporal scales including the electric double layers, enable visualization of instantaneous snapshots of current density directly on the membrane surface, as well as analysis of transport statistics such as concentration variance and fluctuating advective fluxes. Furthermore, we present a full spectral analysis revealing broadband spectra in both concentration and flow fields and deduce the key parameter controlling the range of contributing scales.
NASA Astrophysics Data System (ADS)
da Câmara Santa Clara Gomes, Tristan; De La Torre Medina, Joaquín; Velázquez-Galván, Yenni G.; Martínez-Huerta, Juan Manuel; Encinas, Armando; Piraux, Luc
2016-07-01
We have explored the interplay between the magnetic and magneto-transport properties of 3D interconnected nanowire networks made of various magnetic metals by electrodeposition into nanoporous membranes with crossed channels and controlled topology. The close relationship between their magnetic and structural properties has a direct impact on their magneto-transport behavior. In order to accurately and reliably describe the effective magnetic anisotropy and anisotropic magnetoresistance, an analytical model inherent to the topology of 3D nanowire networks is proposed and validated. The feasibility to obtain magneto-transport responses in nanowire network films based on interconnected nanowires makes them very attractive for the development of mechanically stable superstructures that are suitable for potential technological applications.
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.
Edge Transport Modeling using the 3D EMC3-Eirene code on Tokamaks and Stellarators
NASA Astrophysics Data System (ADS)
Lore, J. D.; Ahn, J. W.; Briesemeister, A.; Ferraro, N.; Labombard, B.; McLean, A.; Reinke, M.; Shafer, M.; Terry, J.
2015-11-01
The fluid plasma edge transport code EMC3-Eirene has been applied to aid data interpretation and understanding the results of experiments with 3D effects on several tokamaks. These include applied and intrinsic 3D magnetic fields, 3D plasma facing components, and toroidally and poloidally localized heat and particle sources. On Alcator C-Mod, a series of experiments explored the impact of toroidally and poloidally localized impurity gas injection on core confinement and asymmetries in the divertor fluxes, with the differences between the asymmetry in L-mode and H-mode qualitatively reproduced in the simulations due to changes in the impurity ionization in the private flux region. Modeling of NSTX experiments on the effect of 3D fields on detachment matched the trend of a higher density at which the detachment occurs when 3D fields are applied. On DIII-D, different magnetic field models were used in the simulation and compared against the 2D Thomson scattering diagnostic. In simulating each device different aspects of the code model are tested pointing to areas where the model must be further developed. The application to stellarator experiments will also be discussed. Work supported by U.S. DOE: DE-AC05-00OR22725, DE AC02-09CH11466, DE-FC02-99ER54512, and DE-FC02-04ER54698.
NASA Technical Reports Server (NTRS)
Davis, Anthony B.; Marshak, Alexander
2010-01-01
The interplay of sunlight with clouds is a ubiquitous and often pleasant visual experience, but it conjures up major challenges for weather, climate, environmental science and beyond. Those engaged in the characterization of clouds (and the clear air nearby) by remote sensing methods are even more confronted. The problem comes, on the one hand, from the spatial complexity of real clouds and, on the other hand, from the dominance of multiple scattering in the radiation transport. The former ingredient contrasts sharply with the still popular representation of clouds as homogeneous plane-parallel slabs for the purposes of radiative transfer computations. In typical cloud scenes the opposite asymptotic transport regimes of diffusion and ballistic propagation coexist. We survey the three-dimensional (3D) atmospheric radiative transfer literature over the past 50 years and identify three concurrent and intertwining thrusts: first, how to assess the damage (bias) caused by 3D effects in the operational 1D radiative transfer models? Second, how to mitigate this damage? Finally, can we exploit 3D radiative transfer phenomena to innovate observation methods and technologies? We quickly realize that the smallest scale resolved computationally or observationally may be artificial but is nonetheless a key quantity that separates the 3D radiative transfer solutions into two broad and complementary classes: stochastic and deterministic. Both approaches draw on classic and contemporary statistical, mathematical and computational physics.
Advanced quadratures and periodic boundary conditions in parallel 3D S{sub n} transport
Manalo, K.; Yi, C.; Huang, M.; Sjoden, G.
2013-07-01
Significant updates in numerical quadratures have warranted investigation with 3D Sn discrete ordinates transport. We show new applications of quadrature departing from level symmetric (S{sub 2}o). investigating 3 recently developed quadratures: Even-Odd (EO), Linear-Discontinuous Finite Element - Surface Area (LDFE-SA), and the non-symmetric Icosahedral Quadrature (IC). We discuss implementation changes to 3D Sn codes (applied to Hybrid MOC-Sn TITAN and 3D parallel PENTRAN) that can be performed to accommodate Icosahedral Quadrature, as this quadrature is not 90-degree rotation invariant. In particular, as demonstrated using PENTRAN, the properties of Icosahedral Quadrature are suitable for trivial application using periodic BCs versus that of reflective BCs. In addition to implementing periodic BCs for 3D Sn PENTRAN, we implemented a technique termed 'angular re-sweep' which properly conditions periodic BCs for outer eigenvalue iterative loop convergence. As demonstrated by two simple transport problems (3-group fixed source and 3-group reflected/periodic eigenvalue pin cell), we remark that all of the quadratures we investigated are generally superior to level symmetric quadrature, with Icosahedral Quadrature performing the most efficiently for problems tested. (authors)
NASA Astrophysics Data System (ADS)
Davis, Anthony B.; Marshak, Alexander
2010-02-01
The interplay of sunlight with clouds is a ubiquitous and often pleasant visual experience, but it conjures up major challenges for weather, climate, environmental science and beyond. Those engaged in the characterization of clouds (and the clear air nearby) by remote sensing methods are even more confronted. The problem comes, on the one hand, from the spatial complexity of real clouds and, on the other hand, from the dominance of multiple scattering in the radiation transport. The former ingredient contrasts sharply with the still popular representation of clouds as homogeneous plane-parallel slabs for the purposes of radiative transfer computations. In typical cloud scenes the opposite asymptotic transport regimes of diffusion and ballistic propagation coexist. We survey the three-dimensional (3D) atmospheric radiative transfer literature over the past 50 years and identify three concurrent and intertwining thrusts: first, how to assess the damage (bias) caused by 3D effects in the operational 1D radiative transfer models? Second, how to mitigate this damage? Finally, can we exploit 3D radiative transfer phenomena to innovate observation methods and technologies? We quickly realize that the smallest scale resolved computationally or observationally may be artificial but is nonetheless a key quantity that separates the 3D radiative transfer solutions into two broad and complementary classes: stochastic and deterministic. Both approaches draw on classic and contemporary statistical, mathematical and computational physics.
Ozone formation during an episode over Europe: A 3-D chemical/transport model simulation
NASA Technical Reports Server (NTRS)
Berntsen, Terje; Isaksen, Ivar S. A.
1994-01-01
A 3-D regional photochemical tracer/transport model for Europe and the Eastern Atlantic has been developed based on the NASA/GISS CTM. The model resolution is 4x5 degrees latitude and longitude with 9 layers in the vertical (7 in the troposphere). Advective winds, convection statistics and other meteorological data from the NASA/GISS GCM are used. An extensive gas-phase chemical scheme based on the scheme used in our global 2D model has been incorporated in the 3D model. In this work ozone formation in the troposphere is studied with the 3D model during a 5 day period starting June 30. Extensive local ozone production is found and the relationship between the source regions and the downwind areas are discussed. Variations in local ozone formation as a function of total emission rate, as well as the composition of the emissions (HC/NO(x)) ratio and isoprene emissions) are elucidated. An important vertical transport process in the troposphere is by convective clouds. The 3D model includes an explicit parameterization of this process. It is shown that this process has significant influence on the calculated surface ozone concentrations.
Optically directed molecular transport and 3D isoelectric positioning of amphoteric biomolecules
Hafeman, Dean G.; Harkins, James B.; WitkowskiII, Charles E.; Lewis, Nathan S.; Brown, Gilbert M; Warmack, Robert J Bruce; Thundat, Thomas George
2006-01-01
We demonstrate the formation of charged molecular packets and their transport within optically created electrical force-field traps in a pH-buffered electrolyte. We call this process photoelectrophoretic localization and transport (PELT). The electrolyte is in contact with a photoconductive semiconductor electrode and a counterelectrode that are connected through an external circuit. A light beam directed to coordinates on the photoconductive electrode surface produces a photocurrent within the circuit and electrolyte. Within the electrolyte, the photocurrent creates localized force-field traps centered at the illuminated coordinates. Charged molecules, including polypeptides and proteins, electrophoretically accumulate into the traps and subsequently can be transported in the electrolyte by moving the traps over the photoconductive electrode in response to movement of the light beam. The molecules in a single trap can be divided into aliquots, and the aliquots can be directed along multiple routes simultaneously by using multiple light beams. This photoelectrophoretic transport of charged molecules by PELT resembles the electrostatic transport of electrons within force-field wells of solid-state charge-coupled devices. The molecules, however, travel in a liquid electrolyte rather than a solid. Furthermore, we have used PELT to position amphoteric biomolecules in three dimensions. A 3D pH gradient was created in an electrolyte medium by controlling the illumination position on a photoconductive anode where protons were generated electrolytically. Photoelectrophoretic transport of amphoteric molecules through the pH gradient resulted in accumulation of the molecules at their apparent 3D isoelectric coordinates in the medium.
2D/1D approximations to the 3D neutron transport equation. II: Numerical comparisons
Kelley, B. W.; Collins, B.; Larsen, E. W.
2013-07-01
In a companion paper [1], (i) several new '2D/1D equations' are introduced as accurate approximations to the 3D Boltzmann transport equation, (ii) the simplest of these approximate equations is systematically discretized, and (iii) a theoretically stable iteration scheme is developed to solve the discrete equations. In this paper, numerical results are presented that confirm the theoretical predictions made in [1]. (authors)
3-D Particl-in-Cell Simulations of Transport Driven Currents
NASA Astrophysics Data System (ADS)
Tsung, F. S.; Dawson, J. M.
1997-11-01
In the advanced tokamak regime, transport phenomena can account for a signficant fraction of the toroidal current, possibly over that driven directly by the ohmic heating electric fields. Although bootstrap theory accounts for contributions of the collisional modification of banana orbits on the toroidal currents, the corresponding transport theory does not accurately predict the transport of particles and heat in present-day tokamak experiments. Furthermore, in our previous simulations in 21/2-D, currents were spontaneously generated in both the cylindrical and the toroidal geometries, contrary to neoclassical predictions. In these calculations, it was believed that the driving mechanism is the preferential loss of particles whose initial velocity is opposite to that of the plasma current. Because the preferential loss mechanism assumes the conservation of toroidal angular momentum, we have extended these simulations to three dimensions to study the effects of toroidal assymetries. A parallel, 3-D electromagnetic PIC code running on the IBM SP, with a localized field-solver has been developed to investigate the effects of perturbations parallel to the field lines, and direct comparisons has been made between the 21/2-D and 3-D simulations, and we have found good agreements between the 2 1/2-D calculations and the 3-D results. We will present these results at the meeting.
GPU accelerated simulations of 3D deterministic particle transport using discrete ordinates method
NASA Astrophysics Data System (ADS)
Gong, Chunye; Liu, Jie; Chi, Lihua; Huang, Haowei; Fang, Jingyue; Gong, Zhenghu
2011-07-01
Graphics Processing Unit (GPU), originally developed for real-time, high-definition 3D graphics in computer games, now provides great faculty in solving scientific applications. The basis of particle transport simulation is the time-dependent, multi-group, inhomogeneous Boltzmann transport equation. The numerical solution to the Boltzmann equation involves the discrete ordinates ( Sn) method and the procedure of source iteration. In this paper, we present a GPU accelerated simulation of one energy group time-independent deterministic discrete ordinates particle transport in 3D Cartesian geometry (Sweep3D). The performance of the GPU simulations are reported with the simulations of vacuum boundary condition. The discussion of the relative advantages and disadvantages of the GPU implementation, the simulation on multi GPUs, the programming effort and code portability are also reported. The results show that the overall performance speedup of one NVIDIA Tesla M2050 GPU ranges from 2.56 compared with one Intel Xeon X5670 chip to 8.14 compared with one Intel Core Q6600 chip for no flux fixup. The simulation with flux fixup on one M2050 is 1.23 times faster than on one X5670.
GPU accelerated simulations of 3D deterministic particle transport using discrete ordinates method
Gong Chunye; Liu Jie; Chi Lihua; Huang Haowei; Fang Jingyue; Gong Zhenghu
2011-07-01
Graphics Processing Unit (GPU), originally developed for real-time, high-definition 3D graphics in computer games, now provides great faculty in solving scientific applications. The basis of particle transport simulation is the time-dependent, multi-group, inhomogeneous Boltzmann transport equation. The numerical solution to the Boltzmann equation involves the discrete ordinates (S{sub n}) method and the procedure of source iteration. In this paper, we present a GPU accelerated simulation of one energy group time-independent deterministic discrete ordinates particle transport in 3D Cartesian geometry (Sweep3D). The performance of the GPU simulations are reported with the simulations of vacuum boundary condition. The discussion of the relative advantages and disadvantages of the GPU implementation, the simulation on multi GPUs, the programming effort and code portability are also reported. The results show that the overall performance speedup of one NVIDIA Tesla M2050 GPU ranges from 2.56 compared with one Intel Xeon X5670 chip to 8.14 compared with one Intel Core Q6600 chip for no flux fixup. The simulation with flux fixup on one M2050 is 1.23 times faster than on one X5670.
Impact of 3D root uptake on solute transport: a numerical study
NASA Astrophysics Data System (ADS)
Schröder, N.; Javaux, M.; Vanderborght, J.; Steffen, B.; Vereecken, H.
2011-12-01
Plant transpiration is an important component of the hydrological cycle. Through root water uptake, plants do not only affect the 3D soil water flow velocity distribution, but also solute movement in soil. This numerical study aims at investigating how solute fate is impacted by root uptake using the 3D biophysical model R-SWMS (Javaux et al., 2008). This model solves the Richards equation in 3D in the soil and the flow equation within the plant root xylem vessels. Furthermore, for solute transport simulations, the 3D particle tracker PARTRACE (Bechtold et al., 2011) was used. . We generated 3D virtual steady-state breakthrough curves (BTC) experiments in soils with transpiring plants. The averaged BTCs were then fitted with a 1D numerical flow model under steady-state conditions to obtain apparent CDE parameters. Two types of root architecture, a fibrous and a taprooted structure, were compared in virtual 3D experiments. The solute uptake type or the transpiration rate were also modified and we analyzed how these parameters affected apparent disperisivity and velocity profiles. Our simulation results show, that both, apparent velocity and dispersivity length are affected by water and solute root uptake. In addition, under high exclusion processes (slight or no active uptake), solute accumulates around roots and generates a long tailing to the breakthrough curves, which cannot be reproduced by 1D models that simulate root water uptake with solute exclusion. This observation may have an important impact on how to model pollutant mass transfer to groundwater at larger scales. Javaux, M., T. Schröder, J. Vanderborght, and H. Vereecken. 2008. Use of a three-dimensional detailed modeling approach for predicting root water uptake. Vadose Zone J. 7:1079-1088.doi: 10.2136/vzj2007.0115. Bechtold, M., S. Haber-Pohlmeier, J. Vanderborght, A. Pohlmeier, P.A. Ferre, and H. Vereecken. 2011. Near-surface solute redistribution during evaporation. Submitted to Geophys. Res. Lett
Click chemistry, 3D-printing, and omics: the future of drug development.
Kurzrock, Razelle; Stewart, David J
2016-01-19
Genomics is a disruptive technology, having revealed that cancers are tremendously complex and differ from patient to patient. Therefore, conventional treatment approaches fit poorly with genomic reality. Furthermore, it is likely that this type of complexity will also be observed in other illnesses. Precision medicine has been posited as a way to better target disease-related aberrations, but developing drugs and tailoring therapy to each patient's complicated problem is a major challenge. One solution would be to match patients to existing compounds based on in silico modeling. However, optimization of complex therapy will eventually require designing compounds for patients using computer modeling and just-in-time production, perhaps achievable in the future by three-dimensional (3D) printing. Indeed, 3D printing is potentially transformative by virtue of its ability to rapidly generate almost limitless numbers of objects that previously required manufacturing facilities. Companies are already endeavoring to develop affordable 3D printers for home use. An attractive, but as yet scantily explored, application is to place chemical design and production under digital control. This could be accomplished by utilizing a 3D printer to initiate chemical reactions, and print the reagents and/or the final compounds directly. Of interest, the Food and Drug Administration (FDA) has recently approved a 3D printed drug-levetiracetam-indicated for seizures. Further, it is now increasingly clear that biologic materials-tissues, and eventually organs-can also be "printed." In the near future, it is plausible that high-throughput computing may be deployed to design customized drugs, which will reshape medicine. PMID:26734837
Click chemistry, 3D-printing, and omics: the future of drug development
Kurzrock, Razelle; Stewart, David J.
2016-01-01
Genomics is a disruptive technology, having revealed that cancers are tremendously complex and differ from patient to patient. Therefore, conventional treatment approaches fit poorly with genomic reality. Furthermore, it is likely that this type of complexity will also be observed in other illnesses. Precision medicine has been posited as a way to better target disease-related aberrations, but developing drugs and tailoring therapy to each patient's complicated problem is a major challenge. One solution would be to match patients to existing compounds based on in silico modeling. However, optimization of complex therapy will eventually require designing compounds for patients using computer modeling and just-in-time production, perhaps achievable in the future by three-dimensional (3D) printing. Indeed, 3D printing is potentially transformative by virtue of its ability to rapidly generate almost limitless numbers of objects that previously required manufacturing facilities. Companies are already endeavoring to develop affordable 3D printers for home use. An attractive, but as yet scantily explored, application is to place chemical design and production under digital control. This could be accomplished by utilizing a 3D printer to initiate chemical reactions, and print the reagents and/or the final compounds directly. Of interest, the Food and Drug Administration (FDA) has recently approved a 3D printed drug—levetiracetam—indicated for seizures. Further, it is now increasingly clear that biologic materials—tissues, and eventually organs—can also be “printed.” In the near future, it is plausible that high-throughput computing may be deployed to design customized drugs, which will reshape medicine. PMID:26734837
3D nonrigid registration via optimal mass transport on the GPU.
Ur Rehman, Tauseef; Haber, Eldad; Pryor, Gallagher; Melonakos, John; Tannenbaum, Allen
2009-12-01
In this paper, we present a new computationally efficient numerical scheme for the minimizing flow approach for optimal mass transport (OMT) with applications to non-rigid 3D image registration. The approach utilizes all of the gray-scale data in both images, and the optimal mapping from image A to image B is the inverse of the optimal mapping from B to A. Further, no landmarks need to be specified, and the minimizer of the distance functional involved is unique. Our implementation also employs multigrid, and parallel methodologies on a consumer graphics processing unit (GPU) for fast computation. Although computing the optimal map has been shown to be computationally expensive in the past, we show that our approach is orders of magnitude faster then previous work and is capable of finding transport maps with optimality measures (mean curl) previously unattainable by other works (which directly influences the accuracy of registration). We give results where the algorithm was used to compute non-rigid registrations of 3D synthetic data as well as intra-patient pre-operative and post-operative 3D brain MRI datasets. PMID:19135403
3D nonrigid registration via optimal mass transport on the GPU
Rehman, Tauseef ur; Haber, Eldad; Pryor, Gallagher; Melonakos, John; Tannenbaum, Allen
2009-01-01
In this paper, we present a new computationally efficient numerical scheme for the minimizing flow approach for optimal mass transport (OMT) with applications to non-rigid 3D image registration. The approach utilizes all of the gray-scale data in both images, and the optimal mapping from image A to image B is the inverse of the optimal mapping from B to A. Further, no landmarks need to be specified, and the minimizer of the distance functional involved is unique. Our implementation also employs multigrid, and parallel methodologies on a consumer graphics processing unit (GPU) for fast computation. Although computing the optimal map has been shown to be computationally expensive in the past, we show that our approach is orders of magnitude faster then previous work and is capable of finding transport maps with optimality measures (mean curl) previously unattainable by other works (which directly influences the accuracy of registration). We give results where the algorithm was used to compute non-rigid registrations of 3D synthetic data as well as intra-patient pre-operative and post-operative 3D brain MRI datasets. PMID:19135403
Quasi 3D modeling of water flow and solute transport in vadose zone and groundwater
NASA Astrophysics Data System (ADS)
Yakirevich, A.; Kuznetsov, M.; Weisbrod, N.; Pachepsky, Y. A.
2013-12-01
The complexity of subsurface flow systems calls for a variety of concepts leading to the multiplicity of simplified flow models. One commonly used simplification is based on the assumption that lateral flow and transport in unsaturated zone is insignificant unless the capillary fringe is involved. In such cases the flow and transport in the unsaturated zone above groundwater level can be simulated as a 1D phenomenon, whereas through groundwater they are viewed as 2D or 3D phenomena. A new approach for a numerical scheme for 3D variably saturated flow and transport is presented. A Quasi-3D approach allows representing flow in the 'vadose zone - aquifer' system by a series of 1D Richards' equations solved in variably-saturated zone and by 3D-saturated flow equation in groundwater (modified MODFLOW code). The 1D and 3D equations are coupled at the phreatic surface in a way that aquifer replenishment is calculated using the Richards' equation, and solving for the moving water table does not require definition of the specific yield parameter. The 3D advection-dispersion equation is solved in the entire domain by the MT3D code. Using implicit finite differences approximation to couple processes in the vadose zone and groundwater provides mass conservation and increase of computational efficiency. The above model was applied to simulate the impact of irrigation on groundwater salinity in the Alto Piura aquifer (Northern Peru). Studies on changing groundwater quality in arid and semi-arid lands show that irrigation return flow is one of the major factors contributing to aquifer salinization. Existing mathematical models do not account explicitly for the solute recycling during irrigation on a daily scale. Recycling occurs throughout the unsaturated and saturated zones, as function of the solute mass extracted from pumping wells. Salt concentration in irrigation water is calculated at each time step as a function of concentration of both surface water and groundwater
Optically directed molecular transport and 3D isoelectric positioning of amphoteric biomolecules
Hafeman, Dean G.; Harkins, James B.; Witkowski, Charles E.; Lewis, Nathan S.; Warmack, Robert J.; Brown, Gilbert M.; Thundat, Thomas
2006-01-01
We demonstrate the formation of charged molecular packets and their transport within optically created electrical force-field traps in a pH-buffered electrolyte. We call this process photoelectrophoretic localization and transport (PELT). The electrolyte is in contact with a photoconductive semiconductor electrode and a counterelectrode that are connected through an external circuit. A light beam directed to coordinates on the photoconductive electrode surface produces a photocurrent within the circuit and electrolyte. Within the electrolyte, the photocurrent creates localized force-field traps centered at the illuminated coordinates. Charged molecules, including polypeptides and proteins, electrophoretically accumulate into the traps and subsequently can be transported in the electrolyte by moving the traps over the photoconductive electrode in response to movement of the light beam. The molecules in a single trap can be divided into aliquots, and the aliquots can be directed along multiple routes simultaneously by using multiple light beams. This photoelectrophoretic transport of charged molecules by PELT resembles the electrostatic transport of electrons within force-field wells of solid-state charge-coupled devices. The molecules, however, travel in a liquid electrolyte rather than a solid. Furthermore, we have used PELT to position amphoteric biomolecules in three dimensions. A 3D pH gradient was created in an electrolyte medium by controlling the illumination position on a photoconductive anode where protons were generated electrolytically. Photoelectrophoretic transport of amphoteric molecules through the pH gradient resulted in accumulation of the molecules at their apparent 3D isoelectric coordinates in the medium. PMID:16618926
Transport of iron oxide nanoparticles in saturated porous media: a large-scale 3D study
NASA Astrophysics Data System (ADS)
Velimirovic, Milica; Schmid, Doris; Micić, Vesna; Miyajima, Kumiko; Klaas, Norbert; Braun, Jürgen; Bosch, Julian; Meckenstock, Rainer; von der Kammer, Frank; Hofmann, Thilo
2016-04-01
Iron oxide nanoparticles (FeOxNp) have a high potential as electron acceptor for in situ microbial oxidation of a wide range of recalcitrant groundwater contaminants (Bosch et al., 2010). Tosco et al. (2012) reported on high colloidal stability of FeOxNp dispersed in water, their low deposition behavior, and consequently improved transport in column experiments compared to extensively studied zerovalent iron nanoparticles. However, determination of FeOxNp transport behavior at the field-relevant conditions has not been done before. The present work is aimed to evaluate different complementary methods for detection, quantification and transport characterization of FeOxNp in a large-scale three-dimensional (3D) model aquifer. Prior to that, batch-scale experiments were performed in order to elucidate the potential of the selected methods for direct and indirect characterization and detection of FeOxNp. Direct methods included measurements of particle size distribution, particle concentration, Fetot content and turbidity of the FeOxNp suspension. Indirect methods included measurements of particle zeta potential, as well as TOC content and pH of the FeOxNp suspension. The results of the batch experiments indicated that the most suitable approach for detecting and quantifying FeOxNp was measuring Fetot content and suspension turbidity, as well as particle size determined using dynamic light scattering principle. These complementary methods were further applied in a large-scale 3D study containing medium and coarse sand in order to 1) assess the transport of FeOxNp in saturated porous medium during injection (VFeOx = 6 m3, cparticle = 20 g/L, Qinj = 0.7 m3/h), and 2) illustrate their spatial distribution after injection. The outcomes of the large-scale 3D study confirmed that FeOxNp transport can be successfully investigated applying complementary methods. Monitoring data including Fetot content, turbidity and particle size showed the transport of particles towards the
ERIC Educational Resources Information Center
Kaliakin, Danil S.; Zaari, Ryan R.; Varganov, Sergey A.
2015-01-01
Teaching fundamental physical chemistry concepts such as the potential energy surface, transition state, and reaction path is a challenging task. The traditionally used oversimplified 2D representation of potential and free energy surfaces makes this task even more difficult and often confuses students. We show how this 2D representation can be…
3D Neutron Transport PWR Full-core Calculation with RMC code
NASA Astrophysics Data System (ADS)
Qiu, Yishu; She, Ding; Fan, Xiao; Wang, Kan; Li, Zeguang; Liang, Jingang; Leroyer, Hadrien
2014-06-01
Nowadays, there are more and more interests in the use of Monte Carlo codes to calculate the detailed power density distributions in full-core reactors. With the Inspur TS1000 HPC Server of Tsinghua University, several calculations have been done based on the EDF 3D Neutron Transport PWR Full-core benchmark through large-scale parallelism. To investigate and compare the results of the deterministic method and Monte Carlo method, EDF R&D and Department of Engineering Physics of Tsinghua University are having a collaboration to make code to code verification. So in this paper, two codes are used. One is the code COCAGNE developed by the EDF R&D, a deterministic core code, and the other is the Monte Carlo code RMC developed by Department of Engineering Physics in Tsinghua University. First, the full-core model is described and a 26-group calculation was performed by these two codes using the same 26-group cross-section library provided by EDF R&D. Then the parallel and tally performance of RMC is discussed. RMC employs a novel algorithm which can cut down most of the communications. It can be seen clearly that the speedup ratio almost linearly increases with the nodes. Furthermore the cell-mapping method applied by RMC consumes little time to tally even millions of cells. The results of the codes COCAGNE and RMC are compared in three ways. The results of these two codes agree well with each other. It can be concluded that both COCAGNE and RMC are able to provide 3D-transport solutions associated with detailed power density distributions calculation in PWR full-core reactors. Finally, to investigate how many histories are needed to obtain a given standard deviation for a full 3D solution, the non-symmetrized condensed 2-group fluxes of RMC are discussed.
