High-resolution 2D3V simulations of forced hybrid-kinetic turbulence
NASA Astrophysics Data System (ADS)
Cerri, Silvio Sergio; Califano, Francesco; Rincon, Francois; Told, Daniel; Jenko, Frank; Pegoraro, Francesco
2016-10-01
The understanding of the kinetic processes at play in plasma turbulence is a frontier problem in plasma physics and among the topics currently of most interest in space plasma research. Here we investigate the properties of turbulence from the end of the magnetohydrodynamic (MHD) cascade to scales well below the ion gyroradius (i.e., the so-called ``dissipation'' or ``dispersion'' range) by means of unprecedented high-resolution simulations of forced hybrid-kinetic turbulence in a 2D3V phase-space (two real-space and three velocity-space dimensions). Different values of the plasma beta parameter typical of the solar wind (SW) are investigated. Several aspects of turbulence at small-scales emerging from the simulations are presented and discussed. Even within the limitations of the hybrid approach in 2D3V, a reasonable agreement with SW observations and with theory is found. Finally, we identify possible implications and questions related to SW turbulence which arise from this study. This research has been funded by European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No.277870 and by Euratom research and training programme 2014-2018. Simulations were performed on Fermi (CINECA, IT) and Hydra (MPCDF, DE).
2D Kinetic Particle in Cell Simulations of a Shear-Flow Stabilized Z-Pinch
NASA Astrophysics Data System (ADS)
Tummel, Kurt; Higginson, Drew; Schmidt, Andrea; Link, Anthony; McLean, Harry; Shumlak, Uri; Nelson, Brian; Golingo, Raymond; Claveau, Elliot; Lawrence Livermore National Lab Team; University of Washington Team
2016-10-01
The Z-pinch is a relatively simple and attractive potential fusion reactor design, but attempts to develop such a reactor have consistently struggled to overcome Z-pinch instabilities. The ``sausage'' and ``kink'' modes are among the most robust and prevalent Z-pinch instabilities, but theory and simulations suggest that axial flow-shear, dvz / dr ≠ 0 , can suppress these modes. Experiments have confirmed that Z-pinch plasmas with embedded axial flow-shear display a significantly enhanced resilience to the sausage and kink modes at a demonstration current of 50kAmps. A new experiment is under way to test the concept at higher current, and efforts to model these plasmas are being expanded. The performance and stability of these devices will depend on features like the plasma viscosity, anomalous resistivity, and finite Larmor radius effects, which are most accurately characterized in kinetic models. To predict these features, kinetic simulations using the particle in cell code LSP are now in development, and initial benchmarking and 2D stability analyses of the sausage mode are presented here. These results represent the first kinetic modeling of the flow-shear stabilized Z-pinch. This work is funded by the USDOE/ARPAe Alpha Program. Prepared by LLNL under Contract DE-AC52-07NA27344.
Simulation of 2D Kinetic Effects in Plasmas using the Grid Based Continuum Code LOKI
NASA Astrophysics Data System (ADS)
Banks, Jeffrey; Berger, Richard; Chapman, Tom; Brunner, Stephan
2016-10-01
Kinetic simulation of multi-dimensional plasma waves through direct discretization of the Vlasov equation is a useful tool to study many physical interactions and is particularly attractive for situations where minimal fluctuation levels are desired, for instance, when measuring growth rates of plasma wave instabilities. However, direct discretization of phase space can be computationally expensive, and as a result there are few examples of published results using Vlasov codes in more than a single configuration space dimension. In an effort to fill this gap we have developed the Eulerian-based kinetic code LOKI that evolves the Vlasov-Poisson system in 2+2-dimensional phase space. The code is designed to reduce the cost of phase-space computation by using fully 4th order accurate conservative finite differencing, while retaining excellent parallel scalability that efficiently uses large scale computing resources. In this poster I will discuss the algorithms used in the code as well as some aspects of their parallel implementation using MPI. I will also overview simulation results of basic plasma wave instabilities relevant to laser plasma interaction, which have been obtained using the code.
Reconnection and small-scale fields in 2D-3V hybrid-kinetic driven turbulence simulations
NASA Astrophysics Data System (ADS)
Cerri, S. S.; Califano, F.
2017-02-01
The understanding of the fundamental properties of turbulence in collisionless plasmas, such as the solar wind, is a frontier problem in plasma physics. In particular, the occurrence of magnetic reconnection in turbulent plasmas and its interplay with a fully-developed turbulent state is still a matter of great debate. Here we investigate the properties of small-scale electromagnetic fluctuations and the role of fast magnetic reconnection in the development of a quasi-steady turbulent state by means of 2D-3V high-resolution Vlasov–Maxwell simulations. At the largest scales turbulence is fed by external random forcing. We show that large-scale turbulent motions establish a -5/3 spectrum at {k}\\perp {d}i< 1 and, at the same time, feed the formation of current sheets where magnetic reconnection occurs. As a result coherent magnetic structures are generated which, together with the rise of the associated small-scale non-ideal electric field, mediate the transition between the inertial and the subproton-scale spectrum. A mechanism that boosts the magnetic reconnection process is identified, making the generation of coherent structures rapid enough to be competitive with wave mode interactions and leading to the formation of a fully-developed turbulent spectrum across the so-called ion break.
Multi-GPU unsteady 2D flow simulation coupled with a state-to-state chemical kinetics
NASA Astrophysics Data System (ADS)
Tuttafesta, Michele; Pascazio, Giuseppe; Colonna, Gianpiero
2016-10-01
In this work we are presenting a GPU version of a CFD code for high enthalpy reacting flow, using the state-to-state approach. In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma and state-to-state kinetics is the most accurate approach used for this kind of problems. This model consists in writing a continuity equation for the population of each vibrational level of the molecules in the mixture, determining at the same time the species densities and the distribution of the population in internal levels. An explicit scheme is employed here to integrate the governing equations, so as to exploit the GPU structure and obtain an efficient algorithm. The best performances are obtained for reacting flows in state-to-state approach, reaching speedups of the order of 100, thanks to the use of an operator splitting scheme for the kinetics equations.
Realistic and efficient 2D crack simulation
NASA Astrophysics Data System (ADS)
Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek
2010-04-01
Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.
RNA folding pathways and kinetics using 2D energy landscapes.
Senter, Evan; Dotu, Ivan; Clote, Peter
2015-01-01
RNA folding pathways play an important role in various biological processes, such as (i) the hok/sok (host-killing/suppression of killing) system in E. coli to check for sufficient plasmid copy number, (ii) the conformational switch in spliced leader (SL) RNA from Leptomonas collosoma, which controls trans splicing of a portion of the '5 exon, and (iii) riboswitches--portions of the 5' untranslated region of messenger RNA that regulate genes by allostery. Since RNA folding pathways are determined by the energy landscape, we describe a novel algorithm, FFTbor2D, which computes the 2D projection of the energy landscape for a given RNA sequence. Given two metastable secondary structures A, B for a given RNA sequence, FFTbor2D computes the Boltzmann probability p(x, y) = Z(x,y)/Z that a secondary structure has base pair distance x from A and distance y from B. Using polynomial interpolationwith the fast Fourier transform,we compute p(x, y) in O(n(5)) time and O(n(2)) space, which is an improvement over an earlier method, which runs in O(n(7)) time and O(n(4)) space. FFTbor2D has potential applications in synthetic biology, where one might wish to design bistable switches having target metastable structures A, B with favorable pathway kinetics. By inverting the transition probability matrix determined from FFTbor2D output, we show that L. collosoma spliced leader RNA has larger mean first passage time from A to B on the 2D energy landscape, than 97.145% of 20,000 sequences, each having metastable structures A, B. Source code and binaries are freely available for download at http://bioinformatics.bc.edu/clotelab/FFTbor2D. The program FFTbor2D is implemented in C++, with optional OpenMP parallelization primitives.
Simulation of Yeast Cooperation in 2D.
Wang, M; Huang, Y; Wu, Z
2016-03-01
Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse.
Shocks in 2D Yukawa systems : thermodynamics and kinetic properties
NASA Astrophysics Data System (ADS)
Murillo, Michael S.; Marciante, Mathieu
2016-10-01
The study of shock propagation has become a common way to obtain statistical information on a medium, as one can relate properties of the undisturbed medium to the shock dynamics through the Rankine-Hugoniot relations. However, theoretical investigations of shock dynamics are often done through idealized fluid models, which neglect kinetic properties. In this poster we study the propagation of shock waves in plasmas at the particle level, using molecular dynamics simulations to model the propagation of stationary shock waves in a two-dimensional Yukawa plasma. Stationary shocks are generated by a piston moving at constant speed, and macroscopic thermodynamic quantities such as temperature and pressure are computed from statistical averages. This theoretical investigation comprises two parts. First, we present the thermodynamic equilibrium properties of Yukawa plasmas under shock dynamics. Next, we focus on the influence of the kinetic aspects of the plasma, showing how transport coefficients of fluid models are related to the microscopic dynamics in phase-space and apply it to the Yukawa plasma case. Contract DE-AC52-06NA25396.
Aggregation kinetics of carbonyl iron based magnetic suspensions in 2D.
Shahrivar, Keshvad; Carreón-González, Elizabeth; Morillas, Jose R; de Vicente, Juan
2017-04-05
We investigate the (irreversible) two-dimensional aggregation kinetics of dilute non-Brownian magnetic suspensions in rectangular microchannels using video-microscopy, image analysis and particle-level dynamics simulations. Special emphasis is given to carbonyl iron suspensions that are of interest in the formulation of magnetorheological fluids. The results are compared to non-Brownian suspensions of magnetic latexes. We demonstrate that both suspensions follow a deterministic aggregation process. Furthermore, experimental and simulation aggregation curves can be collapsed onto a master curve when using the appropriate scaling time (∝λ(-1)ϕ2D(-2.5)) as a function of only two dimensionless numbers: the lambda ratio (λ) and the particle surface fraction (ϕ2D).
2-D Clinostat for Simulated Microgravity Experiments with Arabidopsis Seedlings
NASA Astrophysics Data System (ADS)
Wang, Hui; Li, Xugang; Krause, Lars; Görög, Mark; Schüler, Oliver; Hauslage, Jens; Hemmersbach, Ruth; Kircher, Stefan; Lasok, Hanna; Haser, Thomas; Rapp, Katja; Schmidt, Jürgen; Yu, Xin; Pasternak, Taras; Aubry-Hivet, Dorothée; Tietz, Olaf; Dovzhenko, Alexander; Palme, Klaus; Ditengou, Franck Anicet
2016-04-01
Ground-based simulators of microgravity such as fast rotating 2-D clinostats are valuable tools to study gravity related processes. We describe here a versatile g-value-adjustable 2-D clinostat that is suitable for plant analysis. To avoid seedling adaptation to 1 g after clinorotation, we designed chambers that allow rapid fixation. A detailed protocol for fixation, RNA isolation and the analysis of selected genes is described. Using this clinostat we show that mRNA levels of LONG HYPOCOTYL 5 (HY5), MIZU-KUSSEI 1 (MIZ1) and microRNA MIR163 are down-regulated in 5-day-old Arabidopsis thaliana roots after 3 min and 6 min of clinorotation using a maximal reduced g-force of 0.02 g, hence demonstrating that this 2-D clinostat enables the characterization of early transcriptomic events during root response to microgravity. We further show that this 2-D clinostat is able to compensate the action of gravitational force as both gravitropic-dependent statolith sedimentation and subsequent auxin redistribution (monitoring D R5 r e v :: G F P reporter) are abolished when plants are clinorotated. Our results demonstrate that 2-D clinostats equipped with interchangeable growth chambers and tunable rotation velocity are suitable for studying how plants perceive and respond to simulated microgravity.
Kinetic parameter estimation in N. europaea biofilms using a 2-D reactive transport model.
Lauchnor, Ellen G; Semprini, Lewis; Wood, Brian D
2015-06-01
Biofilms of the ammonia oxidizing bacterium Nitrosomonas europaea were cultivated to study microbial processes associated with ammonia oxidation in pure culture. We explored the hypothesis that the kinetic parameters of ammonia oxidation in N. europaea biofilms were in the range of those determined with batch suspended cells. Oxygen and pH microelectrodes were used to measure dissolved oxygen (DO) concentrations and pH above and inside biofilms and reactive transport modeling was performed to simulate the measured DO and pH profiles. A two dimensional (2-D) model was used to simulate advection parallel to the biofilm surface and diffusion through the overlying fluid while reaction and diffusion were simulated in the biofilm. Three experimental studies of microsensor measurements were performed with biofilms: i) NH3 concentrations near the Ksn value of 40 μM determined in suspended cell tests ii) Limited buffering capacity which resulted in a pH gradient within the biofilms and iii) NH3 concentrations well below the Ksn value. Very good fits to the DO concentration profiles both in the fluid above and in the biofilms were achieved using the 2-D model. The modeling study revealed that the half-saturation coefficient for NH3 in N. europaea biofilms was close to the value measured in suspended cells. However, the third study of biofilms with low availability of NH3 deviated from the model prediction. The model also predicted shifts in the DO profiles and the gradient in pH that resulted for the case of limited buffering capacity. The results illustrate the importance of incorporating both key transport and chemical processes in a biofilm reactive transport model.
Spatially Resolved Synthetic Spectra from 2D Simulations of Stainless Steel Wire Array Implosions
Clark, R. W.; Giuliani, J. L.; Thornhill, J. W.; Chong, Y. K.; Dasgupta, A.; Davis, J.
2009-01-21
A 2D radiation MHD model has been developed to investigate stainless steel wire array implosion experiments on the Z and refurbished Z machines. This model incorporates within the Mach2 MHD code a self-consistent calculation of the non-LTE kinetics and ray trace based radiation transport. Such a method is necessary in order to account for opacity effects in conjunction with ionization kinetics of K-shell emitting plasmas. Here the model is used to investigate multi-dimensional effects of stainless steel wire implosions. In particular, we are developing techniques to produce non-LTE, axially and/or radially resolved synthetic spectra based upon snapshots of our 2D simulations. Comparisons between experimental spectra and these synthetic spectra will allow us to better determine the state of the experimental pinches.
Numerical simulation of rock cutting using 2D AUTODYN
NASA Astrophysics Data System (ADS)
Woldemichael, D. E.; Rani, A. M. Abdul; Lemma, T. A.; Altaf, K.
2015-12-01
In a drilling process for oil and gas exploration, understanding of the interaction between the cutting tool and the rock is important for optimization of the drilling process using polycrystalline diamond compact (PDC) cutters. In this study the finite element method in ANSYS AUTODYN-2D is used to simulate the dynamics of cutter rock interaction, rock failure, and fragmentation. A two-dimensional single PDC cutter and rock model were used to simulate the orthogonal cutting process and to investigate the effect of different parameters such as depth of cut, and back rake angle on two types of rocks (sandstone and limestone). In the simulation, the cutting tool was dragged against stationary rock at predetermined linear velocity and the depth of cut (1,2, and 3 mm) and the back rake angles(-10°, 0°, and +10°) were varied. The simulation result shows that the +10° back rake angle results in higher rate of penetration (ROP). Increasing depth of cut leads to higher ROP at the cost of higher cutting force.
Ion acoustic wave collapse via two-ion wave decay: 2D Vlasov simulation and theory
NASA Astrophysics Data System (ADS)
Chapman, Thomas; Berger, Richard; Banks, Jeffrey; Brunner, Stephan
2015-11-01
The decay of ion acoustic waves (IAWs) via two-ion wave decay may transfer energy from the electric field of the IAWs to the particles, resulting in a significant heating of resonant particles. This process has previously been shown in numerical simulations to decrease the plasma reflectivity due to stimulated Brillouin scattering. Two-ion wave decay is a fundamental property of ion acoustic waves that occurs over most if not all of the parameter space of relevance to inertial confinement fusion experiments, and can lead to a sudden collapse of IAWs. The treatment of all species kinetically, and in particular the electrons, is required to describe the decay process correctly. We present fully kinetic 2D+2V Vlasov simulations of IAWs undergoing decay to a highly nonlinear turbulent state using the code LOKI. The scaling of the decay rate with characteristic plasma parameters and wave amplitude is shown. A new theory describing two-ion wave decay in 2D, that incorporates key kinetic properties of the electrons, is presented and used to explain quantitatively for the first time the observed decay of IAWs. Work performed under auspices of U.S. DoE by LLNL, Contract DE-AC52-07NA2734. Funded by LDRD 15-ERD-038 and supported by LLNL Grand Challenge allocation.
Interrogating Fiber Formation Kinetics with Automated 2D-IR Spectroscopy
NASA Astrophysics Data System (ADS)
Strasfeld, David B.; Ling, Yun L.; Shim, Sang-Hee; Zanni, Martin T.
A new method for collecting 2D-IR spectra that utilizes both a pump-probe beam geometry and a mid-IR pulse shaper is used to gain a fuller understanding of fiber formation in the human islet amyloid polypeptide (hIAPP). We extract structural kinetics in order to better understand aggregation in hIAPP, the protein component of the amyloid fibers found to inhibit insulin production in type II diabetes patients.
2D and 3D Numerical Simulations of Flux Cancellation
NASA Technical Reports Server (NTRS)
Karpen, Judith T.; DeVore, C.; Antiochos, S. K.; Linton, M. G.
2009-01-01
Cancellation of magnetic flux in the solar photosphere and chromosphere has been linked observationally and theoretically to a broad range of solar activity, from filament channel formation to CME initiation. Because this phenomenon is typically measured at only a single layer in the atmosphere, in the radial (line of sight) component of the magnetic field, the actual processes behind this observational signature are ambiguous. It is clear that reconnection is involved in some way, but the location of the reconnection sites and associated connectivity changes remain uncertain in most cases. We are using numerical modeling to demystify flux cancellation, beginning with the simplest possible configuration: a subphotospheric Lundquist flux tube surrounded by a potential field, immersed in a gravitationally stratified atmosphere, spanning many orders of magnitude in plasma beta. In this system, cancellation is driven slowly by a 2-cell circulation pattern imposed in the convection zone, such that the tops of the cells are located around the beta=1 level (i.e., the photosphere) and the flows converge and form a downdraft at the polarity inversion line; note however that no flow is imposed along the neutral line. We will present the results of 2D and 3D MHD-AMR simulations of flux cancellation, in which the flux at the photosphere begins in either an unsheared or sheared state. In all cases, a low-lying flux rope is formed by reconnection at the polarity inversion line within a few thousand seconds. The flux rope remains stable and does not rise, however, in contrast to models which do not include the presence of significant mass loading.
Application of 2-D simulations to hollow z-pinch implosions
Peterson, D.L.; Bowers, R.L.; Brownell, J.H.
1997-12-01
The application of simulations of z-pinch implosions should have at least two goals: first, to properly model the most important physical processes occurring in the pinch allowing for a better understanding of the experiments and second, provide a design capability for future experiments. Beginning with experiments fielded at Los Alamos on the Pegasus 1 and Pegasus 2 capacitor banks, the authors have developed a methodology for simulating hollow z-pinches in two dimensions which has reproduced important features of the measured experimental current drive, spectrum, radiation pulse shape, peak power and total radiated energy. This methodology employs essentially one free parameter, the initial level of the random density perturbations imposed at the beginning of the 2-D simulation, but in general no adjustments to other parameters are required. Currently the authors are applying this capability to the analysis of recent Saturn and PBFA-Z experiments. The code results provide insight into the nature of the pinch plasma prior to arrival on-axis, during thermalization and development after peak pinch time. Among other things, the simulation results provide an explanation for the production of larger amounts of radiated energy than would be expected from a simple slug-model kinetic energy analysis and the appearance of multiple peaks in the radiation power. The 2-D modeling has also been applied to the analysis of Saturn dynamic hohlraum experiments and is being used in the design of this and other Z-Pinch applications on PBFA-Z.
A 2D simulation model for urban flood management
NASA Astrophysics Data System (ADS)
Price, Roland; van der Wielen, Jonathan; Velickov, Slavco; Galvao, Diogo
2014-05-01
The European Floods Directive, which came into force on 26 November 2007, requires member states to assess all their water courses and coast lines for risk of flooding, to map flood extents and assets and humans at risk, and to take adequate and coordinated measures to reduce the flood risk in consultation with the public. Flood Risk Management Plans are to be in place by 2015. There are a number of reasons for the promotion of this Directive, not least because there has been much urban and other infrastructural development in flood plains, which puts many at risk of flooding along with vital societal assets. In addition there is growing awareness that the changing climate appears to be inducing more frequent extremes of rainfall with a consequent increases in the frequency of flooding. Thirdly, the growing urban populations in Europe, and especially in the developing countries, means that more people are being put at risk from a greater frequency of urban flooding in particular. There are urgent needs therefore to assess flood risk accurately and consistently, to reduce this risk where it is important to do so or where the benefit is greater than the damage cost, to improve flood forecasting and warning, to provide where necessary (and possible) flood insurance cover, and to involve all stakeholders in decision making affecting flood protection and flood risk management plans. Key data for assessing risk are water levels achieved or forecasted during a flood. Such levels should of course be monitored, but they also need to be predicted, whether for design or simulation. A 2D simulation model (PriceXD) solving the shallow water wave equations is presented specifically for determining flood risk, assessing flood defense schemes and generating flood forecasts and warnings. The simulation model is required to have a number of important properties: -Solve the full shallow water wave equations using a range of possible solutions; -Automatically adjust the time step and
Catalog of velocity distributions around a reconnection site in 2D PIC simulations
NASA Astrophysics Data System (ADS)
Lechner, Lukas; Bourdin, Philippe-A.; Nakamura, Takuma K. M.; Nakamura, Rumi; Narita, Yasuhito
2016-04-01
The velocity distribution of electrons and ions are known to be a marker for regions where magnetic reconnection develops. Past theoretical and computational works demonstrated that non-gyrotropic and anisotropic distributions depending on particle meandering motions and accelerations are seen around the reconnection point. The Magnetospheric Multiscale (MMS) mission is expected to resolve such kinetic scale reconnection regions. We present a catalog of velocity distribution functions that can give hints on the location within the current sheet relative to the reconnection point, which is sometimes unclear from pure spacecraft observations. We use 2D PIC simulations of anti-parallel magnetic reconnection to obtain velocity distributions at different locations, like in the center of the reconnection site, the ion and electron diffusion regions, or the reconnection inflow and outflow regions. With sufficiently large number of particles we resolve the distribution functions also in rather small regions. Such catalog may be compared with future MMS observations of the Earth's magnetotail.
Zhang, Jin; Germann, Markus W.
2011-01-01
Secondary amide cis peptide bonds are of even lower abundance than the cis tertiary amide bonds of prolines, yet they are of biochemical importance. Using 2D NMR exchange spectroscopy we investigated the formation of cis peptide bonds in several oligopeptides: Ac-G-G-G-NH2, Ac-I-G-G-NH2, Ac-I-G-G-N-NH2 and its cyclic form: I-G-G-N in DMSO. From the NMR studies, using the amide protons as monitors, an occurrenc.e of 0.13% – 0.23% of cis bonds was obtained at 296 K. The rate constants for the trans to cis conversion determined from 2D EXSY spectroscopy were 4–9·10−3 s−1. Multiple minor conformations were detected for most peptide bonds. From their thermodynamic and kinetic properties the cis isomers are distinguished from minor trans isomers that appear because of an adjacent cis peptide bond. Solvent and sequence effects were investigated utilizing N-methylacetamide and various peptides, which revealed an unique enthalpy profile in DMSO. The cyclization of a tetrapeptide resulted in greatly lowered cis populations and slower isomerization rate compared to its linear counterpart, further highlighting the impact of structural constraints. PMID:21538331
Electrostatic drift waves in a 2D magnetic current sheet - a new kinetic theory
NASA Astrophysics Data System (ADS)
Fruit, G.; Louarn, P.; Tur, A.
2015-12-01
In the general context of understanding the possible destabilization of the magnetotail before a substorm, a kinetic model for electromagnetic instabilities in resonant interaction with trapped bouncing electrons has been proposed for several years. Fruit et al. 2013 already used it to investigate the possibilities for electrostatic instabilities. Tur et al. 2014 generalizes the model for full electromagnetic perturbations.It turns out that some corrections should be added to the electrostatic version of Fruit et al. 2013. We propose to revist the theory in this present paper.Starting with a modified 2D Harris sheet as equilibrium state, the linearized gyrokinetic Vlasov equation is solved for electrostatic fluctuations with period of the order of the electron bounce period (a few seconds). The particle motion is restricted to its first Fourier component along the magnetic field and this allows the complete time integration of the non local perturbed distribution functions. The dispersion relation for electrostatic modes is finally obtained through the quasineutrality condition.The new feature of the present model is the inclusion of diamagnetic drift effects due to the density gradient in the tail. It is well known in MHD theory that drift waves are driven unstable through collisions or other dissipative effects. Here electrostatic drift waves are revisited in this more complete kinetic model including bouncing electrons and finite Larmor radius effects. A new mode has been found with original propagation proprieties. It is moreover mildly unstable due to electron or ion damping (dissipative instability).
Reactor2D: A tool for simulation of shock deformation
NASA Astrophysics Data System (ADS)
Kraus, Eugeny I.; Shabalin, Ivan I.
2016-10-01
The basic steps for creating a numerical tool to simulate the deformation and failure processes of complex technical objects (CTO) are presented. Calculations of shock loading of CTO both at low and high speeds, showing the efficiency of the numerical tools created are carried out.
Simulation of subgrid orographic precipitation with an embedded 2-D cloud-resolving model
NASA Astrophysics Data System (ADS)
Jung, Joon-Hee; Arakawa, Akio
2016-03-01
By explicitly resolving cloud-scale processes with embedded two-dimensional (2-D) cloud-resolving models (CRMs), superparameterized global atmospheric models have successfully simulated various atmospheric events over a wide range of time scales. Up to now, however, such models have not included the effects of topography on the CRM grid scale. We have used both 3-D and 2-D CRMs to simulate the effects of topography with prescribed "large-scale" winds. The 3-D CRM is used as a benchmark. The results show that the mean precipitation can be simulated reasonably well by using a 2-D representation of topography as long as the statistics of the topography such as the mean and standard deviation are closely represented. It is also shown that the use of a set of two perpendicular 2-D grids can significantly reduce the error due to a 2-D representation of topography.
Representativeness of 2D models to simulate 3D unstable variable density flow in porous media
NASA Astrophysics Data System (ADS)
Knorr, Bastian; Xie, Yueqing; Stumpp, Christine; Maloszewski, Piotr; Simmons, Craig T.
2016-11-01
Variable density flow in porous media has been studied primarily using numerical models because it is a semi-chaotic and transient process. Most of these studies have been 2D, owing to the computational restrictions on 3D simulations, and the ability to observe variable density flow in 2D experimentation. However, it is recognised that variable density flow is a three-dimensional process. A 3D system may cause weaker variable density flow than a 2D system due to stronger dispersion, but may also result in bigger fingers and hence stronger variable density flow because of more space for fingers to coalesce. This study aimed to determine the representativeness of 2D modelling to simulate 3D variable density flow. 3D homogeneous sand column experiments were conducted at three different water flow velocities with three different bromide tracer solutions mixed with methanol resulting in different density ratios. Both 2D axisymmetric and 3D numerical simulations were performed to reproduce experimental data. Experimental results showed that the magnitude of variable density flow increases with decreasing flow rates and decreasing density ratios. The shapes of the observed breakthrough curves differed significantly from those produced by 2D axisymmetric and 3D simulations. Compared to 2D simulations, the onset of instabilities was delayed but the growth was more pronounced in 3D simulations. Despite this difference, both 2D axisymmetric and 3D models successfully simulated mass recovery with high efficiency (between 77% and 99%). This study indicates that 2D simulations are sufficient to understand integrated features of variable density flow in homogeneous sand column experiments.
Time resolved spectroscopic investigation of SiD2 + D2: kinetic study
NASA Astrophysics Data System (ADS)
Al-Rubaiey, Najem A.; Walsh, Robin
2017-03-01
Silylenes (silanediyls) have made an important impact on organosilicon chemistry even if it is of more recent foundation than carbenes in organic chemistry and much less complete. These species are highly reactive intermediates. They play a central role in the chemical vapour deposition (CVD) of various silicon-containing thin films which have a technological importance in microelectronics as well as in the dry etching processes of silicon wafers. Spectroscopic methods have been developed to observe these species, a necessary pre-requisite to their direct monitoring. In this work, deuterated phenylsilane precursor, PhSiD3 was chosen for SiD2 because its analogue phenylsilane, PhSiH3 proved to be a good precursor for SiH2 and the high quality decay signals observed revealed that SiD2 be readily detected from PhSiD3 and that if other decomposition pathways (e.g. PhSiD + D2) are occurring, they do not effect measurements of the rate constants for SiD2. The absorption spectrum of SiD2 formed from the flash photolysis of a mixture of PhSiD3 and SF6 at 193nm were found in the region 17384-17391 cm-1 with strong band at 17387.07 cm-1. This single rotational line of pQ1 was chosen to monitor SiD2 removal. Time-resolved studies of SiD2 have been carried out to obtain rate constants for its bimolecular reactions with D2. The reactions were studied over the pressure range 5-100 Torr (in SF6 bath gas) at four temperatures in the range 298-498K. Single decay from 10 photolysis laser shots were averaged and found to give reasonable first-order kinetics fits. Second order kinetics were obtained by pressure dependence of the pseudo first order decay constants and substance D2 pressures within experimental error. The reaction was found to be weakly pressure dependent at all temperatures, consistent with a third-body mediated association process. In addition, SiH2+ H2 reaction is approximately ca. 60% faster than SiD2+D2 reaction. Theoretical extrapolations (using Lindemann
2-D simulation of a waveguide free electron laser having a helical undulator
Kim, S.K.; Lee, B.C.; Jeong, Y.U.
1995-12-31
We have developed a 2-D simulation code for the calculation of output power from an FEL oscillator having a helical undulator and a cylindrical waveguide. In the simulation, the current and the energy of the electron beam is 2 A and 400 keV, respectively. The parameters of the permanent-magnet helical undulator are : period = 32 mm, number of periods = 20, magnetic field = 1.3 kG. The gain per pass is 10 and the output power is calculated to be higher than 10 kW The results of the 2-D simulation are compared with those of 1-D simulation.
Lin, Shangchao; Shih, Chih-Jen; Sresht, Vishnu; Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel
2016-08-03
The colloidal dispersion stability of 1D and 2D materials in the liquid phase is critical for scalable nano-manufacturing, chemical modification, composites production, and deployment as conductive inks or nanofluids. Here, we review recent computational and theoretical studies carried out by our group to model the dispersion stability of 1D and 2D materials, including single-walled carbon nanotubes, graphene, and graphene oxide in aqueous surfactant solutions or organic solvents. All-atomistic (AA) molecular dynamics (MD) simulations can probe the molecular level details of the adsorption morphology of surfactants and solvents around these materials, as well as quantify the interaction energy between the nanomaterials mediated by surfactants or solvents. Utilizing concepts from reaction kinetics and diffusion, one can directly predict the rate constants for the aggregation kinetics and dispersion life times using MD outputs. Furthermore, the use of coarse-grained (CG) MD simulations allows quantitative prediction of surfactant adsorption isotherms. Combined with the Poisson-Boltzmann equation, the Langmuir isotherm, and the DLVO theory, one can directly use CGMD outputs to: (i) predict electrostatic potentials around the nanomaterial, (ii) correlate surfactant surface coverages with surfactant concentrations in the bulk dispersion medium, and (iii) determine energy barriers against coagulation. Finally, we discuss challenges associated with studying emerging 2D materials, such as, hexagonal boron nitride (h-BN), phosphorene, and transition metal dichalcogenides (TMDCs), including molybdenum disulfide (MoS2). An outlook is provided to address these challenges with plans to develop force-field parameters for MD simulations to enable predictive modeling of emerging 2D materials in the liquid phase.
Simulation and calculation of particle trapping using a quasistatic 2D simulation code
NASA Astrophysics Data System (ADS)
Morshed, Sepehr; Antonsen, Thomas; Huang, Chengkun; Mori, Warren
2008-11-01
In LWFA schemes the laser pulse must propagate several centimeters and maintain its coherence over this distance, which corresponds to many Rayleigh lengths. These Wakefields and their effect on the laser can be simulated in quasistatic approximation [1, 2]. In this approximation the assumption is that the driver (laser) does not change shape during the time it takes for it to pass by a plasma particle. As a result the particles that are trapped and moving with near-luminal velocity can not be treated with this approximation. Here we have modified the 2D code WAKE with an alternate algorithm so that when a plasma particle gains sufficient energy from wakefields it is promoted to beam particle status which later on may become trapped in the wakefields of laser. Similar implementations have been made in the 3D code QUICKPIC [2]. We also have done comparison between WAKE and results from 200 TW laser simulations using OSIRIS [3]. These changes in WAKE will give users a tool that can be used on a desk top machine to simulate GeV acceleration.[0pt] [1] P. Mora and T. M. Antonsen Jr., Phys Plasma 4, 217 (1997)[0pt] [2] C. Huang et al. Comp Phys. 217 (2006)[0pt] [3] W. Lu et al. PRST, Accelerators and Beams 10, 061301 (2007)
A 2D spring model for the simulation of ultrasonic wave propagation in nonlinear hysteretic media.
Delsanto, P P; Gliozzi, A S; Hirsekorn, M; Nobili, M
2006-07-01
A two-dimensional (2D) approach to the simulation of ultrasonic wave propagation in nonclassical nonlinear (NCNL) media is presented. The approach represents the extension to 2D of a previously proposed one dimensional (1D) Spring Model, with the inclusion of a PM space treatment of the intersticial regions between grains. The extension to 2D is of great practical relevance for its potential applications in the field of quantitative nondestructive evaluation and material characterization, but it is also useful, from a theoretical point of view, to gain a better insight of the interaction mechanisms involved. The model is tested by means of virtual 2D experiments. The expected NCNL behaviors are qualitatively well reproduced.
The simulation of 3D microcalcification clusters in 2D digital mammography and breast tomosynthesis
Shaheen, Eman; Van Ongeval, Chantal; Zanca, Federica; Cockmartin, Lesley; Marshall, Nicholas; Jacobs, Jurgen; Young, Kenneth C.; Dance, David R.; Bosmans, Hilde
2011-12-15
Purpose: This work proposes a new method of building 3D models of microcalcification clusters and describes the validation of their realistic appearance when simulated into 2D digital mammograms and into breast tomosynthesis images. Methods: A micro-CT unit was used to scan 23 breast biopsy specimens of microcalcification clusters with malignant and benign characteristics and their 3D reconstructed datasets were segmented to obtain 3D models of microcalcification clusters. These models were then adjusted for the x-ray spectrum used and for the system resolution and simulated into 2D projection images to obtain mammograms after image processing and into tomographic sequences of projection images, which were then reconstructed to form 3D tomosynthesis datasets. Six radiologists were asked to distinguish between 40 real and 40 simulated clusters of microcalcifications in two separate studies on 2D mammography and tomosynthesis datasets. Receiver operating characteristic (ROC) analysis was used to test the ability of each observer to distinguish between simulated and real microcalcification clusters. The kappa statistic was applied to assess how often the individual simulated and real microcalcification clusters had received similar scores (''agreement'') on their realistic appearance in both modalities. This analysis was performed for all readers and for the real and the simulated group of microcalcification clusters separately. ''Poor'' agreement would reflect radiologists' confusion between simulated and real clusters, i.e., lesions not systematically evaluated in both modalities as either simulated or real, and would therefore be interpreted as a success of the present models. Results: The area under the ROC curve, averaged over the observers, was 0.55 (95% confidence interval [0.44, 0.66]) for the 2D study, and 0.46 (95% confidence interval [0.29, 0.64]) for the tomosynthesis study, indicating no statistically significant difference between real and simulated
2D Mesoscale Simulations of Quasielastic Reloading and Unloading in Shock Compressed Aluminum
NASA Astrophysics Data System (ADS)
Dwivedi, S. K.
2007-06-01
2D mesoscale simulations of planar shock compression, followed by either reloading or unloading, are presented that predict quasi-elastic (QE) response observed experimentally in shocked polycrystalline aluminum. The representative volume element (RVE) of the plate impact experiments included a realistic representation of a grain ensemble with apparent heterogeneities in the polycrystalline sample. Simulations were carried out using a 2D updated Lagrangian finite element code ISP-TROTP incorporating elastic-plastic deformation in grain interior and contact/cohesive methodology to analyze finite strength grain boundaries. Local heterogeneous response was quantified by calculating appropriate material variables along in-situ Lagrangian tracer lines and comparing the temporal variation of their mean values with results from 2D continuum simulations. Simulations were carried out by varying a large number of individual heterogeneities to predict QE response on reloading and unloading from shock state. The heterogeneities important for simulating the QE response identified from these simulations were: hardened grain boundaries, hard inclusions, and micro-porosity. It is shown that the shock-deformed state of polycrystalline aluminum in the presence of these effects is strongly heterogeneous with considerable variations in lateral stresses. This distributed stress state unloads the shear stress from flow stress causing QE response on reloading as well as unloading. The simulated velocity profiles and calculated shear strength and shear stresses for a representative reloading and unloading experimental configuration were found to agree well with the reported experimental data. Work supported by DOE.
NASA Astrophysics Data System (ADS)
Sirait, S. H.; Edison, R. E.; Baidillah, M. R.; Taruno, W. P.; Haryanto, F.
2016-08-01
The aim of this study is to simulate the potential distribution of 2D brain geometry based on two electrodes ECVT. ECVT (electrical capacitance tomography) is a tomography modality which produces dielectric distribution image of a subject from several capacitance electrodes measurements. This study begins by producing the geometry of 2D brain based on MRI image and then setting the boundary conditions on the boundaries of the geometry. The values of boundary conditions follow the potential values used in two electrodes brain ECVT, and for this reason the first boundary is set to 20 volt and 2.5 MHz signal and another boundary is set to ground. Poisson equation is implemented as the governing equation in the 2D brain geometry and finite element method is used to solve the equation. Simulated Hodgkin-Huxley action potential is applied as disturbance potential in the geometry. We divide this study into two which comprises simulation without disturbance potential and simulation with disturbance potential. From this study, each of time dependent potential distributions from non-disturbance and disturbance potential of the 2D brain geometry has been generated.
Transverse instability of electron plasma waves study via direct 2 +2D Vlasov simulations
NASA Astrophysics Data System (ADS)
Silantyev, Denis; Lushnikov, Pavel; Rose, Harvey
2016-10-01
Transverse instability can be viewed as initial stage of electron plasma waves (EPWs) filamentation. We performed direct 2 +2D Vlasov-Poisson simulations of collisionless plasma to systematically study the growth rates of oblique modes of finite-amplitude EPW depending on its amplitude, wavenumber, angle of the oblique mode wavevector relative to the EPW's wavevector and the configuration of the trapped electrons in the EPW. Simulation results are compared to the predictions of theoretical models.
2-D MHD numerical simulations of EML plasma armatures with ablation
NASA Astrophysics Data System (ADS)
Boynton, G. C.; Huerta, M. A.; Thio, Y. C.
1993-01-01
We use a 2-D) resistive MHD code to simulate an EML plasma armature. The energy equation includes Ohmic heating, radiation heat transport and the ideal gas equation of state, allowing for variable ionization using the Saha equations. We calculate rail ablation taking into account the flow of heat into the interior of the rails. Our simulations show the development of internal convective flows and secondary arcs. We use an explicit Flux Corrected Transport algorithm to advance all quantities in time.
Microcomputer Simulation of Enzyme Kinetic Behaviour.
ERIC Educational Resources Information Center
Gill, R. A.
1984-01-01
Describes a program which simulates the kinetic behavior of a "typical" enzyme. Program objectives, background to the kinetic model used in the simulation, major program features, typical results obtained, and a note on the availability of the program (written in BASIC for Commodore microcomputer) are included. (JN)
The simulation of 3D mass models in 2D digital mammography and breast tomosynthesis
Shaheen, Eman De Keyzer, Frederik; Bosmans, Hilde; Ongeval, Chantal Van; Dance, David R.; Young, Kenneth C.
2014-08-15
Purpose: This work proposes a new method of building 3D breast mass models with different morphological shapes and describes the validation of the realism of their appearance after simulation into 2D digital mammograms and breast tomosynthesis images. Methods: Twenty-five contrast enhanced MRI breast lesions were collected and each mass was manually segmented in the three orthogonal views: sagittal, coronal, and transversal. The segmented models were combined, resampled to have isotropic voxel sizes, triangularly meshed, and scaled to different sizes. These masses were referred to as nonspiculated masses and were then used as nuclei onto which spicules were grown with an iterative branching algorithm forming a total of 30 spiculated masses. These 55 mass models were projected into 2D projection images to obtain mammograms after image processing and into tomographic sequences of projection images, which were then reconstructed to form 3D tomosynthesis datasets. The realism of the appearance of these mass models was assessed by five radiologists via receiver operating characteristic (ROC) analysis when compared to 54 real masses. All lesions were also given a breast imaging reporting and data system (BIRADS) score. The data sets of 2D mammography and tomosynthesis were read separately. The Kendall's coefficient of concordance was used for the interrater observer agreement assessment for the BIRADS scores per modality. Further paired analysis, using the Wilcoxon signed rank test, of the BIRADS assessment between 2D and tomosynthesis was separately performed for the real masses and for the simulated masses. Results: The area under the ROC curves, averaged over all observers, was 0.54 (95% confidence interval [0.50, 0.66]) for the 2D study, and 0.67 (95% confidence interval [0.55, 0.79]) for the tomosynthesis study. According to the BIRADS scores, the nonspiculated and the spiculated masses varied in their degrees of malignancy from normal (BIRADS 1) to highly
2D-3D hybrid stabilized finite element method for tsunami runup simulations
NASA Astrophysics Data System (ADS)
Takase, S.; Moriguchi, S.; Terada, K.; Kato, J.; Kyoya, T.; Kashiyama, K.; Kotani, T.
2016-09-01
This paper presents a two-dimensional (2D)-three-dimensional (3D) hybrid stabilized finite element method that enables us to predict a propagation process of tsunami generated in a hypocentral region, which ranges from offshore propagation to runup to urban areas, with high accuracy and relatively low computational costs. To be more specific, the 2D shallow water equation is employed to simulate the propagation of offshore waves, while the 3D Navier-Stokes equation is employed for the runup in urban areas. The stabilized finite element method is utilized for numerical simulations for both of the 2D and 3D domains that are independently discretized with unstructured meshes. The multi-point constraint and transmission methods are applied to satisfy the continuity of flow velocities and pressures at the interface between the resulting 2D and 3D meshes, since neither their spatial dimensions nor node arrangements are consistent. Numerical examples are presented to demonstrate the performance of the proposed hybrid method to simulate tsunami behavior, including offshore propagation and runup to urban areas, with substantially lower computation costs in comparison with full 3D computations.
PFC2D simulation of thermally induced cracks in concrete specimens
NASA Astrophysics Data System (ADS)
Liu, Xinghong; Chang, Xiaolin; Zhou, Wei; Li, Shuirong
2013-06-01
The appearance of cracks exposed to severe environmental conditions can be critical for concrete structures. The research is to validate Particle Flow Code(PFC2D) method in the context of concrete thermally-induced cracking simulations. First, concrete was discreted as meso-level units of aggregate, cement mortar and the interfaces between them. Parallel bonded-particle model in PFC2D was adapted to describe the constitutive relation of the cementing material. Then, the concrete mechanics meso-parameters were obtained through several groups of biaxial tests, in order to make the numerical results comply with the law of the indoor test. The concrete thermal meso-parameters were determined by compared with the parameters in the empirical formula through the simulations imposing a constant heat flow to the left margin of concrete specimens. At last, a case of 1000mm×500mm concrete specimen model was analyzed. It simulated the formation and development process of the thermally-induced cracks under the cold waves of different durations and temperature decline. Good agreements in fracture morphology and process were observed between the simulations, previous studies and laboratory data. The temperature decline limits during cold waves were obtained when its tensile strength was given as 3MPa. And it showed the feasibility of using PFC2D to simulate concrete thermally-induced cracking.
FRANC2D: A two-dimensional crack propagation simulator. Version 2.7: User's guide
NASA Technical Reports Server (NTRS)
Wawrzynek, Paul; Ingraffea, Anthony
1994-01-01
FRANC 2D (FRacture ANalysis Code, 2 Dimensions) is a menu driven, interactive finite element computer code that performs fracture mechanics analyses of 2-D structures. The code has an automatic mesh generator for triangular and quadrilateral elements. FRANC2D calculates the stress intensity factor using linear elastic fracture mechanics and evaluates crack extension using several methods that may be selected by the user. The code features a mesh refinement and adaptive mesh generation capability that is automatically developed according to the predicted crack extension direction and length. The code also has unique features that permit the analysis of layered structure with load transfer through simulated mechanical fasteners or bonded joints. The code was written for UNIX workstations with X-windows graphics and may be executed on the following computers: DEC DecStation 3000 and 5000 series, IBM RS/6000 series, Hewlitt-Packard 9000/700 series, SUN Sparc stations, and most Silicon Graphics models.
Simulation of Cardiac Arrhythmias Using a 2D Heterogeneous Whole Heart Model
Balakrishnan, Minimol; Chakravarthy, V. Srinivasa; Guhathakurta, Soma
2015-01-01
Simulation studies of cardiac arrhythmias at the whole heart level with electrocardiogram (ECG) gives an understanding of how the underlying cell and tissue level changes manifest as rhythm disturbances in the ECG. We present a 2D whole heart model (WHM2D) which can accommodate variations at the cellular level and can generate the ECG waveform. It is shown that, by varying cellular-level parameters like the gap junction conductance (GJC), excitability, action potential duration (APD) and frequency of oscillations of the auto-rhythmic cell in WHM2D a large variety of cardiac arrhythmias can be generated including sinus tachycardia, sinus bradycardia, sinus arrhythmia, sinus pause, junctional rhythm, Wolf Parkinson White syndrome and all types of AV conduction blocks. WHM2D includes key components of the electrical conduction system of the heart like the SA (Sino atrial) node cells, fast conducting intranodal pathways, slow conducting atriovenctricular (AV) node, bundle of His cells, Purkinje network, atrial, and ventricular myocardial cells. SA nodal cells, AV nodal cells, bundle of His cells, and Purkinje cells are represented by the Fitzhugh-Nagumo (FN) model which is a reduced model of the Hodgkin-Huxley neuron model. The atrial and ventricular myocardial cells are modeled by the Aliev-Panfilov (AP) two-variable model proposed for cardiac excitation. WHM2D can prove to be a valuable clinical tool for understanding cardiac arrhythmias. PMID:26733873
Simulation of Cardiac Arrhythmias Using a 2D Heterogeneous Whole Heart Model.
Balakrishnan, Minimol; Chakravarthy, V Srinivasa; Guhathakurta, Soma
2015-01-01
Simulation studies of cardiac arrhythmias at the whole heart level with electrocardiogram (ECG) gives an understanding of how the underlying cell and tissue level changes manifest as rhythm disturbances in the ECG. We present a 2D whole heart model (WHM2D) which can accommodate variations at the cellular level and can generate the ECG waveform. It is shown that, by varying cellular-level parameters like the gap junction conductance (GJC), excitability, action potential duration (APD) and frequency of oscillations of the auto-rhythmic cell in WHM2D a large variety of cardiac arrhythmias can be generated including sinus tachycardia, sinus bradycardia, sinus arrhythmia, sinus pause, junctional rhythm, Wolf Parkinson White syndrome and all types of AV conduction blocks. WHM2D includes key components of the electrical conduction system of the heart like the SA (Sino atrial) node cells, fast conducting intranodal pathways, slow conducting atriovenctricular (AV) node, bundle of His cells, Purkinje network, atrial, and ventricular myocardial cells. SA nodal cells, AV nodal cells, bundle of His cells, and Purkinje cells are represented by the Fitzhugh-Nagumo (FN) model which is a reduced model of the Hodgkin-Huxley neuron model. The atrial and ventricular myocardial cells are modeled by the Aliev-Panfilov (AP) two-variable model proposed for cardiac excitation. WHM2D can prove to be a valuable clinical tool for understanding cardiac arrhythmias.
NASA Technical Reports Server (NTRS)
Tang, H. T.; Hofmann, R.; Yee, G.; Vaughan, D. K.
1980-01-01
Transient, nonlinear soil-structure interaction simulations of an Electric Power Research Institute, SIMQUAKE experiment were performed using the large strain, time domain STEALTH 2D code and a cyclic, kinematically hardening cap soil model. Results from the STEALTH simulations were compared to identical simulations performed with the TRANAL code and indicate relatively good agreement between all the STEALTH and TRANAL calculations. The differences that are seen can probably be attributed to: (1) large (STEALTH) vs. small (TRANAL) strain formulation and/or (2) grid discretization differences.
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.
Kinetic inductance driven nanoscale 2D and 3D THz transmission lines
Mousavi, S. Hossein; Williamson, Ian A. D.; Wang, Zheng
2016-01-01
We examine the unusual dispersion and attenuation of transverse electromagnetic waves in the few-THz regime on nanoscale graphene and copper transmission lines. Conventionally, such propagation has been considered to be highly dispersive, due to the RC time constant-driven voltage diffusion below 1 THz and plasmonic effects at higher optical frequencies. Our numerical modeling across the microwave, THz, and optical frequency ranges reveals that the conductor kinetic inductance creates an ultra-broadband linear-dispersion and constant-attenuation region in the THz regime. This so-called LC region is an ideal characteristic that is known to be absent in macro-scale transmission lines. The kinetic-LC frequency range is dictated by the structural dimensionality and the free-carrier scattering rate of the conductor material. Moreover, up to 40x wavelength reduction is observed in graphene transmission lines. PMID:27137628
Long ranged interactions in computer simulations and for quasi-2D systems
NASA Astrophysics Data System (ADS)
Mazars, Martial
2011-03-01
Taking correctly into account long ranged interactions in molecular simulations of molecular models based on classical atomistic representations are essential to obtain reliable results on model systems and in simulations of biological systems. A lot of numerical methods have been developed to this end; the most important of them are reviewed in this paper. Particular attention is paid to the analytical relations between the methods, this allows comparisons on efficiency and accuracy between them and also to proceed to precise implementations of these techniques. While most of the methods have been developed for Coulomb interactions, we give also some analytical details to apply these methods to screened Coulomb (Yukawa interactions), inverse power law and dipolar interactions. Particular types of systems, the quasi-2D systems, are also considered in this paper. Quasi-2D systems represent a large class of physical systems where the spatial extension in one direction of the space is very small by comparison to the other two. These representations are very useful to describe the properties of interfaces, surfaces, fluids confined in slab geometry, etc. In computer simulations, these systems are studied with partial periodic boundary conditions: periodic boundary conditions are taken in directions where spatial extensions are large and some other boundary conditions are taken in directions with smaller extensions. In this review, we describe also the numerical methods developed to handle long ranged interactions in numerical simulations of quasi-2D systems. The properties of quasi-2D systems depend strongly on interactions between components; more specifically electrostatic and magnetic interactions and interactions with external fields are of particular interest in these systems.
Modeling and 2-D discrete simulation of dislocation dynamics for plastic deformation of metal
NASA Astrophysics Data System (ADS)
Liu, Juan; Cui, Zhenshan; Ou, Hengan; Ruan, Liqun
2013-05-01
Two methods are employed in this paper to investigate the dislocation evolution during plastic deformation of metal. One method is dislocation dynamic simulation of two-dimensional discrete dislocation dynamics (2D-DDD), and the other is dislocation dynamics modeling by means of nonlinear analysis. As screw dislocation is prone to disappear by cross-slip, only edge dislocation is taken into account in simulation. First, an approach of 2D-DDD is used to graphically simulate and exhibit the collective motion of a large number of discrete dislocations. In the beginning, initial grains are generated in the simulation cells according to the mechanism of grain growth and the initial dislocation is randomly distributed in grains and relaxed under the internal stress. During the simulation process, the externally imposed stress, the long range stress contribution of all dislocations and the short range stress caused by the grain boundaries are calculated. Under the action of these forces, dislocations begin to glide, climb, multiply, annihilate and react with each other. Besides, thermal activation process is included. Through the simulation, the distribution of dislocation and the stress-strain curves can be obtained. On the other hand, based on the classic dislocation theory, the variation of the dislocation density with time is described by nonlinear differential equations. Finite difference method (FDM) is used to solve the built differential equations. The dislocation evolution at a constant strain rate is taken as an example to verify the rationality of the model.
2-D and 3-D PIC simulations of a SLAC Klystrino
NASA Astrophysics Data System (ADS)
Spencer, Thomas; Luginsland, John; Hackett, Kirk; Haworth, Michael; Song, Liqun; Scheitrum, Glenn
2000-10-01
The Air Force Research Laboratory is collaborating with the Stanford Linear Accelerator Center in performing 3-D PIC simulations using ARGUS and ICEPIC on a klystrino with the following parameters: voltage of 110 kV, current of 2.4 A, frequency of 94 GHz, peak magnetic field of 4 kG. Results wll be presented and will be compared to 2-D MAGIC simulations, as well as to experimental test data. This work is supported in part by the Air Force Office of Scientific Research.
Penetration of tungsten-alloy rods into composite ceramic targets: Experiments and 2-D simulations
NASA Astrophysics Data System (ADS)
Rosenberg, Z.; Dekel, E.; Hohler, V.; Stilp, A. J.; Weber, K.
1998-07-01
A series of terminal ballistics experiments, with scaled tungsten-alloy penetrators, was performed on composite targets consisting of ceramic tiles glued to thick steel backing plates. Tiles of silicon-carbide, aluminum nitride, titanium-dibroide and boron-carbide were 20-80 mm thick, and impact velocity was 1.7 km/s. 2-D numerical simulations, using the PISCES code, were performed in order to simulate these shots. It is shown that a simplified version of the Johnson-Holmquist failure model can account for the penetration depths of the rods but is not enough to capture the effect of lateral release waves on these penetrations.
Kinetic distance and kinetic maps from molecular dynamics simulation.
Noé, Frank; Clementi, Cecilia
2015-10-13
Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly interconverting states. Here, we build upon diffusion map theory and define a kinetic distance metric for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here, we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets.
An interactive 2-D power-line modeling and simulation tool
NASA Astrophysics Data System (ADS)
Hull, David; Adelman, Ross
2012-06-01
The U.S. Army Research Laboratory's Power-Line unmanned aerial vehicle (UAV) Modeling and Simulation (ARL-PLUMS) is a tool for estimating and analyzing quasi-static electric and magnetic fields due to power lines. This tool consists of an interactive 2-D graphical user interface (GUI) and a compute engine that can be used to calculate and visualize the E-Field and H-Field due to as many as seven conductors (two 3-phase circuits and a ground wire). ARL-PLUMS allows the user to set the geometry of the lines and the load conditions on those lines, and then calculate Ey, Ez, Hy, or Hz along a linear path or cutting plane, or in the form of a movie. The path can be along the ground or in the air to simulate the fields that might be observed, for example, by a robotic vehicle or a UAV. ARL-PLUMS makes several simplifying assumptions in order to allow simulations to be completed on a laptop PC interactively. In most cases, the results are excellent, providing a "90% solution" in just a few minutes of total modeling and simulation time. This paper describes the physics used by ARL-PLUMS, including the simplifying assumptions and the 2-D Method of Moments solver. Examples of electric and magnetic fields for different wire configurations, including typical 3-phase distribution and transmissions lines, are provided. Comparisons to similar results using a full 3-D model are also shown, and a discussion of errors that may be expected from the 2-D simulations is provided.
Quantum simulation of 2D topological physics in a 1D array of optical cavities.
Luo, Xi-Wang; Zhou, Xingxiang; Li, Chuan-Feng; Xu, Jin-Shi; Guo, Guang-Can; Zhou, Zheng-Wei
2015-07-06
Orbital angular momentum of light is a fundamental optical degree of freedom characterized by unlimited number of available angular momentum states. Although this unique property has proved invaluable in diverse recent studies ranging from optical communication to quantum information, it has not been considered useful or even relevant for simulating nontrivial physics problems such as topological phenomena. Contrary to this misconception, we demonstrate the incredible value of orbital angular momentum of light for quantum simulation by showing theoretically how it allows to study a variety of important 2D topological physics in a 1D array of optical cavities. This application for orbital angular momentum of light not only reduces required physical resources but also increases feasible scale of simulation, and thus makes it possible to investigate important topics such as edge-state transport and topological phase transition in a small simulator ready for immediate experimental exploration.
A faster method for 3D/2D medical image registration—a simulation study
NASA Astrophysics Data System (ADS)
Birkfellner, Wolfgang; Wirth, Joachim; Burgstaller, Wolfgang; Baumann, Bernard; Staedele, Harald; Hammer, Beat; Claudius Gellrich, Niels; Jacob, Augustinus Ludwig; Regazzoni, Pietro; Messmer, Peter
2003-08-01
3D/2D patient-to-computed-tomography (CT) registration is a method to determine a transformation that maps two coordinate systems by comparing a projection image rendered from CT to a real projection image. Iterative variation of the CT's position between rendering steps finally leads to exact registration. Applications include exact patient positioning in radiation therapy, calibration of surgical robots, and pose estimation in computer-aided surgery. One of the problems associated with 3D/2D registration is the fact that finding a registration includes solving a minimization problem in six degrees of freedom (dof) in motion. This results in considerable time requirements since for each iteration step at least one volume rendering has to be computed. We show that by choosing an appropriate world coordinate system and by applying a 2D/2D registration method in each iteration step, the number of iterations can be grossly reduced from n6 to n5. Here, n is the number of discrete variations around a given coordinate. Depending on the configuration of the optimization algorithm, this reduces the total number of iterations necessary to at least 1/3 of it's original value. The method was implemented and extensively tested on simulated x-ray images of a tibia, a pelvis and a skull base. When using one projective image and a discrete full parameter space search for solving the optimization problem, average accuracy was found to be 1.0 +/- 0.6(°) and 4.1 +/- 1.9 (mm) for a registration in six parameters, and 1.0 +/- 0.7(°) and 4.2 +/- 1.6 (mm) when using the 5 + 1 dof method described in this paper. Time requirements were reduced by a factor 3.1. We conclude that this hardware-independent optimization of 3D/2D registration is a step towards increasing the acceptance of this promising method for a wide number of clinical applications.
A faster method for 3D/2D medical image registration--a simulation study.
Birkfellner, Wolfgang; Wirth, Joachim; Burgstaller, Wolfgang; Baumann, Bernard; Staedele, Harald; Hammer, Beat; Gellrich, Niels Claudius; Jacob, Augustinus Ludwig; Regazzoni, Pietro; Messmer, Peter
2003-08-21
3D/2D patient-to-computed-tomography (CT) registration is a method to determine a transformation that maps two coordinate systems by comparing a projection image rendered from CT to a real projection image. Iterative variation of the CT's position between rendering steps finally leads to exact registration. Applications include exact patient positioning in radiation therapy, calibration of surgical robots, and pose estimation in computer-aided surgery. One of the problems associated with 3D/2D registration is the fact that finding a registration includes solving a minimization problem in six degrees of freedom (dof) in motion. This results in considerable time requirements since for each iteration step at least one volume rendering has to be computed. We show that by choosing an appropriate world coordinate system and by applying a 2D/2D registration method in each iteration step, the number of iterations can be grossly reduced from n6 to n5. Here, n is the number of discrete variations around a given coordinate. Depending on the configuration of the optimization algorithm, this reduces the total number of iterations necessary to at least 1/3 of it's original value. The method was implemented and extensively tested on simulated x-ray images of a tibia, a pelvis and a skull base. When using one projective image and a discrete full parameter space search for solving the optimization problem, average accuracy was found to be 1.0 +/- 0.6(degrees) and 4.1 +/- 1.9 (mm) for a registration in six parameters, and 1.0 +/- 0.7(degrees) and 4.2 +/- 1.6 (mm) when using the 5 + 1 dof method described in this paper. Time requirements were reduced by a factor 3.1. We conclude that this hardware-independent optimization of 3D/2D registration is a step towards increasing the acceptance of this promising method for a wide number of clinical applications.
Matrone, G; Quaglia, F; Magenes, G
2010-01-01
Modern ultrasound imaging instrumentation for clinical applications allows real-time volumetric scanning of the patients' body. 4D imaging has been made possible thanks to the development of new echographic probes which consist in 2D phased arrays of piezoelectric transducers. In these new devices it is the system electronics which properly drives the matrix elements and focuses the beam in order to obtain a sequence of volumetric images. This paper introduces an ultrasound field simulator based on the Spatial Impulse Response method which is being properly developed to analyze the characteristics of the ultrasound field generated by a 2D phased array of transducers. Thanks to its high configurability by the user, it will represent a very useful tool for electronics designers in developing 4D ultrasound imaging systems components.
2D PIC simulations of a curved supercritical shock: dynamics of the whistler precursor
NASA Astrophysics Data System (ADS)
Stienlet, Joël.; Savoini, Philippe; Lembege, Bertrand
2010-05-01
The whistler precursor emitted from the curved terrestrial shock front plays an important role in pre-decelerating and heating the incoming solar wind. Most previous works have mainly analyzed the features of the whistler precursor emission for a 1D planar shock where it is forced to propagate along the shock normal (Liewer and al, 1991) or to propagate obliquely with respect to a fixed shock normal direction in 2D planar shock simulation (Krauss-Varban et al., 1995). In the present case, the dynamics of the precursor is analyzed with the help of a 2D full particle simulation for a continuously curved shock within the angular range 90o ≥ ?Bn ≥ 45o where ?Bn is the angle between the shock normal and the upstream magnetostatic field. Both electrons and ions dynamics are described by a self consistent approach. Our results show that (i) the whistler precursor extends far from the shock front mainly along the magnetostatic field (projected on the simulation plane) and not along the shock normal; (ii) the width of these curved wave fronts (precursor) strongly decreases when moving far from the shock front; (iii) at the shock front, the precursor is emitted within an angular range much larger than that predicted by linear theory; (iv) the damping rate of the whistler precursor is analyzed for different directions of the shock normal. Wave particle energy transfer is analysed, and these results will be discussed and compared with previous 1D and 2D simulations of planar shocks; (v) the whistler precursor is not monochromatic, and interferences between modes are evidenced by beats and wave-packets in front of the shock. The impact of this effect on damping rate measurements will be discussed.
Fast Acceleration of 2D Wave Propagation Simulations Using Modern Computational Accelerators
Wang, Wei; Xu, Lifan; Cavazos, John; Huang, Howie H.; Kay, Matthew
2014-01-01
Recent developments in modern computational accelerators like Graphics Processing Units (GPUs) and coprocessors provide great opportunities for making scientific applications run faster than ever before. However, efficient parallelization of scientific code using new programming tools like CUDA requires a high level of expertise that is not available to many scientists. This, plus the fact that parallelized code is usually not portable to different architectures, creates major challenges for exploiting the full capabilities of modern computational accelerators. In this work, we sought to overcome these challenges by studying how to achieve both automated parallelization using OpenACC and enhanced portability using OpenCL. We applied our parallelization schemes using GPUs as well as Intel Many Integrated Core (MIC) coprocessor to reduce the run time of wave propagation simulations. We used a well-established 2D cardiac action potential model as a specific case-study. To the best of our knowledge, we are the first to study auto-parallelization of 2D cardiac wave propagation simulations using OpenACC. Our results identify several approaches that provide substantial speedups. The OpenACC-generated GPU code achieved more than speedup above the sequential implementation and required the addition of only a few OpenACC pragmas to the code. An OpenCL implementation provided speedups on GPUs of at least faster than the sequential implementation and faster than a parallelized OpenMP implementation. An implementation of OpenMP on Intel MIC coprocessor provided speedups of with only a few code changes to the sequential implementation. We highlight that OpenACC provides an automatic, efficient, and portable approach to achieve parallelization of 2D cardiac wave simulations on GPUs. Our approach of using OpenACC, OpenCL, and OpenMP to parallelize this particular model on modern computational accelerators should be applicable to other computational models of wave propagation in
NASA Astrophysics Data System (ADS)
Mendoza-Torres, F.; Diaz-Viera, M. A.
2015-12-01
In many natural fractured porous media, such as aquifers, soils, oil and geothermal reservoirs, fractures play a crucial role in their flow and transport properties. An approach that has recently gained popularity for modeling fracture systems is the Discrete Fracture Network (DFN) model. This approach consists in applying a stochastic boolean simulation method, also known as object simulation method, where fractures are represented as simplified geometric objects (line segments in 2D and polygons in 3D). One of the shortcomings of this approach is that it usually does not consider the dependency relationships that may exist between the geometric properties of fractures (direction, length, aperture, etc), that is, each property is simulated independently. In this work a method for modeling such dependencies by copula theory is introduced. In particular, a nonparametric model using Bernstein copulas for direction-length fracture dependency in 2D is presented. The application of this method is illustrated in a case study for a fractured rock sample from a carbonate reservoir outcrop.
Tuning and simulating a 193-nm resist for 2D applications
NASA Astrophysics Data System (ADS)
Howard, William B.; Wiaux, Vincent; Ercken, Monique; Bui, Bang; Byers, Jeff D.; Pochkowski, Mike
2002-07-01
For some applications, the usefulness of lithography simulation results depends strongly on the matching between experimental conditions and the simulation input parameters. If this matching is optimized and other sources of error are minimized, then the lithography model can be used to explain printed wafer experimental results. Further, simulation can be useful in predicting the results or in choosing the correct set of experiments. In this paper, PROLITH and ProDATA AutoTune were used to systematically vary simulation input parameters to match measured results on printed wafers used in a 193 nm process. The validity of the simulation parameters was then checked using 3D simulation compared to 2D top-down SEM images. The quality of matching was evaluated using the 1D metrics of average gate CD and Line End Shortening (LES). To ensure the most accurate simulation, a new approach was taken to create a compound mask from GDSII contextual information surrounding an accurate SEM image of the reticle region of interest. Corrections were made to account for all metrology offsets.
2-D/3-D ECE imaging data for validation of turbulence simulations
NASA Astrophysics Data System (ADS)
Choi, Minjun; Lee, Jaehyun; Yun, Gunsu; Lee, Woochang; Park, Hyeon K.; Park, Young-Seok; Sabbagh, Steve A.; Wang, Weixing; Luhmann, Neville C., Jr.
