The Plasma Simulation Code: A modern particle-in-cell code with patch-based load-balancing

NASA Astrophysics Data System (ADS)

Germaschewski, Kai; Fox, William; Abbott, Stephen; Ahmadi, Narges; Maynard, Kristofor; Wang, Liang; Ruhl, Hartmut; Bhattacharjee, Amitava

2016-08-01

This work describes the Plasma Simulation Code (PSC), an explicit, electromagnetic particle-in-cell code with support for different order particle shape functions. We review the basic components of the particle-in-cell method as well as the computational architecture of the PSC code that allows support for modular algorithms and data structure in the code. We then describe and analyze in detail a distinguishing feature of PSC: patch-based load balancing using space-filling curves which is shown to lead to major efficiency gains over unbalanced methods and a previously used simpler balancing method.

Improvement of Mishchenko's T-matrix code for absorbing particles.

PubMed

Moroz, Alexander

2005-06-10

The use of Gaussian elimination with backsubstitution for matrix inversion in scattering theories is discussed. Within the framework of the T-matrix method (the state-of-the-art code by Mishchenko is freely available at http://www.giss.nasa.gov/-crmim), it is shown that the domain of applicability of Mishchenko's FORTRAN 77 (F77) code can be substantially expanded in the direction of strongly absorbing particles where the current code fails to converge. Such an extension is especially important if the code is to be used in nanoplasmonic or nanophotonic applications involving metallic particles. At the same time, convergence can also be achieved for large nonabsorbing particles, in which case the non-Numerical Algorithms Group option of Mishchenko's code diverges. Computer F77 implementation of Mishchenko's code supplemented with Gaussian elimination with backsubstitution is freely available at http://www.wave-scattering.com.

Two-dimensional implosion simulations with a kinetic particle code [2D implosion simulations with a kinetic particle code

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

Sagert, Irina; Even, Wesley Paul; Strother, Terrance Timothy

Here, we perform two-dimensional implosion simulations using a Monte Carlo kinetic particle code. The application of a kinetic transport code is motivated, in part, by the occurrence of nonequilibrium effects in inertial confinement fusion capsule implosions, which cannot be fully captured by hydrodynamic simulations. Kinetic methods, on the other hand, are able to describe both continuum and rarefied flows. We perform simple two-dimensional disk implosion simulations using one-particle species and compare the results to simulations with the hydrodynamics code rage. The impact of the particle mean free path on the implosion is also explored. In a second study, we focusmore » on the formation of fluid instabilities from induced perturbations. We find good agreement with hydrodynamic studies regarding the location of the shock and the implosion dynamics. Differences are found in the evolution of fluid instabilities, originating from the higher resolution of rage and statistical noise in the kinetic studies.« less

Two-dimensional implosion simulations with a kinetic particle code [2D implosion simulations with a kinetic particle code

DOE PAGES

Sagert, Irina; Even, Wesley Paul; Strother, Terrance Timothy

2017-05-17

Here, we perform two-dimensional implosion simulations using a Monte Carlo kinetic particle code. The application of a kinetic transport code is motivated, in part, by the occurrence of nonequilibrium effects in inertial confinement fusion capsule implosions, which cannot be fully captured by hydrodynamic simulations. Kinetic methods, on the other hand, are able to describe both continuum and rarefied flows. We perform simple two-dimensional disk implosion simulations using one-particle species and compare the results to simulations with the hydrodynamics code rage. The impact of the particle mean free path on the implosion is also explored. In a second study, we focusmore » on the formation of fluid instabilities from induced perturbations. We find good agreement with hydrodynamic studies regarding the location of the shock and the implosion dynamics. Differences are found in the evolution of fluid instabilities, originating from the higher resolution of rage and statistical noise in the kinetic studies.« less

An Extended Proof-Carrying Code Framework for Security Enforcement

NASA Astrophysics Data System (ADS)

Pirzadeh, Heidar; Dubé, Danny; Hamou-Lhadj, Abdelwahab

The rapid growth of the Internet has resulted in increased attention to security to protect users from being victims of security threats. In this paper, we focus on security mechanisms that are based on Proof-Carrying Code (PCC) techniques. In a PCC system, a code producer sends a code along with its safety proof to the consumer. The consumer executes the code only if the proof is valid. Although PCC has been shown to be a useful security framework, it suffers from the sheer size of typical proofs -proofs of even small programs can be considerably large. In this paper, we propose an extended PCC framework (EPCC) in which, instead of the proof, a proof generator for the program in question is transmitted. This framework enables the execution of the proof generator and the recovery of the proof on the consumer's side in a secure manner using a newly created virtual machine called the VEP (Virtual Machine for Extended PCC).

Parallelization Issues and Particle-In Codes.

NASA Astrophysics Data System (ADS)

Elster, Anne Cathrine

1994-01-01

"Everything should be made as simple as possible, but not simpler." Albert Einstein. The field of parallel scientific computing has concentrated on parallelization of individual modules such as matrix solvers and factorizers. However, many applications involve several interacting modules. Our analyses of a particle-in-cell code modeling charged particles in an electric field, show that these accompanying dependencies affect data partitioning and lead to new parallelization strategies concerning processor, memory and cache utilization. Our test-bed, a KSR1, is a distributed memory machine with a globally shared addressing space. However, most of the new methods presented hold generally for hierarchical and/or distributed memory systems. We introduce a novel approach that uses dual pointers on the local particle arrays to keep the particle locations automatically partially sorted. Complexity and performance analyses with accompanying KSR benchmarks, have been included for both this scheme and for the traditional replicated grids approach. The latter approach maintains load-balance with respect to particles. However, our results demonstrate it fails to scale properly for problems with large grids (say, greater than 128-by-128) running on as few as 15 KSR nodes, since the extra storage and computation time associated with adding the grid copies, becomes significant. Our grid partitioning scheme, although harder to implement, does not need to replicate the whole grid. Consequently, it scales well for large problems on highly parallel systems. It may, however, require load balancing schemes for non-uniform particle distributions. Our dual pointer approach may facilitate this through dynamically partitioned grids. We also introduce hierarchical data structures that store neighboring grid-points within the same cache -line by reordering the grid indexing. This alignment produces a 25% savings in cache-hits for a 4-by-4 cache. A consideration of the input data's effect on

Uncoupling cis-Acting RNA Elements from Coding Sequences Revealed a Requirement of the N-Terminal Region of Dengue Virus Capsid Protein in Virus Particle Formation

PubMed Central

Samsa, Marcelo M.; Mondotte, Juan A.; Caramelo, Julio J.

2012-01-01

Little is known about the mechanism of flavivirus genome encapsidation. Here, functional elements of the dengue virus (DENV) capsid (C) protein were investigated. Study of the N-terminal region of DENV C has been limited by the presence of overlapping cis-acting RNA elements within the protein-coding region. To dissociate these two functions, we used a recombinant DENV RNA with a duplication of essential RNA structures outside the C coding sequence. By the use of this system, the highly conserved amino acids FNML, which are encoded in the RNA cyclization sequence 5′CS, were found to be dispensable for C function. In contrast, deletion of the N-terminal 18 amino acids of C impaired DENV particle formation. Two clusters of basic residues (R5-K6-K7-R9 and K17-R18-R20-R22) were identified as important. A systematic mutational analysis indicated that a high density of positive charges, rather than particular residues at specific positions, was necessary. Furthermore, a differential requirement of N-terminal sequences of C for viral particle assembly was observed in mosquito and human cells. While no viral particles were observed in human cells with a virus lacking the first 18 residues of C, DENV propagation was detected in mosquito cells, although to a level about 50-fold less than that observed for a wild-type (WT) virus. We conclude that basic residues at the N terminus of C are necessary for efficient particle formation in mosquito cells but that they are crucial for propagation in human cells. This is the first report demonstrating that the N terminus of C plays a role in DENV particle formation. In addition, our results suggest that this function of C is differentially modulated in different host cells. PMID:22072762

Extending the Host Range of Bacteriophage Particles for DNA Transduction.

PubMed

Yosef, Ido; Goren, Moran G; Globus, Rea; Molshanski-Mor, Shahar; Qimron, Udi

2017-06-01

A major limitation in using bacteriophage-based applications is their narrow host range. Approaches for extending the host range have focused primarily on lytic phages in hosts supporting their propagation rather than approaches for extending the ability of DNA transduction into phage-restrictive hosts. To extend the host range of T7 phage for DNA transduction, we have designed hybrid particles displaying various phage tail/tail fiber proteins. These modular particles were programmed to package and transduce DNA into hosts that restrict T7 phage propagation. We have also developed an innovative generalizable platform that considerably enhances DNA transfer into new hosts by artificially selecting tails that efficiently transduce DNA. In addition, we have demonstrated that the hybrid particles transduce desired DNA into desired hosts. This study thus critically extends and improves the ability of the particles to transduce DNA into novel phage-restrictive hosts, providing a platform for myriad applications that require this ability. Copyright © 2017 Elsevier Inc. All rights reserved.

The Particle Accelerator Simulation Code PyORBIT

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

Gorlov, Timofey V; Holmes, Jeffrey A; Cousineau, Sarah M

2015-01-01

The particle accelerator simulation code PyORBIT is presented. The structure, implementation, history, parallel and simulation capabilities, and future development of the code are discussed. The PyORBIT code is a new implementation and extension of algorithms of the original ORBIT code that was developed for the Spallation Neutron Source accelerator at the Oak Ridge National Laboratory. The PyORBIT code has a two level structure. The upper level uses the Python programming language to control the flow of intensive calculations performed by the lower level code implemented in the C++ language. The parallel capabilities are based on MPI communications. The PyORBIT ismore » an open source code accessible to the public through the Google Open Source Projects Hosting service.« less

N-MODY: A Code for Collisionless N-body Simulations in Modified Newtonian Dynamics

NASA Astrophysics Data System (ADS)

Londrillo, Pasquale; Nipoti, Carlo

2011-02-01

N-MODY is a parallel particle-mesh code for collisionless N-body simulations in modified Newtonian dynamics (MOND). N-MODY is based on a numerical potential solver in spherical coordinates that solves the non-linear MOND field equation, and is ideally suited to simulate isolated stellar systems. N-MODY can be used also to compute the MOND potential of arbitrary static density distributions. A few applications of N-MODY indicate that some astrophysically relevant dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter.

A fast ellipse extended target PHD filter using box-particle implementation

NASA Astrophysics Data System (ADS)

Zhang, Yongquan; Ji, Hongbing; Hu, Qi

2018-01-01

This paper presents a box-particle implementation of the ellipse extended target probability hypothesis density (ET-PHD) filter, called the ellipse extended target box particle PHD (EET-BP-PHD) filter, where the extended targets are described as a Poisson model developed by Gilholm et al. and the term "box" is here equivalent to the term "interval" used in interval analysis. The proposed EET-BP-PHD filter is capable of dynamically tracking multiple ellipse extended targets and estimating the target states and the number of targets, in the presence of clutter measurements, false alarms and missed detections. To derive the PHD recursion of the EET-BP-PHD filter, a suitable measurement likelihood is defined for a given partitioning cell, and the main implementation steps are presented along with the necessary box approximations and manipulations. The limitations and capabilities of the proposed EET-BP-PHD filter are illustrated by simulation examples. The simulation results show that a box-particle implementation of the ET-PHD filter can avoid the high number of particles and reduce computational burden, compared to a particle implementation of that for extended target tracking.

Coupling extended magnetohydrodynamic fluid codes with radiofrequency ray tracing codes for fusion modeling

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Held, Eric D.

2015-09-01

Neoclassical tearing modes are macroscopic (L ∼ 1 m) instabilities in magnetic fusion experiments; if unchecked, these modes degrade plasma performance and may catastrophically destroy plasma confinement by inducing a disruption. Fortunately, the use of properly tuned and directed radiofrequency waves (λ ∼ 1 mm) can eliminate these modes. Numerical modeling of this difficult multiscale problem requires the integration of separate mathematical models for each length and time scale (Jenkins and Kruger, 2012 [21]); the extended MHD model captures macroscopic plasma evolution while the RF model tracks the flow and deposition of injected RF power through the evolving plasma profiles. The scale separation enables use of the eikonal (ray-tracing) approximation to model the RF wave propagation. In this work we demonstrate a technique, based on methods of computational geometry, for mapping the ensuing RF data (associated with discrete ray trajectories) onto the finite-element/pseudospectral grid that is used to model the extended MHD physics. In the new representation, the RF data can then be used to construct source terms in the equations of the extended MHD model, enabling quantitative modeling of RF-induced tearing mode stabilization. Though our specific implementation uses the NIMROD extended MHD (Sovinec et al., 2004 [22]) and GENRAY RF (Smirnov et al., 1994 [23]) codes, the approach presented can be applied more generally to any code coupling requiring the mapping of ray tracing data onto Eulerian grids.

Particle Number Dependence of the N-body Simulations of Moon Formation

NASA Astrophysics Data System (ADS)

Sasaki, Takanori; Hosono, Natsuki

2018-04-01

The formation of the Moon from the circumterrestrial disk has been investigated by using N-body simulations with the number N of particles limited from 104 to 105. We develop an N-body simulation code on multiple Pezy-SC processors and deploy Framework for Developing Particle Simulators to deal with large number of particles. We execute several high- and extra-high-resolution N-body simulations of lunar accretion from a circumterrestrial disk of debris generated by a giant impact on Earth. The number of particles is up to 107, in which 1 particle corresponds to a 10 km sized satellitesimal. We find that the spiral structures inside the Roche limit radius differ between low-resolution simulations (N ≤ 105) and high-resolution simulations (N ≥ 106). According to this difference, angular momentum fluxes, which determine the accretion timescale of the Moon also depend on the numerical resolution.

Progress on the Development of the hPIC Particle-in-Cell Code

NASA Astrophysics Data System (ADS)

Dart, Cameron; Hayes, Alyssa; Khaziev, Rinat; Marcinko, Stephen; Curreli, Davide; Laboratory of Computational Plasma Physics Team

2017-10-01

Advancements were made in the development of the kinetic-kinetic electrostatic Particle-in-Cell code, hPIC, designed for large-scale simulation of the Plasma-Material Interface. hPIC achieved a weak scaling efficiency of 87% using the Algebraic Multigrid Solver BoomerAMG from the PETSc library on more than 64,000 cores of the Blue Waters supercomputer at the University of Illinois at Urbana-Champaign. The code successfully simulates two-stream instability and a volume of plasma over several square centimeters of surface extending out to the presheath in kinetic-kinetic mode. Results from a parametric study of the plasma sheath in strongly magnetized conditions will be presented, as well as a detailed analysis of the plasma sheath structure at grazing magnetic angles. The distribution function and its moments will be reported for plasma species in the simulation domain and at the material surface for plasma sheath simulations. Membership Pending.

IMPLEMENTATION OF SINK PARTICLES IN THE ATHENA CODE

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

Gong Hao; Ostriker, Eve C., E-mail: hgong@astro.umd.edu, E-mail: eco@astro.princeton.edu

2013-01-15

We describe the implementation and tests of sink particle algorithms in the Eulerian grid-based code Athena. The introduction of sink particles enables the long-term evolution of systems in which localized collapse occurs, and it is impractical (or unnecessary) to resolve the accretion shocks at the centers of collapsing regions. We discuss the similarities and differences of our methods compared to other implementations of sink particles. Our criteria for sink creation are motivated by the properties of the Larson-Penston collapse solution. We use standard particle-mesh methods to compute particle and gas gravity together. Accretion of mass and momenta onto sinks ismore » computed using fluxes returned by the Riemann solver. A series of tests based on previous analytic and numerical collapse solutions is used to validate our method and implementation. We demonstrate use of our code for applications with a simulation of planar converging supersonic turbulent flow, in which multiple cores form and collapse to create sinks; these sinks continue to interact and accrete from their surroundings over several Myr.« less

Shielding evaluation for solar particle events using MCNPX, PHITS and OLTARIS codes

NASA Astrophysics Data System (ADS)

Aghara, S. K.; Sriprisan, S. I.; Singleterry, R. C.; Sato, T.

2015-01-01

Detailed analyses of Solar Particle Events (SPE) were performed to calculate primary and secondary particle spectra behind aluminum, at various thicknesses in water. The simulations were based on Monte Carlo (MC) radiation transport codes, MCNPX 2.7.0 and PHITS 2.64, and the space radiation analysis website called OLTARIS (On-Line Tool for the Assessment of Radiation in Space) version 3.4 (uses deterministic code, HZETRN, for transport). The study is set to investigate the impact of SPEs spectra transporting through 10 or 20 g/cm2 Al shield followed by 30 g/cm2 of water slab. Four historical SPE events were selected and used as input source spectra particle differential spectra for protons, neutrons, and photons are presented. The total particle fluence as a function of depth is presented. In addition to particle flux, the dose and dose equivalent values are calculated and compared between the codes and with the other published results. Overall, the particle fluence spectra from all three codes show good agreement with the MC codes showing closer agreement compared to the OLTARIS results. The neutron particle fluence from OLTARIS is lower than the results from MC codes at lower energies (E < 100 MeV). Based on mean square difference analysis the results from MCNPX and PHITS agree better for fluence, dose and dose equivalent when compared to OLTARIS results.

Extending self-organizing particle systems to problem solving.

PubMed

Rodríguez, Alejandro; Reggia, James A

2004-01-01

Self-organizing particle systems consist of numerous autonomous, purely reflexive agents ("particles") whose collective movements through space are determined primarily by local influences they exert upon one another. Inspired by biological phenomena (bird flocking, fish schooling, etc.), particle systems have been used not only for biological modeling, but also increasingly for applications requiring the simulation of collective movements such as computer-generated animation. In this research, we take some first steps in extending particle systems so that they not only move collectively, but also solve simple problems. This is done by giving the individual particles (agents) a rudimentary intelligence in the form of a very limited memory and a top-down, goal-directed control mechanism that, triggered by appropriate conditions, switches them between different behavioral states and thus different movement dynamics. Such enhanced particle systems are shown to be able to function effectively in performing simulated search-and-collect tasks. Further, computational experiments show that collectively moving agent teams are more effective than similar but independently moving ones in carrying out such tasks, and that agent teams of either type that split off members of the collective to protect previously acquired resources are most effective. This work shows that the reflexive agents of contemporary particle systems can readily be extended to support goal-directed problem solving while retaining their collective movement behaviors. These results may prove useful not only for future modeling of animal behavior, but also in computer animation, coordinated movement control in robotic teams, particle swarm optimization, and computer games.

LIGKA: A linear gyrokinetic code for the description of background kinetic and fast particle effects on the MHD stability in tokamaks

NASA Astrophysics Data System (ADS)

Lauber, Ph.; Günter, S.; Könies, A.; Pinches, S. D.

2007-09-01

In a plasma with a population of super-thermal particles generated by heating or fusion processes, kinetic effects can lead to the additional destabilisation of MHD modes or even to additional energetic particle modes. In order to describe these modes, a new linear gyrokinetic MHD code has been developed and tested, LIGKA (linear gyrokinetic shear Alfvén physics) [Ph. Lauber, Linear gyrokinetic description of fast particle effects on the MHD stability in tokamaks, Ph.D. Thesis, TU München, 2003; Ph. Lauber, S. Günter, S.D. Pinches, Phys. Plasmas 12 (2005) 122501], based on a gyrokinetic model [H. Qin, Gyrokinetic theory and computational methods for electromagnetic perturbations in tokamaks, Ph.D. Thesis, Princeton University, 1998]. A finite Larmor radius expansion together with the construction of some fluid moments and specification to the shear Alfvén regime results in a self-consistent, electromagnetic, non-perturbative model, that allows not only for growing or damped eigenvalues but also for a change in mode-structure of the magnetic perturbation due to the energetic particles and background kinetic effects. Compared to previous implementations [H. Qin, mentioned above], this model is coded in a more general and comprehensive way. LIGKA uses a Fourier decomposition in the poloidal coordinate and a finite element discretisation in the radial direction. Both analytical and numerical equilibria can be treated. Integration over the unperturbed particle orbits is performed with the drift-kinetic HAGIS code [S.D. Pinches, Ph.D. Thesis, The University of Nottingham, 1996; S.D. Pinches et al., CPC 111 (1998) 131] which accurately describes the particles' trajectories. This allows finite-banana-width effects to be implemented in a rigorous way since the linear formulation of the model allows the exchange of the unperturbed orbit integration and the discretisation of the perturbed potentials in the radial direction. Successful benchmarks for toroidal Alfvén

Extended micro objects as dark matter particles

NASA Astrophysics Data System (ADS)

Belotsky, K.; Rubin, S.; Svadkovsky, I.

2017-05-01

Models of various forms of composite dark matter (DM) predicted by particle theory and the DM constituents formed by gravity that are not reduced to new elementary particle candidates are discussed. Main attention is paid to a gravitational origin of the DM. The influence of extended mass spectrum of primordial black holes on observational limits is considered. It is shown that non-uniformly deformed extra space can be considered as point-like masses which possess only gravitational interaction with each other and with the ordinary particles. The recently discussed six-dimensional stable wormholes could contribute to the DM. The contribution of dark atoms is also considered.

VINE-A NUMERICAL CODE FOR SIMULATING ASTROPHYSICAL SYSTEMS USING PARTICLES. I. DESCRIPTION OF THE PHYSICS AND THE NUMERICAL METHODS

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

Wetzstein, M.; Nelson, Andrew F.; Naab, T.

2009-10-01

We present a numerical code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is written in Fortran 95 and is designed to be versatile, flexible, and extensible, with modular options that can be selected either at the time the code is compiled or at run time through a text input file. We include a number of general purpose modules describing a variety of physical processes commonly required in the astrophysical community and we expect that the effort required to integrate additional or alternate modules into the code will be small. Inmore » its simplest form the code can evolve the dynamical trajectories of a set of particles in two or three dimensions using a module which implements either a Leapfrog or Runge-Kutta-Fehlberg integrator, selected by the user at compile time. The user may choose to allow the integrator to evolve the system using individual time steps for each particle or with a single, global time step for all. Particles may interact gravitationally as N-body particles, and all or any subset may also interact hydrodynamically, using the smoothed particle hydrodynamic (SPH) method by selecting the SPH module. A third particle species can be included with a module to model massive point particles which may accrete nearby SPH or N-body particles. Such particles may be used to model, e.g., stars in a molecular cloud. Free boundary conditions are implemented by default, and a module may be selected to include periodic boundary conditions. We use a binary 'Press' tree to organize particles for rapid access in gravity and SPH calculations. Modules implementing an interface with special purpose 'GRAPE' hardware may also be selected to accelerate the gravity calculations. If available, forces obtained from the GRAPE coprocessors may be transparently substituted for those obtained from the tree, or both tree and GRAPE may be used as a combination GRAPE/tree code. The code may be run without

Vine—A Numerical Code for Simulating Astrophysical Systems Using Particles. I. Description of the Physics and the Numerical Methods

NASA Astrophysics Data System (ADS)

Wetzstein, M.; Nelson, Andrew F.; Naab, T.; Burkert, A.

2009-10-01

We present a numerical code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is written in Fortran 95 and is designed to be versatile, flexible, and extensible, with modular options that can be selected either at the time the code is compiled or at run time through a text input file. We include a number of general purpose modules describing a variety of physical processes commonly required in the astrophysical community and we expect that the effort required to integrate additional or alternate modules into the code will be small. In its simplest form the code can evolve the dynamical trajectories of a set of particles in two or three dimensions using a module which implements either a Leapfrog or Runge-Kutta-Fehlberg integrator, selected by the user at compile time. The user may choose to allow the integrator to evolve the system using individual time steps for each particle or with a single, global time step for all. Particles may interact gravitationally as N-body particles, and all or any subset may also interact hydrodynamically, using the smoothed particle hydrodynamic (SPH) method by selecting the SPH module. A third particle species can be included with a module to model massive point particles which may accrete nearby SPH or N-body particles. Such particles may be used to model, e.g., stars in a molecular cloud. Free boundary conditions are implemented by default, and a module may be selected to include periodic boundary conditions. We use a binary "Press" tree to organize particles for rapid access in gravity and SPH calculations. Modules implementing an interface with special purpose "GRAPE" hardware may also be selected to accelerate the gravity calculations. If available, forces obtained from the GRAPE coprocessors may be transparently substituted for those obtained from the tree, or both tree and GRAPE may be used as a combination GRAPE/tree code. The code may be run without

Shielding evaluation for solar particle events using MCNPX, PHITS and OLTARIS codes.