Momentum Transport: 2D and 3D Cloud Resolving Model Simulations
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo
2001-01-01
The major objective of this study is to investigate the momentum budgets associated with several convective systems that developed during the TOGA COARE IOP (west Pacific warm pool region) and GATE (east Atlantic region). The tool for this study is the improved Goddard Cumulas Ensemble (GCE) model which includes a 3-class ice-phase microphysical scheme, explicit cloud radiative interactive processes and air-sea interactive surface processes. The model domain contains 256 x 256 grid points (with 2 km resolution) in the horizontal and 38 grid points (to a depth of 22 km) in the vertical. The 2D domain has 1024 grid points. The simulations were performed over a 7-day time period (December 19-26, 1992, for TOGA COARE and September 1-7, 1994 for GATE). Cyclic literal boundary conditions are required for this type of long-term integration. Two well organized squall systems (TOGA, COARE February 22, 1993, and GATE September 12, 1994) were also simulated using the 3D GCE model. Only 9 h simulations were required to cover the life time of the squall systems. the lateral boundary conditions were open for these two squall systems simulations. the following will be examined: (1) the momentum budgets in the convective and stratiform regions, (2) the relationship between momentum transport and cloud organization (i.e., well organized squall lines versus less organized convective), (3) the differences and similarities in momentum transport between 2D and 3D simulated convective systems, and (4) the differences and similarities in momentum budgets between cloud systems simulated with open and cyclic lateral boundary conditions. Preliminary results indicate that there are only small differences between 2D and 3D simulated momentum budgets. Major differences occur, however, between momentum budgets associated with squall systems simulated using different lateral boundary conditions.
Domain Decomposition PN Solutions to the 3D Transport Benchmark over a Range in Parameter Space
NASA Astrophysics Data System (ADS)
Van Criekingen, S.
2014-06-01
The objectives of this contribution are twofold. First, the Domain Decomposition (DD) method used in the parafish parallel transport solver is re-interpreted as a Generalized Schwarz Splitting as defined by Tang [SIAM J Sci Stat Comput, vol.13 (2), pp. 573-595, 1992]. Second, parafish provides spherical harmonic (i.e., PN) solutions to the NEA benchmark suite for 3D transport methods and codes over a range in parameter space. To the best of the author's knowledge, these are the first spherical harmonic solutions provided for this demanding benchmark suite. They have been obtained using 512 CPU cores of the JuRoPa machine installed at the Jülich Computing Center (Germany).
M3D-K simulations of sawteeth and energetic particle transport in tokamak plasmas
NASA Astrophysics Data System (ADS)
Shen, Wei; Fu, G. Y.; Sheng, Zheng-Mao; Breslau, J. A.; Wang, Feng
2014-09-01
Nonlinear simulations of sawteeth and related energetic particle transport are carried out using the kinetic/magnetohydrodynamic (MHD) hybrid code M3D-K. MHD simulations show repeated sawtooth cycles for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in the plasma core, depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with existing theories. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases with increasing particle energy.
M3D-K Simulations of Sawteeth and Energetic Particle Transport in Tokamak Plasmas
NASA Astrophysics Data System (ADS)
Shen, Wei; Fu, Guoyong; Sheng, Zhengmao; Breslau, Joshua; Wang, Feng
2013-10-01
Nonlinear simulations of Sawteeth and energetic particle transport are carried out using the kinetic/MHD hybrid code M3D-K. MHD simulations show repeated sawtooth cycles due to a resistive (1,1) internal kink mode for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in plasma core depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with previous theory. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases as particle energy becomes large.
M3D-K simulations of sawteeth and energetic particle transport in tokamak plasmas
Shen, Wei; Sheng, Zheng-Mao; Fu, G. Y.; Breslau, J. A.; Wang, Feng
2014-09-15
Nonlinear simulations of sawteeth and related energetic particle transport are carried out using the kinetic/magnetohydrodynamic (MHD) hybrid code M3D-K. MHD simulations show repeated sawtooth cycles for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in the plasma core, depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with existing theories. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases with increasing particle energy.
Ash3d: A finite-volume, conservative numerical model for ash transport and tephra deposition
Schwaiger, Hans F.; Denlinger, Roger P.; Mastin, Larry G.
2012-01-01
We develop a transient, 3-D Eulerian model (Ash3d) to predict airborne volcanic ash concentration and tephra deposition during volcanic eruptions. This model simulates downwind advection, turbulent diffusion, and settling of ash injected into the atmosphere by a volcanic eruption column. Ash advection is calculated using time-varying pre-existing wind data and a robust, high-order, finite-volume method. Our routine is mass-conservative and uses the coordinate system of the wind data, either a Cartesian system local to the volcano or a global spherical system for the Earth. Volcanic ash is specified with an arbitrary number of grain sizes, which affects the fall velocity, distribution and duration of transport. Above the source volcano, the vertical mass distribution with elevation is calculated using a Suzuki distribution for a given plume height, eruptive volume, and eruption duration. Multiple eruptions separated in time may be included in a single simulation. We test the model using analytical solutions for transport. Comparisons of the predicted and observed ash distributions for the 18 August 1992 eruption of Mt. Spurr in Alaska demonstrate to the efficacy and efficiency of the routine.
3D numerical simulation of the transport of chemical signature compounds from buried landmines
NASA Astrophysics Data System (ADS)
Irrazabal, Maik; Borrero, Ernesto; Briano, Julio G.; Castro, Miguel; Hernandez, Samuel P.
2005-06-01
The transport of the chemical signature compounds from buried landmines in a three-dimensional (3D) array has been numerically modeled using the finite-volume technique. Compounds such as trinitrotoluene, dinitrotoluene, and their degradation products, are semi volatile and somewhat soluble in water. Furthermore, they can strongly adsorb to the soil and undergo chemical and biological degradation. Consequently, the spatial and temporal concentration distributions of such chemicals depend on the mobility of the water and gaseous phases, their molecular and mechanical diffusion, adsorption characteristics, soil water content, compaction, and environmental factors. A 3D framework is required since two-dimensional (2D) symmetry may easily fade due to terrain topography: non-flat surfaces, soil heterogeneity, or underground fractures. The spatial and temporal distribution of the chemical-signature-compounds, in an inclined grid has been obtained. The fact that the chemicals may migrate horizontally, giving higher surface concentrations at positions not directly on top of the objects, emphasizes the need for understanding the transport mechanism when a chemical detector is used. Deformation in the concentration contours after rainfall is observed in the inclined surface and is attributed to both: the advective flux, and to the water flux at the surface caused by the slope. The analysis of the displacements in the position of the maximum concentrations at the surface, respect to the actual location of the mine, in an inclined system, is presented.
NASA Astrophysics Data System (ADS)
Nair, Nikila; Majumder, Sutripto; Sankapal, Babasaheb R.
2016-08-01
Two step soft chemical route has been utilized for the fabrication of CdS nanowire electrode in 3D architecture at room temperature (300 K). The electrochemical pseudocapacitive behavior of thin film consisting of CdS nanowires has been evaluated by using cyclic voltammetry, charge-discharge and electrochemical impedance spectroscopy in an aqueous media. The electrochemical test revealed that CdS nanowire attained a specific capacitance of 181 F/g at a scan rate of 5 mV/s. An energy density of 1.72 Wh/kg and power density of 27.14 W/kg has been achieved at 89 mA/g current density in 1 M Na2SO3 solution.
Analysis of transport connectivity in karstic aquifers spanned by 3D conduit networks
NASA Astrophysics Data System (ADS)
Ronayne, M. J.
2013-12-01
Karst aquifers are characterized by interconnected conduits that behave as structural pathways for groundwater and solutes. This modeling study assesses the influence of conduit network geometry on solute transport behavior within karst systems. Synthetic karst aquifers containing 3D conduit networks were considered. Networks of varying complexity were generated using a directed percolation model. Flow and transport simulations were conducted for each synthetic aquifer by modeling the conduits as discretized high-permeability features within a uniform matrix material. Transport connectivity and dispersive properties were evaluated using statistical moments of the solute arrival time distribution at the downgradient conduit outlet (karst spring). In addition, a new connectivity metric that quantifies solute residence time within conduits was considered. Results show that a more complex network leads to enhanced mixing between the conduit and matrix domains, which has the effect of reducing transport connectivity. This modeling study illustrates how typically available transport data (e.g., solute breakthrough curves at the conduit outlet) may reveal information about the internal network structure, thus providing guidance for future inverse modeling.
MODIS volcanic ash retrievals vs FALL3D transport model: a quantitative comparison
NASA Astrophysics Data System (ADS)
Corradini, S.; Merucci, L.; Folch, A.
2010-12-01
Satellite retrievals and transport models represents the key tools to monitor the volcanic clouds evolution. Because of the harming effects of fine ash particles on aircrafts, the real-time tracking and forecasting of volcanic clouds is key for aviation safety. Together with the security reasons also the economical consequences of a disruption of airports must be taken into account. The airport closures due to the recent Icelandic Eyjafjöll eruption caused millions of passengers to be stranded not only in Europe, but across the world. IATA (the International Air Transport Association) estimates that the worldwide airline industry has lost a total of about 2.5 billion of Euro during the disruption. Both security and economical issues require reliable and robust ash cloud retrievals and trajectory forecasting. The intercomparison between remote sensing and modeling is required to assure precise and reliable volcanic ash products. In this work we perform a quantitative comparison between Moderate Resolution Imaging Spectroradiometer (MODIS) retrievals of volcanic ash cloud mass and Aerosol Optical Depth (AOD) with the FALL3D ash dispersal model. MODIS, aboard the NASA-Terra and NASA-Aqua polar satellites, is a multispectral instrument with 36 spectral bands operating in the VIS-TIR spectral range and spatial resolution varying between 250 and 1000 m at nadir. The MODIS channels centered around 11 and 12 micron have been used for the ash retrievals through the Brightness Temperature Difference algorithm and MODTRAN simulations. FALL3D is a 3-D time-dependent Eulerian model for the transport and deposition of volcanic particles that outputs, among other variables, cloud column mass and AOD. Three MODIS images collected the October 28, 29 and 30 on Mt. Etna volcano during the 2002 eruption have been considered as test cases. The results show a general good agreement between the retrieved and the modeled volcanic clouds in the first 300 km from the vents. Even if the
An unstaggered constrained transport method for the 3D ideal magnetohydrodynamic equations
NASA Astrophysics Data System (ADS)
Helzel, Christiane; Rossmanith, James A.; Taetz, Bertram
2011-05-01
Numerical methods for solving the ideal magnetohydrodynamic (MHD) equations in more than one space dimension must either confront the challenge of controlling errors in the discrete divergence of the magnetic field, or else be faced with nonlinear numerical instabilities. One approach for controlling the discrete divergence is through a so-called constrained transport method, which is based on first predicting a magnetic field through a standard finite volume solver, and then correcting this field through the appropriate use of a magnetic vector potential. In this work we develop a constrained transport method for the 3D ideal MHD equations that is based on a high-resolution wave propagation scheme. Our proposed scheme is the 3D extension of the 2D scheme developed by Rossmanith [J.A. Rossmanith, An unstaggered, high-resolution constrained transport method for magnetohydrodynamic flows, SIAM J. Sci. Comput. 28 (2006) 1766], and is based on the high-resolution wave propagation method of Langseth and LeVeque [J.O. Langseth, R.J. LeVeque, A wave propagation method for threedimensional hyperbolic conservation laws, J. Comput. Phys. 165 (2000) 126]. In particular, in our extension we take great care to maintain the three most important properties of the 2D scheme: (1) all quantities, including all components of the magnetic field and magnetic potential, are treated as cell-centered; (2) we develop a high-resolution wave propagation scheme for evolving the magnetic potential; and (3) we develop a wave limiting approach that is applied during the vector potential evolution, which controls unphysical oscillations in the magnetic field. One of the key numerical difficulties that is novel to 3D is that the transport equation that must be solved for the magnetic vector potential is only weakly hyperbolic. In presenting our numerical algorithm we describe how to numerically handle this problem of weak hyperbolicity, as well as how to choose an appropriate gauge condition. The
BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations
Ghaffarizadeh, Ahmadreza; Friedman, Samuel H.; Macklin, Paul
2016-01-01
Motivation: Computational models of multicellular systems require solving systems of PDEs for release, uptake, decay and diffusion of multiple substrates in 3D, particularly when incorporating the impact of drugs, growth substrates and signaling factors on cell receptors and subcellular systems biology. Results: We introduce BioFVM, a diffusive transport solver tailored to biological problems. BioFVM can simulate release and uptake of many substrates by cell and bulk sources, diffusion and decay in large 3D domains. It has been parallelized with OpenMP, allowing efficient simulations on desktop workstations or single supercomputer nodes. The code is stable even for large time steps, with linear computational cost scalings. Solutions are first-order accurate in time and second-order accurate in space. The code can be run by itself or as part of a larger simulator. Availability and implementation: BioFVM is written in C ++ with parallelization in OpenMP. It is maintained and available for download at http://BioFVM.MathCancer.org and http://BioFVM.sf.net under the Apache License (v2.0). Contact: paul.macklin@usc.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26656933
NASA Astrophysics Data System (ADS)
Childs, Scott L.; Hagen, Karl S.
1996-10-01
The visualization of molecular and solid state chemical structures in three dimensions is a particularly difficult problem for students to overcome when the primary means of communication is the two-dimensional world of textbooks, blackboards, and overhead projector screens. Recent editions of popular textbooks in organic, inorganic, and biochemistry have included stereoviews of molecules to aid the student, and stereoviews of crystal structures have been used in inorganic chemistry publications for many years. These are powerful aids for visualizing complex molecules, but with the exception of the biochemistry text mentioned above, they are limited to single, static images generally in black and white. Molecular model kits are routinely used very effectively in organic chemistry but their utility in inorganic chemistry is limited to all but the most simple molecules encountered. Now that personal computers are generally accessible and multimedia tools are starting to make an appearance in chemistry lecture halls (1), we can make our inorganic and bioinorganic chemistry and crystallography lectures come alive with the aid of the computer-based resources, which are the essence of this project. As part of this project we are accumulating a database of representative crystal structures of main group molecules, coordination complexes, organometallic compounds, small metalloproteins, bioinorganic model complexes, clusters, and solid state materials in Chem3D Plus format to be viewed with Chem3D Viewer, which is free software from Cambridge Scientific Computing. We are also generating a library of high-quality graphic images of these same molecules and structures using Cerius2 package from Molecular Simulations. These include polyhedral representations of clusters and solid state structures (see Fig. 1). Figure 1. Representation of the user interface: the title page and an example of polyhedral and ball-and-stick representation of an octanuclear iron-oxo cluster. The
Time-dependent 3-D dterministic transport on parallel architectures using Dantsys/MPI
Baker, R.S.; Alcouffe, R.E.
1996-12-31
In addition to the ability to solve the static transport equation, we have also incorporated time dependence into our parallel 3-D S{sub {ital N}} code DANTSYS/MPI. Using a semi-implicit scheme, DANTSYS/MPI is capable of performing time-dependent calculations for both fissioning and pure source driven problems. We have applied this to various types of problems such as nuclear well logging and prompt fission experiments. This paper describes the form of the time- dependent equations implemented, their solution strategies in DANTSYS/MPI including iteration acceleration, and the strategies used for time-step control. Results are presented for a model nuclear well logging calculation.
Coupling 2-D cylindrical and 3-D x-y-z transport computations
Abu-Shumays, I.K.; Yehnert, C.E.; Pitcairn, T.N.
1998-06-30
This paper describes a new two-dimensional (2-D) cylindrical geometry to three-dimensional (3-D) rectangular x-y-z splice option for multi-dimensional discrete ordinates solutions to the neutron (photon) transport equation. Of particular interest are the simple transformations developed and applied in order to carry out the required spatial and angular interpolations. The spatial interpolations are linear and equivalent to those applied elsewhere. The angular interpolations are based on a high order spherical harmonics representation of the angular flux. Advantages of the current angular interpolations over previous work are discussed. An application to an intricate streaming problem is provided to demonstrate the advantages of the new method for efficient and accurate prediction of particle behavior in complex geometries.
3D Structure of Saharan Dust Transport Towards Europe as Seen by CALIPSO
NASA Astrophysics Data System (ADS)
Marinou, Eleni; Amiridis, Vassilis; Tsekeri, Alexandra; Solomos, Stavros; Kokkalis, Panos; Proestakis, Emmanouil; Kottas, Michael; Binietoglou, Ioannis; Zanis, Prodromos; Kazadzis, Stelios; Wandinger, Ulla; Ansmann, Albert
2016-06-01
We present a 3D multi-year monthly mean climatology of Saharan dust advection over Europe using an area-optimized pure dust CALIPSO product. The product has been developed by applying EARLINET-measured dust lidar ratios and depolarization-based dust discrimination methods and it is shown to have a very good agreement in terms of AOD when compared to AERONET over Europe/North Africa and MODIS over Mediterranean. The processing of such purely observational data reveals the certain seasonal patterns of dust transportation towards Europe and the Atlantic Ocean. The physical and optical properties of the dust layer are identified for several areas near the Saharan sources, over the Mediterranean and over continental Europe.
Distributed network of integrated 3D sensors for transportation security applications
NASA Astrophysics Data System (ADS)
Hejmadi, Vic; Garcia, Fred
2009-05-01
The US Port Security Agency has strongly emphasized the needs for tighter control at transportation hubs. Distributed arrays of miniature CMOS cameras are providing some solutions today. However, due to the high bandwidth required and the low valued content of such cameras (simple video feed), large computing power and analysis algorithms as well as control software are needed, which makes such an architecture cumbersome, heavy, slow and expensive. We present a novel technique by integrating cheap and mass replicable stealth 3D sensing micro-devices in a distributed network. These micro-sensors are based on conventional structures illumination via successive fringe patterns on the object to be sensed. The communication bandwidth between each sensor remains very small, but is of very high valued content. Key technologies to integrate such a sensor are digital optics and structured laser illumination.
Multi-scale self-organisation of edge plasma turbulent transport in 3D global simulations
NASA Astrophysics Data System (ADS)
Tamain, P.; Ghendrih, Ph; Bufferand, H.; Ciraolo, G.; Colin, C.; Fedorczak, N.; Nace, N.; Schwander, F.; Serre, E.
2015-05-01
The 3D global edge turbulence code TOKAM3X is used to study the properties of edge particle turbulent transport in circular limited plasmas, including both closed and open flux surfaces. Turbulence is driven by an incoming particle flux from the core plasma and no scale separation between the equilibrium and the fluctuations is assumed. Simulations show the existence of a complex self-organization of turbulence transport coupling scales ranging from a few Larmor radii up to the machine scale. Particle transport is largely dominated by small scale turbulence with fluctuations forming quasi field-aligned filaments. Radial particle transport is intermittent and associated with the propagation of coherent structures on long distances via avalanches. Long range correlations are also found in the poloidal and toroidal direction. The statistical properties of fluctuations vary with the radial and poloidal directions, with larger fluctuation levels and intermittency found in the outboard scrape-off layer (SOL). Radial turbulent transport is strongly ballooned, with 90% of the flux at the separatrix flowing through the low-field side. One of the main consequences is the existence of quasi-sonic asymmetric parallel flows driving a net rotation of the plasma. Simulations also show the spontaneous onset of an intermittent E × B rotation characterized by a larger shear at the separatrix. Strong correlation is found between the turbulent particle flux and the E × B flow shear in a phenomenology reminiscent of H-mode physics. The poloidal position of the limiter is a key player in the observed dynamics.
Calculations of Arctic ozone chemistry using objectively analyzed data in a 3-D CTM
NASA Technical Reports Server (NTRS)
Kaminski, J. W.; Mcconnell, J. C.; Sandilands, J. W.
1994-01-01
A three-dimensional chemical transport model (CTM) (Kaminski, 1992) has been used to study the evolution of the Arctic ozone during the winter of 1992. The continuity equation has been solved using a spectral method with Rhomboidal 15 (R15) truncation and leap-frog time stepping. Six-hourly meteorological fields from the Canadian Meteorological Center global objective analysis routines run at T79 were degraded to the model resolution. In addition, they were interpolated to the model time grid and were used to drive the model from the surface to 10 mb. In the model, processing of Cl(x) occurred over Arctic latitudes but some of the initial products were still present by mid-January. Also, the large amounts of ClO formed in the model in early January were converted to ClNO3. The results suggest that the model resolution may be insufficient to resolve the details of the Arctic transport during this time period. In particular, the wind field does not move the ClO(x) 'cloud' to the south over Europe as seen in the MLS measurements.
NASA Astrophysics Data System (ADS)
Hostache, Renaud; Krein, Andreas; Barrière, Julien
2014-05-01
Coupling the 3D hydro-morphodynamic model Telemac-3D-sisyphe and seismic measurements to estimate bedload transport rates in a small gravel-bed river. Renaud Hostache, Andreas Krein, Julien Barrière During flood events, amounts of river bed material are transported via bedload. This causes problems, like the silting of reservoirs or the disturbance of biological habitats. Some current bedload measuring techniques have limited possibilities for studies in high temporal resolutions. Optical systems are usually not applicable because of high turbidity due to concentrated suspended sediment transported. Sediment traps or bedload samplers yield only summative information on bedload transport with low temporal resolution. An alternative bedload measuring technique is the use of seismological systems installed next to the rivers. The potential advantages are observations in real time and under undisturbed conditions. The study area is a 120 m long reach of River Colpach (21.5 km2), a small gravel bed river in Northern Luxembourg. A combined approach of hydro-climatological observations, hydraulic measurements, sediment sampling, and seismological measurements is used in order to investigate bedload transport phenomena. Information derived from seismic measurements and results from a 3-dimensional hydro-morphodynamic model are exemplarily discussed for a November 2013 flood event. The 3-dimensional hydro-morphodynamic model is based on the Telemac hydroinformatic system. This allows for dynamically coupling a 3D hydrodynamic model (Telemac-3D) and a morphodynamic model (Sisyphe). The coupling is dynamic as these models exchange their information during simulations. This is a main advantage as it allows for taking into account the effects of the morphologic changes of the riverbed on the water hydrodynamic and the bedload processes. The coupled model has been calibrated using time series of gauged water depths and time series of bed material collected sequentially (after
NASA Technical Reports Server (NTRS)
Strahan, Susan E.; Douglass, Anne R.; Einaudi, Franco (Technical Monitor)
2001-01-01
The Global Modeling Initiative (GMI) Team developed objective criteria for model evaluation in order to identify the best representation of the stratosphere. This work created a method to quantitatively and objectively discriminate between different models. In the original GMI study, 3 different meteorological data sets were used to run an offline chemistry and transport model (CTM). Observationally-based grading criteria were derived and applied to these simulations and various aspects of stratospheric transport were evaluated; grades were assigned. Here we report on the application of the GMI evaluation criteria to CTM simulations integrated with a new assimilated wind data set and a new general circulation model (GCM) wind data set. The Finite Volume Community Climate Model (FV-CCM) is a new GCM developed at Goddard which uses the NCAR CCM physics and the Lin and Rood advection scheme. The FV-Data Assimilation System (FV-DAS) is a new data assimilation system which uses the FV-CCM as its core model. One year CTM simulations of 2.5 degrees longitude by 2 degrees latitude resolution were run for each wind data set. We present the evaluation of temperature and annual transport cycles in the lower and middle stratosphere in the two new CTM simulations. We include an evaluation of high latitude transport which was not part of the original GMI criteria. Grades for the new simulations will be compared with those assigned during the original GMT evaluations and areas of improvement will be identified.
NASA Astrophysics Data System (ADS)
Thomas, Justin W.
2006-12-01
The Numerical Nuclear Reactor (NNR) is a code suite that is being developed to provide high-fidelity multi-physics capability for the analysis of light water nuclear reactors. The focus of the work here is to extend the capability of the NNR by incorporation of the neutronics module, DeCART, for Boiling Water Reactor (BWR) applications. The DeCART code has been coupled to the NNR fluid mechanics and heat transfer module STAR-CD for light water reactor applications. The coupling has been accomplished via an interface program, which is responsible for mapping the STAR-CD and DeCART meshes, managing communication, and monitoring convergence. DeCART obtains the solution of the 3-D Boltzmann transport equation by performing a series of 2-D modular ray tracing-based method of characteristics problems that are coupled within the framework of 3-D coarse-mesh finite difference. The relatively complex geometry and increased axial heterogeneity found in BWRs are beyond the modeling capability of the original version of DeCART. In this work, DeCART is extended in three primary areas. First, the geometric capability is generalized by extending the modular ray tracing scheme and permitting an unstructured mesh in the global finite difference kernel. Second, numerical instabilities, which arose as a result of the severe axial heterogeneity found in BWR cores, have been resolved. Third, an advanced nodal method has been implemented to improve the accuracy of the axial flux distribution. In this semi-analytic nodal method, the analytic solution to the transverse-integrated neutron diffusion equation is obtained, where the nonhomogeneous neutron source was first approximated by a quartic polynomial. The successful completion of these three tasks has allowed the application of the coupled DeCART/STAR-CD code to practical BWR problems.
Simulation of bacteria transport processes in a river with Flow3D
NASA Astrophysics Data System (ADS)
Schwarzwälder, Kordula; Bui, Minh Duc; Rutschmann, Peter
2014-05-01
Water quality aspects are getting more and more important due to the European water Framework directive (WFD). One problem related to this topic is the inflow of untreated wastewater due to combined sewer overflows into a river. The wastewater mixture contains even bacteria like E. coli and Enterococci which are markers for water quality. In our work we investigated the transport of these bacteria in river Isar by using a large-scale flume in the outside area of our lab (Oskar von Miller Institute). Therefor we could collect basic data and knowledge about the processes which occur during bacteria sedimentation and remobilisation. In our flume we could use the real grain with the exact size distribution curve as in the river Isar which we want to simulate and we had the chance to nurture a biofilm which is realistic for the analysed situation. This biofilm plays an important role in the remobilisation processes, because the bacteria are hindered to be washed out back into the bulk phase as fast and in such an amount as this would happen without biofilm. The results of our experiments are now used for a module in the 3D software Flow3D to simulate the effects of a point source inlet of raw wastewater on the water quality. Therefor we have to implement the bacteria not as a problem of concentration with advection and diffusion but as single particles which can be inactivated during the process of settling and need to be hindered from remobilisation by the biofilm. This biofilm has special characteristic, it is slippery and has a special thickness which influences the chance of bacteria being removed. To achieve realistic results we have to include the biofilm with more than a probabilistic-tool to make sure that our module is transferable. The module should be as flexible as possible to be improved step by step with increasing quality of dataset.
A 3D transport model study of chlorine activation during EASOE
Chipperfield, M.P.; Cariolle, D.; Simon, P. )
1994-06-22
The authors present the results of a chemical transport model which was applied to the problem of atmospheric chemistry of trace species in the stratosphere during EASOE. The model uses a comprehensive set of gas phase reactions, as well as modeling reactions occuring on nuclei in polar stratospheric clouds. This model has been used to study the development of chlorine compounds during the winter of 1991-92. Meteorological data is used as a boundary condition for the model. Significant increases in reactive chlorine are shown to occur in the lower stratosphere through mid January, when warming reduced the occurrence of polar stratospheric clouds. Even with the enhanced active chlorine presence, the lack of sunlight inhibited substantial chemical destruction of ozone.
Simulation of light transport in scintillators based on 3D characterization of crystal surfaces
Cherry, Simon R.
2013-01-01
In the development of positron emission tomography (PET) detectors, understanding and optimizing scintillator light collection is critical for achieving high performance, particularly when the design incorporates depth-of-interaction (DOI) encoding or time-of-flight information. Monte-Carlo simulations play an important role in guiding research in detector designs and popular software such as GATE now include models of light transport in scintillators. Although current simulation toolkits are able to provide accurate models of perfectly polished surfaces, they do not successfully predict light output for other surface finishes, for example those often used in DOI-encoding detectors. The lack of accuracy of those models mainly originates from a simplified description of rough surfaces as an ensemble of micro-facets determined by the distribution of their normal, typically a Gaussian distribution. The user can specify the standard deviation of this distribution, but this parameter does not provide a full description of the surface reflectance properties. We propose a different approach based on 3D measurements of the surface using atomic force microscopy (AFM). Polished and rough (unpolished) crystals were scanned to compute the surface reflectance properties. The angular distributions of reflectance and reflected rays were computed and stored in look-up tables (LUTs). The LUTs account for the effect of incidence angle and were integrated in a light transport model. Crystals of different sizes were simulated with and without reflector. The simulated maximum light output and the light output as a function of DOI showed very good agreement with experimental characterization of the crystals, indicating that our approach provides an accurate model of polished and rough surfaces and could be used to predict light collection in scintillators. This model is based on a true 3D representation of the surface, makes no assumption about the surface and provides insight on the
NASA Astrophysics Data System (ADS)
Viscardy, S.; Errera, Q.; Pitts, M. C.; Daerden, F.