2015-11-01
The 2-D/3-D KSTAR ECEI diagnostic can provide a local 2-D/3-D measurement of ECE intensity. Application of spectral analysis techniques to the ECEI data allows local estimation of frequency spectra S (f) , wavenumber spectra S (k) , wavernumber and frequency spectra S (k , f) , and bispectra b (f1 ,f2) of ECE intensity over the 2-D/3-D space, which can be used to validate turbulence simulations. However, the minimum detectable fluctuation amplitude and the maximum detectable wavenumber are limited by the temporal and spatial resolutions of the diagnostic system, respectively. Also, the finite measurement area of the diagnostic channel could introduce uncertainty in the spectra estimation. The limitations and accuracy of the ECEI estimated spectra have been tested by a synthetic ECEI diagnostic with the model and/or fluctuations calculated by GTS. Supported by the NRF of Korea under Contract No. NRF-2014M1A7A1A03029881 and NRF-2014M1A7A1A03029865 and by U.S. DOE grant DE-FG02-99ER54524.
2012-11-08
Comparison between adaptive and uniform discontinuous Galerkin simulations in dry 2D bubble experiments Andreas Müllera,∗, Jörn Behrensb, Francis X...joern.behrens@zmaw.de (Jörn Behrens), fxgirald@nps.edu ( Francis X. Giraldo), vwirth@uni-mainz.de (Volkmar Wirth) Accepted by Journal of Computational...Mon. Weather Rev. 120 (1992) 1675–1706. [3] D. P. Bacon , N. N. Ahmad, Z. Boybeyi, T. J. Dunn, M. S. Hall, P. C. S. Lee, R. A. Sarma, M. D. Turner, K. T
Simulations of two-particle interactions with 2D quantum walks in time
Schreiber, A.; Laiho, K.; Silberhorn, C.; Rohde, P. P.; Štefaňak, M.; Potoček, V.; Hamilton, C.; Jex, I.
2014-12-04
We present the experimental implementation of a quantum walk on a two-dimensional lattice and show how to employ the optical system to simulate the quantum propagation of two interacting particles. Our quantum walk in time transfers the spatial spread of a quantum walk into the time domain, which guarantees a high stability and scalability of the setup. We present with our device quantum walks over 12 steps on a 2D lattice. By changing the properties of the driving quantum coin, we investigate different kinds of two-particle interactions and reveal their impact on the occurring quantum propagation.
Solution of the field equations for 2-D electromagnetic direct implicit plasma simulation
NASA Astrophysics Data System (ADS)
Hewett, D. W.; Langdon, A. B.
1985-01-01
A direct implicit particle-in-cell (PIC) simulation model with full electromagnetic (EM) effects has been implemented in 2-D Cartesian geometry. The model, implemented with the D1 time differencing scheme, was first implemented in a 1-D electrostatic (ES) version to gain some experience with spatial differencing in forms suitable for extension to the full EM field in two dimensions. The implicit EM field solve is considerably different from the implicit ES code. The EM field calculation requires an inductive part as well as the electrostatic and the B field must be self-consistently advanced.
GMC COLLISIONS AS TRIGGERS OF STAR FORMATION. I. PARAMETER SPACE EXPLORATION WITH 2D SIMULATIONS
Wu, Benjamin; Loo, Sven Van; Tan, Jonathan C.; Bruderer, Simon
2015-09-20
We utilize magnetohydrodynamic (MHD) simulations to develop a numerical model for giant molecular cloud (GMC)–GMC collisions between nearly magnetically critical clouds. The goal is to determine if, and under what circumstances, cloud collisions can cause pre-existing magnetically subcritical clumps to become supercritical and undergo gravitational collapse. We first develop and implement new photodissociation region based heating and cooling functions that span the atomic to molecular transition, creating a multiphase ISM and allowing modeling of non-equilibrium temperature structures. Then in 2D and with ideal MHD, we explore a wide parameter space of magnetic field strength, magnetic field geometry, collision velocity, and impact parameter and compare isolated versus colliding clouds. We find factors of ∼2–3 increase in mean clump density from typical collisions, with strong dependence on collision velocity and magnetic field strength, but ultimately limited by flux-freezing in 2D geometries. For geometries enabling flow along magnetic field lines, greater degrees of collapse are seen. We discuss observational diagnostics of cloud collisions, focussing on {sup 13}CO(J = 2–1), {sup 13}CO(J = 3–2), and {sup 12}CO(J = 8–7) integrated intensity maps and spectra, which we synthesize from our simulation outputs. We find that the ratio of J = 8–7 to lower-J emission is a powerful diagnostic probe of GMC collisions.
Well-posedness and generalized plane waves simulations of a 2D mode conversion model
Imbert-Gérard, Lise-Marie
2015-12-15
Certain types of electro-magnetic waves propagating in a plasma can undergo a mode conversion process. In magnetic confinement fusion, this phenomenon is very useful to heat the plasma, since it permits to transfer the heat at or near the plasma center. This work focuses on a mathematical model of wave propagation around the mode conversion region, from both theoretical and numerical points of view. It aims at developing, for a well-posed equation, specific basis functions to study a wave mode conversion process. These basis functions, called generalized plane waves, are intrinsically based on variable coefficients. As such, they are particularly adapted to the mode conversion problem. The design of generalized plane waves for the proposed model is described in detail. Their implementation within a discontinuous Galerkin method then provides numerical simulations of the process. These first 2D simulations for this model agree with qualitative aspects studied in previous works.
Superclusters of galaxies from the 2dF redshift survey. 2. Comparison with simulations
Einasto, Jaan; Einasto, M.; Saar, E.; Tago, E.; Liivamagi, L.J.; Joeveer, M.J; Suhhonenko, I.; Hutsi, G.; Jaaniste, J.; Heinamaki, P.; Muller, V.; Knebe, A.; Tucker, D.; /Fermilab
2006-04-01
We investigate properties of superclusters of galaxies found on the basis of the 2dF Galaxy Redshift Survey, and compare them with properties of superclusters from the Millennium Simulation.We study the dependence of various characteristics of superclusters on their distance from the observer, on their total luminosity, and on their multiplicity. The multiplicity is defined by the number of Density Field (DF) clusters in superclusters. Using the multiplicity we divide superclusters into four richness classes: poor, medium, rich and extremely rich.We show that superclusters are asymmetrical and have multi-branching filamentary structure, with the degree of asymmetry and filamentarity being higher for the more luminous and richer superclusters. The comparison of real superclusters with Millennium superclusters shows that most properties of simulated superclusters agree very well with real data, the main differences being in the luminosity and multiplicity distributions.
NASA Astrophysics Data System (ADS)
Bezzeccheri, E.; Colasanti, S.; Falco, A.; Liguori, R.; Rubino, A.; Lugli, P.
2016-05-01
Vertical Organic Transistors and Phototransistors have been proven to be promising technologies due to the advantages of reduced channel length and larger sensitive area with respect to planar devices. Nevertheless, a real improvement of their performance is subordinate to the quantitative description of their operation mechanisms. In this work, we present a comparative study on the modeling of vertical and planar Organic Phototransistor (OPT) structures. Computer-based simulations of the devices have been carried out with Synopsys Sentaurus TCAD in a 2D Drift-Diffusion framework. The photoactive semiconductor material has been modeled using the virtual semiconductor approach as the archetypal P3HT:PC61BM bulk heterojunction. It has been found that both simulated devices have comparable electrical and optical characteristics, accordingly to recent experimental reports on the subject.
Highly-resolved 2D HYDRA simulations of Double-Shell Ignition Designs
Milovich, J L; Amendt, P; Hamza, A; Marinak, M; Robey, H
2006-06-30
Double-shell (DS) targets (Amendt, P. A. et al., 2002) offer a complementary approach to the cryogenic baseline design (Lindl, J. et al., 2004) for achieving ignition on the National Ignition Facility (NIF). Among the expected benefits are the ease of room temperature preparation and fielding, the potential for lower laser backscatter and the reduced need for careful shock timing. These benefits are offset, however, by demanding fabrication tolerances, e.g., shell concentricity and shell surface smoothness. In particular, the latter is of paramount importance since DS targets are susceptible to the growth of interface perturbations from impulsive and time-dependent accelerations. Previous work (Milovich, J. L. et al., 2004) has indicated that the growth of perturbations on the outer surface of the inner shell is potentially disruptive. To control this instability new designs have been proposed requiring bimetallic inner shells and material-matching mid-Z nanoporous foam. The challenges in manufacturing such exotic foams have led to a further evaluation of the densities and pore sizes needed to reduce the seeding of perturbations on the outer surface of the inner shell, thereby guiding the ongoing material science research efforts. Highly-resolved 2D simulations of porous foams have been performed to establish an upper limit on the allowable pore sizes for instability growth. Simulations indicate that foams with higher densities than previously thought are now possible. Moreover, while at the present time we are only able to simulate foams with average pore sizes larger than 1 micron (due to computational limitations), we can conclude that these pore sizes are potentially problematic. Furthermore, the effect of low-order hohlraum radiation asymmetries on the growth of intrinsic surface perturbations is also addressed. Highly-resolved 2D simulations indicate that the transverse flows that are set up by these low-order mode features (which can excite Kelvin
Spot size variation FCS in simulations of the 2D Ising model.
Burns, Margaret C; Nouri, Mariam; Veatch, Sarah L
2016-06-02
Spot variation fluorescence correlation spectroscopy (svFCS) was developed to study the movement and organization of single molecules in plasma membranes. This experimental technique varies the size of an illumination area while measuring correlations in time using standard fluorescence correlation methods. Frequently, this data is interpreted using the assumption that correlation measurements reflect the dynamics of single molecule motions, and not motions of the average composition. Here, we explore how svFCS measurements report on the dynamics of components diffusing within simulations of a 2D Ising model with a conserved order parameter. Simulated correlation functions report on both the fast dynamics of single component mobility and the slower dynamics of the average composition. Over a range of simulation conditions, a conventional svFCS analysis suggests the presence of anomalous diffusion even though single molecule motions are nearly Brownian in these simulations. This misinterpretation is most significant when the surface density of the fluorescent label is elevated, therefore we suggest future measurements be made over a range of tracer densities. Some simulation conditions reproduce qualitative features of published svFCS experimental data. Overall, this work emphasizes the need to probe membranes using multiple complimentary experimental methodologies in order to draw conclusions regarding the nature of spatial and dynamical heterogeneity in these systems.
Reynolds-Averaged Navier-Stokes Simulation of a 2D Circulation Control Wind Tunnel Experiment
NASA Technical Reports Server (NTRS)
Allan, Brian G.; Jones, Greg; Lin, John C.
2011-01-01
Numerical simulations are performed using a Reynolds-averaged Navier-Stokes (RANS) flow solver for a circulation control airfoil. 2D and 3D simulation results are compared to a circulation control wind tunnel test conducted at the NASA Langley Basic Aerodynamics Research Tunnel (BART). The RANS simulations are compared to a low blowing case with a jet momentum coefficient, C(sub u), of 0:047 and a higher blowing case of 0.115. Three dimensional simulations of the model and tunnel walls show wall effects on the lift and airfoil surface pressures. These wall effects include a 4% decrease of the midspan sectional lift for the C(sub u) 0.115 blowing condition. Simulations comparing the performance of the Spalart Allmaras (SA) and Shear Stress Transport (SST) turbulence models are also made, showing the SST model compares best to the experimental data. A Rotational/Curvature Correction (RCC) to the turbulence model is also evaluated demonstrating an improvement in the CFD predictions.
Tropical Oceanic Precipitation Processes over Warm Pool: 2D and 3D Cloud Resolving Model Simulations
NASA Technical Reports Server (NTRS)
Tao, W.- K.; Johnson, D.
1998-01-01
Rainfall is a key link in the hydrologic cycle as well as the primary heat source for the atmosphere, The vertical distribution of convective latent-heat release modulates the large-scale circulations of the tropics, Furthermore, changes in the moisture distribution at middle and upper levels of the troposphere can affect cloud distributions and cloud liquid water and ice contents. How the incoming solar and outgoing longwave radiation respond to these changes in clouds is a major factor in assessing climate change. Present large-scale weather and climate models simulate cloud processes only crudely, reducing confidence in their predictions on both global and regional scales. One of the most promising methods to test physical parameterizations used in General Circulation Models (GCMS) and climate models is to use field observations together with Cloud Resolving Models (CRMs). The CRMs use more sophisticated and physically realistic parameterizations of cloud microphysical processes, and allow for their complex interactions with solar and infrared radiative transfer processes. The CRMs can reasonably well resolve the evolution, structure, and life cycles of individual clouds and cloud systems, The major objective of this paper is to investigate the latent heating, moisture and momenti,im budgets associated with several convective systems developed during the TOGA COARE IFA - westerly wind burst event (late December, 1992). The tool for this study is the Goddard Cumulus Ensemble (CCE) model which includes a 3-class ice-phase microphysical scheme, The model domain contains 256 x 256 grid points (using 2 km resolution) in the horizontal and 38 grid points (to a depth of 22 km depth) in the vertical, The 2D domain has 1024 grid points. The simulations are performed over a 7 day time period. We will examine (1) the precipitation processes (i.e., condensation/evaporation) and their interaction with warm pool; (2) the heating and moisture budgets in the convective and
NASA Astrophysics Data System (ADS)
Berger, Richard; Chapman, T.; Banks, J. W.; Brunner, S.
2015-11-01
We present 2D+2V Vlasov simulations of Ion Acoustic waves (IAWs) driven by an external traveling-wave potential, ϕ0 (x , t) , with frequency, ω, and wavenumber, k, obeying the kinetic dispersion relation. Both electrons and ions are treated kinetically. Simulations with ϕ0 (x , t) , localized transverse to the propagation direction, model IAWs driven in a laser speckle. The waves bow with a positive or negative curvature of the wave fronts that depends on the sign of the nonlinear frequency shift ΔωNL , which is in turn determined by the magnitude of ZTe /Ti where Z is the charge state and Te , i is the electron, ion temperature. These kinetic effects result can cause modulational and self-focusing instabilities that transfer wave energy to kinetic energy. Linear dispersion properties of IAWs are used in laser propagation codes that predict the amount of light reflected by stimulated Brillouin scattering. At high enough amplitudes, the linear dispersion is invalid and these kinetic effects should be incorporated. Including the spatial and time scales of these instabilities is computationally prohibitive. We report progress including kinetic models in laser propagation codes. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 and funded by the Laboratory Research and Development Program at LLNL under project tracking code 15.
Efficient simulation of 2+2-D multi-species plasmas waves using an Eulerian Vlasov code
NASA Astrophysics Data System (ADS)
Banks, Jeffrey; Berger, Richard; Chapman, Thomas; Hittinger, Jeffrey; Bruner, Stephan
2013-10-01
We discuss multi-species aspects of the Eulerian-based kinetic code LOKI that evolves the Vlasov-Poisson system in 2+2-dimensional phase space (Banks et al., Phys. Plasmas 18, 052102 (2011)). In order to control the inherent cost associated with phase-space simulation, our approach uses a minimally diffuse, fourth-order-accurate finite-volume discretization (Banks and Hittinger, IEEE T. Plasma Sci. 39, 2198-2207). The scheme is discretely conservative and controls unphysical oscillations. The details of the numerical scheme will be presented, and the implementation on modern highly concurrent parallel computers will be discussed. We will present results of 2D simulations of propagating ion acoustic waves (IAWs) created using an external driving potential. The evolution of the plasma wave field and associated self-consistent distribution of trapped electrons and ions is studied after the external drive is turned off. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and funded by the Laboratory Research and Development Program at LLNL under project tracking code 12-ERD-061.
Numerical simulation of 2D buoyant jets in ice-covered and temperature-stratified water
NASA Astrophysics Data System (ADS)
Gu, Ruochuan
A two-dimensional (2D) unsteady simulation model is applied to the problem of a submerged warm water discharge into a stratified lake or reservoir with an ice cover. Numerical simulations and analyses are conducted to gain insight into large-scale convective recirculation and flow processes in a cold waterbody induced by a buoyant jet. Jet behaviors under various discharge temperatures are captured by directly modeling flow and thermal fields. Flow structures and processes are described by the simulated spatial and temporal distributions of velocity and temperature in various regions: deflection, recirculation, attachment, and impingement. Some peculiar hydrothermal and dynamic features, e.g. reversal of buoyancy due to the dilution of a warm jet by entraining cold ambient water, are identified and examined. Simulation results show that buoyancy is the most important factor controlling jet behavior and mixing processes. The inflow boundary is treated as a liquid wall from which the jet is offset. Similarity and difference in effects of boundaries perpendicular and parallel to flow, and of buoyancy on jet attachment and impingement, are discussed. Symmetric flow configuration is used to de-emphasize the Coanda effect caused by offset.
Rise characteristics of gas bubbles in a 2D rectangular column: VOF simulations vs experiments
Krishna, R.; Baten, J.M. van
1999-10-01
About five centuries ago, Leonardo da Vinci described the sinuous motion of gas bubbles rising in water. The authors have attempted to simulate the rise trajectories of bubbles of 4, 5, 7, 8, 9, 12, and 20 mm in diameter rising in a 2D rectangular column filled with water. The simulations were carried out using the volume-of-fluid (VOF) technique developed by Hirt and Nichols (J. Computational Physics, 39, 201--225 (1981)). To solve the Navier-Stokes equations of motion the authors used a commercial solver, CFX 4.1c of AEA Technology, UK. They developed their own bubble-tracking algorithm to capture sinuous bubble motions. The 4 and 5 mm bubbles show large lateral motions observed by Da Vinci. The 7, 8 and 9 mm bubble behave like jellyfish. The 12 mm bubble flaps its wings like a bird. The extent of lateral motion of the bubbles decreases with increasing bubble size. Bubbles larger than 20 mm in size assume a spherical cap form and simulations of the rise characteristics match experiments exactly. VOF simulations are powerful tools for a priori determination of the morphology and rise characteristics of bubbles rising in a liquid. Bubble-bubble interactions are also properly modeled by the VOF technique.
Atomistic simulations of J-integral in 2D graphene nanosystems.
Jin, Y; Yuan, F G
2005-12-01
The J-integral is investigated in discrete atomic systems using molecular mechanics simulations. A method of calculating J-integral in specified atomic domains is developed. Two cases, a semiinfinite crack in an infinite domain under the remote K-field deformation and a finite crack length in a finite geometry under the tensile and shear deformation prescribed on the boundary, are studied in the two-dimensional graphene sheets and the values of J-integral are obtained under small-strain deformation. The comparison with energy release rates in Mode I and Mode II based on continuum theory of linear elastic fracture mechanics show good agreements. Meanwhile, the nonlinear strain and stress relation of a 2D graphene sheet is evaluated and is fitted with a power law curve. With necessary modifications on the Tersoff-Brenner potential, the critical values of J-integral of 2D graphene systems, which denoted as Jc, are eventually obtained. The results are then compared with those from the relevant references.
Fanchi, J.R.
1985-04-01
Under the sponsorship of the US Department of Energy, a publicly available chemical simulator has been evaluated and substantially enhanced to serve as a useful tool for projecting polymer or chemical flood performance. The program, CHEM2D, is a two-dimensional, three-phase, nine-component finite-difference numerical simulator. It can model primary depletion, waterfloods, polymer floods, and micellar/polymer floods using heterogeneous linear, areal, or cross-sectional reservoir descriptions. The user may specify well performance as either pressure or rate constrained. Both a constant time step size and a variable time step size based on extrapolation of concentration changes are available as options. A solution technique which is implicit in pressure and explicit in saturations and concentrations is used. The major physical mechanisms that are modeled include adsorption, capillary trapping, cation exchange, dilution, dispersion, interfacial tension, binary or ternary phase behavior, non-Newtonian polymer rheology, and two-phase or three-phase relative permeability. Typical components include water, oil, surfactant, polymer, and three ions (chloride, calcium, and sodium). Components may partition amongst the aqueous, oleic, and microemulsion phases. Volume I of this report provides a discussion of the formulation and algorithms used within CHEM2D. Included in Volume I are a number of validation and illustrative examples, as well as the FORTRAN code. The CHEM2D user's manual, Volume II, contains both the input data sets for the examples presented in Volume I and an example output. All appendices and a phase behavior calculation program are collected in Volume III. 20 references.
Simulating ultrasound fields for 2D phased-array probes design optimization.
Matrone, Giulia; Quaglia, Fabio; Magenes, Giovanni
2011-01-01
Nowadays, ultrasound diagnostic imaging is one of the non-invasive techniques mostly used in the clinical practice. Recent advances in this field have brought to the development of small and portable systems. New bidimensional probes consisting of 2D phased arrays, allow to obtain real-time 3D representations of moving organs and blood vessels anatomy. Being the complexity of such 4D ultrasound imaging systems significantly increased, new challenges concerning electronics integration arise for designers. In this paper a software simulator is described, which has been developed in order to model ultrasound wave generation, pressure field distribution and echoes reception, with the aim to become a useful tool for optimizing the probe design. The paper mainly focuses on linear ultrasound field modeling; preliminary results on non-linear interactions with contrast agents are also here introduced.
NASA Astrophysics Data System (ADS)
Li, Jinghe; Song, Linping; Liu, Qing Huo
2016-02-01
A simultaneous multiple frequency contrast source inversion (CSI) method is applied to reconstructing hydrocarbon reservoir targets in a complex multilayered medium in two dimensions. It simulates the effects of a salt dome sedimentary formation in the context of reservoir monitoring. In this method, the stabilized biconjugate-gradient fast Fourier transform (BCGS-FFT) algorithm is applied as a fast solver for the 2D volume integral equation for the forward computation. The inversion technique with CSI combines the efficient FFT algorithm to speed up the matrix-vector multiplication and the stable convergence of the simultaneous multiple frequency CSI in the iteration process. As a result, this method is capable of making quantitative conductivity image reconstruction effectively for large-scale electromagnetic oil exploration problems, including the vertical electromagnetic profiling (VEP) survey investigated here. A number of numerical examples have been demonstrated to validate the effectiveness and capacity of the simultaneous multiple frequency CSI method for a limited array view in VEP.
NASA Astrophysics Data System (ADS)
Deca, Jan; Lapenta, Giovanni; Lembège, Bertrand; Divin, Andrey; Markidis, Stefano; Amaya, Jorge
2013-04-01
We present the first 2D/3D fully kinetic Particle-in-Cell simulations of the solar wind interaction with lunar crustal magnetic anomalies. The simulations are performed using the implicit electromagnetic Particle-in-Cell code iPIC3D [Markidis, Lapenta & Rizwan-uddin, 2010]. Multiscale physics is resolved for all plasma components (heavy ions, protons and electrons) in the code, recently updated with a set of open boundary conditions designed for solar wind-body interactions. We use a dipole to model the crustal anomaly. The dipole center is located outside the computational domain and the boundary representing the lunar surface is modeled as a particle-absorbing plane. Photo-emission from the lunar surface is at this point not included, but will be in future work. We study the behaviour of the dipole model with variable surface magnetic field strength under changing solar wind conditions and confirm that lunar crustal magnetic fields may indeed be strong enough to stand off the solar wind and form a mini-magnetosphere, as suggested by MHD simulations [Harnett & Winglee, 2000, 2002, 2003] and spacecraft observations [Kurata et al., 2005; Halekas et al., 2008; Wieser et al., 2010]. 3D-PIC simulations reveal to be very helpful to analyze the diversion/braking of the particle flux and the characteristics of the resulting particles accumulation. The particle flux to the surface is significantly reduced at the magnetic anomaly, surrounded by a region of enhanced density due to the magnetic mirror effect. Finally we will present preliminary results on the interaction of the solar wind with weaker magnetic anomalies in which highly non-adiabatic interactions are expected.
Hall-Effect Thruster Simulations with 2-D Electron Transport and Hydrodynamic Ions
NASA Technical Reports Server (NTRS)
Mikellides, Ioannis G.; Katz, Ira; Hofer, Richard H.; Goebel, Dan M.
2009-01-01
A computational approach that has been used extensively in the last two decades for Hall thruster simulations is to solve a diffusion equation and energy conservation law for the electrons in a direction that is perpendicular to the magnetic field, and use discrete-particle methods for the heavy species. This "hybrid" approach has allowed for the capture of bulk plasma phenomena inside these thrusters within reasonable computational times. Regions of the thruster with complex magnetic field arrangements (such as those near eroded walls and magnets) and/or reduced Hall parameter (such as those near the anode and the cathode plume) challenge the validity of the quasi-one-dimensional assumption for the electrons. This paper reports on the development of a computer code that solves numerically the 2-D axisymmetric vector form of Ohm's law, with no assumptions regarding the rate of electron transport in the parallel and perpendicular directions. The numerical challenges related to the large disparity of the transport coefficients in the two directions are met by solving the equations in a computational mesh that is aligned with the magnetic field. The fully-2D approach allows for a large physical domain that extends more than five times the thruster channel length in the axial direction, and encompasses the cathode boundary. Ions are treated as an isothermal, cold (relative to the electrons) fluid, accounting for charge-exchange and multiple-ionization collisions in the momentum equations. A first series of simulations of two Hall thrusters, namely the BPT-4000 and a 6-kW laboratory thruster, quantifies the significance of ion diffusion in the anode region and the importance of the extended physical domain on studies related to the impact of the transport coefficients on the electron flow field.
A new model for two-dimensional numerical simulation of pseudo-2D gas-solids fluidized beds
Li, Tingwen; Zhang, Yongmin
2013-10-11
Pseudo-two dimensional (pseudo-2D) fluidized beds, for which the thickness of the system is much smaller than the other two dimensions, is widely used to perform fundamental studies on bubble behavior, solids mixing, or clustering phenomenon in different gas-solids fluidization systems. The abundant data from such experimental systems are very useful for numerical model development and validation. However, it has been reported that two-dimensional (2D) computational fluid dynamic (CFD) simulations of pseudo-2D gas-solids fluidized beds usually predict poor quantitative agreement with the experimental data, especially for the solids velocity field. In this paper, a new model is proposed to improve the 2D numerical simulations of pseudo-2D gas-solids fluidized beds by properly accounting for the frictional effect of the front and back walls. Two previously reported pseudo-2D experimental systems were simulated with this model. Compared to the traditional 2D simulations, significant improvements in the numerical predictions have been observed and the predicted results are in better agreement with the available experimental data.
Simulation of abrasive flow machining process for 2D and 3D mixture models
NASA Astrophysics Data System (ADS)
Dash, Rupalika; Maity, Kalipada
2015-12-01
Improvement of surface finish and material removal has been quite a challenge in a finishing operation such as abrasive flow machining (AFM). Factors that affect the surface finish and material removal are media viscosity, extrusion pressure, piston velocity, and particle size in abrasive flow machining process. Performing experiments for all the parameters and accurately obtaining an optimized parameter in a short time are difficult to accomplish because the operation requires a precise finish. Computational fluid dynamics (CFD) simulation was employed to accurately determine optimum parameters. In the current work, a 2D model was designed, and the flow analysis, force calculation, and material removal prediction were performed and compared with the available experimental data. Another 3D model for a swaging die finishing using AFM was simulated at different viscosities of the media to study the effects on the controlling parameters. A CFD simulation was performed by using commercially available ANSYS FLUENT. Two phases were considered for the flow analysis, and multiphase mixture model was taken into account. The fluid was considered to be a
What Can We Learn about Magnetotail Reconnection from 2D PIC Harris-Sheet Simulations?
NASA Astrophysics Data System (ADS)
Goldman, M. V.; Newman, D. L.; Lapenta, G.
2016-03-01
The Magnetosphere Multiscale Mission (MMS) will provide the first opportunity to probe electron-scale physics during magnetic reconnection in Earth's magnetopause and magnetotail. This article will address only tail reconnection—as a non-steady-state process in which the first reconnected field lines advance away from the x-point in flux pile-up fronts directed Earthward and anti-Earthward. An up-to-date microscopic physical picture of electron and ion-scale collisionless tail reconnection processes is presented based on 2-D Particle-In-Cell (PIC) simulations initiated from a Harris current sheet and on Cluster and Themis measurements of tail reconnection. The successes and limitations of simulations when compared to measured reconnection are addressed in detail. The main focus is on particle and field diffusion region signatures in the tail reconnection geometry. The interpretation of these signatures is vital to enable spacecraft to identify physically significant reconnection events, to trigger meaningful data transfer from MMS to Earth and to construct a useful overall physical picture of tail reconnection. New simulation results and theoretical interpretations are presented for energy transport of particles and fields, for the size and shape of electron and ion diffusion regions, for processes occurring near the fronts and for the j × B (Hall) electric field.
NASA Astrophysics Data System (ADS)
Simmons, Daniel; Cools, Kristof; Sewell, Phillip
2016-11-01
Time domain electromagnetic simulation tools have the ability to model transient, wide-band applications, and non-linear problems. The Boundary Element Method (BEM) and the Transmission Line Modeling (TLM) method are both well established numerical techniques for simulating time-varying electromagnetic fields. The former surface based method can accurately describe outwardly radiating fields from piecewise uniform objects and efficiently deals with large domains filled with homogeneous media. The latter volume based method can describe inhomogeneous and non-linear media and has been proven to be unconditionally stable. Furthermore, the Unstructured TLM (UTLM) enables modelling of geometrically complex objects by using triangular meshes which removes staircasing and unnecessary extensions of the simulation domain. The hybridization of BEM and UTLM which is described in this paper is named the Boundary Element Unstructured Transmission-line (BEUT) method. It incorporates the advantages of both methods. The theory and derivation of the 2D BEUT method is described in this paper, along with any relevant implementation details. The method is corroborated by studying its correctness and efficiency compared to the traditional UTLM method when applied to complex problems such as the transmission through a system of Luneburg lenses and the modelling of antenna radomes for use in wireless communications.
Advancing Nucleosynthesis in Core-Collapse Supernovae Models Using 2D CHIMERA Simulations
NASA Astrophysics Data System (ADS)
Harris, J. A.; Hix, W. R.; Chertkow, M. A.; Bruenn, S. W.; Lentz, E. J.; Messer, O. B.; Mezzacappa, A.; Blondin, J. M.; Marronetti, P.; Yakunin, K.
2014-01-01
The deaths of massive stars as core-collapse supernovae (CCSN) serve as a crucial link in understanding galactic chemical evolution since the birth of the universe via the Big Bang. We investigate CCSN in polar axisymmetric simulations using the multidimensional radiation hydrodynamics code CHIMERA. Computational costs have traditionally constrained the evolution of the nuclear composition in CCSN models to, at best, a 14-species α-network. However, the limited capacity of the α-network to accurately evolve detailed composition, the neutronization and the nuclear energy generation rate has fettered the ability of prior CCSN simulations to accurately reproduce the chemical abundances and energy distributions as known from observations. These deficits can be partially ameliorated by "post-processing" with a more realistic network. Lagrangian tracer particles placed throughout the star record the temporal evolution of the initial simulation and enable the extension of the nuclear network evolution by incorporating larger systems in post-processing nucleosynthesis calculations. We present post-processing results of the four ab initio axisymmetric CCSN 2D models of Bruenn et al. (2013) evolved with the smaller α-network, and initiated from stellar metallicity, non-rotating progenitors of mass 12, 15, 20, and 25 M⊙ from Woosley & Heger (2007). As a test of the limitations of post-processing, we provide preliminary results from an ongoing simulation of the 15 M⊙ model evolved with a realistic 150 species nuclear reaction network in situ. With more accurate energy generation rates and an improved determination of the thermodynamic trajectories of the tracer particles, we can better unravel the complicated multidimensional "mass-cut" in CCSN simulations and probe for less energetically significant nuclear processes like the νp-process and the r-process, which require still larger networks.
Transport simulations of the C-2 and C-2U Field Reversed Configurations with the Q2D code
NASA Astrophysics Data System (ADS)
Onofri, Marco; Dettrick, Sean; Barnes, Daniel; Tajima, Toshiki; TAE Team
2016-10-01
The Q2D code is a 2D MHD code, which includes a neutral fluid and separate ion and electron temperatures, coupled with a 3D Monte Carlo code, which is used to calculate source terms due to neutral beams. Q2D has been benchmarked against the 1D transport code Q1D and is used to simulate the evolution of the C-2 and C-2U field reversed configuration experiments [1]. Q2D simulations start from an initial equilibrium and transport coefficients are chosen to match C-2 experimental data. C-2U is an upgrade of C-2, with more beam power and angled beam injection, which demonstrates plasma sustainment for 5 + ms. The simulations use the same transport coefficients for C-2 and C-2U, showing the formation of a steady state in C-2U, sustained by fast ion pressure and current drive.
Impact of phase change kinetics on the Mariana slab within the framework of 2-D mantle convection
NASA Astrophysics Data System (ADS)
Yoshioka, Shoichi; Torii, Yoku; Riedel, Michael R.
2015-03-01
Recent high-pressure and high-temperature experiments indicate that metastable olivine might persist in the cold core of a slab due to the low reaction rate of the olivine-wadsleyite phase transformation. Recent seismological observations detected a metastable olivine wedge that survives to a depth of 630 km in the Mariana slab. To consider the problem of non-equilibrium phase transformation, we developed a two-dimensional (2-D) Cartesian numerical code that incorporates the effects of kinetics into a thermal convection model. We consider the kinetics of the 410-km olivine-wadsleyite and the 660-km ringwoodite-Pv + Mw phase transformations, including the effects of water content at the 410-km phase boundary. The latent heat release of the 410-km non-equilibrium phase transformations inside the slab is also considered. The results show positive correlations between some of the controlling parameters and the length of the metastable olivine wedge: the faster the subducting velocity, and the lower the water content, the deeper is the metastable olivine wedge. With increasing depth of phase transformation, the effect of latent heat release is enhanced: heating of, at most, 100 °C occurs if olivine transforms into wadsleyite at a depth of approximately 570 km in our model setting. Temperature increase due to the latent heat released stimulates further phase transformation, resulting in further temperature increase, acting as a positive feedback effect. We also attempt to explain the seismological observations by calculating the temperature and phase structures in the Mariana slab. If we assume that the age of the Mariana slab is 150 Myr, the subduction velocity is 9.5 cm/yr, phase transformation occurs from the grain boundary of the parental phase, and the water content is 250 wt. ppm for a grain size of 1 mm, 300 wt. ppm for one of 5 mm, and 100 wt. ppm for intracrystalline transformation, then the metastable olivine wedge survives to a depth of 630 km, which is in
2D PIC simulations of a curved supercritical shock: dynamics of the whistler precursor
NASA Astrophysics Data System (ADS)
Stienlet, J.; Lembege, B.; Savoini, P.
2009-12-01
The whistler precursor emitted from the curved terrestrial shock front plays an important role in pre-decelerating and heating the incoming solar wind. Most previous works have mainly analyzed the features of the whistler precursor emission for a 1D planar shock where it is forced to propagate along the shock normal (Liewer and al, 1991) or to propagate obliquely with respect to a fixed shock normal direction in 2D planar shock simulation (Krauss-Varban et al., 1995). In the present case, the dynamics of the precursor is analyzed for a full curved shock with the help of a 2D full particle simulation where full curvature effects and both electrons and ions dynamics are described by a self consistent approach. Curvature effects continously cover all shock normal directions within the angular range 90° ≤ θBn ≤ 45° where θBn is the angle between the shock normal and the upstream magnetostatic field. This approach allows a free accessibility of the whistler precursor to a large angular range without any constraint. Preliminary results show that : (i) the whistler precursor strongly extends far from the shock front mainly along the magnetostatic field (projected on the simulation plane) but this extension is progressively reduced outside this privileged direction; (ii) wave fronts of the whistler precursor have a curvature similar to that of the main curved shock front but the width of these curved wave fronts strongly decreases when moving far from the shock front; (iii) near the shock front, the precursor is emitted within an angular range much larger than that predicted by linear theory; (iv) the critical angle of occurrence of the precursor fits with the theoretical value expected from Krasnoselskikh et al. (2002) model but this angle is not associated to a transition between stationary and non-stationary shocks in contrast with a statement announced by this theoretical model; and (v) the damping rate of the whistler precursor is analyzed for different
1D and 2D simulations of seismic wave propagation in fractured media
NASA Astrophysics Data System (ADS)
Möller, Thomas; Friederich, Wolfgang
2016-04-01
Fractures and cracks have a significant influence on the propagation of seismic waves. Their presence causes reflections and scattering and makes the medium effectively anisotropic. We present a numerical approach to simulation of seismic waves in fractured media that does not require direct modelling of the fracture itself, but uses the concept of linear slip interfaces developed by Schoenberg (1980). This condition states that at an interface between two imperfectly bonded elastic media, stress is continuous across the interface while displacement is discontinuous. It is assumed that the jump of displacement is proportional to stress which implies a jump in particle velocity at the interface. We use this condition as a boundary condition to the elastic wave equation and solve this equation in the framework of a Nodal Discontinuous Galerkin scheme using a velocity-stress formulation. We use meshes with tetrahedral elements to discretise the medium. Each individual element face may be declared as a slip interface. Numerical fluxes have been derived by solving the 1D Riemann problem for slip interfaces with elastic and viscoelastic rheology. Viscoelasticity is realised either by a Kelvin-Voigt body or a Standard Linear Solid. These fluxes are not limited to 1D and can - with little modification - be used for simulations in higher dimensions as well. The Nodal Discontinuous Galerkin code "neXd" developed by Lambrecht (2013) is used as a basis for the numerical implementation of this concept. We present examples of simulations in 1D and 2D that illustrate the influence of fractures on the seismic wavefield. We demonstrate the accuracy of the simulation through comparison to an analytical solution in 1D.
Self-Consistent, 2D Magneto-Hydrodynamic Simulations of Magnetically Driven Flyer Plates
NASA Astrophysics Data System (ADS)
Lemke, Raymond W.
2002-11-01
The intense magnetic field generated in the 20 MA Z-machine is used to accelerate flyer plates to high velocity for equation of state experiments. A peak magnetic drive pressure on the order of 2 Mbar can be generated, which accelerates an approximately 0.2 g aluminum disc to 21 km/s [1]. We have used 2D magneto-hydrodynamic (MHD) simulation to investigate the physics of accelerating flyer plates using multi-megabar magnetic drive pressures. A typical shock physics load is formed by a rectangular slab cathode enclosed by a hollow rectangular duct (the anode). The anode and cathode are connected (shorted) at one end. The electrodes are highly compressible at multi-megabar pressures. Electrode deformation that occurs during the rise time of the current pulse causes significant inductance increase, which reduces the peak current (drive pressure) relative to a static geometry. This important dynamic effect is modeled self-consistently by driving the MHD simulation with a circuit model of Z. Comparison of simulation results with highly accurate velocity interferometry measurements shows that the drive pressure waveform is affected by current losses and short circuiting in the machine, in conjunction with time varying load inductance. The understanding gained from these comparisons has allowed us to optimize shock physics loads using simulation. In this way a load was designed to produce a flyer velocity of 28 km/s, which was achieved experimentally on Z. We have identified paths to producing a flyer velocity of 40 km/s and peak isentropic pressure of 10 Mbar on the refurbished Z-machine [2]. Details of the modeling, the physics and comparisons with experiment are presented. [1] M. D. Knudson et al., Phys. Rev. Letters 87 (22), 22550-1 (2002). [2] R. W. Lemke et al., to be published in Proc. of the Int. Conf. on High Power Particle Beams and Dense Z-Pinches, Albuquerque, NM, June 23-28, 2002.
Simulation and analysis of solute transport in 2D fracture/pipe networks: the SOLFRAC program.
Bodin, Jacques; Porel, Gilles; Delay, Fred; Ubertosi, Fabrice; Bernard, Stéphane; de Dreuzy, Jean-Raynald
2007-01-05
The Time Domain Random Walk (TDRW) method has been recently developed by Delay and Bodin [Delay, F. and Bodin, J., 2001. Time domain random walk method to simulate transport by advection-dispersion and matrix diffusion in fracture networks. Geophys. Res. Lett., 28(21): 4051-4054.] and Bodin et al. [Bodin, J., Porel, G. and Delay, F., 2003c. Simulation of solute transport in discrete fracture networks using the time domain random walk method. Earth Planet. Sci. Lett., 6566: 1-8.] for simulating solute transport in discrete fracture networks. It is assumed that the fracture network can reasonably be represented by a network of interconnected one-dimensional pipes (i.e. flow channels). Processes accounted for are: (1) advection and hydrodynamic dispersion in the channels, (2) matrix diffusion, (3) diffusion into stagnant zones within the fracture planes, (4) sorption reactions onto the fracture walls and in the matrix, (5) linear decay, and (6) mass sharing at fracture intersections. The TDRW method is handy and very efficient in terms of computation costs since it allows for the one-step calculation of the particle residence time in each bond of the network. This method has been programmed in C++, and efforts have been made to develop an efficient and user-friendly software, called SOLFRAC. This program is freely downloadable at the URL (labo.univ-poitiers.fr/hydrasa/intranet/telechargement.htm). It calculates solute transport into 2D pipe networks, while considering different types of injections and different concepts of local dispersion within each flow channel. Post-simulation analyses are also available, such as the mean velocity or the macroscopic dispersion at the scale of the entire network. The program may be used to evaluate how a given transport mechanism influences the macroscopic transport behaviour of fracture networks. It may also be used, as is the case, e.g., with analytical solutions, to interpret laboratory or field tracer test experiments performed
Transient state kinetics tutorial using the kinetics simulation program, KINSIM.
Wachsstock, D H; Pollard, T D
1994-01-01
This article provides an introduction to a computer tutorial on transient state kinetics. The tutorial uses our Macintosh version of the computer program, KINSIM, that calculates the time course of reactions. KINSIM is also available for other popular computers. This program allows even those investigators not mathematically inclined to evaluate the rate constants for the transitions between the intermediates in any reaction mechanism. These rate constants are one of the insights that are essential for understanding how biochemical processes work at the molecular level. The approach is applicable not only to enzyme reactions but also to any other type of process of interest to biophysicists, cell biologists, and molecular biologists in which concentrations change with time. In principle, the same methods could be used to characterize time-dependent, large-scale processes in ecology and evolution. Completion of the tutorial takes students 6-10 h. This investment is rewarded by a deep understanding of the principles of chemical kinetics and familiarity with the tools of kinetics simulation as an approach to solve everyday problems in the laboratory. PMID:7811941
NASA Technical Reports Server (NTRS)
Li, Xiaofan; Sui, C.-H.; Lau, K.-M.
1999-01-01
The phase relation between the perturbation kinetic energy (K') associated with the tropical convection and the horizontal-mean moist available potential energy (bar-P) associated with environmental conditions is investigated by an energetics analysis of a numerical experiment. This experiment is performed using a 2-D cloud resolving model forced by the TOGA-COARE derived vertical velocity. The imposed upward motion leads to a decrease of bar-P directly through the associated vertical advective cooling, and to an increase of K' directly through cloud related processes, feeding the convection. The maximum K' and its maximum growth rate lags and leads, respectively, the maximum imposed large-scale upward motion by about 1-2 hours, indicating that convection is phase locked with large-scale forcing. The dominant life cycle of the simulated convection is about 9 hours, whereas the time scales of the imposed large-scale forcing are longer than the diurnal cycle. In the convective events, maximum growth of K' leads maximum decay of the perturbation moist available potential energy (P') by about 3 hours through vertical heat transport by perturbation circulation, and perturbation cloud heating. Maximum decay of P' leads maximum decay of bar-P by about one hour through the perturbation radiative, processes, the horizontal-mean cloud heating, and the large-scale vertical advective cooling. Therefore, maximum gain of K' occurs about 4-5 hours before maximum decay of bar-P.
Lee, K. H.; Lee, L. C.; Omura, Y.
2011-09-15
We carried out a series of 2D simulations to study the beam instability and cyclotron maser instability (CMI) with the initial condition that a population of tenuous energetic electrons with a ring-beam distribution is present in a magnetized background plasma. In this paper, weakly relativistic cases are discussed with the ring-beam kinetic energy ranging from 25 to 100 keV. The beam component leads to the two-stream or beam instability at an earlier stage, and the beam mode is coupled with Langmuir or whistler mode, leading to excitation of beam-Langmuir or beam-whistler waves. When the beam velocity is large with a strong beam instability, the initial ring-beam distribution is diffused in the parallel direction rapidly. The diffused distribution may still support CMI to amplify the X1 mode (the fundamental X mode). On the contrary, when the beam velocity is small and the beam instability is weak, CMI can amplify the Z1 (the fundamental Z mode) effectively while the O1 (the fundamental O mode) and X2 (the second harmonic X mode) modes are very weak and the X1 mode is not excited. In this report, different cases with various parameters are presented and discussed for a comprehensive understanding of ring-beam instabilities.
Extended MHD simulations of Rayleigh-Taylor instability with real frequency in a 2D slab
NASA Astrophysics Data System (ADS)
Goto, Ryosuke; Miura, Hideaki; Ito, Atsushi; Sato, Masahiko; Hatori, Tomoharu
2014-10-01
Small scale effects such as the Finite Larmor Radius (FLR) effect and the Hall term can change the linear and non-linear growth of the high wave number unstable modes of the pressure driven instability considerably. Here we consider a simple Rayleigh-Taylor (R-T) instability in a 2D slab, and study the effect of the Hall term and the FLR effect to the R-T instability by means of numerical simulations of the Braginskii-type extended MHD equations. As we have reported earlier, the linear growth rates of the high wave number modes are highly reduced when the Hall term and the FLR effect are added simultaneously. However, there appears little real frequency in the previous work. Since the diamagnetic drift associated with the real frequency is considered to affect the growth of the linear and nonlinear evolutions, we provide a new equilibrium in which appearance of the real frequency is expected and carry out numerical simulations. Influences of the real frequency on the growth rates as well as on the nonlinear mixing width for some combinations of the Hall and the FLR parameters are going to be presented.
2D IR spectra of cyanide in water investigated by molecular dynamics simulations
Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus
2013-01-01
Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.
2D properties of core turbulence on DIII-D and comparison to gyrokinetic simulations
Shafer, Morgan W; Fonck, R. J.; McKee, G. R.; Holland, Chris; White, A. E.; Schlossberg, D J
2012-01-01
Quantitative 2D characteristics of localized density fluctuations are presented over the range of 0.3 < r/a < 0.9 in L-mode plasmas on DIII-D [J. L. Luxon, Nucl. Fusion 42, 614 (2002)]. Broadband density fluctuations increase in amplitude from (n) over tilde/n < 0.5% in the deep core to (n) over tilde/n similar to 2.5% near the outer region. The observed Doppler-shift due to the E x B velocity matches well with the measured turbulence group and phase velocities (in toroidally rotating neutral beam heated plasmas). Turbulence decorrelation rates are found to be similar to 200 kHz at the edge and to decrease toward the core (0.45 < r/a < 0.9) where they approach the E x B shearing rate (similar to 50 kHz). Radial and poloidal correlation lengths are found to scale with the ion gyroradius and exhibit an asymmetric poloidally elongated eddy structure. The ensemble-averaged turbulent eddy structure changes its tilt with respect to the radial-poloidal coordinates in the core, consistent with an E x B shear mechanism. The 2D spatial correlation and wavenumber spectra [S(k(r); k(theta))] are presented and compared to nonlinear flux-tube GYRO simulations at two radii, r/a = 0.5 and r/a = 0.75, showing reasonable overall agreement, but the GYRO spectrum exhibits a peak at finite kr for r/a = 0.75 that is not observed experimentally; E x B shear may cause this discrepancy. (C) 2012 American Institute of Physics.
NASA Astrophysics Data System (ADS)
Jung, J.; Arakawa, A.
2015-12-01
Through explicitly resolved cloud-scale processes by embedded 2-D cloud-resolving models (CRMs), the Multiscale Modeling Framework (MMF) known as the superparameterization has been reasonably successful to simulate various atmospheric events over a wide range of time scales. One thing to be justified is, however, if the influence of complex 3-D topography can be adequately represented by the embedded 2-D CRMs. In this study, simulations are performed in the presence of a variety of topography with embedded 3-D and 2-D CRMs in a single-column inactive GCM. Through the comparison between these simulations, it is demonstrated that the 2-D representation of topography is able to simulate the statistics of precipitation due to 3-D topography reasonably well as long as the topographic characteristics, such as the mean and standard deviation, are closely recognized. It is also shown that the use of two perpendicular sets of 2-D representations tends to reduce the error due to a 2-D representation.
Magnetic Null Points in Kinetic Simulations of Space Plasmas
NASA Astrophysics Data System (ADS)
Olshevsky, Vyacheslav; Deca, Jan; Divin, Andrey; Peng, Ivy Bo; Markidis, Stefano; Innocenti, Maria Elena; Cazzola, Emanuele; Lapenta, Giovanni
2016-03-01
We present a systematic attempt to study magnetic null points and the associated magnetic energy conversion in kinetic particle-in-cell simulations of various plasma configurations. We address three-dimensional simulations performed with the semi-implicit kinetic electromagnetic code iPic3D in different setups: variations of a Harris current sheet, dipolar and quadrupolar magnetospheres interacting with the solar wind, and a relaxing turbulent configuration with multiple null points. Spiral nulls are more likely created in space plasmas: in all our simulations except lunar magnetic anomaly (LMA) and quadrupolar mini-magnetosphere the number of spiral nulls prevails over the number of radial nulls by a factor of 3-9. We show that often magnetic nulls do not indicate the regions of intensive energy dissipation. Energy dissipation events caused by topological bifurcations at radial nulls are rather rare and short-lived. The so-called X-lines formed by the radial nulls in the Harris current sheet and LMA simulations are rather stable and do not exhibit any energy dissipation. Energy dissipation is more powerful in the vicinity of spiral nulls enclosed by magnetic flux ropes with strong currents at their axes (their cross sections resemble 2D magnetic islands). These null lines reminiscent of Z-pinches efficiently dissipate magnetic energy due to secondary instabilities such as the two-stream or kinking instability, accompanied by changes in magnetic topology. Current enhancements accompanied by spiral nulls may signal magnetic energy conversion sites in the observational data.
2D fluid simulations of discharges at atmospheric pressure in reactive gas mixtures
NASA Astrophysics Data System (ADS)
Bourdon, Anne
2015-09-01
Since a few years, low-temperature atmospheric pressure discharges have received a considerable interest as they efficiently produce many reactive chemical species at a low energy cost. This potential is of great interest for a wide range of applications as plasma assisted combustion or biomedical applications. Then, in current simulations of atmospheric pressure discharges, there is the need to take into account detailed kinetic schemes. It is interesting to note that in some conditions, the kinetics of the discharge may play a role on the discharge dynamics itself. To illustrate this, we consider the case of the propagation of He-N2 discharges in long capillary tubes, studied for the development of medical devices for endoscopic applications. Simulation results put forward that the discharge dynamics and structure depend on the amount of N2 in the He-N2 mixture. In particular, as the amount of N2 admixture increases, the discharge propagation velocity in the tube increases, reaches a maximum for about 0 . 1 % of N2 and then decreases, in agreement with experiments. For applications as plasma assisted combustion with nanosecond repetitively pulsed discharges, there is the need to handle the very different timescales of the nanosecond discharge with the much longer (micro to millisecond) timescales of combustion processes. This is challenging from a computational point of view. It is also important to better understand the coupling of the plasma induced chemistry and the gas heating. To illustrate this, we present the simulation of the flame ignition in lean mixtures by a nanosecond pulsed discharge between two point electrodes. In particular, among the different discharge regimes of nanosecond repetitively pulsed discharges, a ``spark'' regime has been put forward in the experiments, with an ultra-fast local heating of the gas. For other discharge regimes, the gas heating is much weaker. We have simulated the nanosecond spark regime and have observed shock waves
Schmidt, Michael P; Martínez, Carmen Enid
2016-08-09
Protein adsorption onto clay minerals is a process with wide-ranging impacts on the environmental cycling of nutrients and contaminants. This process is influenced by kinetic and conformational factors that are often challenging to probe in situ. This study represents an in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopic investigation of the adsorption of a model protein (bovine serum albumin (BSA)) onto a clay mineral (montmorillonite) at four concentrations (1.50, 3.75, 7.50, and 15.0 μM) under environmentally relevant conditions. At all concentrations probed, FTIR spectra show that BSA readily adsorbs onto montmorillonite. Adsorption kinetics follow an Elovich model, suggesting that primary limitations on adsorption rates are surface-related heterogeneous energetic restrictions associated with protein rearrangement and lateral protein-protein interaction. BSA adsorption onto montmorillonite fits the Langmuir model, yielding K = 5.97 × 10(5) M(-1). Deconvolution and curve fitting of the amide I band at the end of the adsorption process (∼120 min) shows a large extent of BSA unfolding upon adsorption at 1.50 μM, with extended chains and turns increasing at the expense of α-helices. At higher concentrations/surface coverages, BSA unfolding is less pronounced and a more compact structure is assumed. Two-dimensional correlation spectroscopic (2D-COS) analysis reveals three different pathways corresponding to adsorbed conformations. At 1.50 μM, adsorption increases extended chains, followed by a loss in α-helices and a subsequent increase in turns. At 3.75 μM, extended chains decrease and then aggregated strands increase and side chains decrease, followed by a decrease in turns. With 7.50 and 15.0 μM BSA, the loss of side-chain vibrations is followed by an increase in aggregated strands and a subsequent decrease in turns and extended chains. Overall, the BSA concentration and resultant surface coverage have a profound
Kinetic simulation of hydrodynamic equivalent capsule implosions
NASA Astrophysics Data System (ADS)
Kwan, Thomas; Le, Ari; Schmitt, Mark; Herrmann, Hans
2016-10-01
We have carried out simulations of direct-drive hydrodynamic equivalent capsule implosion experiments conducted on Omega laser facility at the Laboratory of Laser Energetics of the University of Rochester. The capsules had a glass shell (SiO2) 4.87 μm with an inner diameter of 1086 μm. One was filled with deuterium (D) and tritium (T) at 6.635 and 2.475 atmospheric pressure respectively. The other capsule with D, T, and He-3 at 2.475, 2.475, and 5.55 atmospheric pressure respectively. The capsules were imploded with 60 laser beams with a square pulse length of 0.6ns of total energy of 15.6 kJ. One-dimensional radiation hydrodynamic calculations with HYDRA and kinetic particle/hybrid simulations with LSP are carried out for the post-shot analysis. HYDRA outputs at 0.6ns are linked to LSP, in which the electrons are treated as a fluid while all the ion dynamics is simulated by the standard particle-in-cell technique. Additionally, simulations with the new photon package in LSP are initiated at the beginning of the implosion to include the implosion phase of the capsule. The simulation results of density, temperature, and velocity profiles of the electrons, D, T, He-3, and SiO2species are compared with HYDRA. Detail comparisons among the kinetic simulations, rad-hydro simulations, and experimental results of neutron yield, yield ratio, fusion burn histories, and shell convergence will be presented to assess plasma kinetic effects. Work performed under the auspices of the US DOE by the Los Alamos National Laboratory under Contract No. W7405-ENG-36.
Simulation of bootstrap current in 2D and 3D ideal magnetic fields in tokamaks
NASA Astrophysics Data System (ADS)
Raghunathan, M.; Graves, J. P.; Cooper, W. A.; Pedro, M.; Sauter, O.
2016-09-01
We aim to simulate the bootstrap current for a MAST-like spherical tokamak using two approaches for magnetic equilibria including externally caused 3D effects such as resonant magnetic perturbations (RMPs), the effect of toroidal ripple, and intrinsic 3D effects such as non-resonant internal kink modes. The first approach relies on known neoclassical coefficients in ideal MHD equilibria, using the Sauter (Sauter et al 1999 Phys. Plasmas 6 2834) expression valid for all collisionalities in axisymmetry, and the second approach being the quasi-analytic Shaing-Callen (Shaing and Callen 1983 Phys. Fluids 26 3315) model in the collisionless regime for 3D. Using the ideal free-boundary magnetohydrodynamic code VMEC, we compute the flux-surface averaged bootstrap current density, with the Sauter and Shaing-Callen expressions for 2D and 3D ideal MHD equilibria including an edge pressure barrier with the application of resonant magnetic perturbations, and equilibria possessing a saturated non-resonant 1/1 internal kink mode with a weak internal pressure barrier. We compare the applicability of the self-consistent iterative model on the 3D applications and discuss the limitations and advantages of each bootstrap current model for each type of equilibrium.
NASA Astrophysics Data System (ADS)
Schaerlaekens, J.; Mallants, D.; Imûnek, J.; van Genuchten, M. Th.; Feyen, J.
1999-12-01
Microbiological degradation of perchloroethylene (PCE) under anaerobic conditions follows a series of chain reactions, in which, sequentially, trichloroethylene (TCE), cis-dichloroethylene (c-DCE), vinylchloride (VC) and ethene are generated. First-order degradation rate constants, partitioning coefficients and mass exchange rates for PCE, TCE, c-DCE and VC were compiled from the literature. The parameters were used in a case study of pump-and-treat remediation of a PCE-contaminated site near Tilburg, The Netherlands. Transport, non-equilibrium sorption and biodegradation chain processes at the site were simulated using the CHAIN_2D code without further calibration. The modelled PCE compared reasonably well with observed PCE concentrations in the pumped water. We also performed a scenario analysis by applying several increased reductive dechlorination rates, reflecting different degradation conditions (e.g. addition of yeast extract and citrate). The scenario analysis predicted considerably higher concentrations of the degradation products as a result of enhanced reductive dechlorination of PCE. The predicted levels of the very toxic compound VC were now an order of magnitude above the maximum permissible concentration levels.
Kinetic Vlasov simulations of collisionless magnetic reconnection
Schmitz, H.; Grauer, R.
2006-09-15
A fully kinetic Vlasov simulation of the Geospace Environment Modeling Magnetic Reconnection Challenge is presented. Good agreement is found with previous kinetic simulations using particle in cell (PIC) codes, confirming both the PIC and the Vlasov code. In the latter the complete distribution functions f{sub k} (k=i,e) are discretized on a numerical grid in phase space. In contrast to PIC simulations, the Vlasov code does not suffer from numerical noise and allows a more detailed investigation of the distribution functions. The role of the different contributions of Ohm's law are compared by calculating each of the terms from the moments of the f{sub k}. The important role of the off-diagonal elements of the electron pressure tensor could be confirmed. The inductive electric field at the X line is found to be dominated by the nongyrotropic electron pressure, while the bulk electron inertia is of minor importance. Detailed analysis of the electron distribution function within the diffusion region reveals the kinetic origin of the nongyrotropic terms.
Kinetic Simulations of Ion Beam Neutralization
Wang, Joseph
2010-05-21
Ion beam emission/neutralization is one of the most fundamental problems in spacecraft plasma interactions and electric propulsion. Although ion beam neutralization is readily achieved in experiments, the understanding of the underlying physical process remains at a rather primitive level. No theoretical or simulation models have convincingly explained the detailed neutralization mechanism, and no conclusions have been reached. This paper presents a fully kinetic simulation of ion beam neutralization and plasma beam propagation and discusses the physics of electron-ion coupling and the resulting propagation of a neutralized mesothermal plasma.
Accelerated simulation methods for plasma kinetics
NASA Astrophysics Data System (ADS)
Caflisch, Russel
2016-11-01
Collisional kinetics is a multiscale phenomenon due to the disparity between the continuum (fluid) and the collisional (particle) length scales. This paper describes a class of simulation methods for gases and plasmas, and acceleration techniques for improving their speed and accuracy. Starting from the Landau-Fokker-Planck equation for plasmas, the focus will be on a binary collision model that is solved using a Direct Simulation Monte Carlo (DSMC) method. Acceleration of this method is achieved by coupling the particle method to a continuum fluid description. The velocity distribution function f is represented as a combination of a Maxwellian M (the thermal component) and a set of discrete particles fp (the kinetic component). For systems that are close to (local) equilibrium, this reduces the number N of simulated particles that are required to represent f for a given level of accuracy. We present two methods for exploiting this representation. In the first method, equilibration of particles in fp, as well as disequilibration of particles from M, due to the collision process, is represented by a thermalization/dethermalization step that employs an entropy criterion. Efficiency of the representation is greatly increased by inclusion of particles with negative weights. This significantly complicates the simulation, but the second method is a tractable approach for negatively weighted particles. The accelerated simulation method is compared with standard PIC-DSMC method for both spatially homogeneous problems such as a bump-on-tail and inhomogeneous problems such as nonlinear Landau damping.
NASA Technical Reports Server (NTRS)
Shie, Chung-Lin; Tao, Wei-Kuo; Simpson, Joanne
2003-01-01
The 1999 Kwajalein Atoll field experiment (KWAJEX), one of several major TRMM (Tropical Rainfall Measuring Mission) field experiments, has successfully obtained a wealth of information and observation data on tropical convective systems over the western Central Pacific region. In this paper, clouds and convective systems that developed during three active periods (Aug 7-12, Aug 17-21, and Aug 29-Sep 13) around Kwajalein Atoll site are simulated using both 2D and 3D Goddard Cumulus Ensemble (GCE) models. Based on numerical results, the clouds and cloud systems are generally unorganized and short lived. These features are validated by radar observations that support the model results. Both the 2D and 3D simulated rainfall amounts and their stratiform contribution as well as the heat, water vapor, and moist static energy budgets are examined for the three convective episodes. Rainfall amounts are quantitatively similar between the two simulations, but the stratiform contribution is considerably larger in the 2D simulation. Regardless of dimension, fo all three cases, the large-scale forcing and net condensation are the two major physical processes that account for the evolution of the budgets with surface latent heat flux and net radiation solar and long-wave radiation)being secondary processes. Quantitative budget differences between 2D and 3D as well as between various episodes will be detailed.Morover, simulated radar signatures and Q1/Q2 fields from the three simulations are compared to each other and with radar and sounding observations.
Direct numerical simulation of a 2D-stented aortic heart valve at physiological flow rates.
Dimakopoulos, Y; Bogaerds, A C B; Anderson, P D; Hulsen, M A; Baaijens, F P T
2012-01-01
We study the nonlinear interaction of an aortic heart valve, composed of hyperelastic corrugated leaflets of finite density attached to a stented vessel under physiological flow conditions. In our numerical simulations, we use a 2D idealised representation of this arrangement. Blood flow is caused by a time-varying pressure gradient that mimics that of the aortic valve and corresponds to a peak Reynolds number equal to 4050. Here, we fully account for the shear-thinning behaviour of the blood and large deformations and contact between the leaflets by solving the momentum and mass balances for blood and leaflets. The mixed finite element/Galerkin method along with linear discontinuous Lagrange multipliers for coupling the fluid and elastic domains is adopted. Moreover, a series of challenging numerical issues such as the finite length of the computational domain and the conditions that should be imposed on its inflow/outflow boundaries, the accurate time integration of the parabolic and hyperbolic momentum equations, the contact between the leaflets and the non-conforming mesh refinement in part of the domain are successfully resolved. Calculations for the velocity and the shear stress fields of the blood reveal that boundary layers appear on both sides of a leaflet. The one along the ventricular side transfers blood with high momentum from the core region of the vessel to the annulus or the sinusoidal expansion, causing the continuous development of flow instabilities. At peak systole, vortices are convected in the flow direction along the annulus of the vessel, whereas during the closure stage of the valve, an extremely large vortex develops in each half of the flow domain.
NASA Astrophysics Data System (ADS)
Chen, Xihui; Sun, Zhigang; Sun, Jianfen; Song, Yingdong
2017-02-01
In this paper, a numerical model which incorporates the oxidation damage model and the finite element model of 2D plain woven composites is presented for simulation of the oxidation behaviors of 2D plain woven C/SiC composite under preloading oxidation atmosphere. The equal proportional reduction method is firstly proposed to calculate the residual moduli and strength of unidirectional C/SiC composite. The multi-scale method is developed to simulate the residual elastic moduli and strength of 2D plain woven C/SiC composite. The multi-scale method is able to accurately predict the residual elastic modulus and strength of the composite. Besides, the simulated residual elastic moduli and strength of 2D plain woven C/SiC composites under preloading oxidation atmosphere show good agreements with experimental results. Furthermore, the preload, oxidation time, temperature and fiber volume fractions of the composite are investigated to show their influences upon the residual elastic modulus and strength of 2D plain woven C/SiC composites.
NASA Technical Reports Server (NTRS)
Kapoor, Kamlesh; Anderson, Bernhard H.; Shaw, Robert J.
1994-01-01
A two-dimensional computational code, PRLUS2D, which was developed for the reactive propulsive flows of ramjets and scramjets, was validated for two-dimensional shock-wave/turbulent-boundary-layer interactions. The problem of compression corners at supersonic speeds was solved using the RPLUS2D code. To validate the RPLUS2D code for hypersonic speeds, it was applied to a realistic hypersonic inlet geometry. Both the Baldwin-Lomax and the Chien two-equation turbulence models were used. Computational results showed that the RPLUS2D code compared very well with experimentally obtained data for supersonic compression corner flows, except in the case of large separated flows resulting from the interactions between the shock wave and turbulent boundary layer. The computational results compared well with the experiment results in a hypersonic NASA P8 inlet case, with the Chien two-equation turbulence model performing better than the Baldwin-Lomax model.
Stability and accuracy of 3D neutron transport simulations using the 2D/1D method in MPACT
Collins, Benjamin; Stimpson, Shane; Kelley, Blake W.; ...
2016-08-25
We derived a consistent “2D/1D” neutron transport method from the 3D Boltzmann transport equation, to calculate fuel-pin-resolved neutron fluxes for realistic full-core Pressurized Water Reactor (PWR) problems. The 2D/1D method employs the Method of Characteristics to discretize the radial variables and a lower order transport solution to discretize the axial variable. Our paper describes the theory of the 2D/1D method and its implementation in the MPACT code, which has become the whole-core deterministic neutron transport solver for the Consortium for Advanced Simulations of Light Water Reactors (CASL) core simulator VERA-CS. We also performed several applications on both leadership-class and industry-classmore » computing clusters. Results are presented for whole-core solutions of the Watts Bar Nuclear Power Station Unit 1 and compared to both continuous-energy Monte Carlo results and plant data.« less
Stability and accuracy of 3D neutron transport simulations using the 2D/1D method in MPACT
NASA Astrophysics Data System (ADS)
Collins, Benjamin; Stimpson, Shane; Kelley, Blake W.; Young, Mitchell T. H.; Kochunas, Brendan; Graham, Aaron; Larsen, Edward W.; Downar, Thomas; Godfrey, Andrew
2016-12-01
A consistent "2D/1D" neutron transport method is derived from the 3D Boltzmann transport equation, to calculate fuel-pin-resolved neutron fluxes for realistic full-core Pressurized Water Reactor (PWR) problems. The 2D/1D method employs the Method of Characteristics to discretize the radial variables and a lower order transport solution to discretize the axial variable. This paper describes the theory of the 2D/1D method and its implementation in the MPACT code, which has become the whole-core deterministic neutron transport solver for the Consortium for Advanced Simulations of Light Water Reactors (CASL) core simulator VERA-CS. Several applications have been performed on both leadership-class and industry-class computing clusters. Results are presented for whole-core solutions of the Watts Bar Nuclear Power Station Unit 1 and compared to both continuous-energy Monte Carlo results and plant data.