PubMed

Aghara, S K; Sriprisan, S I; Singleterry, R C; Sato, T

2015-01-01

Detailed analyses of Solar Particle Events (SPE) were performed to calculate primary and secondary particle spectra behind aluminum, at various thicknesses in water. The simulations were based on Monte Carlo (MC) radiation transport codes, MCNPX 2.7.0 and PHITS 2.64, and the space radiation analysis website called OLTARIS (On-Line Tool for the Assessment of Radiation in Space) version 3.4 (uses deterministic code, HZETRN, for transport). The study is set to investigate the impact of SPEs spectra transporting through 10 or 20 g/cm(2) Al shield followed by 30 g/cm(2) of water slab. Four historical SPE events were selected and used as input source spectra particle differential spectra for protons, neutrons, and photons are presented. The total particle fluence as a function of depth is presented. In addition to particle flux, the dose and dose equivalent values are calculated and compared between the codes and with the other published results. Overall, the particle fluence spectra from all three codes show good agreement with the MC codes showing closer agreement compared to the OLTARIS results. The neutron particle fluence from OLTARIS is lower than the results from MC codes at lower energies (E<100 MeV). Based on mean square difference analysis the results from MCNPX and PHITS agree better for fluence, dose and dose equivalent when compared to OLTARIS results. Copyright © 2015 The Committee on Space Research (COSPAR). All rights reserved.

A novel neutron energy spectrum unfolding code using particle swarm optimization

NASA Astrophysics Data System (ADS)

Shahabinejad, H.; Sohrabpour, M.

2017-07-01

A novel neutron Spectrum Deconvolution using Particle Swarm Optimization (SDPSO) code has been developed to unfold the neutron spectrum from a pulse height distribution and a response matrix. The Particle Swarm Optimization (PSO) imitates the bird flocks social behavior to solve complex optimization problems. The results of the SDPSO code have been compared with those of the standard spectra and recently published Two-steps Genetic Algorithm Spectrum Unfolding (TGASU) code. The TGASU code have been previously compared with the other codes such as MAXED, GRAVEL, FERDOR and GAMCD and shown to be more accurate than the previous codes. The results of the SDPSO code have been demonstrated to match well with those of the TGASU code for both under determined and over-determined problems. In addition the SDPSO has been shown to be nearly two times faster than the TGASU code.

Optimization of Particle-in-Cell Codes on RISC Processors

NASA Technical Reports Server (NTRS)

Decyk, Viktor K.; Karmesin, Steve Roy; Boer, Aeint de; Liewer, Paulette C.

1996-01-01

General strategies are developed to optimize particle-cell-codes written in Fortran for RISC processors which are commonly used on massively parallel computers. These strategies include data reorganization to improve cache utilization and code reorganization to improve efficiency of arithmetic pipelines.

Adaptation of multidimensional group particle tracking and particle wall-boundary condition model to the FDNS code

NASA Technical Reports Server (NTRS)

Chen, Y. S.; Farmer, R. C.

1992-01-01

A particulate two-phase flow CFD model was developed based on the FDNS code which is a pressure based predictor plus multi-corrector Navier-Stokes flow solver. Turbulence models with compressibility correction and the wall function models were employed as submodels. A finite-rate chemistry model was used for reacting flow simulation. For particulate two-phase flow simulations, a Eulerian-Lagrangian solution method using an efficient implicit particle trajectory integration scheme was developed in this study. Effects of particle-gas reaction and particle size change to agglomeration or fragmentation were not considered in this investigation. At the onset of the present study, a two-dimensional version of FDNS which had been modified to treat Lagrangian tracking of particles (FDNS-2DEL) had already been written and was operational. The FDNS-2DEL code was too slow for practical use, mainly because it had not been written in a form amenable to vectorization on the Cray, nor was the full three-dimensional form of FDNS utilized. The specific objective of this study was to reorder to calculations into long single arrays for automatic vectorization on the Cray and to implement the full three-dimensional version of FDNS to produce the FDNS-3DEL code. Since the FDNS-2DEL code was slow, a very limited number of test cases had been run with it. This study was also intended to increase the number of cases simulated to verify and improve, as necessary, the particle tracking methodology coded in FDNS.

Particle In Cell Codes on Highly Parallel Architectures

NASA Astrophysics Data System (ADS)

Tableman, Adam

2014-10-01

We describe strategies and examples of Particle-In-Cell Codes running on Nvidia GPU and Intel Phi architectures. This includes basic implementations in skeletons codes and full-scale development versions (encompassing 1D, 2D, and 3D codes) in Osiris. Both the similarities and differences between Intel's and Nvidia's hardware will be examined. Work supported by grants NSF ACI 1339893, DOE DE SC 000849, DOE DE SC 0008316, DOE DE NA 0001833, and DOE DE FC02 04ER 54780.

StarSmasher: Smoothed Particle Hydrodynamics code for smashing stars and planets

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Lombardi, James C., Jr.; Portegies Zwart, Simon; Rasio, F. A.

2018-05-01

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian particle method that approximates a continuous fluid as discrete nodes, each carrying various parameters such as mass, position, velocity, pressure, and temperature. In an SPH simulation the resolution scales with the particle density; StarSmasher is able to handle both equal-mass and equal number-density particle models. StarSmasher solves for hydro forces by calculating the pressure for each particle as a function of the particle's properties - density, internal energy, and internal properties (e.g. temperature and mean molecular weight). The code implements variational equations of motion and libraries to calculate the gravitational forces between particles using direct summation on NVIDIA graphics cards. Using a direct summation instead of a tree-based algorithm for gravity increases the accuracy of the gravity calculations at the cost of speed. The code uses a cubic spline for the smoothing kernel and an artificial viscosity prescription coupled with a Balsara Switch to prevent unphysical interparticle penetration. The code also implements an artificial relaxation force to the equations of motion to add a drag term to the calculated accelerations during relaxation integrations. Initially called StarCrash, StarSmasher was developed originally by Rasio.

Monte Carlo N Particle code - Dose distribution of clinical electron beams in inhomogeneous phantoms

PubMed Central

Nedaie, H. A.; Mosleh-Shirazi, M. A.; Allahverdi, M.

2013-01-01

Electron dose distributions calculated using the currently available analytical methods can be associated with large uncertainties. The Monte Carlo method is the most accurate method for dose calculation in electron beams. Most of the clinical electron beam simulation studies have been performed using non- MCNP [Monte Carlo N Particle] codes. Given the differences between Monte Carlo codes, this work aims to evaluate the accuracy of MCNP4C-simulated electron dose distributions in a homogenous phantom and around inhomogeneities. Different types of phantoms ranging in complexity were used; namely, a homogeneous water phantom and phantoms made of polymethyl methacrylate slabs containing different-sized, low- and high-density inserts of heterogeneous materials. Electron beams with 8 and 15 MeV nominal energy generated by an Elekta Synergy linear accelerator were investigated. Measurements were performed for a 10 cm × 10 cm applicator at a source-to-surface distance of 100 cm. Individual parts of the beam-defining system were introduced into the simulation one at a time in order to show their effect on depth doses. In contrast to the first scattering foil, the secondary scattering foil, X and Y jaws and applicator provide up to 5% of the dose. A 2%/2 mm agreement between MCNP and measurements was found in the homogenous phantom, and in the presence of heterogeneities in the range of 1-3%, being generally within 2% of the measurements for both energies in a "complex" phantom. A full-component simulation is necessary in order to obtain a realistic model of the beam. The MCNP4C results agree well with the measured electron dose distributions. PMID:23533162

Balancing Particle and Mesh Computation in a Particle-In-Cell Code

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

Worley, Patrick H; D'Azevedo, Eduardo; Hager, Robert

2016-01-01

The XGC1 plasma microturbulence particle-in-cell simulation code has both particle-based and mesh-based computational kernels that dominate performance. Both of these are subject to load imbalances that can degrade performance and that evolve during a simulation. Each separately can be addressed adequately, but optimizing just for one can introduce significant load imbalances in the other, degrading overall performance. A technique has been developed based on Golden Section Search that minimizes wallclock time given prior information on wallclock time, and on current particle distribution and mesh cost per cell, and also adapts to evolution in load imbalance in both particle and meshmore » work. In problems of interest this doubled the performance on full system runs on the XK7 at the Oak Ridge Leadership Computing Facility compared to load balancing only one of the kernels.« less

FLUKA: A Multi-Particle Transport Code

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

Ferrari, A.; Sala, P.R.; /CERN /INFN, Milan

2005-12-14

This report describes the 2005 version of the Fluka particle transport code. The first part introduces the basic notions, describes the modular structure of the system, and contains an installation and beginner's guide. The second part complements this initial information with details about the various components of Fluka and how to use them. It concludes with a detailed history and bibliography.

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code.

NASA Astrophysics Data System (ADS)

Chacon, L.; Knoll, D. A.

2004-11-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended primitive-variable MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field, non-dissipative, and stable in the absence of physical dissipation.(L. Chacón , phComput. Phys. Comm.) submitted (2004) PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, first and second-order implicit schemes are available, although higher-order temporal implicit schemes can be effortlessly implemented within the Newton-Krylov framework. A successful, scalable, MG physics-based preconditioning strategy, similar in concept to previous 2D MHD efforts,(L. Chacón et al., phJ. Comput. Phys). 178 (1), 15- 36 (2002); phJ. Comput. Phys., 188 (2), 573-592 (2003) has been developed. We are currently in the process of parallelizing the code using the PETSc library, and a Newton-Krylov-Schwarz approach for the parallel treatment of the preconditioner. In this poster, we will report on both the serial and parallel performance of PIXIE3D, focusing primarily on scalability and CPU speedup vs. an explicit approach.

Control and formation mechanism of extended nanochannel geometry in colloidal mesoporous silica particles.

PubMed

Sokolov, I; Kalaparthi, V; Volkov, D O; Palantavida, S; Mordvinova, N E; Lebedev, O I; Owens, J

2017-01-04

A large class of colloidal multi-micron mesoporous silica particles have well-defined cylindrical nanopores, nanochannels which self-assembled in the templated sol-gel process. These particles are of broad interest in photonics, for timed drug release, enzyme stabilization, separation and filtration technologies, catalysis, etc. Although the pore geometry and mechanism of pore formation of such particles has been widely investigated at the nanoscale, their pore geometry and its formation mechanism at a larger (extended) scale is still under debate. The extended geometry of nanochannels is paramount for all aforementioned applications because it defines accessibility of nanochannels, and subsequently, kinetics of interaction of the nanochannel content with the particle surrounding. Here we present both experimental and theoretical investigation of the extended geometry and its formation mechanism in colloidal multi-micron mesoporous silica particles. We demonstrate that disordered (and consequently, well accessible) nanochannels in the initially formed colloidal particles gradually align and form extended self-sealed channels. This knowledge allows to control the percentage of disordered versus self-sealed nanochannels, which defines accessibility of nanochannels in such particles. We further show that the observed aligning the channels is in agreement with theory; it is thermodynamically favored as it decreases the Gibbs free energy of the particles. Besides the practical use of the obtained results, developing a fundamental understanding of the mechanisms of morphogenesis of complex geometry of nanopores will open doors to efficient and controllable synthesis that will, in turn, further fuel the practical utilization of these particles.

Sigma 1 protein of mammalian reoviruses extends from the surfaces of viral particles

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

Furlong, D.B.; Nibert, M.L.; Fields, B.N.

1988-01-01

Electron microscopy revealed structures consisting of long fibers topped with knobs extending from the surfaces of virions of mammalian reoviruses. The morphology of these structures was reminiscent of the fiber protein of adenovirus. Fibers were also seen extending from the reovirus top component and intermediate subviral particles but not from cores, suggesting that the fibers consist of either the ..mu..1C or sigma1 outer capsid protein. Amino acid sequence analysis predicts that the reovirus cell attachment protein sigma1 contains an extended fiber domain. When sigma1 protein was released from viral particles with mild heat and subsequently obtained in isolation, it wasmore » found to have a morphology identical to that of the fiber structures seen extending from the viral particles. The identification of an extended form of sigma1 has important implications for its function in cell attachment. Other evidence suggest that sigma1 protein may occur in virions in both an extended and an unextended state.« less

General Relativistic Smoothed Particle Hydrodynamics code developments: A progress report

NASA Astrophysics Data System (ADS)

Faber, Joshua; Silberman, Zachary; Rizzo, Monica

2017-01-01

We report on our progress in developing a new general relativistic Smoothed Particle Hydrodynamics (SPH) code, which will be appropriate for studying the properties of accretion disks around black holes as well as compact object binary mergers and their ejecta. We will discuss in turn the relativistic formalisms being used to handle the evolution, our techniques for dealing with conservative and primitive variables, as well as those used to ensure proper conservation of various physical quantities. Code tests and performance metrics will be discussed, as will the prospects for including smoothed particle hydrodynamics codes within other numerical relativity codebases, particularly the publicly available Einstein Toolkit. We acknowledge support from NSF award ACI-1550436 and an internal RIT D-RIG grant.

Parallelization of a Monte Carlo particle transport simulation code

NASA Astrophysics Data System (ADS)

Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.

2010-05-01

We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.

Collision Models for Particle Orbit Code on SSX

NASA Astrophysics Data System (ADS)

Fisher, M. W.; Dandurand, D.; Gray, T.; Brown, M. R.; Lukin, V. S.

2011-10-01

Coulomb collision models are being developed and incorporated into the Hamiltonian particle pushing code (PPC) for applications to the Swarthmore Spheromak eXperiment (SSX). A Monte Carlo model based on that of Takizuka and Abe [JCP 25, 205 (1977)] performs binary collisions between test particles and thermal plasma field particles randomly drawn from a stationary Maxwellian distribution. A field-based electrostatic fluctuation model scatters particles from a spatially uniform random distribution of positive and negative spherical potentials generated throughout the plasma volume. The number, radii, and amplitude of these potentials are chosen to mimic the correct particle diffusion statistics without the use of random particle draws or collision frequencies. An electromagnetic fluctuating field model will be presented, if available. These numerical collision models will be benchmarked against known analytical solutions, including beam diffusion rates and Spitzer resistivity, as well as each other. The resulting collisional particle orbit models will be used to simulate particle collection with electrostatic probes in the SSX wind tunnel, as well as particle confinement in typical SSX fields. This work has been supported by US DOE, NSF and ONR.

2D Implosion Simulations with a Kinetic Particle Code

NASA Astrophysics Data System (ADS)

Sagert, Irina; Even, Wesley; Strother, Terrance

2017-10-01

Many problems in laboratory and plasma physics are subject to flows that move between the continuum and the kinetic regime. We discuss two-dimensional (2D) implosion simulations that were performed using a Monte Carlo kinetic particle code. The application of kinetic transport theory is motivated, in part, by the occurrence of non-equilibrium effects in inertial confinement fusion (ICF) capsule implosions, which cannot be fully captured by hydrodynamics simulations. Kinetic methods, on the other hand, are able to describe both, continuum and rarefied flows. We perform simple 2D disk implosion simulations using one particle species and compare the results to simulations with the hydrodynamics code RAGE. The impact of the particle mean-free-path on the implosion is also explored. In a second study, we focus on the formation of fluid instabilities from induced perturbations. I.S. acknowledges support through the Director's fellowship from Los Alamos National Laboratory. This research used resources provided by the LANL Institutional Computing Program.

ECG Denoising Using Marginalized Particle Extended Kalman Filter With an Automatic Particle Weighting Strategy.

PubMed

Hesar, Hamed Danandeh; Mohebbi, Maryam

2017-05-01

In this paper, a model-based Bayesian filtering framework called the "marginalized particle-extended Kalman filter (MP-EKF) algorithm" is proposed for electrocardiogram (ECG) denoising. This algorithm does not have the extended Kalman filter (EKF) shortcoming in handling non-Gaussian nonstationary situations because of its nonlinear framework. In addition, it has less computational complexity compared with particle filter. This filter improves ECG denoising performance by implementing marginalized particle filter framework while reducing its computational complexity using EKF framework. An automatic particle weighting strategy is also proposed here that controls the reliance of our framework to the acquired measurements. We evaluated the proposed filter on several normal ECGs selected from MIT-BIH normal sinus rhythm database. To do so, artificial white Gaussian and colored noises as well as nonstationary real muscle artifact (MA) noise over a range of low SNRs from 10 to -5 dB were added to these normal ECG segments. The benchmark methods were the EKF and extended Kalman smoother (EKS) algorithms which are the first model-based Bayesian algorithms introduced in the field of ECG denoising. From SNR viewpoint, the experiments showed that in the presence of Gaussian white noise, the proposed framework outperforms the EKF and EKS algorithms in lower input SNRs where the measurements and state model are not reliable. Owing to its nonlinear framework and particle weighting strategy, the proposed algorithm attained better results at all input SNRs in non-Gaussian nonstationary situations (such as presence of pink noise, brown noise, and real MA). In addition, the impact of the proposed filtering method on the distortion of diagnostic features of the ECG was investigated and compared with EKF/EKS methods using an ECG diagnostic distortion measure called the "Multi-Scale Entropy Based Weighted Distortion Measure" or MSEWPRD. The results revealed that our proposed

CPIC: a curvilinear Particle-In-Cell code for plasma-material interaction studies

NASA Astrophysics Data System (ADS)

Delzanno, G.; Camporeale, E.; Moulton, J. D.; Borovsky, J. E.; MacDonald, E.; Thomsen, M. F.

2012-12-01

We present a recently developed Particle-In-Cell (PIC) code in curvilinear geometry called CPIC (Curvilinear PIC) [1], where the standard PIC algorithm is coupled with a grid generation/adaptation strategy. Through the grid generator, which maps the physical domain to a logical domain where the grid is uniform and Cartesian, the code can simulate domains of arbitrary complexity, including the interaction of complex objects with a plasma. At present the code is electrostatic. Poisson's equation (in logical space) can be solved with either an iterative method based on the Conjugate Gradient (CG) or the Generalized Minimal Residual (GMRES) coupled with a multigrid solver used as a preconditioner, or directly with multigrid. The multigrid strategy is critical for the solver to perform optimally or nearly optimally as the dimension of the problem increases. CPIC also features a hybrid particle mover, where the computational particles are characterized by position in logical space and velocity in physical space. The advantage of a hybrid mover, as opposed to more conventional movers that move particles directly in the physical space, is that the interpolation of the particles in logical space is straightforward and computationally inexpensive, since one does not have to track the position of the particle. We will present our latest progress on the development of the code and document the code performance on standard plasma-physics tests. Then we will present the (preliminary) application of the code to a basic dynamic-charging problem, namely the charging and shielding of a spherical spacecraft in a magnetized plasma for various level of magnetization and including the pulsed emission of an electron beam from the spacecraft. The dynamical evolution of the sheath and the time-dependent current collection will be described. This study is in support of the ConnEx mission concept to use an electron beam from a magnetospheric spacecraft to trace magnetic field lines from the

Fast decoding techniques for extended single-and-double-error-correcting Reed Solomon codes

NASA Technical Reports Server (NTRS)

Costello, D. J., Jr.; Deng, H.; Lin, S.

1984-01-01

A problem in designing semiconductor memories is to provide some measure of error control without requiring excessive coding overhead or decoding time. For example, some 256K-bit dynamic random access memories are organized as 32K x 8 bit-bytes. Byte-oriented codes such as Reed Solomon (RS) codes provide efficient low overhead error control for such memories. However, the standard iterative algorithm for decoding RS codes is too slow for these applications. Some special high speed decoding techniques for extended single and double error correcting RS codes. These techniques are designed to find the error locations and the error values directly from the syndrome without having to form the error locator polynomial and solve for its roots.

Comprehensive Benchmark Suite for Simulation of Particle Laden Flows Using the Discrete Element Method with Performance Profiles from the Multiphase Flow with Interface eXchanges (MFiX) Code

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

Liu, Peiyuan; Brown, Timothy; Fullmer, William D.

Five benchmark problems are developed and simulated with the computational fluid dynamics and discrete element model code MFiX. The benchmark problems span dilute and dense regimes, consider statistically homogeneous and inhomogeneous (both clusters and bubbles) particle concentrations and a range of particle and fluid dynamic computational loads. Several variations of the benchmark problems are also discussed to extend the computational phase space to cover granular (particles only), bidisperse and heat transfer cases. A weak scaling analysis is performed for each benchmark problem and, in most cases, the scalability of the code appears reasonable up to approx. 103 cores. Profiling ofmore » the benchmark problems indicate that the most substantial computational time is being spent on particle-particle force calculations, drag force calculations and interpolating between discrete particle and continuum fields. Hardware performance analysis was also carried out showing significant Level 2 cache miss ratios and a rather low degree of vectorization. These results are intended to serve as a baseline for future developments to the code as well as a preliminary indicator of where to best focus performance optimizations.« less

Applications of the microdosimetric function implemented in the macroscopic particle transport simulation code PHITS.

PubMed

Sato, Tatsuhiko; Watanabe, Ritsuko; Sihver, Lembit; Niita, Koji

2012-01-01

Microdosimetric quantities such as lineal energy are generally considered to be better indices than linear energy transfer (LET) for expressing the relative biological effectiveness (RBE) of high charge and energy particles. To calculate their probability densities (PD) in macroscopic matter, it is necessary to integrate microdosimetric tools such as track-structure simulation codes with macroscopic particle transport simulation codes. As an integration approach, the mathematical model for calculating the PD of microdosimetric quantities developed based on track-structure simulations was incorporated into the macroscopic particle transport simulation code PHITS (Particle and Heavy Ion Transport code System). The improved PHITS enables the PD in macroscopic matter to be calculated within a reasonable computation time, while taking their stochastic nature into account. The microdosimetric function of PHITS was applied to biological dose estimation for charged-particle therapy and risk estimation for astronauts. The former application was performed in combination with the microdosimetric kinetic model, while the latter employed the radiation quality factor expressed as a function of lineal energy. Owing to the unique features of the microdosimetric function, the improved PHITS has the potential to establish more sophisticated systems for radiological protection in space as well as for the treatment planning of charged-particle therapy.

Microfluidic CODES: a scalable multiplexed electronic sensor for orthogonal detection of particles in microfluidic channels.

PubMed

Liu, Ruxiu; Wang, Ningquan; Kamili, Farhan; Sarioglu, A Fatih

2016-04-21

Numerous biophysical and biochemical assays rely on spatial manipulation of particles/cells as they are processed on lab-on-a-chip devices. Analysis of spatially distributed particles on these devices typically requires microscopy negating the cost and size advantages of microfluidic assays. In this paper, we introduce a scalable electronic sensor technology, called microfluidic CODES, that utilizes resistive pulse sensing to orthogonally detect particles in multiple microfluidic channels from a single electrical output. Combining the techniques from telecommunications and microfluidics, we route three coplanar electrodes on a glass substrate to create multiple Coulter counters producing distinct orthogonal digital codes when they detect particles. We specifically design a digital code set using the mathematical principles of Code Division Multiple Access (CDMA) telecommunication networks and can decode signals from different microfluidic channels with >90% accuracy through computation even if these signals overlap. As a proof of principle, we use this technology to detect human ovarian cancer cells in four different microfluidic channels fabricated using soft lithography. Microfluidic CODES offers a simple, all-electronic interface that is well suited to create integrated, low-cost lab-on-a-chip devices for cell- or particle-based assays in resource-limited settings.

Alfvén eigenmode evolution computed with the VENUS and KINX codes for the ITER baseline scenario

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

Isaev, M. Yu., E-mail: isaev-my@nrcki.ru; Medvedev, S. Yu.; Cooper, W. A.

A new application of the VENUS code is described, which computes alpha particle orbits in the perturbed electromagnetic fields and its resonant interaction with the toroidal Alfvén eigenmodes (TAEs) for the ITER device. The ITER baseline scenario with Q = 10 and the plasma toroidal current of 15 MA is considered as the most important and relevant for the International Tokamak Physics Activity group on energetic particles (ITPA-EP). For this scenario, typical unstable TAE-modes with the toroidal index n = 20 have been predicted that are localized in the plasma core near the surface with safety factor q = 1.more » The spatial structure of ballooning and antiballooning modes has been computed with the ideal MHD code KINX. The linear growth rates and the saturation levels taking into account the damping effects and the different mode frequencies have been calculated with the VENUS code for both ballooning and antiballooning TAE-modes.« less

A Particle Module for the PLUTO Code. I. An Implementation of the MHD–PIC Equations

NASA Astrophysics Data System (ADS)

Mignone, A.; Bodo, G.; Vaidya, B.; Mattia, G.