2012-04-01
A 3-D Chemical Transport Model (CTM), with full stratospheric chemistry and driven by the ECMWF temperature and wind fields, is coupled to the PSC microphysical model PSCBox. This interactively describes the formation and evolution of four types of PSC particles (STS, SAT, NAT, and ice) through relevant microphysical processes. The number density and composition of each type of particles are computed for a binned size distribution. As a result, the calculation of surface area densities is accurately performed, of which the computation of the heterogeneous reaction constants takes advantage. The explicit computation of the particle size distributions allows obtaining the same optical properties as those measured by CALIPSO. Hence, the evolution of PSC coverage and composition will be studied and compared to the CALIPSO observations during Antarctic winters. The relationship between the presence of PSCs and the heterogeneous chemistry will also be investigated. In particular, two issues will be considered: (i) how the ozone depletion is related to the PSC coverage, and (ii) how each PSC particle type contributes to the chlorine activation.
A parametric study of mucociliary transport by numerical simulations of 3D non-homogeneous mucus.
Chatelin, Robin; Poncet, Philippe
2016-06-14
Mucociliary clearance is the natural flow of the mucus which covers and protects the lung from the outer world. Pathologies, like cystic fibrosis, highly change the biological parameters of the mucus flow leading to stagnation situations and pathogens proliferation. As the lung exhibits a complex dyadic structure, in-vivo experimental study of mucociliary clearance is almost impossible and numerical simulations can bring important knowledge about this biological flow. This paper brings a detailed study of the biological parameters influence on the mucociliary clearance, in particular for pathological situations such as cystic fibrosis. Using recent suitable numerical methods, a non-homogeneous mucus flow (including non-linearities) can be simulated efficiently in 3D, allowing the identification of the meaningful parameters involved in this biological flow. Among these parameters, it is shown that the mucus viscosity, the stiffness transition between pericilliary fluid and mucus, the pericilliary fluid height as well as both cilia length and beating frequency have a great influence on the mucociliary transport. PMID:27126985
3D imaging of amplitude objects embedded in phase objects using transport of intensity
NASA Astrophysics Data System (ADS)
Banerjee, Partha; Basunia, Mahmudunnabi
2015-09-01
The amplitude and phase of the complex optical field in the Helmholtz equation obey a pair of coupled equations, arising from equating the real and imaginary parts. The imaginary part yields the transport of intensity equation (TIE), which can be used to derive the phase distribution at the observation plane. If a phase object is approximately imaged on the recording plane(s), TIE yields the phase without the need for phase unwrapping. In our experiment, the 3D image of a phase object and an amplitude object embedded in a phase object is recovered. The phase object is created by heating a liquid, comprising a solution of red dye in alcohol, using a focused 514 nm laser beam to the point where self-phase modulation of the beam is observed. The optical intensities are recorded at various planes during propagation of a low power 633 nm laser beam through the liquid. In the process of applying TIE to derive the phase at the observation plane, the real part of the complex equation is also examined as a cross-check of our calculations. For pure phase objects, it is shown that the real part of the complex equation is best satisfied around the image plane. Alternatively, it is proposed that this information can be used to determine the optimum image plane.
NASA Astrophysics Data System (ADS)
Oh, J.; Jiang, X.; Waliser, D. E.; Moncrieff, M. W.; Johnson, R. H.
2013-12-01
As one of the most prominent tropical atmospheric variability modes, the Madden-Julian Oscillation (MJO) exerts profound influences on global weather and climate, and serves as a critical predictability source for extend-range forecast. While credible representation of the MJO still represents a great challenge for current general circulation models (GCMs), previous studies on the vertical structure of the MJO have largely focused on collective impacts from multi-scale convective systems on thermodynamic properties of the MJO. Most recently, limited observational studies and idealized modeling work suggested that convective momentum transport (CMT) could also play an important role in interpreting the observed MJO features. In this study, the 3D CMT structure associated with the MJO is examined by analyzing model output from three recent high-quality reanalysis systems, including NOAA's Climate Forecast System Reanalysis (CFSR), NASA's Modern Era Retrospective-analysis for Research and Applications (MERRA), and ECMWF-the Year of Tropical Convection (YOTC) reanalysis. Consistent with previous cloud-resolving model study, a well-organized three-layer vertical structure in the CMT associated with the MJO is also discerned based on reanalyses. The result suggests that CMT tends to intensify the MJO circulation, particularly in the lower troposphere. Relative roles of meso-scale systems (MCS) and synoptic waves in contributing the total CMT profiles of the MJO will also be explored. Differences in CMT profiles in these several reanalysis models will be discussed.
3-D simulation of gases transport under condition of inert gas injection into goaf
NASA Astrophysics Data System (ADS)
Liu, Mao-Xi; Shi, Guo-Qing; Guo, Zhixiong; Wang, Yan-Ming; Ma, Li-Yang
2016-02-01
To prevent coal spontaneous combustion in mines, it is paramount to understand O2 gas distribution under condition of inert gas injection into goaf. In this study, the goaf was modeled as a 3-D porous medium based on stress distribution. The variation of O2 distribution influenced by CO2 or N2 injection was simulated based on the multi-component gases transport and the Navier-Stokes equations using Fluent. The numerical results without inert gas injection were compared with field measurements to validate the simulation model. Simulations with inert gas injection show that CO2 gas mainly accumulates at the goaf floor level; however, a notable portion of N2 gas moves upward. The evolution of the spontaneous combustion risky zone with continuous inert gas injection can be classified into three phases: slow inerting phase, rapid accelerating inerting phase, and stable inerting phase. The asphyxia zone with CO2 injection is about 1.25-2.4 times larger than that with N2 injection. The efficacy of preventing and putting out mine fires is strongly related with the inert gas injecting position. Ideal injections are located in the oxidation zone or the transitional zone between oxidation zone and heat dissipation zone.
3D electro-thermal Monte Carlo study of transport in confined silicon devices
NASA Astrophysics Data System (ADS)
Mohamed, Mohamed Y.
The simultaneous explosion of portable microelectronics devices and the rapid shrinking of microprocessor size have provided a tremendous motivation to scientists and engineers to continue the down-scaling of these devices. For several decades, innovations have allowed components such as transistors to be physically reduced in size, allowing the famous Moore's law to hold true. As these transistors approach the atomic scale, however, further reduction becomes less probable and practical. As new technologies overcome these limitations, they face new, unexpected problems, including the ability to accurately simulate and predict the behavior of these devices, and to manage the heat they generate. This work uses a 3D Monte Carlo (MC) simulator to investigate the electro-thermal behavior of quasi-one-dimensional electron gas (1DEG) multigate MOSFETs. In order to study these highly confined architectures, the inclusion of quantum correction becomes essential. To better capture the influence of carrier confinement, the electrostatically quantum-corrected full-band MC model has the added feature of being able to incorporate subband scattering. The scattering rate selection introduces quantum correction into carrier movement. In addition to the quantum effects, scaling introduces thermal management issues due to the surge in power dissipation. Solving these problems will continue to bring improvements in battery life, performance, and size constraints of future devices. We have coupled our electron transport Monte Carlo simulation to Aksamija's phonon transport so that we may accurately and efficiently study carrier transport, heat generation, and other effects at the transistor level. This coupling utilizes anharmonic phonon decay and temperature dependent scattering rates. One immediate advantage of our coupled electro-thermal Monte Carlo simulator is its ability to provide an accurate description of the spatial variation of self-heating and its effect on non
Crossover from 3D to 2D Quantum Transport in Bi2Se3/In2Se3 Superlattices
NASA Astrophysics Data System (ADS)
Yanfei, Zhao; Haiwen, Liu; Xin, Guo; Ying, Jiang; Yi, Sun; Huichao, Wang; Yong, Wang; Handong, Li; Maohai, Xie; Xincheng, Xie; Jian, Wang
2015-03-01
The topological insulator/normal insulator (TI/NI) superlattices (SLs) with multiple Dirac channels are predicted to offer great opportunity to design novel materials and investigate new quantum phenomena. Here, we report first transport studies on the SLs composed of TI Bi2Se3 layers sandwiched by NI In2Se3 layers artificially grown by molecular beam epitaxy (MBE). The transport properties of two kinds of SL samples show convincing evidence that the transport dimensionality changes from three-dimensional (3D) to two-dimensional (2D) when decreasing the thickness of building block Bi2Se3 layers, corresponding to the crossover from coherent TI transport to separated TI channels. Our findings provide the possibility to realizing 3D surface states in TI/NI SLs.
Crossover from 3D to 2D quantum transport in Bi2Se3/In2Se3 superlattices.
Zhao, Yanfei; Liu, Haiwen; Guo, Xin; Jiang, Ying; Sun, Yi; Wang, Huichao; Wang, Yong; Li, Han-Dong; Xie, Mao-Hai; Xie, Xin-Cheng; Wang, Jian
2014-09-10
The topological insulator/normal insulator (TI/NI) superlattices (SLs) with multiple Dirac channels are predicted to offer great opportunity to design novel materials and investigate new quantum phenomena. Here, we report first transport studies on the SLs composed of TI Bi2Se3 layers sandwiched by NI In2Se3 layers artificially grown by molecular beam epitaxy (MBE). The transport properties of two kinds of SL samples show convincing evidence that the transport dimensionality changes from three-dimensional (3D) to two-dimensional (2D) when decreasing the thickness of building block Bi2Se3 layers, corresponding to the crossover from coherent TI transport to separated TI channels. Our findings provide the possibility to realizing "3D surface states" in TI/NI SLs. PMID:25102289
An iterative KP1 method for solving the transport equation in 3D domains on unstructured grids
NASA Astrophysics Data System (ADS)
Kokonkov, N. I.; Nikolaeva, O. V.
2015-10-01
A two-step iterative KP1 method for solving systems of grid equations that approximate the integro-differential transport equation in 3D domains on unstructured grids using nodal SN methods is described. Results of testing the efficiency of the proposed method in solving benchmark problems of reactor protection on tetrahedral grids are presented.
3D modelling of the transport and fate of riverine fine sediment exported to a semi-enclosed system
NASA Astrophysics Data System (ADS)
Delandmeter, Philippe; Lambrechts, Jonathan; Lewis, Stephen; Legat, Vincent; Deleersnijder, Eric; Wolanski, Eric
2015-04-01
Understanding the transport and fate of suspended sediment exported by rivers is crucial for the management of sensitive marine ecosystems. Sediment transport and fate can vary considerably depending on the geophysical characteristics of the offshore environment (i.e. open, semi-enclosed and enclosed systems and the nature of the continental shelf). In this presentation, we focus on a semi-enclosed setting in the Great Barrier Reef, NE Australia. In this system, the large tropical Burdekin River discharges to a long and narrow continental shelf containing numerous headlands and embayments. Using a new 3D sediment model we developed and SLIM 3D, a Finite Element 3D model for coastal flows, we highlight the key processes of sediment transport for such a system. We validate the model with available measured data from the region. Wind direction and speed during the high river flows are showed to largely control the dynamics and final fate of the sediments. Most (71%) of the sediment load delivered by the river is deposited and retained near the river mouth. The remaining sediment is transported further afield in riverine freshwater plumes. The suspended sediment transported longer distances in the freshwater plumes can reach sensitive marine ecosystems. These results are compared to previous studies on the Burdekin River sediment fate and differences are analysed. The model suggests that wind-driven resuspension events will redistribute sediments within an embayment but have little influence on transporting sediments from bay to bay.
GEOS-5 Chemistry Transport Model User's Guide
NASA Technical Reports Server (NTRS)
Kouatchou, J.; Molod, A.; Nielsen, J. E.; Auer, B.; Putman, W.; Clune, T.
2015-01-01
The Goddard Earth Observing System version 5 (GEOS-5) General Circulation Model (GCM) makes use of the Earth System Modeling Framework (ESMF) to enable model configurations with many functions. One of the options of the GEOS-5 GCM is the GEOS-5 Chemistry Transport Model (GEOS-5 CTM), which is an offline simulation of chemistry and constituent transport driven by a specified meteorology and other model output fields. This document describes the basic components of the GEOS-5 CTM, and is a user's guide on to how to obtain and run simulations on the NCCS Discover platform. In addition, we provide information on how to change the model configuration input files to meet users' needs.
Energy Science and Technology Software Center (ESTSC)
2013-06-24
Version 07 TART2012 is a coupled neutron-photon Monte Carlo transport code designed to use three-dimensional (3-D) combinatorial geometry. Neutron and/or photon sources as well as neutron induced photon production can be tracked. It is a complete system to assist you with input preparation, running Monte Carlo calculations, and analysis of output results. TART2012 is also incredibly FAST; if you have used similar codes, you will be amazed at how fast this code is compared tomore » other similar codes. Use of the entire system can save you a great deal of time and energy. TART2012 extends the general utility of the code to even more areas of application than available in previous releases by concentrating on improving the physics, particularly with regard to improved treatment of neutron fission, resonance self-shielding, molecular binding, and extending input options used by the code. Several utilities are included for creating input files and displaying TART results and data. TART2012 uses the latest ENDF/B-VI, Release 8, data. New for TART2012 is the use of continuous energy neutron cross sections, in addition to its traditional multigroup cross sections. For neutron interaction, the data are derived using ENDF-ENDL2005 and include both continuous energy cross sections and 700 group neutron data derived using a combination of ENDF/B-VI, Release 8, and ENDL data. The 700 group structure extends from 10-5 eV up to 1 GeV. Presently nuclear data are only available up to 20 MeV, so that only 616 of the groups are currently used. For photon interaction, 701 point photon data were derived using the Livermore EPDL97 file. The new 701 point structure extends from 100 eV up to 1 GeV, and is currently used over this entire energy range. TART2012 completely supersedes all older versions of TART, and it is strongly recommended that one use only the most recent version of TART2012 and its data files. Check authors homepage for related information: http
Reactor Dosimetry Applications Using RAPTOR-M3G:. a New Parallel 3-D Radiation Transport Code
NASA Astrophysics Data System (ADS)
Longoni, Gianluca; Anderson, Stanwood L.
2009-08-01
The numerical solution of the Linearized Boltzmann Equation (LBE) via the Discrete Ordinates method (SN) requires extensive computational resources for large 3-D neutron and gamma transport applications due to the concurrent discretization of the angular, spatial, and energy domains. This paper will discuss the development RAPTOR-M3G (RApid Parallel Transport Of Radiation - Multiple 3D Geometries), a new 3-D parallel radiation transport code, and its application to the calculation of ex-vessel neutron dosimetry responses in the cavity of a commercial 2-loop Pressurized Water Reactor (PWR). RAPTOR-M3G is based domain decomposition algorithms, where the spatial and angular domains are allocated and processed on multi-processor computer architectures. As compared to traditional single-processor applications, this approach reduces the computational load as well as the memory requirement per processor, yielding an efficient solution methodology for large 3-D problems. Measured neutron dosimetry responses in the reactor cavity air gap will be compared to the RAPTOR-M3G predictions. This paper is organized as follows: Section 1 discusses the RAPTOR-M3G methodology; Section 2 describes the 2-loop PWR model and the numerical results obtained. Section 3 addresses the parallel performance of the code, and Section 4 concludes this paper with final remarks and future work.
Estimation of Atmospheric Methane Surface Fluxes Using a Global 3-D Chemical Transport Model
NASA Astrophysics Data System (ADS)
Chen, Y.; Prinn, R.
2003-12-01
Accurate determination of atmospheric methane surface fluxes is an important and challenging problem in global biogeochemical cycles. We use inverse modeling to estimate annual, seasonal, and interannual CH4 fluxes between 1996 and 2001. The fluxes include 7 time-varying seasonal (3 wetland, rice, and 3 biomass burning) and 3 steady aseasonal (animals/waste, coal, and gas) global processes. To simulate atmospheric methane, we use the 3-D chemical transport model MATCH driven by NCEP reanalyzed observed winds at a resolution of T42 ( ˜2.8° x 2.8° ) in the horizontal and 28 levels (1000 - 3 mb) in the vertical. By combining existing datasets of individual processes, we construct a reference emissions field that represents our prior guess of the total CH4 surface flux. For the methane sink, we use a prescribed, annually-repeating OH field scaled to fit methyl chloroform observations. MATCH is used to produce both the reference run from the reference emissions, and the time-dependent sensitivities that relate individual emission processes to observations. The observational data include CH4 time-series from ˜15 high-frequency (in-situ) and ˜50 low-frequency (flask) observing sites. Most of the high-frequency data, at a time resolution of 40-60 minutes, have not previously been used in global scale inversions. In the inversion, the high-frequency data generally have greater weight than the weekly flask data because they better define the observational monthly means. The Kalman Filter is used as the optimal inversion technique to solve for emissions between 1996-2001. At each step in the inversion, new monthly observations are utilized and new emissions estimates are produced. The optimized emissions represent deviations from the reference emissions that lead to a better fit to the observations. The seasonal processes are optimized for each month, and contain the methane seasonality and interannual variability. The aseasonal processes, which are less variable, are
NASA Astrophysics Data System (ADS)
Viscardy, Sébastien; Errera, Quentin; Pitts, Michael C.; Poole, Lamont R.; Chabrillat, Simon; Daerden, Frank
2013-04-01
A 3-D Chemical Transport Model (CTM), with full stratospheric chemistry and driven by the ECMWF temperature and wind fields, has been coupled to a detailed PSC microphysical model to simulate polar winters. The formation and evolution of four types of PSC particles (STS, SAT, NAT, and ice) are described through relevant microphysical processes which alter interactively the nitric acid and water vapor concentrations of the atmosphere. Each particle type is described by a binned size distribution for the number density and chemical composition. This set-up allows for detailed calculation of optical properties and surface area densities used to compute the heterogeneous reaction rates. After comparing the evolution of the stratospheric chemical structure to satellite observations, we will investigate how the model reproduces the PSC coverage detected by CALIPSO. A comparison between the model and CALIPSO optical properties will be used to discuss the PSC composition. Finally, we aim at estimating the contribution of each PSC particle type to the chlorine activation.
NASA Astrophysics Data System (ADS)
Teruzzi, Anna; Dobricic, Srdjan; Solidoro, Cosimo; Cossarini, Gianpiero
2014-01-01
Increasing attention is dedicated to the implementation of suitable marine forecast systems for the estimate of the state of the ocean. Within the framework of the European MyOcean infrastructure, the pre-existing short-term Mediterranean Sea biogeochemistry operational forecast system has been upgraded by assimilating remotely sensed ocean color data in the coupled transport-biogeochemical model OPATM-BFM using a 3-D variational data assimilation (3D-VAR) procedure. In the present work, the 3D-VAR scheme is used to correct the four phytoplankton functional groups included in the OPATM-BFM in the period July 2007 to September 2008. The 3D-VAR scheme decomposes the error covariance matrix using a sequence of different operators that account separately for vertical covariance, horizontal covariance, and covariance among biogeochemical variables. The assimilation solution is found in a reduced dimensional space, and the innovation for the biogeochemical variables is obtained by the sequential application of the covariance operators. Results show a general improvement in the forecast skill, providing a correction of the basin-scale bias of surface chlorophyll concentration and of the local-scale spatial and temporal dynamics of typical bloom events. Further, analysis of the assimilation skill provides insights into the functioning of the model. The computational costs of the assimilation scheme adopted are low compared to other assimilation techniques, and its modular structure facilitates further developments. The 3D-VAR scheme results especially suitable for implementation within a biogeochemistry operational forecast system.
[Global Atmospheric Chemistry/Transport Modeling and Data-Analysis
NASA Technical Reports Server (NTRS)
Prinn, Ronald G.
1999-01-01
This grant supported a global atmospheric chemistry/transport modeling and data- analysis project devoted to: (a) development, testing, and refining of inverse methods for determining regional and global transient source and sink strengths for trace gases; (b) utilization of these inverse methods which use either the Model for Atmospheric Chemistry and Transport (MATCH) which is based on analyzed observed winds or back- trajectories calculated from these same winds for determining regional and global source and sink strengths for long-lived trace gases important in ozone depletion and the greenhouse effect; (c) determination of global (and perhaps regional) average hydroxyl radical concentrations using inverse methods with multiple "titrating" gases; and (d) computation of the lifetimes and spatially resolved destruction rates of trace gases using 3D models. Important ultimate goals included determination of regional source strengths of important biogenic/anthropogenic trace gases and also of halocarbons restricted by the Montreal Protocol and its follow-on agreements, and hydrohalocarbons now used as alternatives to the above restricted halocarbons.
3D Space Radiation Transport in a Shielded ICRU Tissue Sphere
NASA Technical Reports Server (NTRS)
Wilson, John W.; Slaba, Tony C.; Badavi, Francis F.; Reddell, Brandon D.; Bahadori, Amir A.
2014-01-01
A computationally efficient 3DHZETRN code capable of simulating High Charge (Z) and Energy (HZE) and light ions (including neutrons) under space-like boundary conditions with enhanced neutron and light ion propagation was recently developed for a simple homogeneous shield object. Monte Carlo benchmarks were used to verify the methodology in slab and spherical geometry, and the 3D corrections were shown to provide significant improvement over the straight-ahead approximation in some cases. In the present report, the new algorithms with well-defined convergence criteria are extended to inhomogeneous media within a shielded tissue slab and a shielded tissue sphere and tested against Monte Carlo simulation to verify the solution methods. The 3D corrections are again found to more accurately describe the neutron and light ion fluence spectra as compared to the straight-ahead approximation. These computationally efficient methods provide a basis for software capable of space shield analysis and optimization.
Reconstruction of 3D structure using stochastic methods: morphology and transport properties
NASA Astrophysics Data System (ADS)
Karsanina, Marina; Gerke, Kirill; Čapek, Pavel; Vasilyev, Roman; Korost, Dmitry; Skvortsova, Elena
2013-04-01
One of the main factors defining numerous flow phenomena in rocks, soils and other porous media, including fluid and solute movements, is pore structure, e.g., pore sizes and their connectivity. Numerous numerical methods were developed to quantify single and multi-phase flow in such media on microscale. Among most popular ones are: 1) a wide range of finite difference/element/volume solutions of Navier-Stokes equations and its simplifications; 2) lattice-Boltzmann method; 3) pore-network models, among others. Each method has some advantages and shortcomings, so that different research teams usually utilize more than one, depending on the study case. Recent progress in 3D imaging of internal structure, e.g., X-ray tomography, FIB-SEM and confocal microscopy, made it possible to obtain digitized input pore parameters for such models, however, a trade-off between resolution and sample size is usually unavoidable. There are situations then only standard two-dimensional information of porous structure is known due to tomography high cost or resolution limitations. However, physical modeling on microscale requires 3D information. There are three main approaches to reconstruct (using 2D cut(s) or some other limited information/properties) porous media: 1) statistical methods (correlation functions and simulated annealing, multi-point statistics, entropy methods), 2) sequential methods (sphere or other granular packs) and 3) morphological methods. Stochastic reconstructions using correlation functions possess some important advantage - they provide a statistical description of the structure, which is known to have relationships with all physical properties. In addition, this method is more flexible for other applications to characterize porous media. Taking different 3D scans of natural and artificial porous materials (sandstones, soils, shales, ceramics) we choose some 2D cut/s as sources of input correlation functions. Based on different types of correlation functions
NASA Astrophysics Data System (ADS)
Daughney, C.; Toews, M. W.; Morgenstern, U.; Cornaton, F. J.; Jackson, B. M.
2013-12-01
Lake Rotorua is a focus of culture and tourism in New Zealand. The lake's water quality has declined since the 1970s, partly due to nutrient inputs that reach the lake via the groundwater system. Improved land use management within the catchment requires prediction of the spatial variations of groundwater transit time from land surface to the lake, and from this the prediction of current and future nutrient inflows to the lake. This study combines the two main methods currently available for determination of water age: numerical groundwater models and hydrological tracers. A steady-state 3D finite element model was constructed to simulate groundwater flow and transport of tritium and age at the catchment scale (555 km2). The model materials were defined using a 3D geologic model and included ignimbrites, rhyolites, alluvial and lake bottom sediments. The steady-state saturated groundwater flow model was calibrated using observed groundwater levels in boreholes (111 locations) and stream flow measurements from groundwater-fed streams and springs (61 locations). Hydraulic conductivities and Cauchy boundary conditions associated with the streams, springs and lake were parameterized. The transport parameters for the model were calibrated using 191 tritium samples from 105 locations (springs, streams and boreholes), with most locations having two sample dates. The transport model used steady-state flow, but simulated the transient transport and decay of tritium from rainfall recharge between 1945 and 2012. An additional 1D unsaturated sub-model was added to account for tritium decay from the ground surface to the water table. The sub-model is linked on top of the 3D model, and uses the water table depths and material properties from the 3D model. The adjustable calibration parameters for the transport model were porosity and van Genuchten parameters related to the unsaturated sub-models. Calibration of the flow model was achieved using a combination of automated least
3D multi-scale analysis of coupled heat and moisture transport and its parallel implementation
NASA Astrophysics Data System (ADS)
Kruis, Jaroslav
2016-06-01
Parallel implementation of two-scale model of coupled heat and moisture transport is described. The coupled heat and moisture transport is based on the Künzel model. Motivation for the two-scale analysis comes from the requirement to describe distribution of the relative humidity and temperature in historical masonry structures.
NASA Astrophysics Data System (ADS)
Kobayashi, M.; Xu, Y.; Ida, K.; Corre, Y.; Feng, Y.; Schmitz, O.; Frerichs, H.; Tabares, F. L.; Evans, T. E.; Coenen, J. W.; Liang, Y.; Bader, A.; Itoh, K.; Yamada, H.; Ghendrih, Ph.; Ciraolo, G.; Tafalla, D.; Lopez-Fraguas, A.; Guo, H. Y.; Cui, Z. Y.; Reiter, D.; Asakura, N.; Wenzel, U.; Morita, S.; Ohno, N.; Peterson, B. J.; Masuzaki, S.
2015-10-01
This paper assesses the three-dimensional (3D) effects of the edge magnetic field structure on divertor/scrape-off layer transport, based on an inter-machine comparison of experimental data and on the recent progress of 3D edge transport simulation. The 3D effects are elucidated as a consequence of competition between transports parallel (\\parallel ) and perpendicular (\\bot ) to the magnetic field, in open field lines cut by divertor plates, or in magnetic islands. The competition has strong impacts on divertor functions, such as determination of the divertor density regime, impurity screening and detachment control. The effects of magnetic perturbation on the edge electric field and turbulent transport are also discussed. Parameterization to measure the 3D effects on the edge transport is attempted for the individual divertor functions. Based on the suggested key parameters, an operation domain of the 3D divertor configuration is discussed for future devices.
NASA Astrophysics Data System (ADS)
Levandowski, W.; Jones, C. H.