Stability and accuracy of 3D neutron transport simulations using the 2D/1D method in MPACT
Collins, Benjamin; Stimpson, Shane; Kelley, Blake W.; Young, Mitchell T. H.; Kochunas, Brendan; Graham, Aaron; Larsen, Edward W.; Downar, Thomas; Godfrey, Andrew
2016-08-25
We derived a consistent “2D/1D” neutron transport method from the 3D Boltzmann transport equation, to calculate fuel-pin-resolved neutron fluxes for realistic full-core Pressurized Water Reactor (PWR) problems. The 2D/1D method employs the Method of Characteristics to discretize the radial variables and a lower order transport solution to discretize the axial variable. Our paper describes the theory of the 2D/1D method and its implementation in the MPACT code, which has become the whole-core deterministic neutron transport solver for the Consortium for Advanced Simulations of Light Water Reactors (CASL) core simulator VERA-CS. We also performed several applications on both leadership-class and industry-class computing clusters. Results are presented for whole-core solutions of the Watts Bar Nuclear Power Station Unit 1 and compared to both continuous-energy Monte Carlo results and plant data.
Kinetic Monte Carlo simulation of titin unfolding
NASA Astrophysics Data System (ADS)
Makarov, Dmitrii E.; Hansma, Paul K.; Metiu, Horia
2001-06-01
Recently, it has become possible to unfold a single protein molecule titin, by pulling it with an atomic-force-microscope tip. In this paper, we propose and study a stochastic kinetic model of this unfolding process. Our model assumes that each immunoglobulin domain of titin is held together by six hydrogen bonds. The external force pulls on these bonds and lowers the energy barrier that prevents the hydrogen bond from breaking; this increases the rate of bond breaking and decreases the rate of bond healing. When all six bonds are broken, the domain unfolds. Since the experiment controls the pulling rate, not the force, the latter is calculated from a wormlike chain model for the protein. In the limit of high pulling rate, this kinetic model is solved by a novel simulation method. In the limit of low pulling rate, we develop a quasiequilibrium rate theory, which is tested by simulations. The results are in agreement with the experiments: the distribution of the unfolding force and the dependence of the mean unfolding force on the pulling rate are similar to those measured. The simulations also explain why the work of the force to break bonds is less than the bond energy and why the breaking-force distribution varies from sample to sample. We suggest that one can synthesize polymers that are well described by our model and that they may have unusual mechanical properties.
SmaggIce 2D Version 1.8: Software Toolkit Developed for Aerodynamic Simulation Over Iced Airfoils
NASA Technical Reports Server (NTRS)
Choo, Yung K.; Vickerman, Mary B.
2005-01-01
SmaggIce 2D version 1.8 is a software toolkit developed at the NASA Glenn Research Center that consists of tools for modeling the geometry of and generating the grids for clean and iced airfoils. Plans call for the completed SmaggIce 2D version 2.0 to streamline the entire aerodynamic simulation process--the characterization and modeling of ice shapes, grid generation, and flow simulation--and to be closely coupled with the public-domain application flow solver, WIND. Grid generated using version 1.8, however, can be used by other flow solvers. SmaggIce 2D will help researchers and engineers study the effects of ice accretion on airfoil performance, which is difficult to do with existing software tools because of complex ice shapes. Using SmaggIce 2D, when fully developed, to simulate flow over an iced airfoil will help to reduce the cost of performing flight and wind-tunnel tests for certifying aircraft in natural and simulated icing conditions.
NASA Astrophysics Data System (ADS)
Wang, X.; Cai, M.
2016-11-01
A nonlinear velocity model that considers the influence of confinement and rock mass failure on wave velocity is developed. A numerical method, which couples FLAC and SPECFEM2D, is developed for ground motion modeling near excavation boundaries in underground mines. The motivation of developing the FLAC/SPECFEM2D coupled approach is to take merits of each code, such as the stress analysis capability in FLAC and the powerful wave propagation analysis capability in SPECFEM2D. Because stress redistribution and failure of the rock mass around an excavation are considered, realistic non-uniform velocity fields for the SPECFEM2D model can be obtained, and this is a notable feature of this study. Very large differences in wavefields and ground motion are observed between the results from the non-uniform and the uniform velocity models. If the non-uniform velocity model is used, the ground motion around a stope can be amplified up to five times larger than that given by the design scaling law. If a uniform velocity model is used, the amplification factor is only about three. Using the FLAC/SPECFEM2D coupled modeling approach, accurate velocity models can be constructed and this in turn will assist in predicting ground motions accurately around underground excavations.
Origin of energetic ions observed in the terrestrial ion foreshock : 2D full-particle simulations
NASA Astrophysics Data System (ADS)
Savoini, Philippe; Lembege, bertrand
2016-04-01
Collisionless shocks are well-known structures in astrophysical environments which dissipate bulk flow kinetic energy and accelerate large fraction of particle. Spacecrafts have firmly established the existence of the so-called terrestrial foreshock region magnetically connected to the shock and filled by two distinct populations in the quasi-perpendicular shock region (i.e. for 45r{ } ≤ quad θ Bn quad ≤ 90r{ }, where θ Bn is the angle between the shock normal and the upstream magnetic field) : (i) the field-aligned ion beams or `` FAB '' characterized by a gyrotropic distributionsout{,} and (ii) the gyro-phase bunched ions or `` GPB '' characterized by a NON gyrotropic distribution. The present work is based on the use of two dimensional PIC simulation of a curved shock and associated foreshock region where full curvature effects, time of flight effects and both electrons and ions dynamics are fully described by a self consistent approach. Our previous analysis (Savoini et Lembège, 2015) has evidenced that these two types of backstreaming populations can originate from the shock front itself without invoking any local diffusion by ion beam instabilities. Present results are focussed on individual ion trajectories and evidence that "FAB" population is injected into the foreshock mainly along the shock front whereas the "GPB" population penetrates more deeply the shock front. Such differences explain why the "FAB" population loses their gyro-phase coherency and become gyrotropic which is not the case for the "GPB". The impact of these different injection features on the energy gain for each ion population will be presented in détails. Savoini, P. and B. Lembège (2015), `` Production of nongyrotropic and gyrotropic backstreaming ion distributions in the quasi-perpendicular ion foreshock région '', J. Geophys. Res., 120, pp 7154-7171, doi = 10.1002/2015JA021018.
Middleton, Chris T.; Woys, Ann Marie; Mukherjee, Sudipta S.; Zanni, Martin T.
2010-01-01
We describe a methodology for studying protein kinetics using a rapid-scan technology for collecting 2D IR spectra. In conjunction with isotope labeling, 2D IR spectroscopy is able to probe the secondary structure and environment of individual residues in polypeptides and proteins. It is particularly useful for membrane and aggregate proteins. Our rapid-scan technology relies on a mid-IR pulse shaper that computer generates the pulse shapes, much like in an NMR spectrometer. With this device, data collection is faster, easier, and more accurate. We describe our 2D IR spectrometer, as well as protocols for 13C=18O isotope labeling, and then illustrate the technique with an application to the aggregation of the human islet amyloid polypeptide form type 2 diabetes. PMID:20472067
Tyndale, R F; Li, Y; Li, N Y; Messina, E; Miksys, S; Sellers, E M
1999-08-01
We investigated the enzymatic function, stability, and regional distribution of rat brain cytochrome P-450 (CYP) 2D1 activity. CYP2D1 is the homolog of human CYP2D6, a genetically variable enzyme that activates or inactivates many clinical drugs acting on the central nervous system (e.g., antidepressants, monoamine oxidase inhibitors, serotonin uptake inhibitors, and neuroleptics), drugs of abuse (e.g., amphetamine and codeine), neurotoxins (e.g., 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, 1,2,3, 4-tetrahydroquinoline), and endogenous neurochemicals (e.g., tryptamine). The CYP2D family has been identified in rodent, canine, and primate brain. Conversion of dextromethorphan to dextrorphan by rat brain membranes was assayed by HPLC and was dependent on NADPH, protein concentration, and incubation time. Significant loss of activity was observed in some homogenizing buffers and after freezing of whole tissues or membrane preparations. Dextromethorphan (0.5-640 microM) metabolism was mediated by high- and low-affinity enzyme systems; K(m1) was 2.7 +/- 2.6 and K(m2) was 757 +/- 156 microM (n = 3 rats, mean +/- S.E.). The enzyme activity was significantly (p <.01) and stereoselectively inhibited by CYP2D1 inhibitors quinine and quinidine (not by CYP2C or CYP3A inhibitors), and by anti-CYP2D6 peptide antiserum (not by anti-CYP2C, -CYP2B, or -CYP3A antibodies). The enzymatic activity demonstrated significant brain regional variation (n = 10 regions, p <.001). These data characterize CYP2D1-mediated dextromethorphan metabolism in rat brain and suggest that localized metabolism of other CYP2D1 substrates (drugs, neurotoxins, and possibly endogenous compounds) within the brain will occur. In humans, CYP2D6 is genetically polymorphic; the variable expression of brain CYP2D6 may result in interindividual differences in central drug and neurotoxin metabolism, possibly contributing to interindividual differences in drug effects and neurotoxicity.
MAGNETIC NULL POINTS IN KINETIC SIMULATIONS OF SPACE PLASMAS
Olshevsky, Vyacheslav; Innocenti, Maria Elena; Cazzola, Emanuele; Lapenta, Giovanni; Deca, Jan; Divin, Andrey; Peng, Ivy Bo; Markidis, Stefano
2016-03-01
We present a systematic attempt to study magnetic null points and the associated magnetic energy conversion in kinetic particle-in-cell simulations of various plasma configurations. We address three-dimensional simulations performed with the semi-implicit kinetic electromagnetic code iPic3D in different setups: variations of a Harris current sheet, dipolar and quadrupolar magnetospheres interacting with the solar wind, and a relaxing turbulent configuration with multiple null points. Spiral nulls are more likely created in space plasmas: in all our simulations except lunar magnetic anomaly (LMA) and quadrupolar mini-magnetosphere the number of spiral nulls prevails over the number of radial nulls by a factor of 3–9. We show that often magnetic nulls do not indicate the regions of intensive energy dissipation. Energy dissipation events caused by topological bifurcations at radial nulls are rather rare and short-lived. The so-called X-lines formed by the radial nulls in the Harris current sheet and LMA simulations are rather stable and do not exhibit any energy dissipation. Energy dissipation is more powerful in the vicinity of spiral nulls enclosed by magnetic flux ropes with strong currents at their axes (their cross sections resemble 2D magnetic islands). These null lines reminiscent of Z-pinches efficiently dissipate magnetic energy due to secondary instabilities such as the two-stream or kinking instability, accompanied by changes in magnetic topology. Current enhancements accompanied by spiral nulls may signal magnetic energy conversion sites in the observational data.
Kinetic simulations of collisionless magnetic reconnection
NASA Astrophysics Data System (ADS)
Aunai, N.; Dargent, J.; Lavraud, B.; Ciardi, A.; Drouin, M.; Smets, R.
2016-12-01
This paper focuses on magnetic reconnection and its role in magnetospheric physics, where collisions are inexistant. In this context, the presence of a very cold ion population of ionospheric origin is known to have an important contribution to the particle density at the magnetopause. However, besides this mass loading effect, consequences of their extremely low temperature, and therefore of their must smaller gyroscale, have not yet been addressed from a modeling viewpoint. This study presents two fully kinetic simulations with and without cold ions in the magnetosphere and highlights how their small Larmor radius can change signatures expected to be proxy of the X line in spacecraft measurements. In a second part, this paper addresses shortly the problem of the X line orientation in an asymmetric system. Using this time hybrid kinetic simulations, we show the X line aligned with the bisector of upstream magnetic field vectors results in faster reconnection rate. This have consequences regarding where reconnection at the magnetopause, although models here do not include large scale dynamics. We conclude with perspectives regarding future developments to address multi-scale magnetic reconnection dynamics at the magnetopause.
Kinetic Simulations of Dense Plasma Focus Breakdown
NASA Astrophysics Data System (ADS)
Schmidt, A.; Higginson, D. P.; Jiang, S.; Link, A.; Povilus, A.; Sears, J.; Bennett, N.; Rose, D. V.; Welch, D. R.
2015-11-01
A dense plasma focus (DPF) device is a type of plasma gun that drives current through a set of coaxial electrodes to assemble gas inside the device and then implode that gas on axis to form a Z-pinch. This implosion drives hydrodynamic and kinetic instabilities that generate strong electric fields, which produces a short intense pulse of x-rays, high-energy (>100 keV) electrons and ions, and (in deuterium gas) neutrons. A strong factor in pinch performance is the initial breakdown and ionization of the gas along the insulator surface separating the two electrodes. The smoothness and isotropy of this ionized sheath are imprinted on the current sheath that travels along the electrodes, thus making it an important portion of the DPF to both understand and optimize. Here we use kinetic simulations in the Particle-in-cell code LSP to model the breakdown. Simulations are initiated with neutral gas and the breakdown modeled self-consistently as driven by a charged capacitor system. We also investigate novel geometries for the insulator and electrodes to attempt to control the electric field profile. The initial ionization fraction of gas is explored computationally to gauge possible advantages of pre-ionization which could be created experimentally via lasers or a glow-discharge. Prepared by LLNL under Contract DE-AC52-07NA27344.
Simulation study of 2D spectrum of molecular aggregates coupled to correlated vibrations
NASA Astrophysics Data System (ADS)
Abramavicius, Darius; Butkus, Vytautas; Valkunas, Leonas; Mukamel, Shaul
2011-03-01
Oscillatory dynamics of two-dimensional (2D) spectra of photosynthetic pigment-protein complexes raise the questions of how to disentangle various origins of these oscillations, which may include quantum beats, quantum transport, or molecular vibrations. We study the effects of correlated overdamped fluctuations and under-damped vibrations on the 2D spectra of Fenna-Matthews-Olson (FMO) aggregate, which has well-resolved exciton resonances, and a circular porphyrin aggregate (P6), whose absorption shows vibrational progression. We use a generic exciton Hamiltonian coupled to a bath, characterized by a spectral density. Fluctuations have smooth, while vibtations have δ -type spectral densities. We show how various scenarios of correlated molecular fluctuations lead to some highly oscillatory crosspeaks. Molecular vibrations cause progression of diagonal peaks in the 2D spectrum and make their corresponding cross-peaks highly oscillatory. We, thus, demonstrate that bath fluctuations and molecular vibrations of realistic molecular aggregates are highly entangled in 2D spectroscopy. DA acknowledges grant VP1-3.1-SMM-07-V, SM - the grants CHE0745892 (NSF), DRPA BAA-10-40 QUBE.
NASA Technical Reports Server (NTRS)
Proffitt, M. H.; Solomon, S.; Loewenstein, M.
1992-01-01
A linear reference relationship between O3 and N2O has been used to estimate polar winter O3 loss from aircraft data taken in the lower stratosphere. Here, this relationship is evaluated at high latitudes by comparing it with a 2D model simulation and with NIMBUS 7 satellite measurements. Although comparisons with satellite measurements are limited to January through May, the model simulations are compared during other seasons. The model simulations and the satellite data are found to be consistent with the winter O3 loss analysis. It is shown that such analyses are likely to be inappropriate during other seasons.
2D Numerical simulations of intraoceanic subduction: the case study of the Ligurian Alps.
NASA Astrophysics Data System (ADS)
Malatesta, Cristina; Gerya, Taras; Federico, Laura; Scambelluri, Marco; Crispini, Laura; Capponi, Giovanni
2010-05-01
Intraoceanic subduction is an important part of the present and past subduction systems, and some features of such process are not yet fully understood. We therefore studied intraoceanic subduction zones with the help of 2D numerical models, analyzing the parameters influencing their evolution in time and space. We applied the finite differences method on a rectangular grid, to calculate properties such as pressure, temperatures and velocities inside the models solving a set of equations. The latter comprise the Stokes equation of motion, the continuity equation and the heat transport equation. Temperature and velocities are computed on the nodes of the grid whereas pressures are calculated for the geometrical centers of the cells. We defined material properties such as density or viscosity on marker points, initially positioned on a regular rectangular grid. The markers and therefore the material properties are moved through the mesh according to the velocity field using the forth order Runge-Kutta method (Gerya et al. 2002). Subduction is forced to begin at a weak zone in the lithospheric mantle within an oceanic basin of prescribed width. The effect of different arrangements of rock bodies inside the subducting lithosphere on the evolution of the process was carefully analyzed. In particular we reproduced two distinct structures of the oceanic lithosphere: i) the layered oceanic crust made up of a stratified succession typical of fast-spreading ridges and ii) the oceanic lithosphere typical of slow and ultra-slow spreading centers, where an incomplete sequence is observable. The latter structure lacks a sheeted dike complex, has a low volume of gabbros and basalts and gabbros form discrete intrusions in variably serpentinized peridotites (Lagabrielle et al., 1997; Mével, 2003). Such an "heterogeneous" structure is characteristic of the Alpine and Appennine ophiolites that characterized the Mesozoic Ligurian Tethys located between Europe and Adria. The depth of
Mach number validation of a new zonal CFD method (ZAP2D) for airfoil simulations
NASA Technical Reports Server (NTRS)
Strash, Daniel J.; Summa, Michael; Yoo, Sungyul
1991-01-01
A closed-loop overlapped velocity coupling procedure has been utilized to combine a two-dimensional potential-flow panel code and a Navier-Stokes code. The fully coupled two-zone code (ZAP2D) has been used to compute the flow past a NACA 0012 airfoil at Mach numbers ranging from 0.3 to 0.84 near the two-dimensional airfoil C(lmax) point for a Reynolds number of 3 million. For these cases, the grid domain size can be reduced to 3 chord lengths with less than 3-percent loss in accuracy for freestream Mach numbers through 0.8. Earlier validation work with ZAP2D has demonstrated a reduction in the required Navier-Stokes computation time by a factor of 4 for subsonic Mach numbers. For this more challenging condition of high lift and Mach number, the saving in CPU time is reduced to a factor of 2.
EDGE2D Simulations of JET{sup 13}C Migration Experiments
J.D. Strachan; J.P. Coad; G. Corrigan; G.F. Matthews; J. Spence
2004-06-16
Material migration has received renewed interest due to tritium retention associated with carbon transport to remote vessel locations. Those results influence the desirability of carbon usage on ITER. Subsequently, additional experiments have been performed, including tracer experiments attempting to identify material migration from specific locations. In this paper, EDGE2D models a well-diagnosed JET{sup 13}C tracer migration experiment. The role of SOL flows upon the migration patterns is identified.
Simulation of multi-steps thermal transition in 2D spin-crossover nanoparticles
NASA Astrophysics Data System (ADS)
Jureschi, Catalin-Maricel; Pottier, Benjamin-Louis; Linares, Jorge; Richard Dahoo, Pierre; Alayli, Yasser; Rotaru, Aurelian
2016-04-01
We have used an Ising like model to study the thermal behavior of a 2D spin crossover (SCO) system embedded in a matrix. The interaction parameter between edge SCO molecules and its local environment was included in the standard Ising like model as an additional term. The influence of the system's size and the ratio between the number of edge molecules and the other molecules were also discussed.
Numerical Simulation of Slinger Combustor Using 2-D Axisymmetric Computational Model
NASA Astrophysics Data System (ADS)
Lee, Semin; Park, Soo Hyung; Lee, Donghun
2010-06-01
Small-size turbojet engines have difficulties in maintaining the chemical reaction due to the limitation of chamber size. The combustion chamber is generally designed to improve the reaction efficiency by the generation of vortices in the chamber and to enhance air-fuel mixing characteristics. In the initial stage of designing the combustor, analysis of the 3-D full configuration is not practical due to the huge time consuming computation and grid generation followed by modifications of the geometry. In the present paper, an axisymmetric model maintaining geometric similarity and flow characteristic of 3-D configuration is developed. Based on numerical results from the full 3-D configuration, model reduction is achieved toward 2-D axisymmetric configuration. In the modeling process, the area and location of each hole in 3-D full configuration are considered reasonably and replaced to the 2-D axisymmetric model. By using the 2-D axisymmetric model, the factor that can affect the performance is investigated with the assumption that the flow is non-reacting and turbulent. Numerical results from the present model show a good agreement with numerical results from 3-D full configuration model such as existence of vortex pair in forward region and total pressure loss. By simplifying the complex 3-D model, computing time can be remarkably reduced and it makes easy to find effects of geometry modification.
Global kinetic ballooning mode simulations in BOUT++
NASA Astrophysics Data System (ADS)
Ma, C. H.; Xu, X. Q.
2017-01-01
We report on simulation results of a 3+1 gyro-Landau-fluid (GLF) model in BOUT++ framework, which contributes to increasing the physics understanding of the edge turbulence. We find that there is no second stability region of kinetic ballooning modes (KBM) in the concentric circular geometry. The first unstable β of KBM decreases below the ideal ballooning mode threshold with increasing {ηi} . In order to study the KBM in the real tokamak equilibrium, we find that the approximation of shifted circular geometry (β \\ll {{\\varepsilon}2} ) is not valid for a high β global equilibrium near the second stability region of KBM. Thus we generate a series of real equilibria from a global equilibrium solver CORSICA, including both Shafranov shift and elongation effects, but not including bootstrap current. In these real equilibria, the second stability region of KBM are observed in our global linear simulations. The most unstable mode for different β are the same while the mode number spectrum near the second stability region is wider than the case near the first stability region. The nonlinear simulations show that the energy loss of an ELM keeps increasing with β, because the linear drive of the turbulence remains strong for the case near the second stability region during profile evolution.
Carbon monoxide kinetics following simulated cigarette smoking
Karnik, A.S.; Coin, E.J.
1980-05-01
Carbon monoxide kinetics were measured in the blood (% carboxyhemoglobin) and alveolar phase (ppM carbon monoxide) after simulated cigarette smoking. Cigarette smoking was siumlated using the same amount of carbon monoxide that 2R1F cigarettes manufactured by the Tobacco Research Institute would contain. Ten boluses of air containing carbon monoxide equivalent to smoking one cigarette were inhaled by six healthy nonsmoker volunteers. Carbon monoxide in the air phase was measured by an Ecolyzer and carboxyhemoglobin was measured by a CO-Oximeter. The mean rise in alveolar carbon monoxide immediately and 20 min after inhaling the last bolus was 3.3 and 3.1 ppM, respectively (p<.005). The mean rise in carboxyhemoglobin immediately and 20 min after inhalation of the last bolus was 0.8 and 0.5% respectively (P<.005). The changes in carboxyhemoglobin were found to be similar to changes that occur when one cigarette is actually smoked.
Continuum-kinetic approach to sheath simulations
NASA Astrophysics Data System (ADS)
Cagas, Petr; Hakim, Ammar; Srinivasan, Bhuvana
2016-10-01
Simulations of sheaths are performed using a novel continuum-kinetic model with collisions including ionization/recombination. A discontinuous Galerkin method is used to directly solve the Boltzmann-Poisson system to obtain a particle distribution function. Direct discretization of the distribution function has advantages of being noise-free compared to particle-in-cell methods. The distribution function, which is available at each node of the configuration space, can be readily used to calculate the collision integrals in order to get ionization and recombination operators. Analytical models are used to obtain the cross-sections as a function of energy. Results will be presented incorporating surface physics with a classical sheath in Hall thruster-relevant geometry. This work was sponsored by the Air Force Office of Scientific Research under Grant Number FA9550-15-1-0193.
Sengupta, Neelanjana; Maekawa, Hiroaki; Zhuang, Wei; Toniolo, Claudio; Mukamel, Shaul; Tobias, Douglas J.; Ge, Nien-Hui
2010-01-01
We have investigated the sensitivity of two-dimensional infrared (2D IR) spectroscopy to peptide helicity with an experimental and theoretical study of Z-[L-(αMe)Val]8-OtBu in CDCl3. 2D IR experiments were carried out in the amide-I region under the parallel and the double-crossed polarization configurations. In the latter polarization configuration, the 2D spectra taken with the rephasing and nonrephasing pulse sequences exhibit a doublet feature and a single peak, respectively. These cross-peak patterns are highly sensitive to the underlying peptide structure. Spectral calculations were performed on the basis of a vibrational exciton model, with the local mode frequencies and couplings calculated from snapshots of molecular dynamics (MD) simulation trajectories using six different models for the Hamiltonian. Conformationally variant segments of the MD trajectory, while reproducing the main features of the experimental spectra, are characterized by extraneous features, suggesting that the structural ensembles sampled by the simulation are too broad. By imposing periodic restraints on the peptide dihedral angles with the crystal structure as a reference, much better agreement between the measured and the calculated spectra was achieved. The result indicates that the structure of Z-[L-(αMe)Val]8-OtBu in CDCl3 is a fully developed 310-helix with only a small fraction of α-helical or nonhelical conformations in the middle of the peptide. Of the four different combinations of pulse sequences and polarization configurations, the nonrephasing double-crossed polarization 2D IR spectrum exhibits the highest sensitivity in detecting conformational variation. Of the six local mode frequency models tested, the electrostatic maps of Mukamel and Cho perform the best. Our results show that the high sensitivity of 2D IR spectroscopy can provide a useful basis for developing methods to improve the sampling accuracy of force fields and for characterizing the relative merits of
Karavitis, G.A.
1984-01-01
The SIMSYS2D two-dimensional water-quality simulation system is a large-scale digital modeling software system used to simulate flow and transport of solutes in freshwater and estuarine environments. Due to the size, processing requirements, and complexity of the system, there is a need to easily move the system and its associated files between computer sites when required. A series of job control language (JCL) procedures was written to allow transferability between IBM and IBM-compatible computers. (USGS)
Kinetic simulations of magnetized capacitively coupled discharges
NASA Astrophysics Data System (ADS)
Trieschmann, Jan; Shihab, Mohammed; Eremin, Denis; Brinkmann, Ralf Peter; Schulze, Julian; Mussenbrock, Thomas
2012-10-01
Capacitive high frequency discharges are of crucial importance in the context of plasma etching, deposition and surface modification. As these single or multiple frequency discharges are oftentimes operated at low pressures of less than a few pascal, a high plasma density is commonly achieved with the use of external magnetic fields. In this work kinetic simulations are used to investigate the effect of inhomogeneous external magnetic fields on the discharge dynamics in a strongly nonlocal pressure regime. We found that capacitively coupled discharges can be largely asymmetrized by applying strong magnetic fields in front of a given target electrode. This not only has an effect on the plasma density, but also on the ion energy distribution functions (IEDF) at the electrodes and on the acceleration of fast electrons in the plasma sheath regions. In consequence in the discharge currents a generation of higher harmonics of the driving frequency can be observed. We investigate these scenarios in terms of 1D-3V Particle in Cell simulations.
Simulations of kinetically irreversible protein aggregate structure.
Patro, S Y; Przybycien, T M
1994-01-01
We have simulated the structure of kinetically irreversible protein aggregates in two-dimensional space using a lattice-based Monte-Carlo routine. Our model specifically accounts for the intermolecular interactions between hydrophobic and hydrophilic protein surfaces and a polar solvent. The simulations provide information about the aggregate density, the types of inter-monomer contacts and solvent content within the aggregates, the type and extent of solvent exposed perimeter, and the short- and long-range order all as a function of (i) the extent of monomer hydrophobic surface area and its distribution on the model protein surface and (ii) the magnitude of the hydrophobic-hydrophobic contact energy. An increase in the extent of monomer hydrophobic surface area resulted in increased aggregate densities with concomitant decreased system free energies. These effects are accompanied by increases in the number of hydrophobic-hydrophobic contacts and decreases in the solvent-exposed hydrophobic surface area of the aggregates. Grouping monomer hydrophobic surfaces in a single contiguous stretch resulted in lower aggregate densities and lower short range order. More favorable hydrophobic-hydrophobic contact energies produced structures with higher densities but the number of unfavorable protein-protein contacts was also observed to increase; greater configurational entropy produced the opposite effect. Properties predicted by our model are in good qualitative agreement with available experimental observations. Images FIGURE 6 FIGURE 13 PMID:8061184
Simulation of Ultra-Small MOSFETs Using a 2-D Quantum-Corrected Drift-Diffusion Model
NASA Technical Reports Server (NTRS)
Biegal, Bryan A.; Rafferty, Connor S.; Yu, Zhiping; Ancona, Mario G.; Dutton, Robert W.; Saini, Subhash (Technical Monitor)
1998-01-01
The continued down-scaling of electronic devices, in particular the commercially dominant MOSFET, will force a fundamental change in the process of new electronics technology development in the next five to ten years. The cost of developing new technology generations is soaring along with the price of new fabrication facilities, even as competitive pressure intensifies to bring this new technology to market faster than ever before. To reduce cost and time to market, device simulation must become a more fundamental, indeed dominant, part of the technology development cycle. In order to produce these benefits, simulation accuracy must improve markedly. At the same time, device physics will become more complex, with the rapid increase in various small-geometry and quantum effects. This work describes both an approach to device simulator development and a physical model which advance the effort to meet the tremendous electronic device simulation challenge described above. The device simulation approach is to specify the physical model at a high level to a general-purpose (but highly efficient) partial differential equation solver (in this case PROPHET, developed by Lucent Technologies), which then simulates the model in 1-D, 2-D, or 3-D for a specified device and test regime. This approach allows for the rapid investigation of a wide range of device models and effects, which is certainly essential for device simulation to catch up with, and then stay ahead of, electronic device technology of the present and future. The physical device model used in this work is the density-gradient (DG) quantum correction to the drift-diffusion model [Ancona, Phys. Rev. B 35(5), 7959 (1987)]. This model adds tunneling and quantum smoothing of carrier density profiles to the drift-diffusion model. We used the DG model in 1-D and 2-D (for the first time) to simulate both bipolar and unipolar devices. Simulations of heavily-doped, short-base diodes indicated that the DG quantum
HEAT.PRO - THERMAL IMBALANCE FORCE SIMULATION AND ANALYSIS USING PDE2D
NASA Technical Reports Server (NTRS)
Vigue, Y.
1994-01-01
HEAT.PRO calculates the thermal imbalance force resulting from satellite surface heating. The heated body of a satellite re-radiates energy at a rate that is proportional to its temperature, losing the energy in the form of photons. By conservation of momentum, this momentum flux out of the body creates a reaction force against the radiation surface, and the net thermal force can be observed as a small perturbation that affects long term orbital behavior of the satellite. HEAT.PRO calculates this thermal imbalance force and then determines its effects on satellite orbits, especially where the Earth's shadowing of an orbiting satellite causes periodic changes in the spacecraft's thermal environment. HEAT.PRO implements a finite element method routine called PDE2D which incorporates material properties to determine the solar panel surface temperatures. The nodal temperatures are computed at specified time steps and are used to determine the magnitude and direction of the thermal force on the spacecraft. These calculations are based on the solar panel orientation and satellite's position with respect to the earth and sun. It is necessary to have accurate, current knowledge of surface emissivity, thermal conductivity, heat capacity, and material density. These parameters, which may change due to degradation of materials in the environment of space, influence the nodal temperatures that are computed and thus the thermal force calculations. HEAT.PRO was written in FORTRAN 77 for Cray series computers running UNICOS. The source code contains directives for and is used as input to the required partial differential equation solver, PDE2D. HEAT.PRO is available on a 9-track 1600 BPI magnetic tape in UNIX tar format (standard distribution medium) or a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation in Macintosh Microsoft Word format is included on the distribution tape. HEAT.PRO was developed in 1991. Cray and UNICOS are
2D Quantum Simulation of MOSFET Using the Non Equilibrium Green's Function Method
NASA Technical Reports Server (NTRS)
Svizhenko, Alexel; Anantram, M. P.; Govindan, T. R.; Yan, Jerry (Technical Monitor)
2000-01-01
The objectives this viewgraph presentation summarizes include: (1) the development of a quantum mechanical simulator for ultra short channel MOSFET simulation, including theory, physical approximations, and computer code; (2) explore physics that is not accessible by semiclassical methods; (3) benchmarking of semiclassical and classical methods; and (4) study other two-dimensional devices and molecular structure, from discretized Hamiltonian to tight-binding Hamiltonian.
Aerosol kinetic code "AERFORM": Model, validation and simulation results
NASA Astrophysics Data System (ADS)
Gainullin, K. G.; Golubev, A. I.; Petrov, A. M.; Piskunov, V. N.
2016-06-01
The aerosol kinetic code "AERFORM" is modified to simulate droplet and ice particle formation in mixed clouds. The splitting method is used to calculate condensation and coagulation simultaneously. The method is calibrated with analytic solutions of kinetic equations. Condensation kinetic model is based on cloud particle growth equation, mass and heat balance equations. The coagulation kinetic model includes Brownian, turbulent and precipitation effects. The real values are used for condensation and coagulation growth of water droplets and ice particles. The model and the simulation results for two full-scale cloud experiments are presented. The simulation model and code may be used autonomously or as an element of another code.
Implementation, study and calibration of a modified ASM2d for the simulation of SBR processes.
Marsili Libelli, S; Ratini, P; Spagni, A; Bortone, G
2001-01-01
An enhanced process model for SBRs has been developed. Though the basic mechanism largely draws on the Activated Sludge Model n. 2d, its new features are the splitting of the nitrification stage in a two-step process, according to the well known Nitrosomonas-Nitrobacter oxidation sequence, and an improved XPAO dynamics, involved in the anaerobic/aerobic phosphorus removal process. The model was implemented through the DLL technique allowing complied C++ modules to be linked to an ordinary Simulink block diagram. The static sensitivity study revealed that if the parameter vector is partitioned into subsets of biologically related parameters and calibrated separately, the calibration procedure does not present particularly difficult aspects. Trajectory sensitivity showed also to which extent data collection could be optimised in order to improve calibration accuracy. The study of the shape of the error functional generated by parameters couples allows a much more effective calibration strategy.
NASA Astrophysics Data System (ADS)
Hidrovo, Carlos; Salamat, Yasamin
2016-11-01
Capacitive Deionization (CDI) is a relatively new electrically based desalination method that uses porous media to adsorb ions in solution from water, with the potential to recover part of the energy used during the desalination process. Previous studies have investigated the physics underlying the electro-adsorption process in the electrical double layers in the CDI porous electrodes. In order to improve CDI performance in terms of minimum average concentration, total amount of water treated, and duration of the desalination process, herein we propose and evaluate different CDI architectures. Two previously validated 2D and 1D models are used alongside each other to study different CDI system configurations based on various convective-diffusive layer regimes. Moreover, the effects of micro pore and macro pore capacities on the total number of ions adsorbed in the porous media is investigated. This will open new opportunities for further researches toward engineered CDI units for better desalination.
Numerical Simulations of High-Frequency Respiratory Flows in 2D and 3D Lung Bifurcation Models
NASA Astrophysics Data System (ADS)
Chen, Zixi; Parameswaran, Shamini; Hu, Yingying; He, Zhaoming; Raj, Rishi; Parameswaran, Siva
2014-07-01
To better understand the human pulmonary system and optimize the high-frequency oscillatory ventilation (HFOV) design, numerical simulations were conducted under normal breathing frequency and HFOV condition using a CFD code Ansys Fluent and its user-defined C programs. 2D and 3D double bifurcating lung models were created, and the geometry corresponds to fifth to seventh generations of airways with the dimensions based on the Weibel's pulmonary model. Computations were carried out for different Reynolds numbers (Re = 400 and 1000) and Womersley numbers (α = 4 and 16) to study the air flow fields, gas transportation, and wall shear stresses in the lung airways. Flow structure was compared with experimental results. Both 2D and 3D numerical models successfully reproduced many results observed in the experiment. The oxygen concentration distribution in the lung model was investigated to analyze the influence of flow oscillation on gas transport inside the lung model.
Tracer dispersion simulation in low wind speed conditions with a new 2D Langevin equation system
NASA Astrophysics Data System (ADS)
Anfossi, D.; Alessandrini, S.; Trini Castelli, S.; Ferrero, E.; Oettl, D.; Degrazia, G.
The simulation of atmospheric dispersion in low wind speed conditions (LW) is still recognised as a challenge for modellers. Recently, a new system of two coupled Langevin equations that explicitly accounts for meandering has been proposed. It is based on the study of turbulence and dispersion properties in LW. The new system was implemented in the Lagrangian stochastic particle models LAMBDA and GRAL. In this paper we present simulations with this new approach applying it to the tracer experiments carried out in LW by Idaho National Engineering Laboratory (INEL, USA) in 1974 and by the Graz University of Technology and CNR-Torino near Graz in 2003. To assess the improvement obtained with the present model with respect to previous models not taking into account the meandering effect, the simulations for the INEL experiments were also performed with the old version of LAMBDA. The results of the comparisons clearly indicate that the new approach improves the simulation results.
Lindenschmidt, Karl-Erich; Huang, Shaochun; Baborowski, Martina
2008-07-01
In flood modeling, many one-dimensional (1D) hydrodynamic and water quality models are too restricted in capturing the spatial differentiation of processes within a polder or system of polders and two-dimensional (2D) models are too demanding in data requirements and computational resources, especially if Monte-Carlo techniques are to be used for model uncertainty analyses. The first goal of this paper is to show the successful development of a quasi-2D modeling approach which still calculates the dynamic wave in 1D but the discretisation of the computational units is in 2D, allowing a better spatial representation of the flow and substance transport processes in the polders without a large additional expenditure on data pre-processing and simulation processing. The models DYNHYD (1D hydrodynamics) and TOXI (sediment and micro-pollutant transport) were used as a basis for the hydrodynamic and water quality simulations. An extreme flood event on the Elbe River, Germany, with a proposed polder system variant was used as a test case. The results show a plausible differentiation of suspended sediment and zinc concentrations within the polders both spatially and temporally. This fulfills the second goal of this research. The third goal of this work is to provide an example methodology of carrying out an environmental risk assessment in inundated areas by flood waters, as required by the European Union floods directive. The deposition of zinc in polders was used for this example, due to its high contamination potential in the Elbe River. The extended quasi-2D modeling system incorporates a Monte-Carlo uncertainty analysis to assess the environmental impact of heavy metal deposition in the polders during extreme flooding. The environmental risk computed gives a 48% chance of exceeding the inspection value of 500 mg zinc/kg sediment for a flood such as the August 2002 event.
Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores
Burris, Paul C.; Laage, Damien; Thompson, Ward H.
2016-05-20
Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this Paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D_{2}O is considered. An empirical mapping approach is used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. Lastly, the simulated spectra indicate that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra.
Burris, Paul C; Laage, Damien; Thompson, Ward H
2016-05-21
Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D2O is considered. An empirical mapping approach is used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. The simulated spectra indicates that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra.
Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores
Burris, Paul C.; Laage, Damien; Thompson, Ward H.
2016-05-20
Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this Paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D2O is considered. An empirical mapping approach is usedmore » to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. Lastly, the simulated spectra indicate that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra.« less
Evans, J. W.; Thiel, P. A.; Li, Maozhi
2007-06-14
We consider homoepitaxy (or low-misfit heteroepitaxy) via vapor deposition or MBE under UHV conditions. Thin film growth is initiated by nucleation and growth of 2D islands in the submonolayer regime. For atoms subsequently deposited on top of islands, a step edge barrier often inhibits downward transport and produces kinetic roughening during multilayer growth. Such unstable growth is characterized by the formation of 3D mounds (multilayer stacks of 2D islands). Kinetic Monte Carlo (KMC) simulation of suitable atomistic lattice-gas models can address fundamental or general issues related to both submonolayer and multilayer film evolution, and can also provide a predictive tool for morphological evolution in specific systems. Examples of the successes of KMC modeling are provided for metal homoepitaxial film growth, specifically for contrasting behavior in the classic Ag/Ag(100) and Ag/Ag(111) systems.
NASA Astrophysics Data System (ADS)
Michelson, Sara; Bao, Jian-Wen; Grell, Evelyn
2016-04-01
In this study, numerical model simulations of an idealized 2-D squall line are investigated using microphysics budget analysis. Four commonly-used microphysics schemes of various complexity are used in the simulations. Diagnoses of the source and sink terms of the hydrometeor budget equations reveal that the differences related to the assumptions of hydrometeor size-distributions between the schemes lead to the differences in the simulations due to the net effect of various microphysical processes on the interaction between latent heating/evaporative cooling and flow dynamics as the squall line develops. Results from this study also highlight the possibility that the advantage of double-moment formulations can be overshadowed by the uncertainties in the spectral definition of individual hydrometeor categories and spectrum-dependent microphysical processes.
The 2-D simulations of the NRL (Naval Research Laboratory) laser experiment
NASA Astrophysics Data System (ADS)
Lyon, J. G.
1985-05-01
Two-dimensional gas-dynamic simulations of the NRL laser experiment have been performed to study the formation of aneurysms in the blast wave and to study the formation of structure internal to the blast front itself. In one set of simulations the debris shell was perturbed sinusoidally in mass and position and also perturbed to mimic the action of a slow jet of material leaving the target at slower speeds than the bulk of the debris. In all cases the blast wave remained stable to any aneurysm-like instability. Internal structure, however, was quite easily produced and grew as a function of time. In the other set of simulations the effect of a pre-heated channel upon the propagation of the blast wave was examined. Bulges in the blast wave shock front were produced in these simulations that could be the beginning of the aneurysm phenomenon, but the preheated channel by itself appears to be insufficient to produce the observed aneurysm.
NASA Astrophysics Data System (ADS)
Sellmeier, B.; Thuro, K.
2012-04-01
In between the last years rock falls seem to occur more often in high mountainous regions. Linked with the climate change problem, this topic is mentioned in the media more and more frequently. As a consequence, especially in populated alpine regions in Europe, public authorities have to act more and more towards prevention of rock fall events. Important questions in that context are how events can be predicted more precisely in the future and how mitigation methods can be improved in endangered areas. On that purpose, a research project has been established giving an input in different ways by means of a project site which is situated along the federal road B 305 between Unterjettenberg and Schwarzbachwacht near Berchtesgaden in the Bavarian Alps, Germany. In that context the uncertainties concerning field work in difficult terrain are considered with regard to the subsequent simulations. It is often the case that not every part of the rock fall site can be examined in the same way. A further origin of uncertainty is the variation of the initial parameters in between a certain period of time. For example the variation of forest stands parameters because of windbreakage or avalanches. Consequently the factors of uncertainty and their possible consequences for the simulations will be analyzed. As further aspects of the project it is intended to compare the possibilities and limitations of 2D and 3D rock fall simulations concerning the runout zones. In particular the application ranges of both methods will be analyzed using the 2 dimensional simulation codes Rockfall (Dr. Spang) and Rofmod 2D (Geotest) in comparison with the 3 dimensional simulation code Rofmod 3D (Geotest). In this contribution the results of the field work, the analyses of the uncertainties concerning the initial parameters of rockfall simulations will be presented. (SELLMEIER & THURO 2011)
NASA Astrophysics Data System (ADS)
Darvini, G.; Salandin, P.
2009-12-01
To analyze the impact of the hydraulic conductivity K spatial variability in a real field case (as an example to delimitate a well catchment), numerical simulations can be reasonably developed in a two-dimensional vertical average context. Nevertheless the plume evolution is a consequence of a more complex three-dimensional heterogeneous structure whose vertical variability dominates the dispersion phenomena at local scale. In larger domains, the effect of the vertical heterogeneity combines itself with that one due to the horizontal variability of K, and only when the plume has travelled a large number of (horizontal) integral scales, its evolution can be analyzed in a regional context, under the hypothesis that the transmissivity spatial distribution prevails. Until this limit is reached, the vertical and horizontal variability of K are combined to give a fully 3-D dispersion process. In all these situations, to successfully accomplish the 3-D heterogeneous structure of the aquifer in 2-D simulations, more than the planimetric depth-averaged variability of K must be accounted for. To define the uncertainty related to the use of different planimetric schematizations of the real hydraulic conductivity spatial distribution, we present here the results of some numerical experiments that compare the 3-D plume evolution with 2-D simulations developed by tacking into account different hydraulic conductivity distribution schematization, by considering a hierarchical architecture of media also. This description of a sedimentary formation combined with the finite size of the plume requires theoretical and numerical tools able to take into account the flow field inhomogeneity and the ergodicity lack that characterize the transport phenomena. Following this way it will be possible to quantify / reduce the uncertainty related to a 2-D schematization in a large number of real cases where the domain spans between the local and the regional scale and whose dimension may lead to
NASA Astrophysics Data System (ADS)
Smirnov, E. M.; Smirnovsky, A. A.; Schur, N. A.; Zaitsev, D. K.; Smirnov, P. E.
2016-09-01
The contribution covers results of numerical study of air flow and heat transfer past a backward-facing step at the Reynolds number of 28,000. The numerical simulation was carried out under conditions of the experiments of Vogel&Eaton (1985), where nominally 2D fluid dynamics and heat transfer in a channel with expansion ratio of 1.25 was investigated. Two approaches were used for turbulence modelling. First, the Menter SST turbulence model was used to perform refined 2D and 3D RANS steady-state computations. The 3D analysis was undertaken to evaluate effects of boundary layers developing on the sidewalls of the experimental channel. Then, 3D time-dependent computations were carried out using the vortex-resolving IDDES method and applying the spanwise-periodicity conditions. Comparative computations were performed using an in-house finite-volume code SINF/Flag-S and the ANSYS Fluent. The codes produced practically identical RANS solutions, showing in particular a difference of 4% in the central-line peak Stanton number calculated in 2D and 3D cases. The IDDES results obtained with two codes are in a satisfactory agreement. Comparing with the experimental data, the IDDES produces the best agreement for the wall friction, whereas the RANS solutions show superiority in predictions of the local Stanton number distribution.
Efficient simulation of pitch angle collisions in a 2+2-D Eulerian Vlasov code
NASA Astrophysics Data System (ADS)
Banks, Jeff; Berger, R.; Brunner, S.; Tran, T.
2014-10-01
Here we discuss pitch angle scattering collisions in the context of the Eulerian-based kinetic code LOKI that evolves the Vlasov-Poisson system in 2+2-dimensional phase space. The collision operator is discretized using 4th order accurate conservative finite-differencing. The treatment of the Vlasov operator in phase-space uses an approach based on a minimally diffuse, fourth-order-accurate discretization (Banks and Hittinger, IEEE T. Plasma Sci. 39, 2198). The overall scheme is therefore discretely conservative and controls unphysical oscillations. Some details of the numerical scheme will be presented, and the implementation on modern highly concurrent parallel computers will be discussed. We will present results of collisional effects on linear and non-linear Landau damping of electron plasma waves (EPWs). In addition we will present initial results showing the effect of collisions on the evolution of EPWs in two space dimensions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and funded by the LDRD program at LLNL under project tracking code 12-ERD-061.
NASA Astrophysics Data System (ADS)
Krause, M.; Camenzind, M.
2001-12-01
In the present paper, we examine the convergence behavior and inter-code reliability of astrophysical jet simulations in axial symmetry. We consider both pure hydrodynamic jets and jets with a dynamically significant magnetic field. The setups were chosen to match the setups of two other publications, and recomputed with the MHD code NIRVANA. We show that NIRVANA and the two other codes give comparable, but not identical results. We explain the differences by the different application of artificial viscosity in the three codes and numerical details, which can be summarized in a resolution effect, in the case without magnetic field: NIRVANA turns out to be a fair code of medium efficiency. It needs approximately twice the resolution as the code by Lind (Lind et al. 1989) and half the resolution as the code by Kössl (Kössl & Müller 1988). We find that some global properties of a hydrodynamical jet simulation, like e.g. the bow shock velocity, converge at 100 points per beam radius (ppb) with NIRVANA. The situation is quite different after switching on the toroidal magnetic field: in this case, global properties converge even at 10 ppb. In both cases, details of the inner jet structure and especially the terminal shock region are still insufficiently resolved, even at our highest resolution of 70 ppb in the magnetized case and 400 ppb for the pure hydrodynamic jet. The magnetized jet even suffers from a fatal retreat of the Mach disk towards the inflow boundary, which indicates that this simulation does not converge, in the end. This is also in definite disagreement with earlier simulations, and challenges further studies of the problem with other codes. In the case of our highest resolution simulation, we can report two new features: first, small scale Kelvin-Helmholtz instabilities are excited at the contact discontinuity next to the jet head. This slows down the development of the long wavelength Kelvin-Helmholtz instability and its turbulent cascade to smaller
Fully kinetic particle simulations of high pressure streamer propagation
NASA Astrophysics Data System (ADS)
Rose, David; Welch, Dale; Thoma, Carsten; Clark, Robert
2012-10-01
Streamer and leader formation in high pressure devices is a dynamic process involving a hierarchy of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. We have performed 2D and 3D fully EM implicit particle-in-cell simulation model of gas breakdown leading to streamer formation under DC and RF fields. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm [D. R. Welch, et al., J. Comp. Phys. 227, 143 (2007)] that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge. These models are being applied to the analysis of high-pressure gas switches [D. V. Rose, et al., Phys. Plasmas 18, 093501 (2011)] and gas-filled RF accelerator cavities [D. V. Rose, et al. Proc. IPAC12, to appear].
Mixed-RKDG Finite Element Methods for the 2-D Hydrodynamic Model for Semiconductor Device Simulation
Chen, Zhangxin; Cockburn, Bernardo; Jerome, Joseph W.; ...
1995-01-01
In this paper we introduce a new method for numerically solving the equations of the hydrodynamic model for semiconductor devices in two space dimensions. The method combines a standard mixed finite element method, used to obtain directly an approximation to the electric field, with the so-called Runge-Kutta Discontinuous Galerkin (RKDG) method, originally devised for numerically solving multi-dimensional hyperbolic systems of conservation laws, which is applied here to the convective part of the equations. Numerical simulations showing the performance of the new method are displayed, and the results compared with those obtained by using Essentially Nonoscillatory (ENO) finite difference schemes. Frommore » the perspective of device modeling, these methods are robust, since they are capable of encompassing broad parameter ranges, including those for which shock formation is possible. The simulations presented here are for Gallium Arsenide at room temperature, but we have tested them much more generally with considerable success.« less
NASA Astrophysics Data System (ADS)
Zhao, J. W.; Ding, G. H.; Yin, W. Y.; Yang, X. J.; Shi, W. C.; Zhang, X. L.
The objective of this study is to investigate the effect of hemodynamic parameters on the formation, growth and rupture of an aneurysm. Our simulation of the elastic and rigid aneurysm is based on a DSA or other clinic image. The simulatied results are that there are great differences in the distribution of velocity magnitude at some sections which are predicted by the two models. For the elastic wall model, the distribution of velocity magnitude of one outlet is obviously off-center, which influences the distribution of wall shear stress (WSS) and exchange of substance through the vessel wall. The currents of the distributions of WSS along the wall of aneurysm for the two models are similar. But there are obvious differences between the two models in the values especially at the neck of aneurysm. This study demonstrates obviously that the elastic wall model suits the simulation for growth and rupture of an aneurysm better.
Generalized source method in curvilinear coordinates for 2D grating diffraction simulation
NASA Astrophysics Data System (ADS)
Shcherbakov, Alexey A.; Tishchenko, Alexandre V.
2017-01-01
The article presents a curvilinear coordinate Fourier space integral method for linear optical rigorous grating diffraction simulation in 3D (crossed grating diffraction). The presented formulation extends our previous work on a related method for 1D periodic grating diffraction. Following this previous work we exploit a concept of the generalized metric sources to efficiently solve the Maxwell's equations. The article provides a general description of the method together with a detailed formulation and analysis of sinusoidal corrugation crossed grating diffraction.
Zhou, Y. L.; Wang, Z. H.; Xu, X. Q.; Li, H. D.; Feng, H.; Sun, W. G.
2015-01-09
Plasma fueling with high efficiency and deep injection is very important to enable fusion power performance requirements. It is a powerful and efficient way to study neutral transport dynamics and find methods of improving the fueling performance by doing large scale simulations. Furthermore, two basic fueling methods, gas puffing (GP) and supersonic molecular beam injection (SMBI), are simulated and compared in realistic divertor geometry of the HL-2A tokamak with a newly developed module, named trans-neut, within the framework of BOUT++ boundary plasma turbulence code [Z. H. Wang et al., Nucl. Fusion 54, 043019 (2014)]. The physical model includes plasma density, heat and momentum transport equations along with neutral density, and momentum transport equations. In transport dynamics and profile evolutions of both plasma and neutrals are simulated and compared between GP and SMBI in both poloidal and radial directions, which are quite different from one and the other. It finds that the neutrals can penetrate about four centimeters inside the last closed (magnetic) flux surface during SMBI, while they are all deposited outside of the LCF during GP. Moreover, it is the radial convection and larger inflowing flux which lead to the deeper penetration depth of SMBI and higher fueling efficiency compared to GP.
Zhou, Y. L.; Wang, Z. H.; Xu, X. Q.; Li, H. D.; Feng, H.; Sun, W. G.
2015-01-15
Plasma fueling with high efficiency and deep injection is very important to enable fusion power performance requirements. It is a powerful and efficient way to study neutral transport dynamics and find methods of improving the fueling performance by doing large scale simulations. Two basic fueling methods, gas puffing (GP) and supersonic molecular beam injection (SMBI), are simulated and compared in realistic divertor geometry of the HL-2A tokamak with a newly developed module, named trans-neut, within the framework of BOUT++ boundary plasma turbulence code [Z. H. Wang et al., Nucl. Fusion 54, 043019 (2014)]. The physical model includes plasma density, heat and momentum transport equations along with neutral density, and momentum transport equations. Transport dynamics and profile evolutions of both plasma and neutrals are simulated and compared between GP and SMBI in both poloidal and radial directions, which are quite different from one and the other. It finds that the neutrals can penetrate about four centimeters inside the last closed (magnetic) flux surface during SMBI, while they are all deposited outside of the LCF during GP. It is the radial convection and larger inflowing flux which lead to the deeper penetration depth of SMBI and higher fueling efficiency compared to GP.
Zhou, Y. L.; Wang, Z. H.; Xu, X. Q.; ...
2015-01-09
Plasma fueling with high efficiency and deep injection is very important to enable fusion power performance requirements. It is a powerful and efficient way to study neutral transport dynamics and find methods of improving the fueling performance by doing large scale simulations. Furthermore, two basic fueling methods, gas puffing (GP) and supersonic molecular beam injection (SMBI), are simulated and compared in realistic divertor geometry of the HL-2A tokamak with a newly developed module, named trans-neut, within the framework of BOUT++ boundary plasma turbulence code [Z. H. Wang et al., Nucl. Fusion 54, 043019 (2014)]. The physical model includes plasma density,more » heat and momentum transport equations along with neutral density, and momentum transport equations. In transport dynamics and profile evolutions of both plasma and neutrals are simulated and compared between GP and SMBI in both poloidal and radial directions, which are quite different from one and the other. It finds that the neutrals can penetrate about four centimeters inside the last closed (magnetic) flux surface during SMBI, while they are all deposited outside of the LCF during GP. Moreover, it is the radial convection and larger inflowing flux which lead to the deeper penetration depth of SMBI and higher fueling efficiency compared to GP.« less
Development of a 2-D large-scale micellar/polymer simulator
Wang, B.
1982-01-01
A large-scale, two-dimensional, multicomponent, multiphase, compositional simulator for micellar/polymer flooding has been developed and applied. It can be used to calculate the areal sweep with any well pattern and any irregular reservoir boundary. This model involves both streamline and finite-difference techniques. Time invariant streamlines without transverse dispersion are assumed. The change in the flow rates into each streamline is accounted for as a function of mobility ratio. The sensitivity of the oil recovery for micellar/polymer flood to several reservoir and process variables was investigated. The reservoir variables included the well spacing, pattern type, pattern orientation in an anisotropic reservoir, and degree of confinement. The process variables included the salinity gradient, surfactant content of the slug, slug and polymer bank sizes, mobility ratio of polymer drive to oil bank, and polymer shear thinning effect. In order to demonstrate that this model is capable of handling large field problems, a large-scale simulation of the north lease of the El Dorado micellar/polymer pilot test was made. The simulated final oil recovery and the production histories of each producer are illustrated.
NASA Astrophysics Data System (ADS)
Croes, Vivien; Lafleur, Trevor; Bonaventura, Zdeněk; Bourdon, Anne; Chabert, Pascal
2017-03-01
In this work we study the electron drift instability in Hall-effect thrusters (HETs) using a 2D electrostatic particle-in-cell (PIC) simulation. The simulation is configured with a Cartesian coordinate system modeling the radial-azimuthal (r{--}θ ) plane for large radius thrusters. A magnetic field, {{B}}0, is aligned along the Oy axis (r direction), a constant applied electric field, {{E}}0, along the Oz axis (perpendicular to the simulation plane), and the {{E}}0× {{B}}0 direction is along the Ox axis (θ direction). Although electron transport can be well described by electron–neutral collisions for low plasma densities, at high densities (similar to those in typical HETs), a strong instability is observed that enhances the electron cross-field mobility; even in the absence of electron–neutral collisions. The instability generates high frequency (of the order of MHz) and short wavelength (of the order of mm) fluctuations in both the azimuthal electric field and charged particle densities, and propagates in the {{E}}0× {{B}}0 direction with a velocity close to the ion sound speed. The correlation between the electric field and density fluctuations (which leads to an enhanced electron–ion friction force) is investigated and shown to be directly responsible for the increased electron transport. Results are compared with a recent kinetic theory, showing good agreement with the instability properties and electron transport.
A GPU Simulation Tool for Training and Optimisation in 2D Digital X-Ray Imaging.
Gallio, Elena; Rampado, Osvaldo; Gianaria, Elena; Bianchi, Silvio Diego; Ropolo, Roberto
2015-01-01
Conventional radiology is performed by means of digital detectors, with various types of technology and different performance in terms of efficiency and image quality. Following the arrival of a new digital detector in a radiology department, all the staff involved should adapt the procedure parameters to the properties of the detector, in order to achieve an optimal result in terms of correct diagnostic information and minimum radiation risks for the patient. The aim of this study was to develop and validate a software capable of simulating a digital X-ray imaging system, using graphics processing unit computing. All radiological image components were implemented in this application: an X-ray tube with primary beam, a virtual patient, noise, scatter radiation, a grid and a digital detector. Three different digital detectors (two digital radiography and a computed radiography systems) were implemented. In order to validate the software, we carried out a quantitative comparison of geometrical and anthropomorphic phantom simulated images with those acquired. In terms of average pixel values, the maximum differences were below 15%, while the noise values were in agreement with a maximum difference of 20%. The relative trends of contrast to noise ratio versus beam energy and intensity were well simulated. Total calculation times were below 3 seconds for clinical images with pixel size of actual dimensions less than 0.2 mm. The application proved to be efficient and realistic. Short calculation times and the accuracy of the results obtained make this software a useful tool for training operators and dose optimisation studies.
A GPU Simulation Tool for Training and Optimisation in 2D Digital X-Ray Imaging
Gallio, Elena; Rampado, Osvaldo; Gianaria, Elena; Bianchi, Silvio Diego; Ropolo, Roberto
2015-01-01
Conventional radiology is performed by means of digital detectors, with various types of technology and different performance in terms of efficiency and image quality. Following the arrival of a new digital detector in a radiology department, all the staff involved should adapt the procedure parameters to the properties of the detector, in order to achieve an optimal result in terms of correct diagnostic information and minimum radiation risks for the patient. The aim of this study was to develop and validate a software capable of simulating a digital X-ray imaging system, using graphics processing unit computing. All radiological image components were implemented in this application: an X-ray tube with primary beam, a virtual patient, noise, scatter radiation, a grid and a digital detector. Three different digital detectors (two digital radiography and a computed radiography systems) were implemented. In order to validate the software, we carried out a quantitative comparison of geometrical and anthropomorphic phantom simulated images with those acquired. In terms of average pixel values, the maximum differences were below 15%, while the noise values were in agreement with a maximum difference of 20%. The relative trends of contrast to noise ratio versus beam energy and intensity were well simulated. Total calculation times were below 3 seconds for clinical images with pixel size of actual dimensions less than 0.2 mm. The application proved to be efficient and realistic. Short calculation times and the accuracy of the results obtained make this software a useful tool for training operators and dose optimisation studies. PMID:26545097
Towards adaptive kinetic-fluid simulations of weakly ionized plasmas
NASA Astrophysics Data System (ADS)
Kolobov, V. I.; Arslanbekov, R. R.
2012-02-01
This paper describes an Adaptive Mesh and Algorithm Refinement (AMAR) methodology for multi-scale simulations of gas flows and the challenges associated with extending this methodology for simulations of weakly ionized plasmas. The AMAR method combines Adaptive Mesh Refinement (AMR) with automatic selection of kinetic or continuum solvers in different parts of computational domains. We first review the discrete velocity method for solving Boltzmann and Wang Chang-Uhlenbeck kinetic equations for rarefied gases. Then, peculiarities of AMR implementation with octree Cartesian mesh are discussed. A Unified Flow Solver (UFS) uses AMAR method with adaptive Cartesian mesh to dynamically introduce kinetic patches for multi-scale simulations of gas flows. We describe fluid plasma models with AMR capabilities and illustrate how physical models affect simulation results for gas discharges, especially in the areas where electron kinetics plays an important role. We introduce Eulerian solvers for plasma kinetic equations and illustrate the concept of adaptive mesh in velocity space. Specifics of electron kinetics in collisional plasmas are described focusing on deterministic methods of solving kinetic equations for electrons under different conditions. We illustrate the appearance of distinct groups of electrons in the cathode region of DC discharges and discuss the physical models appropriate for each group. These kinetic models are currently being incorporated into AMAR methodology for multi-scale plasma simulations.
Dunbar, Josef A; Arthur, Evan J; White, Aaron M; Kubarych, Kevin J
2015-05-21
Using a derivative of the vitamin biotin labeled with a transition-metal carbonyl vibrational probe in a series of aqueous N,N-dimethylformamide (DMF) solutions, we observe a striking slowdown in spectral diffusion dynamics with decreased DMF concentration. Equilibrium solvation dynamics, measured with the rapidly acquired spectral diffusion (RASD) technique, a variant of heterodyne-detected photon-echo peak shift experiments, range from 1 ps in neat DMF to ∼3 ps in 0.07 mole fraction DMF/water solution. Molecular dynamics simulations of the biotin-metal carbonyl solute in explicit aqueous DMF solutions show marked preferential solvation by DMF, which becomes more pronounced at lower DMF concentrations. The simulations and the experimental data are consistent with an interpretation where the slowdown in spectral diffusion is due to solvent exchange involving distinct cosolvent species. A simple two-component model reproduces the observed spectral dynamics as well as the DMF concentration dependence, enabling the extraction of the solvent exchange time scale of 8 ps. This time scale corresponds to the diffusive motion of a few Å, consistent with a solvent-exchange mechanism. Unlike most previous studies of solvation dynamics in binary mixtures of polar solvents, our work highlights the ability of vibrational probes to sense solvent exchange as a new, slow component in the spectral diffusion dynamics.
Real-time 2D floating-point fast Fourier transforms for seeker simulation
NASA Astrophysics Data System (ADS)
Chamberlain, Richard; Lord, Eric; Shand, David J.
2002-07-01
The floating point Fast Fourier Transform (FFT) is one of the most useful basic functions available to the image and signal processing engineer allowing many complex and detailed special functions to be implemented more simply in the frequency domain. In the Hardware-in-the-Loop field an image transformed using FFT would allow the designer to think about accurate frequency based simulation of seeker lens effects, motion blur, detector transfer functions and much more. Unfortunately, the transform requires many hundreds of thousands or millions of floating point operations on a single modest sized image making it impractical for realtime Hardware-in-the-Loop systems. .until now. This paper outlines the development, by Nallatech, of an FPGA based IEEE floating point core. It traces the subsequent use of this core to develop a full 256 X 256 FFT and filter process implemented on COTS hardware at frame rates up to 150Hz. This transform can be demonstrated to model optical transfer functions at a far greater accuracy than the current spatial models. Other applications and extensions of this technique will be discussed such as filtering for image tracking algorithms and in the simulation of radar processing in the frequency domain.
Evans, T.E.; Leonard, A.W.; West, W.P.; Finkenthal, D.F.; Fenstermacher, M.E.; Porter, G.D.
1998-08-01
Experimentally measured carbon line emissions and total radiated power distributions from the DIII-D divertor and Scrape-Off Layer (SOL) are compared to those calculated with the Monte Carlo Impurity (MCI) model. A UEDGE background plasma is used in MCI with the Roth and Garcia-Rosales (RG-R) chemical sputtering model and/or one of six physical sputtering models. While results from these simulations do not reproduce all of the features seen in the experimentally measured radiation patterns, the total radiated power calculated in MCI is in relatively good agreement with that measured by the DIII-D bolometric system when the Smith78 physical sputtering model is coupled to RG-R chemical sputtering in an unaltered UEDGE plasma. Alternatively, MCI simulations done with UEDGE background ion temperatures along the divertor target plates adjusted to better match those measured in the experiment resulted in three physical sputtering models which when coupled to the RG-R model gave a total radiated power that was within 10% of measured value.
Fan, D.; Geng, C.; Chen, L.Q.
1997-03-01
The local kinetics and topological phenomena during normal grain growth were studied in two dimensions by computer simulations employing a continuum diffuse-interface field model. The relationships between topological class and individual grain growth kinetics were examined, and compared with results obtained previously from analytical theories, experimental results and Monte Carlo simulations. It was shown that both the grain-size and grain-shape (side) distributions are time-invariant and the linear relationship between the mean radii of individual grains and topological class n was reproduced. The moments of the shape distribution were determined, and the differences among the data from soap froth. Potts model and the present simulation were discussed. In the limit when the grain size goes to zero, the average number of grain edges per grain is shown to be between 4 and 5, implying the direct vanishing of 4- and 5-sided grains, which seems to be consistent with recent experimental observations on thin films. Based on the simulation results, the conditions for the applicability of the familiar Mullins-Von Neumann law and the Hillert`s equation were discussed.
NASA Astrophysics Data System (ADS)
Pérez-Corona, M.; García, J. A.; Taller, G.; Polgár, D.; Bustos, E.; Plank, Z.
2016-02-01
The purpose of geophysical electrical surveys is to determine the subsurface resistivity distribution by making measurements on the ground surface. From these measurements, the true resistivity of the subsurface can be estimated. The ground resistivity is related to various geological parameters, such as the mineral and fluid content, porosity and degree of water saturation in the rock. Electrical resistivity surveys have been used for many decades in hydrogeological, mining and geotechnical investigations. More recently, they have been used for environmental surveys. To obtain a more accurate subsurface model than is possible with a simple 1-D model, a more complex model must be used. In a 2-D model, the resistivity values are allowed to vary in one horizontal direction (usually referred to as the x direction) but are assumed to be constant in the other horizontal (the y) direction. A more realistic model would be a fully 3-D model where the resistivity values are allowed to change in all three directions. In this research, a simulation of the cone penetration test and 2D imaging resistivity are used as tools to simulate the distribution of hydrocarbons in soil.