2018-05-01

We describe an implementation of a particle physics module available for the PLUTO code appropriate for the dynamical evolution of a plasma consisting of a thermal fluid and a nonthermal component represented by relativistic charged particles or cosmic rays (CRs). While the fluid is approached using standard numerical schemes for magnetohydrodynamics, CR particles are treated kinetically using conventional Particle-In-Cell (PIC) techniques. The module can be used either to describe test-particle motion in the fluid electromagnetic field or to solve the fully coupled magnetohydrodynamics (MHD)–PIC system of equations with particle backreaction on the fluid as originally introduced by Bai et al. Particle backreaction on the fluid is included in the form of momentum–energy feedback and by introducing the CR-induced Hall term in Ohm’s law. The hybrid MHD–PIC module can be employed to study CR kinetic effects on scales larger than the (ion) skin depth provided that the Larmor gyration scale is properly resolved. When applicable, this formulation avoids resolving microscopic scales, offering substantial computational savings with respect to PIC simulations. We present a fully conservative formulation that is second-order accurate in time and space, and extends to either the Runge–Kutta (RK) or the corner transport upwind time-stepping schemes (for the fluid), while a standard Boris integrator is employed for the particles. For highly energetic relativistic CRs and in order to overcome the time-step restriction, a novel subcycling strategy that retains second-order accuracy in time is presented. Numerical benchmarks and applications including Bell instability, diffusive shock acceleration, and test-particle acceleration in reconnecting layers are discussed.

Performance tuning of N-body codes on modern microprocessors: I. Direct integration with a hermite scheme on x86_64 architecture

NASA Astrophysics Data System (ADS)

Nitadori, Keigo; Makino, Junichiro; Hut, Piet

2006-12-01

The main performance bottleneck of gravitational N-body codes is the force calculation between two particles. We have succeeded in speeding up this pair-wise force calculation by factors between 2 and 10, depending on the code and the processor on which the code is run. These speed-ups were obtained by writing highly fine-tuned code for x86_64 microprocessors. Any existing N-body code, running on these chips, can easily incorporate our assembly code programs. In the current paper, we present an outline of our overall approach, which we illustrate with one specific example: the use of a Hermite scheme for a direct N2 type integration on a single 2.0 GHz Athlon 64 processor, for which we obtain an effective performance of 4.05 Gflops, for double-precision accuracy. In subsequent papers, we will discuss other variations, including the combinations of N log N codes, single-precision implementations, and performance on other microprocessors.

Particle merging algorithm for PIC codes

NASA Astrophysics Data System (ADS)

Vranic, M.; Grismayer, T.; Martins, J. L.; Fonseca, R. A.; Silva, L. O.

2015-06-01

Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in previous works, none of them seemed to be able to conserve fully charge, momentum, energy and their associated distributions. We describe here an alternative algorithm based on the coalescence of N massive or massless particles, considered to be close enough in phase space, into two new macro-particles. The local conservation of charge, momentum and energy are ensured by the resolution of a system of scalar equations. Various simulation comparisons have been carried out with and without the merging algorithm, from classical plasma physics problems to extreme scenarios where quantum electrodynamics is taken into account, showing in addition to the conservation of local quantities, the good reproducibility of the particle distributions. In case where the number of particles ought to increase exponentially in the simulation box, the dynamical merging permits a considerable speedup, and significant memory savings that otherwise would make the simulations impossible to perform.

Development of 1D Particle-in-Cell Code and Simulation of Plasma-Wall Interactions

NASA Astrophysics Data System (ADS)

Rose, Laura P.

This thesis discusses the development of a 1D particle-in-cell (PIC) code and the analysis of plasma-wall interactions. The 1D code (Plasma and Wall Simulation -- PAWS) is a kinetic simulation of plasma done by treating both electrons and ions as particles. The goal of this thesis is to study near wall plasma interaction to better understand the mechanism that occurs in this region. The main focus of this investigation is the effects that secondary electrons have on the sheath profile. The 1D code is modeled using the PIC method. Treating both the electrons and ions as macroparticles the field is solved on each node and weighted to each macro particle. A pre-ionized plasma was loaded into the domain and the velocities of particles were sampled from the Maxwellian distribution. An important part of this code is the boundary conditions at the wall. If a particle hits the wall a secondary electron may be produced based on the incident energy. To study the sheath profile the simulations were run for various cases. Varying background neutral gas densities were run with the 2D code and compared to experimental values. Different wall materials were simulated to show their effects of SEE. In addition different SEE yields were run, including one study with very high SEE yields to show the presence of a space charge limited sheath. Wall roughness was also studied with the 1D code using random angles of incidence. In addition to the 1D code, an external 2D code was also used to investigate wall roughness without secondary electrons. The roughness profiles where created upon investigation of wall roughness inside Hall Thrusters based off of studies done on lifetime erosion of the inner and outer walls of these devices. The 2D code, Starfish[33], is a general 2D axisymmetric/Cartesian code for modeling a wide a range of plasma and rarefied gas problems. These results show that higher SEE yield produces a smaller sheath profile and that wall roughness produces a lower SEE yield

Generalized power-spectrum Larmor formula for an extended charged particle embedded in a harmonic oscillator

NASA Astrophysics Data System (ADS)

Marengo, Edwin A.; Khodja, Mohamed R.

2006-09-01

The nonrelativistic Larmor radiation formula, giving the power radiated by an accelerated charged point particle, is generalized for a spatially extended particle in the context of the classical charged harmonic oscillator. The particle is modeled as a spherically symmetric rigid charge distribution that possesses both translational and spinning degrees of freedom. The power spectrum obtained exhibits a structure that depends on the form factor of the particle, but reduces, in the limit of an infinitesimally small particle and for the charge distributions considered, to Larmor’s familiar result. It is found that for finite-duration small-enough accelerations as well as perpetual uniform accelerations the power spectrum of the spatially extended particle reduces to that of a point particle. It is also found that when the acceleration is violent or the size parameter of the particle is very large compared to the wavelength of the emitted radiation the power spectrum is highly suppressed. Possible applications are discussed.

Hybrid simulations of Alfvén modes driven by energetic particles

NASA Astrophysics Data System (ADS)

Zhu, J.; Ma, Z. W.; Wang, S.

2016-12-01

A hybrid kinetic-magnetohydrodynamic code (CLT-K) is developed to study nonlinear dynamics of Alfvén modes driven by energetic particles (EP). A n = 2 toroidicity-induced discrete shear Alfvén eigenmode (TAE)-type energetic particle mode (EPM) with two dominant poloidal harmonics (m = 2 and 3) is first excited and its frequency remains unchanged in the early phase. Later, a new branch of the n = 2 frequency with a single dominant poloidal mode (m = 3) splits from the original TAE-type EPM. The new single m EPM (m = 3) slowly moves radially outward with the downward chirping of the frequency and the mode amplitude remains at a higher level. The original EPM remains at its original position without the frequency chirping, but its amplitude decays with time. Finally, the m = 3 EPM becomes dominant and the frequency falls into the β-induced gap of the Alfvén continuum. The redistribution of the δf in the phase space is consistent with the mode frequency downward chirping and the drifting direction of the resonance region is mainly due to the biased free energy profile. The transition from a TAE-type EPM to a single m EPM is mainly caused by extension of the p = 0 trapped particle resonance in the phase space.

Verification of long wavelength electromagnetic modes with a gyrokinetic-fluid hybrid model in the XGC code

PubMed Central

Lang, Jianying; Ku, S.; Chen, Y.; Parker, S. E.; Adams, M. F.

2017-01-01

As an alternative option to kinetic electrons, the gyrokinetic total-f particle-in-cell (PIC) code XGC1 has been extended to the MHD/fluid type electromagnetic regime by combining gyrokinetic PIC ions with massless drift-fluid electrons analogous to Chen and Parker [Phys. Plasmas 8, 441 (2001)]. Two representative long wavelength modes, shear Alfvén waves and resistive tearing modes, are verified in cylindrical and toroidal magnetic field geometries. PMID:29104419

Blow-up in nonlinear models of extended particles with confined constituents

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

Alvarez, A.; Ranada, A.F.

1988-11-15

It is shown that the indefinite character of the charge in classical models of extended particles with confined constituents is a serious handicap since infinite amounts of positive and negative charge can be emitted in some solutions, causing a blow-up in finite time.

Edge localized linear ideal magnetohydrodynamic instability studies in an extended-magnetohydrodynamic code

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

Burke, B. J.; Kruger, S. E.; Hegna, C. C.

A linear benchmark between the linear ideal MHD stability codes ELITE [H. R. Wilson et al., Phys. Plasmas 9, 1277 (2002)], GATO [L. Bernard et al., Comput. Phys. Commun. 24, 377 (1981)], and the extended nonlinear magnetohydrodynamic (MHD) code, NIMROD [C. R. Sovinec et al.., J. Comput. Phys. 195, 355 (2004)] is undertaken for edge-localized (MHD) instabilities. Two ballooning-unstable, shifted-circle tokamak equilibria are compared where the stability characteristics are varied by changing the equilibrium plasma profiles. The equilibria model an H-mode plasma with a pedestal pressure profile and parallel edge currents. For both equilibria, NIMROD accurately reproduces the transition tomore » instability (the marginally unstable mode), as well as the ideal growth spectrum for a large range of toroidal modes (n=1-20). The results use the compressible MHD model and depend on a precise representation of 'ideal-like' and 'vacuumlike' or 'halo' regions within the code. The halo region is modeled by the introduction of a Lundquist-value profile that transitions from a large to a small value at a flux surface location outside of the pedestal region. To model an ideal-like MHD response in the core and a vacuumlike response outside the transition, separate criteria on the plasma and halo Lundquist values are required. For the benchmarked equilibria the critical Lundquist values are 10{sup 8} and 10{sup 3} for the ideal-like and halo regions, respectively. Notably, this gives a ratio on the order of 10{sup 5}, which is much larger than experimentally measured values using T{sub e} values associated with the top of the pedestal and separatrix. Excellent agreement with ELITE and GATO calculations are made when sharp boundary transitions in the resistivity are used and a small amount of physical dissipation is added for conditions very near and below marginal ideal stability.« less

Rate-compatible punctured convolutional codes (RCPC codes) and their applications

NASA Astrophysics Data System (ADS)

Hagenauer, Joachim

1988-04-01

The concept of punctured convolutional codes is extended by punctuating a low-rate 1/N code periodically with period P to obtain a family of codes with rate P/(P + l), where l can be varied between 1 and (N - 1)P. A rate-compatibility restriction on the puncturing tables ensures that all code bits of high rate codes are used by the lower-rate codes. This allows transmission of incremental redundancy in ARQ/FEC (automatic repeat request/forward error correction) schemes and continuous rate variation to change from low to high error protection within a data frame. Families of RCPC codes with rates between 8/9 and 1/4 are given for memories M from 3 to 6 (8 to 64 trellis states) together with the relevant distance spectra. These codes are almost as good as the best known general convolutional codes of the respective rates. It is shown that the same Viterbi decoder can be used for all RCPC codes of the same M. The application of RCPC codes to hybrid ARQ/FEC schemes is discussed for Gaussian and Rayleigh fading channels using channel-state information to optimize throughput.

A NEW HYBRID N-BODY-COAGULATION CODE FOR THE FORMATION OF GAS GIANT PLANETS

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

Bromley, Benjamin C.; Kenyon, Scott J., E-mail: bromley@physics.utah.edu, E-mail: skenyon@cfa.harvard.edu

2011-04-20

We describe an updated version of our hybrid N-body-coagulation code for planet formation. In addition to the features of our 2006-2008 code, our treatment now includes algorithms for the one-dimensional evolution of the viscous disk, the accretion of small particles in planetary atmospheres, gas accretion onto massive cores, and the response of N-bodies to the gravitational potential of the gaseous disk and the swarm of planetesimals. To validate the N-body portion of the algorithm, we use a battery of tests in planetary dynamics. As a first application of the complete code, we consider the evolution of Pluto-mass planetesimals in amore » swarm of 0.1-1 cm pebbles. In a typical evolution time of 1-3 Myr, our calculations transform 0.01-0.1 M{sub sun} disks of gas and dust into planetary systems containing super-Earths, Saturns, and Jupiters. Low-mass planets form more often than massive planets; disks with smaller {alpha} form more massive planets than disks with larger {alpha}. For Jupiter-mass planets, masses of solid cores are 10-100 M{sub +}.« less

EASY-II Renaissance: n, p, d, α, γ-induced Inventory Code System

NASA Astrophysics Data System (ADS)

Sublet, J.-Ch.; Eastwood, J. W.; Morgan, J. G.

2014-04-01

The European Activation SYstem has been re-engineered and re-written in modern programming languages so as to answer today's and tomorrow's needs in terms of activation, transmutation, depletion, decay and processing of radioactive materials. The new FISPACT-II inventory code development project has allowed us to embed many more features in terms of energy range: up to GeV; incident particles: alpha, gamma, proton, deuteron and neutron; and neutron physics: self-shielding effects, temperature dependence and covariance, so as to cover all anticipated application needs: nuclear fission and fusion, accelerator physics, isotope production, stockpile and fuel cycle stewardship, materials characterization and life, and storage cycle management. In parallel, the maturity of modern, truly general purpose libraries encompassing thousands of target isotopes such as TENDL-2012, the evolution of the ENDF-6 format and the capabilities of the latest generation of processing codes PREPRO, NJOY and CALENDF have allowed the activation code to be fed with more robust, complete and appropriate data: cross sections with covariance, probability tables in the resonance ranges, kerma, dpa, gas and radionuclide production and 24 decay types. All such data for the five most important incident particles (n, p, d, α, γ), are placed in evaluated data files up to an incident energy of 200 MeV. The resulting code system, EASY-II is designed as a functional replacement for the previous European Activation System, EASY-2010. It includes many new features and enhancements, but also benefits already from the feedback from extensive validation and verification activities performed with its predecessor.

PARAVT: Parallel Voronoi tessellation code

NASA Astrophysics Data System (ADS)

González, R. E.

2016-10-01

In this study, we present a new open source code for massive parallel computation of Voronoi tessellations (VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several serial Voronoi tessellation codes, however no open source and parallel implementations are available to handle the large number of particles/galaxies in current N-body simulations and sky surveys. Parallelization is implemented under MPI and VT using Qhull library. Domain decomposition takes into account consistent boundary computation between tasks, and includes periodic conditions. In addition, the code computes neighbors list, Voronoi density, Voronoi cell volume, density gradient for each particle, and densities on a regular grid. Code implementation and user guide are publicly available at https://github.com/regonzar/paravt.

SoAx: A generic C++ Structure of Arrays for handling particles in HPC codes

NASA Astrophysics Data System (ADS)

Homann, Holger; Laenen, Francois

2018-03-01

The numerical study of physical problems often require integrating the dynamics of a large number of particles evolving according to a given set of equations. Particles are characterized by the information they are carrying such as an identity, a position other. There are generally speaking two different possibilities for handling particles in high performance computing (HPC) codes. The concept of an Array of Structures (AoS) is in the spirit of the object-oriented programming (OOP) paradigm in that the particle information is implemented as a structure. Here, an object (realization of the structure) represents one particle and a set of many particles is stored in an array. In contrast, using the concept of a Structure of Arrays (SoA), a single structure holds several arrays each representing one property (such as the identity) of the whole set of particles. The AoS approach is often implemented in HPC codes due to its handiness and flexibility. For a class of problems, however, it is known that the performance of SoA is much better than that of AoS. We confirm this observation for our particle problem. Using a benchmark we show that on modern Intel Xeon processors the SoA implementation is typically several times faster than the AoS one. On Intel's MIC co-processors the performance gap even attains a factor of ten. The same is true for GPU computing, using both computational and multi-purpose GPUs. Combining performance and handiness, we present the library SoAx that has optimal performance (on CPUs, MICs, and GPUs) while providing the same handiness as AoS. For this, SoAx uses modern C++ design techniques such template meta programming that allows to automatically generate code for user defined heterogeneous data structures.

Comprehensive Model of Single Particle Pulverized Coal Combustion Extended to Oxy-Coal Conditions

DOE PAGES

Holland, Troy; Fletcher, Thomas H.

2017-02-22

Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive CFD simulations are valuable tools in evaluating and deploying oxy-fuel and other carbon capture technologies either as retrofit technologies or for new construction. But, accurate predictive simulations require physically realistic submodels with low computational requirements. In particular, comprehensive char oxidation and gasification models have been developed that describe multiple reaction and diffusion processes. Our work extends a comprehensive char conversion code (CCK), which treats surface oxidation and gasification reactions as well as processes such as film diffusion, pore diffusion, ash encapsulation, and annealing. In this work several submodels inmore » the CCK code were updated with more realistic physics or otherwise extended to function in oxy-coal conditions. Improved submodels include the annealing model, the swelling model, the mode of burning parameter, and the kinetic model, as well as the addition of the chemical percolation devolatilization (CPD) model. We compare our results of the char combustion model to oxy-coal data, and further compared to parallel data sets near conventional conditions. A potential method to apply the detailed code in CFD work is given.« less

Comprehensive Model of Single Particle Pulverized Coal Combustion Extended to Oxy-Coal Conditions

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

Holland, Troy; Fletcher, Thomas H.

Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive CFD simulations are valuable tools in evaluating and deploying oxy-fuel and other carbon capture technologies either as retrofit technologies or for new construction. But, accurate predictive simulations require physically realistic submodels with low computational requirements. In particular, comprehensive char oxidation and gasification models have been developed that describe multiple reaction and diffusion processes. Our work extends a comprehensive char conversion code (CCK), which treats surface oxidation and gasification reactions as well as processes such as film diffusion, pore diffusion, ash encapsulation, and annealing. In this work several submodels inmore » the CCK code were updated with more realistic physics or otherwise extended to function in oxy-coal conditions. Improved submodels include the annealing model, the swelling model, the mode of burning parameter, and the kinetic model, as well as the addition of the chemical percolation devolatilization (CPD) model. We compare our results of the char combustion model to oxy-coal data, and further compared to parallel data sets near conventional conditions. A potential method to apply the detailed code in CFD work is given.« less

Improvements of the particle-in-cell code EUTERPE for petascaling machines

NASA Astrophysics Data System (ADS)

Sáez, Xavier; Soba, Alejandro; Sánchez, Edilberto; Kleiber, Ralf; Castejón, Francisco; Cela, José M.

2011-09-01

In the present work we report some performance measures and computational improvements recently carried out using the gyrokinetic code EUTERPE (Jost, 2000 [1] and Jost et al., 1999 [2]), which is based on the general particle-in-cell (PIC) method. The scalability of the code has been studied for up to sixty thousand processing elements and some steps towards a complete hybridization of the code were made. As a numerical example, non-linear simulations of Ion Temperature Gradient (ITG) instabilities have been carried out in screw-pinch geometry and the results are compared with earlier works. A parametric study of the influence of variables (step size of the time integrator, number of markers, grid size) on the quality of the simulation is presented.

Extension of the XGC code for global gyrokinetic simulations in stellarator geometry

NASA Astrophysics Data System (ADS)

Cole, Michael; Moritaka, Toseo; White, Roscoe; Hager, Robert; Ku, Seung-Hoe; Chang, Choong-Seock

2017-10-01

In this work, the total-f, gyrokinetic particle-in-cell code XGC is extended to treat stellarator geometries. Improvements to meshing tools and the code itself have enabled the first physics studies, including single particle tracing and flux surface mapping in the magnetic geometry of the heliotron LHD and quasi-isodynamic stellarator Wendelstein 7-X. These have provided the first successful test cases for our approach. XGC is uniquely placed to model the complex edge physics of stellarators. A roadmap to such a global confinement modeling capability will be presented. Single particle studies will include the physics of energetic particles' global stochastic motions and their effect on confinement. Good confinement of energetic particles is vital for a successful stellarator reactor design. These results can be compared in the core region with those of other codes, such as ORBIT3d. In subsequent work, neoclassical transport and turbulence can then be considered and compared to results from codes such as EUTERPE and GENE. After sufficient verification in the core region, XGC will move into the stellarator edge region including the material wall and neutral particle recycling.

Application of electron closures in extended MHD

NASA Astrophysics Data System (ADS)

Held, Eric; Adair, Brett; Taylor, Trevor

2017-10-01

Rigorous closure of the extended MHD equations in plasma fluid codes includes the effects of electron heat conduction along perturbed magnetic fields and contributions of the electron collisional friction and stress to the extended Ohms law. In this work we discuss application of a continuum numerical solution to the Chapman-Enskog-like electron drift kinetic equation using the NIMROD code. The implementation is a tightly-coupled fluid/kinetic system that carefully addresses time-centering in the advance of the fluid variables with their kinetically-computed closures. Comparisons of spatial accuracy, computational efficiency and required velocity space resolution are presented for applications involving growing magnetic islands in cylindrical and toroidal geometry. The reduction in parallel heat conduction due to particle trapping in toroidal geometry is emphasized. Work supported by DOE under Grant Nos. DE-FC02-08ER54973 and DE-FG02-04ER54746.

Modelling of aircrew radiation exposure from galactic cosmic rays and solar particle events.

PubMed

Takada, M; Lewis, B J; Boudreau, M; Al Anid, H; Bennett, L G I

2007-01-01

Correlations have been developed for implementation into the semi-empirical Predictive Code for Aircrew Radiation Exposure (PCAIRE) to account for effects of extremum conditions of solar modulation and low altitude based on transport code calculations. An improved solar modulation model, as proposed by NASA, has been further adopted to interpolate between the bounding correlations for solar modulation. The conversion ratio of effective dose to ambient dose equivalent, as applied to the PCAIRE calculation (based on measurements) for the legal regulation of aircrew exposure, was re-evaluated in this work to take into consideration new ICRP-92 radiation-weighting factors and different possible irradiation geometries of the source cosmic-radiation field. A computational analysis with Monte Carlo N-Particle eXtended Code was further used to estimate additional aircrew exposure that may result from sporadic solar energetic particle events considering real-time monitoring by the Geosynchronous Operational Environmental Satellite. These predictions were compared with the ambient dose equivalent rates measured on-board an aircraft and to count rate data observed at various ground-level neutron monitors.

pycola: N-body COLA method code

NASA Astrophysics Data System (ADS)

Tassev, Svetlin; Eisenstein, Daniel J.; Wandelt, Benjamin D.; Zaldarriagag, Matias

2015-09-01

pycola is a multithreaded Python/Cython N-body code, implementing the Comoving Lagrangian Acceleration (COLA) method in the temporal and spatial domains, which trades accuracy at small-scales to gain computational speed without sacrificing accuracy at large scales. This is especially useful for cheaply generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing. The COLA method achieves its speed by calculating the large-scale dynamics exactly using LPT while letting the N-body code solve for the small scales, without requiring it to capture exactly the internal dynamics of halos.

Towards robust algorithms for current deposition and dynamic load-balancing in a GPU particle in cell code

NASA Astrophysics Data System (ADS)

Rossi, Francesco; Londrillo, Pasquale; Sgattoni, Andrea; Sinigardi, Stefano; Turchetti, Giorgio

2012-12-01

We present `jasmine', an implementation of a fully relativistic, 3D, electromagnetic Particle-In-Cell (PIC) code, capable of running simulations in various laser plasma acceleration regimes on Graphics-Processing-Units (GPUs) HPC clusters. Standard energy/charge preserving FDTD-based algorithms have been implemented using double precision and quadratic (or arbitrary sized) shape functions for the particle weighting. When porting a PIC scheme to the GPU architecture (or, in general, a shared memory environment), the particle-to-grid operations (e.g. the evaluation of the current density) require special care to avoid memory inconsistencies and conflicts. Here we present a robust implementation of this operation that is efficient for any number of particles per cell and particle shape function order. Our algorithm exploits the exposed GPU memory hierarchy and avoids the use of atomic operations, which can hurt performance especially when many particles lay on the same cell. We show the code multi-GPU scalability results and present a dynamic load-balancing algorithm. The code is written using a python-based C++ meta-programming technique which translates in a high level of modularity and allows for easy performance tuning and simple extension of the core algorithms to various simulation schemes.

Study of premixing phase of steam explosion with JASMINE code in ALPHA program

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

Moriyama, Kiyofumi; Yamano, Norihiro; Maruyama, Yu

Premixing phase of steam explosion has been studied in ALPHA Program at Japan Atomic Energy Research Institute (JAERI). An analytical model to simulate the premixing phase, JASMINE (JAERI Simulator for Multiphase Interaction and Explosion), has been developed based on a multi-dimensional multi-phase thermal hydraulics code MISTRAL (by Fuji Research Institute Co.). The original code was extended to simulate the physics in the premixing phenomena. The first stage of the code validation was performed by analyzing two mixing experiments with solid particles and water: the isothermal experiment by Gilbertson et al. (1992) and the hot particle experiment by Angelini et al.more » (1993) (MAGICO). The code predicted reasonably well the experiments. Effectiveness of the TVD scheme employed in the code was also demonstrated.« less

An electrostatic Particle-In-Cell code on multi-block structured meshes

NASA Astrophysics Data System (ADS)

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; Vernon, Louis J.; Moulton, J. David

2017-12-01

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. Despite the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where an arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma-material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. Compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.