2014-12-01
Although seismic velocity generally reflects material density, density models drawn solely from seismic interpretations suffer from the fact that temperature, melt-depletion, variations in quartz content, and in-situ melt—as well as myriad other factors—have different effects on the relationship between velocity and density. To wit, such models generally do not accurately recover gravity and/or topography variations. We have developed a probabilistic density modeling method that estimates density from seismic velocity and heat flow and refines these initial estimates in order to reproduce gravity and topography, accounting for lithospheric flexure. Both the input seismic velocity modeling and the refinement are Monte Carlo-type approaches, so the posterior distribution of models provides a direct measure of uncertainty. We leverage the aforementioned difference in sensitivity to separate density variations into thermal and compositional components, providing information on the chemistry and physical state of the crust and upper mantle. Using this approach and Transportable Array seismic data, we present a density model of the western US lithosphere (from central Kansas west) to a depth of 150 km that reveals: 1) remarkably uniform, near- to supra-solidus mantle temperatures beneath regions deformed in the Cenozoic--including the Colorado Plateau--that are ~400 °C higher than those beneath the nominally stable interior of North America; 2) crustal melt (~1%) beneath Miocene-Recent volcanic provinces; 3) depleted mantle lithosphere beneath the Wyoming craton and northern High Plains; 4) likely hydrated lower crust in the Colorado Plateau and Great Plains; and 5) that horizontal differences in lithostatic pressure create deviatoric extensional stress of ~10 MPa in the northern Basin and Range and along the margins of the Colorado Plateau. This density model is a rich source of information, shedding light on the causes and consequences of tectonism, crust
Teruzzi, Anna; Dobricic, Srdjan; Solidoro, Cosimo; Cossarini, Gianpiero
2014-01-01
[1] Increasing attention is dedicated to the implementation of suitable marine forecast systems for the estimate of the state of the ocean. Within the framework of the European MyOcean infrastructure, the pre-existing short-term Mediterranean Sea biogeochemistry operational forecast system has been upgraded by assimilating remotely sensed ocean color data in the coupled transport-biogeochemical model OPATM-BFM using a 3-D variational data assimilation (3D-VAR) procedure. In the present work, the 3D-VAR scheme is used to correct the four phytoplankton functional groups included in the OPATM-BFM in the period July 2007 to September 2008. The 3D-VAR scheme decomposes the error covariance matrix using a sequence of different operators that account separately for vertical covariance, horizontal covariance, and covariance among biogeochemical variables. The assimilation solution is found in a reduced dimensional space, and the innovation for the biogeochemical variables is obtained by the sequential application of the covariance operators. Results show a general improvement in the forecast skill, providing a correction of the basin-scale bias of surface chlorophyll concentration and of the local-scale spatial and temporal dynamics of typical bloom events. Further, analysis of the assimilation skill provides insights into the functioning of the model. The computational costs of the assimilation scheme adopted are low compared to other assimilation techniques, and its modular structure facilitates further developments. The 3D-VAR scheme results especially suitable for implementation within a biogeochemistry operational forecast system. PMID:26213670
The coordination chemistry and magnetism of some 3d-4f and 4f amino-polyalcohol compounds.
Sharples, Joseph W; Collison, David
2014-02-01
Triethanolamine, teaH3, and diethanolamine, RdeaH2, 3d-4f and 4f compounds demonstrate an enormous variety in their structure and bonding. This review examines the synthetic strategies to these molecules and their magnetic properties, whilst trying to assess these ligands' suitability towards new SMMs and magnetic refrigerants. PMID:25009361
ERIC Educational Resources Information Center
Zhong, Ying
2013-01-01
Virtual worlds are well-suited for building virtual laboratories for educational purposes to complement hands-on physical laboratories. However, educators may face technical challenges because developing virtual worlds requires skills in programming and 3D design. Current virtual world building tools are developed for users who have programming…
Photons, Electrons and Positrons Transport in 3D by Monte Carlo Techniques
Energy Science and Technology Software Center (ESTSC)
2014-12-01
Version 04 FOTELP-2014 is a new compact general purpose version of the previous FOTELP-2K6 code designed to simulate the transport of photons, electrons and positrons through three-dimensional material and sources geometry by Monte Carlo techniques, using subroutine package PENGEOM from the PENELOPE code under Linux-based and Windows OS. This new version includes routine ELMAG for electron and positron transport simulation in electric and magnetic fields, RESUME option and routine TIMER for obtaining starting random numbermore » and for measuring the time of simulation.« less
Photons, Electrons and Positrons Transport in 3D by Monte Carlo Techniques
2014-12-01
Version 04 FOTELP-2014 is a new compact general purpose version of the previous FOTELP-2K6 code designed to simulate the transport of photons, electrons and positrons through three-dimensional material and sources geometry by Monte Carlo techniques, using subroutine package PENGEOM from the PENELOPE code under Linux-based and Windows OS. This new version includes routine ELMAG for electron and positron transport simulation in electric and magnetic fields, RESUME option and routine TIMER for obtaining starting random number and for measuring the time of simulation.
Age, double porosity, and simple reaction modifications for the MOC3D ground-water transport model
Goode, Daniel J.
1999-01-01
This report documents modifications for the MOC3D ground-water transport model to simulate (a) ground-water age transport; (b) double-porosity exchange; and (c) simple but flexible retardation, decay, and zero-order growth reactions. These modifications are incorporated in MOC3D version 3.0. MOC3D simulates the transport of a single solute using the method-ofcharacteristics numerical procedure. The age of ground water, that is the time since recharge to the saturated zone, can be simulated using the transport model with an additional source term of unit strength, corresponding to the rate of aging. The output concentrations of the model are in this case the ages at all locations in the model. Double porosity generally refers to a separate immobilewater phase within the aquifer that does not contribute to ground-water flow but can affect solute transport through diffusive exchange. The solute mass exchange rate between the flowing water in the aquifer and the immobile-water phase is the product of the concentration difference between the two phases and a linear exchange coefficient. Conceptually, double porosity can approximate the effects of dead-end pores in a granular porous media, or matrix diffusion in a fractured-rock aquifer. Options are provided for decay and zero-order growth reactions within the immobilewater phase. The simple reaction terms here extend the original model, which included decay and retardation. With these extensions, (a) the retardation factor can vary spatially within each model layer, (b) the decay rate coefficient can vary spatially within each model layer and can be different for the dissolved and sorbed phases, and (c) a zero-order growth reaction is added that can vary spatially and can be different in the dissolved and sorbed phases. The decay and growth reaction terms also can change in time to account for changing geochemical conditions during transport. The report includes a description of the theoretical basis of the model, a
NASA Astrophysics Data System (ADS)
Ghita, Gabriel; Sjoden, Glenn; Baciak, James; Huang, Nancy
2006-05-01
The Florida Institute for Nuclear Detection and Security (FINDS) is currently working on the design and evaluation of a prototype neutron detector array that may be used for parcel screening systems and homeland security applications. In order to maximize neutron detector response over a wide spectrum of energies, moderator materials of different compositions and amounts are required, and can be optimized through 3-D discrete ordinates and Monte Carlo model simulations verified through measurement. Pu-Be sources can be used as didactic source materials to augment the design, optimization, and construction of detector arrays with proper characterization via transport analysis. To perform the assessments of the Pu-Be Source Capsule, 3-D radiation transport computations are used, including Monte Carlo (MCNP5) and deterministic (PENTRAN) methodologies. In establishing source geometry, we based our model on available source schematic data. Because both the MCNP5 and PENTRAN codes begin with source neutrons, exothermic (α,n) reactions are modeled using the SCALE5 code from ORNL to define the energy spectrum and the decay of the source. We combined our computational results with experimental data to fully validate our computational schemes, tools and models. Results from our computational models will then be used with experiment to generate a mosaic of the radiation spectrum. Finally, we discuss follow-up studies that highlight response optimization efforts in designing, building, and testing an array of detectors with varying moderators/thicknesses tagged to specific responses predicted using 3-D radiation transport models to augment special nuclear materials detection.
3D Numerical Simulation of Turbulent Buoyant Flow and Heat Transport in a Curved Open Channel
Technology Transfer Automated Retrieval System (TEKTRAN)
A three-dimensional buoyancy-extended version of kappa-epsilon turbulence model was developed for simulating the turbulent flow and heat transport in a curved open channel. The density- induced buoyant force was included in the model, and the influence of temperature stratification on flow field was...
Intercomparison of 3D pore-scale flow and solute transport simulation methods
Mehmani, Yashar; Schoenherr, Martin; Pasquali, Andrea; Perkins, William A.; Kim, Kyungjoo; Perego, Mauro; Parks, Michael L.; Balhoff, Matthew T.; Richmond, Marshall C.; Geier, Martin; et al
2015-09-28
Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based onmore » the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This paper provides support for
Intercomparison of 3D pore-scale flow and solute transport simulation methods
Mehmani, Yashar; Schoenherr, Martin; Pasquali, Andrea; Perkins, William A.; Kim, Kyungjoo; Perego, Mauro; Parks, Michael L.; Balhoff, Matthew T.; Richmond, Marshall C.; Geier, Martin; Krafczyk, Manfred; Luo, Li -Shi; Tartakovsky, Alexandre M.; Yang, Xiaofan; Scheibe, Timothy D.; Trask, Nathaniel
2015-09-28
Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based on the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This paper provides support for confidence
NASA Astrophysics Data System (ADS)
Makra, László; Matyasovszky, István; Guba, Zoltán; Karatzas, Kostas; Anttila, Pia
2011-05-01
The purpose of the study is to identify long-range transport patterns that may have an important influence on PM10 levels in three European cities at different latitudes, namely Thessaloniki, Szeged and Helsinki. A further aim is to separate medium- and long-range PM10 transport for these cities. 4-day, 6-hourly three-dimensional (3D) backward trajectories arriving at these locations at 1200 GMT were computed using the HYSPLIT model over a 5-year period from 2001 to 2005. A k-means clustering algorithm using the Mahalanobis metric was applied in order to develop trajectory types. The 3D delimination of the clusters by the function "convhull" is a novel approach. Two statistical indices were used to evaluate and compare critical daily PM10 exceedances corresponding to the trajectory clusters. For Thessaloniki, the major PM10 transport can be clearly associated with air masses arriving from Central and Southern Europe. Occasional North African dust intrusions over Greece are also found. The transport of particulate matter from North-western Europe to Thessaloniki is of limited importance. For Szeged, Central Europe, Southern Europe and Mid-eastern Europe are the most important sources of PM10. The occasional appearance of North African-origin dust over Hungary is also detected. Local PM10 levels tend to be diluted when air masses arrive at the Carpathian Basin from North-western Europe, the Mid-Atlantic - Western Europe and Northern Europe. For Helsinki, high PM10 concentrations are due to air masses coming from Northern and Eastern Europe including North-western Russia. An occasional Caspian Sea desert influence on particulate levels can also be identified. However, air currents coming from the Northern Atlantics, Northern and North-western Europe tend to dilute PM10 levels. A simple approach is developed in order to separate medium- and long-range PM10 transport for each city.
A 3D Model for Ion Beam Formation and Transport Simulation
Qiang, J.; Todd, D.; Leitner, D.
2006-02-07
In this paper, we present a three-dimensional model forself-consistently modeling ion beam formation from plasma ion sources andtransporting in low energy beam transport systems. A multi-sectionoverlapped computational domain has been used to break the originaltransport system into a number of weakly coupled subsystems. Within eachsubsystem, macro-particle tracking is used to obtain the charge densitydistribution in this subdomain. The three-dimensional Poisson equation issolved within the subdomain after each particle tracking to obtain theself-consistent space-charge forces and the particle tracking is repeateduntil the solution converges. Two new Poisson solvers based on acombination of the spectral method and the finite difference multigridmethod have been developed to solve the Poisson equation in cylindricalcoordinates for the straight beam transport section and in Frenet-Serretcoordinates for the bending magnet section. This model can have importantapplication in design and optimization of the low energy beam line opticsof the proposed Rare Isotope Accelerator (RIA) front end.
Full 3D visualization tool-kit for Monte Carlo and deterministic transport codes
Frambati, S.; Frignani, M.
2012-07-01
We propose a package of tools capable of translating the geometric inputs and outputs of many Monte Carlo and deterministic radiation transport codes into open source file formats. These tools are aimed at bridging the gap between trusted, widely-used radiation analysis codes and very powerful, more recent and commonly used visualization software, thus supporting the design process and helping with shielding optimization. Three main lines of development were followed: mesh-based analysis of Monte Carlo codes, mesh-based analysis of deterministic codes and Monte Carlo surface meshing. The developed kit is considered a powerful and cost-effective tool in the computer-aided design for radiation transport code users of the nuclear world, and in particular in the fields of core design and radiation analysis. (authors)
Barlebo, H.C.; Rosbjerg, D.; Hill, M.C.
1996-01-01
An extensive amount of data including hydraulic heads, hydraulic conductivities and concentrations of several solutes from controlled injections have been collected during the MADE 1 and MADE 2 experiments at a heterogeneous site near Columbus, Mississippi. In this paper the use of three-dimensional inverse groundwater models including simultaneous estimation of flow and transport parameters is proposed to help identify the dominant characteristics at the site. Simulations show that using a hydraulic conductivity distribution obtained from 2187 borehole flowmeter tests directly in the model produces poor matches to the measured hydraulic heads and tritium concentrations. Alternatively, time averaged hydraulic head maps are used to define zones of constant hydraulic conductivity to be estimated. Preliminary simulations suggest that in the case of conservative transport many, but not all, of the major plume characteristics can be explained by large-scale heterogeneity in recharge and hydraulic conductivity.
Importance of 3D Processes Near the Ocean's Surface for Material Transport
NASA Astrophysics Data System (ADS)
Ozgokmen, T. M.
2014-12-01
There are a number of practical problems that demand an accurate knowledge of ocean currents near the surface of the ocean. It is known that oceanic coherent features transport heat and carry out vertical exchange of biogeochemical tracers. Ocean currents can affect biological primary production, air-sea gas exchanges and global tracer budgets. Ocean currents are also important for the dispersion of substances that pose a danger to society, economy and human health. Examples of such events include algal blooms, the Fukushima nuclear plant incident in the Pacific Ocean in 2011, and repeated large oil spills in the Gulf of Mexico, namely the IXTOC in 1978 and the Deepwater Horizon event in 2010. Such incidents demand accurate answers to questions such as ``where will the pollutant go?", ``how fast will it get there?" and ``how much pollutant will arrive there?", and in some instances ``where did the pollutant come from?". The answers to these questions are critical to the allocation of limited response resources, and in determining the overall impact of the events. We will summarize the efforts by the Consortium for Advanced Research on Transport of Hydrocarbon in the Environment (CARTHE). One of the primary objectives of CARTHE is to improve predictive modeling capability for flows near the air-sea interface. In particular, two large experiments, Grand Lagrangian Deployment (GLAD) and Surf-zone and Coastal Oil Pathways Experiment (SCOPE), coordinated with real-time modeling were instructive on processes influencing near-surface material transport. Findings on submesoscale flows as well as model deficiencies to capture processes relevant to transport will be discussed. Insight into future modeling and observational plans will be provided.
Quantum transport theory of 3D time-reversal invariant topological insulators
NASA Astrophysics Data System (ADS)
Dellabetta, Brian Jon
We consider the potential technological role of a recently predicted and discovered phase of quantum matter - topological insulators (TIs), which are characterized by an insulating bulk and topologically protected, gapless, spin-momentum locked surface modes. Precise engineering of these gapless modes may yield new potential materials for novel electronic devices, but many materials issues and open questions in application remain in the nascent field. The quasiparticle dynamics of TI systems can be elegantly written in terms of a low-energy effective momentum-space Hamiltonian, but analytic methods quickly become intractable in multifarious systems and disordered heterostructures which in general lack translational invariance, as momentum is no longer a good quantum number. Computational methods possess a clear advantage in this regime, for understanding systems in which geometry, contact layout, and disorder play a dominant role. We employ computationally intensive methods to calculate observable, non-equilibrium transport dynamics of real-space topological systems, to propose and identify experimental signatures of topological behavior, and to connect interesting experimental observations to the underlying topological properties in normal, disordered, and superconducting systems. The customizability of these computational methods allows us to determine the salient underlying physics involved in a number of different scenarios, including surface transport corrugated TI channels, the Aharonov-Bohm effect in TI nanowires, supercurrent in TI Josephson junctions, and the superconducting proximity effect and resulting transport in TI-superconductor heterostructures. In doing so, we expand the understanding of quantum and mesoscopic transport in heterostructured TI systems as a first step in exploring their long-term place in novel device applications.
Applications of the 3-D Deterministic Transport Code Attlla for Core Safety Analysis
D. S. Lucas
2004-10-01
An LDRD (Laboratory Directed Research and Development) project is ongoing at the Idaho National Engineering and Environmental Laboratory (INEEL) for applying the three-dimensional multi-group deterministic neutron transport code (Attila®) to criticality, flux and depletion calculations of the Advanced Test Reactor (ATR). This paper discusses the model development, capabilities of Attila, generation of the cross-section libraries, and comparisons to an ATR MCNP model and future.
Applications of the 3-D Deterministic Transport Attila{reg_sign} for Core Safety Analysis
Lucas, D.S.; Gougar, D.; Roth, P.A.; Wareing, T.; Failla, G.; McGhee, J.; Barnett, A.
2004-10-06
An LDRD (Laboratory Directed Research and Development) project is ongoing at the Idaho National Engineering and Environmental Laboratory (INEEL) for applying the three-dimensional multi-group deterministic neutron transport code (Attila{reg_sign}) to criticality, flux and depletion calculations of the Advanced Test Reactor (ATR). This paper discusses the model development, capabilities of Attila, generation of the cross-section libraries, and comparisons to an ATR MCNP model and future.
NASA Astrophysics Data System (ADS)
Janssen, G.; Del Val Alonso, L.; Groenendijk, P.; Griffioen, J.
2012-12-01
We developed an on-line coupling between the 1D/quasi-2D nutrient transport model ANIMO and the 3D groundwater transport model code MT3DMS. ANIMO is a detailed, process-oriented model code for the simulation of nitrate leaching to groundwater, N- and P-loads on surface waters and emissions of greenhouse gasses. It is the leading nutrient fate and transport code in the Netherlands where it is used primarily for the evaluation of fertilization related legislation. In addition, the code is applied frequently in international research projects. MT3DMS is probably the most commonly used groundwater solute transport package worldwide. The on-line model coupling ANIMO-MT3DMS combines the state-of-the-art descriptions of the biogeochemical cycles in ANIMO with the advantages of using a 3D approach for the transport through the saturated domain. These advantages include accounting for regional lateral transport, considering groundwater-surface water interactions more explicitly, and the possibility of using MODFLOW to obtain the flow fields. An additional merit of the on-line coupling concept is that it preserves feedbacks between the saturated and unsaturated zone. We tested ANIMO-MT3DMS by simulating nutrient transport for the period 1970-2007 in a Dutch agricultural polder catchment covering an area of 118 km2. The transient groundwater flow field had a temporal resolution of one day and was calculated with MODFLOW-MetaSWAP. The horizontal resolution of the model grid was 100x100m and consisted of 25 layers of varying thickness. To keep computation times manageable, we prepared MT3DMS for parallel computing, which in itself is a relevant development for a large community of groundwater transport modelers. For the parameterization of the soil, we applied a standard classification approach, representing the area by 60 units with unique combinations of soil type, land use and geohydrological setting. For the geochemical parameterization of the deeper subsurface, however, we
NASA Astrophysics Data System (ADS)
Brueck, C. L.; Meisenheimer, D.; Wildenschild, D.
2015-12-01
Understanding the mechanisms controlling colloid transport and deposition in the vadose zone is an important step in protecting our water resources. Not only may these particles themselves be undesirable contaminants, but they can also aid in the transport of smaller, molecular-scale contaminants by chemical attachment. In this research, we examined the influence that air-water interfaces (AWI) and air-water-solid contact lines (AWS) have on colloid deposition and mobilization in three-dimensional systems. We used x-ray microtomography to visualize the transport of hydrophobic colloids as they move through a partially saturated glass bead pack. Drainage and imbibition experiments were conducted using syringe pumps to control the flow of a colloid suspension through the porous media at 0.6 mL/hr. The high ionic strength fluid was adjusted to a pH of 9.5 and a concentration of 1.0 mol/L KI. During the drainage and imbibition, the flow was periodically halted and allowed to equilibrate before collecting the microtomography scans. Dopants were used to enhance the contrast between the four phases (water, air, beads, and colloids), including potassium iodide dissolved in the fluid, and an outer layer of silver coating the colloids. We hypothesized that AWIs and AWSs will scour and mobilize a significant percentage of colloids, and therefore reduce the concentration of colloids along the vertical profile of the column. The concentration of potassium iodide, and thus the ionic strength, necessary for adequate image segmentation was also explored in separate experiments so that the influence of ionic strength on colloid deposition and mobilization can be studied.
Benchmark Study of 3D Pore-scale Flow and Solute Transport Simulation Methods
NASA Astrophysics Data System (ADS)
Scheibe, T. D.; Yang, X.; Mehmani, Y.; Perkins, W. A.; Pasquali, A.; Schoenherr, M.; Kim, K.; Perego, M.; Parks, M. L.; Trask, N.; Balhoff, M.; Richmond, M. C.; Geier, M.; Krafczyk, M.; Luo, L. S.; Tartakovsky, A. M.
2015-12-01
Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that benchmark study to include additional models of the first type based on the immersed-boundary method (IMB), lattice Boltzmann method (LBM), and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries in the manner of PNMs has not been fully determined. We apply all five approaches (FVM-based CFD, IMB, LBM, SPH and PNM) to simulate pore-scale velocity distributions and nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The benchmark study was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for confidence in a variety of pore-scale modeling methods, and motivates further development and application of pore-scale simulation methods.
Investigating the Use of 3-D Deterministic Transport for Core Safety Analysis
H. D. Gougar; D. Scott
2004-04-01
An LDRD (Laboratory Directed Research and Development) project is underway at the Idaho National Laboratory (INL) to demonstrate the feasibility of using a three-dimensional multi-group deterministic neutron transport code (Attila®) to perform global (core-wide) criticality, flux and depletion calculations for safety analysis of the Advanced Test Reactor (ATR). This paper discusses the ATR, model development, capabilities of Attila, generation of the cross-section libraries, comparisons to experimental results for Advanced Fuel Cycle (AFC) concepts, and future work planned with Attila.
McGhee, J.M.; Roberts, R.M.; Morel, J.E.
1997-06-01
A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner for scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated.
Finite-Orbit-Width version of the CQL3D for description of RF-enhanced neoclassical transport
NASA Astrophysics Data System (ADS)
Petrov, Yu. V.; Harvey, R. W.
2015-12-01
The CQL3D bounce-averaged Fokker-Planck (FP) code [l] has been upgraded to include Finite-Orbit-Width (FOW) effects. The calculations can be done either with a fast Hybrid-FOW option or with a slower but neoclassically complete full-FOW option. The neoclassical radial transport appears naturally in the full-FOW version by averaging the local collision coefficients along guiding center orbits, with a proper transformation matrix from local (R, Z) coordinates to the midplane computational coordinates, where the FP equation is solved. In a similar way, the local quasilinear rf diffusion terms give rise to additional radial transport of orbits. The results of validation tests for the full-FOW version are presented.
GROUNDWATER MASS TRANSPORT AND EQUILIBRIUM CHEMISTRY MODEL FOR MULTICOMPONENT SYSTEMS
A mass transport model, TRANQL, for a multicomponent solution system has been developed. The equilibrium interaction chemistry is posed independently of the mass transport equations which leads to a set of algebraic equations for the chemistry coupled to a set of differential equ...
Development of a 3D to 1D Particle Transport Model to Predict Deposition in the Lungs
NASA Astrophysics Data System (ADS)
Oakes, Jessica M.; Grandmont, Celine; Shadden, Shawn C.; Vignon-Clementel, Irene E.
2014-11-01
Aerosolized particles are commonly used for therapeutic drug delivery as they can be delivered to the body systemically or be used to treat lung diseases. Recent advances in computational resources have allowed for sophisticated pulmonary simulations, however it is currently impossible to solve for airflow and particle transport for all length and time scales of the lung. Instead, multi-scale methods must be used. In our recent work, where computational methods were employed to solve for airflow and particle transport in the rat airways (Oakes et al. (2014), Annals of Biomedical Engineering 42, 899), the number of particles to exit downstream of the 3D domain was determined. In this current work, the time-dependent Lagrangian description of particles was used to numerically solve a 1D convection-diffusion model (trumpet model, Taulbee and Yu (1975), Journal of Applied Physiology, 38, 77) parameterized specifically for the lung. The expansion of the airway dimensions was determined based on data collected from our aerosol exposure experiments (Oakes et al. (2014), Journal of Applied Physiology, 116, 1561). This 3D-1D framework enables us to predict the fate of particles in the whole lung. This work was supported by the Whitaker Foundation at the IIE, a INRIA Associated Team Postdoc Grant, and a UC Presidential Fellowship.
Three-fluid, 3D MHD solar wind modeling with turbulence transport and eddy viscosity
NASA Astrophysics Data System (ADS)
Usmanov, A. V.; Goldstein, M. L.; Matthaeus, W. H.
2014-12-01
We present results from a three-fluid, fully three-dimensional MHD solar wind model that includes turbulence transport, eddy viscosity, turbulent resistivity, and turbulent heating. The solar wind plasma is described as a co-moving system of three species: the solar wind protons, electrons, and interstellar pickup protons. Separate energy equations are employed for each species. We obtain numerical solutions of Reynolds-averaged solar wind equations coupled with turbulence transport equations in the region from 0.3 to 100 AU. The integrated system of equations includes the effects of electron heat conduction, Coulomb collisions, photoionization of interstellar hydrogen atoms and their charge exchange with the solar wind protons, turbulence energy generation by pickup protons, and turbulent heating of solar wind protons and electrons. Using either a dipole approximation for the solar magnetic field or synoptic solar magnetograms from the Wilcox Solar Observatory for assigning boundary conditions at the coronal base, we apply the model to study the global structure of the solar wind and its three-dimensional properties, including turbulence parameters, throughout the heliosphere. The model results are compared with observations on WIND, Ulysses and Voyager 2 spacecraft. This work is partially supported by LWS and Heliophysics Grand Challenges programs.
Reactive transport in 3D models of irregularly fractured rock masses
NASA Astrophysics Data System (ADS)
Driesner, T.; Mindel, J. E.
2014-12-01
Reactive transport through irregularly fractured rock masses is a key phenomenon in ore-forming hydrothermal systems, geothermal systems, and many other geological processes and will affect the mechanical properties and hydraulic apertures of fractures. Realistic representations of such systems have so far been hampered by technical limitations of most hydrothermal reactive transport codes, namely the ability to represent discrete fracture networks in a porous rock matrix. We present the first three-dimensional simulation results obtained from coupling a combined finite element - finite volume scheme of the revised CSMP++ flow simulation platform (1) with the GEMIPM3K (2) chemical equilibration code. In these, we represented fracture zones as thin, porous zones of higher permeability. The simulations demonstrate the effects of fracture zone orientation relative to the pressure field and fracture zone intersections on the differential advance of reaction fronts. We outline our numerical approaches for testing and comparing the effect of various ways of representing fractures and fracture zones in irregular meshes, namely the possibility of using layers of prism elements to represent fractures of finite thickness with internally varying properties and the possibility to represent thin fractures as lower dimensional (=2D) elements. We intend to make use of the "split node" capabilities of CSMP++ (3) to maintain sharp interfaces at material boundaries in order to be able to study the transient influence of reactive flow on fracture and matrix permeability in irregularly fractured rock masses.
ERIC Educational Resources Information Center
Kumi, Bryna C.; Olimpo, Jeffrey T.; Bartlett, Felicia; Dixon, Bonnie L.
2013-01-01
The use of two-dimensional (2D) representations to communicate and reason about micromolecular phenomena is common practice in chemistry. While experts are adept at using such representations, research suggests that novices often exhibit great difficulty in understanding, manipulating, and translating between various representational forms. When…
Coordination Chemistry of Microbial Iron Transport.