Simulation of a pulsatile non-Newtonian flow past a stenosed 2D artery with atherosclerosis.
Tian, Fang-Bao; Zhu, Luoding; Fok, Pak-Wing; Lu, Xi-Yun
2013-09-01
Atherosclerotic plaque can cause severe stenosis in the artery lumen. Blood flow through a substantially narrowed artery may have different flow characteristics and produce different forces acting on the plaque surface and artery wall. The disturbed flow and force fields in the lumen may have serious implications on vascular endothelial cells, smooth muscle cells, and circulating blood cells. In this work a simplified model is used to simulate a pulsatile non-Newtonian blood flow past a stenosed artery caused by atherosclerotic plaques of different severity. The focus is on a systematic parameter study of the effects of plaque size/geometry, flow Reynolds number, shear-rate dependent viscosity and flow pulsatility on the fluid wall shear stress and its gradient, fluid wall normal stress, and flow shear rate. The computational results obtained from this idealized model may shed light on the flow and force characteristics of more realistic blood flow through an atherosclerotic vessel.
Simulating HFIR Core Thermal Hydraulics Using 3D-2D Model Coupling
Travis, Adam R; Freels, James D; Ekici, Kivanc
2013-01-01
A model utilizing interdimensional variable coupling is presented for simulating the thermal hydraulic interactions of the High Flux Isotope Reactor (HFIR) core at Oak Ridge National Laboratory (ORNL). The model s domain consists of a single, explicitly represented three-dimensional fuel plate and a simplified two-dimensional coolant channel slice. In simplifying the coolant channel, and thus the number of mesh points in which the Navier-Stokes equations must be solved, the computational cost and solution time are both greatly reduced. In order for the reduced-dimension coolant channel to interact with the explicitly represented fuel plate, however, interdimensional variable coupling must be enacted along all shared boundaries. The primary focus of this paper is in detailing the collection, storage, passage, and application of variables across this interdimensional interface. Comparisons are made showing the general speed-up associated with this simplified coupled model.
Simulation of the kinetics of oxygen complexes in crystalline silicon
NASA Astrophysics Data System (ADS)
Joo Lee, Young; von Boehm, J.; Nieminen, R. M.
2002-10-01
The formation kinetics of thermal double donors (TDD's) is studied by a general kinetic model with parameters based on accurate ab initio total-energy calculations. The kinetic model includes all relevant association, dissociation, and restructuring processes. The simulated kinetics agrees qualitatively and in most cases quantitatively with the experimentally found consecutive kinetics of TDD's. It also supports our earlier assignments of the ring-type oxygen chains to TDD's [Pesola et al., Phys. Rev. Lett. 84, 5343 (2000)]. We demonstrate with the kinetic model that the most common assumption that only the O2 dimer acts as a fast diffusing species would lead to an unrealistic steady increase of the concentration of O3. The neglect of restructuring processes leads to an anomalous increase of oxygen dimers and negligible concentrations of TDD's. The capture of interstitial oxygens by diffusing oxygen chains and the escaping of interstitial oxygens from the chains fully dominate the formation kinetics.
Gomez, Juan F.; Cardona, Karen; Martinez, Laura; Saiz, Javier; Trenor, Beatriz
2014-01-01
Background Heart failure is operationally defined as the inability of the heart to maintain blood flow to meet the needs of the body and it is the final common pathway of various cardiac pathologies. Electrophysiological remodeling, intercellular uncoupling and a pro-fibrotic response have been identified as major arrhythmogenic factors in heart failure. Objective In this study we investigate vulnerability to reentry under heart failure conditions by incorporating established electrophysiological and anatomical remodeling using computer simulations. Methods The electrical activity of human transmural ventricular tissue (5 cm×5 cm) was simulated using the human ventricular action potential model Grandi et al. under control and heart failure conditions. The MacCannell et al. model was used to model fibroblast electrical activity, and their electrotonic interactions with myocytes. Selected degrees of diffuse fibrosis and variations in intercellular coupling were considered and the vulnerable window (VW) for reentry was evaluated following cross-field stimulation. Results No reentry was observed in normal conditions or in the presence of HF ionic remodeling. However, defined amount of fibrosis and/or cellular uncoupling were sufficient to elicit reentrant activity. Under conditions where reentry was generated, HF electrophysiological remodeling did not alter the width of the VW. However, intermediate fibrosis and cellular uncoupling significantly widened the VW. In addition, biphasic behavior was observed, as very high fibrotic content or very low tissue conductivity hampered the development of reentry. Detailed phase analysis of reentry dynamics revealed an increase of phase singularities with progressive fibrotic components. Conclusion Structural remodeling is a key factor in the genesis of vulnerability to reentry. A range of intermediate levels of fibrosis and intercellular uncoupling can combine to favor reentrant activity. PMID:25054335
A hierarchical lattice spring model to simulate the mechanics of 2-D materials-based composites
NASA Astrophysics Data System (ADS)
Brely, Lucas; Bosia, Federico; Pugno, Nicola
2015-07-01
In the field of engineering materials, strength and toughness are typically two mutually exclusive properties. Structural biological materials such as bone, tendon or dentin have resolved this conflict and show unprecedented damage tolerance, toughness and strength levels. The common feature of these materials is their hierarchical heterogeneous structure, which contributes to increased energy dissipation before failure occurring at different scale levels. These structural properties are the key to exceptional bioinspired material mechanical properties, in particular for nanocomposites. Here, we develop a numerical model in order to simulate the mechanisms involved in damage progression and energy dissipation at different size scales in nano- and macro-composites, which depend both on the heterogeneity of the material and on the type of hierarchical structure. Both these aspects have been incorporated into a 2-dimensional model based on a Lattice Spring Model, accounting for geometrical nonlinearities and including statistically-based fracture phenomena. The model has been validated by comparing numerical results to continuum and fracture mechanics results as well as finite elements simulations, and then employed to study how structural aspects impact on hierarchical composite material properties. Results obtained with the numerical code highlight the dependence of stress distributions on matrix properties and reinforcement dispersion, geometry and properties, and how failure of sacrificial elements is directly involved in the damage tolerance of the material. Thanks to the rapidly developing field of nanocomposite manufacture, it is already possible to artificially create materials with multi-scale hierarchical reinforcements. The developed code could be a valuable support in the design and optimization of these advanced materials, drawing inspiration and going beyond biological materials with exceptional mechanical properties.
Fully kinetic simulations of megajoule-scale dense plasma focus
Schmidt, A.; Link, A.; Tang, V.; Halvorson, C.; May, M.; Welch, D.; Meehan, B. T.; Hagen, E. C.
2014-10-15
Dense plasma focus (DPF) Z-pinch devices are sources of copious high energy electrons and ions, x-rays, and neutrons. Megajoule-scale DPFs can generate 10{sup 12} neutrons per pulse in deuterium gas through a combination of thermonuclear and beam-target fusion. However, the details of the neutron production are not fully understood and past optimization efforts of these devices have been largely empirical. Previously, we reported on the first fully kinetic simulations of a kilojoule-scale DPF and demonstrated that both kinetic ions and kinetic electrons are needed to reproduce experimentally observed features, such as charged-particle beam formation and anomalous resistivity. Here, we present the first fully kinetic simulation of a MegaJoule DPF, with predicted ion and neutron spectra, neutron anisotropy, neutron spot size, and time history of neutron production. The total yield predicted by the simulation is in agreement with measured values, validating the kinetic model in a second energy regime.
Tropical Oceanic Precipitation Processes Over Warm Pool: 2D and 3D Cloud Resolving Model Simulations
NASA Technical Reports Server (NTRS)
Tao, W.-K.; Johnson, D.; Simpson, J.; Einaudi, Franco (Technical Monitor)
2001-01-01
Rainfall is a key link in the hydrologic cycle as well as the primary heat source for the atmosphere. The vertical distribution of convective latent-heat release modulates the large-scale circulations of the topics. Furthermore, changes in the moisture distribution at middle and upper levels of the troposphere can affect cloud distributions and cloud liquid water and ice contents. How the incoming solar and outgoing longwave radiation respond to these changes in clouds is a major factor in assessing climate change. Present large-scale weather and climate model simulate processes only crudely, reducing confidence in their predictions on both global and regional scales. One of the most promising methods to test physical parameterizations used in General Circulation Models (GCMs) and climate models is to use field observations together with Cloud Resolving Models (CRMs). The CRMs use more sophisticated and physically realistic parameterizations of cloud microphysical processes, and allow for their complex interactions with solar and infrared radiative transfer processes. The CRMs can reasonably well resolve the evolution, structure, and life cycles of individual clouds and clouds systems. The major objective of this paper is to investigate the latent heating, moisture and momentum budgets associated with several convective systems developed during the TOGA COARE IFA - westerly wind burst event (late December, 1992). The tool for this study is the Goddard Cumulus Ensemble (GCE) model which includes a 3-class ice-phase microphysics scheme.
A Parallel 2D Numerical Simulation of Tumor Cells Necrosis by Local Hyperthermia
NASA Astrophysics Data System (ADS)
Reis, R. F.; Loureiro, F. S.; Lobosco, M.
2014-03-01
Hyperthermia has been widely used in cancer treatment to destroy tumors. The main idea of the hyperthermia is to heat a specific region like a tumor so that above a threshold temperature the tumor cells are destroyed. This can be accomplished by many heat supply techniques and the use of magnetic nanoparticles that generate heat when an alternating magnetic field is applied has emerged as a promise technique. In the present paper, the Pennes bioheat transfer equation is adopted to model the thermal tumor ablation in the context of magnetic nanoparticles. Numerical simulations are carried out considering different injection sites for the nanoparticles in an attempt to achieve better hyperthermia conditions. Explicit finite difference method is employed to solve the equations. However, a large amount of computation is required for this purpose. Therefore, this work also presents an initial attempt to improve performance using OpenMP, a parallel programming API. Experimental results were quite encouraging: speedups around 35 were obtained on a 64-core machine.
NASA Technical Reports Server (NTRS)
Zimmerman, Michael I.; Farrell, W. M.; Snubbs, T. J.; Halekas, J. S.
2011-01-01
Anticipating the plasma and electrical environments in permanently shadowed regions (PSRs) of the moon is critical in understanding local processes of space weathering, surface charging, surface chemistry, volatile production and trapping, exo-ion sputtering, and charged dust transport. In the present study, we have employed the open-source XOOPIC code [I] to investigate the effects of solar wind conditions and plasma-surface interactions on the electrical environment in PSRs through fully two-dimensional pattic1e-in-cell simulations. By direct analogy with current understanding of the global lunar wake (e.g., references) deep, near-terminator, shadowed craters are expected to produce plasma "mini-wakes" just leeward of the crater wall. The present results (e.g., Figure I) are in agreement with previous claims that hot electrons rush into the crater void ahead of the heavier ions, fanning a negative cloud of charge. Charge separation along the initial plasma-vacuum interface gives rise to an ambipolar electric field that subsequently accelerates ions into the void. However, the situation is complicated by the presence of the dynamic lunar surface, which develops an electric potential in response to local plasma currents (e.g., Figure Ia). In some regimes, wake structure is clearly affected by the presence of the charged crater floor as it seeks to achieve current balance (i.e. zero net current to the surface).
Study of liquid water by computer simulations. I. Static properties of a 2D model
NASA Astrophysics Data System (ADS)
Okazaki, Keiji; Nosé, Shuichi; Kataoka, Yosuke; Yamamoto, Tsunenobu
1981-12-01
A computer-simulation study of a water-like system is carried out by making use of a two-dimensional version of the Ben-Naim and Stillinger potential. The pair potential is set up such that at 0 K it yields a square net structure at low pressures and an interpretation of two square nets at high pressures. The liquid state is surveyed over a wide range of temperature and pressure. Various kinds of molecular distribution functions are derived to see how the hydrogen-bond network structure depends on temperature and density. The pressure and thermal equations of state are ''experimentally'' determined by a least square fitting to the pressures and energies calculated for about 200 different state points. The well-known anomalous behavior of liquid water is reproduced at least in a semiquantitative way. The singular properties of supercooled water also are reproduced and their origin is ascribed to the thermodynamical instability. New anomalies are predicted at high temperatures and pressures.
The 1963 Vajont landslide (Italy) simulated through a numerical 2D code
NASA Astrophysics Data System (ADS)
Zaniboni, Filippo; Ausilia Paparo, Maria; Elsen, Katharina; Tinti, Stefano
2013-04-01
On October 9th, 1963, a huge mass of about 260 million m3 collapsed along Mt. Toc flank into the artificial lake called Vajont and generated a gigantic wave that invested the town of Longarone (North-East Italy, about 100 km north of Venice), provoking about 2000 casualties. The event started a public debate on the responsibilities for the disaster, and also raised crucial issues for the scientific and engineering community, regarding reservoir flank instability and safety of the hydroelectric plant. The peculiar features of the event were immediately evident. The clay layers remained uncovered in the upper part of the detachment niche, supporting the hypothesis of a well-defined pre-existing sliding surface, that could explain the high falling velocity (around 20 m/s as a maximum) and the compactness of the deposit layers that were found to sit almost unperturbed on the bottom of the valley. The numerical study presented here contributes to the understanding of dynamics of the Vajont landslide. It is found that the accurate knowledge of the pre- and post-slide morphology provides tight constraints on the parameters of the numerical model, that are tuned to fit the observed deposit. Numerical simulations are carried out by means of the in-house built code UBO-BLOCK2. The initial sliding body is divided into a mesh of interacting volume-conserving blocks, whose motion is computed numerically. The friction coefficient at the base of the landslide is determined through a best fit search by maximizing the degree of overlapping between the calculated and observed deposits. Our best solution is also able to account for the observed slight easterly rotation of the mass, the different behaviors of the eastern and western part of the sliding surface and the retrogressive motion of the slide that after climbing up the opposite flank of the valley reverted velocity to settle down on the bottom of the valley.
NASA Astrophysics Data System (ADS)
Dages, Cecile; Samouelian, Anatja; Lanoix, Marthe; Dollinger, Jeanne; Chakkour, Sara; Chovelon, Gabrielle; Trabelsi, Khouloud; Voltz, Marc
2015-04-01
Ditches are involved in the transfer of pesticide to surface and groundwaters (e.g. Louchart et al., 2001). Soil horizons underlying ditch beds may present specific soil characteristics compared to neighbouring field soils due to erosion/deposition processes, to the specific biological activities (rooting dynamic and animal habitat) in the ditches (e.g. Vaughan et al., 2008) and to management practices (burning, dredging, mowing,...). Moreover, in contrast to percolation processes in field soils that can be assumed to be mainly 1D vertical, those occurring in the ditch beds are by essence 2D or even 3D. Nevertheless, due to a lake of knowledge, these specific aspects of transfer within ditch beds are generally omitted for hydrological simulation at the catchment scale (Mottes et al., 2014). Accordingly, the aims of this study were i) to characterize subsurface solute transfer through ditch beds and ii) to determine equivalent hydraulic parameters of the ditch beds for use in catchment scale hydrological simulations. A complementary aim was to evaluate the error in predictions performed when percolation in ditches is assumed to be similar to that in the neighbouring field soil. First, bromide transfer experiments were performed on undisturbed soil column (15 cm long with a 15 cm inner-diameter), horizontally and vertically sampled within each soil horizon underlying a ditch bed and within the neighboring field. Columns were sampled at the Roujan catchment (Hérault, France), which belongs to the long term Mediterranean hydrological observatory OMERE (Voltz and Albergel, 2002). Second, for each column, a set of parameters was determined by inverse optimization with mobile-immobile or dual permeability models, with CXTFIT (Toride et al., 1999) or with HYDRUS (Simunek et al., 1998). Third, infiltration and percolation in the ditch was simulated by a 2D flow domain approach considering the 2D variation in hydraulic properties of the cross section of a ditch bed. Last
NASA Astrophysics Data System (ADS)
Campforts, Benjamin; Vanacker, Veerle; Vanderborght, Jan; Baken, Stijn; Smolders, Erik; Govers, Gerard
2016-04-01
Meteoric 10Be allows for the quantification of vertical and lateral soil fluxes over long time scales (103-105 yr). However, the mobility of meteoric 10Be in the soil system makes a translation of meteoric 10Be inventories into erosion and deposition rates complex. Here, we present a spatially explicit 2D model simulating the behaviour of meteoric 10Be on a hillslope. The model consists of two parts. The first component deals with advective and diffusive mobility of meteoric 10Be within the soil profile, and the second component describes lateral soil and meteoric 10Be fluxes over the hillslope. Soil depth is calculated dynamically, accounting for soil production through weathering as well as downslope fluxes of soil due to creep, water and tillage erosion. Synthetic model simulations show that meteoric 10Be inventories can be related to erosion and deposition across a wide range of geomorphological and pedological settings. Our results also show that meteoric 10Be can be used as a tracer to detect human impact on soil fluxes for soils with a high affinity for meteoric 10Be. However, the quantification of vertical mobility is essential for a correct interpretation of the observed variations in meteoric 10Be profiles and inventories. Application of the Be2D model to natural conditions using data sets from the Southern Piedmont (Bacon et al., 2012) and Appalachian Mountains (Jungers et al., 2009; West et al., 2013) allows to reliably constrain parameter values. Good agreement between simulated and observed meteoric 10Be concentrations and inventories is obtained with realistic parameter values. Furthermore, our results provide detailed insights into the processes redistributing meteoric 10Be at the soil-hillslope scale.
FireStem2D--a two-dimensional heat transfer model for simulating tree stem injury in fires.
Chatziefstratiou, Efthalia K; Bohrer, Gil; Bova, Anthony S; Subramanian, Ravishankar; Frasson, Renato P M; Scherzer, Amy; Butler, Bret W; Dickinson, Matthew B
2013-01-01
FireStem2D, a software tool for predicting tree stem heating and injury in forest fires, is a physically-based, two-dimensional model of stem thermodynamics that results from heating at the bark surface. It builds on an earlier one-dimensional model (FireStem) and provides improved capabilities for predicting fire-induced mortality and injury before a fire occurs by resolving stem moisture loss, temperatures through the stem, degree of bark charring, and necrotic depth around the stem. We present the results of numerical parameterization and model evaluation experiments for FireStem2D that simulate laboratory stem-heating experiments of 52 tree sections from 25 trees. We also conducted a set of virtual sensitivity analysis experiments to test the effects of unevenness of heating around the stem and with aboveground height using data from two studies: a low-intensity surface fire and a more intense crown fire. The model allows for improved understanding and prediction of the effects of wildland fire on injury and mortality of trees of different species and sizes.
FireStem2D – A Two-Dimensional Heat Transfer Model for Simulating Tree Stem Injury in Fires
Chatziefstratiou, Efthalia K.; Bohrer, Gil; Bova, Anthony S.; Subramanian, Ravishankar; Frasson, Renato P. M.; Scherzer, Amy; Butler, Bret W.; Dickinson, Matthew B.
2013-01-01
FireStem2D, a software tool for predicting tree stem heating and injury in forest fires, is a physically-based, two-dimensional model of stem thermodynamics that results from heating at the bark surface. It builds on an earlier one-dimensional model (FireStem) and provides improved capabilities for predicting fire-induced mortality and injury before a fire occurs by resolving stem moisture loss, temperatures through the stem, degree of bark charring, and necrotic depth around the stem. We present the results of numerical parameterization and model evaluation experiments for FireStem2D that simulate laboratory stem-heating experiments of 52 tree sections from 25 trees. We also conducted a set of virtual sensitivity analysis experiments to test the effects of unevenness of heating around the stem and with aboveground height using data from two studies: a low-intensity surface fire and a more intense crown fire. The model allows for improved understanding and prediction of the effects of wildland fire on injury and mortality of trees of different species and sizes. PMID:23894599
Bolmatov, Dima; Zhernenkov, Mikhail; Zav’yalov, Dmitry; ...
2016-08-19
Here in this work we report on terahertz phononic excitations in 2D gold nanoparticle arrays in a water matrix through a series of large-scale molecular dynamics simulations. For the first time, we observe acoustic Dirac-like crossings in H (H2O) atomic (molecular) networks which emerge due to an intraband phononic scattering. These crossings are the phononic fingerprints of ice-like arrangements of H (H2O) atomic (molecular) networks at nanometer scale. We reveal how phononic excitations in metallic nanoparticles and the water matrix reciprocally impact on one another providing the mechanism for the THz phononics manipulation via structural engineering. In addition, we showmore » that by tuning the arrangement of 2D gold nanoparticle assemblies the Au phononic polarizations experience sub-terahertz hybridization (Kohn anomaly) due to surface electron-phonon relaxation processes. This opens the way for the sound control and manipulation in soft matter metamaterials at nanoscale.« less
Bolmatov, Dima; Zhernenkov, Mikhail; Zav’yalov, Dmitry; Cai, Yong Q.; Cunsolo, Alessandro
2016-08-19
Here in this work we report on terahertz phononic excitations in 2D gold nanoparticle arrays in a water matrix through a series of large-scale molecular dynamics simulations. For the first time, we observe acoustic Dirac-like crossings in H (H_{2}O) atomic (molecular) networks which emerge due to an intraband phononic scattering. These crossings are the phononic fingerprints of ice-like arrangements of H (H_{2}O) atomic (molecular) networks at nanometer scale. We reveal how phononic excitations in metallic nanoparticles and the water matrix reciprocally impact on one another providing the mechanism for the THz phononics manipulation via structural engineering. In addition, we show that by tuning the arrangement of 2D gold nanoparticle assemblies the Au phononic polarizations experience sub-terahertz hybridization (Kohn anomaly) due to surface electron-phonon relaxation processes. This opens the way for the sound control and manipulation in soft matter metamaterials at nanoscale.
NASA Astrophysics Data System (ADS)
Humair, F.; Matasci, B.; Carrea, D.; Pedrazzini, A.; Loye, A.; Pedrozzi, G.; Nicolet, P.; Jaboyedoff, M.
2012-04-01
account the results of the experimental testing are performed and compared with the a-priori simulations. 3D simulations were performed using a software that takes into account the effect of the forest cover in the blocky trajectory (RockyFor 3D) and an other that neglects this aspect (Rotomap; geo&soft international). 2D simulation (RocFall; Rocscience) profiles were located in the blocks paths deduced from 3D simulations. The preliminary results show that: (1) high speed movies are promising and allow us to track the blocks using video software, (2) the a-priori simulations tend to overestimate the runout distance which is certainly due to an underestimation of the obstacles as well as the breaking of the failing rocks which is not taken into account in the models, (3) the trajectories deduced from both a-priori simulation and real size experiment highlights the major influence of the channelized slope morphology on rock paths as it tends to follow the flow direction. This indicates that the 2D simulation have to be performed along the line of flow direction.
Analysis of Highly-Resolved Simulations of 2-D Humps Toward Improvement of Second-Moment Closures
NASA Technical Reports Server (NTRS)
Jeyapaul, Elbert; Rumsey Christopher
2013-01-01
Fully resolved simulation data of flow separation over 2-D humps has been used to analyze the modeling terms in second-moment closures of the Reynolds-averaged Navier- Stokes equations. Existing models for the pressure-strain and dissipation terms have been analyzed using a priori calculations. All pressure-strain models are incorrect in the high-strain region near separation, although a better match is observed downstream, well into the separated-flow region. Near-wall inhomogeneity causes pressure-strain models to predict incorrect signs for the normal components close to the wall. In a posteriori computations, full Reynolds stress and explicit algebraic Reynolds stress models predict the separation point with varying degrees of success. However, as with one- and two-equation models, the separation bubble size is invariably over-predicted.
Introducing Michaelis-Menten Kinetics through Simulation
ERIC Educational Resources Information Center
Halkides, Christopher J.; Herman, Russell
2007-01-01
We describe a computer tutorial that introduces the concept of the steady state in enzyme kinetics. The tutorial allows students to produce graphs of the concentrations of free enzyme, enzyme-substrate complex, and product versus time in order to learn about the approach to steady state. By using a range of substrate concentrations and rate…
KINEXP: Computer Simulation in Enzyme Kinetics.
ERIC Educational Resources Information Center
Gelpi, Josep Lluis; Domenech, Carlos
1988-01-01
Describes a program which allows students to identify and characterize several kinetic inhibitory mechanisms. Uses the generic model of reversible inhibition of a monosubstrate enzyme but can be easily modified to run other models such as bisubstrate enzymes. Uses MS-DOS BASIC. (MVL)
Kinetic plasma modeling with quiet Monte Carlo direct simulation.
Albright, B. J.; Jones, M. E.; Lemons, D. S.; Winske, D.
2001-01-01
The modeling of collisions among particles in space plasma media poses a challenge for computer simulation. Traditional plasma methods are able to model well the extremes of highly collisional plasmas (MHD and Hall-MHD simulations) and collisionless plasmas (particle-in-cell simulations). However, neither is capable of trealing the intermediate, semi-collisional regime. The authors have invented a new approach to particle simulation called Quiet Monte Carlo Direct Simulation (QMCDS) that can, in principle, treat plasmas with arbitrary and arbitrarily varying collisionality. The QMCDS method will be described, and applications of the QMCDS method as 'proof of principle' to diffusion, hydrodynamics, and radiation transport will be presented. Of particular interest to the space plasma simulation community is the application of QMCDS to kinetic plasma modeling. A method for QMCDS simulation of kinetic plasmas will be outlined, and preliminary results of simulations in the limit of weak pitch-angle scattering will be presented.
NASA Astrophysics Data System (ADS)
Schiettekatte, François; Chicoine, Martin
2016-03-01
Corteo is a program that implements Monte Carlo (MC) method to simulate ion beam analysis (IBA) spectra of several techniques by following the ions trajectory until a sufficiently large fraction of them reach the detector to generate a spectrum. Hence, it fully accounts for effects such as multiple scattering (MS). Here, a version of Corteo is presented where the target can be a 2D or 3D image. This image can be derived from micrographs where the different compounds are identified, therefore bringing extra information into the solution of an IBA spectrum, and potentially significantly constraining the solution. The image intrinsically includes many details such as the actual surface or interfacial roughness, or actual nanostructures shape and distribution. This can for example lead to the unambiguous identification of structures stoichiometry in a layer, or at least to better constraints on their composition. Because MC computes in details the trajectory of the ions, it simulates accurately many of its aspects such as ions coming back into the target after leaving it (re-entry), as well as going through a variety of nanostructures shapes and orientations. We show how, for example, as the ions angle of incidence becomes shallower than the inclination distribution of a rough surface, this process tends to make the effective roughness smaller in a comparable 1D simulation (i.e. narrower thickness distribution in a comparable slab simulation). Also, in ordered nanostructures, target re-entry can lead to replications of a peak in a spectrum. In addition, bitmap description of the target can be used to simulate depth profiles such as those resulting from ion implantation, diffusion, and intermixing. Other improvements to Corteo include the possibility to interpolate the cross-section in angle-energy tables, and the generation of energy-depth maps.
NASA Astrophysics Data System (ADS)
Awad, Esam; Toorman, Erik; Lacor, Chris
2009-06-01
In this study, the performance of the horizontal large eddy simulation module, developed at the University of Leuven (HLES-KULeuven module) is assessed. A comparison between different subgrid scale models has been carried out. The study is concerned with the non-rotating and unstratified flows. The results of the simulation for an oscillatory backward facing (BFS) flow are presented in case of an expanding flume based on a one-length scale approach and a two-length scale approach. Three subgrid scale (SGS) models have been tested: Smagorinsky SGS model (Smagorinsky, J., (1963). General circulation experiments with the primitive equations, I. the basic experiments. Monthly Weather Review, 91(3), 99-164), Uittenbogaard SGS model (Uittenbogaard, R.E., and van Vossen, B., (2004). Subgrid-scale model for quasi-2D turbulence in shallow water. Shallow Flows. Jirka and Uijttewaal (Eds.), Taylor & Francis Group, London, ISBN 90 5809 700 5) and a proposed two-length scale approach. The first two models are considered to be a one-length scale models. A simulation without a subgrid scale model for the horizontal mixing has also been conducted. In all simulations, a quadratic friction model parameterizes the dissipation produced by the 3D-subdepth scale turbulence. The two-length scale concept uses a newly mixing length formulation for the quasi-2D turbulence and doesn't depend on the filter width in contrast to the one-length scale approach, in which the mixing length is function of the filter width. The outputs of the HLES-KULeuven module have been compared with the experimental data taken from Stelling, G.S., and Wang, L.X., (1984). Experiments and computations on separating flow in an expanding flume. Dept. Civil Engineering, Delft University of Technology, Report 2-84.). The two-length scale approach has been validated with experimental data from SERC Flood Channel Facility at HR Wallingford. In general, there is a qualitative agreement with the experimental data. It has
Kinetic particle simulation of discharge and wall erosion of a Hall thruster
Cho, Shinatora; Komurasaki, Kimiya; Arakawa, Yoshihiro
2013-06-15
The primary lifetime limiting factor of Hall thrusters is the wall erosion caused by the ion induced sputtering, which is predominated by dielectric wall sheath and pre-sheath. However, so far only fluid or hybrid simulation models were applied to wall erosion and lifetime studies in which this non-quasi-neutral and non-equilibrium area cannot be treated directly. Thus, in this study, a 2D fully kinetic particle-in-cell model was presented for Hall thruster discharge and lifetime simulation. Because the fully kinetic lifetime simulation was yet to be achieved so far due to the high computational cost, the semi-implicit field solver and the technique of mass ratio manipulation was employed to accelerate the computation. However, other artificial manipulations like permittivity or geometry scaling were not used in order to avoid unrecoverable change of physics. Additionally, a new physics recovering model for the mass ratio was presented for better preservation of electron mobility at the weakly magnetically confined plasma region. The validity of the presented model was examined by various parametric studies, and the thrust performance and wall erosion rate of a laboratory model magnetic layer type Hall thruster was modeled for different operation conditions. The simulation results successfully reproduced the measurement results with typically less than 10% discrepancy without tuning any numerical parameters. It is also shown that the computational cost was reduced to the level that the Hall thruster fully kinetic lifetime simulation is feasible.
Kinetic particle simulation of discharge and wall erosion of a Hall thruster
NASA Astrophysics Data System (ADS)
Cho, Shinatora; Komurasaki, Kimiya; Arakawa, Yoshihiro
2013-06-01
The primary lifetime limiting factor of Hall thrusters is the wall erosion caused by the ion induced sputtering, which is predominated by dielectric wall sheath and pre-sheath. However, so far only fluid or hybrid simulation models were applied to wall erosion and lifetime studies in which this non-quasi-neutral and non-equilibrium area cannot be treated directly. Thus, in this study, a 2D fully kinetic particle-in-cell model was presented for Hall thruster discharge and lifetime simulation. Because the fully kinetic lifetime simulation was yet to be achieved so far due to the high computational cost, the semi-implicit field solver and the technique of mass ratio manipulation was employed to accelerate the computation. However, other artificial manipulations like permittivity or geometry scaling were not used in order to avoid unrecoverable change of physics. Additionally, a new physics recovering model for the mass ratio was presented for better preservation of electron mobility at the weakly magnetically confined plasma region. The validity of the presented model was examined by various parametric studies, and the thrust performance and wall erosion rate of a laboratory model magnetic layer type Hall thruster was modeled for different operation conditions. The simulation results successfully reproduced the measurement results with typically less than 10% discrepancy without tuning any numerical parameters. It is also shown that the computational cost was reduced to the level that the Hall thruster fully kinetic lifetime simulation is feasible.
NASA Astrophysics Data System (ADS)
Simão Ferreira, C. J.; Bijl, H.; van Bussel, G.; van Kuik, G.
2007-07-01
The implementation of wind energy conversion systems in the built environment renewed the interest and the research on Vertical Axis Wind Turbines (VAWT), which in this application present several advantages over Horizontal Axis Wind Turbines (HAWT). The VAWT has an inherent unsteady aerodynamic behavior due to the variation of angle of attack with the angle of rotation, perceived velocity and consequentially Reynolds number. The phenomenon of dynamic stall is then an intrinsic effect of the operation of a Vertical Axis Wind Turbine at low tip speed ratios, having a significant impact in both loads and power. The complexity of the unsteady aerodynamics of the VAWT makes it extremely attractive to be analyzed using Computational Fluid Dynamics (CFD) models, where an approximation of the continuity and momentum equations of the Navier-Stokes equations set is solved. The complexity of the problem and the need for new design approaches for VAWT for the built environment has driven the authors of this work to focus the research of CFD modeling of VAWT on: •comparing the results between commonly used turbulence models: URANS (Spalart-Allmaras and k-epsilon) and large eddy models (Large Eddy Simulation and Detached Eddy Simulation) •verifying the sensitivity of the model to its grid refinement (space and time), •evaluating the suitability of using Particle Image Velocimetry (PIV) experimental data for model validation. The 2D model created represents the middle section of a single bladed VAWT with infinite aspect ratio. The model simulates the experimental work of flow field measurement using Particle Image Velocimetry by Simão Ferreira et al for a single bladed VAWT. The results show the suitability of the PIV data for the validation of the model, the need for accurate simulation of the large eddies and the sensitivity of the model to grid refinement.
Simulations of P-SV wave scattering due to cracks by the 2-D finite difference method
NASA Astrophysics Data System (ADS)
Suzuki, Yuji; Shiina, Takahiro; Kawahara, Jun; Okamoto, Taro; Miyashita, Kaoru
2013-12-01
We simulate P-SV wave scattering by 2-D parallel cracks using the finite difference method (FDM). Here, special emphasis is put on simplicity; we apply a standard FDM (second-order velocity-stress scheme with a staggered grid) to media including traction-free, infinitesimally thin cracks, which are expressed in a simple manner. As an accuracy test of the present method, we calculate the displacement discontinuity along an isolated crack caused by harmonic waves using the method, which is compared with the corresponding results based on a reliable boundary integral equation method. The test resultantly indicates that the present method yields sufficient accuracy. As an application of this method, we also simulate wave propagation in media with randomly distributed cracks. We experimentally determine the attenuation and velocity dispersion induced by scattering from the synthetic seismograms, using a waveform averaging technique. It is shown that the results are well explained by a theory based on the Foldy approximation, if the crack density is sufficiently low. The theory appears valid with a crack density up to at least 0.1 for SV wave incidence, whereas the validity limit appears lower for P wave incidence.
NASA Astrophysics Data System (ADS)
Gramusset, Anneli; Herrera, Paulo; Parada, Miguel Angel
2014-05-01
A thorough understanding of the thermal processes that occur in aquifers is essential to assess local and regional low enthalpy geothermal resources. The relationship between heat convection and heat conduction has been widely studied in basins around the world at a regional scale. However, few studies have focused on smaller, shallower basins containing free aquifers hosted in unconsolidated fluvial-alluvial sediments, like Santiago Basin. We use numerical modeling to simulate the fluid dynamics of the Santiago basin groundwater system under different thermal conditions. Despite the current computational advances, modeling such a complex system with a full 3D approach is still numerically time demanding and unstable. Besides, the basin has irregular geometry and variable hydraulic and thermal features. Thus, we performed a 2D model comprising a thin water saturated slice of sediments beneath the central part of the city, where the basin morphology is well constrained. We simulate coupled groundwater and heat flow throughout this vertical slice and we compare results for different scenarios that comprise different hydraulic, thermal and geometric parameters. Results obtained with certain hydraulic conductivities show that instabilities appear giving rise to free thermal convection in the deepest parts of the basin. If the system is split into several hydrogeological units, the onset of these instabilities is inhibited. Consequently, we suggest that the stratigraphic complexities of a fluvial-alluvial deposit should be considered to better understanding the thermal-driven groundwater fluid dynamics.
2D simulation of active species and ozone production in a multi-tip DC air corona discharge
NASA Astrophysics Data System (ADS)
Meziane, M.; Eichwald, O.; Sarrette, J. P.; Ducasse, O.; Yousfi, M.
2011-11-01
The present paper shows for the first time in the literature a complete 2D simulation of the ozone production in a DC positive multi-tip to plane corona discharge reactor crossed by a dry air flow at atmospheric pressure. The simulation is undertaken until 1 ms and involves tens of successive discharge and post-discharge phases. The air flow is stressed by several monofilament corona discharges generated by a maximum of four anodic tips distributed along the reactor. The nonstationary hydrodynamics model for reactive gas mixture is solved using the commercial FLUENT software. During each discharge phase, thermal and vibrational energies as well as densities of radical and metastable excited species are locally injected as source terms in the gas medium surrounding each tip. The chosen chemical model involves 10 neutral species reacting following 24 reactions. The obtained results allow us to follow the cartography of the temperature and the ozone production inside the corona reactor as a function of the number of high voltage anodic tips.
Gyrokinetic Electron and Fully Kinetic Ion Particle Simulation of Collisionless Plasma Dynamics
Yu Lin; Xueyi Wang; Liu Chen; Zhihong Lin
2009-08-11
Fully kinetic-particle simulations and hybrid simulations have been utilized for decades to investigate various fundamental plasma processes, such as magnetic reconnection, fast compressional waves, and wave-particle interaction. Nevertheless, due to disparate temporal and spatial scales between electrons and ions, existing fully kinetic-particle codes have to employ either unrealistically high electron-to-ion mass ratio, me/mi, or simulation domain limited to a few or a few ten's of the ion Larmor radii, or/and time much less than the global Alfven time scale in order to accommodate available computing resources. On the other hand, in the hybrid simulation, the ions are treated as fully kinetic particles but the electrons are treated as a massless fluid. The electron kinetic effects, e.g., wave-particle resonances and finite electron Larmor radius effects, are completely missing. Important physics, such as the electron transit time damping of fast compressional waves or the triggering mechanism of magnetic reconnection in collisionless plasmas is absent in the hybrid codes. Motivated by these considerations and noting that dynamics of interest to us has frequencies lower than the electron gyrofrequency, we planned to develop an innovative particle simulation model, gyrokinetic (GK) electrons and fully kinetic (FK) ions. In the GK-electron and FK-ion (GKe/FKi) particle simulation model, the rapid electron cyclotron motion is removed, while keeping finite electron Larmor radii, realistic me/mi ratio, wave-particle interactions, and off-diagonal components of electron pressure tensor. The computation power can thus be significantly improved over that of the full-particle codes. As planned in the project DE-FG02-05ER54826, we have finished the development of the new GK-electron and FK-ion scheme, finished its benchmark for a uniform plasma in 1-D, 2-D, and 3-D systems against linear waves obtained from analytical theories, and carried out a further convergence test
2D hybrid simulations of super-diffusion at the magnetopause driven by Kelvin-Helmholtz instability
Cowee, Misa M; Winske, Dan; Gary, S Peter
2009-01-01
This manuscript describes the self-consistent simulation of diffusion at the magnetopause driven by Kelvin-Helmholtz (KH) instability. Two-dimensional hybrid (kinetic ions, fluid electrons) simulations of the most KH-unstable configuration where the shear flow is oriented perpendicular to the uniform magnetic field are carried out. The motion of the simulation particles are tracked during the run and their mean-square displacement normal to the magnetopause is calculated from which diffusion coefficients are determined. The diffusion coefficients are found to be time dependent, with D{sub x} {proportional_to} t{sup {alpha}}, where {alpha} > 1. Additionally, the probability distribution functions (PDF) of the 'jump lengths' the particles make over time are found to be non-gaussian. Such time-dependent diffusion coefficients and non-gaussian PDF's have been associated with so-called 'super-diffusion', in which diffusive mixing of particles is enhanced over classical diffusion. The results indicate that while turbulence associated with the break-down of vortices contributes to this enhanced diffusion, it is the growth of large-scale, coherent vortices is the more important process in facilitating it.
NASA Astrophysics Data System (ADS)
Llanes, F.; dela Resma, M.; Ferrer, P.; Realino, V.; Aquino, D. T.; Eco, R. C.; Lagmay, A.
2013-12-01
From November 14 to December 3, 2004, Luzon Island was ravaged by 4 successive typhoons: Typhoon Mufia, Tropical Storm Merbok, Tropical Depression Winnie, and Super Typhoon Nanmadol. Tropical Depression Winnie was the most destructive of the four when it triggered landslides on November 29 that devastated the municipalities of Infanta, General Nakar, and Real in Quezon Province, southeast Luzon. Winnie formed east of Central Luzon on November 27 before it moved west-northwestward over southeastern Luzon on November 29. A total of 1,068 lives were lost and more than USD 170 million worth of damages to crops and infrastructure were incurred from the landslides triggered by Typhoon Winnie on November 29 and the flooding caused by the 4 typhoons. FLO-2D, a flood routing software for generating flood and debris flow hazard maps, was utilized to simulate the debris flows that could potentially affect the study area. Based from the rainfall intensity-duration-frequency analysis, the cumulative rainfall from typhoon Winnie on November 29 which was approximately 342 mm over a 9-hour period was classified within a 100-year return period. The Infanta station of the Philippine Atmospheric Geophysical and Astronomical Services Administration (PAGASA) was no longer able to measure the amount of rainfall after this period because the rain gauge in that station was washed away by floods. Rainfall data with a 100-year return period was simulated over the watersheds delineated from a SAR-derived digital elevation model. The resulting debris flow hazard map was compared with results from field investigation and previous studies made on the landslide event. The simulation identified 22 barangays (villages) with a total of 45,155 people at risk of turbulent flow and flooding.
Kinetic transport simulation of energetic particles
NASA Astrophysics Data System (ADS)
Sheng, He; Waltz, R. E.
2016-05-01
A kinetic transport code (EPtran) is developed for the transport of the energetic particles (EPs). The EPtran code evolves the EP distribution function in radius, energy, and pitch angle phase space (r, E, λ) to steady state with classical slowing down, pitch angle scattering, as well as radial and energy transport of the injected EPs (neutral beam injection (NBI) or fusion alpha). The EPtran code is illustrated by treating the transport of NBI fast ions from high-n ITG/TEM micro-turbulence and EP driven unstable low-n Alfvén eigenmodes (AEs) in a well-studied DIII-D NBI heated discharge with significant AE central core loss. The kinetic transport code results for this discharge are compared with previous study using a simple EP density moment transport code ALPHA (R.E. Waltz and E.M. Bass 2014 Nucl. Fusion 54 104006). The dominant EP-AE transport is treated with a local stiff critical EP density (or equivalent pressure) gradient radial transport model modified to include energy-dependence and the nonlocal effects EP drift orbits. All previous EP transport models assume that the EP velocity space distribution function is not significantly distorted from the classical ‘no transport’ slowing down distribution. Important transport distortions away from the slowing down EP spectrum are illustrated by a focus on the coefficient of convection: EP energy flux divided by the product of EP average energy and EP particle flux.
NASA Astrophysics Data System (ADS)
Machado, Christiano B.; Pereira, Wagner C. A.; Padilla, Frédéric; Laugier, Pascal
2012-05-01
Ultrasound axial transmission (UAT) has been proposed to the diagnosis and follow-up of fracture healing. Some researchers have already pointed out the influence of fracture length, geometry and callus composition on the ultrasound time-of-flight and attenuation, with experimental and simulation studies. The aim of this work was to develop a pilot study on the effect of bone fracture unevenness on UAT measurements. Two-dimensional (2D) numerical simulations of ultrasound wave propagation were run using a custom-made finite-difference time domain code (SimSonic2D). Numerical models were composed of two 4-mm thick bone plates, with fracture lengths varying from 0 to 4 mm. For each case, an upward (UWun) and downward (DWun) unevenness of 0.5, 1.0 and 1.5 mm was implemented in the second plate. The 1-MHz emitter and receptor transducers were placed at 40 mm from each other, 20 mm apart from the center fracture. Two configurations were considered: 1.5 mm above the plates (for the 0-mm unevenness case) and transducers in contact with bone plate. For each situation, the time-of-flight of the first arriving signal (TOFFAS) and the FAS energy amplitude loss measured by the sound pressure level (SPLFAS) were computed. Results showed that there was a linear increase in TOFFAS with increasing fracture length, and a decrease of SPLFAS with the presence of a discontinuity. TOFFAS values were decreased with UWun (-0.87 μs for UWun = 1.5 mm), and increased with DWun (+0.99 μs for DWun = 1.5 mm). The SPLFAS increased with both UWun (+3.54 dB for UWun = 1.5 mm) and DWun (+8.15 dB for DWun = 1.5 mm). Both parameters showed the same variability. When transducers were put in contact with bone surface, fracture unevenness had no influence on TOF and SPL estimates. Previous works have already demonstrated that a fracture of 3 mm can increase TOFFAS in an order of 1 μs. Considering these preliminary results, it can be concluded that, although the variable fracture unevenness (until 1
Kinetic Simulations of Ion Beam Neutralization
Chang, O.; Wang, J.
2011-05-20
Full particle PIC simulations are performed to study the neutralization of an ion beam in the cohesionless, mesothermal regime. Simulations further confirmed that neutralization is achieved through interactions between the trapped electrons and the potential well established by the propagation of the beam front along the beam direction and is not through plasma instabilities as previous studies suggested. In the transverse direction, the process is similar to that of the expansion of mesothermal plasma into vacuum. Parametric simulations are also performed to investigate the effects of beam radius and domain boundary condition on the neutralization process. The results suggests that, while the qualitative behavior may be similar in ground tests, quantitative parameters such as the beam potential will be affected significantly by the vacuum chamber because of the limits imposed on the expansion process by the finite chamber space.
NASA Astrophysics Data System (ADS)
Williams, Westin B.; Michaels, Thomas E.; Michaels, Jennifer E.
2017-02-01
Reliable detection of damage in composites is critically important for failure prevention in the aerospace industry since these materials are more frequently being used in high stress applications. Structural health monitoring (SHM) via guided wave sensors mounted on or embedded within a composite structure can help detect and localize damage in real-time while potentially reducing overall maintenance costs. One approach to guided wave SHM is sparse array imaging via the minimum variance algorithm, and it has been shown in prior work that incorporating expected scattering from defects of interest can improve the quality of damage localization and characterization. For this study, simulated damage in the form of attached magnets was used for estimating scattering from recorded wavefield data. Data were recorded on a circle centered at the damage location from multiple incident directions before and after the magnets were attached. Baseline subtraction is used to estimate scattering patterns for each incident direction, and these patterns are combined and interpolated to form a full 2-D scattering matrix. This matrix is then incorporated into the minimum variance imaging algorithm, and the efficacy of this scattering estimation methodology is evaluated by comparing the resulting sparse array images to those generated using simpler scattering assumptions.
TITAN2D simulations of pyroclastic flows at Cerro Machín Volcano, Colombia: Hazard implications
NASA Astrophysics Data System (ADS)
Murcia, H. F.; Sheridan, M. F.; Macías, J. L.; Cortés, G. P.
2010-03-01
Cerro Machín is a dacitic tuff ring located in the central part of the Colombian Andes. It lies at the southern end of the Cerro Bravo-Cerro Machín volcanic belt. This volcano has experienced at least six major explosive eruptions during the last 5000 years. These eruptions have generated pyroclastic flows associated with Plinian activity that have traveled up to 8 km from the crater, and pyroclastic flows associated with Vulcanian activity with shorter runouts of 5 km from the source. Today, some 21,000 people live within a 8 km radius of Cerro Machín. The volcano is active with fumaroles and has shown increasing seismic activity since 2004, and therefore represents a potentially increasing threat to the local population. To evaluate the possible effects of future eruptions that may generate pyroclastic density currents controlled by granular flow dynamics we performed flow simulations with the TITAN2D code. These simulations were run in all directions around the volcano, using the input parameters of the largest eruption reported. The results show that an eruption of 0.3 km 3 of pyroclastic flows from a collapsing Plinian column would travel up to 9 km from the vent, emplacing a deposit thicker than 60 m within the Toche River valley. Deposits >45 m thick can be expected in the valleys of San Juan, Santa Marta, and Azufral creeks, while 30 m thick deposits could accumulate within the drainages of the Tochecito, Bermellón, and Coello Rivers. A minimum area of 56 km 2 could be affected directly by this kind of eruption. In comparison, Vulcanian column-collapse pyroclastic flows of 0.1 km 3 would travel up to 6 km from the vent depositing >45 m thick debris inside the Toche River valley and more than 30 m inside the valleys of San Juan, Santa Marta, and Azufral creeks. The minimum area that could be affected directly by this kind of eruption is 33 km 2. The distribution and thickness of the deposits obtained by these simulations are consistent with the hazard
Kinetic energy of rainfall simulation nozzles
Technology Transfer Automated Retrieval System (TEKTRAN)
Different spray nozzles are used frequently to simulate natural rain for soil erosion and chemical transport, particularly phosphorous (P), studies. Oscillating VeeJet nozzles are used mostly in soil erosion research while constant spray FullJet nozzles are commonly used for P transport. Several ch...
FULLY KINETIC SIMULATIONS OF SLOW-MODE SHOCKS
W. DAUGHTON; D. WINSKE; L. YIN
2001-05-01
Much of the theoretical understanding concerning the structure and essential properties of the slow-mode shock has been obtained from extensive hybrid calculations in which a full kinetic description is retained for the ions while the electrons are approximated as a massless adiabatic fluid. Due to the relatively broad spatial and relatively slow temporal scales of the slow shock, one would expect this approximation to be well justified. However, implicit simulations with kinetic electrons have produced significant differences in comparison to standard hybrid results. In this work, we re-examine the importance of electron dynamics to the slow shock using one-dimensional fully kinetic simulations. We employ a simple explicit simulation technique and fully resolve all relevant spatial and temporal electron scales. The resulting shock structure and ion heating are in excellent agreement with hybrid simulations, indicating the total dissipation arising from kinetic electrons is relatively minor. However, the electron heating is somewhat larger than the corresponding hybrid simulation and clear non-Maxwellian features are observed. In the upstream region, back streaming electrons give rise to double peaked distributions while in the downstream region bi-Maxwellian distributions are observed with T{sub e{parallel}} > T{sub e{perpendicular}}.
Enabling Breakthrough Kinetic Simulations of the Magnetosphere Using Petascale Computing
NASA Astrophysics Data System (ADS)
Vu, H. X.; Karimabadi, H.; Omelchenko, Y.; Tatineni, M.; Majumdar, A.; Krauss-Varban, D.; Dorelli, J.
2009-12-01
Currently global magnetospheric simulations are predominantly based on single-fluid magnetohydrodynamics (MHD). MHD simulations have proven useful in studies of the global dynamics of the magnetosphere with the goal of predicting eminent features of substorms and other global events. But it is well known that the magnetosphere is dominated by ion kinetic effects, which is ignored in MHD simulations, and many key aspects of the magnetosphere relating to transport and structure of boundaries await global kinetic simulations. We are using our recent innovations in hybrid (electron fluid, kinetic ions) simulations, as being developed in our Hybrid3D (H3D) code, and the power of massively parallel machines to make, breakthrough 3D global kinetic simulations of the magnetosphere. The innovations include (i) multi-zone (asynchronous) algorithm, (ii) dynamic load balancing, and (iii) code adaptation and optimization to large number of processors. In this presentation we will show preliminary results of our progress to date using from 512 to over 8192 cores. In particular, we focus on what we believe to be the first demonstration of the formation of a flux rope in 3D global hybrid simulations. As in the MHD simulations, the resulting flux rope has a very complex structure, wrapping up field lines from different regions and appears to be connected on at least one end to Earth. Magnetic topology of the FTE is examined to reveal the existence of several separators (3D X-lines). The formation and growth of this structure will be discussed and spatial profile of the magnetic and plasma variables will be compared with those from MHD simulations.
NASA Technical Reports Server (NTRS)
Fleming, Eric L.; Jackman, Charles H.; Considine, David B.; Stolarski, Richard S.
1999-01-01
In this study, we examine the sensitivity of long lived tracers to changes in the base transport components in our 2-D model. Changes to the strength of the residual circulation in the upper troposphere and stratosphere and changes to the lower stratospheric K(sub zz) had similar effects in that increasing the transport rates decreased the overall stratospheric mean age, and increased the rate of removal of material from the stratosphere. Increasing the stratospheric K(sub yy) increased the mean age due to the greater recycling of air parcels through the middle atmosphere, via the residual circulation, before returning to the troposphere. However, increasing K(sub yy) along with self-consistent increases in the corresponding planetary wave drive, which leads to a stronger residual circulation, more than compensates for the K(sub yy)-effect, and produces significantly younger ages throughout the stratosphere. Simulations with very small tropical stratospheric K(sub yy) decreased the globally averaged age of air by as much as 25% in the middle and upper stratosphere, and resulted in substantially weaker vertical age gradients above 20 km in the extratropics. We found only very small stratospheric tracer sensitivity to the magnitude of the horizontal mixing across the tropopause, and to the strength of the mesospheric gravity wave drag and diffusion used in the model. We also investigated the transport influence on chemically active tracers and found a strong age-tracer correlation, both in concentration and calculated lifetimes. The base model transport gives the most favorable overall comparison with a variety of inert tracer observations, and provides a significant improvement over our previous 1995 model transport. Moderate changes to the base transport were found to provide modest agreement with some of the measurements. Transport scenarios with residence times ranging from moderately shorter to slightly longer relative to the base case simulated N2O lifetimes
NASA Astrophysics Data System (ADS)
Sato, Haruo; Fehler, Michael C.
2016-10-01
The envelope broadening and the peak delay of the S-wavelet of a small earthquake with increasing travel distance are results of scattering by random velocity inhomogeneities in the earth medium. As a simple mathematical model, Sato proposed a new stochastic synthesis of the scalar wavelet envelope in 3-D von Kármán type random media when the centre wavenumber of the wavelet is in the power-law spectral range of the random velocity fluctuation. The essential idea is to split the random medium spectrum into two components using the centre wavenumber as a reference: the long-scale (low-wavenumber spectral) component produces the peak delay and the envelope broadening by multiple scattering around the forward direction; the short-scale (high-wavenumber spectral) component attenuates wave amplitude by wide angle scattering. The former is calculated by the Markov approximation based on the parabolic approximation and the latter is calculated by the Born approximation. Here, we extend the theory for the envelope synthesis of a wavelet in 2-D random media, which makes it easy to compare with finite difference (FD) simulation results. The synthetic wavelet envelope is analytically written by using the random medium parameters in the angular frequency domain. For the case that the power spectral density function of the random velocity fluctuation has a steep roll-off at large wavenumbers, the envelope broadening is small and frequency independent, and scattering attenuation is weak. For the case of a small roll-off, however, the envelope broadening is large and increases with frequency, and the scattering attenuation is strong and increases with frequency. As a preliminary study, we compare synthetic wavelet envelopes with the average of FD simulation wavelet envelopes in 50 synthesized random media, which are characterized by the RMS fractional velocity fluctuation ε = 0.05, correlation scale a = 5 km and the background wave velocity V0 = 4 km s-1. We use the radiation
Kinetic Method for Hydrogen-Deuterium-Tritium Mixture Distillation Simulation
Sazonov, A.B.; Kagramanov, Z.G.; Magomedbekov, E.P.
2005-07-15
Simulation of hydrogen distillation plants requires mathematical procedures suitable for multicomponent systems. In most of the present-day simulation methods a distillation column is assumed to be composed of theoretical stages, or plates. However, in the case of a multicomponent mixture theoretical plate does not exist.An alternative kinetic method of simulation is depicted in the work. According to this method a system of mass-transfer differential equations is solved numerically. Mass-transfer coefficients are estimated with using experimental results and empirical equations.Developed method allows calculating the steady state of a distillation column as well as its any non-steady state when initial conditions are given. The results for steady states are compared with ones obtained via Thiele-Geddes theoretical stage technique and the necessity of using kinetic method is demonstrated. Examples of a column startup period and periodic distillation simulations are shown as well.
Simulations of plasma sheaths using continuum kinetic models
NASA Astrophysics Data System (ADS)
Srinivasan, Bhuvana; Hakim, Ammar
2015-11-01
Understanding plasma sheath physics is important for the performance of devices such as Hall thrusters due to the effect of energetic particles on electrode erosion. Plasma sheath physics is studied using kinetic and multi-fluid models with relevance to secondary electron emissions and plasma-surface interactions. Continuum kinetic models are developed to directly solve the Vlasov-Poisson equation using the discontinuous Galerkin method for each of the ion and electron species. A steady-state sheath is simulated by including a simple model for a neutral fluid. Multi-fluid simulations for the plasma sheath are also performed using the discontinuous Galerkin method to solve a complete set of fluid equations for each of the ion and electron species. The kinetic plasma sheath is compared to a multi-fluid plasma sheath. Supported by Air Force Office of Scientific Research.
Fediai, Artem; Ryndyk, Dmitry A; Cuniberti, Gianaurelio
2016-10-05
Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces-for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts-metal/graphene contacts-and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties.
Continuum kinetic and multi-fluid simulations of classical sheaths
NASA Astrophysics Data System (ADS)
Cagas, P.; Hakim, A.; Juno, J.; Srinivasan, B.
2017-02-01
The kinetic study of plasma sheaths is critical, among other things, to understand the deposition of heat on walls, the effect of sputtering, and contamination of the plasma with detrimental impurities. The plasma sheath also provides a boundary condition and can often have a significant global impact on the bulk plasma. In this paper, kinetic studies of classical sheaths are performed with the continuum kinetic code, Gkeyll, which directly solves the Vlasov-Maxwell equations. The code uses a novel version of the finite-element discontinuous Galerkin scheme that conserves energy in the continuous-time limit. The fields are computed using Maxwell equations. Ionization and scattering collisions are included; however, surface effects are neglected. The aim of this work is to introduce the continuum kinetic method and compare its results with those obtained from an already established finite-volume multi-fluid model also implemented in Gkeyll. Novel boundary conditions on the fluids allow the sheath to form without specifying wall fluxes, so the fluids and fields adjust self-consistently at the wall. The work presented here demonstrates that the kinetic and fluid results are in agreement for the momentum flux, showing that in certain regimes, a multi-fluid model can be a useful approximation for simulating the plasma boundary. There are differences in the electrostatic potential between the fluid and kinetic results. Further, the direct solutions of the distribution function presented here highlight the non-Maxwellian distribution of electrons in the sheath, emphasizing the need for a kinetic model. The densities, velocities, and the potential show a good agreement between the kinetic and fluid results. However, kinetic physics is highlighted through higher moments such as parallel and perpendicular temperatures which provide significant differences from the fluid results in which the temperature is assumed to be isotropic. Besides decompression cooling, the heat flux
A Computer Simulated Experiment in Complex Order Kinetics
ERIC Educational Resources Information Center
Merrill, J. C.; And Others
1975-01-01
Describes a computer simulation experiment in which physical chemistry students can determine all of the kinetic parameters of a reaction, such as order of the reaction with respect to each reagent, forward and reverse rate constants for the overall reaction, and forward and reverse activation energies. (MLH)
Nonisothermal Analysis of Solution Kinetics by Spreadsheet Simulation
ERIC Educational Resources Information Center
de Levie, Robert
2012-01-01
A fast and generally applicable alternative solution to the problem of determining the useful shelf life of medicinal solutions is described. It illustrates the power and convenience of the combination of numerical simulation and nonlinear least squares with a practical pharmaceutical application of chemical kinetics and thermodynamics, validated…
Kinetic Simulations of Particle Acceleration at Shocks
Caprioli, Damiano; Guo, Fan
2015-07-16
Collisionless shocks are mediated by collective electromagnetic interactions and are sources of non-thermal particles and emission. The full particle-in-cell approach and a hybrid approach are sketched, simulations of collisionless shocks are shown using a multicolor presentation. Results for SN 1006, a case involving ion acceleration and B field amplification where the shock is parallel, are shown. Electron acceleration takes place in planetary bow shocks and galaxy clusters. It is concluded that acceleration at shocks can be efficient: >15%; CRs amplify B field via streaming instability; ion DSA is efficient at parallel, strong shocks; ions are injected via reflection and shock drift acceleration; and electron DSA is efficient at oblique shocks.
NASA Astrophysics Data System (ADS)
Lembege, B.; Savoini, P.; Stienlet, J.
2013-05-01
Two distinct ion populations backstreaming into the solar wind have been clearly evidenced by various space missions within the quasi-perpendicular region of the ion foreshock located upstream of the Earth's Bow shock (i.e. for 45° ≤ Theta_Bn ≤ 90°, where Theta_Bn is the angle between the shock normal and the upstream magnetostatic field): (i) field-aligned ion beams (« FAB ») characterized by a gyrotropic distribution, and (ii) gyro-phase bunched ions («GPB »), characterized by a NON gyrotropic distribution. The origin of these backstreaming ions has not been clearly identified and is presently analyzed with the help of 2D PIC simulation of a curved shock, where full curvature effects, time of flight effects and both electrons and ions dynamics are fully described within a self consistent approach. Present simulations evidence that these two populations can be effectively created directly by the shock front without invoking microinstabilities. The analysis of both individual and statistical ion trajectories evidences that: (i) two new parameters, namely the interaction time DT_inter and distance of penetration L_depth into the shock wave, play a key role and allow to discriminate these two populations. "GPB" population is characterized by a very short interaction time (DT_inter = 1 to 2 Tci) in comparison to the "FAB" population (DT_inter = 2 Tci to 10 Tci) which moves back and forth between the upstream edge of the shock front and the overshoot, where tci is the upstream ion gyroperiod. (ii) the importance of the injection angle (i.e. the angle between the normal of the shock front and the gyration velocity when ions reach the shock) to understand how the reflection process takes place. (iii) "FAB" population drifts along the curved shock front scanning a large Theta_Bn range from 90°. (iv) "GPB" population is embedded within the "FAB" population near the shock front which explains the difficulty to identify such a population in the experimental
Large Scale Simulations of the Kinetic Ising Model
NASA Astrophysics Data System (ADS)
Münkel, Christian
We present Monte Carlo simulation results for the dynamical critical exponent z of the two- and three-dimensional kinetic Ising model. The z-values were calculated from the magnetization relaxation from an ordered state into the equilibrium state at Tc for very large systems with up to (169984)2 and (3072)3 spins. To our knowledge, these are the largest Ising-systems simulated todate. We also report the successful simulation of very large lattices on a massively parallel MIMD computer with high speedups of approximately 1000 and an efficiency of about 0.93.
NASA Astrophysics Data System (ADS)
Lee, Khil-Ha; Kim, Sung-Wook; Kim, Sang-Hyun
2014-05-01
model, called FLO-2D runs to simulate channel routing downstream to give the maximum water level. Once probable inundation areas are identified by the huge volume of water in the caldera lake, the unique geography, and the limited control capability, a potential hazard assessment can be represented. The study will contribute to build a geohazard map for the decision-makers and practitioners. Keywords: Volcanic flood, Caldera lake, Hazard assessment, Magma effusion Acknowledgement This research was supported by a grant [NEMA-BAEKDUSAN-2012-1-2] from the Volcanic Disaster Preparedness Research Center sponsored by National Emergency Management Agency of Korea.
NASA Astrophysics Data System (ADS)
Savoini, P.; Lembege, B.; Stienlet, J.
2012-04-01
The foreshock region is located upstream of the terrestrial bow shock and is characterized by energetic backstreaming particles (electrons and ions) issued from the shock and by an important wave activity as observed by many space missions. In order to analyse the foreshock region, a curved shock is simulated with the help of a 2 - D full particle (PIC) code, where full curvature and time of flight effects, and where both electrons and ions dynamics are fully described by a self consistent approach. The analysis is presently restricted to the quasi-perpendicular angular range defined by 45°≤ θBn ≤ 90°, where θBn is the angle between the shock normal and the upstream magnetostatic field, and we focus only on the ion foreshock. In a good agreement with experimental data, present preliminary results evidence two distinct ion populations collimated along the interplanetary magnetic field (IMF): (i) the Field-Aligned Beam population (hereafter named "FAB") and (ii) the gyro-phase bunch population (hereafter named "GPB") which differ from each other by their gyrotropic or non-gyrotropic behavior, respectively. Additionally, the "FAB" population is observed at the edge of the ion foreshock and near the curved shock front, while the "'GPB" population is observed deeper in the foreshock and further from the shock front. The analysis shows that no pitch angle scattering mechanism needs to be invoked to account for the generation of the "GPB", but rather additional criteria are necessary namely: the interaction time Δtint of backstreaming ions with the shock front and their downstream penetration depth. These criteria allow to evidence that (i) the "FAB" population corresponds to particles which move back and forth between the upstream edge of the front and the overshoot, and are characterized by a quite large Δtint (covering several local gyro-periods, 4 ≤ τci ≤ 12). In contrast, (ii) the "GPB" ions have suffered a very short interaction time (i.e. Δtint < 1
Allain, Ariane; Chauvot de Beauchêne, Isaure; Langenfeld, Florent; Guarracino, Yann; Laine, Elodie; Tchertanov, Luba
2014-01-01
Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach - MOdular NETwork Analysis (MONETA) - based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non
Kinetic aspects of tail dynamics - Theory and simulation
NASA Technical Reports Server (NTRS)
Speiser, T. W.
1987-01-01
Kinetic theories relevant to the geomagnetic tail are reviewed. The topics discussed include kinetic instabilities, simulations, and current-sheet particle acceleration. Tearing mode and reconnection theories are emphasized. Kinetic treatment is appropriate for these topics since the tail plasma is collisionless. Fluid calculations are appropriate when stochastic processes dominate and for studies where long wavelengths are important. However, fluid treatments of tearing modes and reconnection require a finite resistivity in the diffusion region. Thus, although 'anomalous resistivity' can be guessed or in some cases calculated, ideally the kinetic treatment is often to be preferred. Particle motion and acceleration in the current sheet can give rise to beam-like distributions in the plasma-sheet boundary layer. Studies of current-sheet particle motion have also been used as the basis for 'kinetic' tail equilibrium models. Furthermore, quite recently current-sheet particle motion is used directly in Coroniti's explosive tail reconnection model. The 'inertial conductivity' from the equilibrium models provides the 'dissipation' necessary for reconnection.
Numerical Simulation of SNCR Technology with Simplified Chemical Kinetics Model
NASA Astrophysics Data System (ADS)
Blejchař, T.; Dolníčková, D.
2013-04-01
The paper deals with numerical simulation of SNCR method. For numerical modelling was used CFD code Ansys/CFX. SNCR method was described by dominant chemical reaction, which were look up NIST Chemical database. The reactions including reduction of NOx and concentration change of pollutants, like N2O and CO in flue gas too. Proposed chemical kinetics and CFD model was applied to two boilers. Both simulations were compared with experimental measurements. First simulation was used to validation of chemical mechanism. Second simulation was based on first simulation and it was used to verification of compiled SNCR chemical mechanism. Next the new variant of the reagent penetration lance was proposed and compared with the original variants.