An electrostatic Particle-In-Cell code on multi-block structured meshes

DOE PAGES

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; ...

2017-09-14

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less

An electrostatic Particle-In-Cell code on multi-block structured meshes

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

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less

Investigation of neutral particle dynamics in Aditya tokamak plasma with DEGAS2 code

NASA Astrophysics Data System (ADS)

Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.; Manchanda, R.; Banerjee, S.; Ramaiya, N.; Sharma, Deepti; Srinivasan, R.; Stotler, D. P.; Aditya Team

2017-08-01

Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated and matched with the experimental one. The dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7-40 eV).

Investigation of neutral particle dynamics in Aditya tokamak plasma with DEGAS2 code

DOE PAGES

Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.; ...

2017-06-09

Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated which was matched with the experimental one. Themore » dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~ 2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7 to 40 eV).« less

Extending DIRAC File Management with Erasure-Coding for efficient storage.

NASA Astrophysics Data System (ADS)

Cadellin Skipsey, Samuel; Todev, Paulin; Britton, David; Crooks, David; Roy, Gareth

2015-12-01

The state of the art in Grid style data management is to achieve increased resilience of data via multiple complete replicas of data files across multiple storage endpoints. While this is effective, it is not the most space-efficient approach to resilience, especially when the reliability of individual storage endpoints is sufficiently high that only a few will be inactive at any point in time. We report on work performed as part of GridPP[1], extending the Dirac File Catalogue and file management interface to allow the placement of erasure-coded files: each file distributed as N identically-sized chunks of data striped across a vector of storage endpoints, encoded such that any M chunks can be lost and the original file can be reconstructed. The tools developed are transparent to the user, and, as well as allowing up and downloading of data to Grid storage, also provide the possibility of parallelising access across all of the distributed chunks at once, improving data transfer and IO performance. We expect this approach to be of most interest to smaller VOs, who have tighter bounds on the storage available to them, but larger (WLCG) VOs may be interested as their total data increases during Run 2. We provide an analysis of the costs and benefits of the approach, along with future development and implementation plans in this area. In general, overheads for multiple file transfers provide the largest issue for competitiveness of this approach at present.

Modeling Spectra of Icy Satellites and Cometary Icy Particles Using Multi-Sphere T-Matrix Code

NASA Astrophysics Data System (ADS)

Kolokolova, Ludmilla; Mackowski, Daniel; Pitman, Karly M.; Joseph, Emily C. S.; Buratti, Bonnie J.; Protopapa, Silvia; Kelley, Michael S.

2016-10-01

The Multi-Sphere T-matrix code (MSTM) allows rigorous computations of characteristics of the light scattered by a cluster of spherical particles. It was introduced to the scientific community in 1996 (Mackowski & Mishchenko, 1996, JOSA A, 13, 2266). Later it was put online and became one of the most popular codes to study photopolarimetric properties of aggregated particles. Later versions of this code, especially its parallelized version MSTM3 (Mackowski & Mishchenko, 2011, JQSRT, 112, 2182), were used to compute angular and wavelength dependence of the intensity and polarization of light scattered by aggregates of up to 4000 constituent particles (Kolokolova & Mackowski, 2012, JQSRT, 113, 2567). The version MSTM4 considers large thick slabs of spheres (Mackowski, 2014, Proc. of the Workshop ``Scattering by aggregates``, Bremen, Germany, March 2014, Th. Wriedt & Yu. Eremin, Eds., 6) and is significantly different from the earlier versions. It adopts a Discrete Fourier Convolution, implemented using a Fast Fourier Transform, for evaluation of the exciting field. MSTM4 is able to treat dozens of thousands of spheres and is about 100 times faster than the MSTM3 code. This allows us not only to compute the light scattering properties of a large number of electromagnetically interacting constituent particles, but also to perform multi-wavelength and multi-angular computations using computer resources with rather reasonable CPU and computer memory. We used MSTM4 to model near-infrared spectra of icy satellites of Saturn (Rhea, Dione, and Tethys data from Cassini VIMS), and of icy particles observed in the coma of comet 103P/Hartley 2 (data from EPOXI/DI HRII). Results of our modeling show that in the case of icy satellites the best fit to the observed spectra is provided by regolith made of spheres of radius ~1 micron with a porosity in the range 85% - 95%, which slightly varies for the different satellites. Fitting the spectra of the cometary icy particles requires icy

Further Studies of the NRL Collective Particle Accelerator VIA Numerical Modeling with the MAGIC Code.

DTIC Science & Technology

1984-08-01

COLLFCTIVF PAPTTCLE ACCELERATOR VIA NUMERICAL MODFLINC WITH THF MAGIC CODE Robert 1. Darker Auqust 19F4 Final Report for Period I April. qI84 - 30...NUMERICAL MODELING WITH THE MAGIC CODE Robert 3. Barker August 1984 Final Report for Period 1 April 1984 - 30 September 1984 Prepared for: Scientific...Collective Final Report Particle Accelerator VIA Numerical Modeling with April 1 - September-30, 1984 MAGIC Code. 6. PERFORMING ORG. REPORT NUMBER MRC/WDC-R

Extended Salecker-Wigner formula for optimal accuracy in reading a clock via a massive signal particle

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

Kudaka, Shoju; Matsumoto, Shuichi

2007-07-15

In order to acquire an extended Salecker-Wigner formula from which to derive the optimal accuracy in reading a clock with a massive particle as the signal, von Neumann's classical measurement is employed, by which simultaneously both position and momentum of the signal particle can be measured approximately. By an appropriate selection of wave function for the initial state of the composite system (a clock and a signal particle), the formula is derived accurately. Valid ranges of the running time of a clock with a given optimal accuracy are also given. The extended formula means that contrary to the Salecker-Wigner formulamore » there exists the possibility of a higher accuracy of time measurement, even if the mass of the clock is very small.« less

Overview of Particle and Heavy Ion Transport Code System PHITS

NASA Astrophysics Data System (ADS)

Sato, Tatsuhiko; Niita, Koji; Matsuda, Norihiro; Hashimoto, Shintaro; Iwamoto, Yosuke; Furuta, Takuya; Noda, Shusaku; Ogawa, Tatsuhiko; Iwase, Hiroshi; Nakashima, Hiroshi; Fukahori, Tokio; Okumura, Keisuke; Kai, Tetsuya; Chiba, Satoshi; Sihver, Lembit

2014-06-01

A general purpose Monte Carlo Particle and Heavy Ion Transport code System, PHITS, is being developed through the collaboration of several institutes in Japan and Europe. The Japan Atomic Energy Agency is responsible for managing the entire project. PHITS can deal with the transport of nearly all particles, including neutrons, protons, heavy ions, photons, and electrons, over wide energy ranges using various nuclear reaction models and data libraries. It is written in Fortran language and can be executed on almost all computers. All components of PHITS such as its source, executable and data-library files are assembled in one package and then distributed to many countries via the Research organization for Information Science and Technology, the Data Bank of the Organization for Economic Co-operation and Development's Nuclear Energy Agency, and the Radiation Safety Information Computational Center. More than 1,000 researchers have been registered as PHITS users, and they apply the code to various research and development fields such as nuclear technology, accelerator design, medical physics, and cosmic-ray research. This paper briefly summarizes the physics models implemented in PHITS, and introduces some important functions useful for specific applications, such as an event generator mode and beam transport functions.

Half-Cell RF Gun Simulations with the Electromagnetic Particle-in-Cell Code VORPAL

NASA Astrophysics Data System (ADS)

Paul, K.; Dimitrov, D. A.; Busby, R.; Bruhwiler, D. L.; Smithe, D.; Cary, J. R.; Kewisch, J.; Kayran, D.; Calaga, R.; Ben-Zvi, I.

2009-01-01

We have simulated Brookhaven National Laboratory's half-cell superconducting RF gun design for a proposed high-current ERL using the three-dimensional, electromagnetic particle-in-cell code VORPAL. VORPAL computes the fully self-consistent electromagnetic fields produced by the electron bunches, meaning that it accurately models space-charge effects as well as bunch-to-bunch beam loading effects and the effects of higher-order cavity modes, though these are beyond the scope of this paper. We compare results from VORPAL to the well-established space-charge code PARMELA, using RF fields produced by SUPERFISH, as a benchmarking exercise in which the two codes should agree well.

Relating quantum discord with the quantum dense coding capacity

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

Wang, Xin; Qiu, Liang, E-mail: lqiu@cumt.edu.cn; Li, Song

2015-01-15

We establish the relations between quantum discord and the quantum dense coding capacity in (n + 1)-particle quantum states. A necessary condition for the vanishing discord monogamy score is given. We also find that the loss of quantum dense coding capacity due to decoherence is bounded below by the sum of quantum discord. When these results are restricted to three-particle quantum states, some complementarity relations are obtained.

Extended germa[N]pericyclynes: synthesis and characterization.

PubMed

Tanimoto, Hiroki; Fujiwara, Taro; Mori, Junta; Nagao, Tomohiko; Nishiyama, Yasuhiro; Morimoto, Tsumoru; Ito, Shunichiro; Tanaka, Kazuo; Chujo, Yoshiki; Kakiuchi, Kiyomi

2017-02-14

We herein describe the syntheses and characterization of extended germa[N]pericyclynes, which are macrocycles composed of germanium-butadiyne units. The obtained novel extended germa[4]-[8]pericyclynes were characterized by X-ray crystallography, UV-Vis spectroscopy, fluorescence and phosphorescence emission spectroscopy, and cyclic voltammetry, and exhibited characteristic absorptions and emissions. Density functional theory (DFT) calculations suggested smaller HOMO-LUMO gap energy compared to that of general germapericyclynes.

OCTGRAV: Sparse Octree Gravitational N-body Code on Graphics Processing Units

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Bédorf, Jeroen; Portegies Zwart, Simon

2010-10-01

Octgrav is a very fast tree-code which runs on massively parallel Graphical Processing Units (GPU) with NVIDIA CUDA architecture. The algorithms are based on parallel-scan and sort methods. The tree-construction and calculation of multipole moments is carried out on the host CPU, while the force calculation which consists of tree walks and evaluation of interaction list is carried out on the GPU. In this way, a sustained performance of about 100GFLOP/s and data transfer rates of about 50GB/s is achieved. It takes about a second to compute forces on a million particles with an opening angle of heta approx 0.5. To test the performance and feasibility, we implemented the algorithms in CUDA in the form of a gravitational tree-code which completely runs on the GPU. The tree construction and traverse algorithms are portable to many-core devices which have support for CUDA or OpenCL programming languages. The gravitational tree-code outperforms tuned CPU code during the tree-construction and shows a performance improvement of more than a factor 20 overall, resulting in a processing rate of more than 2.8 million particles per second. The code has a convenient user interface and is freely available for use.

PHITS-2.76, Particle and Heavy Ion Transport code System

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

2015-08-01

Version 03 PHITS can deal with the transport of almost all particles (nucleons, nuclei, mesons, photons, and electrons) over wide energy ranges, using several nuclear reaction models and nuclear data libraries. Geometrical configuration of the simulation can be set with GG (General Geometry) or CG (Combinatorial Geometry). Various quantities such as heat deposition, track length and production yields can be deduced from the simulation, using implemented estimator functions called "tally". The code also has a function to draw 2D and 3D figures of the calculated results as well as the setup geometries, using a code ANGEL. The physical processes includedmore » in PHITS can be divided into two categories, transport process and collision process. In the transport process, PHITS can simulate motion of particles under external fields such as magnetic and gravity. Without the external fields, neutral particles move along a straight trajectory with constant energy up to the next collision point. However, charge particles interact many times with electrons in the material losing energy and changing direction. PHITS treats ionization processes not as collision but as a transport process, using the continuous-slowing-down approximation. The average stopping power is given by the charge density of the material and the momentum of the particle taking into account the fluctuations of the energy loss and the angular deviation. In the collision process, PHITS can simulate the elastic and inelastic interactions as well as decay of particles. The total reaction cross section, or the life time of the particle is an essential quantity in the determination of the mean free path of the transport particle. According to the mean free path, PHITS chooses the next collision point using the Monte Carlo method. To generate the secondary particles of the collision, we need the information of the final states of the collision. For neutron induced reactions in low energy region, PHITS employs

Status of the R-matrix Code AMUR toward a consistent cross-section evaluation and covariance analysis for the light nuclei

NASA Astrophysics Data System (ADS)

Kunieda, Satoshi

2017-09-01

We report the status of the R-matrix code AMUR toward consistent cross-section evaluation and covariance analysis for the light-mass nuclei. The applicable limit of the code is extended by including computational capability for the charged-particle elastic scattering cross-sections and the neutron capture cross-sections as example results are shown in the main texts. A simultaneous analysis is performed on the 17O compound system including the 16O(n,tot) and 13C(α,n)16O reactions together with the 16O(n,n) and 13C(α,α) scattering cross-sections. It is found that a large theoretical background is required for each reaction process to obtain a simultaneous fit with all the experimental cross-sections we analyzed. Also, the hard-sphere radii should be assumed to be different from the channel radii. Although these are technical approaches, we could learn roles and sources of the theoretical background in the standard R-matrix.

An algebraic hypothesis about the primeval genetic code architecture.

PubMed

Sánchez, Robersy; Grau, Ricardo

2009-09-01

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G identical with C and A=U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B(3))(N) of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.

Final Report for "Implimentation and Evaluation of Multigrid Linear Solvers into Extended Magnetohydrodynamic Codes for Petascale Computing"

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

Srinath Vadlamani; Scott Kruger; Travis Austin

Extended magnetohydrodynamic (MHD) codes are used to model the large, slow-growing instabilities that are projected to limit the performance of International Thermonuclear Experimental Reactor (ITER). The multiscale nature of the extended MHD equations requires an implicit approach. The current linear solvers needed for the implicit algorithm scale poorly because the resultant matrices are so ill-conditioned. A new solver is needed, especially one that scales to the petascale. The most successful scalable parallel processor solvers to date are multigrid solvers. Applying multigrid techniques to a set of equations whose fundamental modes are dispersive waves is a promising solution to CEMM problems.more » For the Phase 1, we implemented multigrid preconditioners from the HYPRE project of the Center for Applied Scientific Computing at LLNL via PETSc of the DOE SciDAC TOPS for the real matrix systems of the extended MHD code NIMROD which is a one of the primary modeling codes of the OFES-funded Center for Extended Magnetohydrodynamic Modeling (CEMM) SciDAC. We implemented the multigrid solvers on the fusion test problem that allows for real matrix systems with success, and in the process learned about the details of NIMROD data structures and the difficulties of inverting NIMROD operators. The further success of this project will allow for efficient usage of future petascale computers at the National Leadership Facilities: Oak Ridge National Laboratory, Argonne National Laboratory, and National Energy Research Scientific Computing Center. The project will be a collaborative effort between computational plasma physicists and applied mathematicians at Tech-X Corporation, applied mathematicians Front Range Scientific Computations, Inc. (who are collaborators on the HYPRE project), and other computational plasma physicists involved with the CEMM project.« less

Imaging of spatially extended hot spots with coded apertures for intra-operative nuclear medicine applications

NASA Astrophysics Data System (ADS)

Kaissas, I.; Papadimitropoulos, C.; Potiriadis, C.; Karafasoulis, K.; Loukas, D.; Lambropoulos, C. P.

2017-01-01

Coded aperture imaging transcends planar imaging with conventional collimators in efficiency and Field of View (FOV). We present experimental results for the detection of 141 keV and 122 keV γ-photons emitted by uniformly extended 99mTc and 57Co hot-spots along with simulations of uniformly and normally extended 99mTc hot-spots. These results prove that the method can be used for intra-operative imaging of radio-traced sentinel nodes and thyroid remnants. The study is performed using a setup of two gamma cameras, each consisting of a coded-aperture (or mask) of Modified Uniformly Redundant Array (MURA) of rank 19 positioned on top of a CdTe detector. The detector pixel pitch is 350 μm and its active area is 4.4 × 4.4 cm2, while the mask element size is 1.7 mm. The detectable photon energy ranges from 15 keV up to 200 keV with an energy resolution of 3-4 keV FWHM. Triangulation is exploited to estimate the 3D spatial coordinates of the radioactive spots within the system FOV. Two extended sources, with uniform distributed activity (11 and 24 mm in diameter, respectively), positioned at 16 cm from the system and with 3 cm distance between their centers, can be resolved and localized with accuracy better than 5%. The results indicate that the estimated positions of spatially extended sources lay within their volume size and that neighboring sources, even with a low level of radioactivity, such as 30 MBq, can be clearly distinguished with an acquisition time about 3 seconds.

Recent Improvements of Particle and Heavy Ion Transport code System: PHITS

NASA Astrophysics Data System (ADS)

Sato, Tatsuhiko; Niita, Koji; Iwamoto, Yosuke; Hashimoto, Shintaro; Ogawa, Tatsuhiko; Furuta, Takuya; Abe, Shin-ichiro; Kai, Takeshi; Matsuda, Norihiro; Okumura, Keisuke; Kai, Tetsuya; Iwase, Hiroshi; Sihver, Lembit

2017-09-01

The Particle and Heavy Ion Transport code System, PHITS, has been developed under the collaboration of several research institutes in Japan and Europe. This system can simulate the transport of most particles with energy levels up to 1 TeV (per nucleon for ion) using different nuclear reaction models and data libraries. More than 2,500 registered researchers and technicians have used this system for various applications such as accelerator design, radiation shielding and protection, medical physics, and space- and geo-sciences. This paper summarizes the physics models and functions recently implemented in PHITS, between versions 2.52 and 2.88, especially those related to source generation useful for simulating brachytherapy and internal exposures of radioisotopes.

Comparison of a 3-D multi-group SN particle transport code with Monte Carlo for intracavitary brachytherapy of the cervix uteri.

PubMed

Gifford, Kent A; Wareing, Todd A; Failla, Gregory; Horton, John L; Eifel, Patricia J; Mourtada, Firas

2009-12-03

A patient dose distribution was calculated by a 3D multi-group S N particle transport code for intracavitary brachytherapy of the cervix uteri and compared to previously published Monte Carlo results. A Cs-137 LDR intracavitary brachytherapy CT data set was chosen from our clinical database. MCNPX version 2.5.c, was used to calculate the dose distribution. A 3D multi-group S N particle transport code, Attila version 6.1.1 was used to simulate the same patient. Each patient applicator was built in SolidWorks, a mechanical design package, and then assembled with a coordinate transformation and rotation for the patient. The SolidWorks exported applicator geometry was imported into Attila for calculation. Dose matrices were overlaid on the patient CT data set. Dose volume histograms and point doses were compared. The MCNPX calculation required 14.8 hours, whereas the Attila calculation required 22.2 minutes on a 1.8 GHz AMD Opteron CPU. Agreement between Attila and MCNPX dose calculations at the ICRU 38 points was within +/- 3%. Calculated doses to the 2 cc and 5 cc volumes of highest dose differed by not more than +/- 1.1% between the two codes. Dose and DVH overlays agreed well qualitatively. Attila can calculate dose accurately and efficiently for this Cs-137 CT-based patient geometry. Our data showed that a three-group cross-section set is adequate for Cs-137 computations. Future work is aimed at implementing an optimized version of Attila for radiotherapy calculations.

Design of Optical Systems with Extended Depth of Field: An Educational Approach to Wavefront Coding Techniques

ERIC Educational Resources Information Center

Ferran, C.; Bosch, S.; Carnicer, A.

2012-01-01

A practical activity designed to introduce wavefront coding techniques as a method to extend the depth of field in optical systems is presented. The activity is suitable for advanced undergraduate students since it combines different topics in optical engineering such as optical system design, aberration theory, Fourier optics, and digital image…

Development and Implementation of Photonuclear Cross-Section Data for Mutually Coupled Neutron-Photon Transport Calculations in the Monte Carlo N-Particle (MCNP) Radiation Transport Code

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

White, Morgan C.

2000-07-01

The fundamental motivation for the research presented in this dissertation was the need to development a more accurate prediction method for characterization of mixed radiation fields around medical electron accelerators (MEAs). Specifically, a model is developed for simulation of neutron and other particle production from photonuclear reactions and incorporated in the Monte Carlo N-Particle (MCNP) radiation transport code. This extension of the capability within the MCNP code provides for the more accurate assessment of the mixed radiation fields. The Nuclear Theory and Applications group of the Los Alamos National Laboratory has recently provided first-of-a-kind evaluated photonuclear data for a selectmore » group of isotopes. These data provide the reaction probabilities as functions of incident photon energy with angular and energy distribution information for all reaction products. The availability of these data is the cornerstone of the new methodology for state-of-the-art mutually coupled photon-neutron transport simulations. The dissertation includes details of the model development and implementation necessary to use the new photonuclear data within MCNP simulations. A new data format has been developed to include tabular photonuclear data. Data are processed from the Evaluated Nuclear Data Format (ENDF) to the new class ''u'' A Compact ENDF (ACE) format using a standalone processing code. MCNP modifications have been completed to enable Monte Carlo sampling of photonuclear reactions. Note that both neutron and gamma production are included in the present model. The new capability has been subjected to extensive verification and validation (V&V) testing. Verification testing has established the expected basic functionality. Two validation projects were undertaken. First, comparisons were made to benchmark data from literature. These calculations demonstrate the accuracy of the new data and transport routines to better than 25 percent. Second, the ability

Performance of a multilevel quantum heat engine of an ideal N-particle Fermi system.

PubMed

Wang, Rui; Wang, Jianhui; He, Jizhou; Ma, Yongli

2012-08-01

We generalize the quantum heat engine (QHE) model which was first proposed by Bender et al. [J. Phys. A 33, 4427 (2000)] to the case in which an ideal Fermi gas with an arbitrary number N of particles in a box trap is used as the working substance. Besides two quantum adiabatic processes, the engine model contains two isoenergetic processes, during which the particles are coupled to energy baths at a high constant energy E(h) and a low constant energy E(c), respectively. Directly employing the finite-time thermodynamics, we find that the power output is enhanced by increasing particle number N (or decreasing minimum trap size L(A)) for given L(A) (or N), without reduction in the efficiency. By use of global optimization, the efficiency at possible maximum power output (EPMP) is found to be universal and independent of any parameter contained in the engine model. For an engine model with any particle-number N, the efficiency at maximum power output (EMP) can be determined under the condition that it should be closest to the EPMP. Moreover, we extend the heat engine to a more general multilevel engine model with an arbitrary 1D power-law potential. Comparison between our engine model and the Carnot cycle shows that, under the same conditions, the efficiency η = 1 - E(c)/E(h) of the engine cycle is bounded from above the Carnot value η(c) =1 - T(c)/T(h).

Implementation and Characterization of Three-Dimensional Particle-in-Cell Codes on Multiple-Instruction-Multiple-Data Massively Parallel Supercomputers

NASA Technical Reports Server (NTRS)

Lyster, P. M.; Liewer, P. C.; Decyk, V. K.; Ferraro, R. D.

1995-01-01

A three-dimensional electrostatic particle-in-cell (PIC) plasma simulation code has been developed on coarse-grain distributed-memory massively parallel computers with message passing communications. Our implementation is the generalization to three-dimensions of the general concurrent particle-in-cell (GCPIC) algorithm. In the GCPIC algorithm, the particle computation is divided among the processors using a domain decomposition of the simulation domain. In a three-dimensional simulation, the domain can be partitioned into one-, two-, or three-dimensional subdomains ("slabs," "rods," or "cubes") and we investigate the efficiency of the parallel implementation of the push for all three choices. The present implementation runs on the Intel Touchstone Delta machine at Caltech; a multiple-instruction-multiple-data (MIMD) parallel computer with 512 nodes. We find that the parallel efficiency of the push is very high, with the ratio of communication to computation time in the range 0.3%-10.0%. The highest efficiency (> 99%) occurs for a large, scaled problem with 64(sup 3) particles per processing node (approximately 134 million particles of 512 nodes) which has a push time of about 250 ns per particle per time step. We have also developed expressions for the timing of the code which are a function of both code parameters (number of grid points, particles, etc.) and machine-dependent parameters (effective FLOP rate, and the effective interprocessor bandwidths for the communication of particles and grid points). These expressions can be used to estimate the performance of scaled problems--including those with inhomogeneous plasmas--to other parallel machines once the machine-dependent parameters are known.