Raymond, Kenneth N; Allred, Benjamin E; Sia, Allyson K
2015-09-15
This Account focuses on the coordination chemistry of the microbial iron chelators called siderophores. The initial research (early 1970s) focused on simple analogs of siderophores, which included hydroxamate, catecholate, or hydroxycarboxylate ligands. The subsequent work increasingly focused on the transport of siderophores and their microbial iron transport. Since these are pseudo-octahedral complexes often composed of bidentate ligands, there is chirality at the metal center that in principle is independent of the ligand chirality. It has been shown in many cases that chiral recognition of the complex occurs. Many techniques have been used to elucidate the iron uptake processes in both Gram-positive (single membrane) and Gram-negative (double membrane) bacteria. These have included the use of radioactive labels (of ligand, metal, or both), kinetically inert metal complexes, and Mössbauer spectroscopy. In general, siderophore recognition and transport involves receptors that recognize the metal chelate portion of the iron-siderophore complex. A second, to date less commonly found, mechanism called the siderophore shuttle involves the receptor binding an apo-siderophore. Since one of the primary ways that microbes compete with each other for iron stores is the strength of their competing siderophore complexes, it became important early on to characterize the solution thermodynamics of these species. Since the acidity of siderophores varies significantly, just the stability constant does not give a direct measure of the relative competitive strength of binding. For this reason, the pM value is compared. The pM, like pH, is a measure of the negative log of the free metal ion concentration, typically calculated at pH 7.4, and standard total concentrations of metal and ligand. The characterization of the electronic structure of ferric siderophores has done much to help explain the high stability of these complexes. A new chapter in siderophore science has emerged
Coordination Chemistry of Microbial Iron Transport
2016-01-01
Conspectus This Account focuses on the coordination chemistry of the microbial iron chelators called siderophores. The initial research (early 1970s) focused on simple analogs of siderophores, which included hydroxamate, catecholate, or hydroxycarboxylate ligands. The subsequent work increasingly focused on the transport of siderophores and their microbial iron transport. Since these are pseudo-octahedral complexes often composed of bidentate ligands, there is chirality at the metal center that in principle is independent of the ligand chirality. It has been shown in many cases that chiral recognition of the complex occurs. Many techniques have been used to elucidate the iron uptake processes in both Gram-positive (single membrane) and Gram-negative (double membrane) bacteria. These have included the use of radioactive labels (of ligand, metal, or both), kinetically inert metal complexes, and Mössbauer spectroscopy. In general, siderophore recognition and transport involves receptors that recognize the metal chelate portion of the iron–siderophore complex. A second, to date less commonly found, mechanism called the siderophore shuttle involves the receptor binding an apo-siderophore. Since one of the primary ways that microbes compete with each other for iron stores is the strength of their competing siderophore complexes, it became important early on to characterize the solution thermodynamics of these species. Since the acidity of siderophores varies significantly, just the stability constant does not give a direct measure of the relative competitive strength of binding. For this reason, the pM value is compared. The pM, like pH, is a measure of the negative log of the free metal ion concentration, typically calculated at pH 7.4, and standard total concentrations of metal and ligand. The characterization of the electronic structure of ferric siderophores has done much to help explain the high stability of these complexes. A new chapter in siderophore science
Modelling of transport phenomena in 3D GMAW of thick metals with V groove
NASA Astrophysics Data System (ADS)
Hu, J.; Tsai, H. L.
2008-03-01
This paper analyses the dynamic process of groove filling and the resulting weld pool fluid flow in gas metal arc welding of thick metals with V groove. Filler droplets carrying mass, momentum, thermal energy and sulfur species are periodically impinged onto the workpiece. The complex transport phenomena in the weld pool, caused by the combined effect of droplet impingement, gravity, electromagnetic force, surface tension and plasma arc pressure, were investigated to determine the transient weld pool shape and distributions of velocity, temperature and sulfur species in the weld pool. It was found that the groove provides a channel which can smooth the flow in the weld pool, leading to poor mixing between the filler metal and the base metal.
3D particle simulation of beams using the WARP code: Transport around bends
Friedman, A.; Grote, D.P.; Callahan, D.A.; Langdon, A.B. ); Haber, I. )
1990-11-30
WARP is a discrete-particle simulation program which was developed for studies of space charge dominated ion beams. It combines features of an accelerator code and a particle-in-cell plasma simulation. The code architecture, and techniques employed to enhance efficiency, are briefly described. Current applications are reviewed. In this paper we emphasize the physics of transport of three-dimensional beams around bends. We present a simple bent-beam PIC algorithm. Using this model, we have followed a long, thin beam around a bend in a simple racetrack system (assuming straight-pipe self-fields). Results on beam dynamics are presented; no transverse emittance growth (at mid-pulse) is observed. 11 refs., 5 figs.
TART97 a coupled neutron-photon 3-D, combinatorial geometry Monte Carlo transport code
Cullen, D.E.
1997-11-22
TART97 is a coupled neutron-photon, 3 Dimensional, combinatorial geometry, time dependent Monte Carlo transport code. This code can on any modern computer. It is a complete system to assist you with input preparation, running Monte Carlo calculations, and analysis of output results. TART97 is also incredibly FAST; if you have used similar codes, you will be amazed at how fast this code is compared to other similar codes. Use of the entire system can save you a great deal of time and energy. TART97 is distributed on CD. This CD contains on- line documentation for all codes included in the system, the codes configured to run on a variety of computers, and many example problems that you can use to familiarize yourself with the system. TART97 completely supersedes all older versions of TART, and it is strongly recommended that users only use the most recent version of TART97 and its data riles.
NASA Astrophysics Data System (ADS)
Lamorski, Krzysztof; Sławiński, Cezary; Barna, Gyöngyi
2014-05-01
There are some important macroscopic properties of the soil porous media such as: saturated permeability and water retention characteristics. These soil characteristics are very important as they determine soil transport processes and are commonly used as a parameters of general models of soil transport processes used extensively for scientific developments and engineering practise. These characteristics are usually measured or estimated using some statistical or phenomenological modelling, i.e. pedotransfer functions. On the physical basis, saturated soil permeability arises from physical transport processes occurring at the pore level. Current progress in modelling techniques, computational methods and X-ray micro-tomographic technology gives opportunity to use direct methods of physical modelling for pore level transport processes. Physically valid description of transport processes at micro-scale based on Navier-Stokes type modelling approach gives chance to recover macroscopic porous medium characteristics from micro-flow modelling. Water microflow transport processes occurring at the pore level are dependent on the microstructure of porous body and interactions between the fluid and the medium. In case of soils, i.e. the medium there exist relatively big pores in which water can move easily but also finer pores are present in which water transport processes are dominated by strong interactions between the medium and the fluid - full physical description of these phenomena is a challenge. Ten samples of different soils were scanned using X-ray computational microtomograph. The diameter of samples was 5 mm. The voxel resolution of CT scan was 2.5 µm. Resulting 3D soil samples images were used for reconstruction of the pore space for further modelling. 3D image threshholding was made to determine the soil grain surface. This surface was triangulated and used for computational mesh construction for the pore space. Numerical modelling of water flow through the
NASA Astrophysics Data System (ADS)
Simmons, Gary G.; Howett, Carly J. A.; Young, Leslie A.; Spencer, John R.
2015-11-01
In the last few decades, thermal data from the Galileo and Cassini spacecraft have detected various anomalies on Jovian and Saturnian satellites, including the thermally anomalous “PacMan” regions on Mimas and Tethys and the Pwyll anomaly on Europa (Howett et al. 2011, Howett et al. 2012, Spencer et al. 1999). Yet, the peculiarities of some of these anomalies, like the weak detection of the “PacMan” anomalies on Rhea and Dione and the low thermal inertia values of the widespread anomalies on equatorial Europa, are subjects for on-going research (Howett et al. 2014, Rathbun et al. 2010). Further, analysis and review of all the data both Galileo and Cassini took of these worlds will provide information of the thermal inertia and albedos of their surfaces, perhaps highlighting potential targets of interest for future Jovian and Saturnian system missions. Many previous works have used a thermophysical model for airless planets developed by Spencer (1990). However, the Three Dimensional Volatile-Transport (VT3D) model proposed by Young (2012) is able to predict surface temperatures in significantly faster computation time, incorporating seasonal and diurnal insolation variations. This work is the first step in an ongoing investigation, which will use VT3D’s capabilities to reanalyze Galileo and Cassini data. VT3D, which has already been used to analyze volatile transport on Pluto, is validated by comparing its results to that of the Spencer thermal model. We will also present our initial results using VT3D to reanalyze the thermophysical properties of the PacMan anomaly previous discovered on Mimas by Howett et al. (2011), using temperature constraints of diurnal data from Cassini/CIRS. VT3D is expected to be an efficient tool in identifying new thermal anomalies in future Saturnian and Jovian missions.Bibliography:C.J.A. Howett et al. (2011), Icarus 216, 221.C.J.A. Howett et al. (2012), Icarus 221, 1084.C.J.A. Howett et al. (2014), Icarus 241, 239.J
A Coupled Neutron-Photon 3-D Combinatorial Geometry Monte Carlo Transport Code
Energy Science and Technology Software Center (ESTSC)
1998-06-12
TART97 is a coupled neutron-photon, 3 dimensional, combinatorial geometry, time dependent Monte Carlo transport code. This code can run on any modern computer. It is a complete system to assist you with input preparation, running Monte Carlo calculations, and analysis of output results. TART97 is also incredibly fast: if you have used similar codes, you will be amazed at how fast this code is compared to other similar codes. Use of the entire system canmore » save you a great deal of time and energy. TART 97 is distributed on CD. This CD contains on-line documentation for all codes included in the system, the codes configured to run on a variety of computers, and many example problems that you can use to familiarize yourself with the system. TART97 completely supersedes all older versions of TART, and it is strongly recommended that users only use the most recent version of TART97 and ist data files.« less
Pastura, F C H; Guimarães, C P; Zamberlan, M C P; Cid, G L; Santos, V S; Streit, P; Paranhos, A G; Cobbe, R T; Cobbe, K T; Batista, D S
2012-01-01
The goal of this paper is to present 1D and 3D anthropometric data applied to two distinct design situations: one related to the interior layout of a public transport vehicle and another one related to oil and gas laboratories work environment design. On this study, the 1D anthropometric data were extracted from the Brazilian anthropometric database developed by INT and the 3D anthropometric data were obtained using a Cyberware 3D whole body scanner. A second purpose of this paper is to present the 3D human scanning data as a tool that can help designers on decision making. PMID:22317431
3-D Deep Penetration Neutron Imaging of Thick Absorgin and Diffusive Objects Using Transport Theory
Ragusa, Jean; Bangerth, Wolfgang
2011-08-01
here explores the inverse problem of optical tomography applied to heterogeneous domains. The neutral particle transport equation was used as the forward model for how neutral particles stream through and interact within these heterogeneous domains. A constrained optimization technique that uses Newtons method served as the basis of the inverse problem. Optical tomography aims at reconstructing the material properties using (a) illuminating sources and (b) detector readings. However, accurate simulations for radiation transport require that the particle (gamma and/or neutron) energy be appropriate discretize in the multigroup approximation. This, in turns, yields optical tomography problems where the number of unknowns grows (1) about quadratically with respect to the number of energy groups, G, (notably to reconstruct the scattering matrix) and (2) linearly with respect to the number of unknown material regions. As pointed out, a promising approach could rely on algorithms to appropriately select a material type per material zone rather than G2 values. This approach, though promising, still requires further investigation: (a) when switching from cross-section values unknowns to material type indices (discrete integer unknowns), integer programming techniques are needed since derivative information is no longer available; and (b) the issue of selecting the initial material zoning remains. The work reported here proposes an approach to solve the latter item, whereby a material zoning is proposed using one-group or few-groups transport approximations. The capabilities and limitations of the presented method were explored; they are briefly summarized next and later described in fuller details in the Appendices. The major factors that influenced the ability of the optimization method to reconstruct the cross sections of these domains included the locations of the sources used to illuminate the domains, the number of separate experiments used in the reconstruction, the
Lee, Gang-Young; Han, A-Reum; Kim, Taewan; Lee, Hae Rang; Oh, Joon Hak; Park, Taiho
2016-05-18
To achieve extremely high planarity and processability simultaneously, we have newly designed and synthesized copolymers composed of donor units of 2,2'-(2,5-dialkoxy-1,4-phenylene)dithieno[3,2-b]thiophene (TT-P-TT) and acceptor units of diketopyrrolopyrrole (DPP). These copolymers consist of a highly planar backbone due to intramolecular interactions. We have systematically investigated the effects of intermolecular interactions by controlling the side chain bulkiness on the polymer thin-film morphologies, packing structures, and charge transport. The thin-film microstructures of the copolymers are found to be critically dependent upon subtle changes in the intermolecular interactions, and charge transport dynamics of the copolymer based field-effect transistors (FETs) has been investigated by in-depth structure-property relationship study. Although the size of the fibrillar structures increases as the bulkiness of the side chains in the copolymer increases, the copolymer with the smallest side chain shows remarkably high charge carrier mobility. Our findings reveal the requirement for forming efficient 3-D charge transport pathway and highlight the importance of the molecular packing and interdomain connectivity, rather than the crystalline domain size. The results obtained herein demonstrate the importance of tailoring the side chain bulkiness and provide new insights into the molecular design for high-performance polymer semiconductors. PMID:27117671
NASA Astrophysics Data System (ADS)
Vitousek, S.; Fletcher, C. H.; Storlazzi, C. D.
2006-12-01
Nearshore currents are driven by a number of components including tides, waves winds and even internal tides. To adequately simulate transport of sand and other constituents, the realistic behavior of the dominant current-generating phenomena should be resolved. This often requires sufficient observations and calibration/validation efforts to achieve realistic modeling results. The work explores the capabilities of modeling the currents along West Maui. The West Maui coast has a propagating tide where the observed peak tidal currents, which are directed parallel to the coast, occur very closely to the peak tidal water levels. In 2003, the USGS collected an extensive set of current observations along West Maui, Hawaii, with the goal of better understanding transport mechanisms of sediment, larvae, pollutants and other particles in coral reef settings. The observations included vessel mounted ADCP surveys and an array seafloor instruments at the 10m isobath along the coast. A simple 2DH model of West Maui using Delft3D shows good comparison of the modeled and observed currents. Nearshore currents driven by waves and winds are also considered. During the data collection period a significant erosion event occurred within the study domain at Kaanapali Beach. This event undermined several trees on the shoreline and threatened resort infrastructure. In modeling the nearshore currents of this region we hope to determine the potential for sand transport and shoreline change to hindcast this event.
NASA Astrophysics Data System (ADS)
Wang, Jian; Cheng, Shuang; Li, Wanfei; Zhang, Su; Li, Hongfei; Zheng, Zhaozhao; Li, Fujin; Shi, Liyi; Lin, Hongzhen; Zhang, Yuegang
2016-07-01
Lithium/sulfur (Li/S) battery is a promising next-generation energy storage system owing to its high theoretical energy density. However, for practical use there remains some key problems to be solved, such as low active material utilization and rapid capacity fading, especially at high areal sulfur loadings. Here, we report a facile one-pot method to prepare porous three-dimensional nitrogen, sulfur-codoped graphene through hydrothermal reduction of graphene oxide with multi-ion mixture modulation. We show solid evidence that the results of multi-ion mixture modulation can not only improve the surface affinity of the nanocarbons to polysulfides, but also alter their assembling manner and render the resultant 3D network a more favorable pore morphology for accommodating and confining sulfur. It also had an excellent rate performance and cycling stability, showing an initial capacity of 1304 mA h g-1 at 0.05C, 613 mA h g-1 at 5C and maintaining a reversible capacity of 462 mA h g-1 after 1500 cycles at 2C with capacity fading as low as 0.028% per cycle. Moreover, a high areal capacity of 5.1 mA h cm-2 at 0.2C is achieved at an areal sulfur loading of 6.3 mg cm-2, which are the best values reported so far for dual-doped sulfur cathodes.
NASA Technical Reports Server (NTRS)
Strahan, Susan E.; Douglass, Anne R.
2003-01-01
The Global Modeling Initiative has integrated two 35-year simulations of an ozone recovery scenario with an offline chemistry and transport model using two different meteorological inputs. Physically based diagnostics, derived from satellite and aircraft data sets, are described and then used to evaluate the realism of temperature and transport processes in the simulations. Processes evaluated include barrier formation in the subtropics and polar regions, and extratropical wave-driven transport. Some diagnostics are especially relevant to simulation of lower stratospheric ozone, but most are applicable to any stratospheric simulation. The temperature evaluation, which is relevant to gas phase chemical reactions, showed that both sets of meteorological fields have near climatological values at all latitudes and seasons at 30 hPa and below. Both simulations showed weakness in upper stratospheric wave driving. The simulation using input from a general circulation model (GMI(sub GCM)) showed a very good residual circulation in the tropics and northern hemisphere. The simulation with input from a data assimilation system (GMI(sub DAS)) performed better in the midlatitudes than at high latitudes. Neither simulation forms a realistic barrier at the vortex edge, leading to uncertainty in the fate of ozone-depleted vortex air. Overall, tracer transport in the offline GMI(sub GCM) has greater fidelity throughout the stratosphere than the GMI(sub DAS).
NASA Astrophysics Data System (ADS)
Bergmann, Ryan
Graphics processing units, or GPUs, have gradually increased in computational power from the small, job-specific boards of the early 1990s to the programmable powerhouses of today. Compared to more common central processing units, or CPUs, GPUs have a higher aggregate memory bandwidth, much higher floating-point operations per second (FLOPS), and lower energy consumption per FLOP. Because one of the main obstacles in exascale computing is power consumption, many new supercomputing platforms are gaining much of their computational capacity by incorporating GPUs into their compute nodes. Since CPU-optimized parallel algorithms are not directly portable to GPU architectures (or at least not without losing substantial performance), transport codes need to be rewritten to execute efficiently on GPUs. Unless this is done, reactor simulations cannot take full advantage of these new supercomputers. WARP, which can stand for ``Weaving All the Random Particles,'' is a three-dimensional (3D) continuous energy Monte Carlo neutron transport code developed in this work as to efficiently implement a continuous energy Monte Carlo neutron transport algorithm on a GPU. WARP accelerates Monte Carlo simulations while preserving the benefits of using the Monte Carlo Method, namely, very few physical and geometrical simplifications. WARP is able to calculate multiplication factors, flux tallies, and fission source distributions for time-independent problems, and can run in both criticality or fixed source modes. WARP can transport neutrons in unrestricted arrangements of parallelepipeds, hexagonal prisms, cylinders, and spheres. WARP uses an event-based algorithm, but with some important differences. Moving data is expensive, so WARP uses a remapping vector of pointer/index pairs to direct GPU threads to the data they need to access. The remapping vector is sorted by reaction type after every transport iteration using a high-efficiency parallel radix sort, which serves to keep the
Vannuccini, Elisa; Paccagnini, Eugenio; Cantele, Francesca; Gentile, Mariangela; Dini, Daniele; Fino, Federica; Diener, Dennis; Mencarelli, Caterina; Lupetti, Pietro
2016-05-15
Intraflagellar transport (IFT) is responsible for the bidirectional trafficking of molecular components required for the elongation and maintenance of eukaryotic cilia and flagella. Cargo is transported by IFT 'trains', linear rows of multiprotein particles moved by molecular motors along the axonemal doublets. We have previously described two structurally distinct categories of 'long' and 'short' trains. Here, we analyse the relative number of these trains throughout flagellar regeneration and show that long trains are most abundant at the beginning of flagellar growth whereas short trains gradually increase in number as flagella elongate. These observations are incompatible with the previous hypothesis that short trains are derived solely from the reorganization of long trains at the flagellar tip. We demonstrate with electron tomography the existence of two distinct ultrastructural organizations for the short trains, we name these 'narrow' and 'wide', and provide the first 3D model of the narrow short trains. These trains are characterized by tri-lobed units, which repeat longitudinally every 16 nm and contact protofilament 7 of the B-tubule. Functional implications of the new structural evidence are discussed. PMID:27044756
NASA Astrophysics Data System (ADS)
Rona, Michael; Gasser, Guy; Negev, Ido; Pankratov, Irena; Elhanany, Sara; Lev, Ovadia; Gvirtzman, Haim
2014-05-01
Wastewater recharge facilities are often used as a final water treatment before the discharge to the sea or before water reclamation. These facilities are often located in active aquifers that supply drinking water. Thus, leakage from the water recharge facility and gradual expansion of the underground wastewater plume are of considerable health concern. Hydrological modeling of water recharge systems are widely used as operational and predictive tools. These models rely on distributed water head monitoring and at least one chemical or physical tracer to model solutes' transport. Refractory micropollutants have proven useful in qualitative identification of pollution leakages and for quantification of pollution to a specific site near water recharge facilities. However, their usefulness as tracers for hydrological modeling is still questionable. In this article, we describe a long term, 3-D hydraulic model of a large-scale wastewater effluents recharge system in which a combination of chloride and a refractory micropollutant, carbamazepine is used to trace the solute transport. The combination of the two tracers provides the model with the benefits of the high specificity of the carbamazepine and the extensive historic data base that is available for chloride. The model predicts westward expansion of the pollution plume, whereas a standing front is formed at the east. These trends can be confirmed by the time trace of the carbamazepine concentrations at specific locations. We show that the combination of two tracers accounts better (at least at some locations) for the evolution of the pollution plume than a model based on chloride or carbamazepine alone.
NASA Astrophysics Data System (ADS)
Wehrer, Markus; Slater, Lee
2015-04-01
flow fraction was observed to be independent of precipitation rate. This suggests the presence of a fingering process driven by textural heterogeneities. As a consequence, preferential transport of the conservative and the reactive tracer also occurred. We found that 3D ERT can serve to quantitatively characterize shape measures of both tracer breakthroughs and water content dynamics. In particular, shape measures influenced by the advective propagation of the tracer peak, like mean velocity and normalized first central moment, are highly correlated between ERT data and validation data (consisting of tracer measurements in seepage water samples). Using shape measures proved to be advantageous over interpretation of ERT data with spatially uncertain petrophysical functions for the characterization of heterogeneous flow and transport. Consequently, for future applications of ERT in soil hydrological modeling, the use of temporal moments is recommended.
Holford, D.J.
1994-01-01
This document is a user`s manual for the Rn3D finite element code. Rn3D was developed to simulate gas flow and radon transport in variably saturated, nonisothermal porous media. The Rn3D model is applicable to a wide range of problems involving radon transport in soil because it can simulate either steady-state or transient flow and transport in one-, two- or three-dimensions (including radially symmetric two-dimensional problems). The porous materials may be heterogeneous and anisotropic. This manual describes all pertinent mathematics related to the governing, boundary, and constitutive equations of the model, as well as the development of the finite element equations used in the code. Instructions are given for constructing Rn3D input files and executing the code, as well as a description of all output files generated by the code. Five verification problems are given that test various aspects of code operation, complete with example input files, FORTRAN programs for the respective analytical solutions, and plots of model results. An example simulation is presented to illustrate the type of problem Rn3D is designed to solve. Finally, instructions are given on how to convert Rn3D to simulate systems other than radon, air, and water.
Crandall, K.R.
1987-08-01
TRACE 3-D is an interactive beam-dynamics program that calculates the envelopes of a bunched beam, including linear space-charge forces, through a user-defined transport system. TRACE 3-D provides an immediate graphics display of the envelopes and the phase-space ellipses and allows nine types of beam-matching options. This report describes the beam-dynamics calculations and gives detailed instruction for using the code. Several examples are described in detail.
Unsteady Analysis of Particle Transport and Deposition in the Human Lung: A Hybrid 3D/0D Model
NASA Astrophysics Data System (ADS)
Haworth, Daniel C.; Kunz, Robert F.; Leemhuis, Laura S.; Banks, Syreeta S.; Kriete, Andres
2003-11-01
Three-dimensional CFD meshes including up the sixteenth generation of branching in a human tracheo-bronchial tree have been generated from surface data extracted using novel high-resolution bio-medical imaging and rendering methods. A zero-dimensional model for the deeper generations has been coupled with the three-dimensional model at each of the truncated branches. The 0D model imposes a time-varying volume to simulate realistic breathing cycles; it also includes a simple model for particle deposition. The resulting hybrid 3D/0D model has been exercised to compute the transport and deposition rates of particles of different sizes through full breathing cycles. Results are compared to earlier steady-flow CFD results, to results obtained using one-dimensional functional models of the human lung, and to experimental and modeling results for idealized branching-duct configurations. The aim of the research is to develop a virtual human respiratory system that can be used to address issues in pulmonary health in
Computation of Flow Over a Drag Prediction Workshop Wing/Body Transport Configuration Using CFL3D
NASA Technical Reports Server (NTRS)
Rumsey, Christopher L.; Biedron, Robert T.
2001-01-01
A Drag Prediction Workshop was held in conjunction with the 19th AIAA Applied Aerodynamics Conference in June 2001. The purpose of the workshop was to assess the prediction of drag by computational methods for a wing/body configuration (DLR-F4) representative of subsonic transport aircraft. This report details computed results submitted to this workshop using the Reynolds-averaged Navier-Stokes code CFL3D. Two supplied grids were used: a point-matched 1-to-1 multi-block grid, and an overset multi-block grid. The 1-to-1 grid, generally of much poorer quality and with less streamwise resolution than the overset grid, is found to be too coarse to adequately resolve the surface pressures. However, the global forces and moments are nonetheless similar to those computed using the overset grid. The effect of three different turbulence models is assessed using the 1-to-1 grid. Surface pressures are very similar overall, and the drag variation due to turbulence model is 18 drag counts. Most of this drag variation is in the friction component, and is attributed in part to insufficient grid resolution of the 1-to-1 grid. The misnomer of 'fully turbulent' computations is discussed; comparisons are made using different transition locations and their effects on the global forces and moments are quantified. Finally, the effect of two different versions of a widely used one-equation turbulence model is explored.
Thoma, C.; Welch, D.R.; Yu, S.S.; Henestroza, E.; Roy, P.K.; Eylon, S.; Gilson, E.P.
2004-09-22
The Neutralized Transport Experiment (NTX) at Lawrence Berkeley National Laboratory has been designed to study the final focus and neutralization of high perveance ion beams for applications in heavy ion fusion (HIF) and high energy density physics (HEDP) experiments. Pre-formed plasmas in the last meter before the target of the scaled experiment provide a source of electrons which neutralize the ion current and prevent the space-charge induced spreading of the beam spot. NTX physics issues are discussed and experimental data is analyzed and compared with 3D particle-in-cell simulations. Along with detailed target images, 4D phase-space data of the NTX at the entrance of the neutralization region has been acquired. This data is used to provide a more accurate beam distribution with which to initialize the simulation. Previous treatments have used various idealized beam distributions which lack the detailed features of the experimental ion beam images. Simulation results are compared with NTX experimental measurements for 250 keV K{sup +} ion beams with dimensionless perveance of 1-7 x 10{sup -4}. In both simulation and experiment, the deduced beam charge neutralization is close to the predicted maximum value.
NASA Astrophysics Data System (ADS)
Moustafa, Salli; Févotte, François; Lathuilière, Bruno; Plagne, Laurent
2014-06-01
The past few years have been marked by a noticeable increase in the interest in 3D whole-core heterogeneous deterministic neutron transport solvers for reference calculations. Due to the extremely large problem sizes tackled by such solvers, they need to use adapted numerical methods and need to be efficiently implemented to take advantage of the full computing power of modern systems. As for numerical methods, one possible approach consists in iterating over resolutions of 2D and 1D MOC problems by taking advantage of prismatic geometries. The MICADO solver, developed at EDF R&D, is a parallel implementation of such a method in distributed and shared memory systems. However it is currently unable to use SIMD vectorization to leverage the full computing power of modern CPUs. In this paper, we describe our first effort to support vectorization in MICADO, typically targeting Intel© SSE CPUs. Both the 2D and 1D algorithms are vectorized, allowing for high expected speedups for the whole spatial solver. We present benchmark computations, which show nearly optimal speedups for our vectorized implementation on the TAKEDA case.
NASA Astrophysics Data System (ADS)
Wu, Dongwei
In recent years, Mainland China, and in particular the industrial hotbed of the Pearl River Delta (PRD) has experienced an increasingly serious problem of high concentrations of airborne particulate matter. Following the tightening-up of China's air quality policies in recent years, and with especially fine particles now added to a new air quality objective, the identification of major source regions and major types of pollutants has become critically important. In this study, a source-oriented method (Particulate Source Apportionment Technology: PSAT) implemented in 3-D Comprehensive Air Quality Model (CAMx), has been applied to analyze how different emission activities impact fine particle concentration in the PRD region. By using this method, a detailed source region and emission category contribution matrix is derived for all regions within the Hong Kong/PRD region. Source appointment results shows that, in summer and spring time, emissions inside PRD region are the major fine particle sources, contribution 70.7% (11.2 mug/m3) and 52.5% (13.1 mug/m3) to the total figure. Super-regional transports are found to be significant in autumn and winter, contribution 58.5% (20.2 mug/m3) and 64.6% (27.8 mug/m3) of the total fine particles in PRD and Hong Kong region. Another important cause of high PM levels has been the transport of fine particles between cities within the PRD region, with three different regions selected for detailed analysis. Results show that mobile vehicle and industry emission are the two major sources for fine particles. Meanwhile, over the same period in Hong Kong, marine proved to be another very significant source of particle pollutant in addition to the significant impact from motor vehicle. Results show that for the Hong Kong/PRD region local reduction of mobile sources and collaboration between different areas could have succeeded in alleviating the air pollution problem.