Simulating complex ion channel kinetics with IonChannelLab
Covarrubias, Manuel; Sánchez-Rodríguez, Jorge E; Perez-Cornejo, Patricia; Arreola, Jorge
2010-01-01
In-silico simulation based on Markov chains is a powerful way to describe and predict the activity of many transport proteins including ion channels. However, modeling and simulation using realistic models of voltage- or ligand-gated ion channels exposed to a wide range of experimental conditions require building complex kinetic schemes and solving complicated differential equations. To circumvent these problems, we developed IonChannelLab a software tool that includes a user-friendly Graphical User Interface and a simulation library. This program supports channels with Ohmic or Goldman-Hodgkin-Katz behavior and can simulate the time-course of ionic and gating currents, single channel behavior and steady-state conditions. The program allows the simulation of experiments where voltage, ligand and ionic concentration are varied independently or simultaneously. PMID:20935453
Enabling Global Kinetic Simulations of the Magnetosphere via Petascale Computing
NASA Astrophysics Data System (ADS)
Karimabadi, H.; Vu, H. X.; Omelchenko, Y. A.; Tatineni, M.; Majumdar, A.; Catalyurek, U. V.; Saule, E.
2009-11-01
The ultimate goal in magnetospheric physics is to understand how the solar wind transfers its mass, momentum and energy to the magnetosphere. This problem has turned out to be much more complex intellectually than originally thought. MHD simulations have proven useful in predicting eminent features of substorms and other global events. Given the complexity of solar wind-magnetosphere interactions, hybrid (electron fluid, kinetic ion) simulations have recently been emerging in the studies of the global dynamics of the magnetosphere with the goal of accurately predicting the energetic particle transport and structure of plasma boundaries. We take advantage of our recent innovations in hybrid simulations and the power of massively parallel computers to make breakthrough 3D global kinetic simulations of the magnetosphere. The preliminary results reveal many major differences with global MHD simulations. For example, the hybrid simulations predict the formation of the quadruple structure associated with reconnection events, ion/ion kink instability in the tail, turbulence in the magnetosheath, and formation of the ion foreshock region.
SIMULATIONS OF 2D AND 3D THERMOCAPILLARY FLOWS BY A LEAST-SQUARES FINITE ELEMENT METHOD. (R825200)
Numerical results for time-dependent 2D and 3D thermocapillary flows are presented in this work. The numerical algorithm is based on the Crank-Nicolson scheme for time integration, Newton's method for linearization, and a least-squares finite element method, together with a matri...
Propagation of radiation in fluctuating multiscale plasmas. II. Kinetic simulations
Pal Singh, Kunwar; Robinson, P. A.; Cairns, Iver H.; Tyshetskiy, Yu.
2012-11-15
A numerical algorithm is developed and tested that implements the kinetic treatment of electromagnetic radiation propagating through plasmas whose properties have small scale fluctuations, which was developed in a companion paper. This method incorporates the effects of refraction, damping, mode structure, and other aspects of large-scale propagation of electromagnetic waves on the distribution function of quanta in position and wave vector, with small-scale effects of nonuniformities, including scattering and mode conversion approximated as causing drift and diffusion in wave vector. Numerical solution of the kinetic equation yields the distribution function of radiation quanta in space, time, and wave vector. Simulations verify the convergence, accuracy, and speed of the methods used to treat each term in the equation. The simulations also illustrate the main physical effects and place the results in a form that can be used in future applications.
Threshold kinetics of a solar-simulator-pumped iodine laser
NASA Technical Reports Server (NTRS)
Wilson, J. W.; Lee, Y.; Weaver, W. R.; Humes, D. H.; Lee, J. H.
1984-01-01
A model of the chemical kinetics of the n-C3F7I solar-simulator-pumped iodine laser is utilized to study the major kinetic processes associated with the threshold behavior of this experimental system. Excited-state diffusion to the cell wall is the dominant limiting factor below 5 torr. Excited-state diffusion to the cell wall is the dominant limiting factor below 5 torr. Excited-state recombination with the alkyl radical and quenching by the parent gas control threshold at higher pressures. Treatment of the hyperfine splitting and uncertainty in the pressure broadening are important factors in fixing the threshold level. In spite of scatter in the experimental data caused by instabilities in the simulator high-pressure high-pressure arc, reasonable agreement is achieved between the model and experiment. Model parameters arrived at are within the uncertainty range of values found in the literature.
Global simulation of field-reversed configuration using fully kinetic ion and drift kinetic electron
NASA Astrophysics Data System (ADS)
Lau, Calvin; Fulton, Daniel; Kuley, Animesh; Bao, Jian; Lin, Zhihong; Binderbauer, Michael; Tajima, Toshiki; Schmitz, Lothar; the TAE Team Team
2016-10-01
In the last several years, the C-2/C-2U advanced beam-driven field-reversed configuration (FRC) experiments at Tri Alpha Energy have progressed to consistent, reproducible plasma lifetimes of 10+ ms, i.e. FRCs have reached transport limited regimes. In FRC geometry, the thermal ion gyroradius is on the order of the size of the plasma near the magnetic null-point. Fast ion orbits intersect both the FRC core and the scrape-off layer (SOL) regions. Previous local simulations of electrostatic drift-wave instabilities using the Gyrokinetic Toroidal Code (GTC) find the core to be robustly stable with driftwave instability only in the SOL at frequencies approaching the ion cyclotron frequency. Therefore, FRC transport studies require fully kinetic ion simulations with cross-separatrix coupling between the core and SOL. Here we report progress of such global simulations using fully kinetic ions and drift kinetic electrons, including the implementation of the Boris push scheme for cyclotron motion and cylindrical coordinates for the separatrix. Supported by the Norman Rostoker Fellowship.
Effects of isorhamnetin on tyrosinase: inhibition kinetics and computational simulation.
Si, Yue-Xiu; Wang, Zhi-Jiang; Park, Daeui; Jeong, Hyoung Oh; Ye, Sen; Chung, Hae Young; Yang, Jun-Mo; Yin, Shang-Jun; Qian, Guo-Ying
2012-01-01
We studied the inhibitory effects of isorhamnetin on mushroom tyrosinase by inhibition kinetics and computational simulation. Isorhamnetin reversibly inhibited tyrosinase in a mixed-type manner at Ki=0.235±0.013 mM. Measurements of intrinsic and 1-anilinonaphthalene-8-sulfonate(ANS)-binding fluorescence showed that isorhamnetin did not induce significant changes in the tertiary structure of tyrosinase. To gain insight into the inactivation process, the kinetics were computed via time-interval measurements and continuous substrate reactions. The results indicated that inactivation induced by isorhamnetin was a first-order reaction with biphasic processes. To gain further insight, we simulated docking between tyrosinase and isorhamnetin. Simulation was successful (binding energies for Dock6.3: -32.58 kcal/mol, for AutoDock4.2: -5.66 kcal/mol, and for Fred2.2: -48.86 kcal/mol), suggesting that isorhamnetin interacts with several residues, such as HIS244 and MET280. This strategy of predicting tyrosinase interaction in combination with kinetics based on a flavanone compound might prove useful in screening for potential natural tyrosinase inhibitors.
NASA Astrophysics Data System (ADS)
Zhang, Ning
This thesis presents the parasitic extraction and magnetic analysis for transformers, inductors, and IGBT bridge busbars with Maxwell 2D and Maxwell 3D simulation. In the first chapter, the magnetic field of a transformer in Maxwell 2D is analyzed. The parasitic capacitance between each winding of the transformer are extracted by Maxwell 2D. According to the actual dimensions, the parasitic capacitances are calculated. The results are verified by comparing with the measurement results from 4395A impedance analyzer. In the second chapter, two CM inductors are simulated in Maxwell 3D. One is the conventional winding inductor, the other one is the proposed one. The magnetic field distributions of different winding directions are analyzed. The analysis is verified by the simulation result. The last chapter introduces a technique to analyze, extract, and measure the parasitic inductance of planar busbars. With this technique, the relationship between self-inductance and mutual-inductance is analyzed. Secondly, a total inductance is calculated based on the developed technique. Thirdly, the current paths and the inductance on a planar busbar are investigated with DC-link capacitors. Furthermore, the analysis of the inductance is addressed. Ansys Q3D simulation and analysis are presented. Finally, the experimental verification is shown by the S-parameter measurement.
NASA Astrophysics Data System (ADS)
Chen, T.; Wang, P.; Fehler, M.; Zhang, Y.; Burns, D.
2009-12-01
Localizing subsurface fractures and estimating their mechanical parameters and geometric properties are very important in oil and gas industry as well as geothermal energy research. It is essential to quantitatively understand how the elastic wave propagation is affected by these fractures. In this paper, an analytical expression for the scattered P- and SV waves from a 2D fracture is formulated based on a normal mode method, where the 2D fracture is modeled by a low-aspect ratio elliptical cylinder. The scatter function of this 2D fracture are expressed in terms of the incident angle, the orientation and aspect ratio of the fracture as well as the elastic impedance contrast between the surrounding medium and the inhomogeneity inside the fracture. Results from this analytical solution match well with those from a finite-difference approach. Solutions of this analytical model at two limiting cases (a circular cylinder with aspect ratio equal to one and a strip with aspect ratio equal to zero) are also compared to analytical solutions directly derived for the circular cylinder and strip by other studies.
NASA Astrophysics Data System (ADS)
Brunner, Stephan; Berger, R. L.; Banks, J. W.; Cohen, B. I.; Chapman, T.; Hittinger, J. A. F.; Rozmus, W.; Strozzi, D. J.; Winjum, B. J.; Valeo, E. J.
2012-10-01
Kinetic simulations of nonlinear electron plasma waves (EPW) are presented in 2D with the Vlasov code LOKI (2 space and 2 velocity dimensions; Banks et al., Phys. Plasmas 18, 052102 (2011)). Propagating EPWs are created with an external wave potential with uniform transverse amplitude. The evolution of the plasma wave field and its self-consistent quasi-steady distribution of trapped electrons is studied after the external drive is turned off. For finite-amplitude EPWs, the onset of the trapped-electron-induced filamentation instability (H. Rose, Phys. Plasmas 15, 042311 (2008)) and trapped electron sideband instability (S. Brunner and E. Valeo, PRL 93, 145003 (2004)) are studied as a function of wave amplitude and k0λDe, where k0 is the wavenumber of the external potential. We extend the theory of Kruer et al PRL 23, 1969 to 2D to find growth rates of both instabilities and compare these to the ones obtained from the simulations. In the nonlinear state, the distribution of resonant electrons is dramatically modified
Simulations of Magnetic Reconnection - Kinetic Mechanisms Underlying the Fluid Description of Ions
NASA Technical Reports Server (NTRS)
Aunai, icolas; Belmont, Gerard; Smets, Roch
2012-01-01
Because of its ability to transfer the energy stored in magnetic field together with the breaking of the flux freezing constraint, magnetic reconnection is considered as one of the most important phenomena in plasma physics. When it happens in a collision less environment such as the terrestrial magnetosphere, it should a priori be modelled with in the framework of kinetic physics. The evidence of kinetic features has incidentally for a long time, been shown by researchers with the help of both numerical simulations and satellite observations. However, most of our understanding of the process comes from the more intuitive fluid interpretation with simple closure hypothesis which do not include kinetic effects. To what extent are these two separate descriptions of the same phenomenon related? What is the role of kinetic effects in the averaged/fluid dynamics of reconnection? This thesis addresses these questions for the proton population in the particular case of anti parallel merging with the help of 2D Hybrid simulations. We show that one can not assume, as is usually done, that the acceleration of the proton flow is only due to the Laplace force. Our results show, for symmetric and asymmetric connection, the importance of the pressure force, opposed to the electric one on the separatrices, in the decoupling region. In the symmetric case, we emphasize the kinetic origin of this force by analyzing the proton distribution functions and explain their structure by studying the underlying particle dynamics. Protons, as individual particles, are shown to bounce in the electric potential well created by the Hall effect. The spatial divergence of this well results in a mixing in phase space responsible for the observed structure of the pressure tensor. A detailed energy budget analysis confirms the role of the pressure force for the acceleration; but, contrary to what is sometimes assumed, it also reveals that the major part of the incoming Poynting flux is transferred to
NASA Astrophysics Data System (ADS)
Toda, S.; Nakata, M.; Nunami, M.; Ishizawa, A.; Watanabe, T.-H.; Sugama, H.
2016-10-01
A reduced model of the turbulent ion heat diffusivity is proposed by the gyrokinetic simulation code (GKV-X) with the adiabatic electrons for the high-Ti Large Helical Device discharge. The plasma parameter region of the short poloidal wavelength is studied, where the ion temperature gradient mode becomes unstable. The ion heat diffusivity by the nonlinear simulation with the kinetic electrons is found to be several times larger than the simulation results using the adiabatic electrons in the radial region 0.46 <= r / a <= 0.80 . The electromagnetic contribution is about a several percent in the ion energy flux. The model of the turbulent diffusivity is derived as the function of the squared electrostatic potential fluctuation and the squared zonal flow potential. Next, the squared electrostatic potential fluctuation is approximated with the mixing length estimate. The squared zonal flow potential fluctuation is shown as the linear zonal flow response function. The reduced model of the turbulent diffusivity is derived as the function of the physical parameters by the linear GKV-X simulation with the kinetic electrons. This reduced model is applied to the transport code with the same procedure as.
Collisionless spectral-kinetic Simulation of the Multipole Resonance Probe
NASA Astrophysics Data System (ADS)
Dobrygin, Wladislaw; Szeremley, Daniel; Schilling, Christian; Oberrath, Jens; Eremin, Denis; Mussenbrock, Thomas; Brinkmann, Ralf Peter
2012-10-01
Plasma resonance spectroscopy is a well established plasma diagnostic method realized in several designs. One of these designs is the multipole resonance probe (MRP). In its idealized - geometrically simplified - version it consists of two dielectrically shielded, hemispherical electrodes to which an RF signal is applied. A numerical tool is under development, which is capable of simulating the dynamics of the plasma surrounding the MRP in electrostatic approximation. In the simulation the potential is separeted in an inner and a vacuum potential. The inner potential is influenced by the charged partilces and is calculated by a specialized Poisson solver. The vacuum potential fulfills Laplace's equetion and consists of the applied voltage of the probe as boundary condition. Both potentials are expanded in spherical harmonics. For a practical particle pusher implementation, the expansion must be appropriately truncated. Compared to a PIC simulation a grid is unnecessary to calculate the force on the particles. This work purpose is a collisionless kinetic simulation, which can be used to investigate kinetic effects on the resonance behavior of the MRP.[4pt] [1] M. Lapke et al., Appl. Phys. Lett. 93, 2008, 051502.
Yan, Chang; Yuan, Rongfeng; Pfalzgraff, William C.; Nishida, Jun; Wang, Lu; Markland, Thomas E.; Fayer, Michael D.
2016-01-01
Functionalized self-assembled monolayers (SAMs) are the focus of ongoing investigations because they can be chemically tuned to control their structure and dynamics for a wide variety of applications, including electrochemistry, catalysis, and as models of biological interfaces. Here we combine reflection 2D infrared vibrational echo spectroscopy (R-2D IR) and molecular dynamics simulations to determine the relationship between the structures of functionalized alkanethiol SAMs on gold surfaces and their underlying molecular motions on timescales of tens to hundreds of picoseconds. We find that at higher head group density, the monolayers have more disorder in the alkyl chain packing and faster dynamics. The dynamics of alkanethiol SAMs on gold are much slower than the dynamics of alkylsiloxane SAMs on silica. Using the simulations, we assess how the different molecular motions of the alkyl chain monolayers give rise to the dynamics observed in the experiments. PMID:27044113
2016-06-16
Journal of Wind Engineering ELSEVIER and Industrial Aerodynamics 92 (2004) 117-158 www.elsevier.com/locate/jweia Simulation of mean flow and...detailed and comprehensive wind tunnel data set. Vertical profiles of the mean streamwise velocity and the turbulence kinetic energy are presented and...compared to those measured in the wind tunnel simulation. It is found that the performance of all the turbulence models investigated is generally
Kinetics Modeling and Numerical Simulation of Reactive Materials
NASA Astrophysics Data System (ADS)
Yoo, Sunhee; Stewart, D. Scott; Lambert, David E.; Choi, Sunjin
2011-06-01
Simulations with reduced kinetic models are used to study shock ignition and detonation in reactive materials that may support non-classical detonation. Porous aluminum Teflon oxidizer mixtures that support combustion reactions in air are considered, as a member of a class of materials with intrinsic interest. We recast a phenomenological theory with realistic kinetics with end products; AlF3, C and CO2. Intermediate products include at least thirty elementary reactions; a sub-set can be selected to simplify, but a hard problem remains. We use the multi-scale asymptotic ``G-scheme'' proposed by M. Valorani, S. Paolucci and reduce a dynamical system consisting of the intermediate reactions and rates, conservation laws and porosity evolution. Results of the multi-species evolution and its impact on rapid self-oxidizing combustion and possible detonation conditions and the computational methods are presented. Supported by AFRL/RW and DTRA.
Kinetic Simulation and Energetic Neutral Atom Imaging of the Magnetosphere
NASA Technical Reports Server (NTRS)
Fok, Mei-Ching H.
2011-01-01
Advanced simulation tools and measurement techniques have been developed to study the dynamic magnetosphere and its response to drivers in the solar wind. The Comprehensive Ring Current Model (CRCM) is a kinetic code that solves the 3D distribution in space, energy and pitch-angle information of energetic ions and electrons. Energetic Neutral Atom (ENA) imagers have been carried in past and current satellite missions. Global morphology of energetic ions were revealed by the observed ENA images. We have combined simulation and ENA analysis techniques to study the development of ring current ions during magnetic storms and substorms. We identify the timing and location of particle injection and loss. We examine the evolution of ion energy and pitch-angle distribution during different phases of a storm. In this talk we will discuss the findings from our ring current studies and how our simulation and ENA analysis tools can be applied to the upcoming TRIO-CINAMA mission.
Lanczos and Recursion Techniques for Multiscale Kinetic Monte Carlo Simulations
Rudd, R E; Mason, D R; Sutton, A P
2006-03-13
We review an approach to the simulation of the class of microstructural and morphological evolution involving both relatively short-ranged chemical and interfacial interactions and long-ranged elastic interactions. The calculation of the anharmonic elastic energy is facilitated with Lanczos recursion. The elastic energy changes affect the rate of vacancy hopping, and hence the rate of microstructural evolution due to vacancy mediated diffusion. The elastically informed hopping rates are used to construct the event catalog for kinetic Monte Carlo simulation. The simulation is accelerated using a second order residence time algorithm. The effect of elasticity on the microstructural development has been assessed. This article is related to a talk given in honor of David Pettifor at the DGP60 Workshop in Oxford.
OBJECT KINETIC MONTE CARLO SIMULATIONS OF RADIATION DAMAGE IN TUNGSTEN
Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.; Roche, Kenneth J.; Kurtz, Richard J.; Wirth, Brian D.
2015-04-16
We used our recently developed lattice-based object kinetic Monte Carlo code; KSOME [1] to carryout simulations of radiation damage in bulk tungsten at temperatures of 300, and 2050 K for various dose rates. Displacement cascades generated from molecular dynamics (MD) simulations for PKA energies at 60, 75 and 100 keV provided residual point defect distributions. It was found that the number density of vacancies in the simulation box does not change with dose rate while the number density of vacancy clusters slightly decreases with dose rate indicating that bigger clusters are formed at larger dose rates. At 300 K, although the average vacancy cluster size increases slightly, the vast majority of vacancies exist as mono-vacancies. At 2050 K no accumulation of defects was observed during irradiation over a wide range of dose rates for all PKA energies studied in this work.
Kinetic Monte Carlo simulation of the classical nucleation process
NASA Astrophysics Data System (ADS)
Filipponi, A.; Giammatteo, P.
2016-12-01
We implemented a kinetic Monte Carlo computer simulation of the nucleation process in the framework of the coarse grained scenario of the Classical Nucleation Theory (CNT). The computational approach is efficient for a wide range of temperatures and sample sizes and provides a reliable simulation of the stochastic process. The results for the nucleation rate are in agreement with the CNT predictions based on the stationary solution of the set of differential equations for the continuous variables representing the average population distribution of nuclei size. Time dependent nucleation behavior can also be simulated with results in agreement with previous approaches. The method, here established for the case in which the excess free-energy of a crystalline nucleus is a smooth-function of the size, can be particularly useful when more complex descriptions are required.
Leblanc, M D; Whitehead, J P; Plumer, M L
2013-05-15
A combination of Metropolis and modified Wolff cluster algorithms is used to examine the impact of uniaxial single-ion anisotropy on the phase transition to ferromagnetic order of Heisenberg macrospins on a 2D square lattice. This forms the basis of a model for granular perpendicular recording media where macrospins represent the magnetic moment of grains. The focus of this work is on the interplay between anisotropy D, intragrain exchange J' and intergrain exchange J on the ordering temperature T(C) and extends our previous reported analysis of the granular Ising model. The role of intragrain degrees of freedom in heat assisted magnetic recording is discussed.
NASA Astrophysics Data System (ADS)
Leblanc, M. D.; Whitehead, J. P.; Plumer, M. L.
2013-05-01
A combination of Metropolis and modified Wolff cluster algorithms is used to examine the impact of uniaxial single-ion anisotropy on the phase transition to ferromagnetic order of Heisenberg macrospins on a 2D square lattice. This forms the basis of a model for granular perpendicular recording media where macrospins represent the magnetic moment of grains. The focus of this work is on the interplay between anisotropy D, intragrain exchange J‧ and intergrain exchange J on the ordering temperature TC and extends our previous reported analysis of the granular Ising model. The role of intragrain degrees of freedom in heat assisted magnetic recording is discussed.
Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation
2011-01-01
Background Higher plants and algae are able to fix atmospheric carbon dioxide through photosynthesis and store this fixed carbon in large quantities as starch, which can be hydrolyzed into sugars serving as feedstock for fermentation to biofuels and precursors. Rational engineering of carbon flow in plant cells requires a greater understanding of how starch breakdown fluxes respond to variations in enzyme concentrations, kinetic parameters, and metabolite concentrations. We have therefore developed and simulated a detailed kinetic ordinary differential equation model of the degradation pathways for starch synthesized in plants and green algae, which to our knowledge is the most complete such model reported to date. Results Simulation with 9 internal metabolites and 8 external metabolites, the concentrations of the latter fixed at reasonable biochemical values, leads to a single reference solution showing β-amylase activity to be the rate-limiting step in carbon flow from starch degradation. Additionally, the response coefficients for stromal glucose to the glucose transporter kcat and KM are substantial, whereas those for cytosolic glucose are not, consistent with a kinetic bottleneck due to transport. Response coefficient norms show stromal maltopentaose and cytosolic glucosylated arabinogalactan to be the most and least globally sensitive metabolites, respectively, and β-amylase kcat and KM for starch to be the kinetic parameters with the largest aggregate effect on metabolite concentrations as a whole. The latter kinetic parameters, together with those for glucose transport, have the greatest effect on stromal glucose, which is a precursor for biofuel synthetic pathways. Exploration of the steady-state solution space with respect to concentrations of 6 external metabolites and 8 dynamic metabolite concentrations show that stromal metabolism is strongly coupled to starch levels, and that transport between compartments serves to lower coupling between metabolic
NASA Astrophysics Data System (ADS)
Ito, Y.; Noborio, K.
2015-12-01
In Japan, soil disinfection with hot water has been popular since the use of methyl bromide was restricted in 2005. Decreasing the amount of hot water applied may make farmers reduce the operation cost. To determine the appropriate amount of hot water needed for soil disinfection, HYDRUS-2D was evaluated. A field experiment was conducted and soil water content and soil temperature were measured at 5, 10, 20, 40, 60, 80 and 100 cm deep when 95oC hot water was applied. Irrigation tubing equipped with drippers every 30 cm were laid at the soil surface, z=0 cm. An irrigation rate for each dripper was 0.83 cm min-1 between t=0 and 120 min, and thereafter it was zero. Temperature of irrigation water was 95oC. Total simulation time with HYDRUS-2D was 720 min for a homogeneous soil. A simulating domain was selected as x=60 cm and z=100 cm. A potential evaporation rate was assumed to be 0 cm min-1 because the soil surface was covered with a plastic sheet. The boundary condition at the bottom was free drainage and those of both sides were no-flux conditions. Hydraulic properties and bulk densities measured at each depth were used for simulation. It was assumed that there was no organic matter contained. Soil thermal properties were adopted from previous study and HYDRUS 2D. Simulated temperatures at 5, 10, 20 and 40 cm deep agreed well with those measured although simulated temperatures at 60, 80, and 100 cm deep were overly estimated. Estimates of volumetric water content at 5 cm deep agreed well with measured values. Simulated values at 10 to 100 cm deep were overly estimated by 0.1 to 0.3 (m3 m-3). The deeper the soil became, the more the simulated wetting front lagged behind the measured one. It was speculated that water viscosity estimated smaller at high temperature might attributed to the slower advances of wetting front simulated with HYDRUS 2-D.
NASA Astrophysics Data System (ADS)
Kim, Kyeong-Hyeon; Kim, Dong-Su; Kim, Tae-Ho; Kang, Seong-Hee; Cho, Min-Seok; Suh, Tae Suk
2015-11-01
The phantom-alignment error is one of the factors affecting delivery quality assurance (QA) accuracy in intensity-modulated radiation therapy (IMRT). Accordingly, a possibility of inadequate use of spatial information in gamma evaluation may exist for patient-specific IMRT QA. The influence of the phantom-alignment error on gamma evaluation can be demonstrated experimentally by using the gamma passing rate and the gamma value. However, such experimental methods have a limitation regarding the intrinsic verification of the influence of the phantom set-up error because experimentally measuring the phantom-alignment error accurately is impossible. To overcome this limitation, we aimed to verify the effect of the phantom set-up error within the gamma evaluation formula by using a Monte Carlo simulation. Artificial phantom set-up errors were simulated, and the concept of the true point (TP) was used to represent the actual coordinates of the measurement point for the mathematical modeling of these effects on the gamma. Using dose distributions acquired from the Monte Carlo simulation, performed gamma evaluations in 2D and 3D. The results of the gamma evaluations and the dose difference at the TP were classified to verify the degrees of dose reflection at the TP. The 2D and the 3D gamma errors were defined by comparing gamma values between the case of the imposed phantom set-up error and the TP in order to investigate the effect of the set-up error on the gamma value. According to the results for gamma errors, the 3D gamma evaluation reflected the dose at the TP better than the 2D one. Moreover, the gamma passing rates were higher for 3D than for 2D, as is widely known. Thus, the 3D gamma evaluation can increase the precision of patient-specific IMRT QA by applying stringent acceptance criteria and setting a reasonable action level for the 3D gamma passing rate.
Error propagation in first-principles kinetic Monte Carlo simulation
NASA Astrophysics Data System (ADS)
Döpking, Sandra; Matera, Sebastian
2017-04-01
First-principles kinetic Monte Carlo models allow for the modeling of catalytic surfaces with predictive quality. This comes at the price of non-negligible errors induced by the underlying approximate density functional calculation. On the example of CO oxidation on RuO2(110), we demonstrate a novel, efficient approach to global sensitivity analysis, with which we address the error propagation in these multiscale models. We find, that we can still derive the most important atomistic factors for reactivity, albeit the errors in the simulation results are sizable. The presented approach might also be applied in the hierarchical model construction or computational catalyst screening.
Huang, Chenhua; Yang, Xiangbo; He, Zhihong
2010-06-01
In this paper, based on the evolutionary Monte Carlo (EMC) algorithm, we have made four points of ameliorations and propose a so-called genetic algorithm based on optimal secondary structure (GAOSS) method to predict efficiently the protein folding conformations in the two-dimensional hydrophobic-hydrophilic (2D HP) model. Nine benchmarks are tested to verify the effectiveness of the proposed approach and the results show that for the listed benchmarks GAOSS can find the best solutions so far. It means that reasonable, effective and compact secondary structures (SSs) can avoid blind searches and can reduce time consuming significantly. On the other hand, as examples, we discuss the diversity of protein GSC for the 24-mer and 85-mer sequences. Several GSCs have been found by GAOSS and some of the conformations are quite different from each other. It would be useful for the designing of protein molecules. GAOSS would be an efficient tool for the protein structure predictions (PSP).
A spectral Poisson solver for kinetic plasma simulation
NASA Astrophysics Data System (ADS)
Szeremley, Daniel; Obberath, Jens; Brinkmann, Ralf
2011-10-01
Plasma resonance spectroscopy is a well established plasma diagnostic method, realized in several designs. One of these designs is the multipole resonance probe (MRP). In its idealized - geometrically simplified - version it consists of two dielectrically shielded, hemispherical electrodes to which an RF signal is applied. A numerical tool is under development which is capable of simulating the dynamics of the plasma surrounding the MRP in electrostatic approximation. In this contribution we concentrate on the specialized Poisson solver for that tool. The plasma is represented by an ensemble of point charges. By expanding both the charge density and the potential into spherical harmonics, a largely analytical solution of the Poisson problem can be employed. For a practical implementation, the expansion must be appropriately truncated. With this spectral solver we are able to efficiently solve the Poisson equation in a kinetic plasma simulation without the need of introducing a spatial discretization.
NASA Astrophysics Data System (ADS)
Wu, C.; Chang, T.
2010-12-01
A new method in describing the multifractal characteristics of intermittent events was introduced by Cheng and Wu [Chang T. and Wu C.C., Physical Rev, E77, 045401(R), 2008]. The procedure provides a natural connection between the rank-ordered spectrum and the idea of one-parameter scaling for monofractals. This technique has been demonstrated using results obtained from a 2D MHD simulation. It has also been successfully applied to in-situ solar wind observations [Chang T., Wu, C.C. and Podesta, J., AIP Conf Proc. 1039, 75, 2008], and the broadband electric field oscillations from the auroral zone [Tam, S.W.Y. et al., Physical Rev, E81, 036414, 2010]. We take the next step in this procedure. By using the ROMA spectra and the scaled probability distribution functions (PDFs), raw PDFs can be calculated, which can be compared directly with PDFs from observations or simulation results. In addition to 2D MHD simulation results and in-situ solar wind observation, we show clearly using the ROMA analysis the multifractal character of the 3D fluid simulation data obtained from the JHU turbulence database cluster at http://turbulence.pha.jhu.edu. In particular, we show the scaling of the non-symmetrical PDF for the parallel-velocity fluctuations of this 3D fluid data.
NASA Astrophysics Data System (ADS)
Croes, Vivien; Lafleur, Trevor; Bonaventura, Zdenek; Péchereau, François; Bourdon, Anne; Chabert, Pascal
2016-09-01
This work studies the electron-cyclotron instability in Hall-Effect Thrusters (HETs) using a 2D Particle-In-Cell (PIC) simulation. The simulation is configured with a Cartesian coordinate system where a magnetic field, B0, is aligned along the X-axis (radial direction, including absorbing walls), a constant electric field, E0, along the Z-axis (axial direction, perpendicular to simulation plane), and the E0xB0 direction along the Y-axis (O direction, with periodic boundaries). Although for low plasma densities classical electron-neutral collisions theory describes well electron transport, at sufficiently high densities (as measured in HETs) a strong instability can be observed that enhances the electron mobility, even in the absence of collisions. The instability generates high frequency ( MHz) and short wavelength ( mm) fluctuations in both the electric field and charged particle densities. We investigate the correlation between these fluctuations and their role with anomalous electron transport; complementing previous 1D simulations. Plasma is self-consistently heated by the instability, but since the latter does not reach saturation in an infinitely long 2D system, saturation is achieved through implementation of a finite axial length that models convection in E0 direction. With support of Safran Aircraft Engines.
Kinetics of a Multilamellar Lipid Vesicle Ripening: Simulation and Theory.
Xu, Rui; He, Xuehao
2016-03-10
Lipid vesicle ripening via unimolecular diffusion and exchange greatly influences the evolution of complex vesicle structure. However, this behavior is difficult to capture using conventional experimental technology and molecular simulation. In the present work, the ripening of a multilamellar lipid vesicle (MLV) is effectively explored using a mesoscale coarse-grained molecular model. The simulation reveals that a small MLV evolves into a unilamellar vesicle over a very long time period. In this process, only the outermost bilayer inflates, and the inner bilayers shrink. With increasing MLV size, the ripening process becomes complex and depends on competition between a series of adjacent bilayers in the MLV. To understand the diffusion behavior of the unimolecule, the potentials of mean force (PMFs) of a single lipid molecule across unilamellar vesicles with different sizes are calculated. It is found that the PMF of lipid dissociation from the inner layer is different than that of the outer layer, and the dissociation energy barrier sensitively depends on the curvature of the bilayer. A kinetics theoretical model of MLV ripening that considers the lipid dissociation energy for curved bilayers is proposed. The model successfully interprets the MLV ripening process with various numbers of bilayers and shows potential to predict the ripening kinetics of complex lipid vesicles.
NASA Astrophysics Data System (ADS)
Hallo, L.; Olazabal-Loumé, M.; Maire, P. H.; Breil, J.; Morse, R.-L.; Schurtz, G.
2006-06-01
This paper deals with ablation front instabilities simulations in the context of direct drive ICF. A simplified DT target, representative of realistic target on LIL is considered. We describe here two numerical approaches: the linear perturbation method using the perturbation codes Perle (planar) and Pansy (spherical) and the direct simulation method using our Bi-dimensional hydrodynamic code Chic. Numerical solutions are shown to converge, in good agreement with analytical models.
2006-01-01
choice is asymptotically equivalent to have fixed V on the MESFET gate region depending on Vgate and the oxide thickness δ in such a way that ∆y = κ̃ δ...the Poisson equation modeling semiconductor devices such as the MESFET and MOSFET. We compare the simulation results with those obtained by a direct...Essentially Non-Oscillatory (WENO) schemes; Boltzmann Tran- sport Equation (BTE); semiconductor device simulation; MESFET ; MOSFET; Direct Sim
Efficient kinetic Monte Carlo simulation of annealing in semiconductor materials
NASA Astrophysics Data System (ADS)
Hargrove, Paul Hamilton
As the semiconductor manufacturing industry advances, the length scales of devices are shrinking rapidly, in accordance with the predictions of Moore's Law. As the device dimensions shrink the importance of predictive process modeling to the development of the production process is growing. Of particular importance are predictive models which can be applied to process conditions not easily accessible via experiment. Therefore the importance of models based on physical understanding are gaining importance versus models based on empirical fits alone. One promising research area in physical-based models is kinetic Monte Carlo (kMC) modeling of atomistic processes. This thesis explores kMC modeling of annealing and diffusion processes. After providing the necessary background to understand and motivate the research, a detailed review of simulation using this class of models is presented which exposes the motivation for using these models and establishes the state of the field. The author provides a user's manual for ANISRA ( ANnealIng Simulation libRAry), a computer code for on-lattice kMC simulations. This library is intended as a reusable tool for the development of simulation codes for atomistic models covering a wide variety of problems. Thus care has been taken to separate the core functionality of a simulation from the specification of the model. This thesis also compares the performance of data structures for the kMC simulation problem and recommends some novel approaches. These recommendations are applicable to a wider class of model than is ANISRA, and thus of potential interest even to researchers who implement their own simulators. Three example simulations are built from ANISRA and are presented to show the applicability of this class of model to problems of interest in semiconductor process modeling. The differences between the models simulated display the versatility of the code library. The small amount of code written to construct and modify these
NASA Astrophysics Data System (ADS)
Boukenkoul, M. A.; Li, F. C.; Aounallah, M.
2017-03-01
The present study aims to investigate numerically the flow control possibility using a synthetic jet actuation over a bi-dimensional NACA0015 airfoil manoeuvring at a highly turbulent flow (8.9e105 Reynolds to chord number). The 2-D flow behaviour was computed using the ANSYS Fluent commercial code. The so-called Reynolds Averaged Navier-Stocks (RANS) approach has been tested for one (Spalat-Allmaras S-A) and two (K-ε) transport equations for the turbulence modelling. Both present a weakness to predict the stall angle effectively. The S-A lift coefficient slope seems to be the closest to the experimental data. The synthetic jet control exhibits an extraordinary lift coefficient enhancement at high Angles Of Attack (AOA) but seems to be less obvious at low AOA, where the flow is still attached. A synthetic jet of a Strouhal (St = 2) and momentum (Cμ of 0.56%), delays the stall onset from 15 to 19deg with enhancing the lift coefficient by 40%. The actual work has been enriched by studying the effect of the jet’s frequency and momentum on the lift temporal signal. Also, the interaction between the mean flow and the synthetic jet structures topology was undertaken.
NASA Astrophysics Data System (ADS)
Wendling, A.; Daniel, J. L.; Hivet, G.; Vidal-Sallé, E.; Boisse, P.
2015-12-01
Numerical simulation is a powerful tool to predict the mechanical behavior and the feasibility of composite parts. Among the available numerical approaches, as far as woven reinforced composites are concerned, 3D finite element simulation at the mesoscopic scale leads to a good compromise between realism and complexity. At this scale, the fibrous reinforcement is modeled by an interlacement of yarns assumed to be homogeneous that have to be accurately represented. Among the numerous issues induced by these simulations, the first one consists in providing a representative meshed geometrical model of the unit cell at the mesoscopic scale. The second one consists in enabling a fast data input in the finite element software (contacts definition, boundary conditions, elements reorientation, etc.) so as to obtain results within reasonable time. Based on parameterized 3D CAD modeling tool of unit-cells of dry fabrics already developed, this paper presents an efficient strategy which permits an automated meshing of the models with 3D hexahedral elements and to accelerate of several orders of magnitude the simulation data input. Finally, the overall modeling strategy is illustrated by examples of finite element simulation of the mechanical behavior of fabrics.
NASA Technical Reports Server (NTRS)
Scalapino, D. J.; Sugar, R. L.; White, S. R.; Bickers, N. E.; Scalettar, R. T.
1989-01-01
Numerical simulations on the half-filled three-dimensional Hubbard model clearly show the onset of Neel order. Simulations of the two-dimensional electron-phonon Holstein model show the competition between the formation of a Peierls-CDW state and a superconducting state. However, the behavior of the partly filled two-dimensional Hubbard model is more difficult to determine. At half-filling, the antiferromagnetic correlations grow as T is reduced. Doping away from half-filling suppresses these correlations, and it is found that there is a weak attractive pairing interaction in the d-wave channel. However, the strength of the pair field susceptibility is weak at the temperatures and lattice sizes that have been simulated, and the nature of the low-temperature state of the nearly half-filled Hubbard model remains open.
Peterson, D.L.; Bowers, R.L.; Lebeda, C.F.; Matuska, W.; Benage, J.; Idzorek, G.; Oona, H.; Stokes, J.; Roderick, N.F.
1995-09-01
Two experiments, PegI-41, conducted on the Los Alamos Pegasus I capacitor bank, and PegII-25, on the Pegasus II bank, consisted of the implosions of 13 mg (nominal), 5 cm radius, 2 cm high thin cylindrical aluminum foils resulting in soft x-ray radiation pulses from the plasma thermalization on axis. The implosions were conducted in direct-drive (no intermediate switching) mode with peak currents of about 4 MA and 5 MA respectively, and implosion times of about 2.5 {micro}s and 2.0 {micro}s. A radiation yield of about 250 kJ was measured for PegII-25. The purpose of these experiments was to examine the physics of the implosion and relate this physics to the production of the radiation pulse and to provide detailed experimental data which could be compared with 2-D radiation-magnetohydrodynamic (RMHD) simulations. Included in the experimental diagnostic suites were faraday rotation and dB/dt current measurements, a visible framing camera, an x-ray stripline camera, time-dependent spectroscopy, bolometers and XRD`S. A comparison of the results from these experiments shows agreement with 2-D simulation results in the instability development, current, and radiation pulse data, including the pulsewidth, shape, peak power and total radiation yield as measured by bolometry. Instabilities dominate the behavior of the implosion and largely determine the properties of the resulting radiation pulse. The 2-D simulations can be seen to be an important tool in understanding the implosion physics.
NASA Astrophysics Data System (ADS)
Sengupta, M.; Ganesh, R.
2017-03-01
In this paper, we have investigated, through simulation, the process of destabilization of a cylindrically confined electron cloud due to the presence of a single species of neutral atoms, Ar in the background of the trap at a pressure relevant to experiments. The destabilization occurs because of a gradual accumulation of Ar+ in the cloud by the electron-impact ionization of the background neutrals. The trapped ions gradually collectively form a sizeable ion cloud which engages in a rotational two-stream instability (the ion resonance instability) with the electron cloud. The instability excites a growing fundamental diocotron mode on both components of the mixed non-neutral cloud. With the help of a set of numerical diagnostics, we have investigated the nonlinear evolution of the excited fundamental mode under the combined influence of two ongoing processes viz, (i) the changing electron and ion populations caused by electron impact ionization of the background Ar, and also by the radial loss of both charged species to the grounded trap wall at later stages and (ii) the elastic scattering of electrons and ions that make non-ionizing collisions with the background neutrals. The 2D collisionless dynamics of the instability has been simulated using a 2D Particle-in-Cell code operating on a Cartesian grid laid out on the cylindrical trap's cross-section, and the 3D ionizing and non-ionizing collisions between charged particles and background neutrals have been simulated using the technique of Monte-Carlo-Collisions.
NASA Astrophysics Data System (ADS)
Fares, A.; Simunek, J.; Parsons, L. R.; van Genuchten, T. M.; Wheaton, T. A.; Morgan, K. T.
2001-12-01
Citrus root systems are exposed to different thermal and hydrologic conditions as a result of tree canopy shading and undertree microirrigation. Because microsprinklers wet only part of the soil surface and are located under the tree, roots under the canopy usually receive more water than those outside the tree canopy. The combined effects of different soil temperature and water input on water redistribution under field conditions have not been fully studied in Florida sandy soils. The objective of this study was to investigate shading and irrigation effects on spatial distribution of water content and soil temperature at different soil depths. Real-time capacitance probe systems (EnviroSCAN, SENTEK, Ltd. South Australia) and thermocouples were used to monitor soil water content and temperature at depths of 0, 10, 20, 40, 80 and 150 cm. Weather parameters were monitored simultaneously at the same location. HYDRUS-2D, a two dimensional computer package for simulating movement of water, heat, and multiple solutes in variably saturated media, was used to simulate water flow and heat transport under such conditions. The predicted water contents and soil temperatures compared favorably with their corresponding observed parameters. Shading substantially influenced hydraulic and thermal regimes of the system as shown by both predicted and measured water content and soil temperature. In addition to its accuracy in simulating this system, HYDRUS-2D helped to improve the analysis of this research project.
Huang, Haibing; Lv, Jun; Bao, Yameng; Xuan, Rongwei; Sun, Shenghua; Sneck, Sami; Li, Shuo; Modanese, Chiara; Savin, Hele; Wang, Aihua; Zhao, Jianhua
2017-04-01
This data article is related to our recently published article ('20.8% industrial PERC solar cell: ALD Al2O3 rear surface passivation, efficiency loss mechanisms analysis and roadmap to 24%', Huang et al., 2017 [1]) where we have presented a systematic evaluation of the overall cell processing and a cost-efficient industrial roadmap for PERC cells. Aside from the information already presented in Huang et al., 2017 [1], here we provide data related to Sectin 3 in Huang et al., 2017 [1] concerning the analysis of the recombination losses׳ mechanisms by PC1D V5.9 and PC2D simulations (Clugston and Basore, 1997, Basore and Cabanas-Holmen, 2011, Cabanas-Holmen and Basore, 2012 and Cabanas-Holmen and Basore, 2012.) [2], [3], [4], [5] on our current industrial Al2O3 PERC cell. The data include: i) PC2D simulations on J02, ii) the calculation of series resistance and back surface recombination velocity (BSRV) on the rear side metallization of PERC cell for the case of a point contact, and iii) the PC1D simulation on the cumulative photo-generation and recombination along the distance from the front surface. Finally, the roadmap of the solar cell efficiency for an industrial PERC technology up to 24% is presented, with the aim of providing a potential guideline for industrial researchers.
Qian, A R; Li, D; Han, J; Gao, X; Di, S M; Zhang, W; Hu, L F; Shang, Peng
2012-05-01
Osteoblasts, the bone-forming cells, respond to various mechanical forces, such as stretch and fluid shear force in essentially similar ways. The cytoskeleton, as the load-bearing architecture of the cell, is sensitive to altered inertial forces. Disruption of the cytoskeleton will result in alteration of cellular structure and function. However, it is difficult to quantitatively illustrate cytoskeletal rearrangement because of the complexity of cytoskeletal structure. Usually, the morphological changes in actin organization caused by external stimulus are basically descriptive. In this study, fractal dimensions (D) analysis was used to quantify the morphological changes in the actin cytoskeleton of osteoblast-like cells (MC3T3-E1) under simulated microgravity using 3-D/2-D clinostats. The ImageJ software was used to count the fractal dimension of actin cytoskeleton by box-counting methods. Real-time PCR and immunofluroscent assays were used to further confirm the results obtained by fractal dimension analysis. The results showed significant decreases in D value of actin cytoskeleton, β-actin mRNA expression, and the mean fluorescence intensity of F-actin in osteoblast-like cells after 24 or 48 h of incubation under 3-D/2-D clinorotation condition compared with control. The findings indicate that 3-D/2-D clinorotation affects both actin cytoskeleton architecture and mRNA expression, and fractal may be a promising approach for quantitative analysis of the changes in cytoskeleton in different environments.
Vogel; Rossler
2000-11-01
By carrying out random walk simulations we systematically study the effects of various types of complex molecular dynamics on (2)H NMR experiments in solids. More precisely, we calculate one-dimensional (1D) (2)H NMR spectra and the results of two dimensional (2D) (2)H NMR experiments in time domain, taking into account isotropic as well as highly restricted motions which involve rotational jumps about different finite angles. Although the dynamical models are chosen to mimic the primary and secondary relaxation in supercooled liquids and glasses, we do not intend to describe experimental results quantitatively but rather to show general effects appearing for complex reorientations. We carefully investigate whether 2D (2)H NMR in time domain, which was originally designed to measure correlation times of ultraslow motions (tau >/= 1 ms), can be used to obtain shorter tau, too. It is demonstrated that an extension of the time window to tau >/= 10 &mgr;s is possible when dealing with exponential relaxation, but that it will fail if there is a distribution of correlation times G(lgtau). Vice versa, we show that 1D (2)H NMR spectra, usually recorded to look at dynamics with tau in the microsecond regime, are also applicable for studying ultraslow motions provided that the loss of correlation is achieved step by step. Therefore, it is useful to carry out 1D and 2D NMR experiments simultaneously in order to reveal the mechanism of complex molecular motions. In addition, we demonstrate that highly restricted dynamics can be clearly observed in 1D spectra and in 2D NMR in time domain if long solid-echo delays and large evolution times are applied, respectively. Finally, unexpected observations are described which appear in the latter experiment when considering very broad distributions G(lgtau). Because of these effects, time scale and geometry of a considered motion cannot be extracted from a straightforward analysis of experimental results. Copyright 2000 Academic Press.
NASA Astrophysics Data System (ADS)
Uchino, H.; Machida, S.
2012-12-01
A physical process of the substorm triggering in the Earth's Magnetotail is thought to be closely related to the magnetic reconnection and the tearing instability. Recently we proposed a new scheme of the substorm onset called "Catapult Current Sheet Relaxation (CCSR) Model " to physically understand the results from GEOTAIL and THEMIS data. The CCSR Model has characters that are the decrease of the total pressure and thinning of the current sheet at the distance about -12Re in the magnetotail a few minutes before the substorm onset, and the simultaneous occurrence of the dipolarization at X~-10Re and the magnetic reconnection at X~-20Re at the time of the onset. In this study, we investigate a stability of the current sheet and the particle acceleration via particle simulation in order to assess the validity of the CCSR model and to clarify the mechanism of substorm onset. We give an initial magnetic field structure which is akin to the Earth's dipole magnetic field together with a stretched magnetic field by thin current sheet, and further add a weak northward magnetic field at the place where Near-Earth Neutral Line is expected to be formed. The results of simulation contain similar features that characterize the CCSR Model. A physically interpretation of the simulation result with the linear instability theory as well as comparison with observations will be given.
Roux, Emmanuel; Ramalli, Alessandro; Tortoli, Piero; Cachard, Christian; Robini, Marc; Liebgott, Herve
2016-08-24
Full matrix arrays are excellent tools for 3D ultrasound imaging, but the required number of active elements is too high to be individually controlled by an equal number of scanner channels. The number of active elements is significantly reduced by the sparse array techniques, but the position of the remaining elements must be carefully optimized. This issue is here faced by introducing novel energy functions in the simulated annealing algorithm. At each iteration step of the optimization process, one element is freely translated and the associated radiated pattern is simulated. To control the pressure field behavior at multiple depths, three energy functions inspired by the pressure field radiated by a Blackman-tapered spiral array are introduced. Such energy functions aim at limiting the main lobe width while lowering the side lobe and grating lobe levels at multiple depths. Numerical optimization results illustrate the influence of the number of iterations, pressure measurement points and depths as well as the influence of the energy function definition on the optimized layout. It is also shown that performance close to- or even better than the one provided by a spiral array, here assumed as reference, may be obtained. The finite-time convergence properties of simulated annealing allow the duration of the optimization process to be set in advance.
On the accuracy of simulations of a 2D boundary layer with RANS models implemented in OpenFoam
NASA Astrophysics Data System (ADS)
Graves, Benjamin J.; Gomez, Sebastian; Poroseva, Svetlana V.
2013-11-01
The OpenFoam software is an attractive Computational Fluid Dynamics solver for evaluating new turbulence models due to the open-source nature, and the suite of existing standard model implementations. Before interpreting results obtained with a new model, a baseline for performance of the OpenFoam solver and existing models is required. In the current study we analyze the RANS models in the OpenFoam incompressible solver for two planar (two-dimensional mean flow) benchmark cases generated by the AIAA Turbulence Model Benchmarking Working Group (TMBWG): a zero-pressure-gradient flat plate and a bump-in-channel. The OpenFoam results are compared against both experimental data and simulation results obtained with the NASA CFD codes CFL3D and FUN3D. Sensitivity of simulation results to the grid resolution and model implementation are analyzed. Testing is conducted using the Spalart-Allmaras one-equation model, Wilcox's two-equation k-omega model, and the Launder-Reece-Rodi Reynolds-stress model. Simulations using both wall functions and wall-resolved (low Reynolds number) formulations are considered. The material is based upon work supported by NASA under award NNX12AJ61A.
NASA Astrophysics Data System (ADS)
Matos, J. R.; Welty, C.; Packman, A.
2005-12-01
The main purpose of the simulations in this research is the analysis of three-dimensional surface-groundwater interchange in heterogeneous systems. The effects of channel pattern, bed forms and aquifer heterogeneity on flow interactions between stream and groundwater systems are examined in order to contribute for a better understanding of the hyporheic process. A two-dimensional approach was also adopted to allow comparisons with the three-dimensional results. The grid was designed using the correlation scales of the heterogeneous fields and the scale of the stream meanders. MODFLOW and MODPATH were used to evaluate magnitude, direction and spatial distribution of the exchange flow. PMWIN and PMPATH were used as pre and post-processors during the construction of the models and analysis of results. Gaining and losing streams as well as parallel flow and flow across streams were simulated as idealized cases intended to describe how properties of the streambed and aquifer in low-gradient lowland streams contribute to hyporheic exchange. At first a straight river was analyzed then meandering streams were created with a sine curve and variations on wavelength and amplitude. Bed forms were simulated assuming a sinusoidal distribution of pressure head in the bed surface. Aspects of the influence of bedforms on mechanisms such as "pumping" and "turnover" are expected to be addressed with simulations. Flow velocities between 20 and 40 cm/s in the channel were tested with the objective of showing the influence of river morphology and natural bed forms on the flow exchange in the hyporheic zone. Several meander cycles and four levels of hydraulic conductivity variance were analyzed. Results of flow variances along the cross-sections and wetted perimeter show the increasing on hyporheic exchange as the degree of heterogeneity increases. Particle tracking was performed to define hyporheic residence time distributions. When comparing the homogeneous fields with all degrees of
Gyrokinetic simulation and theory for kinetic ballooning mode
NASA Astrophysics Data System (ADS)
Li, Yue-Yan; Xiao, Yong
2016-10-01
The kinetic ballooning mode (KBM) plays an important role in H mode formation and edge-localized mode (ELM) physics and internal transport barrier. A thorough understanding of the linear KBM physics is crucial to understanding the nonlinear edge physics in tokamaks. The second stability regime in small shear and sufficiently large pressure gradient has been predicted by the ballooning MHD theory. In the present work, a kinetic ballooning mode is found for the second stability regime in s-alpha space. This KBM mode is characterized by a broad-spread eigenfunction in the ballooning space, and destabilized dramatically by the ion temperature gradient. Such KBM mode almost exists in the entire second stability regime. Also KBM has been found in the sufficiently small shear even with negative shear. The gyrokinetic code GTC is employed to study the KBM physics, and finds that the linear KBM growth rate and frequency are very sensitive to the equilibrium profile. The effect of parallel current and density has been investigated, and comparisons between gyrokinetic simulation and analytic theory are carried out. The results shows that parallel current response have a strong effect in stabilize KBM instability, which could have a large effect on nonlinear electromagnetic turbulent transport.
Kinetic particle simulation of turbulence in an FRC geometry
NASA Astrophysics Data System (ADS)
Fulton, Daniel; Lau, Calvin; Holod, Ihor; Lin, Zhihong; Dettrick, Sean; Binderbauer, Michl; Tajima, Toshiki
2014-10-01
Core turbulence in a Field Reversed Configuration (FRC) is studied using the Gyrokinetic Toroidal Code with modified equilibrium geometry. The code solves the gyrokinetic equation for ions and the drift kinetic equation for electrons. The simulation region is an annulus which excludes plasma near the O-point to avoid breakdown of the gyrokinetic dynamics of ions. The C-2 FRC equilibrium is introduced to study similar conditions as found in the C-2 experiments, where the core is found to be relatively quiescent. In simulation, we find the C-2 plasma is stable to ion temperature gradient instabilities using realistic experimental parameters, consistent with experimental results obtained in C-2. When temperature and density gradients are enhanced beyond typical C-2 parameters, we observe a class of instabilities that appear as flute-like drift modes. These results shed light on a possible reason why transport temperature scaling in the C-2 core is radically different from that of typical turbulent transport scaling such as the Bohm-like regime. Progress is also reported on simulations of scrape off layer turbulence and electron driven turbulence.
Hybrid framework for the simulation of stochastic chemical kinetics
NASA Astrophysics Data System (ADS)
Duncan, Andrew; Erban, Radek; Zygalakis, Konstantinos
2016-12-01
Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the "fast" reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when one or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.
Schaffranek, Raymond W.
2004-01-01
A numerical model for simulation of surface-water integrated flow and transport in two (horizontal-space) dimensions is documented. The model solves vertically integrated forms of the equations of mass and momentum conservation and solute transport equations for heat, salt, and constituent fluxes. An equation of state for salt balance directly couples solution of the hydrodynamic and transport equations to account for the horizontal density gradient effects of salt concentrations on flow. The model can be used to simulate the hydrodynamics, transport, and water quality of well-mixed bodies of water, such as estuaries, coastal seas, harbors, lakes, rivers, and inland waterways. The finite-difference model can be applied to geographical areas bounded by any combination of closed land or open water boundaries. The simulation program accounts for sources of internal discharges (such as tributary rivers or hydraulic outfalls), tidal flats, islands, dams, and movable flow barriers or sluices. Water-quality computations can treat reactive and (or) conservative constituents simultaneously. Input requirements include bathymetric and topographic data defining land-surface elevations, time-varying water level or flow conditions at open boundaries, and hydraulic coefficients. Optional input includes the geometry of hydraulic barriers and constituent concentrations at open boundaries. Time-dependent water level, flow, and constituent-concentration data are required for model calibration and verification. Model output consists of printed reports and digital files of numerical results in forms suitable for postprocessing by graphical software programs and (or) scientific visualization packages. The model is compatible with most mainframe, workstation, mini- and micro-computer operating systems and FORTRAN compilers. This report defines the mathematical formulation and computational features of the model, explains the solution technique and related model constraints, describes the
2D/3D quench simulation using ANSYS for epoxy impregnated Nb3Sn high field magnets
Ryuji Yamada et al.
2002-09-19
A quench program using ANSYS is developed for the high field collider magnet for three-dimensional analysis. Its computational procedure is explained. The quench program is applied to a one meter Nb{sub 3}Sn high field model magnet, which is epoxy impregnated. The quench simulation program is used to estimate the temperature and mechanical stress inside the coil as well as over the whole magnet. It is concluded that for the one meter magnet with the presented cross section and configuration, the thermal effects due to the quench is tolerable. But we need much more quench study and improvements in the design for longer magnets.
NASA Astrophysics Data System (ADS)
Palmroth, M.; Hoilijoki, S.; Pfau-Kempf, Y.; Hietala, H.; Nishimura, Y.; Angelopoulos, V.; Pulkkinen, T. I.; Ganse, U.; Hannuksela, O.; von Alfthan, S.; Battarbee, M. C.; Vainio, R. O.
2015-12-01
We investigate the dayside-nightside coupling of the magnetospheric dynamics in a global kinetic simulation displaying the entire magnetosphere. We use the newly developed Vlasiator (http://vlasiator.fmi.fi), which is the world's first global hybrid-Vlasov simulation modelling the ions as distribution functions, while electrons are treated as a charge-neutralising fluid. Here, we run Vlasiator in the 5-dimensional (5D) setup, where the ordinary space is presented in the 2D noon-midnight meridional plane, embedding in each grid cell the 3D velocity space. This approach combines the improved physical solution with fine resolution, allowing to investigate kinetic processes as a consequence of the global magnetospheric evolution. The simulation is during steady southward interplanetary magnetic field. We observe dayside reconnection and the resulting 2D representations of flux transfer events (FTE). FTE's move tailwards and distort the magnetopause, while the largest of them even modify the plasma sheet location. In the nightside, the plasma sheet shows bead-like density enhancements moving slowly earthward. The tailward side of the dipolar field stretches. Strong reconnection initiates first in the near-Earth region, forming a tailward-moving magnetic island that cannibalises other islands forming further down the tail, increasing the island's volume and complexity. After this, several reconnection lines are formed again in the near-Earth region, resulting in several magnetic islands. At first, none of the earthward moving islands reach the closed field region because just tailward of the dipolar region exists a relatively stable X-line, which is strong enough to push most of the magnetic islands tailward. However, finally one of the tailward X-lines is strong enough to overcome the X-line nearest to Earth, forming a strong surge into the dipolar field region as there is nothing anymore to hold back the propagation of the structure. We investigate this substorm
Simulation of Ultra-Small MOSFETs Using a 2-D Quantum-Corrected Drift-Diffusion Model
NASA Technical Reports Server (NTRS)
Biegel, Bryan A.; Rafferty, Conor S.; Yu, Zhiping; Dutton, Robert W.; Ancona, Mario G.; Saini, Subhash (Technical Monitor)
1998-01-01
We describe an electronic transport model and an implementation approach that respond to the challenges of device modeling for gigascale integration. We use the density-gradient (DG) transport model, which adds tunneling and quantum smoothing of carrier density profiles to the drift-diffusion model. We present the current implementation of the DG model in PROPHET, a partial differential equation solver developed by Lucent Technologies. This implementation approach permits rapid development and enhancement of models, as well as run-time modifications and model switching. We show that even in typical bulk transport devices such as P-N diodes and BJTs, DG quantum effects can significantly modify the I-V characteristics. Quantum effects are shown to be even more significant in small, surface transport devices, such as sub-0.1 micron MOSFETs. In thin-oxide MOS capacitors, we find that quantum effects may reduce gate capacitance by 25% or more. The inclusion of quantum effects in simulations dramatically improves the match between C-V simulations and measurements. Significant quantum corrections also occur in the I-V characteristics of short-channel MOSFETs due to the gate capacitance correction.
Roux, Emmanuel; Ramalli, Alessandro; Tortoli, Piero; Cachard, Christian; Robini, Marc C; Liebgott, Herve
2016-12-01
Full matrix arrays are excellent tools for 3-D ultrasound imaging, but the required number of active elements is too high to be individually controlled by an equal number of scanner channels. The number of active elements is significantly reduced by the sparse array techniques, but the position of the remaining elements must be carefully optimized. This issue is faced here by introducing novel energy functions in the simulated annealing (SA) algorithm. At each iteration step of the optimization process, one element is freely translated and the associated radiated pattern is simulated. To control the pressure field behavior at multiple depths, three energy functions inspired by the pressure field radiated by a Blackman-tapered spiral array are introduced. Such energy functions aim at limiting the main lobe width while lowering the side lobe and grating lobe levels at multiple depths. Numerical optimization results illustrate the influence of the number of iterations, pressure measurement points, and depths, as well as the influence of the energy function definition on the optimized layout. It is also shown that performance close to or even better than the one provided by a spiral array, here assumed as reference, may be obtained. The finite-time convergence properties of SA allow the duration of the optimization process to be set in advance.
NASA Astrophysics Data System (ADS)
Suryanarayanan, Saikishan; Narasimha, Roddam
2017-02-01
Although the free-shear or mixing layer has been a subject of extensive research over nearly a century, there are certain fundamental issues that remain controversial. These include the influence of initial and downstream conditions on the flow, the effect of velocity ratio across the layer, and the nature of any possible coupling between small scale dynamics and the large scale evolution of layer thickness. In the spirit of the temporal vortex-gas simulations of Suryanarayanan et al. ["Free turbulent shear layer in a point vortex gas as a problem in nonequilibrium statistical mechanics," Phys. Rev. E 89, 013009 (2014)], we revisit the simple 2D inviscid vortex-gas model with extensive computations and detailed analysis, in order to gain insights into some of the above issues. Simulations of the spatially evolving vortex-gas shear layer are carried out at different velocity ratios using a computational model based on the work of Basu et al. ["Vortex sheet simulation of a plane canonical mixing layer," Comput. Fluids 21, 1-30 (1992) and "Modelling plane mixing layers using vortex points and sheets," Appl. Math. Modell. 19, 66-75 (1995)], but with a crucial improvement that ensures conservation of global circulation. The simulations show that the conditions imposed at the origin of the free shear layer and at the exit to the computational domain can affect flow evolution in their respective downstream and upstream neighbourhoods, the latter being particularly strong in the single stream limit. In between these neighbourhoods at the ends is a regime of universal self-preserving growth rate given by a universal function of velocity ratio. The computed growth rates are generally located within the scatter of experimental data on plane mixing layers and closely agree with recent high Reynolds number experiments and 3D large eddy simulation studies. These findings support the view that observed free-shear layer growth can be largely explained by the 2D vortex dynamics of
NASA Astrophysics Data System (ADS)
Guillemaut, C.; Pitts, R. A.; Kukushkin, A. S.; Gunn, J. P.; Bucalossi, J.; Arnoux, G.; Belo, P.; Brezinsek, S.; Brix, M.; Corrigan, G.; Devaux, S.; Flanagan, J.; Groth, M.; Harting, D.; Huber, A.; Jachmich, S.; Kruezi, U.; Lehnen, M.; Marchetto, C.; Marsen, S.; Meigs, A. G.; Meyer, O.; Stamp, M.; Strachan, J. D.; Wiesen, S.; Wischmeier, M.; EFDA Contributors, JET
2014-09-01
The EDGE2D-EIRENE code is applied for simulation of divertor detachment during matched density ramp experiments in high triangularity, L-mode plasmas in both JET-Carbon (JET-C) and JET-ITER-Like Wall (JET-ILW). The code runs without drifts and includes either C or Be as impurity, but not W, assuming that the W targets have been coated with Be via main chamber migration. The simulations reproduce reasonably well the observed particle flux detachment as density is raised in both JET-C and JET-ILW experiments and can better match the experimental in-out divertor target power asymmetry if the heat flux entering the outer divertor is artificially set at around 2-3 times that entering the inner divertor. A careful comparison between different sets of atomic physics processes used in EIRENE shows that the detachment modelled by EDGE2D-EIRENE relies only on an increase of the particle sinks and not on a decrease of the ionization source. For the rollover and the beginning of the partially detached phase, the particle losses by perpendicular transport and the molecular activated recombination processes are mainly involved. For a deeper detachment with significant target ion flux reduction, volume recombination appears to be the main contributor. The elastic molecule-ion collisions are also important to provide good neutral confinement in the divertor and thus stabilize the simulations at low electron temperature (Te), when the sink terms are strong. Comparison between EDGE2D-EIRENE and SOLPS4.3 simulations of the density ramp in C shows similar detachment trends, but the importance of the elastic ion-molecule collisions is reduced in SOLPS4.3. Both codes suggest that any process capable of increasing the neutral confinement in the divertor should help to improve the modelling of the detachment. A further outcome of this work has been to demonstrate that key JET divertor diagnostic signals—Langmuir probe Te and bolometric tomographic reconstructions—are running beyond
NASA Astrophysics Data System (ADS)
de Garis, Hugo; Korkin, Michael; Guttikonda, Padma; Cooley, Donald
2000-11-01
This paper presents some simulation results of the evolution of 2D visual pattern recognizers to be implemented very shortly on real hardware, namely the 'CAM-Brain Machine' (CBM), an FPGA based piece of evolvable hardware which implements a genetic algorithm (GA) to evolve a 3D cellular automata (CA) based neural network circuit module, of approximately 1,000 neurons, in about a second, i.e. a complete run of a GA, with 10,000s of circuit growths and performance evaluations. Up to 65,000 of these modules, each of which is evolved with a humanly specified function, can be downloaded into a large RAM space, and interconnected according to humanly specified gvdvips -o SPIE-2000.ps SPIE-2000 artificial brain architectures. This RAM, containing an artificial brain with up to 75 million neurons, is then updated by the CBM at a rate of 130 billion CA cells per second. Such speeds will enable real time control of robots and hopefully the birth of a new research field that we call 'brain building.' The first such artificial brain, to be built at STARLAB in 2000 and beyond, will be used to control the behaviors of a life sized kitten robot called 'Robokitty.' This kitten robot will need 2D pattern recognizers in the visual section of its artificial brain. This paper presents simulation results on the evolvability and generalization properties of such recognizers.
Kasinathan, N.; Rajakumar, A.; Vaidyanathan, G.; Chetal, S.C.