Characteristics of large three-dimensional heaps of particles produced by ballistic deposition from extended sources

NASA Astrophysics Data System (ADS)

Topic, Nikola; Gallas, Jason A. C.; Pöschel, Thorsten

2013-11-01

This paper reports a detailed numerical investigation of the geometrical and structural properties of three-dimensional heaps of particles. Our goal is the characterization of very large heaps produced by ballistic deposition from extended circular dropping areas. First, we provide an in-depth study of the formation of monodisperse heaps of particles. We find very large heaps to contain three new geometrical characteristics: they may display two external angles of repose, one internal angle of repose, and four distinct packing fraction (density) regions. Such features are found to be directly connected with the size of the dropping zone. We derive a differential equation describing the boundary of an unexpected triangular packing fraction zone formed under the dropping area. We investigate the impact that noise during the deposition has on the final heap structure. In addition, we perform two complementary experiments designed to test the robustness of the novel features found. The first experiment considers changes due to polydispersity. The second checks what happens when letting the extended dropping zone to become a point-like source of particles, the more common type of source.

n-Nucleotide circular codes in graph theory.

PubMed

Fimmel, Elena; Michel, Christian J; Strüngmann, Lutz

2016-03-13

The circular code theory proposes that genes are constituted of two trinucleotide codes: the classical genetic code with 61 trinucleotides for coding the 20 amino acids (except the three stop codons {TAA,TAG,TGA}) and a circular code based on 20 trinucleotides for retrieving, maintaining and synchronizing the reading frame. It relies on two main results: the identification of a maximal C(3) self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses (Michel 2015 J. Theor. Biol. 380, 156-177. (doi:10.1016/j.jtbi.2015.04.009); Arquès & Michel 1996 J. Theor. Biol. 182, 45-58. (doi:10.1006/jtbi.1996.0142)) and the finding of X circular code motifs in tRNAs and rRNAs, in particular in the ribosome decoding centre (Michel 2012 Comput. Biol. Chem. 37, 24-37. (doi:10.1016/j.compbiolchem.2011.10.002); El Soufi & Michel 2014 Comput. Biol. Chem. 52, 9-17. (doi:10.1016/j.compbiolchem.2014.08.001)). The univerally conserved nucleotides A1492 and A1493 and the conserved nucleotide G530 are included in X circular code motifs. Recently, dinucleotide circular codes were also investigated (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. (doi:10.1155/2013/538631); Fimmel et al. 2015 J. Theor. Biol. 386, 159-165. (doi:10.1016/j.jtbi.2015.08.034)). As the genetic motifs of different lengths are ubiquitous in genes and genomes, we introduce a new approach based on graph theory to study in full generality n-nucleotide circular codes X, i.e. of length 2 (dinucleotide), 3 (trinucleotide), 4 (tetranucleotide), etc. Indeed, we prove that an n-nucleotide code X is circular if and only if the corresponding graph [Formula: see text] is acyclic. Moreover, the maximal length of a path in [Formula: see text] corresponds to the window of nucleotides in a sequence for detecting the correct reading frame. Finally, the graph theory of tournaments is applied to the study of dinucleotide circular codes. It has full equivalence between the combinatorics

COLAcode: COmoving Lagrangian Acceleration code

NASA Astrophysics Data System (ADS)

Tassev, Svetlin V.

2016-02-01

COLAcode is a serial particle mesh-based N-body code illustrating the COLA (COmoving Lagrangian Acceleration) method; it solves for Large Scale Structure (LSS) in a frame that is comoving with observers following trajectories calculated in Lagrangian Perturbation Theory (LPT). It differs from standard N-body code by trading accuracy at small-scales to gain computational speed without sacrificing accuracy at large scales. This is useful for generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing; such catalogs are needed to perform detailed error analysis for ongoing and future surveys of LSS.

Particle-in-cell/accelerator code for space-charge dominated beam simulation

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

2012-05-08

Warp is a multidimensional discrete-particle beam simulation program designed to be applicable where the beam space-charge is non-negligible or dominant. It is being developed in a collaboration among LLNL, LBNL and the University of Maryland. It was originally designed and optimized for heave ion fusion accelerator physics studies, but has received use in a broader range of applications, including for example laser wakefield accelerators, e-cloud studies in high enery accelerators, particle traps and other areas. At present it incorporates 3-D, axisymmetric (r,z) planar (x-z) and transverse slice (x,y) descriptions, with both electrostatic and electro-magnetic fields, and a beam envelope model.more » The code is guilt atop the Python interpreter language.« less

Relativistic Hamiltonian dynamics for N point particles

NASA Astrophysics Data System (ADS)

King, M. J.

1980-08-01

The theory is quantized canonically to give a relativistic quantum mechanics for N particles. The existence of such a theory has been in doubt since the proof of the No-interaction theorem. However, such a theory does exist and was generalized. This dynamics is expressed in terms of N + 1 pairs of canonical fourvectors (center-of-momentum variables or CMV). A gauge independent reduction due to N + 3 first class kinematic constraints leads to a 6N + 2 dimensional minimum kinematic phase space, K. The kinematics and dynamics of particles with intrinsic spin were also considered. To this end known constraint techniques were generalized to make use of graded Lie algebras. The (Poincare) invariant Hamiltonian is specified in terms of the gauge invarient variables of K. The covariant worldline variables of each particle were found to be gauge dependent. As such they will usually not satisfy a canonical algebra. An exception exists for free particles. The No-interaction theorem therefore is not violated.

User Manual and Source Code for a LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)

DTIC Science & Technology

2014-06-01

User Manual and Source Code for a LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E) by James P. Larentzos...Laboratory Aberdeen Proving Ground, MD 21005-5069 ARL-SR-290 June 2014 User Manual and Source Code for a LAMMPS Implementation of Constant...3. DATES COVERED (From - To) September 2013–February 2014 4. TITLE AND SUBTITLE User Manual and Source Code for a LAMMPS Implementation of

New methods in WARP, a particle-in-cell code for space-charge dominated beams

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

Grote, D., LLNL

1998-01-12

The current U.S. approach for a driver for inertial confinement fusion power production is a heavy-ion induction accelerator; high-current beams of heavy ions are focused onto the fusion target. The space-charge of the high-current beams affects the behavior more strongly than does the temperature (the beams are described as being ``space-charge dominated``) and the beams behave like non-neutral plasmas. The particle simulation code WARP has been developed and used to study the transport and acceleration of space-charge dominated ion beams in a wide range of applications, from basic beam physics studies, to ongoing experiments, to fusion driver concepts. WARP combinesmore » aspects of a particle simulation code and an accelerator code; it uses multi-dimensional, electrostatic particle-in-cell (PIC) techniques and has a rich mechanism for specifying the lattice of externally applied fields. There are both two- and three-dimensional versions, the former including axisymmetric (r-z) and transverse slice (x-y) models. WARP includes a number of novel techniques and capabilities that both enhance its performance and make it applicable to a wide range of problems. Some of these have been described elsewhere. Several recent developments will be discussed in this paper. A transverse slice model has been implemented with the novel capability of including bends, allowing more rapid simulation while retaining essential physics. An interface using Python as the interpreter layer instead of Basis has been developed. A parallel version of WARP has been developed using Python.« less

Nyx: Adaptive mesh, massively-parallel, cosmological simulation code

NASA Astrophysics Data System (ADS)

Almgren, Ann; Beckner, Vince; Friesen, Brian; Lukic, Zarija; Zhang, Weiqun

2017-12-01

Nyx code solves equations of compressible hydrodynamics on an adaptive grid hierarchy coupled with an N-body treatment of dark matter. The gas dynamics in Nyx use a finite volume methodology on an adaptive set of 3-D Eulerian grids; dark matter is represented as discrete particles moving under the influence of gravity. Particles are evolved via a particle-mesh method, using Cloud-in-Cell deposition/interpolation scheme. Both baryonic and dark matter contribute to the gravitational field. In addition, Nyx includes physics for accurately modeling the intergalactic medium; in optically thin limits and assuming ionization equilibrium, the code calculates heating and cooling processes of the primordial-composition gas in an ionizing ultraviolet background radiation field.

A smooth particle hydrodynamics code to model collisions between solid, self-gravitating objects

NASA Astrophysics Data System (ADS)

Schäfer, C.; Riecker, S.; Maindl, T. I.; Speith, R.; Scherrer, S.; Kley, W.

2016-05-01

Context. Modern graphics processing units (GPUs) lead to a major increase in the performance of the computation of astrophysical simulations. Owing to the different nature of GPU architecture compared to traditional central processing units (CPUs) such as x86 architecture, existing numerical codes cannot be easily migrated to run on GPU. Here, we present a new implementation of the numerical method smooth particle hydrodynamics (SPH) using CUDA and the first astrophysical application of the new code: the collision between Ceres-sized objects. Aims: The new code allows for a tremendous increase in speed of astrophysical simulations with SPH and self-gravity at low costs for new hardware. Methods: We have implemented the SPH equations to model gas, liquids and elastic, and plastic solid bodies and added a fragmentation model for brittle materials. Self-gravity may be optionally included in the simulations and is treated by the use of a Barnes-Hut tree. Results: We find an impressive performance gain using NVIDIA consumer devices compared to our existing OpenMP code. The new code is freely available to the community upon request. If you are interested in our CUDA SPH code miluphCUDA, please write an email to Christoph Schäfer. miluphCUDA is the CUDA port of miluph. miluph is pronounced [maßl2v]. We do not support the use of the code for military purposes.

SHARP: A Spatially Higher-order, Relativistic Particle-in-cell Code

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

Shalaby, Mohamad; Broderick, Avery E.; Chang, Philip

Numerical heating in particle-in-cell (PIC) codes currently precludes the accurate simulation of cold, relativistic plasma over long periods, severely limiting their applications in astrophysical environments. We present a spatially higher-order accurate relativistic PIC algorithm in one spatial dimension, which conserves charge and momentum exactly. We utilize the smoothness implied by the usage of higher-order interpolation functions to achieve a spatially higher-order accurate algorithm (up to the fifth order). We validate our algorithm against several test problems—thermal stability of stationary plasma, stability of linear plasma waves, and two-stream instability in the relativistic and non-relativistic regimes. Comparing our simulations to exact solutionsmore » of the dispersion relations, we demonstrate that SHARP can quantitatively reproduce important kinetic features of the linear regime. Our simulations have a superior ability to control energy non-conservation and avoid numerical heating in comparison to common second-order schemes. We provide a natural definition for convergence of a general PIC algorithm: the complement of physical modes captured by the simulation, i.e., those that lie above the Poisson noise, must grow commensurately with the resolution. This implies that it is necessary to simultaneously increase the number of particles per cell and decrease the cell size. We demonstrate that traditional ways for testing for convergence fail, leading to plateauing of the energy error. This new PIC code enables us to faithfully study the long-term evolution of plasma problems that require absolute control of the energy and momentum conservation.« less

Particle-in-cell code library for numerical simulation of the ECR source plasma

NASA Astrophysics Data System (ADS)

Shirkov, G.; Alexandrov, V.; Preisendorf, V.; Shevtsov, V.; Filippov, A.; Komissarov, R.; Mironov, V.; Shirkova, E.; Strekalovsky, O.; Tokareva, N.; Tuzikov, A.; Vatulin, V.; Vasina, E.; Fomin, V.; Anisimov, A.; Veselov, R.; Golubev, A.; Grushin, S.; Povyshev, V.; Sadovoi, A.; Donskoi, E.; Nakagawa, T.; Yano, Y.

2003-05-01

The project ;Numerical simulation and optimization of ion accumulation and production in multicharged ion sources; is funded by the International Science and Technology Center (ISTC). A summary of recent project development and the first version of a computer code library for simulation of electron-cyclotron resonance (ECR) source plasmas based on the particle-in-cell method are presented.

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code

NASA Astrophysics Data System (ADS)

Chacon, Luis

2006-10-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field to machine precision, non-dissipative, and linearly and nonlinearly stable in the absence of physical dissipation. PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, second-order implicit schemes such as Crank-Nicolson and BDF2 (2^nd order backward differentiation formula) are available. PIXIE3D is fully parallel (employs PETSc for parallelism), and exhibits excellent parallel scalability. A parallel, scalable, MG preconditioning strategy, based on physics-based preconditioning ideas, has been developed for resistive MHD, and is currently being extended to Hall MHD. In this poster, we will report on progress in the algorithmic formulation for extended MHD, as well as the the serial and parallel performance of PIXIE3D in a variety of problems and geometries. L. Chac'on, Comput. Phys. Comm., 163 (3), 143-171 (2004) L. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002); J. Comput. Phys., 188 (2), 573-592 (2003) L. Chac'on, 32nd EPS Conf. Plasma Physics, Tarragona, Spain, 2005 L. Chac'on et al., 33rd EPS Conf. Plasma Physics, Rome, Italy, 2006

VINE-A NUMERICAL CODE FOR SIMULATING ASTROPHYSICAL SYSTEMS USING PARTICLES. II. IMPLEMENTATION AND PERFORMANCE CHARACTERISTICS

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

Nelson, Andrew F.; Wetzstein, M.; Naab, T.

2009-10-01

We continue our presentation of VINE. In this paper, we begin with a description of relevant architectural properties of the serial and shared memory parallel computers on which VINE is intended to run, and describe their influences on the design of the code itself. We continue with a detailed description of a number of optimizations made to the layout of the particle data in memory and to our implementation of a binary tree used to access that data for use in gravitational force calculations and searches for smoothed particle hydrodynamics (SPH) neighbor particles. We describe the modifications to the codemore » necessary to obtain forces efficiently from special purpose 'GRAPE' hardware, the interfaces required to allow transparent substitution of those forces in the code instead of those obtained from the tree, and the modifications necessary to use both tree and GRAPE together as a fused GRAPE/tree combination. We conclude with an extensive series of performance tests, which demonstrate that the code can be run efficiently and without modification in serial on small workstations or in parallel using the OpenMP compiler directives on large-scale, shared memory parallel machines. We analyze the effects of the code optimizations and estimate that they improve its overall performance by more than an order of magnitude over that obtained by many other tree codes. Scaled parallel performance of the gravity and SPH calculations, together the most costly components of most simulations, is nearly linear up to at least 120 processors on moderate sized test problems using the Origin 3000 architecture, and to the maximum machine sizes available to us on several other architectures. At similar accuracy, performance of VINE, used in GRAPE-tree mode, is approximately a factor 2 slower than that of VINE, used in host-only mode. Further optimizations of the GRAPE/host communications could improve the speed by as much as a factor of 3, but have not yet been implemented in VINE

Implementation of a flexible and scalable particle-in-cell method for massively parallel computations in the mantle convection code ASPECT

NASA Astrophysics Data System (ADS)

Gassmöller, Rene; Bangerth, Wolfgang

2016-04-01

Particle-in-cell methods have a long history and many applications in geodynamic modelling of mantle convection, lithospheric deformation and crustal dynamics. They are primarily used to track material information, the strain a material has undergone, the pressure-temperature history a certain material region has experienced, or the amount of volatiles or partial melt present in a region. However, their efficient parallel implementation - in particular combined with adaptive finite-element meshes - is complicated due to the complex communication patterns and frequent reassignment of particles to cells. Consequently, many current scientific software packages accomplish this efficient implementation by specifically designing particle methods for a single purpose, like the advection of scalar material properties that do not evolve over time (e.g., for chemical heterogeneities). Design choices for particle integration, data storage, and parallel communication are then optimized for this single purpose, making the code relatively rigid to changing requirements. Here, we present the implementation of a flexible, scalable and efficient particle-in-cell method for massively parallel finite-element codes with adaptively changing meshes. Using a modular plugin structure, we allow maximum flexibility of the generation of particles, the carried tracer properties, the advection and output algorithms, and the projection of properties to the finite-element mesh. We present scaling tests ranging up to tens of thousands of cores and tens of billions of particles. Additionally, we discuss efficient load-balancing strategies for particles in adaptive meshes with their strengths and weaknesses, local particle-transfer between parallel subdomains utilizing existing communication patterns from the finite element mesh, and the use of established parallel output algorithms like the HDF5 library. Finally, we show some relevant particle application cases, compare our implementation to a

Spacecraft charging analysis with the implicit particle-in-cell code iPic3D

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

Deca, J.; Lapenta, G.; Marchand, R.

2013-10-15

We present the first results on the analysis of spacecraft charging with the implicit particle-in-cell code iPic3D, designed for running on massively parallel supercomputers. The numerical algorithm is presented, highlighting the implementation of the electrostatic solver and the immersed boundary algorithm; the latter which creates the possibility to handle complex spacecraft geometries. As a first step in the verification process, a comparison is made between the floating potential obtained with iPic3D and with Orbital Motion Limited theory for a spherical particle in a uniform stationary plasma. Second, the numerical model is verified for a CubeSat benchmark by comparing simulation resultsmore » with those of PTetra for space environment conditions with increasing levels of complexity. In particular, we consider spacecraft charging from plasma particle collection, photoelectron and secondary electron emission. The influence of a background magnetic field on the floating potential profile near the spacecraft is also considered. Although the numerical approaches in iPic3D and PTetra are rather different, good agreement is found between the two models, raising the level of confidence in both codes to predict and evaluate the complex plasma environment around spacecraft.« less

PyMercury: Interactive Python for the Mercury Monte Carlo Particle Transport Code

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

Iandola, F N; O'Brien, M J; Procassini, R J

2010-11-29

Monte Carlo particle transport applications are often written in low-level languages (C/C++) for optimal performance on clusters and supercomputers. However, this development approach often sacrifices straightforward usability and testing in the interest of fast application performance. To improve usability, some high-performance computing applications employ mixed-language programming with high-level and low-level languages. In this study, we consider the benefits of incorporating an interactive Python interface into a Monte Carlo application. With PyMercury, a new Python extension to the Mercury general-purpose Monte Carlo particle transport code, we improve application usability without diminishing performance. In two case studies, we illustrate how PyMercury improvesmore » usability and simplifies testing and validation in a Monte Carlo application. In short, PyMercury demonstrates the value of interactive Python for Monte Carlo particle transport applications. In the future, we expect interactive Python to play an increasingly significant role in Monte Carlo usage and testing.« less

Deploying electromagnetic particle-in-cell (EM-PIC) codes on Xeon Phi accelerators boards

NASA Astrophysics Data System (ADS)

Fonseca, Ricardo

2014-10-01

The complexity of the phenomena involved in several relevant plasma physics scenarios, where highly nonlinear and kinetic processes dominate, makes purely theoretical descriptions impossible. Further understanding of these scenarios requires detailed numerical modeling, but fully relativistic particle-in-cell codes such as OSIRIS are computationally intensive. The quest towards Exaflop computer systems has lead to the development of HPC systems based on add-on accelerator cards, such as GPGPUs and more recently the Xeon Phi accelerators that power the current number 1 system in the world. These cards, also referred to as Intel Many Integrated Core Architecture (MIC) offer peak theoretical performances of >1 TFlop/s for general purpose calculations in a single board, and are receiving significant attention as an attractive alternative to CPUs for plasma modeling. In this work we report on our efforts towards the deployment of an EM-PIC code on a Xeon Phi architecture system. We will focus on the parallelization and vectorization strategies followed, and present a detailed performance evaluation of code performance in comparison with the CPU code.

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

DOE PAGES

Vincenti, H.; Lobet, M.; Lehe, R.; ...

2016-09-19

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈20pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD registermore » length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scat;ter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of ×2 to ×2.5 speed-up in double precision for particle shape factor of orders 1–3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles). Program summary Program Title: vec_deposition Program Files doi:http://dx.doi.org/10.17632/nh77fv9k8c.1 Licensing provisions: BSD 3-Clause Programming language: Fortran 90 External routines/libraries:  OpenMP > 4.0 Nature of problem

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

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

Vincenti, H.; Lobet, M.; Lehe, R.

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈20pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD registermore » length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scat;ter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of ×2 to ×2.5 speed-up in double precision for particle shape factor of orders 1–3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles). Program summary Program Title: vec_deposition Program Files doi:http://dx.doi.org/10.17632/nh77fv9k8c.1 Licensing provisions: BSD 3-Clause Programming language: Fortran 90 External routines/libraries:  OpenMP > 4.0 Nature of problem

Application of a Java-based, univel geometry, neutral particle Monte Carlo code to the searchlight problem

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

Charles A. Wemple; Joshua J. Cogliati

2005-04-01

A univel geometry, neutral particle Monte Carlo transport code, written entirely in the Java programming language, is under development for medical radiotherapy applications. The code uses ENDF-VI based continuous energy cross section data in a flexible XML format. Full neutron-photon coupling, including detailed photon production and photonuclear reactions, is included. Charged particle equilibrium is assumed within the patient model so that detailed transport of electrons produced by photon interactions may be neglected. External beam and internal distributed source descriptions for mixed neutron-photon sources are allowed. Flux and dose tallies are performed on a univel basis. A four-tap, shift-register-sequence random numbermore » generator is used. Initial verification and validation testing of the basic neutron transport routines is underway. The searchlight problem was chosen as a suitable first application because of the simplicity of the physical model. Results show excellent agreement with analytic solutions. Computation times for similar numbers of histories are comparable to other neutron MC codes written in C and FORTRAN.« less

Implementation and performance of FDPS: a framework for developing parallel particle simulation codes

NASA Astrophysics Data System (ADS)

Iwasawa, Masaki; Tanikawa, Ataru; Hosono, Natsuki; Nitadori, Keigo; Muranushi, Takayuki; Makino, Junichiro

2016-08-01

We present the basic idea, implementation, measured performance, and performance model of FDPS (Framework for Developing Particle Simulators). FDPS is an application-development framework which helps researchers to develop simulation programs using particle methods for large-scale distributed-memory parallel supercomputers. A particle-based simulation program for distributed-memory parallel computers needs to perform domain decomposition, exchange of particles which are not in the domain of each computing node, and gathering of the particle information in other nodes which are necessary for interaction calculation. Also, even if distributed-memory parallel computers are not used, in order to reduce the amount of computation, algorithms such as the Barnes-Hut tree algorithm or the Fast Multipole Method should be used in the case of long-range interactions. For short-range interactions, some methods to limit the calculation to neighbor particles are required. FDPS provides all of these functions which are necessary for efficient parallel execution of particle-based simulations as "templates," which are independent of the actual data structure of particles and the functional form of the particle-particle interaction. By using FDPS, researchers can write their programs with the amount of work necessary to write a simple, sequential and unoptimized program of O(N2) calculation cost, and yet the program, once compiled with FDPS, will run efficiently on large-scale parallel supercomputers. A simple gravitational N-body program can be written in around 120 lines. We report the actual performance of these programs and the performance model. The weak scaling performance is very good, and almost linear speed-up was obtained for up to the full system of the K computer. The minimum calculation time per timestep is in the range of 30 ms (N = 107) to 300 ms (N = 109). These are currently limited by the time for the calculation of the domain decomposition and communication

A comparison of cosmological hydrodynamic codes

NASA Technical Reports Server (NTRS)

Kang, Hyesung; Ostriker, Jeremiah P.; Cen, Renyue; Ryu, Dongsu; Hernquist, Lars; Evrard, August E.; Bryan, Greg L.; Norman, Michael L.

1994-01-01

We present a detailed comparison of the simulation results of various hydrodynamic codes. Starting with identical initial conditions based on the cold dark matter scenario for the growth of structure, with parameters h = 0.5 Omega = Omega(sub b) = 1, and sigma(sub 8) = 1, we integrate from redshift z = 20 to z = O to determine the physical state within a representative volume of size L(exp 3) where L = 64 h(exp -1) Mpc. Five indenpendent codes are compared: three of them Eulerian mesh-based and two variants of the smooth particle hydrodynamics 'SPH' Lagrangian approach. The Eulerian codes were run at N(exp 3) = (32(exp 3), 64(exp 3), 128(exp 3), and 256(exp 3)) cells, the SPH codes at N(exp 3) = 32(exp 3) and 64(exp 3) particles. Results were then rebinned to a 16(exp 3) grid with the exception that the rebinned data should converge, by all techniques, to a common and correct result as N approaches infinity. We find that global averages of various physical quantities do, as expected, tend to converge in the rebinned model, but that uncertainites in even primitive quantities such as (T), (rho(exp 2))(exp 1/2) persists at the 3%-17% level achieve comparable and satisfactory accuracy for comparable computer time in their treatment of the high-density, high-temeprature regions as measured in the rebinned data; the variance among the five codes (at highest resolution) for the mean temperature (as weighted by rho(exp 2) is only 4.5%. Examined at high resolution we suspect that the density resolution is better in the SPH codes and the thermal accuracy in low-density regions better in the Eulerian codes. In the low-density, low-temperature regions the SPH codes have poor accuracy due to statiscal effects, and the Jameson code gives the temperatures which are too high, due to overuse of artificial viscosity in these high Mach number regions. Overall the comparison allows us to better estimate errors; it points to ways of improving this current generation ofhydrodynamic

Implementation of a 3D version of ponderomotive guiding center solver in particle-in-cell code OSIRIS

NASA Astrophysics Data System (ADS)

Helm, Anton; Vieira, Jorge; Silva, Luis; Fonseca, Ricardo

2016-10-01

Laser-driven accelerators gained an increased attention over the past decades. Typical modeling techniques for laser wakefield acceleration (LWFA) are based on particle-in-cell (PIC) simulations. PIC simulations, however, are very computationally expensive due to the disparity of the relevant scales ranging from the laser wavelength, in the micrometer range, to the acceleration length, currently beyond the ten centimeter range. To minimize the gap between these despair scales the ponderomotive guiding center (PGC) algorithm is a promising approach. By describing the evolution of the laser pulse envelope separately, only the scales larger than the plasma wavelength are required to be resolved in the PGC algorithm, leading to speedups in several orders of magnitude. Previous work was limited to two dimensions. Here we present the implementation of the 3D version of a PGC solver into the massively parallel, fully relativistic PIC code OSIRIS. We extended the solver to include periodic boundary conditions and parallelization in all spatial dimensions. We present benchmarks for distributed and shared memory parallelization. We also discuss the stability of the PGC solver.