NASA Astrophysics Data System (ADS)
Bergmann, Ryan
Graphics processing units, or GPUs, have gradually increased in computational power from the small, job-specific boards of the early 1990s to the programmable powerhouses of today. Compared to more common central processing units, or CPUs, GPUs have a higher aggregate memory bandwidth, much higher floating-point operations per second (FLOPS), and lower energy consumption per FLOP. Because one of the main obstacles in exascale computing is power consumption, many new supercomputing platforms are gaining much of their computational capacity by incorporating GPUs into their compute nodes. Since CPU-optimized parallel algorithms are not directly portable to GPU architectures (or at least not without losing substantial performance), transport codes need to be rewritten to execute efficiently on GPUs. Unless this is done, reactor simulations cannot take full advantage of these new supercomputers. WARP, which can stand for ``Weaving All the Random Particles,'' is a three-dimensional (3D) continuous energy Monte Carlo neutron transport code developed in this work as to efficiently implement a continuous energy Monte Carlo neutron transport algorithm on a GPU. WARP accelerates Monte Carlo simulations while preserving the benefits of using the Monte Carlo Method, namely, very few physical and geometrical simplifications. WARP is able to calculate multiplication factors, flux tallies, and fission source distributions for time-independent problems, and can run in both criticality or fixed source modes. WARP can transport neutrons in unrestricted arrangements of parallelepipeds, hexagonal prisms, cylinders, and spheres. WARP uses an event-based algorithm, but with some important differences. Moving data is expensive, so WARP uses a remapping vector of pointer/index pairs to direct GPU threads to the data they need to access. The remapping vector is sorted by reaction type after every transport iteration using a high-efficiency parallel radix sort, which serves to keep the
A model of CO-CH4 global transport/chemistry. I - Chemistry model
NASA Technical Reports Server (NTRS)
Peters, L. K.; Kitada, T.
1980-01-01
A simplified chemistry model was developed to incorporate the CO-CH4 chemistry into the global transport model of these compounds. CO is important because of its effects on atmospheric chemistry and is partly responsible for controlling the hydroxyl radical (OH) concentration in the troposphere. The model includes the photodissociation rate coefficients expressed as functions of solar zenith angle and altitude, and it was applied to determine the sensitivity of the OH concentration to trace gaseous species, such as NOx, O3, and H2O. Also, the concentrations and diurnal variations of OH and HO2, and the contribution of individual reactions to OH generation and consumption were calculated.
Almeida, P. G. C.; Benilov, M. S.
2013-10-15
The work is aimed at advancing the multiple steady-state solutions that have been found recently in the theory of direct current (DC) glow discharges. It is shown that an account of detailed plasma chemistry and non-locality of electron transport and kinetic coefficients results in an increase of the number of multiple solutions but does not change their pattern. Multiple solutions are shown to exist for discharges in argon and helium provided that discharge pressure is high enough. This result indicates that self-organization in DC glow microdischarges can be observed not only in xenon, which has been the case until recently, but also in other plasma-producing gases; a conclusion that has been confirmed by recent experiments. Existence of secondary bifurcations can explain why patterns of spots grouped in concentric rings, observed in the experiment, possess in many cases higher number of spots in outer rings than in inner ones.
Davidenko, Natalia; Schuster, Carlos F; Bax, Daniel V; Farndale, Richard W; Hamaia, Samir; Best, Serena M; Cameron, Ruth E
2016-10-01
Studies of cell attachment to collagen-based materials often ignore details of the binding mechanisms-be they integrin-mediated or non-specific. In this work, we have used collagen and gelatin-based substrates with different dimensional characteristics (monolayers, thin films and porous scaffolds) in order to establish the influence of composition, crosslinking (using carbodiimide) treatment and 2D or 3D architecture on integrin-mediated cell adhesion. By varying receptor expression, using cells with collagen-binding integrins (HT1080 and C2C12 L3 cell lines, expressing α2β1, and Rugli expressing α1β1) and a parent cell line C2C12 with gelatin-binding receptors (αvβ3 and α5β1), the nature of integrin binding sites was studied in order to explain the bioactivity of different protein formulations. We have shown that alteration of the chemical identity, conformation and availability of free binding motifs (GxOGER and RGD), resulting from addition of gelatin to collagen and crosslinking, have a profound effect on the ability of cells to adhere to these formulations. Carbodiimide crosslinking ablates integrin-dependent cell activity on both two-dimensional and three-dimensional architectures while the three-dimensional scaffold structure also leads to a high level of non-specific interactions remaining on three-dimensional samples even after a rigorous washing regime. This phenomenon, promoted by crosslinking, and attributed to cell entrapment, should be considered in any assessment of the biological activity of three-dimensional substrates. Spreading data confirm the importance of integrin-mediated cell engagement for further cell activity on collagen-based compositions. In this work, we provide a simple, but effective, means of deconvoluting the effects of chemistry and dimensional characteristics of a substrate, on the cell activity of protein-derived materials, which should assist in tailoring their biological properties for specific tissue engineering
Using Transport Diagnostics to Understand Chemistry Climate Model Ozone Simulations
NASA Technical Reports Server (NTRS)
Strahan, S. E.; Douglass, A. R.; Stolarski, R. S.; Akiyoshi, H.; Bekki, S.; Braesicke, P.; Butchart, N.; Chipperfield, M. P.; Cugnet, D.; Dhomse, S.; Frith, S. M.; Gettleman, A.; Hardiman, S. C.; Kinnison, D. E.; Lamarque, J.-F.; Mancini, E.; Marchand, M.; Michou, M.; Morgenstern, O.; Nakamura, T.; Olivie, D.; Pawson, S.; Pitari, G.; Plummer, D. A.; Pyle, J. A.
2010-01-01
We demonstrate how observations of N2O and mean age in the tropical and midlatitude lower stratosphere (LS) can be used to identify realistic transport in models. The results are applied to 15 Chemistry Climate Models (CCMs) participating in the 2010 WMO assessment. Comparison of the observed and simulated N2O/mean age relationship identifies models with fast or slow circulations and reveals details of model ascent and tropical isolation. The use of this process-oriented N2O/mean age diagnostic identifies models with compensating transport deficiencies that produce fortuitous agreement with mean age. We compare the diagnosed model transport behavior with a model's ability to produce realistic LS O3 profiles in the tropics and midlatitudes. Models with the greatest tropical transport problems show the poorest agreement with observations. Models with the most realistic LS transport agree more closely with LS observations and each other. We incorporate the results of the chemistry evaluations in the SPARC CCMVal Report (2010) to explain the range of CCM predictions for the return-to-1980 dates for global (60 S-60 N) and Antarctic column ozone. Later (earlier) Antarctic return dates are generally correlated to higher (lower) vortex Cl(sub y) levels in the LS, and vortex Cl(sub y) is generally correlated with the model's circulation although model Cl(sub y) chemistry or Cl(sub y) conservation can have a significant effect. In both regions, models that have good LS transport produce a smaller range of predictions for the return-to-1980 ozone values. This study suggests that the current range of predicted return dates is unnecessarily large due to identifiable model transport deficiencies.
NASA Astrophysics Data System (ADS)
Atzeni, Stefano; Marocchino, Alberto; Schiavi, Angelo
2016-03-01
Accurate descriptions of laser power coupling to the plasma and electron energy transport are crucial for designing shock-ignition targets and assessing their robustness (in particular with regard to laser and positioning errors). To this purpose, the 2D DUED laser fusion code has been improved with the inclusion of a 3D laser ray-tracing scheme and a model for non-local electron transport. 2D simulations with the upgraded code are presented; the dependence of the fusion yield vs target displacement is studied. Two different irradiation configurations are considered.
NASA Astrophysics Data System (ADS)
Shashkin, Vladimir; Fadeev, Rostislav; Tolstykh, Mikhail
2016-01-01
The article presents conservative cascade scheme using reduced grid (CCS-RG) - a finite volume semi-Lagrangian (FVSL) algorithm for numerical solution of 3D advection equation on the sphere. The CCS-RG is based on the cascade approach that allows to split 3D advected quantity mass remapping between the Lagrangian and Eulerian grids onto 3 1D remappings. Another feature is using a quasi-uniform spaced reduced latitude-longitude grid on the sphere. The scheme is inherently mass-conservative, monotonic and stable with large time-steps. The CCS-RG performance is tested with the advection cases from the Dynamical Core Model Intercomparison Project test suite. The impact of the reduced grids and two different monotonic filters on the solution is investigated. The comparison with the results obtained by other schemes proves competitive accuracy of CCS-RG. In most cases, the numerical solution obtained with various reduced grids is as accurate as the regular grid solution.
NASA Astrophysics Data System (ADS)
Hamer, P. D.; Marécal, V.; Hossaini, R.; Pirre, M.; Warwick, N.; Chipperfield, M.; Samah, A. A.; Harris, N.; Robinson, A.; Quack, B.; Engel, A.; Krüger, K.; Atlas, E.; Subramaniam, K.; Oram, D.; Leedham, E.; Mills, G.; Pfeilsticker, K.; Sala, S.; Keber, T.; Bönisch, H.; Peng, L. K.; Nadzir, M. S. M.; Lim, P. T.; Mujahid, A.; Anton, A.; Schlager, H.; Catoire, V.; Krysztofiak, G.; Fühlbrügge, S.; Dorf, M.; Sturges, W. T.
2013-08-01
We carry out a case study of the transport and chemistry of bromoform and its product gases (PGs) in a sea breeze driven convective episode on 19 November 2011 along the North West coast of Borneo during the "Stratospheric ozone: Halogen Impacts in a Varying Atmosphere" (SHIVA) campaign. We use ground based, ship, aircraft and balloon sonde observations made during the campaign, and a 3-D regional online transport and chemistry model capable of resolving clouds and convection explicitly that includes detailed bromine chemistry. The model simulates the temperature, wind speed, wind direction fairly well for the most part, and adequately captures the convection location, timing, and intensity. The simulated transport of bromoform from the boundary layer up to 12 km compares well to aircraft observations to support our conclusions. The model makes several predictions regarding bromine transport from the boundary layer to the level of convective detrainment (11 to 12 km). First, the majority of bromine undergoes this transport as bromoform. Second, insoluble organic bromine carbonyl species are transported to between 11 and 12 km, but only form a small proportion of the transported bromine. Third, soluble bromine species, which include bromine organic peroxides, hydrobromic acid (HBr), and hypobromous acid (HOBr), are washed out efficiently within the core of the convective column. Fourth, insoluble inorganic bromine species (principally Br2) are not washed out of the convective column, but are also not transported to the altitude of detrainment in large quantities. We expect that Br2 will make a larger relative contribution to the total vertical transport of bromine atoms in scenarios with higher CHBr3 mixing ratios in the boundary layer, which have been observed in other regions. Finally, given the highly detailed description of the chemistry, transport and washout of bromine compounds within our simulations, we make a series of recommendations about the physical and
Moridis, G J; Hu, Q; Wu, Y-S; Bodvarsson, G S
2003-02-01
The U.S. Department of Energy (DOE) is actively investigating the technical feasibility of permanent disposal of high-level nuclear waste in a repository to be situated in the unsaturated zone (UZ) at Yucca Mountain (YM), Nevada. In this study we investigate, by means of numerical simulation, the transport of radioactive colloids under ambient conditions from the potential repository horizon to the water table. The site hydrology and the effects of the spatial distribution of hydraulic and transport properties in the Yucca Mountain subsurface are considered. The study of migration and retardation of colloids accounts for the complex processes in the unsaturated zone of Yucca Mountain, and includes advection, diffusion, hydrodynamic dispersion, kinetic colloid filtration, colloid straining, and radioactive decay. The results of the study indicate that the most important factors affecting colloid transport are the subsurface geology and site hydrology, i.e., the presence of faults (they dominate and control transport), fractures (the main migration pathways), and the relative distribution of zeolitic and vitric tuffs. The transport of colloids is strongly influenced by their size (as it affects diffusion into the matrix, straining at hydrogeologic unit interfaces, and transport velocity) and by the parameters of the kinetic-filtration model used for the simulations. Arrival times at the water table decrease with an increasing colloid size because of smaller diffusion, increased straining, and higher transport velocities. The importance of diffusion as a retardation mechanism increases with a decreasing colloid size, but appears to be minimal in large colloids. PMID:12504362
Carafa, R; Marinov, D; Dueri, S; Wollgast, J; Ligthart, J; Canuti, E; Viaroli, P; Zaldívar, J M
2006-10-01
Sacca di Goro is a shallow coastal microtidal lagoon with a surface area of 26 km2, and an average depth of about 1.5m. Fresh water pollutant loads from Po River branches and several drainage canals lead to anthropogenic eutrophication, frequent summer anoxia crises and chemical contamination. Such events not only affect the lagoon ecosystem but also cause serious economic losses, the lagoon being the second largest producer of clams in Italy. The present work aims at using a fate model coupled with COHERENS 3D hydrodynamic model to simulate and to explain the spatial distribution and temporal variations of s-triazines herbicides in the Sacca di Goro lagoon. The simulation results of spatial and temporal dynamic behaviour of atrazine, simazine and terbuthylazine have been compared with experimental data obtained during an annual monitoring programme. PMID:16643962
NASA Astrophysics Data System (ADS)
Üpping, J.; Bielawny, A.; Lee, S.; Knez, M.; Carius, R.; Wehrspohn, R. B.
2009-08-01
The progress of 3D photonic intermediate reflectors for micromorph silicon tandem cells towards a first prototype cell is presented. Intermediate reflectors enhance the absorption of spectrally-selected light in the top cell and decrease the current mismatch between both junctions. A numerical method to predict filter properties for optimal current matching is presented. Our device is an inverted opal structure made of ZnO and fabricated using self-organized nanoparticles and atomic layer deposition for conformal coating. In particular, the influence of ZnO-doping and replicated cracks during drying of the opal is discussed with respect to conductivity and optical properties. A first prototype is compared to a state-of-the-art reference cell.
Dimensionality-dependent charge transport in close-packed nanoparticle arrays: from 2D to 3D
Wang, Ying; Duan, Chao; Peng, Lianmao; Liao, Jianhui
2014-01-01
Charge transport properties in close-packed nanoparticle arrays with thickness crossing over from two dimensions to three dimensions have been studied. The dimensionality transition of nanoparticle arrays was realized by continually printing spatially well-defined nanoparticle monolayers on top of the device in situ. The evolution of charge transport properties depending on the dimensionality has been investigated in both the Efros-Shaklovskii variable-range-hopping (ES-VRH) (low temperature) regime and the sequential hopping (SH) (medium temperature) regime. We find that the energy barriers to transport decrease when the thickness of nanoparticle arrays increases from monolayer to multilayers, but start to level off at the thickness of 4–5 monolayers. The energy barriers are characterized by the coefficient βD at ES-VRH regime and the activation energy Ea at SH regime. Moreover, a turning point for the temperature coefficient of conductance was observed in multilayer nanoparticle arrays at high temperature, which is attributed to the increasing mobility with decreasing temperature of hopping transport in three dimensions. PMID:25523836
Modeling of tungsten transport in the linear plasma device PSI-2 with the 3D Monte-Carlo code ERO
NASA Astrophysics Data System (ADS)
Marenkov, E.; Eksaeva, A.; Borodin, D.; Kirschner, A.; Laengner, M.; Kurnaev, V.; Kreter, A.; Coenen, J. W.; Rasinski, M.
2015-08-01
The ERO code was modified for modeling of plasma-surface interactions and impurities transport in the PSI-2 installation. Results of experiments on tungsten target irradiation with argon plasma were taken as a benchmark for the new version of the code. Spectroscopy data modeled with the code are in good agreement with experimental ones. Main factors contributing to observed discrepancies are discussed.
Dimensionality-dependent charge transport in close-packed nanoparticle arrays: from 2D to 3D.
Wang, Ying; Duan, Chao; Peng, Lianmao; Liao, Jianhui
2014-01-01
Charge transport properties in close-packed nanoparticle arrays with thickness crossing over from two dimensions to three dimensions have been studied. The dimensionality transition of nanoparticle arrays was realized by continually printing spatially well-defined nanoparticle monolayers on top of the device in situ. The evolution of charge transport properties depending on the dimensionality has been investigated in both the Efros-Shaklovskii variable-range-hopping (ES-VRH) (low temperature) regime and the sequential hopping (SH) (medium temperature) regime. We find that the energy barriers to transport decrease when the thickness of nanoparticle arrays increases from monolayer to multilayers, but start to level off at the thickness of 4-5 monolayers. The energy barriers are characterized by the coefficient βD at ES-VRH regime and the activation energy Ea at SH regime. Moreover, a turning point for the temperature coefficient of conductance was observed in multilayer nanoparticle arrays at high temperature, which is attributed to the increasing mobility with decreasing temperature of hopping transport in three dimensions. PMID:25523836
Dimensionality-dependent charge transport in close-packed nanoparticle arrays: from 2D to 3D
NASA Astrophysics Data System (ADS)
Wang, Ying; Duan, Chao; Peng, Lianmao; Liao, Jianhui
2014-12-01
Charge transport properties in close-packed nanoparticle arrays with thickness crossing over from two dimensions to three dimensions have been studied. The dimensionality transition of nanoparticle arrays was realized by continually printing spatially well-defined nanoparticle monolayers on top of the device in situ. The evolution of charge transport properties depending on the dimensionality has been investigated in both the Efros-Shaklovskii variable-range-hopping (ES-VRH) (low temperature) regime and the sequential hopping (SH) (medium temperature) regime. We find that the energy barriers to transport decrease when the thickness of nanoparticle arrays increases from monolayer to multilayers, but start to level off at the thickness of 4-5 monolayers. The energy barriers are characterized by the coefficient βD at ES-VRH regime and the activation energy Ea at SH regime. Moreover, a turning point for the temperature coefficient of conductance was observed in multilayer nanoparticle arrays at high temperature, which is attributed to the increasing mobility with decreasing temperature of hopping transport in three dimensions.
Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; Gable, Carl W.; Karra, Satish
2015-09-16
The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates massmore » balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.« less
Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; Gable, Carl W.; Karra, Satish
2015-09-16
The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates mass balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.
Yue, Dan; Lu, Wei; Jin, Lin; Li, Chunyang; Luo, Wen; Wang, Mengnan; Wang, Zhenling; Hao, Jianhua
2014-11-21
Lanthanide doped ZnO mushroom-like 3D hierarchical structures have been fabricated by polyol-mediated method and characterized by various microstructural and optical techniques. The results indicate that the as-prepared ZnO:Ln(3+) (Ln = Tb, Eu) samples have a hexagonal phase structure and possess a mushroom-like 3D hierarchical morphology. The length of the whole mushroom from stipe bottom to pileus top is about 1.0 μm, and the diameters of pileus and stipe are about 0.8 μm and 0.4 μm, respectively. It is found that the flow of N2 is the key parameter for the formation of the novel ZnO structure and the addition of (NH4)2HPO4 has a prominent effect on the phase structure and the growth of mushroom-like morphology. The potential mechanism of forming this morphology is proposed. The pileus of the formed mushroom is assembled by several radial ZnO:Ln(3+) nanorods, whereas the stipe is composed of over layered ZnO:Ln(3+) nanosheets. Moreover, asymmetrical I-V characteristic curves of ZnO:Ln(3+) mushrooms indicate that the texture composition of the 3D hierarchical morphology might lead to the asymmetrical transport behavior of electrical conductivity. Lanthanide doped ZnO samples can exhibit red or green emission under the excitation of UV light. PMID:25293373
NASA Astrophysics Data System (ADS)
Zurek, A. J.; Witczak, S.; Dulinski, M.; Wachniew, P.; Rozanski, K.; Kania, J.; Postawa, A.; Karczewski, J.; Moscicki, W. J.
2014-08-01
A dedicated study was launched in 2010 with the main aim to better understand the functioning of groundwater dependent terrestrial ecosystem (GDTE) located in southern Poland. The GDTE consists of a valuable forest stand (Niepolomice Forest) and associated wetland (Wielkie Bloto fen). A wide range of tools (environmental tracers, geochemistry, geophysics, 3-D flow and transport modeling) was used. The research was conducted along three major directions: (i) quantification of the dynamics of groundwater flow in various parts of the aquifer associated with GDTE, (ii) quantification of the degree of interaction between the GDTE and the aquifer, and (iii) 3-D modeling of groundwater flow in the vicinity of the studied GDTE and quantification of possible impact of enhanced exploitation of the aquifer on the status of GDTE. Environmental tracer data (tritium, stable isotopes of water) strongly suggest that upward leakage of the aquifer contributes significantly to the present water balance of the studied wetland and associated forest. Physico-chemical parameters of water (pH, conductivity, Na / Cl ratio) confirm this notion. Model runs indicate that prolonged groundwater abstraction through the newly-established network of water supply wells, conducted at maximum permitted capacity (ca. 10 000 m3 d-1), may trigger drastic changes in the ecosystem functioning, eventually leading to its degradation.
NASA Technical Reports Server (NTRS)
Fung, Inez Y.; Tucker, C. J.; Prentice, Katharine C.
1985-01-01
The 'normalized difference vegetation indices' (NVI) derived from AVHRR radiances are combined with field data of soil respiration and a global map of net primary productivity to prescribe, for the globe, the seasonal exchange of CO2 between the atmosphere and the terrestrial biosphere. The monthly fluxes of CO2 thus obtained are used as inputs to a 3-D tracer transport model which uses winds generated by a 3-D atmospheric general circulation model to advect CO2 as an inert constituent. Analysis of the 3-D model results shows reasonable agreement between the simulated and observed annual cycles of atmospheric CO2 at the locations of the remote monitoring stations. The application is shown of atmospheric CO2 distributions to calibrate the NVI in terms of carbon fluxes. The approach suggests that the NVI may be used to provide quantitative information about long term and global scale variations of photosynthetic activity and of atmospheric CO2 concentrations provided that variations in the atmospheric circulation and in atmospheric composition are known.
Vandersall, K S; Murty, S S; Chidester, S K; Forbes, J W; Garcia, F; Greenwood, D W; Tarver, C M
2003-07-02
The Steven Impact Test and associated modeling offer valuable practical predictions for evaluating numerous safety scenarios involving low velocity impact of energetic materials by different projectile geometries. One such scenario is the impact of energetic material by a transportation hook during shipping, which offers complexity because of the irregular hook projectile shape. Experiments were performed using gauged Steven Test targets with PBX9404 impacted by a transportation hook projectile to compliment previous non-gauged experiments that established an impact threshold of approximately 69 m/s. Modeling of these experiments was performed with LS-DYNA code using an Ignition and Growth reaction criteria with a friction term. Comparison of the experiment to the model shows reasonable agreement with some details requiring more attention. The experimental results (including carbon resistor gauge records), model calculations, and a discussion of the dominant reaction mechanisms in light of comparisons between experiment and model will be presented.
NASA Astrophysics Data System (ADS)
Qin, G.; Wang, Y.
2014-12-01
In solar cycle 24, solar energetic particles (SEPs) are measured by multi-spacecraft at different locations, e.g., STEREO A and B, and ACE. Interplanetary observers located on the opposite sides of the Sun may or may not be connected to the ICME shock by the IMF. And the connected observers may also be connected to different parts of an ICME. In this work, we will numerically solve the Fokker-Planck transport equation to get the fluxes of SEPs accelerated by ICME shocks. In addition, we will compare our simulation results with SEP observations of different spacecraft, e.g., STEREO A and B, and ACE, during solar cycle 24. The simulation and data analysis together can improve our understanding of SEPs acceleration and transport mechanism.
Cheng, Gang; Markenscoff, Pauline; Zygourakis, Kyriacos
2009-01-01
Abstract To provide theoretical guidance for the design and in vitro cultivation of bioartificial tissues, we have developed a multiscale computational model that can describe the complex interplay between cell population and mass transport dynamics that governs the growth of tissues in three-dimensional scaffolds. The model has three components: a transient partial differential equation for the simultaneous diffusion and consumption of a limiting nutrient; a cellular automaton describing cell migration, proliferation, and collision; and equations that quantify how the varying nutrient concentration modulates cell division and migration. The hybrid discrete-continuous model was parallelized and solved on a distributed-memory multicomputer to study how transport limitations affect tissue regeneration rates under conditions encountered in typical bioreactors. Simulation results show that the severity of transport limitations can be estimated by the magnitude of two dimensionless groups: the Thiele modulus and the Biot number. Key parameters including the initial seeding mode, cell migration speed, and the hydrodynamic conditions in the bioreactor are shown to affect not only the overall rate, but also the pattern of tissue growth. This study lays the groundwork for more comprehensive models that can handle mixed cell cultures, multiple nutrients and growth factors, and other cellular processes, such as cell death. PMID:19619455
Voss, Clifford I.; Provost, A.M.
2002-01-01
SUTRA (Saturated-Unsaturated Transport) is a computer program that simulates fluid movement and the transport of either energy or dissolved substances in a subsurface environment. This upgraded version of SUTRA adds the capability for three-dimensional simulation to the former code (Voss, 1984), which allowed only two-dimensional simulation. The code employs a two- or three-dimensional finite-element and finite-difference method to approximate the governing equations that describe the two interdependent processes that are simulated: 1) fluid density-dependent saturated or unsaturated ground-water flow; and 2) either (a) transport of a solute in the ground water, in which the solute may be subject to: equilibrium adsorption on the porous matrix, and both first-order and zero-order production or decay; or (b) transport of thermal energy in the ground water and solid matrix of the aquifer. SUTRA may also be used to simulate simpler subsets of the above processes. A flow-direction-dependent dispersion process for anisotropic media is also provided by the code and is introduced in this report. As the primary calculated result, SUTRA provides fluid pressures and either solute concentrations or temperatures, as they vary with time, everywhere in the simulated subsurface system. SUTRA flow simulation may be employed for two-dimensional (2D) areal, cross sectional and three-dimensional (3D) modeling of saturated ground-water flow systems, and for cross sectional and 3D modeling of unsaturated zone flow. Solute-transport simulation using SUTRA may be employed to model natural or man-induced chemical-species transport including processes of solute sorption, production, and decay. For example, it may be applied to analyze ground-water contaminant transport problems and aquifer restoration designs. In addition, solute-transport simulation with SUTRA may be used for modeling of variable-density leachate movement, and for cross sectional modeling of saltwater intrusion in
Quantum chemistry and charge transport in biomolecules with superconducting circuits
NASA Astrophysics Data System (ADS)
García-Álvarez, L.; Las Heras, U.; Mezzacapo, A.; Sanz, M.; Solano, E.; Lamata, L.
2016-06-01
We propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects.
Quantum chemistry and charge transport in biomolecules with superconducting circuits.
García-Álvarez, L; Las Heras, U; Mezzacapo, A; Sanz, M; Solano, E; Lamata, L
2016-01-01
We propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects. PMID:27324814
Quantum chemistry and charge transport in biomolecules with superconducting circuits
García-Álvarez, L.; Las Heras, U.; Mezzacapo, A.; Sanz, M.; Solano, E.; Lamata, L.