1995-09-01
Post shutdown decay heat removal is an important safety requirement in any nuclear system. In order to improve the reliability of this function, Liquid metal (sodium) cooled fast breeder reactors (LMFBR) are equipped with redundant hot pool dipped immersion coolers connected to natural draught air cooled heat exchangers through intermediate sodium circuits. During decay heat removal, flow through the core, immersion cooler primary side and in the intermediate sodium circuits are also through natural convection. In order to establish the viability and validate computer codes used in making predictions, a 1:20 scale experimental model called RAMONA with water as coolant has been built and experimental simulation of decay heat removal situation has been performed at KfK Karlsruhe. Results of two such experiments have been compiled and published as benchmarks. This paper brings out the results of the numerical simulation of one of the benchmark case through a 1D/2D coupled code system, DHDYN-1D/THYC-2D and the salient features of the comparisons. Brief description of the formulations of the codes are also included.
NASA Astrophysics Data System (ADS)
Lawson, K. D.; Groth, M.; Belo, P.; Brezinsek, S.; Corrigan, G.; Czarnecka, A.; Delabie, E.; Drewelow, P.; Harting, D.; Książek, I.; Maggi, C. F.; Marchetto, C.; Meigs, A. G.; Menmuir, S.; Stamp, M. F.; Wiesen, S.
2015-08-01
A discrepancy in the divertor radiated powers between EDGE2D-EIRENE simulations, both with and without drifts, and JET-ILW experiments employing a set of NBI-heated L-mode discharges with step-wise density variation is investigated. Results from a VUV/visible poloidally scanning spectrometer are used together with bolometric measurements to determine the radiated power and its composition. The analysis shows the importance of D line radiation in contributing to the divertor radiated power, while contributions from D radiative recombination are smaller than expected. Simulations with W divertor plates underestimate the Be content in the divertor, since no allowance is made for Be previously deposited on the plates being re-eroded. An improved version of EDGE2D-EIRENE is used to test the importance of the deposited layer in which the sputtering yield from supposed pure Be divertor plates is reduced to match the spectroscopic signals, while keeping the sputtering yield for the Be main chamber walls unchanged.
NASA Astrophysics Data System (ADS)
Zhang, Wei; Chen, Chen; Jia, Rui; Janssen, G. J. M.; Zhang, Dai-Sheng; Xing, Zhao; Bronsveld, P. C. P.; Weeber, A. W.; Jin, Zhi; Liu, Xin-Yu
2013-07-01
In interdigitated back contact (IBC) solar cells, the metal-electrode coverage on a p-type emitter is optimized by a PC2D simulation. The result shows that the variation of the metal coverage ratio (MCR) will affect both the surface passivation and the electrode-contact properties for the p-type emitter in IBC solar cells. We find that when Rc ranges from 0.08 to 0.16Ω·cm2, the MCR is optimized with a value of 25% and 33%, resulting in a highest energy-conversion efficiency. The dependences of both Voc and fill factor on MCR are simulated in order to explore the mechanism of the IBC solar cells.
NASA Technical Reports Server (NTRS)
Gnoffo, Peter A.; Berry, Scott A.; VanNorman, John W.
2011-01-01
This paper is one of a series of five papers in a special session organized by the NASA Fundamental Aeronautics Program that addresses uncertainty assessments for CFD simulations in hypersonic flow. Simulations of a shock emanating from a compression corner and interacting with a fully developed turbulent boundary layer are evaluated herein. Mission relevant conditions at Mach 7 and Mach 14 are defined for a pre-compression ramp of a scramjet powered vehicle. Three compression angles are defined, the smallest to avoid separation losses and the largest to force a separated flow engaging more complicated flow physics. The Baldwin-Lomax and the Cebeci-Smith algebraic models, the one-equation Spalart-Allmaras model with the Catrix-Aupoix compressibility modification and two-equation models including Menter SST, Wilcox k-omega 98, and Wilcox k-omega 06 turbulence models are evaluated. Each model is fully defined herein to preclude any ambiguity regarding model implementation. Comparisons are made to existing experimental data and Van Driest theory to provide preliminary assessment of model form uncertainty. A set of coarse grained uncertainty metrics are defined to capture essential differences among turbulence models. Except for the inability of algebraic models to converge for some separated flows there is no clearly superior model as judged by these metrics. A preliminary metric for the numerical component of uncertainty in shock-turbulent-boundary-layer interactions at compression corners sufficiently steep to cause separation is defined as 55%. This value is a median of differences with experimental data averaged for peak pressure and heating and for extent of separation captured in new, grid-converged solutions presented here. This value is consistent with existing results in a literature review of hypersonic shock-turbulent-boundary-layer interactions by Roy and Blottner and with more recent computations of MacLean.
Parmar, S.S.; Benson, S.W.
1989-01-04
The bimolecular rate constant for the title reaction has been measured with the very low pressure reactor technique (VLPR) at 295 K. The rate constant at room temperature (295 K) was found to be k/sub 1/ = (8.30 /plus minus/ 0.7) /times/ 10/sup /minus/12/ cm/sup 3//(molecule/center dot/s). The value of K/sub 1/, i.e., equilibrium constant at room temperature, was found to be (4.70 /plus minus/ 0.3) /times/ 10/sup 2/. From third law calculations at 295 K /delta/H/sub f//degree/(C/sub 2/D/sub 5/) = (24.30 /plus minus/ 0.4) kcal/mol and DH/degree/(C/sub 2/D/sub 5/-D) = 102.8 /plus minus/ 0.4 kcal/mol. With use of known zero-point energy differences DH/degree/(C/sub 2/H/sub 5/-H) can be calculated from this as 100.4 kcal/mol and /delta/H/sub f//degree/(C/sub 2/H/sub 5/) = 28.3 kcal/mol in excellent agreement with recent data. 22 references, 4 figures, 3 tables.
Kinetic simulations of X-B and O-X-B mode conversion
NASA Astrophysics Data System (ADS)
Arefiev, A.; Du Toit, E. J.; Kohn, A.; Holzhauer, E.; Shevchenko, V. F.; Vann, R. G. L.
2015-11-01
High-performance spherical tokamaks are usually overdense (typically ωpe /ωce 4 in the core) and so regular electron cyclotron emission is blocked. However, electron Bernstein waves, generated at the local cyclotron frequency (and its harmonics) in the core may be observed outside the plasma via a mode conversion process that takes place typically in the plasma edge between an electromagnetic mode and the (electrostatic) electron Bernstein wave. Understanding the details of this mode conversion process is important in tokamaks with over-dense plasmas both for the interpretation of microwave diagnostic data and to assess the feasibility of EBW heating and/or current drive. To this end, we have performed the first ever 2-D fully-kinetic simulations of O-X-B mode conversion using the particle-in-cell code EPOCH. In addition to benchmarking these numerical results against the linear dispersion relation, we have also investigated nonlinearities associated with a larger incident intensity and the effect of a steeper (and more realistic) density gradient at the mode conversion layer. Simulations were performed on the HELIOS supercomputer at the IFERC-CSC, Rokkasho, Japan and on TACC supercomputers at the University of Texas at Austin.
NASA Astrophysics Data System (ADS)
Ren, Guoli; Pei, Wenbing; Lan, Ke; Gu, Peijun; Li, Xin; Institute of Applied Physics; Computional Mathematics Team
2011-10-01
In current routine 2D simulation of hohlraum physics, we adopt the principal-quantum- number(n-level) average atom model(AAM). However, the experimental frequency-dependant radiative drive differs from our n-level simulated drive, which reminds us the need of a more detailed atomic kinetics description. The orbital-quantum-number(nl-level) AAM is a natural consideration but the in-line calculation consumes much more resources. We use a new method to built up a nl-level bound electron distribution using in-line n-level calculated plasma condition (such as temperature, density, average ionization degree). We name this method ``quasi-steady approximation.'' Using the re-built nl-level bound electron distribution (Pnl) , we acquire a new hohlraum radiative drive by post-processing. Comparison with the n-level post-processed hohlraum drive shows that we get an almost identical radiation flux but with more-detailed frequency-dependant structures.
Variable Charge State Impurities in Coupled Kinetic Plasma-Kinetic Neutral Transport Simulations
NASA Astrophysics Data System (ADS)
Stotler, D. P.; Hager, R.; Kim, K.; Koskela, T.; Park, G.
2015-11-01
A previous version of the XGC0 neoclassical particle transport code with two fully stripped impurity species was used to study kinetic neoclassical transport in the DIII-D H-mode pedestal. To properly simulate impurities in the scrape-off layer and divertor and to account for radiative cooling, however, the impurity charge state distributions must evolve as the particles are transported into regions of different electron temperatures and densities. To do this, the charge state of each particle in XGC0 is included as a parameter in the list that represents the particle's location in phase space. Impurity ionizations and recombinations are handled with a dedicated collision routine. The associated radiative cooling is accumulated during the process and applied to the electron population later in the time step. The density profiles of the neutral impurities are simulated with the DEGAS 2 neutral transport code and then used as a background for electron impact ionization in XGC0 via a test particle Monte Carlo method analogous to that used for deuterium. This work supported by US DOE contracts DE-AC02-09CH11466.
Techniques utilized in the simulated altitude testing of a 2D-CD vectoring and reversing nozzle
NASA Technical Reports Server (NTRS)
Block, H. Bruce; Bryant, Lively; Dicus, John H.; Moore, Allan S.; Burns, Maureen E.; Solomon, Robert F.; Sheer, Irving
1988-01-01
Simulated altitude testing of a two-dimensional, convergent-divergent, thrust vectoring and reversing exhaust nozzle was accomplished. An important objective of this test was to develop test hardware and techniques to properly operate a vectoring and reversing nozzle within the confines of an altitude test facility. This report presents detailed information on the major test support systems utilized, the operational performance of the systems and the problems encountered, and test equipment improvements recommended for future tests. The most challenging support systems included the multi-axis thrust measurement system, vectored and reverse exhaust gas collection systems, and infrared temperature measurement systems used to evaluate and monitor the nozzle. The feasibility of testing a vectoring and reversing nozzle of this type in an altitude chamber was successfully demonstrated. Supporting systems performed as required. During reverser operation, engine exhaust gases were successfully captured and turned downstream. However, a small amount of exhaust gas spilled out the collector ducts' inlet openings when the reverser was opened more than 60 percent. The spillage did not affect engine or nozzle performance. The three infrared systems which viewed the nozzle through the exhaust collection system worked remarkably well considering the harsh environment.
Baryon acoustic oscillations in 2D. II. Redshift-space halo clustering in N-body simulations
NASA Astrophysics Data System (ADS)
Nishimichi, Takahiro; Taruya, Atsushi
2011-08-01
We measure the halo power spectrum in redshift space from cosmological N-body simulations, and test the analytical models of redshift distortions particularly focusing on the scales of baryon acoustic oscillations. Remarkably, the measured halo power spectrum in redshift space exhibits a large-scale enhancement in amplitude relative to the real-space clustering, and the effect becomes significant for the massive or highly biased halo samples. These findings cannot be simply explained by the so-called streaming model frequently used in the literature. By contrast, a physically motivated perturbation theory model developed in the previous paper reproduces the halo power spectrum very well, and the model combining a simple linear scale-dependent bias can accurately characterize the clustering anisotropies of halos in two dimensions, i.e., line-of-sight and its perpendicular directions. The results highlight the significance of nonlinear coupling between density and velocity fields associated with two competing effects of redshift distortions, i.e., Kaiser and Finger-of-God effects, and a proper account of this effect would be important in accurately characterizing the baryon acoustic oscillations in two dimensions.
NASA Astrophysics Data System (ADS)
Westerhof, E.; de Blank, H. J.; Pratt, J.
2016-03-01
Two dimensional reduced MHD simulations of neoclassical tearing mode growth and suppression by ECCD are performed. The perturbation of the bootstrap current density and the EC drive current density perturbation are assumed to be functions of the perturbed flux surfaces. In the case of ECCD, this implies that the applied power is flux surface averaged to obtain the EC driven current density distribution. The results are consistent with predictions from the generalized Rutherford equation using common expressions for Δ \\text{bs}\\prime and Δ \\text{ECCD}\\prime . These expressions are commonly perceived to describe only the effect on the tearing mode growth of the helical component of the respective current perturbation acting through the modification of Ohm’s law. Our results show that they describe in addition the effect of the poloidally averaged current density perturbation which acts through modification of the tearing mode stability index. Except for modulated ECCD, the largest contribution to the mode growth comes from this poloidally averaged current density perturbation.
Kinetic simulation of neutral particle transport in sputtering processes
NASA Astrophysics Data System (ADS)
Trieschmann, Jan; Gallian, Sara; Brinkmann, Ralf Peter; Mussenbrock, Thomas; Ries, Stefan; Bibinov, Nikita; Awakowicz, Peter
2013-09-01
For many physical vapor deposition applications using sputtering processes, knowledge about the detailed spatial and temporal evolution of the involved gas species is of great importance. Modeling of the involved gas dynamic and plasma processes is however challenging, because the operating pressure is typically below 1 Pa. In consequence, only kinetic descriptions are appropriate. In order to approach this problem, the dynamics of sputtered particle transport through a neutral gas background is simulated. For this study, a modified version of the three-dimensional Direct Simulation Monte Carlo (DSMC) code dsmcFoam is utilized. The impact of a transient sputtering wind is investigated in a generic reactor geometry, which may be used for dc Magnetron Sputtering (dcMS), High Power Impulse Magnetron Sputtering (HiPIMS), as well as sputtering in capacitively coupled discharges. In the present work a rarefaction of the background gas is observed. Moreover in pulsed mode the temporal dynamics of the rarefaction and subsequent recovery of the background gas is investigated. This work is supported by the German Research Foundation in the frame of TRR 87.
Hybrid Parallelization of Adaptive MHD-Kinetic Module in Multi-Scale Fluid-Kinetic Simulation Suite
Borovikov, Sergey; Heerikhuisen, Jacob; Pogorelov, Nikolai
2013-04-01
The Multi-Scale Fluid-Kinetic Simulation Suite has a computational tool set for solving partially ionized flows. In this paper we focus on recent developments of the kinetic module which solves the Boltzmann equation using the Monte-Carlo method. The module has been recently redesigned to utilize intra-node hybrid parallelization. We describe in detail the redesign process, implementation issues, and modifications made to the code. Finally, we conduct a performance analysis.
A general kinetic-flow coupling model for FCC riser flow simulation.
Chang, S. L.
1998-05-18
A computational fluid dynamic (CFD) code has been developed for fluid catalytic cracking (FCC) riser flow simulation. Depending on the application of interest, a specific kinetic model is needed for the FCC flow simulation. This paper describes a method to determine a kinetic model based on limited pilot-scale test data. The kinetic model can then be used with the CFD code as a tool to investigate optimum operating condition ranges for a specific FCC unit.
Pitz, William J.; McNenly, Matt J.; Whitesides, Russell; Mehl, Marco; Killingsworth, Nick J.; Westbrook, Charles K.
2015-12-17
Predictive chemical kinetic models are needed to represent next-generation fuel components and their mixtures with conventional gasoline and diesel fuels. These kinetic models will allow the prediction of the effect of alternative fuel blends in CFD simulations of advanced spark-ignition and compression-ignition engines. Enabled by kinetic models, CFD simulations can be used to optimize fuel formulations for advanced combustion engines so that maximum engine efficiency, fossil fuel displacement goals, and low pollutant emission goals can be achieved.
NASA Astrophysics Data System (ADS)
Constantinescu, R.; Thouret, J. C.; Sandri, L.; Irimus, I. A.; Stefanescu, R.
2012-04-01
Pyroclastic density currents, which include pyroclastic surges and pyroclastic flows (PFs), are among the most dangerous volcanic phenomena. We present a probabilistic hazard assessment of the PFs generated from eruptive column collapse at El Misti volcano (5822 m) in South Peru. The high relief of the cone, the location of the city of Arequipa (~1,000,000 people) on two large volcanoclastic fans and the H (3.5 km)/L (17 km) ratio (0.2) between the summit and the city center, make PFs a direct threat. We consider three eruption scenario sizes: small Vulcanian/Phreatomagmatic (VEI 2), medium Sub-Plinian (VEI 3-4), and large Plinian (VEI 4+). We use the Event-Tree approach in a Bayesian scheme with BET_VH (Bayesian Event Tree for Volcanic Hazard) software. Quantitative data that stem from numerical simulations from TITAN2D (termed prior models) and from stratigraphic record (termed past data) are input to BET_VH, which enables us to compute the probabilities (in a 1-year time window) of (i) having an eruption (ii) in a selected location/vent (iii) of a specific size, (iv) and that this eruption will produce PFs (v) that will reach a location of interest around El Misti. TITAN2D simulation runs, expressed as color-coded thicknesses of PDC deposits, fit well the extent of past PFs deposits, including thick confined deposits (0.5-7 m) in the Rio Chili canyon and its tributary ravines (Quebradas San Lazaro, Huarangal and Agua Salada).The unconfined, thinner (≤10cm) deposits, as displayed by simulation runs on the interfluves, is attributed to ash-cloud surges. Such thin, fine ash deposits have not been emphasized in geological maps either because they have been removed away or remain yet unrecognized. The simulated Vulcanian flows, restricted to the upper part of the cone, become confined (0.1-1m thick) in the ravines which converge towards each of the three Quebradas. The simulated Subplinian PF deposits reach 0.1 to 1 m thick in the Quebradas and 1-4 m WNW of El
Sidler, Rolf; Carcione, José M.; Holliger, Klaus
2013-02-15
We present a novel numerical approach for the comprehensive, flexible, and accurate simulation of poro-elastic wave propagation in 2D polar coordinates. An important application of this method and its extensions will be the modeling of complex seismic wave phenomena in fluid-filled boreholes, which represents a major, and as of yet largely unresolved, computational problem in exploration geophysics. In view of this, we consider a numerical mesh, which can be arbitrarily heterogeneous, consisting of two or more concentric rings representing the fluid in the center and the surrounding porous medium. The spatial discretization is based on a Chebyshev expansion in the radial direction and a Fourier expansion in the azimuthal direction and a Runge–Kutta integration scheme for the time evolution. A domain decomposition method is used to match the fluid–solid boundary conditions based on the method of characteristics. This multi-domain approach allows for significant reductions of the number of grid points in the azimuthal direction for the inner grid domain and thus for corresponding increases of the time step and enhancements of computational efficiency. The viability and accuracy of the proposed method has been rigorously tested and verified through comparisons with analytical solutions as well as with the results obtained with a corresponding, previously published, and independently benchmarked solution for 2D Cartesian coordinates. Finally, the proposed numerical solution also satisfies the reciprocity theorem, which indicates that the inherent singularity associated with the origin of the polar coordinate system is adequately handled.
NASA Astrophysics Data System (ADS)
Reddy, K. Sanjeeva; Krishnamurthy, C. V.; Balasubramaniam, Krishnan; Balasubramanian, T.
2010-02-01
This paper discusses the evaluation of diffracted signals from cracks in 2D based on a new Huygen-Fresnel Diffraction Model (H-FDM). The model employs the frequency-domain far-field displacement expressions derived by Miller & Pursey [1] in 2D for a line source located on the free surface of a semi-infinite elastic medium. At each frequency in the bandwidth of a pulsed excitation, the complex diffracted field is obtained by summing over the unblocked virtual sources located in the section containing a vertical crack. The time-domain diffracted signal is obtained using standard FFT procedures. The effect of beam refraction from a wedge-based finite transducer has been modeled by treating the finite transducer as an array of line sources. The model has been used for predicting diffracted signals in time-of-flight from the crack like defect. The model allows the evaluation of back wall signal amplitude and lateral wave amplitude as well. Experiments have been carried out on 10 mm thick aluminum sample with surface breaking crack of lengths 2 mm and 4 mm using shear probe shoe. The simulated A-Scan results for the aluminum sample with 2 mm and 4 mm surface breaking lengths compare very well in relative amplitudes and time of arrivals with experiments. The H-FDM model offers a tool to evaluate diffraction and related phenomena quantitatively with modest computational resources.
NASA Astrophysics Data System (ADS)
Rank, Christopher M.; Heußer, Thorsten; Flach, Barbara; Brehm, Marcus; Kachelrieß, Marc
2015-03-01
We propose a new method for PET/MR respiratory motion compensation, which is based on a 3D-2D registration of strongly undersampled MR data and a) runs in parallel with the PET acquisition, b) can be interlaced with clinical MR sequences, and c) requires less than one minute of the total MR acquisition time per bed position. In our simulation study, we applied a 3D encoded radial stack-of-stars sampling scheme with 160 radial spokes per slice and an acquisition time of 38 s. Gated 4D MR images were reconstructed using a 4D iterative reconstruction algorithm. Based on these images, motion vector fields were estimated using our newly-developed 3D-2D registration framework. A 4D PET volume of a patient with eight hot lesions in the lungs and upper abdomen was simulated and MoCo 4D PET images were reconstructed based on the motion vector fields derived from MR. For evaluation, average SUVmean values of the artificial lesions were determined for a 3D, a gated 4D, a MoCo 4D and a reference (with ten-fold measurement time) gated 4D reconstruction. Compared to the reference, 3D reconstructions yielded an underestimation of SUVmean values due to motion blurring. In contrast, gated 4D reconstructions showed the highest variation of SUVmean due to low statistics. MoCo 4D reconstructions were only slightly affected by these two sources of uncertainty resulting in a significant visual and quantitative improvement in terms of SUVmean values. Whereas temporal resolution was comparable to the gated 4D images, signal-to-noise ratio and contrast-to-noise ratio were close to the 3D reconstructions.
Spectral Kinetic Simulation of the Ideal Multipole Resonance Probe
NASA Astrophysics Data System (ADS)
Gong, Junbo; Wilczek, Sebastian; Szeremley, Daniel; Oberrath, Jens; Eremin, Denis; Dobrygin, Wladislaw; Schilling, Christian; Friedrichs, Michael; Brinkmann, Ralf Peter
2015-09-01
The term Active Plasma Resonance Spectroscopy (APRS) denotes a class of diagnostic techniques which utilize the natural ability of plasmas to resonate on or near the electron plasma frequency ωpe: An RF signal in the GHz range is coupled into the plasma via an electric probe; the spectral response of the plasma is recorded, and a mathematical model is used to determine plasma parameters such as the electron density ne or the electron temperature Te. One particular realization of the method is the Multipole Resonance Probe (MRP). The ideal MRP is a geometrically simplified version of that probe; it consists of two dielectrically shielded, hemispherical electrodes to which the RF signal is applied. A particle-based numerical algorithm is described which enables a kinetic simulation of the interaction of the probe with the plasma. Similar to the well-known particle-in-cell (PIC), it contains of two modules, a particle pusher and a field solver. The Poisson solver determines, with the help of a truncated expansion into spherical harmonics, the new electric field at each particle position directly without invoking a numerical grid. The effort of the scheme scales linearly with the ensemble size N.
Thermodynamics and kinetics of bubble nucleation: Simulation methodology
NASA Astrophysics Data System (ADS)
Meadley, Stacey L.; Escobedo, Fernando A.
2012-08-01
The simulation of homogeneous liquid to vapor nucleation is investigated using three rare-event algorithms, boxed molecular dynamics, hybrid umbrella sampling Monte Carlo, and forward flux sampling. Using novel implementations of these methods for efficient use in the isothermal-isobaric ensemble, the free energy barrier to nucleation and the kinetic rate are obtained for a Lennard-Jones fluid at stretched and at superheated conditions. From the free energy surface mapped as a function of two order parameters, the global density and largest bubble volume, we find that the free energy barrier height is larger when projected over bubble volume. Using a regression analysis of forward flux sampling results, we show that bubble volume is a more ideal reaction coordinate than global density to quantify the progression of the metastable liquid toward the stable vapor phase and the intervening free energy barrier. Contrary to the assumptions of theoretical approaches, we find that the bubble takes on cohesive non-spherical shapes with irregular and (sometimes highly) undulating surfaces. Overall, the resulting free energy barriers and rates agree well between the methods, providing a set of complementary algorithms useful for studies of different types of nucleation events.
Kinetic Monte Carlo Simulation of Oxygen Diffusion in Ytterbium Disilicate
NASA Technical Reports Server (NTRS)
Good, Brian S.
2015-01-01
Ytterbium disilicate is of interest as a potential environmental barrier coating for aerospace applications, notably for use in next generation jet turbine engines. In such applications, the transport of oxygen and water vapor through these coatings to the ceramic substrate is undesirable if high temperature oxidation is to be avoided. In an effort to understand the diffusion process in these materials, we have performed kinetic Monte Carlo simulations of vacancy-mediated and interstitial oxygen diffusion in Ytterbium disilicate. Oxygen vacancy and interstitial site energies, vacancy and interstitial formation energies, and migration barrier energies were computed using Density Functional Theory. We have found that, in the case of vacancy-mediated diffusion, many potential diffusion paths involve large barrier energies, but some paths have barrier energies smaller than one electron volt. However, computed vacancy formation energies suggest that the intrinsic vacancy concentration is small. In the case of interstitial diffusion, migration barrier energies are typically around one electron volt, but the interstitial defect formation energies are positive, with the result that the disilicate is unlikely to exhibit experience significant oxygen permeability except at very high temperature.
Kinetic Monte Carlo Simulation of Oxygen Diffusion in Ytterbium Disilicate
NASA Technical Reports Server (NTRS)
Good, Brian S.
2015-01-01
Silicon-based ceramic components for next-generation jet turbine engines offer potential weight savings, as well as higher operating temperatures, both of which lead to increased efficiency and lower fuel costs. Silicon carbide (SiC), in particular, offers low density, good strength at high temperatures, and good oxidation resistance in dry air. However, reaction of SiC with high-temperature water vapor, as found in the hot section of jet turbine engines in operation, can cause rapid surface recession, which limits the lifetime of such components. Environmental Barrier Coatings (EBCs) are therefore needed if long component lifetime is to be achieved. Rare earth silicates such as Yb2Si2O7 and Yb2SiO5 have been proposed for such applications; in an effort to better understand diffusion in such materials, we have performed kinetic Monte Carlo (kMC) simulations of oxygen diffusion in Ytterbium disilicate, Yb2- Si2O7. The diffusive process is assumed to take place via the thermally activated hopping of oxygen atoms among oxygen vacancy sites or among interstitial sites. Migration barrier energies are computed using density functional theory (DFT).
Hopping electron model with geometrical frustration: kinetic Monte Carlo simulations
NASA Astrophysics Data System (ADS)
Terao, Takamichi
2016-09-01
The hopping electron model on the Kagome lattice was investigated by kinetic Monte Carlo simulations, and the non-equilibrium nature of the system was studied. We have numerically confirmed that aging phenomena are present in the autocorrelation function C ({t,tW )} of the electron system on the Kagome lattice, which is a geometrically frustrated lattice without any disorder. The waiting-time distributions p(τ ) of hopping electrons of the system on Kagome lattice has been also studied. It is confirmed that the profile of p (τ ) obtained at lower temperatures obeys the power-law behavior, which is a characteristic feature of continuous time random walk of electrons. These features were also compared with the characteristics of the Coulomb glass model, used as a model of disordered thin films and doped semiconductors. This work represents an advance in the understanding of the dynamics of geometrically frustrated systems and will serve as a basis for further studies of these physical systems.
NASA Astrophysics Data System (ADS)
Orlić, Ivica; Mekterović, Darko; Mekterović, Igor; Ivošević, Tatjana
2015-11-01
VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster-Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By "running" a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.
Axisymmetric Bernstein modes in a finite-length non-neutral plasma: simulation and kinetic theory
NASA Astrophysics Data System (ADS)
Hart, Grant; Peterson, Bryan G.; Spencer, Ross L.
2016-10-01
We are using a 2-D PIC code to model high-frequency (near the cyclotron frequency) axisymmetric oscillations in a finite-length pure-ion plasma. We previously modeled these modes for infinite-length plasmas, where they are not detectable in the surface charge on the walls because of axisymmetry and lack of z-dependence. This is not true in a finite-length plasma, however, because the eigenfunction of the oscillation has to have nodes a short distance beyond the ends of the plasma. This gives the modes a cos (kz z) or sin (kz z) dependence, with a kz such that an integral number (approximately) of half-wavelengths fit into the plasma. This z-dependence makes the mode detectable in the surface charge on the walls. The modes also have r-dependence. The radial-velocity eigenfunctions of the modes behave as J1 (kr r) . We have simulated the plasma with different kz and kr values and find that increasing kz introduces a small frequency shift, either upward or downward depending on which mode is measured. The damping of the modes also increases as kz or kr increases. We are developing an appropriate kinetic theory of these modes that will include both the finite-Larmour-radius effects and the axial bouncing motion of the particles.
NASA Astrophysics Data System (ADS)
Ren, Guoli; Pei, Wenbing; Lan, Ke; Li, Xin; Hohlraum Physics Team
2014-10-01
In current routine 2D simulation of hohlraum physics, we adopt the principal-quantum-number (n-level) average atom model (AAM) in NLTE plasma description. The more sophisticated atomic kinetics description is better choice, but the in-line calculation consumes much more resource. By distinguishing the much more fast bound-bound atomic processes from the relative slow bound-free atomic processes, we found a method to built up a bound electron distribution (n-level or nl-level) using in-line n-level calculated plasma condition (such as temperature, density, average ionization degree). We name this method ``quasi-steady approximation.'' Using this method and the plasma condition calculated under n-level, we re-build the nl-level bound electron distribution (Pnl), and acquire a new hohlraum radiative drive by post-processing. Comparison with the n-level post-processed hohlraum drive shows that we get an almost identical radiation flux but with more-detailed frequency-dependant structures. Also we use this method in the benchmark gold sphere experiment, the constructed nl-level radiation drive resembles the experimental results and DCA results, while the n-level raditation does not.
Fully Nonlinear Edge Gyrokinetic Simulations of Kinetic Geodesic-Acoustic Modes and Boundary Flows
Xu, X Q; Belli, E; Bodi, K; Candy, J; Chang, C S; Cohen, B I; Cohen, R H; Colella, P; Dimits, A M; Dorr, M R; Gao, Z; Hittinger, J A; Ko, S; Krasheninnikov, S; McKee, G R; Nevins, W M; Rognlien, T D; Snyder, P B; Suh, J; Umansky, M V
2008-09-18
We present edge gyrokinetic neoclassical simulations of tokamak plasmas using the fully nonlinear (full-f) continuum code TEMPEST. A nonlinear Boltzmann model is used for the electrons. The electric field is obtained by solving the 2D gyrokinetic Poisson Equation. We demonstrate the following: (1) High harmonic resonances (n > 2) significantly enhance geodesic-acoustic mode (GAM) damping at high-q (tokamak safety factor), and are necessary to explain both the damping observed in our TEMPEST q-scans and experimental measurements of the scaling of the GAM amplitude with edge q{sub 95} in the absence of obvious evidence that there is a strong q dependence of the turbulent drive and damping of the GAM. (2) The kinetic GAM exists in the edge for steep density and temperature gradients in the form of outgoing waves, its radial scale is set by the ion temperature profile, and ion temperature inhomogeneity is necessary for GAM radial propagation. (3) The development of the neoclassical electric field evolves through different phases of relaxation, including GAMs, their radial propagation, and their long-time collisional decay. (4) Natural consequences of orbits in the pedestal and scrape-off layer region in divertor geometry are substantial non-Maxwellian ion distributions and flow characteristics qualitatively like those observed in experiments.
Zhang, Y; Yang, J; Liu, H; Liu, D
2014-06-01
Purpose: The purpose of this work is to compare the verification results of three solutions (2D/3D ionization chamber arrays measurement and Monte Carlo simulation), the results will help make a clinical decision as how to do our cervical IMRT verification. Methods: Seven cervical cases were planned with Pinnacle 8.0m to meet the clinical acceptance criteria. The plans were recalculated in the Matrixx and Delta4 phantom with the accurate plans parameters. The plans were also recalculated by Monte Carlo using leaf sequences and MUs for individual plans of every patient, Matrixx and Delta4 phantom. All plans of Matrixx and Delta4 phantom were delivered and measured. The dose distribution of iso slice, dose profiles, gamma maps of every beam were used to evaluate the agreement. Dose-volume histograms were also compared. Results: The dose distribution of iso slice and dose profiles from Pinnacle calculation were in agreement with the Monte Carlo simulation, Matrixx and Delta4 measurement. A 95.2%/91.3% gamma pass ratio was obtained between the Matrixx/Delta4 measurement and Pinnacle distributions within 3mm/3% gamma criteria. A 96.4%/95.6% gamma pass ratio was obtained between the Matrixx/Delta4 measurement and Monte Carlo simulation within 2mm/2% gamma criteria, almost 100% gamma pass ratio within 3mm/3% gamma criteria. The DVH plot have slightly differences between Pinnacle and Delta4 measurement as well as Pinnacle and Monte Carlo simulation, but have excellent agreement between Delta4 measurement and Monte Carlo simulation. Conclusion: It was shown that Matrixx/Delta4 and Monte Carlo simulation can be used very efficiently to verify cervical IMRT delivery. In terms of Gamma value the pass ratio of Matrixx was little higher, however, Delta4 showed more problem fields. The primary advantage of Delta4 is the fact it can measure true 3D dosimetry while Monte Carlo can simulate in patients CT images but not in phantom.
NASA Astrophysics Data System (ADS)
Fischer, Jessica; Schoppmann, Kathrin; Knie, Miriam; Laforsch, Christian
2016-06-01
Bioregenerative Life Support Systems (BLSS) are an endeavor to create environments able to maintain human life e.g. on future long-duration space missions like flights to Mars. Based on cyclic biological processes, these systems will be independent from material resupply (such as food, water and oxygen). Due to their central role in limnic ecosystems, herbivorous microcrustaceans could act as key player in aquatic BLSS as they link oxygen liberating, autotrophic producers like algae to higher trophic levels, such as fish. However, before such BLSS can be utilized in space, organisms inhabiting these systems have to be studied thoroughly to disclose the gravitational impact on the biological processes. This is possible in real microgravity, but requires high financial resources, is opportunity-limited or periods of microgravity are very short. Yet, cost-effective and almost permanently accessible tools for gravitational research are ground-based facilities (GBFs), providing simulated microgravity. Among those GBFs is the so called 2D-clinostat. In the present study we demonstrate, that rotation of clinostat tubes does not generate acceleration in form of (predator resembling) small scale turbulence, which can be perceived by Daphnia cucullata. Additionally, embryonal development is not disturbed in subitaneous eggs of Daphnia magna and resting eggs of the ostracod Heterocypris incongruens (besides through restrictions in space within the narrow clinostat tubes), just as subsequent hatching from the respective eggs. Hence, our results indicate that clinorotation is a suitable method to simulate microgravity for microcrustaceans.
NASA Astrophysics Data System (ADS)
Farsi, Mohammad; Ghadimi, Parviz
2014-09-01
Main aim of this paper is to find the best combination of numerical schemes for 2-D SPH simulation of wedge water entry. Diffusion term is considered as laminar, turbulent, and artificial viscosity. Density filter that seriously affects the pressure distribution is investigated by adopting no filter, first order filter, and second order filter. Validation of the results indicates that turbulent model and first order density filter can lead to more reasonable solutions. This simulation was then conducted for wedge water entry with wide range of deadrise angles including 10 degrees, 20 degrees, 30 degrees, 45 degrees, 60 degrees and 81 degrees, with extreme deadrise angles of 10 degrees, 60 degrees and 81 degrees being considered. Comparison of SPH results with BEM solutions has displayed favorable agreement. In two particular cases where experimental data are available, the SPH results are shown to be closer to the experiments than BEM solution. While, accuracy of the obtained results for moderate deadrise angles is desirable, numerical findings for very small or very large deadrise angles are also very reasonable
Zheng, Michael L; Zheng, David C; Wang, Jianping
2010-02-18
Infrared frequency region of 2000-2600 cm(-1) (i.e., ca. 4-5 microm in wavelength) is a well-known open spectral window for peptides and proteins. In this work, six unnatural amino acids (unAAs) were designed to have characteristic absorption bands located in this region. Key chemical groups that served as side chains in these unAAs are C[triple bond]C, Phe-C[triple bond]C, N=C=O, N=C=S, P-H, and Si-H, respectively. Cysteine (a natural AA having S-H in side chain) was also studied for comparison. The anharmonic vibrational properties, including frequencies, anharmonicities, and intermode couplings, were examined using the density functional theory. Broadband linear infrared (IR) and two-dimensional (2D) IR spectra were simulated for each molecule. It is found that all of the side chain modes have significant overtone diagonal anharmonicities. All have moderate transition dipole strengths except the C[triple bond]C and S-H stretching modes, in comparison with the C=O stretching mode. In each case, a collection of 2D IR cross peaks were predicted to appear due to the presence of the side chain groups, whose strengths are closely related to the intramolecular anharmonic interactions, and to the transition dipole strengths of the coupled vibrators. Further, potential energy distribution analysis and high-order anharmonic constant computation showed that these IR probes possess a varying degree of mode localization. The results suggest that these IR probes are potentially useful in complementing the well-studied amide-I mode, to investigate structures and dynamics of peptides and proteins.
NASA Technical Reports Server (NTRS)
Li, Xiaofan; Sui, C.-H.; Lau, K-M.; Adamec, D.
1999-01-01
A two-dimensional coupled ocean-cloud resolving atmosphere model is used to investigate possible roles of convective scale ocean disturbances induced by atmospheric precipitation on ocean mixed-layer heat and salt budgets. The model couples a cloud resolving model with an embedded mixed layer-ocean circulation model. Five experiment are performed under imposed large-scale atmospheric forcing in terms of vertical velocity derived from the TOGA COARE observations during a selected seven-day period. The dominant variability of mixed-layer temperature and salinity are simulated by the coupled model with imposed large-scale forcing. The mixed-layer temperatures in the coupled experiments with 1-D and 2-D ocean models show similar variations when salinity effects are not included. When salinity effects are included, however, differences in the domain-mean mixed-layer salinity and temperature between coupled experiments with 1-D and 2-D ocean models could be as large as 0.3 PSU and 0.4 C respectively. Without fresh water effects, the nocturnal heat loss over ocean surface causes deep mixed layers and weak cooling rates so that the nocturnal mixed-layer temperatures tend to be horizontally-uniform. The fresh water flux, however, causes shallow mixed layers over convective areas while the nocturnal heat loss causes deep mixed layer over convection-free areas so that the mixed-layer temperatures have large horizontal fluctuations. Furthermore, fresh water flux exhibits larger spatial fluctuations than surface heat flux because heavy rainfall occurs over convective areas embedded in broad non-convective or clear areas, whereas diurnal signals over whole model areas yield high spatial correlation of surface heat flux. As a result, mixed-layer salinities contribute more to the density differences than do mixed-layer temperatures.
Coupling Kinetic and Hydrodynamic Models for Simulations of Gas Flows and Weakly Ionized Plasmas
NASA Astrophysics Data System (ADS)
Kolobov, V. I.; Arslanbekov, R. R.
2011-10-01
This paper presents adaptive kinetic/fluid models for simulations of gases and weakly ionized plasmas. We first describe a Unified Flow Solver (UFS), which combines Adaptive Mesh Refinement with automatic selection of kinetic or hydrodynamic models for different parts of flows. This Adaptive Mesh and Algorithm Refinement (AMAR) technique limits expensive atomistic-scale solutions only to the regions where they are needed. We present examples of plasma simulations with fluid models and describe kinetic solvers for electrons which are currently being incorporated into AMAR techniques for plasma simulations.
NASA Astrophysics Data System (ADS)
Winjum, B. J.; Berger, R. L.; Chapman, T.; Banks, J. W.; Brunner, S.; Decyk, V. K.; Mori, W. B.
2013-10-01
We present 2D kinetic simulations, both Vlasov and PIC, of externally-driven, nonlinear electron plasma waves (EPWs) with wavenumber kλD ~ 1 / 3 , and we investigate their link with EPWs that evolve self-consistently in PIC simulations of stimulated Raman scattering (SRS). Simulating externally-driven EPWs is useful for isolating aspects of EPW evolution, while SRS modeling ultimately requires understanding the self-consistent evolution of EPWs with SRS light waves. In the externally-driven EPW simulations, the intrinsically intertwined effects of self-focusing and dissipation of field energy caused by electron trapping are studied. From various initial wave states, the width and field amplitude at focus are shown to be a function of the growth rate of the transverse modulational instability, γtpmi, divided by the loss rate of field energy, νE, to electrons, and we find an amplitude threshold for self-focusing, γtpmi /νE ~ 1 . These results are compared with the EPWs that arise in SRS simulations. Similarities and differences are investigated by varying the external driver and the incident and (seeded) scattered light waves. Performed by LLNL under Contract DE-AC52-07NA27344 and funded under project tracking code 12-ERD-061. Supported also in part under Grants DE-NA0001833 and NSF-Phy-0904039. Simulations performed on UCLA's Hoffman2 and Dawson2 and NERSC's Hopper.
NASA Astrophysics Data System (ADS)
Martelloni, Gianluca; Bagnoli, Franco; Di Cintio, Pierfrancesco
2015-04-01
We integrate existing soil infiltration modeling with particle based methods in order to simulate two and three-dimensional setups of triggered landslides. Commonly, the infiltration models are based on continuum schemes (e.g. Eulerian approach) by means of which it is possible to define the field of the pore pressure within a soil. By contrast, the particle based methods follow a Lagrangian scheme that allows one to identify the particle trajectories and their dynamical properties. In this work, in order to simulate the triggering mechanism, we apply the classical, fractal and fractional Richards equations and the Mohr-Coulomb failure criterion, adapted to the molecular dynamics technique. In our scheme the (local) positive pore pressure is simply implemented as a perturbation of the rest state of each grain. Therefore, the pore pressure function can be interpreted as a time-space dependent scalar field acting on each particle. To initialize the system we generate, using a molecular dynamics based algorithm, a mechanically stable disk (2D) or sphere (3D) packing simulating the consolidated soil. In this way, we can built the micro and macro pore structure related to different infiltration time scales. The inter-particle interactions are modeled with a Lennard-Jones like potential. The particle positions are updated in time, after and during a rainfall, with standard molecular dynamics. We analyze the sensitivity of the model with respect to the variation of some parameters such as hydraulic conductivity, cohesion, slope and friction angle, soil depth and fractional order of the generalized infiltration model. In addition, we consider both regular and random particle configurations. The results of our simulations are found to be in agreement with real landslides. In particular, the mean velocity patterns of the simulated landslides appear extremely similar to the observed ones. Moreover, it is possible to apply the method of the inverse surface displacement
OBJECT KINETIC MONTE CARLO SIMULATIONS OF CASCADE ANNEALING IN TUNGSTEN
Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.; Roche, Kenneth J.; Kurtz, Richard J.; Wirth, Brian D.
2014-03-31
The objective of this work is to study the annealing of primary cascade damage created by primary knock-on atoms (PKAs) of various energies, at various temperatures in bulk tungsten using the object kinetic Monte Carlo (OKMC) method.
Gargett, Maegan Rosenfeld, Anatoly; Oborn, Brad; Metcalfe, Peter
2015-02-15
Purpose: MRI-guided radiation therapy systems (MRIgRT) are being developed to improve online imaging during treatment delivery. At present, the operation of single point dosimeters and an ionization chamber array have been characterized in such systems. This work investigates a novel 2D diode array, named “magic plate,” for both single point calibration and 2D positional performance, the latter being a key element of modern radiotherapy techniques that will be delivered by these systems. Methods: GEANT4 Monte Carlo methods have been employed to study the dose response of a silicon diode array to 6 MV photon beams, in the presence of in-line and perpendicularly aligned uniform magnetic fields. The array consists of 121 silicon diodes (dimensions 1.5 × 1.5 × 0.38 mm{sup 3}) embedded in kapton substrate with 1 cm pitch, spanning a 10 × 10 cm{sup 2} area in total. A geometrically identical, water equivalent volume was simulated concurrently for comparison. The dose response of the silicon diode array was assessed for various photon beam field shapes and sizes, including an IMRT field, at 1 T. The dose response was further investigated at larger magnetic field strengths (1.5 and 3 T) for a 4 × 4 cm{sup 2} photon field size. Results: The magic plate diode array shows excellent correspondence (< ± 1%) to water dose in the in-line orientation, for all beam arrangements and magnetic field strengths investigated. The perpendicular orientation, however, exhibits a dose shift with respect to water at the high-dose-gradient beam edge of jaw-defined fields [maximum (4.3 ± 0.8)% over-response, maximum (1.8 ± 0.8)% under-response on opposing side for 1 T, uncertainty 1σ]. The trend is not evident in areas with in-field dose gradients typical of IMRT dose maps. Conclusions: A novel 121 pixel silicon diode array detector has been characterized by Monte Carlo simulation for its performance inside magnetic fields representative of current prototype and proposed MRI
NASA Astrophysics Data System (ADS)
Prins, Steven L.; Blatchford, James; Olubuyide, Oluwamuyiwa; Riley, Deborah; Chang, Simon; Hong, Qi-Zhong; Kim, T. S.; Borges, Ricardo; Lin, Li
2009-03-01
As design rules and corresponding logic standard cell layouts continue to shrink node-on-node in accordance with Moore's law, complex 2D interactions, both intra-cell and between cells, become much more prominent. For example, in lithography, lack of scaling of λ/NA implies aggressive use of resolution enhancement techniques to meet logic scaling requirements-resulting in adverse effects such as 'forbidden pitches'-and also implies an increasing range of optical influence relative to cell size. These adverse effects are therefore expected to extend well beyond the cell boundary, leading to lithographic marginalities that occur only when a given cell is placed "in context" with other neighboring cells in a variable design environment [1]. This context dependence is greatly exacerbated by increased use of strain engineering techniques such as SiGe and dual-stress liners (DSL) to enhance transistor performance, both of which also have interaction lengths on the order of microns. The use of these techniques also breaks the formerly straightforward connection between lithographic 'shapes' and end-of-line electrical performance, thus making the formulation of design rules that are robust to process variations and complex 2D interactions more difficult. To address these issues, we have developed a first-principles-based simulation flow to study contextdependent electrical effects in layout, arising not only from lithography, but also from stress and interconnect parasitic effects. This flow is novel in that it can be applied to relatively large layout clips- required for context-dependent analysis-without relying on semi-empirical or 'black-box' models for the fundamental electrical effects. The first-principles-based approach is ideal for understanding contextdependent effects early in the design phase, so that they can be mitigated through restrictive design rules. The lithographic simulations have been discussed elsewhere [1] and will not be presented in detail. The
A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition
Zheng Zheming; Stephens, Ryan M.; Braatz, Richard D.; Alkire, Richard C.; Petzold, Linda R.
2008-05-01
A hybrid multiscale kinetic Monte Carlo (HMKMC) method for speeding up the simulation of copper electrodeposition is presented. The fast diffusion events are simulated deterministically with a heterogeneous diffusion model which considers site-blocking effects of additives. Chemical reactions are simulated by an accelerated (tau-leaping) method for discrete stochastic simulation which adaptively selects exact discrete stochastic simulation for the appropriate reaction whenever that is necessary. The HMKMC method is seen to be accurate and highly efficient.
Kinetic study of antibiotic ciprofloxacin ozonation by MWCNT/MnO2 using Monte Carlo simulation.
Jalali, Hamed Moradmand
2016-02-01
Kinetic Monte Carlo simulation was used to investigate kinetics of antibiotic ciprofloxacin degradation by direct and heterogeneous catalytic (MnO2 and carbon nano-tube loaded with MnO2) ozonation. The reaction kinetic mechanisms of each system have been obtained. The rate constant values for the each step of the reaction mechanisms were attained as adjustable parameters by kinetic Monte Carlo simulation. The carbon nano-tube loaded with MnO2 plays important role as catalyst in the ciprofloxacin ozonation by increasing reactivity of ozone and ciprofloxacin drug on the surface of carbon nano-tube. Optimized amount of ozone and catalysts were obtained via studying the effect of inlet ozone concentration and initial amount of catalyst on the rate of ciprofloxacin degradation using Monte Carlo simulation. The simulation results of this study have reasonably agreement with the present experimental data for the ozonation of ciprofloxacin drug.
Icarus: A 2D direct simulation Monte Carlo (DSMC) code for parallel computers. User`s manual - V.3.0
Bartel, T.; Plimpton, S.; Johannes, J.; Payne, J.
1996-10-01
Icarus is a 2D Direct Simulation Monte Carlo (DSMC) code which has been optimized for the parallel computing environment. The code is based on the DSMC method of Bird and models from free-molecular to continuum flowfields in either cartesian (x, y) or axisymmetric (z, r) coordinates. Computational particles, representing a given number of molecules or atoms, are tracked as they have collisions with other particles or surfaces. Multiple species, internal energy modes (rotation and vibration), chemistry, and ion transport are modelled. A new trace species methodology for collisions and chemistry is used to obtain statistics for small species concentrations. Gas phase chemistry is modelled using steric factors derived from Arrhenius reaction rates. Surface chemistry is modelled with surface reaction probabilities. The electron number density is either a fixed external generated field or determined using a local charge neutrality assumption. Ion chemistry is modelled with electron impact chemistry rates and charge exchange reactions. Coulomb collision cross-sections are used instead of Variable Hard Sphere values for ion-ion interactions. The electrostatic fields can either be externally input or internally generated using a Langmuir-Tonks model. The Icarus software package includes the grid generation, parallel processor decomposition, postprocessing, and restart software. The commercial graphics package, Tecplot, is used for graphics display. The majority of the software packages are written in standard Fortran.
NASA Astrophysics Data System (ADS)
Zhao, Yi; Fu, Ceji
2016-10-01
Tailoring the spectrum of thermal emission from the emitter is important for improving the performance of a thermophotovoltaic (TPV) system. In this work, a two-dimensional (2D) layered grating structure made of SiO2 and tungsten (W), which can realize wavelength-selective control of thermal emission, was proposed for a potential emitter in TPV applications. Numerical simulations of the spectral emissivity of the structure from the ultraviolet (UV) to the mid-infrared region reveals that the spectral-normal emissivity of the structure is enhanced to above 0.95 in the wavelength region from 0.55 μm to 1.9 μm for both TE and TM waves, but drops sharply at wavelength larger than 2 μm. Physical mechanisms responsible for the wavelength-selective emissivity were elucidated as due to resonance of magnetic polaritons (MPs) in the SiO2 spacer and in the grooves of the tungsten grating, Wood's anomaly (WA), excitation of surface plasmon polaritons (SPPs) and wave interference. Furthermore, the structure was found to exhibit quasi-diffuse and polarization-insensitive features of thermal emission, suggesting that the proposed structure can serve as the emitter in the design of high performance TPV systems.
NASA Astrophysics Data System (ADS)
Babbick, M.; Dijkstra, C.; Larkin, O. J.; Anthony, P.; Davey, M. R.; Power, J. B.; Lowe, K. C.; Cogoli-Greuter, M.; Hampp, R.
Gravity is an important environmental factor that controls plant growth and development. Studies have shown that the perception of gravity is not only a property of specialized cells, but can also be performed by undifferentiated cultured cells. In this investigation, callus of Arabidopsis thaliana cv. Columbia was used to investigate the initial steps of gravity-related signalling cascades, through altered expression of transcription factors (TFs). TFs are families of small proteins that regulate gene expression by binding to specific promoter sequences. Based on microarray studies, members of the gene families WRKY, MADS-box, MYB, and AP2/EREBP were selected for investigation, as well as members of signalling chains, namely IAA 19 and phosphoinositol-4-kinase. Using qRT-PCR, transcripts were quantified within a period of 30 min in response to hypergravity (8 g), clinorotation [2-D clinostat and 3-D random positioning machine (RPM)] and magnetic levitation (ML). The data indicated that (1) changes in gravity induced stress-related signalling, and (2) exposure in the RPM induced changes in gene expression which resemble those of magnetic levitation. Two dimensional clinorotation resulted in responses similar to those caused by hypergravity. It is suggested that RPM and ML are preferable to simulate microgravity than clinorotation.
NASA Astrophysics Data System (ADS)
Tirupathi, S.; Schiemenz, A. R.; Liang, Y.; Parmentier, E.; Hesthaven, J.
2013-12-01
The style and mode of melt migration in the mantle are important to the interpretation of basalts erupted on the surface. Both grain-scale diffuse porous flow and channelized melt migration have been proposed. To better understand the mechanisms and consequences of melt migration in a heterogeneous mantle, we have undertaken a numerical study of reactive dissolution in an upwelling and viscously deformable mantle where solubility of pyroxene increases upwards. Our setup is similar to that described in [1], except we use a larger domain size in 2D and 3D and a new numerical method. To enable efficient simulations in 3D through parallel computing, we developed a high-order accurate numerical method for the magma dynamics problem using discontinuous Galerkin methods and constructed the problem using the numerical library deal.II [2]. Linear stability analyses of the reactive dissolution problem reveal three dynamically distinct regimes [3] and the simulations reported in this study were run in the stable regime and the unstable wave regime where small perturbations in porosity grows periodically. The wave regime is more relevant to melt migration beneath the mid-ocean ridges but computationally more challenging. Extending the 2D simulations in the stable regime in [1] to 3D using various combinations of sustained perturbations in porosity at the base of the upwelling column (which may result from a viened mantle), we show the geometry and distribution of dunite channel and high-porosity melt channels are highly correlated with inflow perturbation through superposition. Strong nonlinear interactions among compaction, dissolution, and upwelling give rise to porosity waves and high-porosity melt channels in the wave regime. These compaction-dissolution waves have well organized but time-dependent structures in the lower part of the simulation domain. High-porosity melt channels nucleate along nodal lines of the porosity waves, growing downwards. The wavelength scales
NASA Astrophysics Data System (ADS)
Le, Ari; Daughton, William; Chen, Li-Jen; Egedal, Jan
2016-10-01
We present a 3D kinetic simulation of asymmetric reconnection with plasma parameters matching the MMS magetopause diffusion region crossing reported by Burch et al. (Science 2016). The simulation was performed with the code VPIC on LANL's Trinity machine, which enabled relatively high grid resolution and numerical particle numbers to resolve the electron diffusion region dynamics. The simulation not only reproduces the reported crescent distributions but also appears to account for new features observed by MMS in other diffusion region events with weak guide fields. Compared to a 2D simulation with the same plasma parameters, drift turbulence in the 3D simulation substantially enhances the mixing and parallel heating of electrons on the magnetosphere side. This modifies the reconnection rate inferred from a recently introduced electron mixing diagnostic. To the magnetosphere side of the in-plane magnetic null, the parallel electric field exhibits a bipolar structure with polarities opposite to the large-scale parallel electric field. The 3D structure of the X line and the particle signature of the inverted bipolar parallel electric field have been observed by MMS.
NASA Astrophysics Data System (ADS)
López-Venegas, Alberto M.; Horrillo, Juan; Pampell-Manis, Alyssa; Huérfano, Victor; Mercado, Aurelio
2015-06-01
The most recent tsunami observed along the coast of the island of Puerto Rico occurred on October 11, 1918, after a magnitude 7.2 earthquake in the Mona Passage. The earthquake was responsible for initiating a tsunami that mostly affected the northwestern coast of the island. Runup values from a post-tsunami survey indicated the waves reached up to 6 m. A controversy regarding the source of the tsunami has resulted in several numerical simulations involving either fault rupture or a submarine landslide as the most probable cause of the tsunami. Here we follow up on previous simulations of the tsunami from a submarine landslide source off the western coast of Puerto Rico as initiated by the earthquake. Improvements on our previous study include: (1) higher-resolution bathymetry; (2) a 3D-2D coupled numerical model specifically developed for the tsunami; (3) use of the non-hydrostatic numerical model NEOWAVE (non-hydrostatic evolution of ocean WAVE) featuring two-way nesting capabilities; and (4) comprehensive energy analysis to determine the time of full tsunami wave development. The three-dimensional Navier-Stokes model tsunami solution using the Navier-Stokes algorithm with multiple interfaces for two fluids (water and landslide) was used to determine the initial wave characteristic generated by the submarine landslide. Use of NEOWAVE enabled us to solve for coastal inundation, wave propagation, and detailed runup. Our results were in agreement with previous work in which a submarine landslide is favored as the most probable source of the tsunami, and improvement in the resolution of the bathymetry yielded inundation of the coastal areas that compare well with values from a post-tsunami survey. Our unique energy analysis indicates that most of the wave energy is isolated in the wave generation region, particularly at depths near the landslide, and once the initial wave propagates from the generation region its energy begins to stabilize.
Kolkoori, Sanjeevareddy; Chitti Venkata, Krishnamurthy; Balasubramaniam, Krishnan
2015-01-01
This article presents an analytical approach for simulation of ultrasonic diffracted wave signals from cracks in two-dimensional geometries based on a novel Huygens-Fresnel Diffraction Model (HFDM). The model employs the frequency domain far-field displacement expressions derived by Miller and Pursey in 2D for a line source located on the free surface boundary of a semi-infinite elastic medium. At each frequency in the bandwidth of a pulsed excitation, the complex diffracted field is obtained by summation of displacements due to the unblocked virtual sources located in the section containing a vertical crack. The time-domain diffracted wave signal amplitudes in a general isotropic solid are obtained by standard Fast Fourier Transform (FFT) procedures. The wedge based finite aperture transducer refracted beam profiles were modelled by treating the finite dimension transducer as an array of line sources. The proposed model is able to evaluate back-wall signal amplitude and lateral wave signal amplitude, quantitatively. The model predicted range-dependent diffracted amplitudes from the edge of a bottom surface-breaking crack in the isotropic steel specimen were compared with Geometrical Theory of Diffraction (GTD) results. The good agreement confirms the validity of the HFDM method. The simulated ultrasonic time-of-flight diffraction (TOFD) A-scan signals for surface-breaking crack lengths 2 mm and 4 mm in a 10 mm thick aluminium specimen were compared quantitatively with the experimental results. Finally, important applications of HFDM method to the ultrasonic quantitative non-destructive evaluation are discussed.
NASA Astrophysics Data System (ADS)
Franci, Luca; Landi, Simone; Matteini, Lorenzo; Verdini, Andrea; Hellinger, Petr
2016-12-01
We investigate properties of the ion-scale spectral break of solar wind turbulence by means of two-dimensional high-resolution hybrid particle-in-cell simulations. We impose an initial ambient magnetic field perpendicular to the simulation box and add a spectrum of in-plane, large-scale, magnetic and kinetic fluctuations. We perform a set of simulations with different values of the plasma β, distributed over three orders of magnitude, from 0.01 to 10. In all cases, once turbulence is fully developed, we observe a power-law spectrum of the fluctuating magnetic field on large scales (in the inertial range) with a spectral index close to -5/3, while in the sub-ion range we observe another power-law spectrum with a spectral index systematically varying with β (from around -3.6 for small values to around -2.9 for large ones). The two ranges are separated by a spectral break around ion scales. The length scale at which this transition occurs is found to be proportional to the ion inertial length, d i , for β ≪ 1 and to the ion gyroradius, {ρ }i={d}i\\sqrt{β }, for β ≫ 1, i.e., to the larger between the two scales in both the extreme regimes. For intermediate cases, i.e., β ˜ 1, a combination of the two scales is involved. We infer an empiric relation for the dependency of the spectral break on β that provides a good fit over the whole range of values. We compare our results with in situ observations in the solar wind and suggest possible explanations for such a behavior.
Towards adaptive kinetic-fluid simulations of low-temperature plasmas
NASA Astrophysics Data System (ADS)
Kolobov, Vladimir
2013-09-01
The emergence of new types of gaseous electronics in multi-phase systems calls for computational tools with adaptive kinetic-fluid simulation capabilities. We will present an Adaptive Mesh and Algorithm Refinement (AMAR) methodology for multi-scale simulations of gas flows and discuss current efforts towards extending this methodology for weakly ionized plasmas. The AMAR method combines Adaptive Mesh Refinement (AMR) with automatic selection of kinetic or fluid solvers in different parts of computational domains. This AMAR methodology was implemented in our Unified Flow Solver (UFS) for mixed rarefied and continuum flows. UFS uses discrete velocity method for solving Boltzmann kinetic equation under rarefied flow conditions coupled to fluid (Navier-Stokes) solvers for continuum flow regimes. The main challenge of extending AMAR to plasmas comes from the distinction of electron and atom mass. We will present multi-fluid, two-temperature plasma models with AMR capabilities for simulations of glow, corona, and streamer discharges. We will briefly discuss specifics of electron kinetics in collisional plasmas, and deterministic methods of solving kinetic equations for different electron groups. Kinetic solvers with Adaptive Mesh in Phase Space (AMPS) will be introduced to solve Boltzmann equation for electrons in the presence of electric fields, elastic and inelastic collisions with atoms. These kinetic and fluid models are currently being incorporated into AMAR methodology for multi-scale simulations of low-temperature plasmas in multi-phase systems. Supported by AFOSR, NASA, and DoE
NASA Astrophysics Data System (ADS)
Kwan, Thomas; Le, Ari; Schmitt, Mark; Herrmann, Hans; Batha, Steve
2015-11-01
We have carried out simulations of direct-drive capsule implosion experiments conducted on Omega laser facility at the Laboratory of Laser energetics of the University of Rochester. The capsules had a glass shell (SiO2) with D, T, He-3 fills at various proportions. One-dimensional radiation hydrodynamic calculations and kinetic particle/hybrid simulations with LSP were carried out for the post-shot analysis to compare neutron yield, yield ratio, and shell convergence in assessing the effects of plasma kinetic effects. The LSP simulations were initiated with the output from the rad-hydro simulations at the end of the laser-drive. The electrons are treated as a fluid while all the ion species by the kinetic PIC technique. Our LSP simulations clearly showed species separation between the deuterons, tritons and He-3 during the implosion but significantly less after the compression. The neutron yield, gamma bang-time and -width from the LSP simulations compared favorably with experiments. Detail comparison among the kinetic simulations, rad-hydro simulations, and experimental results will be presented. Work performed under the auspices of the US Department of Energy by Los Alamos National Laboratory under Contract No. W-7405-ENG-36.
NASA Astrophysics Data System (ADS)
Karimabadi, Homa
2012-03-01
Recent advances in simulation technology and hardware are enabling breakthrough science where many longstanding problems can now be addressed for the first time. In this talk, we focus on kinetic simulations of the Earth's magnetosphere and magnetic reconnection process which is the key mechanism that breaks the protective shield of the Earth's dipole field, allowing the solar wind to enter the Earth's magnetosphere. This leads to the so-called space weather where storms on the Sun can affect space-borne and ground-based technological systems on Earth. The talk will consist of three parts: (a) overview of a new multi-scale simulation technique where each computational grid is updated based on its own unique timestep, (b) Presentation of a new approach to data analysis that we refer to as Physics Mining which entails combining data mining and computer vision algorithms with scientific visualization to extract physics from the resulting massive data sets. (c) Presentation of several recent discoveries in studies of space plasmas including the role of vortex formation and resulting turbulence in magnetized plasmas.
NASA Astrophysics Data System (ADS)
Mitsui, Y.; Hirahara, K.
2006-12-01
There have been a lot of studies that simulate large earthquakes occurring quasi-periodically at a subduction zone, based on the laboratory-derived rate-and-state friction law [eg. Kato and Hirasawa (1997), Hirose and Hirahara (2002)]. All of them assume that pore fluid pressure in the fault zone is constant. However, in the fault zone, pore fluid pressure changes suddenly, due to coseismic pore dilatation [Marone (1990)] and thermal pressurization [Mase and Smith (1987)]. If pore fluid pressure drops and effective normal stress rises, fault slip is decelerated. Inversely, if pore fluid pressure rises and effective normal stress drops, fault slip is accelerated. The effect of pore fluid may cause slow slip events and low-frequency tremor [Kodaira et al. (2004), Shelly et al. (2006)]. For a simple spring model, how pore dilatation affects slip instability was investigated [Segall and Rice (1995), Sleep (1995)]. When the rate of the slip becomes high, pore dilatation occurs and pore pressure drops, and the rate of the slip is restrained. Then the inflow of pore fluid recovers the pore pressure. We execute 2D earthquake cycle simulations at a subduction zone, taking into account such changes of pore fluid pressure following Segall and Rice (1995), in addition to the numerical scheme in Kato and Hirasawa (1997). We do not adopt hydrostatic pore pressure but excess pore pressure for initial condition, because upflow of dehydrated water seems to exist at a subduction zone. In our model, pore fluid is confined to the fault damage zone and flows along the plate interface. The smaller the flow rate is, the later pore pressure recovers. Since effective normal stress keeps larger, the fault slip is decelerated and stress drop becomes smaller. Therefore the smaller flow rate along the fault zone leads to the shorter earthquake recurrence time. Thus, not only the frictional parameters and the subduction rate but also the fault zone permeability affects the recurrence time of
NASA Astrophysics Data System (ADS)
Savoini, P.; Lembege, B.
2013-12-01
The ion foreshock located upstream of the Earth's bow shock is populated with ions reflected back by the shock front with an high energy gain. In-situ spacecraft measurements have clearly established the existence of two distinct populations in the foreshock upstream of quasi-perpendicular shock region (i.e. for 45° ≤ ΘBn≤ 90°, where ΘBn is the angle between the shock normal and the upstream magnetostatic field): (i) field-aligned (';FAB') ion beams characterized by a gyrotropic distribution, and (ii) gyro-phase bunched (';GPB') ions characterized by a NON gyrotropic distribution, which exhibits a non-vanishing perpendicular bulk velocity. The purpose of the present work is to identify the possible sources of the different backstreaming ions and is based on the use of 2D PIC simulations of a curved shock, where full curvature effects, time of flight effects and both electrons and ions dynamics are fully described by a self consistent approach. Our analysis evidences that the two populations mentionned above may have different origins identified both in terms of interaction time and distance of penetration within the shock front. In particular, ours simulations evidence that "GPB" and ';FAB' populations are characterized by a short (Δinter= 1 to 2 tci) and much larger (Δinter= 1 to 10 tci) interaction time respectively, where τci is the ion upstream gyroperiod. In addition, a deeper statistical analysis of ion trajectories evidences that: (i) both populations can be discriminated in terms of injection angle into the shock front (i.e. defined between the local normal to the shock front and the gyration velocity vector at the time ions reach the front). Such a behavior explains how reflected ions can be splitted in the observed two populations "FAB" and "GPB". (ii) ion trajectories strongly differ between the "FAB" and "GPB" populations at the shock front. In particular, ';FAB' ions suffer multi-bounces whereas ';GPB '; ions make only one bounce. Such
NASA Technical Reports Server (NTRS)
Zimmerman, M. I.; Farrell, W. M.; Poppe, A. R.