Confinement properties of tokamak plasmas with extended regions of low magnetic shear

NASA Astrophysics Data System (ADS)

Graves, J. P.; Cooper, W. A.; Kleiner, A.; Raghunathan, M.; Neto, E.; Nicolas, T.; Lanthaler, S.; Patten, H.; Pfefferle, D.; Brunetti, D.; Lutjens, H.

2017-10-01

Extended regions of low magnetic shear can be advantageous to tokamak plasmas. But the core and edge can be susceptible to non-resonant ideal fluctuations due to the weakened restoring force associated with magnetic field line bending. This contribution shows how saturated non-linear phenomenology, such as 1 / 1 Long Lived Modes, and Edge Harmonic Oscillations associated with QH-modes, can be modelled accurately using the non-linear stability code XTOR, the free boundary 3D equilibrium code VMEC, and non-linear analytic theory. That the equilibrium approach is valid is particularly valuable because it enables advanced particle confinement studies to be undertaken in the ordinarily difficult environment of strongly 3D magnetic fields. The VENUS-LEVIS code exploits the Fourier description of the VMEC equilibrium fields, such that full Lorenzian and guiding centre approximated differential operators in curvilinear angular coordinates can be evaluated analytically. Consequently, the confinement properties of minority ions such as energetic particles and high Z impurities can be calculated accurately over slowing down timescales in experimentally relevant 3D plasmas.

Second order gyrokinetic theory for particle-in-cell codes

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

Tronko, Natalia; Bottino, Alberto; Sonnendrücker, Eric

2016-08-15

The main idea of the gyrokinetic dynamical reduction consists in a systematical removal of the fast scale motion (the gyromotion) from the dynamics of the plasma, resulting in a considerable simplification and a significant gain of computational time. The gyrokinetic Maxwell–Vlasov equations are nowadays implemented in for modeling (both laboratory and astrophysical) strongly magnetized plasmas. Different versions of the reduced set of equations exist, depending on the construction of the gyrokinetic reduction procedure and the approximations performed in the derivation. The purpose of this article is to explicitly show the connection between the general second order gyrokinetic Maxwell–Vlasov system issuedmore » from the modern gyrokinetic theory and the model currently implemented in the global electromagnetic Particle-in-Cell code ORB5. Necessary information about the modern gyrokinetic formalism is given together with the consistent derivation of the gyrokinetic Maxwell–Vlasov equations from first principles. The variational formulation of the dynamics is used to obtain the corresponding energy conservation law, which in turn is used for the verification of energy conservation diagnostics currently implemented in ORB5. This work fits within the context of the code verification project VeriGyro currently run at IPP Max-Planck Institut in collaboration with others European institutions.« less

Visual Tracking via Sparse and Local Linear Coding.

PubMed

Wang, Guofeng; Qin, Xueying; Zhong, Fan; Liu, Yue; Li, Hongbo; Peng, Qunsheng; Yang, Ming-Hsuan

2015-11-01

The state search is an important component of any object tracking algorithm. Numerous algorithms have been proposed, but stochastic sampling methods (e.g., particle filters) are arguably one of the most effective approaches. However, the discretization of the state space complicates the search for the precise object location. In this paper, we propose a novel tracking algorithm that extends the state space of particle observations from discrete to continuous. The solution is determined accurately via iterative linear coding between two convex hulls. The algorithm is modeled by an optimal function, which can be efficiently solved by either convex sparse coding or locality constrained linear coding. The algorithm is also very flexible and can be combined with many generic object representations. Thus, we first use sparse representation to achieve an efficient searching mechanism of the algorithm and demonstrate its accuracy. Next, two other object representation models, i.e., least soft-threshold squares and adaptive structural local sparse appearance, are implemented with improved accuracy to demonstrate the flexibility of our algorithm. Qualitative and quantitative experimental results demonstrate that the proposed tracking algorithm performs favorably against the state-of-the-art methods in dynamic scenes.

Effect of Particle Size and Impact Velocity on Collision Behaviors Between Nano-Scale TiN Particles: MD Simulation.

PubMed

Yao, Hai-Long; Hu, Xiao-Zhen; Yang, Guan-Jun

2018-06-01

Inter-particle bonding formation which determines qualities of nano-scale ceramic coatings is influenced by particle collision behaviors during high velocity collision processes. In this study, collision behaviors between nano-scale TiN particles with different diameters were illuminated by using Molecular Dynamics simulation through controlling impact velocities. Results show that nano-scale TiN particles exhibit three states depending on particle sizes and impact velocities, i.e., bonding, bonding with localized fracturing, and rebounding. These TiN particles states are summarized into a parameter selection map providing an overview of the conditions in terms of particle sizes and velocities. Microstructure results show that localized atoms displacement and partial fracture around the impact region are main reasons for bonding formation of nano-scale ceramic particles, which shows differences from conventional particles refining and amorphization. A relationship between the adhesion energy and the rebound energy is established to understand bonding formation mechanism for nano-scale TiN particle collision. Results show that the energy relationship is depended on the particle sizes and impact velocities, and nano-scale ceramic particles can be bonded together as the adhesion energy being higher than the rebound energy.

Prediction of material strength and fracture of glass using the SPHINX smooth particle hydrodynamics code

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

Mandell, D.A.; Wingate, C.A.

1994-08-01

The design of many military devices involves numerical predictions of the material strength and fracture of brittle materials. The materials of interest include ceramics, that are used in armor packages; glass that is used in truck and jeep windshields and in helicopters; and rock and concrete that are used in underground bunkers. As part of a program to develop advanced hydrocode design tools, the authors have implemented a brittle fracture model for glass into the SPHINX smooth particle hydrodynamics code. The authors have evaluated this model and the code by predicting data from one-dimensional flyer plate impacts into glass, andmore » data from tungsten rods impacting glass. Since fractured glass properties, which are needed in the model, are not available, the authors did sensitivity studies of these properties, as well as sensitivity studies to determine the number of particles needed in the calculations. The numerical results are in good agreement with the data.« less

The PARTRAC code: Status and recent developments

NASA Astrophysics Data System (ADS)

Friedland, Werner; Kundrat, Pavel

Biophysical modeling is of particular value for predictions of radiation effects due to manned space missions. PARTRAC is an established tool for Monte Carlo-based simulations of radiation track structures, damage induction in cellular DNA and its repair [1]. Dedicated modules describe interactions of ionizing particles with the traversed medium, the production and reactions of reactive species, and score DNA damage determined by overlapping track structures with multi-scale chromatin models. The DNA repair module describes the repair of DNA double-strand breaks (DSB) via the non-homologous end-joining pathway; the code explicitly simulates the spatial mobility of individual DNA ends in parallel with their processing by major repair enzymes [2]. To simulate the yields and kinetics of radiation-induced chromosome aberrations, the repair module has been extended by tracking the information on the chromosome origin of ligated fragments as well as the presence of centromeres [3]. PARTRAC calculations have been benchmarked against experimental data on various biological endpoints induced by photon and ion irradiation. The calculated DNA fragment distributions after photon and ion irradiation reproduce corresponding experimental data and their dose- and LET-dependence. However, in particular for high-LET radiation many short DNA fragments are predicted below the detection limits of the measurements, so that the experiments significantly underestimate DSB yields by high-LET radiation [4]. The DNA repair module correctly describes the LET-dependent repair kinetics after (60) Co gamma-rays and different N-ion radiation qualities [2]. First calculations on the induction of chromosome aberrations have overestimated the absolute yields of dicentrics, but correctly reproduced their relative dose-dependence and the difference between gamma- and alpha particle irradiation [3]. Recent developments of the PARTRAC code include a model of hetero- vs euchromatin structures to enable

A Dual-Channel Acquisition Method Based on Extended Replica Folding Algorithm for Long Pseudo-Noise Code in Inter-Satellite Links.

PubMed

Zhao, Hongbo; Chen, Yuying; Feng, Wenquan; Zhuang, Chen

2018-05-25

Inter-satellite links are an important component of the new generation of satellite navigation systems, characterized by low signal-to-noise ratio (SNR), complex electromagnetic interference and the short time slot of each satellite, which brings difficulties to the acquisition stage. The inter-satellite link in both Global Positioning System (GPS) and BeiDou Navigation Satellite System (BDS) adopt the long code spread spectrum system. However, long code acquisition is a difficult and time-consuming task due to the long code period. Traditional folding methods such as extended replica folding acquisition search technique (XFAST) and direct average are largely restricted because of code Doppler and additional SNR loss caused by replica folding. The dual folding method (DF-XFAST) and dual-channel method have been proposed to achieve long code acquisition in low SNR and high dynamic situations, respectively, but the former is easily affected by code Doppler and the latter is not fast enough. Considering the environment of inter-satellite links and the problems of existing algorithms, this paper proposes a new long code acquisition algorithm named dual-channel acquisition method based on the extended replica folding algorithm (DC-XFAST). This method employs dual channels for verification. Each channel contains an incoming signal block. Local code samples are folded and zero-padded to the length of the incoming signal block. After a circular FFT operation, the correlation results contain two peaks of the same magnitude and specified relative position. The detection process is eased through finding the two largest values. The verification takes all the full and partial peaks into account. Numerical results reveal that the DC-XFAST method can improve acquisition performance while acquisition speed is guaranteed. The method has a significantly higher acquisition probability than folding methods XFAST and DF-XFAST. Moreover, with the advantage of higher detection

Simulation of Shear Alfvén Waves in LAPD using the BOUT++ code

NASA Astrophysics Data System (ADS)

Wei, Di; Friedman, B.; Carter, T. A.; Umansky, M. V.

2011-10-01

The linear and nonlinear physics of shear Alfvén waves is investigated using the 3D Braginskii fluid code BOUT++. The code has been verified against analytical calculations for the dispersion of kinetic and inertial Alfvén waves. Various mechanisms for forcing Alfvén waves in the code are explored, including introducing localized current sources similar to physical antennas used in experiments. Using this foundation, the code is used to model nonlinear interactions among shear Alfvén waves in a cylindrical magnetized plasma, such as that found in the Large Plasma Device (LAPD) at UCLA. In the future this investigation will allow for examination of the nonlinear interactions between shear Alfvén waves in both laboratory and space plasmas in order to compare to predictions of MHD turbulence.

Extending the length and time scales of Gram–Schmidt Lyapunov vector computations

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

Costa, Anthony B., E-mail: acosta@northwestern.edu; Green, Jason R., E-mail: jason.green@umb.edu; Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125

Lyapunov vectors have found growing interest recently due to their ability to characterize systems out of thermodynamic equilibrium. The computation of orthogonal Gram–Schmidt vectors requires multiplication and QR decomposition of large matrices, which grow as N{sup 2} (with the particle count). This expense has limited such calculations to relatively small systems and short time scales. Here, we detail two implementations of an algorithm for computing Gram–Schmidt vectors. The first is a distributed-memory message-passing method using Scalapack. The second uses the newly-released MAGMA library for GPUs. We compare the performance of both codes for Lennard–Jones fluids from N=100 to 1300 betweenmore » Intel Nahalem/Infiniband DDR and NVIDIA C2050 architectures. To our best knowledge, these are the largest systems for which the Gram–Schmidt Lyapunov vectors have been computed, and the first time their calculation has been GPU-accelerated. We conclude that Lyapunov vector calculations can be significantly extended in length and time by leveraging the power of GPU-accelerated linear algebra.« less

Extending the length and time scales of Gram-Schmidt Lyapunov vector computations

NASA Astrophysics Data System (ADS)

Costa, Anthony B.; Green, Jason R.

2013-08-01

Lyapunov vectors have found growing interest recently due to their ability to characterize systems out of thermodynamic equilibrium. The computation of orthogonal Gram-Schmidt vectors requires multiplication and QR decomposition of large matrices, which grow as N2 (with the particle count). This expense has limited such calculations to relatively small systems and short time scales. Here, we detail two implementations of an algorithm for computing Gram-Schmidt vectors. The first is a distributed-memory message-passing method using Scalapack. The second uses the newly-released MAGMA library for GPUs. We compare the performance of both codes for Lennard-Jones fluids from N=100 to 1300 between Intel Nahalem/Infiniband DDR and NVIDIA C2050 architectures. To our best knowledge, these are the largest systems for which the Gram-Schmidt Lyapunov vectors have been computed, and the first time their calculation has been GPU-accelerated. We conclude that Lyapunov vector calculations can be significantly extended in length and time by leveraging the power of GPU-accelerated linear algebra.

PHoToNs–A parallel heterogeneous and threads oriented code for cosmological N-body simulation

NASA Astrophysics Data System (ADS)

Wang, Qiao; Cao, Zong-Yan; Gao, Liang; Chi, Xue-Bin; Meng, Chen; Wang, Jie; Wang, Long

2018-06-01

We introduce a new code for cosmological simulations, PHoToNs, which incorporates features for performing massive cosmological simulations on heterogeneous high performance computer (HPC) systems and threads oriented programming. PHoToNs adopts a hybrid scheme to compute gravitational force, with the conventional Particle-Mesh (PM) algorithm to compute the long-range force, the Tree algorithm to compute the short range force and the direct summation Particle-Particle (PP) algorithm to compute gravity from very close particles. A self-similar space filling a Peano-Hilbert curve is used to decompose the computing domain. Threads programming is advantageously used to more flexibly manage the domain communication, PM calculation and synchronization, as well as Dual Tree Traversal on the CPU+MIC platform. PHoToNs scales well and efficiency of the PP kernel achieves 68.6% of peak performance on MIC and 74.4% on CPU platforms. We also test the accuracy of the code against the much used Gadget-2 in the community and found excellent agreement.

Extending Mondrian Memory Protection

DTIC Science & Technology

2010-11-01

a kernel semaphore is locked or unlocked. In addition, we extended the system call interface to receive notifications about user-land locking...operations (such as calls to the mutex and semaphore code provided by the C library). By patching the dynamically loadable GLibC5, we are able to test... semaphores , and spinlocks. RTO-MP-IST-091 10- 9 Extending Mondrian Memory Protection to loading extension plugins. This prevents any untrusted code

TWANG-PIC, a novel gyro-averaged one-dimensional particle-in-cell code for interpretation of gyrotron experiments

NASA Astrophysics Data System (ADS)

Braunmueller, F.; Tran, T. M.; Vuillemin, Q.; Alberti, S.; Genoud, J.; Hogge, J.-Ph.; Tran, M. Q.

2015-06-01

A new gyrotron simulation code for simulating the beam-wave interaction using a monomode time-dependent self-consistent model is presented. The new code TWANG-PIC is derived from the trajectory-based code TWANG by describing the electron motion in a gyro-averaged one-dimensional Particle-In-Cell (PIC) approach. In comparison to common PIC-codes, it is distinguished by its computation speed, which makes its use in parameter scans and in experiment interpretation possible. A benchmark of the new code is presented as well as a comparative study between the two codes. This study shows that the inclusion of a time-dependence in the electron equations, as it is the case in the PIC-approach, is mandatory for simulating any kind of non-stationary oscillations in gyrotrons. Finally, the new code is compared with experimental results and some implications of the violated model assumptions in the TWANG code are disclosed for a gyrotron experiment in which non-stationary regimes have been observed and for a critical case that is of interest in high power gyrotron development.

TWANG-PIC, a novel gyro-averaged one-dimensional particle-in-cell code for interpretation of gyrotron experiments

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

Braunmueller, F., E-mail: falk.braunmueller@epfl.ch; Tran, T. M.; Alberti, S.

A new gyrotron simulation code for simulating the beam-wave interaction using a monomode time-dependent self-consistent model is presented. The new code TWANG-PIC is derived from the trajectory-based code TWANG by describing the electron motion in a gyro-averaged one-dimensional Particle-In-Cell (PIC) approach. In comparison to common PIC-codes, it is distinguished by its computation speed, which makes its use in parameter scans and in experiment interpretation possible. A benchmark of the new code is presented as well as a comparative study between the two codes. This study shows that the inclusion of a time-dependence in the electron equations, as it is themore » case in the PIC-approach, is mandatory for simulating any kind of non-stationary oscillations in gyrotrons. Finally, the new code is compared with experimental results and some implications of the violated model assumptions in the TWANG code are disclosed for a gyrotron experiment in which non-stationary regimes have been observed and for a critical case that is of interest in high power gyrotron development.« less

Study on friction coefficient of soft soil based on particle flow code

NASA Astrophysics Data System (ADS)

Lei, Xiaohong; Zhang, Zhongwei

2017-04-01

There has no uniform method for determining the micro parameters in particle flow code, and the corresponding formulas obtained by each scholar can only be applied to similar situations. In this paper, the relationship between the micro parameters friction coefficient and macro parameters friction angle is established by using the two axis servo compression as the calibration experiment, and the corresponding formula is fitted to solve the difficulties of determining the PFC micro parameters which provide a reference for determination of the micro parameters of soft soil.

Extending the Capture Volume of an Iris Recognition System Using Wavefront Coding and Super-Resolution.

PubMed

Hsieh, Sheng-Hsun; Li, Yung-Hui; Tien, Chung-Hao; Chang, Chin-Chen

2016-12-01

Iris recognition has gained increasing popularity over the last few decades; however, the stand-off distance in a conventional iris recognition system is too short, which limits its application. In this paper, we propose a novel hardware-software hybrid method to increase the stand-off distance in an iris recognition system. When designing the system hardware, we use an optimized wavefront coding technique to extend the depth of field. To compensate for the blurring of the image caused by wavefront coding, on the software side, the proposed system uses a local patch-based super-resolution method to restore the blurred image to its clear version. The collaborative effect of the new hardware design and software post-processing showed great potential in our experiment. The experimental results showed that such improvement cannot be achieved by using a hardware-or software-only design. The proposed system can increase the capture volume of a conventional iris recognition system by three times and maintain the system's high recognition rate.

Understanding large SEP events with the PATH code: Modeling of the 13 December 2006 SEP event

NASA Astrophysics Data System (ADS)

Verkhoglyadova, O. P.; Li, G.; Zank, G. P.; Hu, Q.; Cohen, C. M. S.; Mewaldt, R. A.; Mason, G. M.; Haggerty, D. K.; von Rosenvinge, T. T.; Looper, M. D.

2010-12-01

The Particle Acceleration and Transport in the Heliosphere (PATH) numerical code was developed to understand solar energetic particle (SEP) events in the near-Earth environment. We discuss simulation results for the 13 December 2006 SEP event. The PATH code includes modeling a background solar wind through which a CME-driven oblique shock propagates. The code incorporates a mixed population of both flare and shock-accelerated solar wind suprathermal particles. The shock parameters derived from ACE measurements at 1 AU and observational flare characteristics are used as input into the numerical model. We assume that the diffusive shock acceleration mechanism is responsible for particle energization. We model the subsequent transport of particles originated at the flare site and particles escaping from the shock and propagating in the equatorial plane through the interplanetary medium. We derive spectra for protons, oxygen, and iron ions, together with their time-intensity profiles at 1 AU. Our modeling results show reasonable agreement with in situ measurements by ACE, STEREO, GOES, and SAMPEX for this event. We numerically estimate the Fe/O abundance ratio and discuss the physics underlying a mixed SEP event. We point out that the flare population is as important as shock geometry changes during shock propagation for modeling time-intensity profiles and spectra at 1 AU. The combined effects of seed population and shock geometry will be examined in the framework of an extended PATH code in future modeling efforts.

Inequalities of extended beta and extended hypergeometric functions.

PubMed

Mondal, Saiful R

2017-01-01

We study the log-convexity of the extended beta functions. As a consequence, we establish Turán-type inequalities. The monotonicity, log-convexity, log-concavity of extended hypergeometric functions are deduced by using the inequalities on extended beta functions. The particular cases of those results also give the Turán-type inequalities for extended confluent and extended Gaussian hypergeometric functions. Some reverses of Turán-type inequalities are also derived.

Dual neutral particle induced transmutation in CINDER2008

NASA Astrophysics Data System (ADS)

Martin, W. J.; de Oliveira, C. R. E.; Hecht, A. A.

2014-12-01

Although nuclear transmutation methods for fission have existed for decades, the focus has been on neutron-induced reactions. Recent novel concepts have sought to use both neutrons and photons for purposes such as active interrogation of cargo to detect the smuggling of highly enriched uranium, a concept that would require modeling the transmutation caused by both incident particles. As photonuclear transmutation has yet to be modeled alongside neutron-induced transmutation in a production code, new methods need to be developed. The CINDER2008 nuclear transmutation code from Los Alamos National Laboratory is extended from neutron applications to dual neutral particle applications, allowing both neutron- and photon-induced reactions for this modeling with a focus on fission. Following standard reaction modeling, the induced fission reaction is understood as a two-part reaction, with an entrance channel to the excited compound nucleus, and an exit channel from the excited compound nucleus to the fission fragmentation. Because photofission yield data-the exit channel from the compound nucleus-are sparse, neutron fission yield data are used in this work. With a different compound nucleus and excitation, the translation to the excited compound state is modified, as appropriate. A verification and validation of these methods and data has been performed. This has shown that the translation of neutron-induced fission product yield sets, and their use in photonuclear applications, is appropriate, and that the code has been extended correctly.

Production of energetic light fragments in extensions of the CEM and LAQGSM event generators of the Monte Carlo transport code MCNP6 [Production of energetic light fragments in CEM, LAQGSM, and MCNP6

DOE PAGES

Mashnik, Stepan Georgievich; Kerby, Leslie Marie; Gudima, Konstantin K.; ...

2017-03-23

We extend the cascade-exciton model (CEM), and the Los Alamos version of the quark-gluon string model (LAQGSM), event generators of the Monte Carlo N-particle transport code version 6 (MCNP6), to describe production of energetic light fragments (LF) heavier than 4He from various nuclear reactions induced by particles and nuclei at energies up to about 1 TeV/nucleon. In these models, energetic LF can be produced via Fermi breakup, preequilibrium emission, and coalescence of cascade particles. Initially, we study several variations of the Fermi breakup model and choose the best option for these models. Then, we extend the modified exciton model (MEM)more » used by these codes to account for a possibility of multiple emission of up to 66 types of particles and LF (up to 28Mg) at the preequilibrium stage of reactions. Then, we expand the coalescence model to allow coalescence of LF from nucleons emitted at the intranuclear cascade stage of reactions and from lighter clusters, up to fragments with mass numbers A ≤ 7, in the case of CEM, and A ≤ 12, in the case of LAQGSM. Next, we modify MCNP6 to allow calculating and outputting spectra of LF and heavier products with arbitrary mass and charge numbers. The improved version of CEM is implemented into MCNP6. Lastly, we test the improved versions of CEM, LAQGSM, and MCNP6 on a variety of measured nuclear reactions. The modified codes give an improved description of energetic LF from particle- and nucleus-induced reactions; showing a good agreement with a variety of available experimental data. They have an improved predictive power compared to the previous versions and can be used as reliable tools in simulating applications involving such types of reactions.« less

Production of energetic light fragments in extensions of the CEM and LAQGSM event generators of the Monte Carlo transport code MCNP6 [Production of energetic light fragments in CEM, LAQGSM, and MCNP6

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

Mashnik, Stepan Georgievich; Kerby, Leslie Marie; Gudima, Konstantin K.