2016-01-01
We propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects. PMID:27324814
Wilson, Mike R; Hou, Zhanjun; Yang, Si; Polin, Lisa; Kushner, Juiwanna; White, Kathryn; Huang, Jenny; Ratnam, Manohar; Gangjee, Aleem; Matherly, Larry H
2016-04-01
Pemetrexed (PMX) is a 5-substituted pyrrolo[2,3-d]pyrimidine antifolate used for therapy of nonsquamous nonsmall cell lung cancer (NS-NSCLC). PMX is transported by the reduced folate carrier (RFC) and proton-coupled folate transporter (PCFT). Unlike RFC, PCFT is active at acidic pH levels characterizing the tumor microenvironment. By real-time reverse-transcription polymerase chain reaction (RT-PCR) and immunohistochemistry, PCFT transcripts and proteins were detected in primary NS-NSCLC specimens. In six NS-NSCLC cell lines (A549, H1437, H460, H1299, H1650, and H2030), PCFT transcripts and proteins were detected by real-time RT-PCR and western blots, respectively. 6-Substituted pyrrolo[2,3-d]pyrimidine thienoyl antifolates related to PMX [compound 1 (C1) and compound 2 (C2), respectively] are selective substrates for PCFT over RFC. In the NS-NSCLC cell lines, both [(3)H]PMX and [(3)H]C2 were transported by PCFT. C1 and C2 inhibited proliferation of the NS-NSCLC cell lines; A549, H460, and H2030 cells were more sensitive to C1 than to PMX. C1 and C2 inhibited glycinamide ribonucleotide formyltransferase in de novo purine nucleotide biosynthesis. When treated at pH 6.8, which favors PCFT uptake, C1 and C2 inhibited clonogenicity of H460 cells greater than PMX; PMX inhibited clonogenicity more than C1 or C2 at pH 7.2, which favors RFC transport over PCFT. Knockdown of PCFT in H460 cells resulted in decreased [(3)H]PMX and [(3)H]C2 transport and decreased growth inhibition by C1 and C2, and to a lesser extent by PMX. In vivo efficacy of C1 was seen toward H460 tumor xenografts in severe-combined immunodeficient mice. Our results suggest that 6-substituted pyrrolo[2,3-d]pyrimidine thienoyl antifolates offer significant promise for treating NS-NSCLC by selective uptake by PCFT. PMID:26837243
NASA Astrophysics Data System (ADS)
Rmili, W.; Vivet, N.; Chupin, S.; Le Bihan, T.; Le Quilliec, G.; Richard, C.
2016-04-01
As part of development of a new assembly technology to achieve bonding for an innovative silicon carbide (SiC) power device used in harsh environments, the aim of this study is to compare two silver sintering profiles and then to define the best candidate for die attach material for this new component. To achieve this goal, the solder joints have been characterized in terms of porosity by determination of the morphological characteristics of the material heterogeneities and estimating their thermal and electrical transport properties. The three dimensional (3D) microstructure of sintered silver samples has been reconstructed using a focused ion beam scanning electron microscope (FIB-SEM) tomography technique. The sample preparation and the experimental milling and imaging parameters have been optimized in order to obtain a high quality of 3D reconstruction. Volume fractions and volumetric connectivity of the individual phases (silver and voids) have been determined. Effective thermal and electrical conductivities of the samples and the tortuosity of the silver phase have been also evaluated by solving the diffusive transport equation.
Bekar, Kursat B; Azmy, Yousry
2009-01-01
Improved TORT solutions to the 3D transport codes' suite of benchmarks exercise are presented in this study. Preliminary TORT solutions to this benchmark indicate that the majority of benchmark quantities for most benchmark cases are computed with good accuracy, and that accuracy improves with model refinement. However, TORT fails to compute accurate results for some benchmark cases with aspect ratios drastically different from 1, possibly due to ray effects. In this work, we employ the standard approach of splitting the solution to the transport equation into an uncollided flux and a fully collided flux via the code sequence GRTUNCL3D and TORT to mitigate ray effects. The results of this code sequence presented in this paper show that the accuracy of most benchmark cases improved substantially. Furthermore, the iterative convergence problems reported for the preliminary TORT solutions have been resolved by bringing the computational cells' aspect ratio closer to unity and, more importantly, by using 64-bit arithmetic precision in the calculation sequence. Results of this study are also reported.
Combustion chemistry and an evolving transportation fuel environment.
Taatjes, Craig A.
2010-05-01
The world currently faces tremendous energy challenges stemming from the need to curb potentially catastrophic anthropogenic climate change. In addition, many nations, including the United States, recognize increasing political and economic risks associated with dependence on uncertain and limited energy sources. For these and other reasons the chemical composition of transportation fuels is changing, both through introduction of nontraditional fossil sources, such as oil sands-derived fuels in the US stream, and through broader exploration of biofuels. At the same time the need for clean and efficient combustion is leading engine research towards advanced low-temperature combustion strategies that are increasingly sensitive to this changing fuel chemistry, particularly in the areas of pollutant formation and autoignition. I will highlight the new demands that advanced engine technologies and evolving fuel composition place on investigations of fundamental reaction chemistry. I will focus on recent progress in measuring product formation in elementary reactions by tunable synchrotron photoionization, on the elucidation of pressure-dependent effects in the reactions of alkyl and substituted alkyl radicals with O{sub 2}, and on new combined efforts in fundamental combustion chemistry and engine performance studies of novel potential biofuels.
Ishihara, T.; Kim, J.K.; Kobayashi, Y.
1995-10-01
In this study, martensite-ferrite dual phase steel composed of martensite in hard phase and ferrite in soft phase is made 3 dimensions fabric composite for energy transport and the difference in fatigue crack propagation behavior resulting from the structural size is investigated by fracture mechanics and microstructural method. The main results obtained are as follows: (1) the fatigue crack propagation rate is influenced by the ferrite grain size, in other words, in the low {Delta}K region the fatigue crack propagation rate is decreased with decreasing of the grain size but the difference of propagation rate resulted from the structural size is decreased as {Delta}K is increased; (2) the above results are explained by the degree of crack arrest effect of the martensite phase for the fatigue crack propagation depending on the ratio of reversed plastic zone size to the ferrite grain size.
Cullen, D E
1998-11-22
TART98 is a coupled neutron-photon, 3 Dimensional, combinatorial geometry, time dependent Monte Carlo radiation transport code. This code can run on any modern computer. It is a complete system to assist you with input preparation, running Monte Carlo calculations, and analysis of output results. TART98 is also incredibly FAST; if you have used similar codes, you will be amazed at how fast this code is compared to other similar codes. Use of the entire system can save you a great deal of time and energy. TART98 is distributed on CD. This CD contains on-line documentation for all codes included in the system, the codes configured to run on a variety of computers, and many example problems that you can use to familiarize yourself with the system. TART98 completely supersedes all older versions of TART, and it is strongly recommended that users only use the most recent version of TART98 and its data files.
Future impact of transport emissions on the global atmospheric chemistry
NASA Astrophysics Data System (ADS)
Koffi, B.; Szopa, S.; Cozic, A.
2009-04-01
Emissions of air pollutants by road, air traffic and international shipping affect air quality and climate. Besides their effect on the ozone concentration and its related radiative forcing, they also affect the OH-concentration, i.e. the oxidizing capacity of the atmosphere. The pollutants are emitted by the three transport sectors into highly different environments. The O3 and OH potential productions induced by each of these sectors thus differ strongly. These transport emissions are expected to show drastic quantitative and geographic changes in the next decades, because of new emission regulations, increasing mobility, as well as demographic and economic growths. In addition to changes in emissions, significant changes in climate parameters such as H2O, temperature, and dynamics are expected to occur in the future global atmosphere. They will affect the oxidation processes and thereby the changes in the atmospheric concentrations induced by transport emissions. Within the EU-project QUANTIFY (Quantifying the Climate Impact of Global and European Transport Systems) the LMDz-INCA climate-chemistry model was used to estimate the effect of transport emissions on the global atmospheric chemical composition. In a first step, up-to-date emission datasets were used for the transport and non-transport anthropogenic emissions for present (2000) and future (2050, SRES A1b and B1 scenarios) using 2003 nudged meteorology. A strong reduction of the road emissions and a moderate (B1) to high (A1b) increase of the ship and aircraft emissions are expected by the year 2050. As a consequence, the impact of road emissions on ozone is shown to decrease drastically, whereas aviation would become the major transport sources of tropospheric ozone perturbation at global scale. According to the most likely scenario (A1b), the contribution of all transport modes to the ozone column would increase everywhere, reaching up to 13% in some areas such as Asia. In a second step of the study
Qiang, J.; Leitner, D.; Todd, D.S.; Ryne, R.D.
2005-03-15
The superconducting ECR ion source VENUS serves as the prototype injector ion source for the Rare Isotope Accelerator (RIA) driver linac. The RIA driver linac requires a great variety of high charge state ion beams with up to an order of magnitude higher intensity than currently achievable with conventional ECR ion sources. In order to design the beam line optics of the low energy beam line for the RIA front end for the wide parameter range required for the RIA driver accelerator, reliable simulations of the ion beam extraction from the ECR ion source through the ion mass analyzing system are essential. The RIA low energy beam transport line must be able to transport intense beams (up to 10 mA) of light and heavy ions at 30 keV.For this purpose, LBNL is developing the parallel 3D particle-in-cell code IMPACT to simulate the ion beam transport from the ECR extraction aperture through the analyzing section of the low energy transport system. IMPACT, a parallel, particle-in-cell code, is currently used to model the superconducting RF linac section of RIA and is being modified in order to simulate DC beams from the ECR ion source extraction. By using the high performance of parallel supercomputing we will be able to account consistently for the changing space charge in the extraction region and the analyzing section. A progress report and early results in the modeling of the VENUS source will be presented.
NASA Astrophysics Data System (ADS)
Qiang, J.; Leitner, D.; Todd, D. S.; Ryne, R. D.
2005-03-01
The superconducting ECR ion source VENUS serves as the prototype injector ion source for the Rare Isotope Accelerator (RIA) driver linac. The RIA driver linac requires a great variety of high charge state ion beams with up to an order of magnitude higher intensity than currently achievable with conventional ECR ion sources. In order to design the beam line optics of the low energy beam line for the RIA front end for the wide parameter range required for the RIA driver accelerator, reliable simulations of the ion beam extraction from the ECR ion source through the ion mass analyzing system are essential. The RIA low energy beam transport line must be able to transport intense beams (up to 10 mA) of light and heavy ions at 30 keV. For this purpose, LBNL is developing the parallel 3D particle-in-cell code IMPACT to simulate the ion beam transport from the ECR extraction aperture through the analyzing section of the low energy transport system. IMPACT, a parallel, particle-in-cell code, is currently used to model the superconducting RF linac section of RIA and is being modified in order to simulate DC beams from the ECR ion source extraction. By using the high performance of parallel supercomputing we will be able to account consistently for the changing space charge in the extraction region and the analyzing section. A progress report and early results in the modeling of the VENUS source will be presented.
NASA Astrophysics Data System (ADS)
Yue, Dan; Lu, Wei; Jin, Lin; Li, Chunyang; Luo, Wen; Wang, Mengnan; Wang, Zhenling; Hao, Jianhua
2014-10-01
Lanthanide doped ZnO mushroom-like 3D hierarchical structures have been fabricated by polyol-mediated method and characterized by various microstructural and optical techniques. The results indicate that the as-prepared ZnO:Ln3+ (Ln = Tb, Eu) samples have a hexagonal phase structure and possess a mushroom-like 3D hierarchical morphology. The length of the whole mushroom from stipe bottom to pileus top is about 1.0 μm, and the diameters of pileus and stipe are about 0.8 μm and 0.4 μm, respectively. It is found that the flow of N2 is the key parameter for the formation of the novel ZnO structure and the addition of (NH4)2HPO4 has a prominent effect on the phase structure and the growth of mushroom-like morphology. The potential mechanism of forming this morphology is proposed. The pileus of the formed mushroom is assembled by several radial ZnO:Ln3+ nanorods, whereas the stipe is composed of over layered ZnO:Ln3+ nanosheets. Moreover, asymmetrical I-V characteristic curves of ZnO:Ln3+ mushrooms indicate that the texture composition of the 3D hierarchical morphology might lead to the asymmetrical transport behavior of electrical conductivity. Lanthanide doped ZnO samples can exhibit red or green emission under the excitation of UV light.Lanthanide doped ZnO mushroom-like 3D hierarchical structures have been fabricated by polyol-mediated method and characterized by various microstructural and optical techniques. The results indicate that the as-prepared ZnO:Ln3+ (Ln = Tb, Eu) samples have a hexagonal phase structure and possess a mushroom-like 3D hierarchical morphology. The length of the whole mushroom from stipe bottom to pileus top is about 1.0 μm, and the diameters of pileus and stipe are about 0.8 μm and 0.4 μm, respectively. It is found that the flow of N2 is the key parameter for the formation of the novel ZnO structure and the addition of (NH4)2HPO4 has a prominent effect on the phase structure and the growth of mushroom-like morphology. The potential
NASA Astrophysics Data System (ADS)
Le Fouest, Vincent; Chami, Malik; Verney, Romaric
2015-02-01
The export of riverine suspended particulate matter (SPM) in the coastal ocean has major implications for the biogeochemical cycles. In the Mediterranean Sea (France), the Rhone River inputs of SPM into the Gulf of Lion (GoL) are highly variable in time, which severely impedes the assessment of SPM fluxes. The objectives of this study are (i) to investigate the prediction of the land-to-ocean flux of SPM using the complementarity (i.e., synergy) between a hydrodynamic sediment transport model and satellite observations, and (ii) to analyze the spatial distribution of the SPM export. An original approach that combines the MARS-3D model with satellite ocean color data is proposed. Satellite-derived SPM and light penetration depth are used to initialize MARS-3D and to validate its predictions. A sensitivity analysis is performed to quantify the impact of riverine SPM size composition and settling rate on the horizontal export of SPM. The best agreement between the model and the satellite in terms of SPM spatial distribution and export is obtained for two conditions: (i) when the relative proportion of "heavy and fast" settling particles significantly increases relative to the "light and slow" ones, and (ii) when the settling rate of heavy and light SPM increases by fivefold. The synergy between MARS-3D and the satellite data improved the SPM flux predictions by 48% near the Rhone River mouth. Our results corroborate the importance of implementing satellite observations within initialization procedures of ocean models since data assimilation techniques may fail for river floods showing strong seasonal variability.
Evaluation of Tropical Transport in a Global Chemistry and Transport Model
NASA Technical Reports Server (NTRS)
Douglass, Anne R.; DaSilva, A. M.; Lin, S.-J.; Pawson, S.; Rood, R. B.; Bhartia, P. K. (Technical Monitor)
2001-01-01
Observations of constituents from satellite, aircraft and sondes can be utilized to develop diagnostics of various aspects of tropical transport. These include tropical mid-latitude isolation, the seasonal transport from the upper tropical troposphere to the mid-latitude lowermost stratosphere, the seasonal cycle of the tropical total ozone and its variability. These diagnostics will be applied to constituent fields from an off-line chemistry and transport model (CTM) driven by winds from two sources. These are the Finite Volume Community Climate Model (FV-CCM), a general circulation model that uses the NCAR CCM physics and the Lin and Rood dynamical core, and an assimilation system developed by the Data Assimilation Office at the Goddard Space Flight Center that uses the FV-CCM at its core. Signatures of the quasi-biennial oscillation present in the observations will be emphasized to understand differences between the two model transports and the transport inferred from the observations.
Evaluation of Transport in the Lower Tropical Stratosphere in a Global Chemistry and Transport Model
NASA Technical Reports Server (NTRS)
Douglass, Anne R.; Schoeberl, Mark R.; Rood, Richard B.; Pawson, Steven
2002-01-01
A general circulation model (GCM) relies on various physical parameterizations and provides a solution to the atmospheric equations of motion. A data assimilation system (DAS) combines information from observations with a GCM forecast and produces analyzed meteorological fields that represent the observed atmospheric state. An off-line chemistry and transport model (CTM) can use winds and temperatures from a either a GCM or a DAS. The latter application is in common usage for interpretation of observations from various platforms under the assumption that the DAS transport represents the actual atmospheric transport. Here we compare the transport produced by a DAS with that produced by the particular GCM that is combined with observations to produce the analyzed fields. We focus on transport in the tropics and middle latitudes by comparing the age-of-air inferred from observations of SF6 and CO2 with the age-of-air calculated using GCM fields and DAS fields. We also compare observations of ozone, total reactive nitrogen, and methane with results from the two simulations. These comparisons show that DAS fields produce rapid upward tropical transport and excessive mixing between the tropics and middle latitudes. The unrealistic transport produced by the DAS fields may be due to implicit forcing that is required by the assimilation process when there is bias between the GCM forecast and observations that are combined to produce the analyzed fields. For example, the GCM does not produce a quasi-biennial oscillation (QBO). The QBO is present in the analyzed fields because it is present in the observations, and systematic implicit forcing is required by the DAS. Any systematic bias between observations and the GCM forecast used to produce the DAS analysis is likely to corrupt the transport produced by the analyzed fields. Evaluation of transport in the lower tropical stratosphere in a global chemistry and transport model.
Cheng, Candong; Lee, Joon-Ho; Lim, Kim Hwa; Massoud, Hisham Z.; Liu, Qing Huo
2007-01-01
A 3-D quantum transport solver based on the spectral element method (SEM) and perfectly matched layer (PML) is introduced to solve the 3-D Schrödinger equation with a tensor effective mass. In this solver, the influence of the environment is replaced with the artificial PML open boundary extended beyond the contact regions of the device. These contact regions are treated as waveguides with known incident waves from waveguide mode solutions. As the transmitted wave function is treated as a total wave, there is no need to decompose it into waveguide modes, thus significantly simplifying the problem in comparison with conventional open boundary conditions. The spectral element method leads to an exponentially improving accuracy with the increase in the polynomial order and sampling points. The PML region can be designed such that less than −100 dB outgoing waves are reflected by this artificial material. The computational efficiency of the SEM solver is demonstrated by comparing the numerical and analytical results from waveguide and plane-wave examples, and its utility is illustrated by multiple-terminal devices and semiconductor nanotube devices. PMID:18037971
Wang, Lei; Wallace, Adrianne; Raghavan, Sudhir; Deis, Siobhan M.; Wilson, Mike R.; Yang, Si; Polin, Lisa; White, Kathryn; Kushner, Juiwanna; Orr, Steven; George, Christina; O’Connor, Carrie; Hou, Zhanjun; Mitchell-Ryan, Shermaine; Dann, Charles E.; Matherly, Larry H.; Gangjee, Aleem
2016-01-01
2-Amino-4-oxo-6-substituted-pyrrolo[2,3-d]-pyrimidine antifolate thiophene regioisomers of AGF94 (4) with a thienoyl side chain and three-carbon bridge lengths [AGF150 (5) and AGF154 (7)] were synthesized as potential antitumor agents. These analogues inhibited proliferation of Chinese hamster ovary (CHO) sublines expressing folate receptors (FRs) α or β (IC50s < 1 nM) or the proton-coupled folate transporter (PCFT) (IC50 < 7 nM). Compounds 5 and 7 inhibited KB, IGROV1, and SKOV3 human tumor cells at subnanomolar concentrations, reflecting both FRα and PCFT uptake. AGF152 (6) and AGF163 (8), 2,4-diamino-5-substituted-furo[2,3-d]pyrimidine thiophene regioisomers, also inhibited growth of FR-expressing CHO and KB cells. All four analogues inhibited glycinamide ribonucleotide formyltransferase (GARFTase). Crystal structures of human GARFTase complexed with 5 and 7 were reported. In severe combined immunodeficient mice bearing SKOV3 tumors, 7 was efficacious. The selectivity of these compounds for PCFT and for FRα and β over the ubiquitously expressed reduced folate carrier is a paradigm for selective tumor targeting. PMID:26317331
NASA Astrophysics Data System (ADS)
Elshorbany, Y. F.; Duncan, B. N.; Strode, S. A.; Wang, J. S.; Kouatchou, J.
2015-11-01
We present the Efficient CH4-CO-OH chemistry module (ECCOH) that allows for the simulation of the methane, carbon monoxide and hydroxyl radical (CH4-CO-OH) system, within a chemistry climate model, carbon cycle model, or earth system model. The computational efficiency of the module allows many multi-decadal sensitivity simulations of the CH4-CO-OH system, which primarily determines the global atmospheric oxidizing capacity. This capability is important for capturing the nonlinear feedbacks of the CH4-CO-OH system and understanding the perturbations to methane, CO and OH and the concomitant impacts on climate. We implemented the ECCOH chemistry module into the NASA GEOS-5 Atmospheric Global Circulation Model (AGCM), performed multiple sensitivity simulations of the CH4-CO-OH system over two decades, and evaluated the model output with surface and satellite datasets of methane and CO. The favorable comparison of output from the ECCOH chemistry module (as configured in the GEOS-5 AGCM) with observations demonstrates the fidelity of the module for use in scientific research.
NASA Astrophysics Data System (ADS)
Elshorbany, Yasin F.; Duncan, Bryan N.; Strode, Sarah A.; Wang, James S.; Kouatchou, Jules
2016-02-01
We present the Efficient CH4-CO-OH (ECCOH) chemistry module that allows for the simulation of the methane, carbon monoxide, and hydroxyl radical (CH4-CO-OH) system, within a chemistry climate model, carbon cycle model, or Earth system model. The computational efficiency of the module allows many multi-decadal sensitivity simulations of the CH4-CO-OH system, which primarily determines the global atmospheric oxidizing capacity. This capability is important for capturing the nonlinear feedbacks of the CH4-CO-OH system and understanding the perturbations to methane, CO, and OH, and the concomitant impacts on climate. We implemented the ECCOH chemistry module in the NASA GEOS-5 atmospheric global circulation model (AGCM), performed multiple sensitivity simulations of the CH4-CO-OH system over 2 decades, and evaluated the model output with surface and satellite data sets of methane and CO. The favorable comparison of output from the ECCOH chemistry module (as configured in the GEOS-5 AGCM) with observations demonstrates the fidelity of the module for use in scientific research.
NASA Astrophysics Data System (ADS)
Zurek, A. J.; Witczak, S.; Dulinski, M.; Wachniew, P.; Rozanski, K.; Kania, J.; Postawa, A.; Karczewski, J.; Moscicki, W. J.
2015-02-01
Groundwater-dependent ecosystems (GDEs) have important functions in all climatic zones as they contribute to biological and landscape diversity and provide important economic and social services. Steadily growing anthropogenic pressure on groundwater resources creates a conflict situation between nature and man which are competing for clean and safe sources of water. Such conflicts are particularly noticeable in GDEs located in densely populated regions. A dedicated study was launched in 2010 with the main aim to better understand the functioning of a groundwater-dependent terrestrial ecosystem (GDTE) located in southern Poland. The GDTE consists of a valuable forest stand (Niepolomice Forest) and associated wetland (Wielkie Błoto fen). It relies mostly on groundwater from the shallow Quaternary aquifer and possibly from the deeper Neogene (Bogucice Sands) aquifer. In July 2009 a cluster of new pumping wells abstracting water from the Neogene aquifer was set up 1 km to the northern border of the fen. A conceptual model of the Wielkie Błoto fen area for the natural, pre-exploitation state and for the envisaged future status resulting from intense abstraction of groundwater through the new well field was developed. The main aim of the reported study was to probe the validity of the conceptual model and to quantify the expected anthropogenic impact on the studied GDTE. A wide range of research tools was used. The results obtained through combined geologic, geophysical, geochemical, hydrometric and isotope investigations provide strong evidence for the existence of upward seepage of groundwater from the deeper Neogene aquifer to the shallow Quaternary aquifer supporting the studied GDTE. Simulations of the groundwater flow field in the study area with the aid of a 3-D flow and transport model developed for Bogucice Sands (Neogene) aquifer and calibrated using environmental tracer data and observations of hydraulic head in three different locations on the study area
What do we learn on bromoform transport and chemistry in deep convection from fine scale modelling?
NASA Astrophysics Data System (ADS)
Marécal, V.; Pirre, M.; Krysztofiak, G.; Josse, B.
2011-11-01
Bromoform is one of the main sources of halogenated Very Short-Lived Species (VSLS) that possibly contributes when degradated to the inorganic halogen loading in the stratosphere. Because of its short lifetime of about four weeks, its pathway to the stratosphere is mainly the transport by convection up to the tropical tropopause layer (TTL) and then by radiative ascent in the low stratosphere. Some of its degradation product gases (PGs) that are soluble can be scavenged and not reach the TTL. In this paper we present a detailed modelling study of the transport and the degradation of bromoform and its PGs in convection. We use a 3-D-cloud resolving model coupled with a chemistry model including gaseous and aqueous chemistry. We run idealised simulations up to 10 days, initialised using a tropical radiosounding for atmospheric conditions and using outputs from a global chemistry-transport model for chemical species. Bromoform is initialised only in the low levels. The first simulation is run with stable atmospheric conditions. It shows that the sum of the bromoform and its PGs significantly decreases with time because of dry deposition and that PGs are mainly in the form of HBr after 2 days of simulation. The other simulation is similar to the first simulation but includes perturbations of temperature and of moisture leading to the development of a convective cloud reaching the TTL. Results of this simulation show an efficient vertical transport of the bromoform from the boundary layer in the upper troposphere and TTL (mixing ratio up to 45% of the initial boundary layer mixing ratio). The organic PGs, which are for the most abundant of them not very soluble, are also uplifted efficiently. For the inorganic PGs, which are more abundant than organic PGs, their mixing ratios in the upper troposphere and in the TTL depend on the partitioning between inorganic soluble and inorganic non soluble species in the convective cloud. Important soluble species such as HBr and
NASA Astrophysics Data System (ADS)
Paradis, Hedvig; Andersson, Martin; Sundén, Bengt
2015-09-01
A 3D model at microscale by the lattice Boltzmann method (LBM) is proposed for part of an anode of a solid oxide fuel cell (SOFC) to analyze the interaction between the transport and reaction processes and structural parameters. The equations of charge, momentum, heat and mass transport are simulated in the model. The modeling geometry is created with randomly placed spheres to resemble the part of the anode structure close to the electrolyte. The electrochemical reaction processes are captured at specific sites where spheres representing Ni and YSZ materials are present with void space. This work focuses on analyzing the effect of structural parameters such as porosity, and percentage of active reaction sites on the ionic current density and concentration of H2 using LBM. It is shown that LBM can be used to simulate an SOFC anode at microscale and evaluate the effect of structural parameters on the transport processes to improve the performance of the SOFC anode. It was found that increasing the porosity from 30 to 50 % decreased the ionic current density due to a reduction in the number of reaction sites. Also the consumption of H2 decreased with increasing porosity. When the percentage of active reaction sites was increased while the porosity was kept constant, the ionic current density increased. However, the H2 concentration was slightly reduced when the percentage of active reaction sites was increased. The gas flow tortuosity decreased with increasing porosity.
NASA Astrophysics Data System (ADS)
Paradis, Hedvig; Andersson, Martin; Sundén, Bengt
2016-08-01
A 3D model at microscale by the lattice Boltzmann method (LBM) is proposed for part of an anode of a solid oxide fuel cell (SOFC) to analyze the interaction between the transport and reaction processes and structural parameters. The equations of charge, momentum, heat and mass transport are simulated in the model. The modeling geometry is created with randomly placed spheres to resemble the part of the anode structure close to the electrolyte. The electrochemical reaction processes are captured at specific sites where spheres representing Ni and YSZ materials are present with void space. This work focuses on analyzing the effect of structural parameters such as porosity, and percentage of active reaction sites on the ionic current density and concentration of H2 using LBM. It is shown that LBM can be used to simulate an SOFC anode at microscale and evaluate the effect of structural parameters on the transport processes to improve the performance of the SOFC anode. It was found that increasing the porosity from 30 to 50 % decreased the ionic current density due to a reduction in the number of reaction sites. Also the consumption of H2 decreased with increasing porosity. When the percentage of active reaction sites was increased while the porosity was kept constant, the ionic current density increased. However, the H2 concentration was slightly reduced when the percentage of active reaction sites was increased. The gas flow tortuosity decreased with increasing porosity.