2014-01-01
We present results from a new grid-free 2D plasma simulation code applied to a small, unmagnetized body immersed in the streaming solar wind plasma. The body was purposely modeled as an irregular shape in order to examine photoemission and solar wind plasma flow in high detail on the dayside, night-side, terminator and surface-depressed 'pocket' regions. Our objective is to examine the overall morphology of the various plasma interaction regions that form around a small body like a small near-Earth asteroid (NEA). We find that the object obstructs the solar wind flow and creates a trailing wake region downstream, which involves the interplay between surface charging and ambipolar plasma expansion. Photoemission is modeled as a steady outflow of electrons from illuminated portions of the surface, and under direct illumination the surface forms a non-monotonic or ''double-sheath'' electric potential upstream of the body, which is important for understanding trajectories and equilibria of lofted dust grains in the presence of a complex asteroid geometry. The largest electric fields are found at the terminators, where ambipolar plasma expansion in the body-sized night-side wake merges seamlessly with the thin photoelectric sheath on the dayside. The pocket regions are found to be especially complex, with nearby sunlit regions of positive potential electrically connected to unlit negative potentials and forming adjacent natural electric dipoles. For objects near the surface, we find electrical dissipation times (through collection of local environmental solar wind currents) that vary over at least 5 orders of magnitude: from 39 Micro(s) inside the near-surface photoelectron cloud under direct sunlight to less than 1 s inside the particle-depleted night-side wake and shadowed pocket regions
Becker, Kathrin; Stauber, Martin; Schwarz, Frank; Beißbarth, Tim
2015-09-01
We propose a novel 3D-2D registration approach for micro-computed tomography (μCT) and histology (HI), constructed for dental implant biopsies, that finds the position and normal vector of the oblique slice from μCT that corresponds to HI. During image pre-processing, the implants and the bone tissue are segmented using a combination of thresholding, morphological filters and component labeling. After this, chamfer matching is employed to register the implant edges and fine registration of the bone tissues is achieved using simulated annealing. The method was tested on n=10 biopsies, obtained at 20 weeks after non-submerged healing in the canine mandible. The specimens were scanned with μCT 100 and processed for hard tissue sectioning. After registration, we assessed the agreement of bone to implant contact (BIC) using automated and manual measurements. Statistical analysis was conducted to test the agreement of the BIC measurements in the registered samples. Registration was successful for all specimens and agreement of the respective binary images was high (median: 0.90, 1.-3. Qu.: 0.89-0.91). Direct comparison of BIC yielded that automated (median 0.82, 1.-3. Qu.: 0.75-0.85) and manual (median 0.61, 1.-3. Qu.: 0.52-0.67) measures from μCT were significant positively correlated with HI (median 0.65, 1.-3. Qu.: 0.59-0.72) between μCT and HI groups (manual: R(2)=0.87, automated: R(2)=0.75, p<0.001). The results show that this method yields promising results and that μCT may become a valid alternative to assess osseointegration in three dimensions.
Phase-field simulations of coherent precipitate morphologies and coarsening kinetics
NASA Astrophysics Data System (ADS)
Vaithyanathan, Venugopalan
2002-09-01
The primary aim of this research is to enhance the fundamental understanding of coherent precipitation reactions in advanced metallic alloys. The emphasis is on a particular class of precipitation reactions which result in ordered intermetallic precipitates embedded in a disordered matrix. These precipitation reactions underlie the development of high-temperature Ni-base superalloys and ultra-light aluminum alloys. Phase-field approach, which has emerged as the method of choice for modeling microstructure evolution, is employed for this research with the focus on factors that control the precipitate morphologies and coarsening kinetics, such as precipitate volume fractions and lattice mismatch between precipitates and matrix. Two types of alloy systems are considered. The first involves L1 2 ordered precipitates in a disordered cubic matrix, in an attempt to model the gamma' precipitates in Ni-base superalloys and delta' precipitates in Al-Li alloys. The effect of volume fraction on coarsening kinetics of gamma' precipitates was investigated using two-dimensional (2D) computer simulations. With increase in volume fraction, larger fractions of precipitates were found to have smaller aspect ratios in the late stages of coarsening, and the precipitate size distributions became wider and more positively skewed. The most interesting result was associated with the effect of volume fraction on the coarsening rate constant. Coarsening rate constant as a function of volume fraction extracted from the cubic growth law of average half-edge length was found to exhibit three distinct regimes: anomalous behavior or decreasing rate constant with volume fraction at small volume fractions ( ≲ 20%), volume fraction independent or constant behavior for intermediate volume fractions (˜20--50%), and the normal behavior or increasing rate constant with volume fraction for large volume fractions ( ≳ 50%). The second alloy system considered was Al-Cu with the focus on understanding
Collisionless Spectral Kinetic Simulation of Ideal Multipole Resonance Probe
NASA Astrophysics Data System (ADS)
Gong, Junbo; Wilczek, Sebastian; Szeremley, Daniel; Oberrath, Jens; Eremin, Denis; Dobrygin, Wladislaw; Schilling, Christian; Friedrichs, Michael; Brinkmann, Ralf Peter
2016-09-01
Active Plasma Resonance Spectroscopy denotes a class of industry-compatible plasma diagnostic methods which utilize the natural ability of plasmas to resonate on or near the electron plasma frequency ωpe. One particular realization of APRS with a high degree of geometric and electric symmetry is the Multipole Resonance Probe (MRP). The Ideal MRP(IMRP) is an even more symmetric idealization which is suited for theoretical investigations. In this work, a spectral kinetic scheme is presented to investigate the behavior of the IMRP in the low pressure regime. However, due to the velocity difference, electrons are treated as particles whereas ions are only considered as stationary background. In the scheme, the particle pusher integrates the equations of motion for the studied particles, the Poisson solver determines the electric field at each particle position. The proposed method overcomes the limitation of the cold plasma model and covers kinetic effects like collisionless damping.
NASA Astrophysics Data System (ADS)
Ghizzo, A.; Bertrand, P.; Lebas, J.; Shoucri, M.; Johnston, T.; Fijalkow, E.; Feix, M. R.
1992-10-01
The present 1 1/2D relativistic Euler-Vlasov code has been used to check the validity of a hydrodynamic description used in a 1D version of the Vlasov code. By these means, detailed numerical results can be compared; good agreement furnishes full support for the 1D electromagnetic Vlasov code, which runs faster than the 1 1/2D code. The results obtained assume a nonrelativistic v(y) velocity.
NASA Astrophysics Data System (ADS)
Shi, Feng
This dissertation is organized in two parts, the first part is about fundamental characteristics of multiple dimensional systems, the second part is about parallel KMC calculation of coarsening process. In Part I, we first study the fundamental characteristics of nucleation and growth in 3 dimensional (3D) systems using a simplified model of nucleation and growth. One of the main goals of this work is to compare with previous work on 2D nucleation and growth in order to understand the effects of dimensionality. The scaling of the average island-size, island density, monomer density, island-size distribution (ISD), capture number distribution (CND), and capture zone distribution (CZD) are studied as a function of the fraction of occupied sites (coverage) and the ratio D/F of the monomer hopping rate D to the (per site) monomer creation rate F. Our model may be viewed as a simple model of the early-stages of vacancy cluster nucleation and growth under irradiation. Good agreement is found between our mean-field (MF) rate-equation results for the average island and monomer densities and our simulation results. In addition, we find that due to the decreased influence of correlations and fluctuations in 3D as compared to 2D, the scaled CND depends only weakly on the island-size. As a result the scaled ISD is significantly sharper than obtained in 2D and diverges with increasing D/F. However, the scaled ISD obtained in kinetic Monte Carlo (KMC) simulations appears to diverge more slowly with increasing D/F than the MF prediction while the divergence occurs at a value of the scaled island-size which is somewhat beyond the MF prediction. These results are supported by an analysis of the asymptotic CND. The final goal for understanding the mechanism of nucleation and growth is to develop a theory to concisely and precisely disclose the law underlying the nucleation and growth process. From the theoretical point view, dimension can be taken as a variable to develop theory. In
GPU-based flow simulation with detailed chemical kinetics
NASA Astrophysics Data System (ADS)
Le, Hai P.; Cambier, Jean-Luc; Cole, Lord K.
2013-03-01
The current paper reports on the implementation of a numerical solver on the Graphic Processing Units (GPUs) to model reactive gas mixtures with detailed chemical kinetics. The solver incorporates high-order finite volume methods for solving the fluid dynamical equations coupled with stiff source terms. The chemical kinetics are solved implicitly via an operator-splitting method. We explored different approaches in implementing a fast kinetics solver on the GPU. The detail of the implementation is discussed in the paper. The solver is tested with two high-order shock capturing schemes: MP5 (Suresh and Huynh, 1997) [9] and ADERWENO (Titarev and Toro, 2005) [10]. Considering only the fluid dynamics calculation, the speed-up factors obtained are 30 for the MP5 scheme and 55 for ADERWENO scheme. For the fully-coupled solver, the performance gain depended on the size of the reaction mechanism. Two different examples of chemistry were explored. The first mechanism consisted of 9 species and 38 reactions, resulting in a speed-up factor up to 35. The second, larger mechanism, consisted of 36 species and 308 reactions, resulting in a speed-up factor of up to 40.
NASA Astrophysics Data System (ADS)
Martynenko, Oleg; Ward, William E.; Shepherd, Gordon; Cho, Young-Min; Namgaladze, Alexander; Fomichev, Victor; McConnell, John; Semeniuk, Kirill; Beagley, Stephen
A newly developed Canadian Ionosphere and Atmosphere Model (C-IAM) is introduced. It is being developed on the basis of two existing first principle models: the extended Canadian Middle Atmosphere Model (CMAM) and the ionospheric part of the Upper Atmosphere Model (UAM). The model extends from the surface to the inner magnetosphere and hence, is able to describe in a self-consistent way how lower atmosphere dynamical variability propagates into and affects the upper atmosphere and ionosphere. The C-IAM was applied to model the spatial structure of two different ionospheric emissions: the nighttime 135.6 nm O ( (5) S - (3) P) and daytime 732 nm O (+) ( (2) P - (2) D) emissions. The IMAGE satellite observations showed a wave number 4 (WN4) longitudinal structure in the 135.6 nm ionospheric emission emanating from the equatorial ionization anomaly at 350-400 km near 20:00 local time at each longitude. C-IAM simulations are in a good agreement with the observations. Model result analysis reveals that the main mechanism for generating the WN4 structure in the 135.6 nm emission is a modification of the ionospheric dynamo field caused by longitudinal variation of the zonal wind due to waves penetrating from the lower atmosphere. It was also shown, that during geomagnetic storms and substorms the high-latitudinal electric field fully suppresses the dynamo, so that the emission intensity dramatically decreases and the WN4 structure does not appear. The 732 nm emission simulated with the C-IAM also reveals the WN4 structure. Similar to the 135.6 nm emission, this structure is caused by waves penetrating from the lower atmosphere. However, the mechanism of excitation is quite different. The 732 nm emission is produced by the instant local ionization and excitation, and, hence, its variation is caused by the neutral density variability in the F2 region (above 200 km) without any involvement of the electric field effects. Correspondingly, latitudinal distribution of this
NASA Astrophysics Data System (ADS)
Savoini, Philippe; Lembege, Bertrand
The ion foreshock located upstream of the Earth's bow shock is populated with ions reflected back by the shock front with an high energy gain. In-situ spacecraft measurements have clearly established the existence of two distinct populations in the foreshock upstream of the quasi-perpendicular shock region (i.e. for 45(o) ≤ Theta_{Bn} ≤ 90(o) , where Theta_{Bn} is the angle between the shock normal and the upstream magnetostatic field): (i) field-aligned ion beams (or ‘FAB’) characterized by a gyrotropic distribution, and (ii) gyro-phase bunched ions (or ‘GPB’) characterized by a NON gyrotropic distribution and with a non-vanishing perpendicular bulk velocity. The use of 2D PIC simulations of a curved shock, where full curvature effects and time of flight effects are fully described, has evidenced that the shock front itself can be the possible source of the different backstreaming ions. Our analysis evidences that both populations can be discriminated in terms of interaction time (Δinter) and distance of penetration within the shock front, in particular that "GPB" and ‘FAB’ populations are characterized by a short (Delta_{inter}= 1 to 2 tau_{ci}) and much larger (Delta_{inter}= 1 to 10 tau_{ci}) interaction time respectively, where tau_{ci} is the ion upstream gyroperiod. This discrimination allows a deeper statistical analysis which evidences that: (i) backstreaming ions are splitted into both "FAB" and "GPB populations" depending on their injection angle when hitting the shock front (i.e. defined between the local normal to the shock front and the gyration velocity vector at the time ions hit the front). (ii) As a consequence, ion trajectories strongly differ between the "FAB" and "GPB" populations at the shock front. In particular, "FAB" ions suffer multi-bounces along the curved front whereas "GPB" ions make only one bounce. Such differences can explain why the "FAB" population loses their gyro-phase coherency and become gyrotropic which is
NASA Astrophysics Data System (ADS)
Savoini, Philippe; Lembege, Bertrand
2014-05-01
The ion foreshock located upstream of the Earth's bow shock is populated with ions reflected back by the shock front with an high energy gain. In-situ spacecraft measurements have clearly established the existence of two distinct populations in the foreshock upstream of the quasi-perpendicular shock region (i.e. for 45° ≤ ΘBn ≤ 90° , where ΘBnis the angle between the shock normal and the upstream magnetostatic field): (i) field-aligned ion beams (or ' FAB ') characterized by a gyrotropic distribution, and (ii) gyro-phase bunched ions (or ' GPB ') characterized by a NON gyrotropic distribution, which exhibits a non-vanishing perpendicular bulk velocity. The use of 2D PIC simulations of a curved shock, where full curvature effects, time of flight effects and both electrons and ions dynamics are fully described, has evidenced that the shock front itself can be the possible source of the different backstreaming ions. Our analysis evidences the importance of the interaction time (Δinter) with the shock front, in particular ' GPB ' and ' FAB ' populations are characterized by a short (Δinter= 1 to 2 τci) and much larger (Δinter= 1 to 10 τci) interaction time respectively, where τci is the ion upstream gyroperiod. This discrimination allows a deeper statistical analysis: (i) backstreaming ions are splitted into both ' FAB ' and ' GPB ' populations depending on their injection angle when hitting the shock front (i.e. defined between the local normal to the shock front and the gyration velocity vector at the time ions hit the front). (ii) As a consequence, ion trajectories strongly differ between the ' FAB ' and ' GPB ' populations at the shock front. In particular, ' FAB ' ions suffer multi-bounces along the curved front whereas ' GPB ' ions make only one bounce. Such differences can explain why the ' FAB ' population loses their gyro-phase coherency and become gyrotropic which is not the case for the ' GPB '. As also evidenced by these simulations, the
NASA Astrophysics Data System (ADS)
Sengupta, M.; Ganesh, R.
2016-10-01
This paper is a simulation based investigation of the effect of elastic collisions and effectively elastic-like excitation collisions between electrons and background neutrals on the dynamics of a cylindrically trapped electron cloud that also has an ion contaminant mixed in it. A cross section of the trapped non neutral cloud composed of electrons mixed uniformly with a fractional population of ions is loaded on a 2D PIC grid with the plasma in a state of unstable equilibrium due to differential rotation between the electron and the ion component. The electrons are also loaded with an axial velocity component, vz, that mimics their bouncing motion between the electrostatic end plugs of a Penning-Malmberg trap. This vz loading facilitates 3D elastic and excitation collisions of the electrons with background neutrals under a MCC scheme. In the present set of numerical experiments, the electrons do not ionize the neutrals. This helps in separating out only the effect of non-ionizing collisions of electrons on the dynamics of the cloud. Simulations reveal that these non-ionizing collisions indirectly influence the ensuing collisionless ion resonance instability of the contaminated electron cloud by a feedback process. The collisional relaxation reduces the average density of the electron cloud and thereby increases the fractional density of the ions mixed in it. The dynamically changing electron density and fractional density of ions feed back on the ongoing ion-resonance (two-stream) instability between the two components of the nonneutral cloud and produce deviations in the paths of progression of the instability that are uncorrelated at different background gas pressures. Effects of the collisions on the instability are evident from alteration in the growth rate and energetics of the instability caused by the presence of background neutrals as compared to a vacuum background. Further in order to understand if the non-ionizing collisions can independently be a cause
Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.; Roche, Kenneth J.; Kurtz, Richard J.; Wirth, Brian D.
2014-06-30
The objective of the work is to implement a first-passage time (FPT) approach to deal with very fast 1D diffusing SIA clusters in KSOME (kinetic simulations of microstructural evolution) [1] to achieve longer time-scales during irradiation damage simulations. The goal is to develop FPT-KSOME, which has the same flexibility as KSOME.
Simulation study of overtaking of ion-acoustic solitons in the fully kinetic regime
NASA Astrophysics Data System (ADS)
Hosseini Jenab, S. M.; Spanier, F.
2017-03-01
The overtaking collisions of ion-acoustic solitons in the presence of trapping effects of electrons are studied based on a fully kinetic simulation approach. The method is able to provide all the kinetic details of the process alongside the fluid-level quantities self consistently. Solitons are produced naturally by utilizing the chain formation phenomenon, and then are arranged in a new simulation box to test the different scenarios of overtaking collisions. Three achievements are reported here. First, simulations prove the long-time life span of the ion-acoustic solitons in the presence of trapping effect of electrons (kinetic effects), which serves as the benchmark of the simulation code. Second, their stability against overtaking mutual collisions is established by creating collisions between solitons with different number and shapes of trapped electrons, i.e., different trapping parameter. Finally, details of solitons during collisions for both ions and electrons are provided on both fluid and kinetic levels. These results show that on the kinetic level, trapped electron population accompanying each of the solitons are exchanged between the solitons during the collision. Furthermore, the behavior of electron holes accompanying solitons contradicts the theory about the electron holes interaction developed based on kinetic theory. They also show behaviors much different from other electron holes witnessed in processes such as nonlinear Landau damping (Bernstein-Greene-Kruskal -BGK- modes) or beam-plasma interaction (like two-beam instability).
Theory and simulation of discrete kinetic beta induced Alfvén eigenmode in tokamak plasmas
NASA Astrophysics Data System (ADS)
Wang, X.; Zonca, F.; Chen, L.
2010-11-01
It is shown, both analytically and by numerical simulations, that, in the presence of thermal ion kinetic effects, the beta induced Alfvén eigenmode (BAE)-shear Alfvén wave continuous spectrum can be discretized into radially trapped eigenstates known as kinetic BAE (KBAE). While thermal ion compressibility gives rise to finite BAE accumulation point frequency, the discretization occurs via the finite Larmor radius and finite orbit width effects. Simulations and analytical theories agree both qualitatively and quantitatively. Simulations also demonstrate that KBAE can be readily excited by the finite radial gradients of energetic particles.
Moaty Sayed, A A; Hussein, M A; Becker, T
2010-04-01
Lattice Boltzmann models (LBM) are rapidly showing their ability to simulate a lot of fluid dynamics problems that previously required very complex approaches. This study presents a LBM for simulating diffusion-advection transport of substrate in a 2-D laminar flow. The model considers the substrate influx into a set of active cells placed inside the flow field. A new innovative method was used to simulate the cells activity using the LBM by means of Michaelis-Menten kinetics. The model is validated with some numerical benchmark problems and proved highly accurate results. After validation the model was used to simulate the transport of oxygen substrates that diffuse in water to feed a set of active cartilage cells inside a new designed bioreactor.
Particle kinetic simulation of high altitude hypervelocity flight
NASA Technical Reports Server (NTRS)
Boyd, Iain; Haas, Brian L.
1994-01-01
Rarefied flows about hypersonic vehicles entering the upper atmosphere or through nozzles expanding into a near vacuum may only be simulated accurately with a direct simulation Monte Carlo (DSMC) method. Under this grant, researchers enhanced the models employed in the DSMC method and performed simulations in support of existing NASA projects or missions. DSMC models were developed and validated for simulating rotational, vibrational, and chemical relaxation in high-temperature flows, including effects of quantized anharmonic oscillators and temperature-dependent relaxation rates. State-of-the-art advancements were made in simulating coupled vibration - dissociation - recombination for post-shock flows. Models were also developed to compute vehicle surface temperatures directly in the code rather than requiring isothermal estimates. These codes were instrumental in simulating aerobraking of NASA's Magellan spacecraft during orbital maneuvers to assess heat transfer and aerodynamic properties of the delicate satellite. NASA also depended upon simulations of entry of the Galileo probe into the atmosphere of Jupiter to provide drag and flow field information essential for accurate interpretation of an onboard experiment. Finally, the codes have been used extensively to simulate expanding nozzle flows in low-power thrusters in support of propulsion activities at NASA-Lewis. Detailed comparisons between continuum calculations and DSMC results helped to quantify the limitations of continuum CFD codes in rarefied applications.
Particle kinetic simulation of high altitude hypervelocity flight
NASA Technical Reports Server (NTRS)
Boyd, Iain; Haas, Brian L.
1994-01-01
Rarefied flows about hypersonic vehicles entering the upper atmosphere or through nozzles expanding into a near vacuum may only be simulated accurately with a direct simulation Monte Carlo (DSMC) method. Under this grant, researchers enhanced the models employed in the DSMC method and performed simulations in support of existing NASA projects or missions. DSMC models were developed and validated for simulating rotational, vibrational, and chemical relaxation in high-temperature flows, including effects of quantized anharmonic oscillators and temperature-dependent relaxation rates. State-of-the-art advancements were made in simulating coupled vibration-dissociation recombination for post-shock flows. Models were also developed to compute vehicle surface temperatures directly in the code rather than requiring isothermal estimates. These codes were instrumental in simulating aerobraking of NASA's Magellan spacecraft during orbital maneuvers to assess heat transfer and aerodynamic properties of the delicate satellite. NASA also depended upon simulations of entry of the Galileo probe into the atmosphere of Jupiter to provide drag and flow field information essential for accurate interpretation of an onboard experiment. Finally, the codes have been used extensively to simulate expanding nozzle flows in low-power thrusters in support of propulsion activities at NASA-Lewis. Detailed comparisons between continuum calculations and DSMC results helped to quantify the limitations of continuum CFD codes in rarefied applications.
NASA Astrophysics Data System (ADS)
Castro, Maria Clara; Patriarche, Delphine; Goblet, Patrick
2005-09-01
Because helium and heat production results from a common source, a continental 4He crustal flux of 4.65 * 10 - 14 mol m - 2 s - 1 has been estimated based on heat flow considerations. In addition, because the observed mantle He / heat flux ratio at the proximity of mid-ocean ridges (6.6 * 10 - 14 mol J - 1 ) is significantly lower than the radiogenic production ratio (1.5 * 10 - 12 mol J - 1 ), the presence of a terrestrial helium-heat imbalance was suggested. The latter could be explained by the presence of a layered mantle in which removal of He is impeded from the lower mantle [R.K. O'Nions, E.R. Oxburgh, Heat and helium in the Earth, Nature 306 (1983) 429-431; E.R. Oxburgh, R.K. O'Nions, Helium loss, tectonics, and the terrestrial heat budget, Science 237 (1987) 1583-1588]. van Keken et al. [P.E. van Keken, C.J. Ballentine, D. Porcelli, A dynamical investigation of the heat and helium imbalance, Earth Planet, Sci. Lett. 188 (2001) 421-434] have recently claimed that the helium-heat imbalance remains a robust observation. Such conclusions, however, were reached under the assumption that a steady-state regime was in place for both tracers and that their transport properties are similar at least in the upper portion of the crust. Here, through 2-D simulations of groundwater flow, heat transfer and 4He transport carried out simultaneously in the Carrizo aquifer and surrounding formations in southwest Texas, we assess the legitimacy of earlier assumptions. Specifically, we show that the driving transport mechanisms for He and heat are of a fundamentally different nature for a high range of permeabilities ( k ≤ 10 - 16 m 2) found in metamorphic and volcanic rocks at all depths in the crust. The assumption that transport properties for these two tracers are similar in the crust is thus unsound. We also show that total 4He / heat flux ratios lower than radiogenic production ratios do not reflect a He deficit in the crust or mantle original reservoir. Instead, they
Cellulose pyrolysis kinetics in a simulated solar environment
Tobatabaie-Raissi, A. ); Mok, W.S.- L; Antal, M.J., Jr. . Dept. of Mechanical Engineering)
1989-06-01
The instrumentation and methods required to study rapid, radiative decomposition of highly reactive biopolymers are described and used to determine the kinetic parameters for the pyrolysis of Avicel PH105 microcrystalline cellulose. Experiments were carried out at heating rates greater than 2K/s in a specially fabricated thermogravimetric analyzer system which employed a 30-kW{sub e}/2-kW/th downward-facing beam, arc-image furnace as a heat source. The thermogravimetric data were interpreted assuming a simple, single-step reaction mechanism and using a nonlinear least-squares kinetic analysis. Based on the results, and apparent activation energy of 100.5 {plus minus} 3kJ/mol, a preexonential factor of in (A (s{sup 1})) = 14 {plus minus} 0.5, and nearly a first-order (n = 0.9 {plus minus} 0.05) reaction were obtained. The extent of char formation was determined experimentally and found to be in the range 6.6-8.4% by weight of original dry material depending upon the prevailing reaction conditions.
Modeling and simulation of cement hydration kinetics and microstructure development
Thomas, Jeffrey J.; Biernacki, Joseph J.; Bullard, Jeffrey W.; Bishnoi, Shashank; Dolado, Jorge S.; Scherer, George W.; Luttge, Andreas
2011-12-15
Efforts to model and simulate the highly complex cement hydration process over the past 40 years are reviewed, covering different modeling approaches such as single particle models, mathematical nucleation and growth models, and vector and lattice-based approaches to simulating microstructure development. Particular attention is given to promising developments that have taken place in the past few years. Recent applications of molecular-scale simulation methods to understanding the structure and formation of calcium-silicate-hydrate phases, and to understanding the process of dissolution of cement minerals in water are also discussed, as these topics are highly relevant to the future development of more complete and fundamental hydration models.
NASA Astrophysics Data System (ADS)
Savoini, P.; Lembege, B.
2014-12-01
The ion foreshock located upstream of the Earth's bow shock is populated with ions reflected back by the shock front. In-situ spacecraft measurements have clearly established the existence of two distinct populations in the upstream of the quasi-perpendicular shock region (i.e. for 45o ≤ ΘBn≤ 90o, where ΘBn is the angle between the shock normal and the upstream magnetostatic field): (i) field-aligned ion beams (or 'FAB') characterized by a gyrotropic distribution, and (ii) gyro-phase bunched ions (or 'GPB') characterized by a NON gyrotropic distribution, which exhibits a non-vanishing perpendicular bulk velocity. The use of 2D PIC simulations where full curvature effects, time of flight effects and both electrons and ions dynamics are fully described, has evidenced that the shock front itself can be the possible source of these two characteristic populations. A recent analysis has evidenced that both populations can be discriminated in terms of interaction time (Δtinter) with the shock front. 'GPB' and 'FAB' populations are characterized by a short (Δtinter ~ 1 τci) and much larger (Δtinter ≥ 2 τci) interaction time respectively, where τci is the ion upstream gyroperiod. In addition, present statistical results evidence that: (i) backstreaming ions are splitted into 'FAB' and 'GPB' populations depending on their injection angle when hitting the shock front (defined between the local normal to the shock front and the gyration velocity vector). (ii) As a consequence, ion trajectories strongly differ between the 'FAB' and 'GPB' populations at the shock front. In particular, 'FAB' ions suffer multi-bounces along the curved front whereas 'GPB' ions make only one bounce. Such differences may explain why the 'FAB' population loses their gyro-phase coherency and become gyrotropic which is not the case for the 'GPB'. Then, the differences observed between 'FAB' and 'GPB' populations do not involve some distinct reflection processes as often claimed in the
A CAI System for Simulation of Enzymes Kinetics.
ERIC Educational Resources Information Center
Amorim, G. G.; Leao, F. S.; Martins, M. R.; Santos, J. D.; Novaes, M. A.; Filho, J. L. Lima
1999-01-01
Describes a computer software program that simulates each step of the glycolytic enzyme pathway. Serves as a means of providing interactive learning for undergraduate biochemistry students with the aim of better preparing them for laboratory work. (Author/CCM)
KINETIC ENERGY FROM SUPERNOVA FEEDBACK IN HIGH-RESOLUTION GALAXY SIMULATIONS
Simpson, Christine M.; Bryan, Greg L.; Ostriker, Jeremiah P.; Hummels, Cameron
2015-08-10
We describe a new method for adding a prescribed amount of kinetic energy to simulated gas modeled on a cartesian grid by directly altering grid cells’ mass and velocity in a distributed fashion. The method is explored in the context of supernova (SN) feedback in high-resolution (∼10 pc) hydrodynamic simulations of galaxy formation. Resolution dependence is a primary consideration in our application of the method, and simulations of isolated explosions (performed at different resolutions) motivate a resolution-dependent scaling for the injected fraction of kinetic energy that we apply in cosmological simulations of a 10{sup 9} M{sub ⊙} dwarf halo. We find that in high-density media (≳50 cm{sup −3}) with coarse resolution (≳4 pc per cell), results are sensitive to the initial kinetic energy fraction due to early and rapid cooling. In our galaxy simulations, the deposition of small amounts of SN energy in kinetic form (as little as 1%) has a dramatic impact on the evolution of the system, resulting in an order-of-magnitude suppression of stellar mass. The overall behavior of the galaxy in the two highest resolution simulations we perform appears to converge. We discuss the resulting distribution of stellar metallicities, an observable sensitive to galactic wind properties, and find that while the new method demonstrates increased agreement with observed systems, significant discrepancies remain, likely due to simplistic assumptions that neglect contributions from SNe Ia and stellar winds.
Kinetic Energy from Supernova Feedback in High-resolution Galaxy Simulations
NASA Astrophysics Data System (ADS)
Simpson, Christine M.; Bryan, Greg L.; Hummels, Cameron; Ostriker, Jeremiah P.
2015-08-01
We describe a new method for adding a prescribed amount of kinetic energy to simulated gas modeled on a cartesian grid by directly altering grid cells’ mass and velocity in a distributed fashion. The method is explored in the context of supernova (SN) feedback in high-resolution (˜10 pc) hydrodynamic simulations of galaxy formation. Resolution dependence is a primary consideration in our application of the method, and simulations of isolated explosions (performed at different resolutions) motivate a resolution-dependent scaling for the injected fraction of kinetic energy that we apply in cosmological simulations of a 109 M⊙ dwarf halo. We find that in high-density media (≳50 cm-3) with coarse resolution (≳4 pc per cell), results are sensitive to the initial kinetic energy fraction due to early and rapid cooling. In our galaxy simulations, the deposition of small amounts of SN energy in kinetic form (as little as 1%) has a dramatic impact on the evolution of the system, resulting in an order-of-magnitude suppression of stellar mass. The overall behavior of the galaxy in the two highest resolution simulations we perform appears to converge. We discuss the resulting distribution of stellar metallicities, an observable sensitive to galactic wind properties, and find that while the new method demonstrates increased agreement with observed systems, significant discrepancies remain, likely due to simplistic assumptions that neglect contributions from SNe Ia and stellar winds.
Adiabatic molecular-dynamics-simulation-method studies of kinetic friction
NASA Astrophysics Data System (ADS)
Zhang, J.; Sokoloff, J. B.
2005-06-01
An adiabatic molecular-dynamics method is developed and used to study the Muser-Robbins model for dry friction (i.e., nonzero kinetic friction in the slow sliding speed limit). In this model, dry friction between two crystalline surfaces rotated with respect to each other is due to mobile molecules (i.e., dirt particles) adsorbed at the interface. Our adiabatic method allows us to quickly locate interface potential-well minima, which become unstable during sliding of the surfaces. Since dissipation due to friction in the slow sliding speed limit results from mobile molecules dropping out of such unstable wells, our method provides a way to calculate dry friction, which agrees extremely well with results found by conventional molecular dynamics for the same system, but our method is more than a factor of 10 faster.
Advances in petascale kinetic plasma simulation with VPIC and Roadrunner
Bowers, Kevin J; Albright, Brian J; Yin, Lin; Daughton, William S; Roytershteyn, Vadim; Kwan, Thomas J T
2009-01-01
VPIC, a first-principles 3d electromagnetic charge-conserving relativistic kinetic particle-in-cell (PIC) code, was recently adapted to run on Los Alamos's Roadrunner, the first supercomputer to break a petaflop (10{sup 15} floating point operations per second) in the TOP500 supercomputer performance rankings. They give a brief overview of the modeling capabilities and optimization techniques used in VPIC and the computational characteristics of petascale supercomputers like Roadrunner. They then discuss three applications enabled by VPIC's unprecedented performance on Roadrunner: modeling laser plasma interaction in upcoming inertial confinement fusion experiments at the National Ignition Facility (NIF), modeling short pulse laser GeV ion acceleration and modeling reconnection in magnetic confinement fusion experiments.
Electron Energization in Reconnection Outflows with Kinetic Riemann Simulations
NASA Astrophysics Data System (ADS)
Zhang, Q.; Drake, J. F.; Swisdak, M.
2015-12-01
How electrons are heated during magnetic reconnection in the corona has been a basic puzzle for a long time. Here we carry out PIC Riemann simulations to explore electron energization including its dependence on parameters. One-dimensional Riemann simulations, with its simple magnetic geometry, facilitate the study of the reconnection outflow far downstream of x-line in much more detail than is possible with conventional reconnection simulations. We examine the behavior of the electron temperature in this configuration. We find that the electron temperature in the exhaust increases and approaches a constant. Since the heating is independent of the x-line in the Riemann model, these results suggest that electron heating in the exhausts can extend to macroscopic scales in the corona. In runs with guide field, such heating only weakly depends on the proton-to-electron mass ratio used in the simulation. The scaling of the electron temperature increment with the available magnetic energy is discussed and comparisons with conventional reconnection simulations are made.
Kinetic nucleation model for free expanding water condensation plume simulations.
Li, Zheng; Zhong, Jiaqiang; Levin, Deborah A; Garrison, Barbara J
2009-05-07
Recent direct simulation Monte Carlo (DSMC) simulations of homogeneous condensation in free expansion water plumes [Z. Li, J. Zhong, D. A. Levin, and B. Garrison, AIAA J. 47, 1241 (2009)] show that the nucleation rate is a key factor for accurately modeling condensation phenomenon. In this work, we use molecular dynamics (MD) simulations of a free expansion to explore the microscopic mechanisms of water dimer formation and develop collision models required by DSMC. Bimolecular and termolecular dimer cluster formation mechanisms are considered and the former is found to be the main mechanism in expanding flows to vacuum. MD simulations between two water molecules using the simple point charge intermolecular potential were performed to predict the bimolecular dimer formation probability and the probability was found to decrease with collision energy. The formation probabilities and postcollisional velocity and energy distributions were then integrated into DSMC simulations of a free expansion of an orifice condensation plume with different chamber stagnation temperatures and pressures. The dimer mole fraction was found to increase with distance from the orifice and become constant after a distance of about two orifice diameters. Similar to experiment, the terminal dimer mole fraction was found to decrease with chamber stagnation temperatures and increase linearly with chamber stagnation pressures which is consistent with a bimolecular nucleation mechanism.
NASA Technical Reports Server (NTRS)
Dum, C. T.
1990-01-01
Particle simulation experiments were used to analyze the electron beam-plasma instability. It is shown that there is a transition from the reactive state of the electron beam-plasma instability to the kinetic instability of Langmuir waves. Quantitative tests, which include an evaluation of the dispersion relation for the evolving non-Maxwellian beam distribution, show that a quasi-linear theory describes the onset of this transition and applies again fully to the kinetic stage. This stage is practically identical to the late stage seen in simulations of plasma waves in the electron foreshock described by Dum (1990).
One-dimensional hybrid-direct kinetic simulation of the discharge plasma in a Hall thruster
Hara, Kentaro; Boyd, Iain D.; Kolobov, Vladimir I.
2012-11-15
In order to model the non-equilibrium plasma within the discharge region of a Hall thruster, the velocity distribution functions (VDFs) must be obtained accurately. A direct kinetic (DK) simulation method that directly solves the plasma Boltzmann equation can achieve better resolution of VDFs in comparison to particle simulations, such as the particle-in-cell (PIC) method that inherently include statistical noise. In this paper, a one-dimensional hybrid-DK simulation, which uses a DK simulation for heavy species and a fluid model for electrons, is developed and compared to a hybrid-PIC simulation. Time-averaged results obtained from the hybrid-DK simulation are in good agreement with hybrid-PIC results and experimental data. It is shown from a comparison of using a kinetic simulation and solving the continuity equation that modeling of the neutral atoms plays an important role for simulations of the Hall thruster discharge plasma. In addition, low and high frequency plasma oscillations are observed. Although the kinetic nature of electrons is not resolved due to the use of a fluid model, the hybrid-DK model provides spatially and temporally well-resolved plasma properties and an improved resolution of VDFs for heavy species with less statistical noise in comparison to the hybrid-PIC method.
DBP FORMATION KINETICS IN A SIMULATED DISTRIBUTION SYSTEM
Little is known about how the growth of halogenated disinfection by-products (DBPs) in drinking water is affected by time spent in a distribution system. Experiments were performed to compare the rate of trihalomethane and haloacetic acid production in a simulated pipe environmen...
Saving a Drug Poisoning Victim: A Kinetics Simulation
NASA Astrophysics Data System (ADS)
Selco, Jodye I.; Beery, Janet
2002-05-01
In this project, students, posing as hospital emergency room physicians, must save the life of a child who has accidentally overdosed on the asthma medication, theophylline. The progress of the drug through the child's body can be modeled as a chemical kinetics problem involving first-order consecutive reactions. Students begin by setting up a system of linear first-order differential equations describing the medication's absorption into and elimination from the child's bloodstream using half-lives obtained from the Physician's Desk Reference. By using a computer to solve the differential equations numerically, students discover that the child will almost certainly die if they, as physicians, do not intervene. The students then determine by how much they need to increase the drug's elimination rate in order to save the child. This dictates the appropriate medical action. Students discover that they need to use the more drastic treatment of extracorporeal filtering of the blood through charcoal, rather than simply administering oral doses of charcoal. We've found that this project appeals to a broad range of students; many students are interested in careers in the health professions and all are intrigued by the child's grave situation.
Thermodynamic-kinetic simulation of constrained dendrite growth in steels
Miettinen, J.
2000-04-01
A model of constrained dendritic growth for steels, based on thermodynamic and kinetic theory, is presented. The model links thermodynamic chemical potential-equality equations to an existing, approximate treatment of constrained dendritic growth in multicomponent steels, taking into account the deviation from the local thermodynamic equilibrium of the phase interface caused by interface friction, capillarity, and solute trapping. Due to the thermodynamic approach, with a thermodynamic model and recently assessed data, the present treatment yields a more accurate determination of phase stabilities than the earlier methods. Depending on the steel composition and the growth conditions (growth rate and temperature gradient), the model determines the dendrite tip undercooling, the primary solid phase (ferrite or austenite), the stability of that phase, certain dimensions of the microstructure, and the solute accumulation ahead of the dendrite tip. A special optional calculations is that of the equally probable formation of ferrite and austenite in stainless steels. Calculations for testing the model and for validation it with experimental data are presented.
Scramjet Combustor Simulations Using Reduced Chemical Kinetics for Practical Fuels
2003-12-01
Stochastic Simulation of an HCCI Engine Using an Automatically Reduced Mechanism,� ICE, Vol. 37-2, 2001 Fall Technical Conference...Christopher J. Montgomery, and Wei Zhao Reaction Engineering International (REI) 77 West 200 South, Suite 210 Salt Lake City, UT 84101 Dean R...DOUGLAS L. DAVIS CAPT. BRIAN C. MCDONALD AFRL/PRAS, Project Engineer Branch Chief Propulsion Sciences Branch Propulsion
Improved Kinetic Models for High-Speed Combustion Simulation
2008-06-01
118 83. Results (Not Completely Converged ) for the VULCAN Simulation of the RC-18 Scramjet...Data in the C1 – C3 Submechanism Part of this Report CO + O2, HO2, OH adducts cis and trans rotamers of HOC•O and HOOC•O (vide infra ) Unimolecular...relaxation methods and multigrid convergence acceleration techniques are available. A dual time-stepping methodology is used for time-accurate
NASA Astrophysics Data System (ADS)
Lotsch, Bettina V.
2015-07-01
Graphene's legacy has become an integral part of today's condensed matter science and has equipped a whole generation of scientists with an armory of concepts and techniques that open up new perspectives for the postgraphene area. In particular, the judicious combination of 2D building blocks into vertical heterostructures has recently been identified as a promising route to rationally engineer complex multilayer systems and artificial solids with intriguing properties. The present review highlights recent developments in the rapidly emerging field of 2D nanoarchitectonics from a materials chemistry perspective, with a focus on the types of heterostructures available, their assembly strategies, and their emerging properties. This overview is intended to bridge the gap between two major—yet largely disjunct—developments in 2D heterostructures, which are firmly rooted in solid-state chemistry or physics. Although the underlying types of heterostructures differ with respect to their dimensions, layer alignment, and interfacial quality, there is common ground, and future synergies between the various assembly strategies are to be expected.
Makwana, K. D.; Zhdankin, V.; Li, H.; ...
2015-04-10
We performed simulations of decaying magnetohydrodynamic (MHD) turbulence with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k-1.3⊥k⊥-1.3. The kinetic code shows a spectral slope of k-1.5⊥k⊥-1.5 for smallermore » simulation domain, and k-1.3⊥k⊥-1.3 for larger domain. We then estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. Finally, this work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.« less
Makwana, K. D.; Zhdankin, V.; Li, H.; Daughton, W.; Cattaneo, F.
2015-04-10
We performed simulations of decaying magnetohydrodynamic (MHD) turbulence with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfvén waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k-1.3⊥k⊥-1.3. The kinetic code shows a spectral slope of k-1.5⊥k⊥-1.5 for smaller simulation domain, and k-1.3⊥k⊥-1.3 for larger domain. We then estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the driving scale of the turbulence. In the fluid code, their thickness is determined by the grid resolution as there is no explicit diffusivity. In the kinetic code, their thickness is very close to the skin-depth, irrespective of the grid resolution. Finally, this work shows that kinetic codes can reproduce the MHD inertial range dynamics at large scales, while at the same time capturing important kinetic physics at small scales.
Chara, Osvaldo; Grigera, José Raúl; McCarthy, Andrés N
2007-12-01
The usefulness of computational methods such as molecular dynamics simulation has been extensively established for studying systems in equilibrium. Nevertheless, its application to complex non-equilibrium biological processes such as protein unfolding has been generally regarded as producing results which cannot be interpreted straightforwardly. In the present study, we present results for the kinetics of unfolding of apomyoglobin, based on the analysis of long simulation runs of this protein in solution at 3 kbar (1 atm = 1.01325, bar = 101,325 Pa). We hereby demonstrate that the analysis of the data collected within a simulated time span of 0.18 mus suffices for producing results, which coincide remarkably with the available unfolding kinetics experimental data. This not only validates molecular dynamics simulation as a valuable alternative for studying non-equilibrium processes, but also enables a detailed analysis of the actual structural mechanism which underlies the unfolding process of proteins under elusive denaturing conditions such as high pressure.
Kinetic Monte Carlo simulations of boron activation in implanted Si under laser thermal annealing
NASA Astrophysics Data System (ADS)
Fisicaro, Giuseppe; Pelaz, Lourdes; Aboy, Maria; Lopez, Pedro; Italia, Markus; Huet, Karim; Cristiano, Filadelfo; Essa, Zahi; Yang, Qui; Bedel-Pereira, Elena; Quillec, Maurice; La Magna, Antonino
2014-02-01
We investigate the correlation between dopant activation and damage evolution in boron-implanted silicon under excimer laser irradiation. The dopant activation efficiency in the solid phase was measured under a wide range of irradiation conditions and simulated using coupled phase-field and kinetic Monte Carlo models. With the inclusion of dopant atoms, the presented code extends the capabilities of a previous version, allowing its definitive validation by means of detailed comparisons with experimental data. The stochastic method predicts the post-implant kinetics of the defect-dopant system in the far-from-equilibrium conditions caused by laser irradiation. The simulations explain the dopant activation dynamics and demonstrate that the competitive dopant-defect kinetics during the first laser annealing treatment dominates the activation phenomenon, stabilizing the system against additional laser irradiation steps.
Guo, Zhifang; Hong, Minghua; Du, Aimin; Lin, Yu; Wang, Xueyi; Wu, Mingyu; Lu, Quanming
2015-02-15
In this paper, effects of a fast flow in the tail plasma sheet on the generation of kinetic Alfven waves (KAWs) in the high-latitude of the near-Earth magnetotail are investigated by performing a two-dimensional (2-D) global-scale hybrid simulation, where the plasma flow is initialized by the E×B drift near the equatorial plane due to the existence of the dawn-dusk convection electric field. It is found that firstly, the plasma sheet becomes thinned and the dipolarization of magnetic field appears around (x,z)=(−10.5R{sub E},0.3R{sub E}), where R{sub E} is the radius of the Earth. Then, shear Alfven waves are excited in the plasma sheet, and the strong earthward flow is braked by the dipole-like magnetic field. These waves propagate along the magnetic field lines toward the polar regions later. Subsequently, KAWs with k{sub ⊥}≫k{sub ∥} are generated in the high-latitude magnetotail due to the existence of the non-uniformity of the magnetic field and density in the polar regions. The ratio of the electric field to the magnetic field in these waves is found to obey the relation (δE{sub z})/(δB{sub y} )∼ω/k{sub ∥} of KAWs. Our simulation provides a mechanism for the generation of the observed low-frequency shear Alfven waves in the plasma sheet and kinetic Alfven waves in the high-latitude near-Earth magnetotail, whose source is suggested to be the flow braking in the low-latitude plasma sheet.
Particle kinetic simulation of high altitude hypervelocity flight
NASA Technical Reports Server (NTRS)
Haas, Brian L.
1993-01-01
In this grant period, the focus has been on enhancement and application of the direct simulation Monte Carlo (DSMC) particle method for computing hypersonic flows of re-entry vehicles. Enhancement efforts dealt with modeling gas-gas interactions for thermal non-equilibrium relaxation processes and gas-surface interactions for prediction of vehicle surface temperatures. Both are important for application to problems of engineering interest. The code was employed in a parametric study to improve future applications, and in simulations of aeropass maneuvers in support of the Magellan mission. Detailed comparisons between continuum models for internal energy relaxation and DSMC models reveals that several discrepancies exist. These include definitions of relaxation parameters and the methodologies for implementing them in DSMC codes. These issues were clarified and all differences were rectified in a paper (Appendix A) submitted to Physics of Fluids A, featuring several key figures in the DSMC community as co-authors and B. Haas as first author. This material will be presented at the Fluid Dynamics meeting of the American Physical Society on November 21, 1993. The aerodynamics of space vehicles in highly rarefied flows are very sensitive to the vehicle surface temperatures. Rather than require prescribed temperature estimates for spacecraft as is typically done in DSMC methods, a new technique was developed which couples the dynamic surface heat transfer characteristics into the DSMC flow simulation code to compute surface temperatures directly. This model, when applied to thin planar bodies such as solar panels, was described in AIAA Paper No. 93-2765 (Appendix B) and was presented at the Thermophysics Conference in July 1993. The paper has been submitted to the Journal of Thermophysics and Heat Transfer. Application of the DSMC method to problems of practical interest requires a trade off between solution accuracy and computational expense and limitations. A
Interactive Computer Simulation and Animation for Improving Student Learning of Particle Kinetics
ERIC Educational Resources Information Center
Fang, N.; Guo, Y.
2016-01-01
Computer simulation and animation (CSA) has been receiving growing attention and wide application in engineering education in recent years. A new interactive CSA module was developed in the present study to improve student learning of particle kinetics in an undergraduate engineering dynamics course. The unique feature of this CSA module is that…
Comparisons of dense-plasma-focus kinetic simulations with experimental measurements
Schmidt, A.; Link, A.; Welch, D.; Ellsworth, J.; Falabella, S.; Tang, V.
2014-06-01
Dense-plasma-focus (DPF) Z-pinch devices are sources of copious high-energy electrons and ions, x rays, and neutrons. The mechanisms through which these physically simple devices generate such high-energy beams in a relatively short distance are not fully understood and past optimization efforts of these devices have been largely empirical. Previously we reported on fully kinetic simulations of a DPF and compared them with hybrid and fluid simulations of the same device. Here we present detailed comparisons between fully kinetic simulations and experimental data on a 1.2 kJ DPF with two electrode geometries, including neutron yield and ion beam energy distributions. A more intensive third calculation is presented which examines the effects of a fully detailed pulsed power driver model. We also compare simulated electromagnetic fluctuations with direct measurement of radiofrequency electromagnetic fluctuations in a DPF plasma. These comparisons indicate that the fully kinetic model captures the essential physics of these plasmas with high fidelity, and provide further evidence that anomalous resistivity in the plasma arises due to a kinetic instability near the lower hybrid frequency.
A Simulation Game for the Study of Enzyme Kinetics and Inhibition.
ERIC Educational Resources Information Center
Chayoth, Reuben; Cohen, Annette
1996-01-01
Presents a simulation game that facilitates understanding of the concepts of enzyme kinetics and inhibition. The first part of the game deals with the relationship between enzyme activity and substrate concentration while the second part deals with characterization of competitive and noncompetitive inhibition of enzyme activity. (JRH)
ERIC Educational Resources Information Center
Stern, Luli; Barnea, Nitza; Shauli, Sofia
2008-01-01
The objective of this study was to evaluate the effect of a dynamic software simulation on the understanding of the kinetic molecular theory by 7th graders. Students in the control group (n = 62) studied a curricular unit that addressed the differences in arrangement and motion of molecules in the three phases of matter. The experimental group (n…
A Hands-On Classroom Simulation to Demonstrate Concepts in Enzyme Kinetics
ERIC Educational Resources Information Center
Junker, Matthew
2010-01-01
A classroom exercise is described to introduce enzyme kinetics in an undergraduate biochemistry or chemistry course. The exercise is a simulation in which a student acts as an enzyme that "catalyzes" the unscrewing of a nut from a bolt. With other students assisting, the student enzyme carries out reactions with bolt-nut substrates under different…
ENZVU--An Enzyme Kinetics Computer Simulation Based upon a Conceptual Model of Enzyme Action.
ERIC Educational Resources Information Center
Graham, Ian
1985-01-01
Discusses a simulation on enzyme kinetics based upon the ability of computers to generate random numbers. The program includes: (1) enzyme catalysis in a restricted two-dimensional grid; (2) visual representation of catalysis; and (3) storage and manipulation of data. Suggested applications and conclusions are also discussed. (DH)
Study of kinetic effects arising in simulations of Farley-Buneman instability
Kovalev, D. V.; Smirnov, A. P.; Dimant, Ya. S.
2009-05-15
The Farley-Buneman instability, which has been observed in the E region of the Earth's ionosphere, is studied using fluid equations for electrons, a four-dimensional (in coordinate-velocity space) kinetic equation for ions, and Poisson's equation. Numerical simulations with allowance for Landau damping show that the Farley-Buneman instability results in anisotropy of the ion velocity distribution function.
NASA Technical Reports Server (NTRS)
Card, J. M.; Chen, J. H.; Day, M.; Mahalingam, S.
1994-01-01
Turbulent non-premixed stoichiometric methane-air flames modeled with reduced kinetics have been studied using the direct numerical simulation approach. The simulations include realistic chemical kinetics, and the molecular transport is modeled with constant Lewis numbers for individual species. The effect of turbulence on the internal flame structure and extinction characteristics of methane-air flames is evaluated. Consistent with earlier DNS with simple one-step chemistry, the flame is wrinkled and in some regions extinguished by the turbulence, while the turbulence is weakened in the vicinity of the flame due to a combination of dilatation and an increase in kinematic viscosity. Unlike previous results, reignition is observed in the present simulations. Lewis number effects are important in determining the local stoichiometry of the flame. The results presented in this work are preliminary but demonstrate the feasibility of incorporating reduced kinetics for the oxidation of methane with direct numerical simulations of homogeneous turbulence to evaluate the limitations of various levels of reduction in the kinetics and to address the formation of thermal and prompt NO(x).
Calibration of Chemical Kinetic Models Using Simulations of Small-Scale Cookoff Experiments
Wemhoff, A P; Becker, R C; Burnham, A K
2008-02-26
Establishing safe handling limits for explosives in elevated temperature environments is a difficult problem that often requires extensive simulation. The largest influence on predicting thermal cookoff safety lies in the chemical kinetic model used in these simulations, and these kinetic model reaction sequences often contain multiple steps. Several small-scale cookoff experiments, notably Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TGA), One-Dimensional Time-to-Explosion (ODTX), and the Scaled Thermal Explosion (STEX) have been performed on various explosives to aid in cookoff behavior determination. Past work has used a single test from this group to create a cookoff model, which does not guarantee agreement with the other experiments. In this study, we update the kinetic parameters of an existing model for the common explosive 2,4,6-Trinitrotoluene (TNT) using DSC and ODTX experimental data at the same time by minimizing a global Figure of Merit based on hydrodynamic simulated data. We then show that the new kinetic model maintains STEX agreement, reduces DSC agreement, and improves ODTX and TGA agreement when compared to the original model. In addition, we describe a means to use implicit hydrodynamic simulations of DSC experiments to develop a reaction model for TNT melting.
Multinomial tau-leaping method for stochastic kinetic simulations
NASA Astrophysics Data System (ADS)
Pettigrew, Michel F.; Resat, Haluk
2007-02-01
We introduce the multinomial tau-leaping (MτL) method for general reaction networks with multichannel reactant dependencies. The MτL method is an extension of the binomial tau-leaping method where efficiency is improved in several ways. First, τ-leaping steps are determined simply and efficiently using a priori information and Poisson distribution-based estimates of expectation values for reaction numbers over a tentative τ-leaping step. Second, networks are partitioned into closed groups of reactions and corresponding reactants in which no group reactant set is found in any other group. Third, product formation is factored into upper-bound estimation of the number of times a particular reaction occurs. Together, these features allow larger time steps where the numbers of reactions occurring simultaneously in a multichannel manner are estimated accurately using a multinomial distribution. Furthermore, we develop a simple procedure that places a specific upper bound on the total reaction number to ensure non-negativity of species populations over a single multiple-reaction step. Using two disparate test case problems involving cellular processes—epidermal growth factor receptor signaling and a lactose operon model—we show that the τ-leaping based methods such as the MτL algorithm can significantly reduce the number of simulation steps thus increasing the numerical efficiency over the exact stochastic simulation algorithm by orders of magnitude.
Multinomial Tau-Leaping Method for Stochastic Kinetic Simulations
Pettigrew, Michel F.; Resat, Haluk
2007-02-28
We introduce the multinomial tau-leaping (MtL) method, an improved version of the binomial tau-leaping method, for general reaction networks. Improvements in efficiency are achieved in several ways. Firstly, tau-leaping steps are determined simply and efficiently using a-prior information. Secondly, networks are partitioned into closed groups of reactions and corresponding reactants in which no group reactant or reaction is found in any other group. Thirdly, product formation is factored into upper bound estimation of the number of times a particular reaction occurs. Together, these features allow for larger time steps where the numbers of reactions occurring simultaneously in a multi-channel manner are estimated accurately using a multinomial distribution. Using a wide range of test case problems of scientific and practical interest involving cellular processes, such as epidermal growth factor receptor signaling and lactose operon model incorporating gene transcription and translation, we show that tau-leaping based methods like the MtL algorithm can significantly reduce the number of simulation steps thus increasing the numerical efficiency over the exact stochastic simulation algorithm by orders of magnitude. Furthermore, the simultaneous multi-channel representation capability of the MtL algorithm makes it a candidate for FPGA implementation or for parallelization in parallel computing environments.
DBP formation kinetics in a simulated distribution system.
Rossman, L A; Brown, R A; Singer, P C; Nuckols, J R
2001-10-01
Little is known about how the growth of halogenated disinfection by-products (DBPs) in drinking water is affected by time spent in a distribution system. Experiments were performed to compare the rate of trihalomethane and haloacetic acid production in a simulated pipe environment to that observed for the same water held in glass bottles. Results showed that although the rate of chlorine consumption in the pipe was much greater than in the bottle, there was no decrease in the amount of haloacetic acids produced and that trihalomethane levels actually increased by an average of 15%. Separate tests confirmed that this increase was due to a reservoir of organic precursor material associated with deposits on the pipe wall. This work suggests that the rate of DBP production in a distribution system will not necessarily be reduced by increased chlorine consumption due to non-DBP producing reactions with deposits on the pipe wall.
Kinetic simulation of plasma flows in the inner magnetosphere
NASA Technical Reports Server (NTRS)
Miller, Ronald H.; Rasmussen, Craig E.; Gombosi, Tamas I.; Khazanov, Georgi V.; Winske, Dan
1993-01-01
A one-dimensional hybrid particle code is used to study the interactions between upflowing thermal ions from conjugate ionospheres. The simulation model allows for multiple species, convection of plasmaspheric flux tubes, and Coulomb self-collisions which conserve momentum and energy locally. The model incorporates a variable-flux boundary condition where the flux, at the boundaries, approaches zero as the plasmasphere fills and equilibrium conditions are reached. The effects of two important processes on plasmaspheric refilling have been considered. The first includes convection of the plasmaspheric flux tube. The second is the interaction of ionospheric thermal plasma and particle injection from an external source. Particle injection seems to play an important role in the evolution of the total particle distribution on the early timescales (t less than 1 hour); however, for late timescales (t larger than 8 days) the thermal plasma from the ionosphere dominates the particle distribution.
2D semiconductor optoelectronics
NASA Astrophysics Data System (ADS)
Novoselov, Kostya
The advent of graphene and related 2D materials has recently led to a new technology: heterostructures based on these atomically thin crystals. The paradigm proved itself extremely versatile and led to rapid demonstration of tunnelling diodes with negative differential resistance, tunnelling transistors, photovoltaic devices, etc. By taking the complexity and functionality of such van der Waals heterostructures to the next level we introduce quantum wells engineered with one atomic plane precision. Light emission from such quantum wells, quantum dots and polaritonic effects will be discussed.
NASA Astrophysics Data System (ADS)
Peters, C. A.; Crandell, L. E.; Um, W.; Jones, K. W.; Lindquist, W. B.
2011-12-01
Geochemical reactions in the subsurface can alter the porosity and permeability of a porous medium through mineral precipitation and dissolution. While effects on porosity are relatively well understood, changes in permeability are more difficult to estimate. In this work, pore-network modeling is used to estimate the permeability of a porous medium using pore and throat size distributions. These distributions can be determined from 2D Scanning Electron Microscopy (SEM) images of thin sections or from 3D X-ray Computed Tomography (CT) images of small cores. Each method has unique advantages as well as unique sources of error. 3D CT imaging has the advantage of reconstructing a 3D pore network without the inherent geometry-based biases of 2D images but is limited by resolutions around 1 μm. 2D SEM imaging has the advantage of higher resolution, and the ability to examine sub-grain scale variations in porosity and mineralogy, but is limited by the small size of the sample of pores that are quantified. A pore network model was created to estimate flow permeability in a sand-packed experimental column investigating reaction of sediments with caustic radioactive tank wastes in the context of the Hanford, WA site. Before, periodically during, and after reaction, 3D images of the porous medium in the column were produced using the X2B beam line facility at the National Synchrotron Light Source (NSLS) at Brookhaven National Lab. These images were interpreted using 3DMA-Rock to characterize the pore and throat size distributions. After completion of the experiment, the column was sectioned and imaged using 2D SEM in backscattered electron mode. The 2D images were interpreted using erosion-dilation to estimate the pore and throat size distributions. A bias correction was determined by comparison with the 3D image data. A special image processing method was developed to infer the pore space before reaction by digitally removing the precipitate. The different sets of pore
NASA Astrophysics Data System (ADS)
Stern, Luli; Barnea, Nitza; Shauli, Sofia
2008-08-01
The objective of this study was to evaluate the effect of a dynamic software simulation on the understanding of the kinetic molecular theory by 7th graders. Students in the control group ( n = 62) studied a curricular unit that addressed the differences in arrangement and motion of molecules in the three phases of matter. The experimental group ( n = 71) studied the same unit combined with a few computer lessons using a software simulation. The results indicate that the students in the experimental group scored significantly higher than those in the control group. Nonetheless, while both groups of students improved their understanding of the kinetic molecular theory, the overall achievements were very low. These findings suggest that the simulation improved the understanding of the 7th graders; however, it was insufficient in itself to promote meaningful learning. Statistically significant gender differences were not observed. This paper concludes with a discussion of the educational implications of this study.
Hybrid simulations of magnetic reconnection with kinetic ions and fluid electron pressure anisotropy
Le, A.; Daughton, W.; Karimabadi, H.; ...
2016-03-16
We present the first hybrid simulations with kinetic ions and recently developed equations of state for the electron fluid appropriate for reconnection with a guide field. The equations of state account for the main anisotropy of the electron pressure tensor.Magnetic reconnection is studied in two systems, an initially force-free current sheet and a Harris sheet. The hybrid model with the equations of state is compared to two other models, hybrid simulations with isothermal electrons and fully kinetic simulations. Including the anisotropicequations of state in the hybrid model provides a better match to the fully kinetic model. In agreement with fullymore » kinetic results, the main feature captured is the formation of an electron current sheet that extends several ion inertial lengths. This electron current sheet modifies the Hall magnetic field structure near the X-line, and it is not observed in the standard hybrid model with isotropic electrons. The saturated reconnection rate in this regime nevertheless remains similar in all three models. Here, implications for global modeling are discussed.« less
Hybrid simulations of magnetic reconnection with kinetic ions and fluid electron pressure anisotropy
Le, A.; Daughton, W.; Karimabadi, H.; Egedal, J.
2016-03-16
We present the first hybrid simulations with kinetic ions and recently developed equations of state for the electron fluid appropriate for reconnection with a guide field. The equations of state account for the main anisotropy of the electron pressure tensor.Magnetic reconnection is studied in two systems, an initially force-free current sheet and a Harris sheet. The hybrid model with the equations of state is compared to two other models, hybrid simulations with isothermal electrons and fully kinetic simulations. Including the anisotropicequations of state in the hybrid model provides a better match to the fully kinetic model. In agreement with fully kinetic results, the main feature captured is the formation of an electron current sheet that extends several ion inertial lengths. This electron current sheet modifies the Hall magnetic field structure near the X-line, and it is not observed in the standard hybrid model with isotropic electrons. The saturated reconnection rate in this regime nevertheless remains similar in all three models. Here, implications for global modeling are discussed.
Hybrid simulations of magnetic reconnection with kinetic ions and fluid electron pressure anisotropy
NASA Astrophysics Data System (ADS)
Le, A.; Daughton, W.; Karimabadi, H.; Egedal, J.
2016-03-01
We present the first hybrid simulations with kinetic ions and recently developed equations of state for the electron fluid appropriate for reconnection with a guide field. The equations of state account for the main anisotropy of the electron pressure tensor. Magnetic reconnection is studied in two systems, an initially force-free current sheet and a Harris sheet. The hybrid model with the equations of state is compared to two other models, hybrid simulations with isothermal electrons and fully kinetic simulations. Including the anisotropic equations of state in the hybrid model provides a better match to the fully kinetic model. In agreement with fully kinetic results, the main feature captured is the formation of an electron current sheet that extends several ion inertial lengths. This electron current sheet modifies the Hall magnetic field structure near the X-line, and it is not observed in the standard hybrid model with isotropic electrons. The saturated reconnection rate in this regime nevertheless remains similar in all three models. Implications for global modeling are discussed.
A multiscale model for simulating binding kinetics of proteins with flexible linkers.
Chen, Jiawen; Xie, Zhong-Ru; Wu, Yinghao
2014-10-01
The kinetics of protein interactions are essential determinants in many cellular processes such as signal transduction and transcriptional regulation. Many proteins involved in these functions contain intrinsic disordered regions. This makes conformational flexibility become an unneglectable factor when studying the binding kinetic of these proteins. Compared with the binding of rigid proteins that is limited by diffusions, the binding mechanisms of proteins with internal flexibility are much more complicated. Using a small protein that contains two domains and a connecting loop as a testing system, we developed a multiscale simulation framework to study the role of flexible linkers in regulating kinetics of protein binding. The association and dissociation processes were implemented by a coarse-grained Monte-Carlo algorithm, while the conformational changes of the flexible linker were captured from all-atom molecular dynamic simulations. Our simulations illustrated that the presence of the extended domain linker can enhance the rate of protein association. On the other hand, the full-length flexible molecule is more difficult to dissociate than its two rigid domains but much easier than the molecule with a rigid linker. Overall, our studies demonstrated that both kinetics and thermodynamics of protein binding are closely modulated by the dynamic features of linker regions.
Berry, Hugues
2002-01-01
Conventional equations for enzyme kinetics are based on mass-action laws, that may fail in low-dimensional and disordered media such as biological membranes. We present Monte Carlo simulations of an isolated Michaelis-Menten enzyme reaction on two-dimensional lattices with varying obstacle densities, as models of biological membranes. The model predicts that, as a result of anomalous diffusion on these low-dimensional media, the kinetics are of the fractal type. Consequently, the conventional equations for enzyme kinetics fail to describe the reaction. In particular, we show that the quasi-stationary-state assumption can hardly be retained in these conditions. Moreover, the fractal characteristics of the kinetics are increasingly pronounced as obstacle density and initial substrate concentration increase. The simulations indicate that these two influences are mainly additive. Finally, the simulations show pronounced S-P segregation over the lattice at obstacle densities compatible with in vivo conditions. This phenomenon could be a source of spatial self organization in biological membranes. PMID:12324410
Simulation and assessment of ion kinetic effects in a direct-drive capsule implosion experiment
NASA Astrophysics Data System (ADS)
Le, A.; Kwan, T. J. T.; Schmitt, M. J.; Herrmann, H. W.; Batha, S. H.
2016-10-01
The first simulations employing a kinetic treatment of both fuel and shell ions to model inertial confinement fusion experiments are presented, including results showing the importance of kinetic physics processes in altering fusion burn. A pair of direct drive capsule implosions performed at the OMEGA facility with two different gas fills of deuterium, tritium, and helium-3 are analyzed. During implosion shock convergence, highly non-Maxwellian ion velocity distributions and separations in the density and temperature amongst the ion species are observed. Diffusion of fuel into the capsule shell is identified as a principal process that degrades fusion burn performance.
Simulation and assessment of ion kinetic effects in a direct-drive capsule implosion experiment
Le, Ari Yitzchak; Kwan, Thomas J. T.; Schmitt, Mark J.; ...
2016-10-24
The first simulations employing a kinetic treatment of both fuel and shell ions to model inertial confinement fusion experiments are presented, including results showing the importance of kinetic physics processes in altering fusion burn. A pair of direct drive capsule implosions performed at the OMEGA facility with two different gas fills of deuterium, tritium, and helium-3 are analyzed. During implosion shock convergence, highly non-Maxwellian ion velocity distributions and separations in the density and temperature amongst the ion species are observed. Finally, diffusion of fuel into the capsule shell is identified as a principal process that degrades fusion burn performance.