We extend the cascade-exciton model (CEM), and the Los Alamos version of the quark-gluon string model (LAQGSM), event generators of the Monte Carlo N-particle transport code version 6 (MCNP6), to describe production of energetic light fragments (LF) heavier than 4He from various nuclear reactions induced by particles and nuclei at energies up to about 1 TeV/nucleon. In these models, energetic LF can be produced via Fermi breakup, preequilibrium emission, and coalescence of cascade particles. Initially, we study several variations of the Fermi breakup model and choose the best option for these models. Then, we extend the modified exciton model (MEM)more » used by these codes to account for a possibility of multiple emission of up to 66 types of particles and LF (up to 28Mg) at the preequilibrium stage of reactions. Then, we expand the coalescence model to allow coalescence of LF from nucleons emitted at the intranuclear cascade stage of reactions and from lighter clusters, up to fragments with mass numbers A ≤ 7, in the case of CEM, and A ≤ 12, in the case of LAQGSM. Next, we modify MCNP6 to allow calculating and outputting spectra of LF and heavier products with arbitrary mass and charge numbers. The improved version of CEM is implemented into MCNP6. Lastly, we test the improved versions of CEM, LAQGSM, and MCNP6 on a variety of measured nuclear reactions. The modified codes give an improved description of energetic LF from particle- and nucleus-induced reactions; showing a good agreement with a variety of available experimental data. They have an improved predictive power compared to the previous versions and can be used as reliable tools in simulating applications involving such types of reactions.« less

First experience with particle-in-cell plasma physics code on ARM-based HPC systems

NASA Astrophysics Data System (ADS)

Sáez, Xavier; Soba, Alejandro; Sánchez, Edilberto; Mantsinen, Mervi; Mateo, Sergi; Cela, José M.; Castejón, Francisco

2015-09-01

In this work, we will explore the feasibility of porting a Particle-in-cell code (EUTERPE) to an ARM multi-core platform from the Mont-Blanc project. The used prototype is based on a system-on-chip Samsung Exynos 5 with an integrated GPU. It is the first prototype that could be used for High-Performance Computing (HPC), since it supports double precision and parallel programming languages.

Collisionless stellar hydrodynamics as an efficient alternative to N-body methods

NASA Astrophysics Data System (ADS)

Mitchell, Nigel L.; Vorobyov, Eduard I.; Hensler, Gerhard

2013-01-01

The dominant constituents of the Universe's matter are believed to be collisionless in nature and thus their modelling in any self-consistent simulation is extremely important. For simulations that deal only with dark matter or stellar systems, the conventional N-body technique is fast, memory efficient and relatively simple to implement. However when extending simulations to include the effects of gas physics, mesh codes are at a distinct disadvantage compared to Smooth Particle Hydrodynamics (SPH) codes. Whereas implementing the N-body approach into SPH codes is fairly trivial, the particle-mesh technique used in mesh codes to couple collisionless stars and dark matter to the gas on the mesh has a series of significant scientific and technical limitations. These include spurious entropy generation resulting from discreteness effects, poor load balancing and increased communication overhead which spoil the excellent scaling in massively parallel grid codes. In this paper we propose the use of the collisionless Boltzmann moment equations as a means to model the collisionless material as a fluid on the mesh, implementing it into the massively parallel FLASH Adaptive Mesh Refinement (AMR) code. This approach which we term `collisionless stellar hydrodynamics' enables us to do away with the particle-mesh approach and since the parallelization scheme is identical to that used for the hydrodynamics, it preserves the excellent scaling of the FLASH code already demonstrated on peta-flop machines. We find that the classic hydrodynamic equations and the Boltzmann moment equations can be reconciled under specific conditions, allowing us to generate analytic solutions for collisionless systems using conventional test problems. We confirm the validity of our approach using a suite of demanding test problems, including the use of a modified Sod shock test. By deriving the relevant eigenvalues and eigenvectors of the Boltzmann moment equations, we are able to use high order

Potts glass reflection of the decoding threshold for qudit quantum error correcting codes

NASA Astrophysics Data System (ADS)

Jiang, Yi; Kovalev, Alexey A.; Pryadko, Leonid P.

We map the maximum likelihood decoding threshold for qudit quantum error correcting codes to the multicritical point in generalized Potts gauge glass models, extending the map constructed previously for qubit codes. An n-qudit quantum LDPC code, where a qudit can be involved in up to m stabilizer generators, corresponds to a ℤd Potts model with n interaction terms which can couple up to m spins each. We analyze general properties of the phase diagram of the constructed model, give several bounds on the location of the transitions, bounds on the energy density of extended defects (non-local analogs of domain walls), and discuss the correlation functions which can be used to distinguish different phases in the original and the dual models. This research was supported in part by the Grants: NSF PHY-1415600 (AAK), NSF PHY-1416578 (LPP), and ARO W911NF-14-1-0272 (LPP).

Lorentz symmetric n-particle systems without ``multiple times''

NASA Astrophysics Data System (ADS)

Smith, Felix

2013-05-01

The need for multiple times in relativistic n-particle dynamics is a consequence of Minkowski's postulated symmetry between space and time coordinates in a space-time s = [x1 , . . ,x4 ] = [ x , y , z , ict ] , Eq. (1). Poincaré doubted the need for this space-time symmetry, believing Lorentz covariance could also prevail in some geometries with a three-dimensional position space and a quite different time coordinate. The Hubble expansion observed later justifies a specific geometry of this kind, a negatively curved position 3-space expanding with time at the Hubble rate lH (t) =lH , 0 + cΔt (F. T. Smith, Ann. Fond. L. de Broglie, 30, 179 (2005) and 35, 395 (2010)). Its position 4-vector is not s but q = [x1 , . . ,x4 ] = [ x , y , z , ilH (t) ] , and shows no 4-space symmetry. What is observed is always a difference 4-vector Δq = [ Δx , Δy , Δz , icΔt ] , and this displays the structure of Eq. (1) perfectly. Thus we find the standard 4-vector of special relativity in a geometry that does not require a Minkowski space-time at all, but a quite different geometry with a expanding 3-space symmetry and an independent time. The same Lorentz symmetry with but a single time extends to 2 and n-body systems.

Many-particle-effects in the theory of the extended X-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Tran Thoai, D. B.; Ekardt, W.

1981-10-01

The Lee-Beni-procedure for the calculation of the extended X-ray absorption fine structure (EXAFS) is extended so as to include the effects of the electronic charge density outside the localized muffin-tin potentials. In our scheme EXAFS is caused by back-scattering of an elementary excitation of a homogeneous electron gas by localized energy dependent many-particle muffin-tin potentials. The difference between the two schemes is negligible at large k's, as expected from physical grounds. However, at small and intermediate k-values the difference is quite large. The effect of the outer electrons as compared to the Lee-Beni-model is twofold. First, they renormalize the scattered electron in the usual way. Second, they are missing within the scattering muffin-tins. Hence, we avoid to count some of the electrons twice. Results are presented for Cu as an example.

A comparison of total reaction cross section models used in particle and heavy ion transport codes

NASA Astrophysics Data System (ADS)

Sihver, Lembit; Lantz, M.; Takechi, M.; Kohama, A.; Ferrari, A.; Cerutti, F.; Sato, T.

To be able to calculate the nucleon-nucleus and nucleus-nucleus total reaction cross sections with precision is very important for studies of basic nuclear properties, e.g. nuclear structure. This is also of importance for particle and heavy ion transport calculations because, in all particle and heavy ion transport codes, the probability function that a projectile particle will collide within a certain distance x in the matter depends on the total reaction cross sections. Furthermore, the total reaction cross sections will also scale the calculated partial fragmentation cross sections. It is therefore crucial that accurate total reaction cross section models are used in the transport calculations. In this paper, different models for calculating nucleon-nucleus and nucleus-nucleus total reaction cross sections are compared and discussed.

MHD Code Optimizations and Jets in Dense Gaseous Halos

NASA Astrophysics Data System (ADS)

Gaibler, Volker; Vigelius, Matthias; Krause, Martin; Camenzind, Max

We have further optimized and extended the 3D-MHD-code NIRVANA. The magnetized part runs in parallel, reaching 19 Gflops per SX-6 node, and has a passively advected particle population. In addition, the code is MPI-parallel now - on top of the shared memory parallelization. On a 512^3 grid, we reach 561 Gflops with 32 nodes on the SX-8. Also, we have successfully used FLASH on the Opteron cluster. Scientific results are preliminary so far. We report one computation of highly resolved cocoon turbulence. While we find some similarities to earlier 2D work by us and others, we note a strange reluctancy of cold material to enter the low density cocoon, which has to be investigated further.

Superspace geometrical realization of the N-extended super Virasoro algebra and its dual

NASA Astrophysics Data System (ADS)

Curto, C.; Gates, S. J., Jr.; Rodgers, V. G. J.

2000-05-01

We derive properties of N-extended /GR super Virasoro algebras. These include adding central extensions, identification of all primary fields and the action of the adjoint representation on its dual. The final result suggest identification with the spectrum of fields in supergravity theories and superstring/M-theory constructed from NSR N-extended supersymmetric /GR Virasoro algebras.

Stability, elastic and electronic properties of a novel BN2 sheet with extended hexagons with N-N bonds

NASA Astrophysics Data System (ADS)

Waters, Kevin; Pandey, Ravindra

2018-04-01

A new B-N monolayer material (BN2) consisting of a network of extended hexagons is predicted using density functional theory. The distinguishable nature of this 2D material is found to be the presence of the bonded N atoms (N-N) in the lattice. Analysis of the phonon dispersion curves show this phase of BN2 to be stable. The calculated elastic properties exhibit anisotropic mechanical properties that surpass graphene in the armchair direction. The BN2 monolayer is metallic with in-plane p states dominating the Fermi level. Novel applications resulting from a strong anisotropic mechanical strength together with the metallic properties of the BN2 sheet with the extended hexagons with N-N bonds may enable future innovation at the nanoscale.

nRC: non-coding RNA Classifier based on structural features.

PubMed

Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

2017-01-01

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

A Particle-In-Cell Gun Code for Surface-Converter H- Ion Source Modeling

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

Chacon-Golcher, Edwin; Bowers, Kevin J.

2007-08-10

We present the current status of a particle-in-cell with Monte Carlo collisions (PIC-MCC) gun code under development at Los Alamos for the study of surface-converter H- ion sources. The program preserves a first-principles approach to a significant extent and simulates the production processes without ad hoc models within the plasma region. Some of its features include: solution of arbitrary electrostatic and magnetostatic fields in an axisymmetric (r,z) geometry to describe the self-consistent time evolution of a plasma; simulation of a multi-species (e-,H+,H{sub 2}{sup +},H{sub 3}{sup +},H-) plasma discharge from a neutral hydrogen gas and filament-originated seed electrons; full 2-dimensional (r,z)more » 3-velocity (vr,vz,v{phi}) dynamics for all species with exact conservation of the canonical angular momentum p{phi}; detailed collision physics between charged particles and neutrals and the ability to represent multiple smooth (not stair-stepped) electrodes of arbitrary shape and voltage whose surfaces may be secondary-particle emitters (H- and e-). The status of this development is discussed in terms of its physics content and current implementation details.« less

Monte Carlo N-particle simulation of neutron-based sterilisation of anthrax contamination

PubMed Central

Liu, B; Xu, J; Liu, T; Ouyang, X

2012-01-01

Objective To simulate the neutron-based sterilisation of anthrax contamination by Monte Carlo N-particle (MCNP) 4C code. Methods Neutrons are elementary particles that have no charge. They are 20 times more effective than electrons or γ-rays in killing anthrax spores on surfaces and inside closed containers. Neutrons emitted from a 252Cf neutron source are in the 100 keV to 2 MeV energy range. A 2.5 MeV D–D neutron generator can create neutrons at up to 1013 n s−1 with current technology. All these enable an effective and low-cost method of killing anthrax spores. Results There is no effect on neutron energy deposition on the anthrax sample when using a reflector that is thicker than its saturation thickness. Among all three reflecting materials tested in the MCNP simulation, paraffin is the best because it has the thinnest saturation thickness and is easy to machine. The MCNP radiation dose and fluence simulation calculation also showed that the MCNP-simulated neutron fluence that is needed to kill the anthrax spores agrees with previous analytical estimations very well. Conclusion The MCNP simulation indicates that a 10 min neutron irradiation from a 0.5 g 252Cf neutron source or a 1 min neutron irradiation from a 2.5 MeV D–D neutron generator may kill all anthrax spores in a sample. This is a promising result because a 2.5 MeV D–D neutron generator output >1013 n s−1 should be attainable in the near future. This indicates that we could use a D–D neutron generator to sterilise anthrax contamination within several seconds. PMID:22573293

Monte Carlo N-particle simulation of neutron-based sterilisation of anthrax contamination.

PubMed

Liu, B; Xu, J; Liu, T; Ouyang, X

2012-10-01

To simulate the neutron-based sterilisation of anthrax contamination by Monte Carlo N-particle (MCNP) 4C code. Neutrons are elementary particles that have no charge. They are 20 times more effective than electrons or γ-rays in killing anthrax spores on surfaces and inside closed containers. Neutrons emitted from a (252)Cf neutron source are in the 100 keV to 2 MeV energy range. A 2.5 MeV D-D neutron generator can create neutrons at up to 10(13) n s(-1) with current technology. All these enable an effective and low-cost method of killing anthrax spores. There is no effect on neutron energy deposition on the anthrax sample when using a reflector that is thicker than its saturation thickness. Among all three reflecting materials tested in the MCNP simulation, paraffin is the best because it has the thinnest saturation thickness and is easy to machine. The MCNP radiation dose and fluence simulation calculation also showed that the MCNP-simulated neutron fluence that is needed to kill the anthrax spores agrees with previous analytical estimations very well. The MCNP simulation indicates that a 10 min neutron irradiation from a 0.5 g (252)Cf neutron source or a 1 min neutron irradiation from a 2.5 MeV D-D neutron generator may kill all anthrax spores in a sample. This is a promising result because a 2.5 MeV D-D neutron generator output >10(13) n s(-1) should be attainable in the near future. This indicates that we could use a D-D neutron generator to sterilise anthrax contamination within several seconds.

PoMiN: A Post-Minkowskian N-body Solver

NASA Astrophysics Data System (ADS)

Feng, Justin; Baumann, Mark; Hall, Bryton; Doss, Joel; Spencer, Lucas; Matzner, Richard

2018-06-01

In this paper, we introduce PoMiN, a lightweight N-body code based on the post-Minkowskian N-body Hamiltonian of Ledvinka et al., which includes general relativistic effects up to first order in Newton’s constant G, and all orders in the speed of light c. PoMiN is written in C and uses a fourth-order Runge–Kutta integration scheme. PoMiN has also been written to handle an arbitrary number of particles (both massive and massless), with a computational complexity that scales as O(N 2). We describe the methods we used to simplify and organize the Hamiltonian, and the tests we performed (convergence, conservation, and analytical comparison tests) to validate the code.

The long non-coding RNA PARTICLE is associated with WWOX and the absence of FRA16D breakage in osteosarcoma patients.

PubMed

O'Leary, Valerie Bríd; Maugg, Doris; Smida, Jan; Baumhoer, Daniel; Nathrath, Michaela; Ovsepian, Saak Victor; Atkinson, Michael John

2017-10-20

Breakage of the fragile site FRA16D disrupts the WWOX (WW Domain Containing Oxidoreductase) tumor suppressor gene in osteosarcoma. However, the frequency of breakage is not sufficient to explain the rate of WWOX loss in pathogenesis. The involvement of non-coding RNA transcripts is proposed due to their accumulation at fragile sites, where they are advocated to influence specific chromosomal regions associated with malignancy. The long ncRNA PARTICLE (promoter of MAT2A antisense radiation-induced circulating long non-coding RNA) is transiently elevated in response to irradiation and influences epigenetic silencing modification within WWOX . It now emerges that elevated PARTICLE levels are significantly associated with FRA16D non-breakage in OS patients. Although not associated with overall survival, high PARTICLE levels were found to be significantly linked to metastasis free outcome. The transcription of both PARTICLE and WWOX are transiently responsive to exposure to low doses of radiation in osteosarcoma cell lines. Herein, a relationship between WWOX and PARTICLE transcription is suggested in human osteosarcoma cell lines representing alternative genetic backgrounds. PARTICLE over-expression ameliorated WWOX promoter activity in U2OS harboring FRA16D non-breakage. It can be concluded that the lncRNA PARTICLE influences the WWOX tumor suppressor and in the absence of WWOX FRA16D breakage, it is associated with OS metastasis-free survival.

Introducing a distributed unstructured mesh into gyrokinetic particle-in-cell code, XGC

NASA Astrophysics Data System (ADS)

Yoon, Eisung; Shephard, Mark; Seol, E. Seegyoung; Kalyanaraman, Kaushik

2017-10-01

XGC has shown good scalability for large leadership supercomputers. The current production version uses a copy of the entire unstructured finite element mesh on every MPI rank. Although an obvious scalability issue if the mesh sizes are to be dramatically increased, the current approach is also not optimal with respect to data locality of particles and mesh information. To address these issues we have initiated the development of a distributed mesh PIC method. This approach directly addresses the base scalability issue with respect to mesh size and, through the use of a mesh entity centric view of the particle mesh relationship, provides opportunities to address data locality needs of many core and GPU supported heterogeneous systems. The parallel mesh PIC capabilities are being built on the Parallel Unstructured Mesh Infrastructure (PUMI). The presentation will first overview the form of mesh distribution used and indicate the structures and functions used to support the mesh, the particles and their interaction. Attention will then focus on the node-level optimizations being carried out to ensure performant operation of all PIC operations on the distributed mesh. Partnership for Edge Physics Simulation (EPSI) Grant No. DE-SC0008449 and Center for Extended Magnetohydrodynamic Modeling (CEMM) Grant No. DE-SC0006618.

Gas-particle partitioning of alcohol vapors on organic aerosols.

PubMed

Chan, Lap P; Lee, Alex K Y; Chan, Chak K

2010-01-01

Single particle levitation using an electrodynamic balance (EDB) has been found to give accurate and direct hygroscopic measurements (gas-particle partitioning of water) for a number of inorganic and organic aerosol systems. In this paper, we extend the use of an EDB to examine the gas-particle partitioning of volatile to semivolatile alcohols, including methanol, n-butanol, n-octanol, and n-decanol, on levitated oleic acid particles. The measured K(p) agreed with Pankow's absorptive partitioning model. At high n-butanol vapor concentrations (10(3) ppm), the uptake of n-butanol reduced the average molecular-weight of the oleic acid particle appreciably and hence increased the K(p) according to Pankow's equation. Moreover, the hygroscopicity of mixed oleic acid/n-butanol particles was higher than the predictions given by the UNIFAC model (molecular group contribution method) and the ZSR equation (additive rule), presumably due to molecular interactions between the chemical species in the mixed particles. Despite the high vapor concentrations used, these findings warrant further research on the partitioning of atmospheric organic vapors (K(p)) near sources and how collectively they affect the hygroscopic properties of organic aerosols.

Development Of A Parallel Performance Model For The THOR Neutral Particle Transport Code

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

Yessayan, Raffi; Azmy, Yousry; Schunert, Sebastian

The THOR neutral particle transport code enables simulation of complex geometries for various problems from reactor simulations to nuclear non-proliferation. It is undergoing a thorough V&V requiring computational efficiency. This has motivated various improvements including angular parallelization, outer iteration acceleration, and development of peripheral tools. For guiding future improvements to the code’s efficiency, better characterization of its parallel performance is useful. A parallel performance model (PPM) can be used to evaluate the benefits of modifications and to identify performance bottlenecks. Using INL’s Falcon HPC, the PPM development incorporates an evaluation of network communication behavior over heterogeneous links and a functionalmore » characterization of the per-cell/angle/group runtime of each major code component. After evaluating several possible sources of variability, this resulted in a communication model and a parallel portion model. The former’s accuracy is bounded by the variability of communication on Falcon while the latter has an error on the order of 1%.« less

Beam Dynamics in an Electron Lens with the Warp Particle-in-cell Code

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

Stancari, Giulio; Moens, Vince; Redaelli, Stefano

2014-07-01

Electron lenses are a mature technique for beam manipulation in colliders and storage rings. In an electron lens, a pulsed, magnetically confined electron beam with a given current-density profile interacts with the circulating beam to obtain the desired effect. Electron lenses were used in the Fermilab Tevatron collider for beam-beam compensation, for abort-gap clearing, and for halo scraping. They will be used in RHIC at BNL for head-on beam-beam compensation, and their application to the Large Hadron Collider for halo control is under development. At Fermilab, electron lenses will be implemented as lattice elements for nonlinear integrable optics. The designmore » of electron lenses requires tools to calculate the kicks and wakefields experienced by the circulating beam. We use the Warp particle-in-cell code to study generation, transport, and evolution of the electron beam. For the first time, a fully 3-dimensional code is used for this purpose.« less

Simulations of an accelerator-based shielding experiment using the particle and heavy-ion transport code system PHITS.

PubMed

Sato, T; Sihver, L; Iwase, H; Nakashima, H; Niita, K

2005-01-01

In order to estimate the biological effects of HZE particles, an accurate knowledge of the physics of interaction of HZE particles is necessary. Since the heavy ion transport problem is a complex one, there is a need for both experimental and theoretical studies to develop accurate transport models. RIST and JAERI (Japan), GSI (Germany) and Chalmers (Sweden) are therefore currently developing and bench marking the General-Purpose Particle and Heavy-Ion Transport code System (PHITS), which is based on the NMTC and MCNP for nucleon/meson and neutron transport respectively, and the JAM hadron cascade model. PHITS uses JAERI Quantum Molecular Dynamics (JQMD) and the Generalized Evaporation Model (GEM) for calculations of fission and evaporation processes, a model developed at NASA Langley for calculation of total reaction cross sections, and the SPAR model for stopping power calculations. The future development of PHITS includes better parameterization in the JQMD model used for the nucleus-nucleus reactions, and improvement of the models used for calculating total reaction cross sections, and addition of routines for calculating elastic scattering of heavy ions, and inclusion of radioactivity and burn up processes. As a part of an extensive bench marking of PHITS, we have compared energy spectra of secondary neutrons created by reactions of HZE particles with different targets, with thicknesses ranging from <1 to 200 cm. We have also compared simulated and measured spatial, fluence and depth-dose distributions from different high energy heavy ion reactions. In this paper, we report simulations of an accelerator-based shielding experiment, in which a beam of 1 GeV/n Fe-ions has passed through thin slabs of polyethylene, Al, and Pb at an acceptance angle up to 4 degrees. c2005 Published by Elsevier Ltd on behalf of COSPAR.

Differential Cross Section Kinematics for 3-dimensional Transport Codes

NASA Technical Reports Server (NTRS)

Norbury, John W.; Dick, Frank

2008-01-01

In support of the development of 3-dimensional transport codes, this paper derives the relevant relativistic particle kinematic theory. Formulas are given for invariant, spectral and angular distributions in both the lab (spacecraft) and center of momentum frames, for collisions involving 2, 3 and n - body final states.

Representation of particle motion in the auditory midbrain of a developing anuran.

PubMed

Simmons, Andrea Megela

2015-07-01

In bullfrog tadpoles, a "deaf period" of lessened responsiveness to the pressure component of sounds, evident during the end of the late larval period, has been identified in the auditory midbrain. But coding of underwater particle motion in the vestibular medulla remains stable over all of larval development, with no evidence of a "deaf period." Neural coding of particle motion in the auditory midbrain was assessed to determine if a "deaf period" for this mode of stimulation exists in this brain area in spite of its absence from the vestibular medulla. Recording sites throughout the developing laminar and medial principal nuclei show relatively stable thresholds to z-axis particle motion, up until the "deaf period." Thresholds then begin to increase from this point up through the rest of metamorphic climax, and significantly fewer responsive sites can be located. The representation of particle motion in the auditory midbrain is less robust during later compared to earlier larval stages, overlapping with but also extending beyond the restricted "deaf period" for pressure stimulation. The decreased functional representation of particle motion in the auditory midbrain throughout metamorphic climax may reflect ongoing neural reorganization required to mediate the transition from underwater to amphibious life.

SimTrack: A compact c++ code for particle orbit and spin tracking in accelerators

DOE PAGES

Luo, Yun

2015-08-29

SimTrack is a compact c++ code of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam–beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam–beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam–beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this article, I will present the code architecture,more » physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.« less

Verification of long wavelength electromagnetic modes with a gyrokinetic-fluid hybrid model in the XGC code

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

Hager, Robert; Lang, Jianying; Chang, C. S.

As an alternative option to kinetic electrons, the gyrokinetic total-f particle-in-cell (PIC) code XGC1 has been extended to the MHD/fluid type electromagnetic regime by combining gyrokinetic PIC ions with massless drift-fluid electrons. Here, two representative long wavelength modes, shear Alfven waves and resistive tearing modes, are verified in cylindrical and toroidal magnetic field geometries.