NASA Technical Reports Server (NTRS)
Ott, Lesley; Pickering, Kenneth; Stenchikov, Georgiy; Allen, Dale; DeCaria, Alex; Ridley, Brian; Lin, Ruei-Fong; Lang, Steve; Tao, Wei-Kuo
2009-01-01
A 3-D cloud scale chemical transport model that includes a parameterized source of lightning NO(x), based on observed flash rates has been used to simulate six midlatitude and subtropical thunderstorms observed during four field projects. Production per intracloud (P(sub IC) and cloud-to-ground (P(sub CG)) flash is estimated by assuming various values of P(sub IC) and P(sub CG) for each storm and determining which production scenario yields NO(x) mixing ratios that compare most favorably with in-cloud aircraft observations. We obtain a mean P(sub CG) value of 500 moles NO (7 kg N) per flash. The results of this analysis also suggest that on average, P(sub IC) may be nearly equal to P(sub CG), which is contrary to the common assumption that intracloud flashes are significantly less productive of NO than are cloud-to-ground flashes. This study also presents vertical profiles of the mass of lightning NO(x), after convection based on 3-D cloud-scale model simulations. The results suggest that following convection, a large percentage of lightning NO(x), remains in the middle and upper troposphere where it originated, while only a small percentage is found near the surface. The results of this work differ from profiles calculated from 2-D cloud-scale model simulations with a simpler lightning parameterization that were peaked near the surface and in the upper troposphere (referred to as a "C-shaped" profile). The new model results (a backward C-shaped profile) suggest that chemical transport models that assume a C-shaped vertical profile of lightning NO(x) mass may place too much mass neat the surface and too little in the middle troposphere.
NASA Astrophysics Data System (ADS)
Das, Ronnie; Burfeind, Chris W.; Kramer, Greg M.; Seibel, Eric J.
2014-03-01
A minimally-invasive diagnosis of pancreatic cancer is accomplished by obtaining a fine needle aspirate and observing the cell preparations under conventional optical microscopy. As an unavoidable artifact, native tissue architecture is lost, making definite diagnosis of malignancy, or invasive neoplasm, impossible. One solution is the preparation of core biopsies (CBs) within a microfluidic device that are subsequently imaged in 3D. In this paper, porcine pancreas CBs (L = 1-2 cm, D = 0.4-2.0 mm) were formalin-fixed, stained and optically cleared (FocusClear®). In brightfield at 40x, light transmission through the ordinarily opaque CBs was increased 5-15x, and internal islet structures were easily identified 250-300 μm beneath the tissue surface. Typically, specimen preparation is time intensive and requires precise handling since CBs are delicate; thus, fixative, absorptive stain and FocusClear® diffusion were done slowly and manually. To significantly speed up tissue processing, we developed a microfluidic device consisting of both a main channel (L = 12.5 cm, D = 1.415 mm) with a circular cross section used for fixing and transporting the CB and an intersecting U-channel employed for staining. Space between the CB and channel wall provided a key feature not traditionally employed in microfluidic devices, such that at low flow rates (5-10 mL/min) CBs were fixed and stained while the specimen remained stationary. By switching quickly to higher flow rates (15-20 mL/min), we could precisely overcome adhesion and transport the specimen within the channel towards the imaging platform for 3D pathology.
Gifford, Kent A; Wareing, Todd A; Failla, Gregory; Horton, John L; Eifel, Patricia J; Mourtada, Firas
2010-01-01
A patient dose distribution was calculated by a 3D multi-group S N particle transport code for intracavitary brachytherapy of the cervix uteri and compared to previously published Monte Carlo results. A Cs-137 LDR intracavitary brachytherapy CT data set was chosen from our clinical database. MCNPX version 2.5.c, was used to calculate the dose distribution. A 3D multi-group S N particle transport code, Attila version 6.1.1 was used to simulate the same patient. Each patient applicator was built in SolidWorks, a mechanical design package, and then assembled with a coordinate transformation and rotation for the patient. The SolidWorks exported applicator geometry was imported into Attila for calculation. Dose matrices were overlaid on the patient CT data set. Dose volume histograms and point doses were compared. The MCNPX calculation required 14.8 hours, whereas the Attila calculation required 22.2 minutes on a 1.8 GHz AMD Opteron CPU. Agreement between Attila and MCNPX dose calculations at the ICRU 38 points was within +/- 3%. Calculated doses to the 2 cc and 5 cc volumes of highest dose differed by not more than +/- 1.1% between the two codes. Dose and DVH overlays agreed well qualitatively. Attila can calculate dose accurately and efficiently for this Cs-137 CT-based patient geometry. Our data showed that a three-group cross-section set is adequate for Cs-137 computations. Future work is aimed at implementing an optimized version of Attila for radiotherapy calculations. PMID:20160682
Evaluation of the MOCAGE Chemistry Transport Model during the ICARTT/ITOP Experiment
NASA Technical Reports Server (NTRS)
Bousserez, N.; Attie, J. L.; Peuch, V. H.; Michou, M.; Pfister, G.; Edwards, D.; Emmons, L.; Arnold, S.; Heckel, A.; Richter, A.; Shlager, H.; Lewis A.; Avery, M.; Sachse, G.; Browell, E.; Ferrare, R.
2007-01-01
We evaluate the Meteo-France global chemistry transport 3D model MOCAGE (MOdele de Chimie Atmospherique a Grande Echelle) using the important set of aircraft measurements collected during the ICARRT/ITOP experiment. This experiment took place between US and Europe during summer 2004 (July 15-August 15). Four aircraft were involved in this experiment providing a wealth of chemical data in a large area including the North East of US and western Europe. The model outputs are compared to the following species of which concentration is measured by the aircraft: OH, H2O2, CO, NO, NO2, PAN, HNO3, isoprene, ethane, HCHO and O3. Moreover, to complete this evaluation at larger scale, we used also satellite data such as SCIAMACHY NO2 and MOPITT CO. Interestingly, the comprehensive dataset allowed us to evaluate separately the model representation of emissions, transport and chemical processes. Using a daily emission source of biomass burning, we obtain a very good agreement for CO while the evaluation of NO2 points out incertainties resulting from inaccurate ratio of emission factors of NOx/CO. Moreover, the chemical behavior of O3 is satisfactory as discussed in the paper.
NASA Astrophysics Data System (ADS)
Pletinckx, D.
2011-09-01
The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.
NASA Astrophysics Data System (ADS)
Marécal, V.; Pirre, M.; Krysztofiak, G.; Hamer, P. D.; Josse, B.
2012-07-01
Bromoform is one of the most abundant halogenated Very Short-Lived Substances (VSLS) that possibly contributes, when degradated, to the inorganic halogen loading in the stratosphere. In this paper we present a detailed modelling study of the transport and the photochemical degradation of bromoform and its product gases (PGs) in a tropical convective cloud. The aim was to explore the transport and chemistry of bromoform under idealised conditions at the cloud scale. We used a 3-D cloud-resolving model coupled with a chemistry model including gaseous and aqueous chemistry. In particular, our model features explicit partitioning of the PGs between the gas phase and the aqueous phase based on newly calculated Henry's law coefficients using theoretical methods. We ran idealised simulations for up to 10 days that were initialised using a tropical radiosounding of atmospheric conditions and using outputs from a global chemistry-transport model for chemical species. Two simulations were run with stable atmospheric conditions with a bromoform initial mixing ratio of 40 pptv (part per trillion by volume) and 1.6 pptv up to 1 km altitude. The first simulation corresponds to high bromoform mixing ratios that are representative of real values found near strong localised sources (e.g. tropical coastal margins) and the second to the global tropical mean mixing ratio from observations. Both of these simulations show that the sum of bromoform and its PGs significantly decreases with time because of dry deposition, and that PGs are mainly in the form of HBr after 2 days of simulation. Two further simulations are conducted; these are similar to the first two simulations but include perturbations of temperature and moisture leading to the development of a convective cloud reaching the tropical tropopause layer (TTL). Results of these simulations show an efficient vertical transport of the bromoform from the boundary layer to the upper troposphere and the TTL. The bromoform mixing
Implications of Lagrangian transport for coupled chemistry-climate simulations
NASA Astrophysics Data System (ADS)
Stenke, A.; Dameris, M.; Grewe, V.; Garny, H.
2008-10-01
For the first time a purely Lagrangian transport algorithm is applied in a fully coupled chemistry-climate model (CCM). We use the Lagrangian scheme ATTILA for the transport of water vapour, cloud water and chemical trace species in the ECHAM4.L39(DLR)/CHEM (E39C) CCM. The advantage of the Lagrangian approach is that it is numerically non-diffusive and therefore maintains steeper and more realistic gradients than the operational semi-Lagrangian transport scheme. In case of radiatively active species changes in the simulated distributions feed back to model dynamics which in turn affect the modelled transport. The implications of the Lagrangian transport scheme for stratospheric model dynamics and tracer distributions in the upgraded model version E39C-ATTILA (E39C-A) are evaluated by comparison with observations and results of the E39C model with the operational semi-Lagrangian advection scheme. We find that several deficiencies in stratospheric dynamics in E39C seem to originate from a pronounced modelled wet bias and an associated cold bias in the extra-tropical lowermost stratosphere. The reduction of the simulated moisture and temperature bias in E39C-A leads to a significant advancement of stratospheric dynamics in terms of the mean state as well as annual and interannual variability. As a consequence of the favourable numerical characteristics of the Lagrangian transport scheme and the improved model dynamics, E39C-A generally shows more realistic stratospheric tracer distributions: Compared to E39C high stratospheric chlorine (Cly) concentrations extend further downward and agree now well with analyses derived from observations. Therefore E39C-A realistically covers the altitude of maximum ozone depletion in the stratosphere. The location of the ozonopause, i.e. the transition from low tropospheric to high stratospheric ozone values, is also clearly improved in E39C-A. Furthermore, the simulated temporal evolution of stratospheric Cly in the past is
A new model for plasma transport and chemistry at Saturn
NASA Technical Reports Server (NTRS)
Richardson, John D.
1992-01-01
A model of plasma transport and chemistry is described which calculates the evolution of a plasma population in latitude and radial distance. This model is applied to the magnetosphere of Saturn, where it is used to fit the density profile of the heavy ions assuming both satellite and ring sources of plasma. Use of an extended source region is found to significantly alter the resulting plasma profile. Water ions cannot fit the observed density profile inside L = 6 even with a large ring source. Oxygen ions can fit the density profile throughout the region inside L = 12 given a suitable profile of neutral hydrogen; a suitable profile contains up to 5 H/cu cm outside L = 4 with the number increasing inside this. Preferred values of K are 1-3 x 10 exp -10 R(S)2/s, but any value K less than 10 exp -9 R(S)2/s can be accommodated. The temperature profile is shown to favor models invoking in situ plasma formation and loss as opposed to models where transport is important.
Kipp, K.L.
1987-01-01
The Heat- and Soil-Transport Program (HST3D) simulates groundwater flow and associated heat and solute transport in three dimensions. The three governing equations are coupled through the interstitial pore velocity, the dependence of the fluid density on pressure, temperature, the solute-mass fraction , and the dependence of the fluid viscosity on temperature and solute-mass fraction. The solute transport equation is for only a single, solute species with possible linear equilibrium sorption and linear decay. Finite difference techniques are used to discretize the governing equations using a point-distributed grid. The flow-, heat- and solute-transport equations are solved , in turn, after a particle Gauss-reduction scheme is used to modify them. The modified equations are more tightly coupled and have better stability for the numerical solutions. The basic source-sink term represents wells. A complex well flow model may be used to simulate specified flow rate and pressure conditions at the land surface or within the aquifer, with or without pressure and flow rate constraints. Boundary condition types offered include specified value, specified flux, leakage, heat conduction, and approximate free surface, and two types of aquifer influence functions. All boundary conditions can be functions of time. Two techniques are available for solution of the finite difference matrix equations. One technique is a direct-elimination solver, using equations reordered by alternating diagonal planes. The other technique is an iterative solver, using two-line successive over-relaxation. A restart option is available for storing intermediate results and restarting the simulation at an intermediate time with modified boundary conditions. This feature also can be used as protection against computer system failure. Data input and output may be in metric (SI) units or inch-pound units. Output may include tables of dependent variables and parameters, zoned-contour maps, and plots of the
Hoyer, Andrea B; Wittmann, Marion E; Chandra, Sudeep; Schladow, S Geoffrey; Rueda, Francisco J
2014-12-01
The unwanted impacts of non-indigenous species have become one of the major ecological and economic threats to aquatic ecosystems worldwide. Assessing the potential dispersal and colonization of non-indigenous species is necessary to prevent or reduce deleterious effects that may lead to ecosystem degradation and a range of economic impacts. A three dimensional (3D) numerical model has been developed to evaluate the local dispersal of the planktonic larvae of an invasive bivalve, Asian clam (Corbicula fluminea), by passive hydraulic transport in Lake Tahoe, USA. The probability of dispersal of Asian clam larvae from the existing high density populations to novel habitats is determined by the magnitude and timing of strong wind events. The probability of colonization of new near-shore areas outside the existing beds is low, but sensitive to the larvae settling velocity ws. High larvae mortality was observed due to settling in unsuitable deep habitats. The impact of UV-radiation during the pelagic stages, on the Asian clam mortality was low. This work provides a quantification of the number of propagules that may be successfully transported as a result of natural processes and in function of population size. The knowledge and understanding of the relative contribution of different dispersal pathways, may directly inform decision-making and resource allocation associated with invasive species management. PMID:25108183
Soft metal thiol chemistry is not involved in the transport of arsenite by the Ars pump.
Chen, Y; Dey, S; Rosen, B P
1996-01-01
The single cysteine in the ArsB protein subunit of the arsenite resistance pump was changed to serine and alanine residues. Resistance in cells expressing the two mutant arsB genes was the same as in the wild type, and the serine substitution had no effect on the arsenite transport properties. These results eliminate possible thiol chemistry in translocation. Thus, the pump uses soft metal chemistry for metalloactivation and nonmetal chemistry for oxyanion transport. PMID:8550532
Evolution of Bromoform in a Global Chemistry and Transport Model
NASA Technical Reports Server (NTRS)
Douglass, Anne R.; Pierson, J. M.; Douglass, Anne R.; Einaudi, Franco (Technical Monitor)
2000-01-01
It is well known that many chlorine and bromine compounds that are inert in the troposphere are destroyed in the stratosphere and contribute to the stratospheric burden of reactive chlorine and bromine species. But the contribution from those chlorine and bromine compounds which are reactive in the troposphere is less certain because it is not known whether convection can transport these gases to the upper troposphere rapidly enough to overcome their short tropospheric lifetimes. We examine this issue using a three-dimensional chemistry and transport model to simulate the evolution of three gases which have surface sources, bromoform (CHBr3), methyl chloroform (CH3CCl3), and carbon dioxide (CO2). Our objective is to determine if CHBr3 might enhance the lower stratospheric burden of reactive bromine. The other two gases provide tests of the quality of the simulation. Both CHBr3 and CH3CCl3 are destroyed in the troposphere by reaction with hydroxyl (OH), whose latitudinal and monthly variation is provided by a two-dimensional model and upon which a diurnal variation is imposed. Comparison of the lifetime of CH3CCl3 computed from observations (5 years) with the lifetime computed from the simulation provides an integrated test of the model's transport and photochemistry. Observations also show that CO2 exhibits a strong seasonal cycle in the northern hemisphere troposphere that is not propagated directly across the tropopause into the lower stratosphere. Thus, maintenance of the observed troposphere-stratosphere distinctness of CO2 in the presence of convection is a critical benchmark for meeting our objective.
NASA Technical Reports Server (NTRS)
Bidwell, Colin, S.
2012-01-01
Ice Particle trajectory calculations with phase change were made for the Energy Efficient Engine (E(sup 3)) using the LEWICE3D Version 3.2 software. The particle trajectory computations were performed using the new Glenn Ice Particle Phase Change Model which has been incorporated into the LEWICE3D Version 3.2 software. The E(sup 3) was developed by NASA and GE in the early 1980 s as a technology demonstrator and is representative of a modern high bypass turbofan engine. The E(sup 3) flow field was calculated using the NASA Glenn ADPAC turbomachinery flow solver. Computations were performed for the low pressure compressor of the E(sup 3) for a Mach 0.8 cruise condition at 11,887 m assuming a standard warm day for ice particle sizes of 5, 20, and 100 microns and a free stream particle concentration of 0.3 g/cu m. The impingement efficiency results showed that as particle size increased average impingement efficiencies and scoop factors increased for the various components. The particle analysis also showed that the amount of mass entering the inner core decreased with increased particle size because the larger particles were less able to negotiate the turn into the inner core due to particle inertia. The particle phase change analysis results showed that the larger particles warmed less as they were transported through the low pressure compressor. Only the smallest 5 micron particles were warmed enough to produce melting and the amount of melting was relatively small with a maximum average melting fraction of 0.836. The results also showed an appreciable amount of particle sublimation and evaporation for the 5 micron particles entering the engine core (22 percent).
NASA Technical Reports Server (NTRS)
Chatfield, Robert; Houben, Howard; Sachse, Glenn; Hipskind, R. Stephen (Technical Monitor)
1998-01-01
We report on two aspects of the simulation of global transport of plumes originating from subtropical biomass fires. We use of meteorological assimilation (MM5) at 2-degree resolution with a Grail cloud parameterization and a Blackadar-based planetary boundary layer parameterization. Ames's GRACES model provides emissions, transport, and an appropriate level of simulated chemical transformation. We have worked with passive-tracer CO or linear chemistry. This is appropriate since we find major work to be done in evaluating CO source strengths and transport mechanisms before chemical integrations could be meaningful. First, we present mechanisms by which CO and other pollutants are introduced into the free troposphere, and are then transported with hate dilution from approx. 0 to approx. 180 degrees longitude. One principal conduit for these plumes is the vernal subtropical jet; however the plumes appear at various altitudes and latitudes as they influenced by frontal motions and (most likely) radiative processes. A common, repeated pattern of transport has pollutant plumes arriving in the distant Pacific Ocean from Africa and South America at 25 degrees south and 14 km altitude. Following this, there is then a general appearance of pollution at extending down to 5 kin at more equatorial (10 S) and polar latitudes (to 45 S). Second, we evaluate the quantitative success of our simulation. (Such success requires efforts considerably beyond trajectory analyses, and is necessary for our community to claim an understanding of the effects of biomass burning on global atmospheric chemistry and the planet's trend in oxidizing capacity.) We find that we simulate most pollution episodes sampled by Glenn Sachse's CO instrument and the Blake hydrocarbon analyses during PENT A. We will present our current ideas on why our general levels appear satisfactory when the observations are within 20 ppb of background levels, but substantially miss the variability associated with the most
NASA Astrophysics Data System (ADS)
Bertrand, Tanguy; Forget, Francois
2016-04-01
subsurface conditions as initial conditions, we run the GCM from 1975 to 2015, so that the model become insensitive to the assumed atmospheric initial states (that are not constrained by the volatile transport model). The simulated thermal structure and waves can be compared to the New Horizons occultations measurements. As observed, the horizontal variability is very limited, for fundamental reasons. In addition, we have developed a 3D model of the formation of organic hazes within the GCM. It includes the different steps of aerosols formation as understood on Titan: photolysis of CH4 in the upper atmosphere by the Lyman-alpha radiation, production of various gaseous precursor species, conversion into solid particles through chemistry and aggregation processes, and gravitational sedimentation. Significant amount of haze particles are found to be present at all latitudes up to 100 km. However, if N2 ice is already condensing in the polar night, the majority of the haze particles tend to accumulate in the polar night because of the transport of the haze precursors and aerosols by the condensation flow.
3d-3d correspondence revisited
NASA Astrophysics Data System (ADS)
Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr
2016-04-01
In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.
ERIC Educational Resources Information Center
Matz, Rebecca L.
2012-01-01
Chapter 1: The role of cell division in protein expression is important to understand in order to guide the development of better nonviral gene delivery materials that can transport DNA to the nucleus with high efficiency for a variety of cell types, particularly when nondividing cells are targets of gene therapy. We evaluated the relationship…
NASA Astrophysics Data System (ADS)
Dalla Valle, Giacomo; Gamberi, Fabiano; Rocchini, Patrizia; Minisini, Daniel; Errera, Alessia; Baglioni, Luca; Trincardi, Fabio
2013-08-01
Three-dimensional (3D) seismic-reflection data has shed light on the character of a series of mass transport complexes (MTCs) emplaced during the Pleistocene in the Pescara Basin (Central Adriatic Sea, Italy). The Pescara Basin is the Plio-Pleistocene inner foredeep of the Central Apennines orogen, which was filled by a rapidly prograding, margin-scale clinoforms system. Three MTCs punctuate the normal turbiditic and hemipelagic sedimentary succession of the Pescara Basin foredeep. MTC_0 is the oldest one and covers an area of around 74 km2. It is composed of three different mass transport deposits (MTDs) resulting from individual collapses that involved a shelf-edge delta during a period of relative sea level rise. MTC_1, the intermediate age MTC, is the largest one, with an area of 90 km2. It has a 10 km wide cookie-bite headwall region that indents the upper slope and, in places, reaches the continental shelf-break. MTC_1 is made up of four laterally and vertically stacked MTDs which are the result of a composite set of failures that migrated progressively upslope in a sedimentary setting dominated by contourite deposits. MTC_2 is the youngest and the smallest one, with an area of 55 km2. It has a 5 km long headwall confined in correspondence with a sedimentary bulge developed in the upper slope. Its geomorphic setting leads us to consider two different episodes of failure rooted at different depths. The investigation of the MTCs, through the coupling of 3D seismic geomorphology, seismic facies analysis and rollover trajectory analysis, reveals that the type of sedimentary environment, the rate of sediment accumulation, the source region and the depth of rooting of the failure, are the major controlling factors on MTC evolution and emplacement. Each MTC of the Pescara Basin foredeep is generally confined within a discrete clinotheme. Finally, the rollover trajectory analysis has shown that, in the PB foredeep, a sediment failure can possibly occur at any
Runkel, Robert L.
2010-01-01
OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption. Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale. This report details the development and application of OTEQ. Sections of the report describe model theory, input/output specifications, model applications, and installation instructions. OTEQ may be obtained over the Internet at http://water.usgs.gov/software/OTEQ.
NASA Astrophysics Data System (ADS)
Fraser, Annemarie; Chan Miller, Christopher; Palmer, Paul I.; Deutscher, Nicholas M.; Jones, Nicholas B.; Griffith, David W. T.
2011-10-01
We investigate the Australian methane budget from 2005-2008 using the GEOS-Chem 3D chemistry transport model, focusing on the relative contribution of emissions from different sectors and the influence of long-range transport. To evaluate the model, we use in situ surface measurements of methane, methane dry air column average (XCH4) from ground-based Fourier transform spectrometers (FTSs), and train-borne surface concentration measurements from an in situ FTS along the north-south continental transect. We use gravity anomaly data from Gravity Recovery and Climate Experiment to describe the spatial and temporal distribution of wetland emissions and scale it to a prior emission estimate, which better describes observed atmospheric methane variability at tropical latitudes. The clean air sites of Cape Ferguson and Cape Grim are the least affected by local emissions, while Wollongong, located in the populated southeast with regional coal mining, samples the most locally polluted air masses (2.5% of the total air mass versus <1% at other sites). Averaged annually, the largest single source above background of methane at Darwin is long-range transport, mainly from Southeast Asia, accounting for ˜25% of the change in surface concentration above background. At Cape Ferguson and Cape Grim, emissions from ruminant animals are the largest source of methane above background, at approximately 20% and 30%, respectively, of the surface concentration. At Wollongong, emissions from coal mining are the largest source above background representing 60% of the surface concentration. The train data provide an effective way of observing transitions between urban, desert, and tropical landscapes.
NASA Technical Reports Server (NTRS)
Douglass, A. R.; Schoeberl, M. R.; Browell, E. V.
1999-01-01
An ozone simulation from the Goddard three-dimensional chemistry and transport model for the 1995-96 northern hemisphere winter is compared with ozone observations from airborne Differential Absorption Lidar (DIAL), from the Polar Ozone and Aerosol Measurement (POAM), from the Microwave Limb Sounder (MLS), and from the Halogen Occultation Experiment (HALOE). The 3D model uses winds from the Goddard Data Assimilation System. The 3D model reproduces the latitude dependence of the horizontal and vertical ozone gradients of the subtropical DIAL observations. Comparisons with subtropical satellite observations, which lack the spatial resolution of DIAL but provide near continuous coverage throughout the subtropics, show that the model also reproduces longitude and temporal dependence in the tropical-midlatitude boundary. At polar latitudes, observations from DIAL flights on December 9 and January 30, and POAM and MLS between late December and late January are compared with the 3D model. Data from the three platforms consistently show that the observed ozone has a negative trend relative to the modeled ozone, and that the trend is uniform in time between early and mid winter, with no obvious dependence on proximity to the vortex edge.
3D Direct Simulation Monte Carlo Code Which Solves for Geometrics
Energy Science and Technology Software Center (ESTSC)
1998-01-13
Pegasus is a 3D Direct Simulation Monte Carlo Code which solves for geometries which can be represented by bodies of revolution. Included are all the surface chemistry enhancements in the 2D code Icarus as well as a real vacuum pump model. The code includes multiple species transport.
PEGASUS. 3D Direct Simulation Monte Carlo Code Which Solves for Geometrics
Bartel, T.J.
1998-12-01
Pegasus is a 3D Direct Simulation Monte Carlo Code which solves for geometries which can be represented by bodies of revolution. Included are all the surface chemistry enhancements in the 2D code Icarus as well as a real vacuum pump model. The code includes multiple species transport.
Merritt, Michael L.; Konikow, Leonard F.
2000-01-01
Heads and flow patterns in surficial aquifers can be strongly influenced by the presence of stationary surface-water bodies (lakes) that are in direct contact, vertically and laterally, with the aquifer. Conversely, lake stages can be significantly affected by the volume of water that seeps through the lakebed that separates the lake from the aquifer. For these reasons, a set of computer subroutines called the Lake Package (LAK3) was developed to represent lake/aquifer interaction in numerical simulations using the U.S. Geological Survey three-dimensional, finite-difference, modular ground-water flow model MODFLOW and the U.S. Geological Survey three-dimensional method-of-characteristics solute-transport model MOC3D. In the Lake Package described in this report, a lake is represented as a volume of space within the model grid which consists of inactive cells extending downward from the upper surface of the grid. Active model grid cells bordering this space, representing the adjacent aquifer, exchange water with the lake at a rate determined by the relative heads and by conductances that are based on grid cell dimensions, hydraulic conductivities of the aquifer material, and user-specified leakance distributions that represent the resistance to flow through the material of the lakebed. Parts of the lake may become ?dry? as upper layers of the model are dewatered, with a concomitant reduction in lake surface area, and may subsequently rewet when aquifer heads rise. An empirical approximation has been encoded to simulate the rewetting of a lake that becomes completely dry. The variations of lake stages are determined by independent water budgets computed for each lake in the model grid. This lake budget process makes the package a simulator of the response of lake stage to hydraulic stresses applied to the aquifer. Implementation of a lake water budget requires input of parameters including those representing the rate of lake atmospheric recharge and evaporation
NASA Astrophysics Data System (ADS)
Meulien Ohlmann, Odile
2013-02-01
Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?
Assimilation of surface NO2 and O3 observations into the SILAM chemistry transport model
NASA Astrophysics Data System (ADS)
Vira, J.; Sofiev, M.
2015-02-01
This paper describes the assimilation of trace gas observations into the chemistry transport model SILAM (System for Integrated modeLling of Atmospheric coMposition) using the 3D-Var method. Assimilation results for the year 2012 are presented for the prominent photochemical pollutants ozone (O3) and nitrogen dioxide (NO2). Both species are covered by the AirBase observation database, which provides the observational data set used in this study. Attention was paid to the background and observation error covariance matrices, which were obtained primarily by the iterative application of a posteriori diagnostics. The diagnostics were computed separately for 2 months representing summer and winter conditions, and further disaggregated by time of day. This enabled the derivation of background and observation error covariance definitions, which included both seasonal and diurnal variation. The consistency of the obtained covariance matrices was verified using χ2 diagnostics. The analysis scores were computed for a control set of observation stations withheld from assimilation. Compared to a free-running model simulation, the correlation coefficient for daily maximum values was improved from 0.8 to 0.9 for O3 and from 0.53 to 0.63 for NO2.