NASA Astrophysics Data System (ADS)
Martin-Bragado, Ignacio; Rivera, Antonio; Valles, Gonzalo; Gomez-Selles, Jose Luis; Caturla, María J.
2013-12-01
In this work, we introduce the Object Kinetic Monte Carlo (OKMC) simulator MMonCa and simulate the defect evolution in three different materials. We start by explaining the theory of OKMC and showing some details of how such theory is implemented by creating generic structures and algorithms in the objects that we want to simulate. Then we successfully reproduce simulated results for defect evolution in iron, silicon and tungsten using our simulator and compare with available experimental data and similar simulations. The comparisons validate MMonCa showing that it is powerful and flexible enough to be customized and used to study the damage evolution of defects in a wide range of solid materials.
NASA Astrophysics Data System (ADS)
Oulaid, Othmane; Chen, Qing; Zhang, Junfeng
2013-11-01
In this paper a novel boundary method is proposed for lattice Boltzmann simulations of electric potential fields with complex boundary shapes and conditions. A shifted boundary from the physical surface location is employed in simulations to achieve a better finite-difference approximation of the potential gradient at the physical surface. Simulations are presented to demonstrate the accuracy and capability of this method in dealing with complex surface situations. An example simulation of the electrical double layer and electro-osmotic flow around a three-dimensional spherical particle is also presented. These simulated results are compared with analytical predictions and are found to be in excellent agreement. This method could be useful for electro-kinetic and colloidal simulations with complex boundaries, and can also be readily extended to other phenomena and processes, such as heat transfer and convection-diffusion systems.
Evaporation kinetics of Mg2SiO4 crystals and melts from molecular dynamics simulations
NASA Technical Reports Server (NTRS)
Kubicki, J. D.; Stolper, E. M.
1993-01-01
Computer simulations based on the molecular dynamics (MD) technique were used to study the mechanisms and kinetics of free evaporation from crystalline and molten forsterite (i.e., Mg2SiO4) on an atomic level. The interatomic potential employed for these simulations reproduces the energetics of bonding in forsterite and in gas-phase MgO and SiO2 reasonably accurately. Results of the simulation include predicted evaporation rates, diffusion rates, and reaction mechanisms for Mg2SiO4(s or l) yields 2Mg(g) + 20(g) + SiO2(g).
NASA Astrophysics Data System (ADS)
Field, A. R.; Dunai, D.; Ghim, Y.-c.; Hill, P.; McMillan, B.; Roach, C. M.; Saarelma, S.; Schekochihin, A. A.; Zoletnik, S.; the MAST Team
2014-02-01
Observations of ion-scale (kyρi ⩽ 1) density turbulence of relative amplitude ≳0.2% are available on the Mega Amp Spherical Tokamak (MAST) using a 2D (8 radial × 4 poloidal channel) imaging beam emission spectroscopy diagnostic. Spatial and temporal characteristics of this turbulence, i.e., amplitudes, correlation times, radial and perpendicular correlation lengths and apparent phase velocities of the density contours, are determined by means of correlation analysis. For a low-density, L-mode discharge with strong equilibrium flow shear exhibiting an internal transport barrier in the ion channel, the observed turbulence characteristics are compared with synthetic density turbulence data generated from global, non-linear, gyro-kinetic simulations using the particle-in-cell code NEMORB. This validation exercise highlights the need to include increasingly sophisticated physics, e.g., kinetic treatment of trapped electrons, equilibrium flow shear and collisions, to reproduce most of the characteristics of the observed turbulence. Even so, significant discrepancies remain: an underprediction by the simulations of the turbulence amplitude and heat flux at plasma periphery and the finding that the correlation times of the numerically simulated turbulence are typically two orders of magnitude longer than those measured in MAST. Comparison of these correlation times with various linear timescales suggests that, while the measured turbulence is strong and may be ‘critically balanced’, the simulated turbulence is weak.
Object Kinetic Monte Carlo Simulations of Annealing of Cascade Damage in Tungsten
NASA Astrophysics Data System (ADS)
Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard; Kurtz, Richard; Roche, Kenneth; Roche, Brian
2013-10-01
Results are presented for a series of annealing simulations of displacement cascades in tungsten (W) using the kinetic Monte Carlo (KMC) code kSOME (kinetic simulation of microstructure evolution), which is our newly developed lattice-based Object KMC simulation code. In principle, kSOME can deal with migration, emission, transformation and recombination of all types of intrinsic point defects and their complexes. In addition, the interaction of these point defects with sinks such as dislocations, grain boundaries and free surfaces is also treated. We have studied the long-time annealing of displacement cascades in W obtained from molecular dynamics (MD) simulations. A database of displacement cascades in W was obtained using MD simulations for temperatures of 800-1300K and primary knock-on atom (PKA) energies in the range of 2 to 40 keV. The input data for the KMC simulations, such as activation energies for migration and dissociation of defects, and their capture radii were obtained from atomic-level calculations. The evolution of radiation damage was investigated as a function of time, temperature, dose and dose-rate. The results for W are compared with those for similar simulations of cascades in α-Fe.
Kinetic Electron Closures for Electromagnetic Simulation of Drift and Shear-Alfven Waves (II)
Cohen, B I; Dimits, A M; Nevins, W M; Chen, Y; Parker, S
2001-10-11
An electromagnetic hybrid scheme (fluid electrons and gyrokinetic ions) is elaborated in example calculations and extended to toroidal geometry. The scheme includes a kinetic electron closure valid for {beta}{sub e} > m{sub e}/m{sub i} ({beta}{sub e} is the ratio of the plasma electron pressure to the magnetic field energy density). The new scheme incorporates partially linearized ({delta}f) drift-kinetic electrons whose pressure and number density moments are used to close the fluid momentum equation for the electron fluid (Ohm's law). The test cases used are small-amplitude kinetic shear-Alfven waves with electron Landau damping, the ion-temperature-gradient instability, and the collisionless drift instability (universal mode) in an unsheared slab as a function of the plasma {beta}{sub e}. Attention is given to resolution and convergence issues in simulations of turbulent steady states.
NASA Astrophysics Data System (ADS)
Gharaee, H.; Rankin, R.; Marchand, R.; Paral, J.
2014-12-01
The ARTEMIS mission has made extensive measurements on the density and magnetic field structure of the lunar wake under different solar wind and magnetosphere conditions. Hybrid-kinetic simulations of the lunar wake have been found to be generally in good agreement with observations [Wiehle, S., et al., Planet. Space Sci., 2011], but are not readily available as they require access to large computers and human resources with expertise using this technology. It would be very useful to have an analytic model of the lunar wake, and one such model will be presented. It is based on an approach outlined by Hutchinson [Hutchinson, I., Physics Of Plasmas, 2008], and makes assumptions of cylindrical geometry, a strong and constant magnetic field, and fixed transverse velocity and temperature. Under these approximations the ion fluid equations (with massless electrons assumed) can be solved analytically by the method of characteristics. This paper demonstrates that the analytic model under these assumptions provides excellent agreement with observations and hybrid-kinetic simulations of the lunar wake. The approach outlined by Hutchinson is generalized to include an arbitrary angle between the interplanetary magnetic field and solar wind flow. This results in two angle-dependent characteristics for the fluid flow that can be solved for the density inside the wake region. The Density profiles for different orientations of magnetic field with respect to solar wind flow are in a good qualitative agreement with 2D Hybrid simulation results of the model developed by [Paral and Rankin, Nature Comms, 2012], and with ARTEMIS observations. Refrences, -Wiehle, S., et al. (2011), First Lunar wake passage of Artemis: Discrimination of wake effects and solar wind flactuations by 3D hybrid simulations, Planet. Space Sci., 59, 661-671, doi:10.1016/j.pss.2011.01.012. -Hutchinson, I. (2008),Oblique ion collection in the drift approximation:How magnetized Mach probes really work, Physics Of
Kinetic electron and ion instability of the lunar wake simulated at physical mass ratio
Haakonsen, Christian Bernt Hutchinson, Ian H. Zhou, Chuteng
2015-03-15
The solar wind wake behind the moon is studied with 1D electrostatic particle-in-cell (PIC) simulations using a physical ion to electron mass ratio (unlike prior investigations); the simulations also apply more generally to supersonic flow of dense magnetized plasma past non-magnetic objects. A hybrid electrostatic Boltzmann electron treatment is first used to investigate the ion stability in the absence of kinetic electron effects, showing that the ions are two-stream unstable for downstream wake distances (in lunar radii) greater than about three times the solar wind Mach number. Simulations with PIC electrons are then used to show that kinetic electron effects can lead to disruption of the ion beams at least three times closer to the moon than in the hybrid simulations. This disruption occurs as the result of a novel wake phenomenon: the non-linear growth of electron holes spawned from a narrow dimple in the electron velocity distribution. Most of the holes arising from the dimple are small and quickly leave the wake, approximately following the unperturbed electron phase-space trajectories, but some holes originating near the center of the wake remain and grow large enough to trigger disruption of the ion beams. Non-linear kinetic-electron effects are therefore essential to a comprehensive understanding of the 1D electrostatic stability of such wakes, and possible observational signatures in ARTEMIS data from the lunar wake are discussed.
Simulated single-cycle kinetics improves the design of surface plasmon resonance assays.
Palau, William; Di Primo, Carmelo
2013-09-30
Instruments based on the surface plasmon resonance (SPR) principle are widely used to monitor in real time molecular interactions between a partner, immobilized on a sensor chip surface and another one injected in a continuous flow of buffer. In a classical SPR experiment, several cycles of binding and regeneration of the surface are performed in order to determine the rate and the equilibrium constants of the reaction. In 2006, Karlsson and co-workers introduced a new method named single-cycle kinetics (SCK) to perform SPR assays. The method consists in injecting sequentially increasing concentrations of the partner in solution, with only one regeneration step performed at the end of the complete binding cycle. A 10 base-pair DNA duplex was characterized kinetically to show how simulated sensorgrams generated by the BiaEvaluation software provided by Biacore™ could really improve the design of SPR assays performed with the SCK method. The DNA duplex was investigated at three temperatures, 10, 20 and 30 °C, to analyze fast and slow rate constants. The results show that after a short obligatory preliminary experiment, simulations provide users with the best experimental conditions to be used, in particular, the maximum concentration used to reach saturation, the dilution factor for the serial dilutions of the sample injected and the duration of the dissociation and association phases. The use of simulated single-cycle kinetics saves time and reduces sample consumption. Simulations can also be used to design SPR experiments with ternary complexes.
NASA Technical Reports Server (NTRS)
Mikellides, Ioannis G.; Katz, Ira; Goebel, Dan M.; Jameson, Kristina K.
2006-01-01
Numerical simulations with the time-dependent Orificed Cathode (OrCa2D-II) computer code show that classical enhancements of the plasma resistivity can not account for the elevated electron temperatures and steep plasma potential gradients measured in the plume of a 25-27.5 A discharge hollow cathode. The cathode, which employs a 0.11-in diameter orifice, was operated at 5.5 sccm without an applied magnetic field using two different anode geometries. It is found that anomalous resistivity based on electron-driven instabilities improves the comparison between theory and experiment. It is also estimated that other effects such as the Hall-effect from the self-induced magnetic field, not presently included in OrCa2D-II, may contribute to the constriction of the current density streamlines thus explaining the higher plasma densities observed along the centerline.
3D nozzle flow simulations including state-to-state kinetics calculation
NASA Astrophysics Data System (ADS)
Cutrone, L.; Tuttafesta, M.; Capitelli, M.; Schettino, A.; Pascazio, G.; Colonna, G.
2014-12-01
In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma. In this paper, we present an optimized methodology to approach plasma numerical simulation by state-to-state kinetics calculations in a fully 3D Navier-Stokes CFD solver. Numerical simulations of an expanding flow are presented aimed at comparing the behavior of state-to-state chemical kinetics models with respect to the macroscopic thermochemical non-equilibrium models that are usually used in the numerical computation of high temperature hypersonic flows. The comparison is focused both on the differences in the numerical results and on the computational effort associated with each approach.
Robiche, J.; Rax, J.-M.; Bonnaud, G.; Gremillet, L.
2010-03-15
The collisional dynamics of a relativistic electron jet in a magnetized plasma are investigated within the framework of kinetic theory. The relativistic Fokker-Planck equation describing slowing down, pitch angle scattering, and cyclotron rotation is derived and solved. Based on the solution of this Fokker-Planck equation, an analytical formula for the root mean square spot size transverse to the magnetic field is derived and this result predicts a reduction in radial transport. Some comparisons with particle-in-cell simulation are made and confirm striking agreement between the theory and the simulation. For fast electron with 1 MeV typical kinetic energy interacting with a solid density hydrogen plasma, the energy deposition density in the transverse direction increases by a factor 2 for magnetic field of the order of 1 T. Along the magnetic field, the energy deposition profile is unaltered compared with the field-free case.
Wang, Xu; Ding, Jie; Guo, Wan-Qian; Ren, Nan-Qi
2010-12-01
Investigating how a bioreactor functions is a necessary precursor for successful reactor design and operation. Traditional methods used to investigate flow-field cannot meet this challenge accurately and economically. Hydrodynamics model can solve this problem, but to understand a bioreactor in sufficient depth, it is often insufficient. In this paper, a coupled hydrodynamics-reaction kinetics model was formulated from computational fluid dynamics (CFD) code to simulate a gas-liquid-solid three-phase biotreatment system for the first time. The hydrodynamics model is used to formulate prediction of the flow field and the reaction kinetics model then portrays the reaction conversion process. The coupled model is verified and used to simulate the behavior of an expanded granular sludge bed (EGSB) reactor for biohydrogen production. The flow patterns were visualized and analyzed. The coupled model also demonstrates a qualitative relationship between hydrodynamics and biohydrogen production. The advantages and limitations of applying this coupled model are discussed.
NASA Astrophysics Data System (ADS)
Shim, Yunsic; Amar, Jacques G.
2005-03-01
The standard kinetic Monte Carlo algorithm is an extremely efficient method to carry out serial simulations of dynamical processes such as thin film growth. However, in some cases it is necessary to study systems over extended time and length scales, and therefore a parallel algorithm is desired. Here we describe an efficient, semirigorous synchronous sublattice algorithm for parallel kinetic Monte Carlo simulations. The accuracy and parallel efficiency are studied as a function of diffusion rate, processor size, and number of processors for a variety of simple models of epitaxial growth. The effects of fluctuations on the parallel efficiency are also studied. Since only local communications are required, linear scaling behavior is observed, e.g., the parallel efficiency is independent of the number of processors for fixed processor size.
The Lattice Kinetic Monte Carlo Simulation of Atomic Diffusion and Structural Transition for Gold
He, Xiang; Cheng, Feng; Chen, Zhao-Xu
2016-01-01
For the kinetic simulation of metal nanoparticles, we developed a self-consistent coordination-averaged energies for Au atoms based on energy properties of gold bulk phases. The energy barrier of the atom pairing change is proposed and holds for the microscopic reversibility principle. By applying the lattice kinetic Monte Carlo simulation on gold films, we found that the atomic diffusion of Au on the Au(111) surface undergoes a late transition state with an energy barrier of about 0.2 eV and a prefactor between 40~50 Å2/ps. This study also investigates the structural transition from spherical to faceted gold nanoparticles upon heating. The temperatures of structural transition are in agreement with the experimental melting temperatures of gold nanoparticles with diameters ranging from 2 nm to 8 nm. PMID:27629538
Stochastic method for accommodation of equilibrating basins in kinetic Monte Carlo simulations
Van Siclen, Clinton D
2007-02-01
A computationally simple way to accommodate "basins" of trapping states in standard kinetic Monte Carlo simulations is presented. By assuming the system is effectively equilibrated in the basin, the residence time (time spent in the basin before escape) and the probabilities for transition to states outside the basin may be calculated. This is demonstrated for point defect diffusion over a periodic grid of sites containing a complex basin.
Horowitz, Y S; Eliyahu, I; Oster, L
2016-12-01
The reader will time-travel through almost seven decades of kinetic models and mathematical simulations of thermoluminescence (TL) characteristics based on the band-gap theory of the solid state. From post-World-War II, ideas concerning electron trapping mechanisms to the highly idealised one trap-one recombination (OTOR) model first elaborated in 1956 but still in 'high gear' today. The review caresses but purposely avoids in-depth discussion of the endless stream of papers discussing the intricacies of glow peak shapes arising from first-order, second-order, mixed-order and general-order kinetics predominantly based on non-interacting systems, and then on to the more physically realistic scenarios that have attempted to analyse complex systems involving ever greater numbers of interacting trapping centres, luminescent centres and non-luminescent centres. The review emphasises the difficulty the band-gap models have in the simulation of dose response linear/supralinear behaviour and especially the dependence of the supralinearity on ionisation density. The significance of the non-observation of filling-rate supralinearity in the absorption stage is emphasised since it removes from consideration the possibility of TL supralinearity arising from irradiation stage supralinearity. The importance of the simultaneous action of both localised and delocalised transitions has gradually penetrated the mindset of the community of kinetic researchers, but most simulations have concentrated on the shape of glow peaks and the extraction of the glow peak parameters, E (the thermal activation energy) and s (the attempt-to-escape frequency). The simulation of linear/supralinear dose response and its dependence on ionisation density have been largely avoided until recently due to the fundamental schism between the effects of ionisation density and some basic assumptions of the band-gap model. The review finishes with an in-depth presentation and discussion of the most recent
Kinetic simulations of X-B and O-X-B mode conversion
Arefiev, A. V.; Du Toit, E. J.; Vann, R. G. L.; Köhn, A.; Holzhauer, E.; Shevchenko, V. F.
2015-12-10
We have performed fully-kinetic simulations of X-B and O-X-B mode conversion in one and two dimensional setups using the PIC code EPOCH. We have recovered the linear dispersion relation for electron Bernstein waves by employing relatively low amplitude incoming waves. The setups presented here can be used to study non-linear regimes of X-B and O-X-B mode conversion.
R. Skartlien; E. Sollum; A. Akselsen; P. Meakin; B. Grimes; J. Sjoblom
2012-12-01
Lattice Boltzmann simulations were used to study the coalescence kinetics in emulsions with amphiphilic surfactant, under neutrally buoyant conditions, and with a significant kinematic viscosity contrast between the phases (emulating water in oil emulsions). The 3D simulation domain was large enough (256 3rd power -- 10 7th power grid points) to obtain good statistics with droplet numbers ranging from a few thousand at early times to a few hundred near equilibrium. Increased surfactant contents slowed down the coalescence rate between droplets due to the Gibbs-Marangoni effect, and the coalescence was driven by a quasi-turbulent velocity field. The kinetic energy decayed at a relatively slow rate at early times, due to conversion of interfacial energy to kinetic energy in the flow during coalescence. Phenomenological, coupled differential equations for the mean droplet diameter D(t) and the number density nd(t) were obtained from the simulation data and from film draining theories. Local (in time) power law exponents for the growth of the mean diameter (and for the concomitant decrease of nd) were established in terms of the instantaneous values of the kinetic energy, coalescence probability, Gibbs elasticity, and interfacial area. The model studies indicated that true power laws for the growth of the droplet size and decrease of the number of droplets with time may not be justified, since the exponents derived using the phenomenological model were time dependent. In contrast to earlier simulation results for symmetric blends with surfactant, we found no evidence for stretched logarithmic scaling of the formD -- [ln (ct)]a for the morphology length, or exponential scalings associated with arrested growth, on the basis of the phenomenological model.
Kinetic simulations of X-B and O-X-B mode conversion
NASA Astrophysics Data System (ADS)
Arefiev, A. V.; Du Toit, E. J.; Köhn, A.; Holzhauer, E.; Shevchenko, V. F.; Vann, R. G. L.
2015-12-01
We have performed fully-kinetic simulations of X-B and O-X-B mode conversion in one and two dimensional setups using the PIC code EPOCH. We have recovered the linear dispersion relation for electron Bernstein waves by employing relatively low amplitude incoming waves. The setups presented here can be used to study non-linear regimes of X-B and O-X-B mode conversion.
Schlesinger, Daniel; Sellberg, Jonas A; Nilsson, Anders; Pettersson, Lars G M
2016-03-28
In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.
Schlesinger, Daniel; Sellberg, Jonas A.; Nilsson, Anders; ...
2016-03-22
In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Lastly, our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.
NASA Astrophysics Data System (ADS)
Benezech, Laurent Jean-Michel
A methodology based on the comparison of flame simulations relying on reacting flow models with experiment is applied to C1-C3 stagnation flames. The work reported targets the assessment and validation of the modeled reactions and reaction rates relevant to (C1-C3)-flame propagation in several detailed combustion kinetic models. A concensus does not, as yet, exist on the modeling of the reasonably well-understood oxidation of C1-C2 flames, and a better knowledge of C3 hydrocarbon combustion chemistry is required before attempting to bridge the gap between the oxidation of C1-C2 hydrocarbons and the more complex chemistry of heavier hydrocarbons in a single kinetic model. Simultaneous measurements of velocity and CH-radical profiles were performed in atmospheric propane(C3H8)- and propylene(C3H6)-air laminar premixed stagnation flames stabilized in a jet-wall configuration. These nearly-flat flames can be modeled by one-dimensional simulations, providing a means to validate kinetic models. Experimental data for these C3 flames and similar experimental data for atmospheric methane(CH4)-, ethane(C2H6)-, and ethylene(C2H4)-air flames are compared to numerical simulations performed with a one-dimensional hydrodynamic model, a multi-component transport formulation including thermal diffusion, and different detailed-chemistry models, in order to assess the adequacy of the models employed. A novel continuation technique between kinetic models was developed and applied successfully to obtain solutions with the less-robust models. The 2005/12 and 2005/10 releases of the San Diego mechanism are found to have the best overall performance in C3H8 and C3H6 flames, and in CH4, C2H6, and C2H4 flames, respectively. Flame position provides a good surrogate for flame speed in stagnation-flow stabilized flames. The logarithmic sensitivities of the simulated flame locations to variations in the kinetic rates are calculated via the "brute-force" method for fifteen representative flames
NASA Astrophysics Data System (ADS)
Lantz, Jonas; Ebbers, Tino; Karlsson, Matts
2012-11-01
In this study, turbulent kinetic energy (TKE) in an aortic coarctation was studied using both a numerical technique (large eddy simulation, LES) and in vivo measurements using magnetic resonance imaging (MRI). High levels of TKE are undesirable, as kinetic energy is extracted from the mean flow to feed the turbulent fluctuations. The patient underwent surgery to widen the coarctation, and the flow before and after surgery was computed and compared to MRI measurements. The resolution of the MRI was about 7 × 7 voxels in axial cross-section while 50x50 mesh cells with increased resolution near the walls was used in the LES simulation. In general, the numerical simulations and MRI measurements showed that the aortic arch had no or very low levels of TKE, while elevated values were found downstream the coarctation. It was also found that TKE levels after surgery were lowered, indicating that the diameter of the constriction was increased enough to decrease turbulence effects. In conclusion, both the numerical simulation and MRI measurements gave very similar results, thereby validating the simulations and suggesting that MRI measured TKE can be used as an initial estimation in clinical practice, while LES results can be used for detailed quantification and further research of aortic flows.
NASA Astrophysics Data System (ADS)
Pfeiffer, M.; Copplestone, S.; Binder, T.; Fasoulas, S.; Munz, C.-D.
2016-11-01
The expansion of a plasma plume resulting from laser ablation plays an important role in a large number of applications, e.g., material processing, medical laser applications or novel space propulsion concepts. Here, a high-order three-dimensional Particle-In-Cell code is used to simulate such a plasma plume expansion. A major challenge in this kind of simulation is the handling of the electrons due to their low inertia and resultant high acceleration. Therefore, two separate treatments of electron modeling are compared. Firstly, the electrons are simulated as a normal particle species in a kinetic manner, which strongly decreases the time step size and thereby increases the computational effort. Secondly, the electrons are simulated using an electron fluid model that reduces the computational cost but is less accurate [1]. Additionally, the results from the fully kinetic model are compared regarding chemical reactions, in this case ionization and ion recombination. The electron potential is solved using a high-order highly parallel Hybrid Discontinuous Galerkin (HDG) method [2]. This method also allows simulating computationally expensive three-dimensional setups.
Noe, F; Diadone, Isabella; Lollmann, Marc; Sauer, Marcus; Chondera, John D; Smith, Jeremy C
2011-01-01
There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is dynamical fingerprints which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.
Verification of particle-in-cell simulations against exact solutions of kinetic equations
NASA Astrophysics Data System (ADS)
Turner, Miles
2015-09-01
Demonstrating correctness of computer simulations (or verification) has become a matter of increasing concern in recent years. The strongest type of verification is a demonstration that the simulation converges to an exact solution of the mathematical model that is supposed to be solved. Of course, this is possible only if such an exact solution is available. In this paper, we are interested in kinetic simulation using the particle-in-cell method, and consequently a relevant exact solution must be a solution of a kinetic equation. While we know of no such solutions that exercise all the features of a typical particle-in-cell simulation, in this paper we show that the mathematical literature contains several such solutions that involve a large fraction of the functionality of such a code, and which collectively exercise essentially all of the code functionality. These solutions include the plane diode, the neutron criticality problem, and the calculation of ion energy distribution functions in oscillating fields. In each of theses cases, we can show the the particle-in-cell simulation converges to the exact solution in the expected way. These demonstrations are strong evidence of correct implementation. Work supported by Science Foundation Ireland under grant 08/SRC/I1411.
NASA Astrophysics Data System (ADS)
Dekker, T.; de Zwart, S. T.; Willemsen, O. H.; Hiddink, M. G. H.; IJzerman, W. L.
2006-02-01
A prerequisite for a wide market acceptance of 3D displays is the ability to switch between 3D and full resolution 2D. In this paper we present a robust and cost effective concept for an auto-stereoscopic switchable 2D/3D display. The display is based on an LCD panel, equipped with switchable LC-filled lenticular lenses. We will discuss 3D image quality, with the focus on display uniformity. We show that slanting the lenticulars in combination with a good lens design can minimize non-uniformities in our 20" 2D/3D monitors. Furthermore, we introduce fractional viewing systems as a very robust concept to further improve uniformity in the case slanting the lenticulars and optimizing the lens design are not sufficient. We will discuss measurements and numerical simulations of the key optical characteristics of this display. Finally, we discuss 2D image quality, the switching characteristics and the residual lens effect.
Consistent kinetic simulation of plasma and sputtering in low temperature plasmas
NASA Astrophysics Data System (ADS)
Schmidt, Frederik; Trieschmann, Jan; Mussenbrock, Thomas
2016-09-01
Plasmas are commonly used in sputtering applications for the deposition of thin films. Although magnetron sources are a prominent choice, capacitively coupled plasmas have certain advantages (e.g., sputtering of non-conducting and/or ferromagnetic materials, aside of excellent control of the ion energy distribution). In order to understand the collective plasma and sputtering dynamics, a kinetic simulation model is helpful. Particle-in-Cell has been proven to be successful in simulating the plasma dynamics, while the Test-Multi-Particle-Method can be used to describe the sputtered neutral species. In this talk a consistent combination of these methods is presented by consistently coupling the simulated ion flux as input to a neutral particle transport model. The combined model is used to simulate and discuss the spatially dependent densities, fluxes and velocity distributions of all particles. This work is supported by the German Research Foundation (DFG) in the frame of Transregional Collaborative Research Center (SFB) TR-87.
Khalil, Nagi; Garzó, Vicente
2014-04-28
The homogeneous state of a binary mixture of smooth inelastic hard disks or spheres is analyzed. The mixture is driven by a thermostat composed by two terms: a stochastic force and a drag force proportional to the particle velocity. The combined action of both forces attempts to model the interaction of the mixture with a bath or surrounding fluid. The problem is studied by means of two independent and complementary routes. First, the Enskog kinetic equation with a Fokker-Planck term describing interactions of particles with thermostat is derived. Then, a scaling solution to the Enskog kinetic equation is proposed where the dependence of the scaled distributions φi of each species on the granular temperature occurs not only through the dimensionless velocity c = v/v0 (v0 being the thermal velocity) but also through the dimensionless driving force parameters. Approximate forms for φi are constructed by considering the leading order in a Sonine polynomial expansion. The ratio of kinetic temperatures T1/T2 and the fourth-degree velocity moments λ1 and λ2 (which measure non-Gaussian properties of φ1 and φ2, respectively) are explicitly determined as a function of the mass ratio, size ratio, composition, density, and coefficients of restitution. Second, to assess the reliability of the theoretical results, molecular dynamics simulations of a binary granular mixture of spheres are performed for two values of the coefficient of restitution (α = 0.9 and 0.8) and three different solid volume fractions (ϕ = 0.00785, 0.1, and 0.2). Comparison between kinetic theory and computer simulations for the temperature ratio shows excellent agreement, even for moderate densities and strong dissipation. In the case of the cumulants λ1 and λ2, good agreement is found for the lower densities although significant discrepancies between theory and simulation are observed with increasing density.
Kinetic Simulations of Unsteady Vortex Structures in the Wake of a Cylinder
NASA Astrophysics Data System (ADS)
Arslanbekov, Robert R.; Kolobov, Vladimir I.; Frolova, Anna A.
2008-12-01
The development of an unsteady vortex street in the wake of a cylinder has been studied in computational experiments using recently developed Unified Flow Solver (UFS). A major objective was to investigate a spontaneous breakdown of flow symmetry in the wake and effects of gas compressibility and rarefaction on the laminar vortex shedding. The boundary of the wake instability on the (Kn, M) plane was found with a maximum at Kn˜0.01 for M˜0.6. We have used direct Boltzmann solver, gas kinetic compressible Navier-Stokes solver, incompressible GFS solver, and a hybrid kinetic/continuum UFS capability to analyze the appearance of oscillatory flow regimes. It was found that the wake becomes more stable as the free stream Mach number increases to sonic values. Effects of the flow solver (kinetic vs continuum, compressible vs incompressible) and of the size of computational domain on the Strouhal number were investigated. In all our cases, spontaneous breakdown of the flow symmetry took place without external perturbations. We believe that the procedure of Cartesian mesh cutting by a (curved) solid surface generated sufficient perturbations to break the symmetry of the flow. We compared our results with other simulations and experiments reviewed. It was found that the Adaptive Mesh and Algorithm Refinement (AMAR) procedure implemented in UFS works well for unsteady problems and offers substantial saving of computational time for complex flows with dynamically changing kinetic and continuum domains.
Numerical Simulations of the Kinetic Energy Transfer in the Bath of a BOF Converter
NASA Astrophysics Data System (ADS)
Zhou, Xiaobin; Ersson, Mikael; Zhong, Liangcai; Jönsson, Pär
2016-02-01
The paper focuses on the fundamental aspects of the kinetic energy transfer from a top and bottom gas injection to the bath of the basic oxygen furnace (BOF) by applying a mathematical model. The analyses revealed that the energy transfer is less efficient when top lance height is lowered or the flowrate is increased in the top blowing operations. However, an inverse trend was found that the kinetic energy transfer is increased when the bottom flowrate is increased for the current bottom blowing operation conditions. The kinetic energy transfer index results indicated that the energy transfer for the bottom blowing is much more efficient than that of the top blowing operations. To understand the effects of the upper buoyant phase on the energy dissipation of the bulk liquid in the bath, different mass and physical properties of slag and foam were considered in the bottom blowing simulations. The slag on top of the bath is found to dissipate by 6.6, 9.4, and 11.2 pct for slag mass values of 5, 9, and 15 t compared to the case without slag atop the surface of the bath, respectively. The results showed that the kinetic energy transfer is not largely influenced by the viscosity of the upper slag or the foaming phases.
2013-01-01
Background PQS (PseudomonasQuinolone Signal) and its precursor HHQ are signal molecules of the P. aeruginosa quorum sensing system. They explicate their role in mammalian pathogenicity by binding to the receptor PqsR that induces virulence factor production and biofilm formation. The enzyme PqsD catalyses the biosynthesis of HHQ. Results Enzyme kinetic analysis and surface plasmon resonance (SPR) biosensor experiments were used to determine mechanism and substrate order of the biosynthesis. Comparative analysis led to the identification of domains involved in functionality of PqsD. A kinetic cycle was set up and molecular dynamics (MD) simulations were used to study the molecular bases of the kinetics of PqsD. Trajectory analysis, pocket volume measurements, binding energy estimations and decompositions ensured insights into the binding mode of the substrates anthraniloyl-CoA and β-ketodecanoic acid. Conclusions Enzyme kinetics and SPR experiments hint at a ping-pong mechanism for PqsD with ACoA as first substrate. Trajectory analysis of different PqsD complexes evidenced ligand-dependent induced-fit motions affecting the modified ACoA funnel access to the exposure of a secondary channel. A tunnel-network is formed in which Ser317 plays an important role by binding to both substrates. Mutagenesis experiments resulting in the inactive S317F mutant confirmed the importance of this residue. Two binding modes for β-ketodecanoic acid were identified with distinct catalytic mechanism preferences. PMID:23916145
NASA Astrophysics Data System (ADS)
Hu, Yuan; Wang, Joseph
2017-03-01
This paper presents a fully kinetic particle particle-in-cell simulation study on the emission of a collisionless plasma plume consisting of cold beam ions and thermal electrons. Results are presented for both the two-dimensional macroscopic plume structure and the microscopic electron kinetic characteristics. We find that the macroscopic plume structure exhibits several distinctive regions, including an undisturbed core region, an electron cooling expansion region, and an electron isothermal expansion region. The properties of each region are determined by microscopic electron kinetic characteristics. The division between the undisturbed region and the cooling expansion region approximately matches the Mach line generated at the edge of the emission surface, and that between the cooling expansion region and the isothermal expansion region approximately matches the potential well established in the beam. The interactions between electrons and the potential well lead to a new, near-equilibrium state different from the initial distribution for the electrons in the isothermal expansion region. The electron kinetic characteristics in the plume are also very anisotropic. As the electron expansion process is mostly non-equilibrium and anisotropic, the commonly used assumption that the electrons in a collisionless, mesothermal plasma plume may be treated as a single equilibrium fluid in general is not valid.
NASA Astrophysics Data System (ADS)
Shay, M. A.; Drake, J. F.
2009-12-01
In a recent substorm case study using THEMIS data [1], it was inferred that auroral intensification occurred 96 seconds after reconnection onset initiated a substorm in the magnetotail. These conclusions have been the subject of some controversy [2,3]. The time delay between reconnection and auroral intensification requires a propagation speed significantly faster than can be explained by Alfvén waves. Kinetic Alfvén waves, however, can be much faster and could possibly explain the time lag. To test this possiblity, we simulate large scale reconnection events with the kinetic PIC code P3D and examine the disturbances on a magnetic field line as it propagates through a reconnection region. In the regions near the separatrices but relatively far from the x-line, the propagation physics is expected to be governed by the physics of kinetic Alfvén waves. Indeed, we find that the propagation speed of the magnetic disturbance roughly scales with kinetic Alfvén speeds. We also examine energization of electrons due to this disturbance. Consequences for our understanding of substorms will be discussed. [1] Angelopoulos, V. et al., Science, 321, 931, 2008. [2] Lui, A. T. Y., Science, 324, 1391-b, 2009. [3] Angelopoulos, V. et al., Science, 324, 1391-c, 2009.
Hoffman, E.L.; Ammerman, D.J.
1993-08-01
A series of tests investigating dynamic pulse buckling of a cylindrical shell under axial impact is compared to several finite element simulations of the event. The purpose of the study is to compare the performance of the various analysis codes and element types with respect to a problem which is applicable to radioactive material transport packages, and ultimately to develop a benchmark problem to qualify finite element analysis codes for the transport package design industry.
Cluster Observations and Kinetic Simulations of Slow Mode Shocks at the Earth's Bow Shock
NASA Astrophysics Data System (ADS)
Kucharek, H.; Mouikis, C.; Scholer, M.; Eriksson, S.
2007-12-01
Slow shocks in association with reconnection are thought to be the main engine of the plasma heating, acceleration and dynamical changes of the magnetosphere. It is therefore very important to study their structure and the related physical processes. Measurements, from CLUSTER spacecraft show clear evidence for slow- mode shocks associated with magnetic reconnection in the near Earth magnetotail in connection with a substorm onset [S. Eriksson et al., 2004]. Most of the knowledge of slow mode shocks was derived from two-fluid theory together with extensive small-scale hybrid simulations of the shock transition. However, it is difficult to perform numerical simulations under realistic plasma conditions. First, it is important to use realistic proton electron mass ratios to study downstream electron heating. Second, the method to initiate a slow mode shock is Might have an impact of the obtained results. Using the piston method the slow mode shock will run into the downstream region of a preceding fast shock wave. Using switch off shock conditions the slow mode shock will run into a quite plasma environment. However, at the Earth's bow shock turbulence will always be around. Finally, dimensional effects in numerical simulations have effects on the results. For instance in 1D simulations all wave vectors are forced in the simulation direction. Furthermore, full particle simulations predict lower downstream ion temperature than predicted by hybrid simulations. This is attributed to electron kinetic processes. We performed a number of 1D full particle simulations with real proton to electron mass ratio and multi-dimensional hybrid simulations to address the above-mentioned topics. As input for the numerical simulations we used plasma- parameters from the established Cluster database. We investigated the dynamics, the structure, and the evolution of the simulated slow mode shocks using the piston and the "switch-off" method for hybrid and the 1D full particle simulations
Korla, Kalyani; Vadlakonda, Lakshmipathi; Mitra, Chanchal K
2015-01-01
In the present work, we have kinetically simulated two mitochondrial shuttles, malate-aspartate shuttle (used for transferring reducing equivalents) and citrate-pyruvate shuttle (used for transferring carbon skeletons). However, the functions of these shuttles are not limited to the points mentioned above, and they can be used in different arrangements to meet different cellular requirements. Both the shuttles are intricately associated with Krebs cycle through the metabolites involved. The study of this system of shuttles and Krebs cycle explores the response of the system in different metabolic environments. Here, we have simulated these subsets individually and then combined them to study the interactions among them and to bring out the dynamics of these pathways in focus. Four antiports and a pyruvate pump were modelled along with the metabolic reactions on both sides of the inner mitochondrial membrane. Michaelis-Menten approach was extended for deriving rate equations of every component of the system. Kinetic simulation was carried out using ordinary differential equation solver in GNU Octave. It was observed that all the components attained steady state, sooner or later, depending on the system conditions. Progress curves and phase plots were plotted to understand the steady state behaviour of the metabolites involved. A comparative analysis between experimental and simulated data show fair agreement thus validating the usefulness and applicability of the model.
Kinetic Monte Carlo Simulation of Cation Diffusion in Low-K Ceramics
NASA Technical Reports Server (NTRS)
Good, Brian
2013-01-01
Low thermal conductivity (low-K) ceramic materials are of interest to the aerospace community for use as the thermal barrier component of coating systems for turbine engine components. In particular, zirconia-based materials exhibit both low thermal conductivity and structural stability at high temperature, making them suitable for such applications. Because creep is one of the potential failure modes, and because diffusion is a mechanism by which creep takes place, we have performed computer simulations of cation diffusion in a variety of zirconia-based low-K materials. The kinetic Monte Carlo simulation method is an alternative to the more widely known molecular dynamics (MD) method. It is designed to study "infrequent-event" processes, such as diffusion, for which MD simulation can be highly inefficient. We describe the results of kinetic Monte Carlo computer simulations of cation diffusion in several zirconia-based materials, specifically, zirconia doped with Y, Gd, Nb and Yb. Diffusion paths are identified, and migration energy barriers are obtained from density functional calculations and from the literature. We present results on the temperature dependence of the diffusivity, and on the effects of the presence of oxygen vacancies in cation diffusion barrier complexes as well.
Chara, Osvaldo; Grigera, José Raúl
2008-01-01
The usefulness of computational methods such as molecular dynamics simulation has been extensively established for studying systems in equilibrium. Nevertheless, its application to complex non-equilibrium biological processes such as protein unfolding has been generally regarded as producing results which cannot be interpreted straightforwardly. In the present study, we present results for the kinetics of unfolding of apomyoglobin, based on the analysis of long simulation runs of this protein in solution at 3 kbar (1 atm = 1.01325, bar = 101 325 Pa). We hereby demonstrate that the analysis of the data collected within a simulated time span of 0.18 μs suffices for producing results, which coincide remarkably with the available unfolding kinetics experimental data. This not only validates molecular dynamics simulation as a valuable alternative for studying non-equilibrium processes, but also enables a detailed analysis of the actual structural mechanism which underlies the unfolding process of proteins under elusive denaturing conditions such as high pressure. PMID:19669536
The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.
Shimada, J; Kussell, E L; Shakhnovich, E I
2001-04-20
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding, all side-chain and backbone torsions, and uses a Go potential. In this study, we focus on the 46 residue alpha/beta protein crambin and two of its structural components, the helix and helix hairpin. For a wide range of temperatures, we recorded multiple folding events of these three structures from random coils to native conformations that differ by less than 1 A C(alpha) dRMS from their crystal structure coordinates. The thermodynamics and kinetic mechanism of the helix-coil transition obtained from our simulation shows excellent agreement with currently available experimental and molecular dynamics data. Based on insights obtained from folding its smaller structural components, a possible folding mechanism for crambin is proposed. We observed that the folding occurs via a cooperative, first order-like process, and that many folding pathways to the native state exist. One particular sequence of events constitutes a "fast-folding" pathway where kinetic traps are avoided. At very low temperatures, a kinetic trap arising from the incorrect packing of side-chains was observed. These results demonstrate that folding to the native state can be observed in a reasonable amount of time on desktop computers even when an all-atom representation is used, provided the energetics sufficiently stabilize the native state.
Simulating galaxy formation with black hole driven thermal and kinetic feedback
NASA Astrophysics Data System (ADS)
Weinberger, Rainer; Springel, Volker; Hernquist, Lars; Pillepich, Annalisa; Marinacci, Federico; Pakmor, Rüdiger; Nelson, Dylan; Genel, Shy; Vogelsberger, Mark; Naiman, Jill; Torrey, Paul
2017-03-01
The inefficiency of star formation in massive elliptical galaxies is widely believed to be caused by the interactions of an active galactic nucleus (AGN) with the surrounding gas. Achieving a sufficiently rapid reddening of moderately massive galaxies without expelling too many baryons has however proven difficult for hydrodynamical simulations of galaxy formation, prompting us to explore a new model for the accretion and feedback effects of supermassive black holes. For high-accretion rates relative to the Eddington limit, we assume that a fraction of the accreted rest mass energy heats the surrounding gas thermally, similar to the 'quasar mode' in previous work. For low-accretion rates, we invoke a new, pure kinetic feedback model that imparts momentum to the surrounding gas in a stochastic manner. These two modes of feedback are motivated both by theoretical conjectures for the existence of different types of accretion flows as well as recent observational evidence for the importance of kinetic AGN winds in quenching galaxies. We find that a large fraction of the injected kinetic energy in this mode thermalizes via shocks in the surrounding gas, thereby providing a distributed heating channel. In cosmological simulations, the resulting model produces red, non-star-forming massive elliptical galaxies, and achieves realistic gas fractions, black hole growth histories and thermodynamic profiles in large haloes.
Multiscale gas-kinetic simulation for continuum and near-continuum flows.
Xu, Kun; Liu, Hongwei
2007-01-01
It is well known that for increasingly rarefied flow fields, predictions from continuum formulations, such as the Navier-Stokes equations, lose accuracy. The inclusion of higher-order terms, such as Burnett or high-order moment equations, could improve the predictive capabilities of such continuum formulations, but there has been only limited success. Here, we present a multiscale model. On the macroscopic level, the flow variables are updated based on the mass, momentum, and energy conservation through the fluxes. On the other hand, the fluxes are constructed on the microscopic level based on the gas-kinetic equation, which is valid in both continuum and near-continuum flow regimes. Based on this model, the nonequilibrium shock structure, Poiseuille flow, nonlinear heat conduction problems, and unsteady Rayleigh problem will be studied. In the near-continuum flow regime, the current gas-kinetic simulation is more efficient than microscopic methods, such as the direction Boltzmann solver and direct-simulation Monte Carlo method. In the continuum flow limit, the current formulation will go back to the gas-kinetic Navier-Stokes flow solver automatically.
Bai, Song; Jiang, Jun; Zhang, Qun; Xiong, Yujie
2015-05-21
Charge kinetics is highly critical in determining the quantum efficiency of solar-to-chemical conversion in photocatalysis, and this includes, but is not limited to, the separation of photoexcited electron-hole pairs, utilization of plasmonic hot carriers and delivery of photo-induced charges to reaction sites, as well as activation of reactants by energized charges. In this review, we highlight the recent progress on probing and steering charge kinetics toward designing highly efficient photocatalysts and elucidate the fundamentals behind the combinative use of controlled synthesis, characterization techniques (with a focus on spectroscopic characterizations) and theoretical simulations in photocatalysis studies. We first introduce the principles of various processes associated with charge kinetics that account for or may affect photocatalysis, from which a set of parameters that are critical to photocatalyst design can be summarized. We then outline the design rules for photocatalyst structures and their corresponding synthetic approaches. The implementation of characterization techniques and theoretical simulations in different steps of photocatalysis, together with the associated fundamentals and working mechanisms, are also presented. Finally, we discuss the challenges and opportunities for photocatalysis research at this unique intersection as well as the potential impact on other research fields.
Julin, Jan; Shiraiwa, Manabu; Miles, Rachael E H; Reid, Jonathan P; Pöschl, Ulrich; Riipinen, Ilona
2013-01-17
The condensational growth of submicrometer aerosol particles to climate relevant sizes is sensitive to their ability to accommodate vapor molecules, which is described by the mass accommodation coefficient. However, the underlying processes are not yet fully understood. We have simulated the mass accommodation and evaporation processes of water using molecular dynamics, and the results are compared to the condensation equations derived from the kinetic gas theory to shed light on the compatibility of the two. Molecular dynamics simulations were performed for a planar TIP4P-Ew water surface at four temperatures in the range 268-300 K as well as two droplets, with radii of 1.92 and 4.14 nm at T = 273.15 K. The evaporation flux from molecular dynamics was found to be in good qualitative agreement with that predicted by the simple kinetic condensation equations. Water droplet growth was also modeled with the kinetic multilayer model KM-GAP of Shiraiwa et al. [Atmos. Chem. Phys. 2012, 12, 2777]. It was found that, due to the fast transport across the interface, the growth of a pure water droplet is controlled by gas phase diffusion. These facts indicate that the simple kinetic treatment is sufficient in describing pure water condensation and evaporation. The droplet size was found to have minimal effect on the value of the mass accommodation coefficient. The mass accommodation coefficient was found to be unity (within 0.004) for all studied surfaces, which is in agreement with previous simulation work. Additionally, the simulated evaporation fluxes imply that the evaporation coefficient is also unity. Comparing the evaporation rates of the mass accommodation and evaporation simulations indicated that the high collision flux, corresponding to high supersaturation, present in typical molecular dynamics mass accommodation simulations can under certain conditions lead to an increase in the evaporation rate. Consequently, in such situations the mass accommodation coefficient
Falvo, Cyril; Hayashi, Tomoyuki; Zhuang, Wei; Mukamel, Shaul
2009-01-01
The two dimensional infrared photon echo spectrum of Antamanide (-1Val-2Pro-3Pro-4Ala-5Phe-6Phe-7Pro-8Pro-9Phe-10Pro-) in chloroform is calculated using an explicit solvent MD simulation combined with a DFT map for the effective vibrational Hamiltonian. Evidence for a strong intramolecular hydrogen bonding network is found. Comparison with experimental absorption allows to identify the dominant conformation. Multidimensional spectroscopy reveals intramolecular couplings and gives information on its dynamics. A two color amide-I and amide-A cross peak is predicted and analyzed in term of local structure. PMID:18781709
Alternative fatty food simulants and diffusion kinetics of nylon 12 food packaging.
Stoffers, N H; Dekker, M; Linssen, J P H; Störmer, A; Franz, R
2003-10-01
The migration of laurolactam and cyclic di- and trimer of nylon 12 was assessed using three different films and five food simulants (olive oil, isooctane, 95% ethanol, 50% ethanol, water). Substitute test conditions for migration into olive oil according to European Union Directive EC/97/48 were applied using 95% ethanol and isooctane. Results showed that 95% ethanol overestimated while isooctane underestimated the respective migration into olive oil. Water was the best olive oil substitute, as migration of laurolactam into water and olive oil using the same temperature gave similar results. Additionally, diffusion kinetics of laurolactam were investigated by migration kinetic studies using isooctane and olive oil. Diffusion coefficients determined with isooctane were significantly higher than those found using olive oil. It was proved that isooctane had an interaction and olive oil was inert to the polymer. The diffusion conductance parameter, A(p), for nylon 12 determined using olive oil ranged from 0.3 to 0.6.
3-D kinetics simulations of the NRU reactor using the DONJON code
Leung, T. C.; Atfield, M. D.; Koclas, J.
2006-07-01
The NRU reactor is highly heterogeneous, heavy-water cooled and moderated, with online refuelling capability. It is licensed to operate at a maximum power of 135 MW, with a peak thermal flux of approximately 4.0 x 10{sup 18} n.m{sup -2} . s{sup -1}. In support of the safe operation of NRU, three-dimensional kinetics calculations for reactor transients have been performed using the DONJON code. The code was initially designed to perform space-time kinetics calculations for the CANDU{sup R} power reactors. This paper describes how the DONJON code can be applied to perform neutronic simulations for the analysis of reactor transients in NRU, and presents calculation results for some transients. (authors)
Ma, Dujuan; Liu, Guoguang; Lv, Wenying; Yao, Kun; Zhang, Xiangdan; Xiao, Huahua
2014-01-01
The main objective of this study was to investigate the degradation mechanism, the reaction kinetics, and the evolution of toxicity of naproxen in waters under simulated solar radiation. These criteria were investigated by conducting quenching experiments with reactive oxygen species (ROS), oxygen concentration experiments, and toxicity evaluations with Vibrio fischeri bacteria. The results indicated that the degradation of naproxen proceeds via pseudo first-order kinetics in all cases and that photodegradation included degradation by direct photolysis and by self-sensitization via ROS; the contribution rates of self-sensitized photodegradation were 1.4%, 65.8%, and 31.7% via ·OH, (1)O₂ and O₂(•-), respectively. Furthermore, the oxygen concentration experiments indicated that dissolved oxygen inhibited the direct photodegradation of naproxen, and the higher the oxygen content, the more pronounced the inhibitory effect. The toxicity evaluation illustrated that some of the intermediate products formed were more toxic than naproxen.
Ard, Shaun G; Li, Anyang; Martinez, Oscar; Shuman, Nicholas S; Viggiano, Albert A; Guo, Hua
2014-12-11
Thermal rate coefficients for the title reactions computed using a quasi-classical trajectory method on an accurate global potential energy surface fitted to ∼81,000 high-level ab initio points are compared with experimental values measured between 100 and 600 K using a variable temperature selected ion flow tube instrument. Excellent agreement is found across the entire temperature range, showing a subtle, but unusual temperature dependence of the rate coefficients. For both reactions the temperature dependence has a maximum around 350 K, which is a result of H2O(+) rotations increasing the reactivity, while kinetic energy is decreasing the reactivity. A strong isotope effect is found, although the calculations slightly overestimate the kinetic isotope effect. The good experiment-theory agreement not only validates the accuracy of the potential energy surface but also provides more accurate kinetic data over a large temperature range.
Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite
Pogorelov, N.V.; Borovikov, S. N.; Bedford, M. C.; Heerikhuisen, J.; Kim, T. K.; Kryukov, I. A.; Zank, G. P.
2013-04-01
Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS) is a package of numerical codes capable of performing adaptive mesh refinement simulations of complex plasma flows in the presence of discontinuities and charge exchange between ions and neutral atoms. The flow of the ionized component is described with the ideal MHD equations, while the transport of atoms is governed either by the Boltzmann equation or multiple Euler gas dynamics equations. We have enhanced the code with additional physical treatments for the transport of turbulence and acceleration of pickup ions in the interplanetary space and at the termination shock. In this article, we present the results of our numerical simulation of the solar wind (SW) interaction with the local interstellar medium (LISM) in different time-dependent and stationary formulations. Numerical results are compared with the Ulysses, Voyager, and OMNI observations. Finally, the SW boundary conditions are derived from in-situ spacecraft measurements and remote observations.
Simulation of γ' Precipitation Kinetics in a Commercial Ni-Base Superalloy
NASA Astrophysics Data System (ADS)
Fahrmann, M. G.; Metzler, D. A.
2016-11-01
The ability to accurately simulate the precipitation kinetics of γ' and other strengthening phases in Ni-base superalloys is of great interest to industry. Several commercial simulation tools such as TC-PRISMA (Thermo-Calc, Sweden) and PanPrecipitation (Computherm, USA) have been made available in recent years. This paper reports the outcome of a validation study on wrought Ni-base superalloy HAYNES® 282® alloy for two scenarios of commercial interest: (1) the precipitation of γ' during continuous cooling, and (2) the precipitation of γ' during two-step aging. The simulation results are validated against experimental data. Any discrepancies are discussed in the context of the uncertainty in key material properties (such as interfacial energies), model assumptions, and experimental errors.
Brunner, S.; Berger, R. L.; Cohen, B. I.; Hausammann, L.; Valeo, E. J.
2014-10-01
Kinetic Vlasov simulations of one-dimensional finite amplitude Electron Plasma Waves are performed in a multi-wavelength long system. A systematic study of the most unstable linear sideband mode, in particular its growth rate γ and quasi- wavenumber δk, is carried out by scanning the amplitude and wavenumber of the initial wave. Simulation results are successfully compared against numerical and analytical solutions to the reduced model by Kruer et al. [Phys. Rev. Lett. 23, 838 (1969)] for the Trapped Particle Instability (TPI). A model recently suggested by Dodin et al. [Phys. Rev. Lett. 110, 215006 (2013)], which in addition to the TPI accounts for the so-called Negative Mass Instability because of a more detailed representation of the trapped particle dynamics, is also studied and compared with simulations.
Kinetic AGN feedback effects on cluster cool cores simulated using SPH
NASA Astrophysics Data System (ADS)
Barai, Paramita; Murante, Giuseppe; Borgani, Stefano; Gaspari, Massimo; Granato, Gian Luigi; Monaco, Pierluigi; Ragone-Figueroa, Cinthia
2016-09-01
We implement novel numerical models of AGN feedback in the SPH code GADGET-3, where the energy from a supermassive black hole (BH) is coupled to the surrounding gas in the kinetic form. Gas particles lying inside a bi-conical volume around the BH are imparted a one-time velocity (10 000 km s-1) increment. We perform hydrodynamical simulations of isolated cluster (total mass 1014 h-1 M⊙), which is initially evolved to form a dense cool core, having central T ≤ 106 K. A BH resides at the cluster centre, and ejects energy. The feedback-driven fast wind undergoes shock with the slower moving gas, which causes the imparted kinetic energy to be thermalized. Bipolar bubble-like outflows form propagating radially outward to a distance of a few 100 kpc. The radial profiles of median gas properties are influenced by BH feedback in the inner regions (r < 20-50 kpc). BH kinetic feedback, with a large value of the feedback efficiency, depletes the inner cool gas and reduces the hot gas content, such that the initial cool core of the cluster is heated up within a time 1.9 Gyr, whereby the core median temperature rises to above 107 K, and the central entropy flattens. Our implementation of BH thermal feedback (using the same efficiency as kinetic), within the star formation model, cannot do this heating, where the cool core remains. The inclusion of cold gas accretion in the simulations produces naturally a duty cycle of the AGN with a periodicity of 100 Myr.
Intercomparison of the seasonal cycle in 200 hPa kinetic energy in AMIP GCM simulations
Boyle, J.S.
1996-10-01
The 200 hPa kinetic energy is represented by means of the spherical harmonic components for the Atmospheric Model Intercomparison Project (AMIP) simulations, the National Center for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis and the European Centre for Medium Range Weather Forecast Reanalysis (ERA). The data used are the monthly mean wind fields from 1979 to 1988. The kinetic energy is decomposed into the divergent (DKE) and rotational (RKE) components and emphasis is placed on examining the former. The two reanalysis data sets show reasonable agreement that is best for the rotational kinetic energy. The largest difference in the divergent kinetic energy occurs during the northern summer. As might be expected, the two analyses are closet in regions where there are sufficient observations such that the effect of the model used in the assimilation cycle are minimized. The observed RKE show only a slight seasonal cycle with a maximum occuring during the northern winter. The DKE, on the other hand, has a very pronounced seasonal cycle with maxima at the solsticial seasons and minima during the equinoctial seasons. The model results show a very large spread in the magnitudes of the RKE and DKE although the models all evince a seasonal variation in phase with that observed. The median values of the seasonal cycle of RKE and DKE for the models are usually superior to those of any individual model. Results are also presented for simulation following the AMIP protocol but using updated versions of the original AMIP entries. In most cases these new integrations show better agreement with the observations.
NASA Astrophysics Data System (ADS)
De Wilde, Juray; Lorant, Christophe; Descamps, Pierre
2017-04-01
In atmospheric-pressure plasma reactors, the flow dynamics can be complex, determine the reactor performance and complicate scale-up. Coupling computational fluid dynamics to the calculation of the electric field and plasma chemistry is challenging because of the numerical stiffness introduced by the difference in time scale of the different phenomena involved. Focusing on low-temperature, atmospheric-pressure pure nitrogen plasma, a model and model reduction based solution strategy to deal with the numerical stiffness are presented and evaluated. The influence of the electric field on the flow dynamics and species concentration fields is first qualitatively studied by means of 2D simulations of a sharp-end plate-to-plane configuration. Next, a specific reactor prototype for low-temperature, atmospheric-pressure plasma-enhanced chemical vapor deposition for in-line surface treatments is simulated to illustrate the importance of accounting for the detailed flow dynamics.
NASA Astrophysics Data System (ADS)
Savoini, P.; Lembege, B.
2015-12-01
The ion foreshock located upstream of the Earth's shock wave is populated with ions having interacted with the shock, and then, reflected back with an high energy gain. Spacecrafts have clearly established the existence of two distinct populations in the quasi-perpendicular shock region (i.e. for 45° ≤ ΘBn ≤ 90°, where ΘBn is the angle between the shock normal and the upstream magnetic field) : (i) field-aligned ion beams or « FAB » characterized by a gyrotropic distribution, and (ii) gyro-phase bunched ions or « GPB » characterized by a NON gyrotropic distribution. One of the important unresolved problem is the exact origin of the particles contributing to these two populations. To our knowledge, it was the first time that full-particle simulations have been performed including self-consistently the shock front curvature and nonstationarity, and the time-of-flight effects. Our analysis evidences that these two backstreaming populations may be reflected by the front itself and can be differentiated both in terms of interaction time and trajectory within the shock front. In particular, simulations evidence that "GPB" population is characterized by a short interaction time (ΔTinter = 1 to 2 τci) while the "FAB" population corresponds to a much larger time range (from 1 τci to 10 τci), where tci is the upstream ion gyroperiod. Present individual ion trajectories evidence that "FAB" population shows a strong perpendicular drift at the shock front (i.e. strong dependence of the pitch angle to the perpendicular velocity) whereas the "GPB" population shows no perpendicular drift (i.e. its pitch angle is mainly driven by the parallel velocity). Such differences explain why the "FAB" population loses their gyro-phase coherency and become gyrotropic which is not the case for the "GPB". This important result was not expected and greatly simplifies the question of their origin.
Mu, Zhiping; Dobrucki, Lawrence W; Liu, Yi-Hwa
The imaging of distributed sources with near-field coded aperture (CA) remains extremely challenging and is broadly considered unsuitable for single-photon emission computerized tomography (SPECT). This study proposes a novel CA SPECT reconstruction approach and evaluates the feasibilities of imaging and reconstructing distributed hot sources and cold lesions using near-field CA collimation and iterative image reconstruction. Computer simulations were designed to compare CA and pinhole collimations in two-dimensional radionuclide imaging. Digital phantoms were created and CA images of the phantoms were reconstructed using maximum likelihood expectation maximization (MLEM). Errors and the contrast-to-noise ratio (CNR) were calculated and image resolution was evaluated. An ex vivo rat heart with myocardial infarction was imaged using a micro-SPECT system equipped with a custom-made CA module and a commercial 5-pinhole collimator. Rat CA images were reconstructed via the three-dimensional (3-D) MLEM algorithm developed for CA SPECT with and without correction for a large projection angle, and 5-pinhole images were reconstructed using the commercial software provided by the SPECT system. Phantom images of CA were markedly improved in terms of image quality, quantitative root-mean-squared error, and CNR, as compared to pinhole images. CA and pinhole images yielded similar image resolution, while CA collimation resulted in fewer noise artifacts. CA and pinhole images of the rat heart were well reconstructed and the myocardial perfusion defects could be clearly discerned from 3-D CA and 5-pinhole SPECT images, whereas 5-pinhole SPECT images suffered from severe noise artifacts. Image contrast of CA SPECT was further improved after correction for the large projection angle used in the rat heart imaging. The computer simulations and small-animal imaging study presented herein indicate that the proposed 3-D CA SPECT imaging and reconstruction approaches worked reasonably
Zhang, Chao; Chen, Yin-Guang
2013-03-01
Two groups of sequencing batch reactors were used to study the metabolism substrate transformation of phosphorus-accumulating organisms (PAO) and glycogen-accumulating organisms (GAO) fed with mixed acetic and propionic acids. Seven stoichiometry parameters and 24 kinetic parameters were contained in the PAO and GAO kinetic model, and stoichiometry parameters were deduced from the stoichiometry models, while kinetic parameters were determined by experimental results. The kinetic model parameters of stoichiometry and kinetics were determined according the experiments and the literature. Subsequently, the substrate transformations of PAO and GAO were calculated by the Matlab software. The model curves matched the SBR experimental data well, indicating that the kinetic model based on SCFAs metabolism could be used to simulate PAO and GAO in anaerobic-aerobic conditions.
Monte Carlo simulation for kinetic chemotaxis model: An application to the traveling population wave
NASA Astrophysics Data System (ADS)
Yasuda, Shugo
2017-02-01
A Monte Carlo simulation of chemotactic bacteria is developed on the basis of the kinetic model and is applied to a one-dimensional traveling population wave in a microchannel. In this simulation, the Monte Carlo method, which calculates the run-and-tumble motions of bacteria, is coupled with a finite volume method to calculate the macroscopic transport of the chemical cues in the environment. The simulation method can successfully reproduce the traveling population wave of bacteria that was observed experimentally and reveal the microscopic dynamics of bacterium coupled with the macroscopic transports of the chemical cues and bacteria population density. The results obtained by the Monte Carlo method are also compared with the asymptotic solution derived from the kinetic chemotaxis equation in the continuum limit, where the Knudsen number, which is defined by the ratio of the mean free path of bacterium to the characteristic length of the system, vanishes. The validity of the Monte Carlo method in the asymptotic behaviors for small Knudsen numbers is numerically verified.
A Simulation Model for the Toroidal Ion Temperature Gradient Instability with Fully Kinetic Ions
NASA Astrophysics Data System (ADS)
Sturdevant, Benjamin; Parker, Scott; Chen, Yang
2016-10-01
A simulation model for the toroidal ITG mode in which the ions follow the primitive Lorentz force equations of motion is presented. Such a model can provide an important validation tool or replacement for gyrokinetic ion models in applications where higher order terms may be important. A number of multiple-scale simulation techniques are employed in this work, based on the previous success in slab geometry with an implicit orbit averaged and sub-cycled δf model. For the toroidal geometry model, we have derived a particle integration scheme based on variational principles, which is demonstrated to produce stable and accurate ion trajectories on long time scales. Orbit averaging and sub-cycling will be implemented with the variational integration scheme. The inclusion of equilibrium gradients in the fully kinetic δf formulation is achieved through the use of a guiding center coordinate transformation of the weight equation. Simulation results for the fully kinetic ion model will be presented for the cyclone base case and comparisons will be made with gyrokinetic ion models.
Particle Size Effect on Wetting Kinetics of a Nanosuspension Drop: MD Simulations
NASA Astrophysics Data System (ADS)
Shi, Baiou; Webb, Edmund
The behavior of nano-fluids, or fluid suspensions containing nanoparticles, has garnered tremendous attention recently for applications in advanced manufacturing. In our previous results from MD simulations, for a wetting system with different advancing contact angles, cases where self-pinning was observed were compared to cases where it was not and relevant forces on particles at the contact line were computed. To advance this work, the roles of particle size and particle loading are examined. Results presented illustrate how particle size affects spreading kinetics and how this connects to dynamic droplet morphology and relevant forces that exist nearby the contact line region. Furthermore, increased particle size in simulations permits a more detailed investigation of particle/substrate interfacial contributions to behavior observed at the advancing contact line. Based on changes in spreading kinetics with particle size, forces between the particle and liquid front are predicted and compared to those computed from simulations. At high loading, particle/particle interactions become relevant and forces computed between particles entrained to an advancing contact line will be presented.
Chemical kinetic simulation of kerosene combustion in an individual flame tube.
Zeng, Wen; Liang, Shuang; Li, Hai-Xia; Ma, Hong-An
2014-05-01
The use of detailed chemical reaction mechanisms of kerosene is still very limited in analyzing the combustion process in the combustion chamber of the aircraft engine. In this work, a new reduced chemical kinetic mechanism for fuel n-decane, which selected as a surrogate fuel for kerosene, containing 210 elemental reactions (including 92 reversible reactions and 26 irreversible reactions) and 50 species was developed, and the ignition and combustion characteristics of this fuel in both shock tube and flat-flame burner were kinetic simulated using this reduced reaction mechanism. Moreover, the computed results were validated by experimental data. The calculated values of ignition delay times at pressures of 12, 50 bar and equivalence ratio is 1.0, 2.0, respectively, and the main reactants and main products mole fractions using this reduced reaction mechanism agree well with experimental data. The combustion processes in the individual flame tube of a heavy duty gas turbine combustor were simulated by coupling this reduced reaction mechanism of surrogate fuel n-decane and one step reaction mechanism of surrogate fuel C12H23 into the computational fluid dynamics software. It was found that this reduced reaction mechanism is shown clear advantages in simulating the ignition and combustion processes in the individual flame tube over the one step reaction mechanism.
Burchardt, Malte; Träuble, Markus; Wittstock, Gunther
2009-06-15
The formalism for simulating scanning electrochemical microscopy (SECM) experiments by boundary element methods in three space coordinates has been extended to allow consideration of nonlinear boundary conditions. This is achieved by iteratively refining the boundary conditions that are encoded in a boundary condition matrix. As an example, the simulations are compared to experimental approach cu