Verification of long wavelength electromagnetic modes with a gyrokinetic-fluid hybrid model in the XGC code

DOE PAGES

Hager, Robert; Lang, Jianying; Chang, C. S.; ...

2017-05-24

As an alternative option to kinetic electrons, the gyrokinetic total-f particle-in-cell (PIC) code XGC1 has been extended to the MHD/fluid type electromagnetic regime by combining gyrokinetic PIC ions with massless drift-fluid electrons. Here, two representative long wavelength modes, shear Alfven waves and resistive tearing modes, are verified in cylindrical and toroidal magnetic field geometries.

Crystallization and X-ray analysis of the T = 4 particle of hepatitis B capsid protein with an N-terminal extension

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

Tan, Wen Siang; McNae, Iain W.; Ho, Kok Lian

2007-08-01

Hepatitis B virus capsids have significant potential as carriers for immunogenic peptides. The crystal structure of the T = 4 particle of hepatitis B core protein containing an N-terminal extension reveals that the fusion peptide is exposed on the exterior of the particle. Hepatitis B core (HBc) particles have been extensively exploited as carriers for foreign immunological epitopes in the development of multicomponent vaccines and diagnostic reagents. Crystals of the T = 4 HBc particle were grown in PEG 20 000, ammonium sulfate and various types of alcohols. A temperature jump from 277 or 283 to 290 K was foundmore » to enhance crystal growth. A crystal grown using MPD as a cryoprotectant diffracted X-rays to 7.7 Å resolution and data were collected to 99.6% completeness at 8.9 Å. The crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 352.3, b = 465.5, c = 645.0 Å. The electron-density map reveals a protrusion that is consistent with the N-terminus extending out from the surface of the capsid. The structure presented here supports the idea that N-terminal insertions can be exploited in the development of diagnostic reagents, multicomponent vaccines and delivery vehicles into mammalian cells.« less

Validation of extended magnetohydrodynamic simulations of the HIT-SI3 experiment using the NIMROD code

NASA Astrophysics Data System (ADS)

Morgan, K. D.; Jarboe, T. R.; Hossack, A. C.; Chandra, R. N.; Everson, C. J.

2017-12-01

The HIT-SI3 experiment uses a set of inductively driven helicity injectors to apply a non-axisymmetric current drive on the edge of the plasma, driving an axisymmetric spheromak equilibrium in a central confinement volume. These helicity injectors drive a non-axisymmetric perturbation that oscillates in time, with relative temporal phasing of the injectors modifying the mode structure of the applied perturbation. A set of three experimental discharges with different perturbation spectra are modelled using the NIMROD extended magnetohydrodynamics code, and comparisons are made to both magnetic and fluid measurements. These models successfully capture the bulk dynamics of both the perturbation and the equilibrium, though disagreements related to the pressure gradients experimentally measured exist.

Authorship attribution of source code by using back propagation neural network based on particle swarm optimization

PubMed Central

Xu, Guoai; Li, Qi; Guo, Yanhui; Zhang, Miao

2017-01-01

Authorship attribution is to identify the most likely author of a given sample among a set of candidate known authors. It can be not only applied to discover the original author of plain text, such as novels, blogs, emails, posts etc., but also used to identify source code programmers. Authorship attribution of source code is required in diverse applications, ranging from malicious code tracking to solving authorship dispute or software plagiarism detection. This paper aims to propose a new method to identify the programmer of Java source code samples with a higher accuracy. To this end, it first introduces back propagation (BP) neural network based on particle swarm optimization (PSO) into authorship attribution of source code. It begins by computing a set of defined feature metrics, including lexical and layout metrics, structure and syntax metrics, totally 19 dimensions. Then these metrics are input to neural network for supervised learning, the weights of which are output by PSO and BP hybrid algorithm. The effectiveness of the proposed method is evaluated on a collected dataset with 3,022 Java files belong to 40 authors. Experiment results show that the proposed method achieves 91.060% accuracy. And a comparison with previous work on authorship attribution of source code for Java language illustrates that this proposed method outperforms others overall, also with an acceptable overhead. PMID:29095934

Implementation of ASME Code, Section XI, Code Case N-770, on Alternative Examination Requirements for Class 1 Butt Welds Fabricated with Alloy 82/182

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

Sullivan, Edmund J.; Anderson, Michael T.

In May 2010, the NRC issued a proposed notice of rulemaking that includes a provision to add a new section to its rules to require licensees to implement ASME Code Case N-770, ‘‘Alternative Examination Requirements and Acceptance Standards for Class 1 PWR Piping and Vessel Nozzle Butt Welds Fabricated with UNS N06082 or UNS W86182 Weld Filler Material With or Without the Application of Listed Mitigation Activities, Section XI, Division 1,’’ with 15 conditions. Code Case N-770 contains baseline and inservice inspection (ISI) requirements for unmitigated butt welds fabricated with Alloy 82/182 material and preservice and ISI requirements for mitigatedmore » butt welds. The NRC stated that application of ASME Code Case N-770 is necessary because the inspections currently required by the ASME Code, Section XI, were not written to address stress corrosion cracking Alloy 82/182 butt welds, and the safety consequences of inadequate inspections can be significant. The NRC expects to issue the final rule incorporating this code case into its regulations in the spring 2011 time frame. This paper discusses the new examination requirements, the conditions that NRC is imposing , and the major concerns with implementation of the new Code Case.« less

Extended optical model for fission

DOE PAGES

Sin, M.; Capote, R.; Herman, M. W.; ...

2016-03-07

A comprehensive formalism to calculate fission cross sections based on the extension of the optical model for fission is presented. It can be used for description of nuclear reactions on actinides featuring multi-humped fission barriers with partial absorption in the wells and direct transmission through discrete and continuum fission channels. The formalism describes the gross fluctuations observed in the fission probability due to vibrational resonances, and can be easily implemented in existing statistical reaction model codes. The extended optical model for fission is applied for neutron induced fission cross-section calculations on 234,235,238U and 239Pu targets. A triple-humped fission barrier ismore » used for 234,235U(n,f), while a double-humped fission barrier is used for 238U(n,f) and 239Pu(n,f) reactions as predicted by theoretical barrier calculations. The impact of partial damping of class-II/III states, and of direct transmission through discrete and continuum fission channels, is shown to be critical for a proper description of the measured fission cross sections for 234,235,238U(n,f) reactions. The 239Pu(n,f) reaction can be calculated in the complete damping approximation. Calculated cross sections for 235,238U(n,f) and 239Pu(n,f) reactions agree within 3% with the corresponding cross sections derived within the Neutron Standards least-squares fit of available experimental data. Lastly, the extended optical model for fission can be used for both theoretical fission studies and nuclear data evaluation.« less

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

NASA Technical Reports Server (NTRS)

Winckelmans, G. S.

1995-01-01

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

Non-Maxwellian fast particle effects in gyrokinetic GENE simulations

NASA Astrophysics Data System (ADS)

Di Siena, A.; Görler, T.; Doerk, H.; Bilato, R.; Citrin, J.; Johnson, T.; Schneider, M.; Poli, E.; JET Contributors

2018-04-01

Fast ions have recently been found to significantly impact and partially suppress plasma turbulence both in experimental and numerical studies in a number of scenarios. Understanding the underlying physics and identifying the range of their beneficial effect is an essential task for future fusion reactors, where highly energetic ions are generated through fusion reactions and external heating schemes. However, in many of the gyrokinetic codes fast ions are, for simplicity, treated as equivalent-Maxwellian-distributed particle species, although it is well known that to rigorously model highly non-thermalised particles, a non-Maxwellian background distribution function is needed. To study the impact of this assumption, the gyrokinetic code GENE has recently been extended to support arbitrary background distribution functions which might be either analytical, e.g., slowing down and bi-Maxwellian, or obtained from numerical fast ion models. A particular JET plasma with strong fast-ion related turbulence suppression is revised with these new code capabilities both with linear and nonlinear gyrokinetic simulations. It appears that the fast ion stabilization tends to be less strong but still substantial with more realistic distributions, and this improves the quantitative power balance agreement with experiments.

Apar-T: code, validation, and physical interpretation of particle-in-cell results

NASA Astrophysics Data System (ADS)

Melzani, Mickaël; Winisdoerffer, Christophe; Walder, Rolf; Folini, Doris; Favre, Jean M.; Krastanov, Stefan; Messmer, Peter

2013-10-01

We present the parallel particle-in-cell (PIC) code Apar-T and, more importantly, address the fundamental question of the relations between the PIC model, the Vlasov-Maxwell theory, and real plasmas. First, we present four validation tests: spectra from simulations of thermal plasmas, linear growth rates of the relativistic tearing instability and of the filamentation instability, and nonlinear filamentation merging phase. For the filamentation instability we show that the effective growth rates measured on the total energy can differ by more than 50% from the linear cold predictions and from the fastest modes of the simulation. We link these discrepancies to the superparticle number per cell and to the level of field fluctuations. Second, we detail a new method for initial loading of Maxwell-Jüttner particle distributions with relativistic bulk velocity and relativistic temperature, and explain why the traditional method with individual particle boosting fails. The formulation of the relativistic Harris equilibrium is generalized to arbitrary temperature and mass ratios. Both are required for the tearing instability setup. Third, we turn to the key point of this paper and scrutinize the question of what description of (weakly coupled) physical plasmas is obtained by PIC models. These models rely on two building blocks: coarse-graining, i.e., grouping of the order of p ~ 1010 real particles into a single computer superparticle, and field storage on a grid with its subsequent finite superparticle size. We introduce the notion of coarse-graining dependent quantities, i.e., quantities depending on p. They derive from the PIC plasma parameter ΛPIC, which we show to behave as ΛPIC ∝ 1/p. We explore two important implications. One is that PIC collision- and fluctuation-induced thermalization times are expected to scale with the number of superparticles per grid cell, and thus to be a factor p ~ 1010 smaller than in real plasmas, a fact that we confirm with

RAY-RAMSES: a code for ray tracing on the fly in N-body simulations

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

Barreira, Alexandre; Llinares, Claudio; Bose, Sownak

2016-05-01

We present a ray tracing code to compute integrated cosmological observables on the fly in AMR N-body simulations. Unlike conventional ray tracing techniques, our code takes full advantage of the time and spatial resolution attained by the N-body simulation by computing the integrals along the line of sight on a cell-by-cell basis through the AMR simulation grid. Moroever, since it runs on the fly in the N-body run, our code can produce maps of the desired observables without storing large (or any) amounts of data for post-processing. We implemented our routines in the RAMSES N-body code and tested the implementationmore » using an example of weak lensing simulation. We analyse basic statistics of lensing convergence maps and find good agreement with semi-analytical methods. The ray tracing methodology presented here can be used in several cosmological analysis such as Sunyaev-Zel'dovich and integrated Sachs-Wolfe effect studies as well as modified gravity. Our code can also be used in cross-checks of the more conventional methods, which can be important in tests of theory systematics in preparation for upcoming large scale structure surveys.« less

Py-SPHViewer: Cosmological simulations using Smoothed Particle Hydrodynamics

NASA Astrophysics Data System (ADS)

Benítez-Llambay, Alejandro

2017-12-01

Py-SPHViewer visualizes and explores N-body + Hydrodynamics simulations. The code interpolates the underlying density field (or any other property) traced by a set of particles, using the Smoothed Particle Hydrodynamics (SPH) interpolation scheme, thus producing not only beautiful but also useful scientific images. Py-SPHViewer enables the user to explore simulated volumes using different projections. Py-SPHViewer also provides a natural way to visualize (in a self-consistent fashion) gas dynamical simulations, which use the same technique to compute the interactions between particles.

TORBEAM 2.0, a paraxial beam tracing code for electron-cyclotron beams in fusion plasmas for extended physics applications

NASA Astrophysics Data System (ADS)

Poli, E.; Bock, A.; Lochbrunner, M.; Maj, O.; Reich, M.; Snicker, A.; Stegmeir, A.; Volpe, F.; Bertelli, N.; Bilato, R.; Conway, G. D.; Farina, D.; Felici, F.; Figini, L.; Fischer, R.; Galperti, C.; Happel, T.; Lin-Liu, Y. R.; Marushchenko, N. B.; Mszanowski, U.; Poli, F. M.; Stober, J.; Westerhof, E.; Zille, R.; Peeters, A. G.; Pereverzev, G. V.

2018-04-01

The paraxial WKB code TORBEAM (Poli, 2001) is widely used for the description of electron-cyclotron waves in fusion plasmas, retaining diffraction effects through the solution of a set of ordinary differential equations. With respect to its original form, the code has undergone significant transformations and extensions, in terms of both the physical model and the spectrum of applications. The code has been rewritten in Fortran 90 and transformed into a library, which can be called from within different (not necessarily Fortran-based) workflows. The models for both absorption and current drive have been extended, including e.g. fully-relativistic calculation of the absorption coefficient, momentum conservation in electron-electron collisions and the contribution of more than one harmonic to current drive. The code can be run also for reflectometry applications, with relativistic corrections for the electron mass. Formulas that provide the coupling between the reflected beam and the receiver have been developed. Accelerated versions of the code are available, with the reduced physics goal of inferring the location of maximum absorption (including or not the total driven current) for a given setting of the launcher mirrors. Optionally, plasma volumes within given flux surfaces and corresponding values of minimum and maximum magnetic field can be provided externally to speed up the calculation of full driven-current profiles. These can be employed in real-time control algorithms or for fast data analysis.

Solar wind interaction with Venus and Mars in a parallel hybrid code

NASA Astrophysics Data System (ADS)

Jarvinen, Riku; Sandroos, Arto

2013-04-01

We discuss the development and applications of a new parallel hybrid simulation, where ions are treated as particles and electrons as a charge-neutralizing fluid, for the interaction between the solar wind and Venus and Mars. The new simulation code under construction is based on the algorithm of the sequential global planetary hybrid model developed at the Finnish Meteorological Institute (FMI) and on the Corsair parallel simulation platform also developed at the FMI. The FMI's sequential hybrid model has been used for studies of plasma interactions of several unmagnetized and weakly magnetized celestial bodies for more than a decade. Especially, the model has been used to interpret in situ particle and magnetic field observations from plasma environments of Mars, Venus and Titan. Further, Corsair is an open source MPI (Message Passing Interface) particle and mesh simulation platform, mainly aimed for simulations of diffusive shock acceleration in solar corona and interplanetary space, but which is now also being extended for global planetary hybrid simulations. In this presentation we discuss challenges and strategies of parallelizing a legacy simulation code as well as possible applications and prospects of a scalable parallel hybrid model for the solar wind interactions of Venus and Mars.

GOTHIC: Gravitational oct-tree code accelerated by hierarchical time step controlling

NASA Astrophysics Data System (ADS)

Miki, Yohei; Umemura, Masayuki

2017-04-01

The tree method is a widely implemented algorithm for collisionless N-body simulations in astrophysics well suited for GPU(s). Adopting hierarchical time stepping can accelerate N-body simulations; however, it is infrequently implemented and its potential remains untested in GPU implementations. We have developed a Gravitational Oct-Tree code accelerated by HIerarchical time step Controlling named GOTHIC, which adopts both the tree method and the hierarchical time step. The code adopts some adaptive optimizations by monitoring the execution time of each function on-the-fly and minimizes the time-to-solution by balancing the measured time of multiple functions. Results of performance measurements with realistic particle distribution performed on NVIDIA Tesla M2090, K20X, and GeForce GTX TITAN X, which are representative GPUs of the Fermi, Kepler, and Maxwell generation of GPUs, show that the hierarchical time step achieves a speedup by a factor of around 3-5 times compared to the shared time step. The measured elapsed time per step of GOTHIC is 0.30 s or 0.44 s on GTX TITAN X when the particle distribution represents the Andromeda galaxy or the NFW sphere, respectively, with 224 = 16,777,216 particles. The averaged performance of the code corresponds to 10-30% of the theoretical single precision peak performance of the GPU.

Cellular dosimetry calculations for Strontium-90 using Monte Carlo code PENELOPE.

PubMed

Hocine, Nora; Farlay, Delphine; Boivin, Georges; Franck, Didier; Agarande, Michelle

2014-11-01

To improve risk assessments associated with chronic exposure to Strontium-90 (Sr-90), for both the environment and human health, it is necessary to know the energy distribution in specific cells or tissue. Monte Carlo (MC) simulation codes are extremely useful tools for calculating deposition energy. The present work was focused on the validation of the MC code PENetration and Energy LOss of Positrons and Electrons (PENELOPE) and the assessment of dose distribution to bone marrow cells from punctual Sr-90 source localized within the cortical bone part. S-values (absorbed dose per unit cumulated activity) calculations using Monte Carlo simulations were performed by using PENELOPE and Monte Carlo N-Particle eXtended (MCNPX). Cytoplasm, nucleus, cell surface, mouse femur bone and Sr-90 radiation source were simulated. Cells are assumed to be spherical with the radii of the cell and cell nucleus ranging from 2-10 μm. The Sr-90 source is assumed to be uniformly distributed in cell nucleus, cytoplasm and cell surface. The comparison of S-values calculated with PENELOPE to MCNPX results and the Medical Internal Radiation Dose (MIRD) values agreed very well since the relative deviations were less than 4.5%. The dose distribution to mouse bone marrow cells showed that the cells localized near the cortical part received the maximum dose. The MC code PENELOPE may prove useful for cellular dosimetry involving radiation transport through materials other than water, or for complex distributions of radionuclides and geometries.

Particle decay of proton-unbound levels in N 12

DOE PAGES

Chipps, K. A.; Pain, S. D.; Greife, U.; ...

2017-04-24

Transfer reactions are a useful tool for studying nuclear structure, particularly in the regime of low level densities and strong single-particle strengths. Additionally, transfer reactions can populate levels above particle decay thresholds, allowing for the possibility of studying the subsequent decays and furthering our understanding of the nuclei being probed. In particular, the decay of loosely bound nuclei such as 12 N can help inform and improve structure models.The purpose of this paper is to learn about the decay of excited states in 12 N , to more generally inform nuclear structure models, particularly in the case of particle-unbound levelsmore » in low-mass systems which are within the reach of state-of-the-art ab initio calculations.« less

SEURAT: SPH scheme extended with ultraviolet line radiative transfer

NASA Astrophysics Data System (ADS)

Abe, Makito; Suzuki, Hiroyuki; Hasegawa, Kenji; Semelin, Benoit; Yajima, Hidenobu; Umemura, Masayuki

2018-05-01

We present a novel Lyman alpha (Ly α) radiative transfer code, SEURAT (SPH scheme Extended with Ultraviolet line RAdiative Transfer), where line scatterings are solved adaptively with the resolution of the smoothed particle hydrodynamics (SPH). The radiative transfer method implemented in SEURAT is based on a Monte Carlo algorithm in which the scattering and absorption by dust are also incorporated. We perform standard test calculations to verify the validity of the code; (i) emergent spectra from a static uniform sphere, (ii) emergent spectra from an expanding uniform sphere, and (iii) escape fraction from a dusty slab. Thereby, we demonstrate that our code solves the {Ly} α radiative transfer with sufficient accuracy. We emphasize that SEURAT can treat the transfer of {Ly} α photons even in highly complex systems that have significantly inhomogeneous density fields. The high adaptivity of SEURAT is desirable to solve the propagation of {Ly} α photons in the interstellar medium of young star-forming galaxies like {Ly} α emitters (LAEs). Thus, SEURAT provides a powerful tool to model the emergent spectra of {Ly} α emission, which can be compared to the observations of LAEs.

Particle Acceleration in Mildly Relativistic Shearing Flows: The Interplay of Systematic and Stochastic Effects, and the Origin of the Extended High-energy Emission in AGN Jets

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

Liu, Ruo-Yu; Rieger, F. M.; Aharonian, F. A., E-mail: ruoyu@mpi-hd.mpg.de, E-mail: frank.rieger@mpi-hd.mpg.de, E-mail: aharon@mpi-hd.mpg.de

The origin of the extended X-ray emission in the large-scale jets of active galactic nuclei (AGNs) poses challenges to conventional models of acceleration and emission. Although electron synchrotron radiation is considered the most feasible radiation mechanism, the formation of the continuous large-scale X-ray structure remains an open issue. As astrophysical jets are expected to exhibit some turbulence and shearing motion, we here investigate the potential of shearing flows to facilitate an extended acceleration of particles and evaluate its impact on the resultant particle distribution. Our treatment incorporates systematic shear and stochastic second-order Fermi effects. We show that for typical parametersmore » applicable to large-scale AGN jets, stochastic second-order Fermi acceleration, which always accompanies shear particle acceleration, can play an important role in facilitating the whole process of particle energization. We study the time-dependent evolution of the resultant particle distribution in the presence of second-order Fermi acceleration, shear acceleration, and synchrotron losses using a simple Fokker–Planck approach and provide illustrations for the possible emergence of a complex (multicomponent) particle energy distribution with different spectral branches. We present examples for typical parameters applicable to large-scale AGN jets, indicating the relevance of the underlying processes for understanding the extended X-ray emission and the origin of ultrahigh-energy cosmic rays.« less

Development of new two-dimensional spectral/spatial code based on dynamic cyclic shift code for OCDMA system

NASA Astrophysics Data System (ADS)

Jellali, Nabiha; Najjar, Monia; Ferchichi, Moez; Rezig, Houria

2017-07-01

In this paper, a new two-dimensional spectral/spatial codes family, named two dimensional dynamic cyclic shift codes (2D-DCS) is introduced. The 2D-DCS codes are derived from the dynamic cyclic shift code for the spectral and spatial coding. The proposed system can fully eliminate the multiple access interference (MAI) by using the MAI cancellation property. The effect of shot noise, phase-induced intensity noise and thermal noise are used to analyze the code performance. In comparison with existing two dimensional (2D) codes, such as 2D perfect difference (2D-PD), 2D Extended Enhanced Double Weight (2D-Extended-EDW) and 2D hybrid (2D-FCC/MDW) codes, the numerical results show that our proposed codes have the best performance. By keeping the same code length and increasing the spatial code, the performance of our 2D-DCS system is enhanced: it provides higher data rates while using lower transmitted power and a smaller spectral width.

NIMROD calculations of energetic particle driven toroidal Alfvén eigenmodes

NASA Astrophysics Data System (ADS)

Hou, Yawei; Zhu, Ping; Kim, Charlson C.; Hu, Zhaoqing; Zou, Zhihui; Wang, Zhengxiong; Nimrod Team

2018-01-01

Toroidal Alfvén eigenmodes (TAEs) are gap modes induced by the toroidicity of tokamak plasmas in the absence of continuum damping. They can be excited by energetic particles (EPs) when the EP drive exceeds other dampings, such as electron and ion Landau damping, and collisional and radiative damping. A TAE benchmark case, which was proposed by the International Tokamak Physics Activity group, is studied in this work. The numerical calculations of linear growth of TAEs driven by EPs in a circular-shaped, large aspect ratio tokamak have been performed using the Hybrid Kinetic-MHD (HK-MHD) model implemented in the NIMROD code. This HK-MHD model couples a δf particle-in-cell representation of EPs with the 3D MHD representation of the bulk plasma through moment closure for the momentum conservation equation. Both the excitation of TAEs and their transition to energetic particle modes (EPMs) have been observed. The influence of EP density, temperature, density gradient, and position of the maximum relative density gradient, on the frequency and the growth rate of TAEs are obtained, which are consistent with those from the eigen-analysis calculations, kinetic-MHD, and gyrokinetic simulations for an initial Maxwellian distribution of EPs. The relative pressure gradient of EP at the radial location of the TAE gap, which represents the drive strength of EPs, can strongly affect the growth rate of TAEs. It is demonstrated that the mode transition due to EP drive variation leads to not only the change of frequency but also the change of the mode structure. This mechanism can be helpful in understanding the nonlinear physics of TAE/EPM, such as frequency chirping.

Space Radiation Transport Code Development: 3DHZETRN

NASA Technical Reports Server (NTRS)

Wilson, John W.; Slaba, Tony C.; Badavi, Francis F.; Reddell, Brandon D.; Bahadori, Amir A.

2015-01-01

The space radiation transport code, HZETRN, has been used extensively for research, vehicle design optimization, risk analysis, and related applications. One of the simplifying features of the HZETRN transport formalism is the straight-ahead approximation, wherein all particles are assumed to travel along a common axis. This reduces the governing equation to one spatial dimension allowing enormous simplification and highly efficient computational procedures to be implemented. Despite the physical simplifications, the HZETRN code is widely used for space applications and has been found to agree well with fully 3D Monte Carlo simulations in many circumstances. Recent work has focused on the development of 3D transport corrections for neutrons and light ions (Z < 2) for which the straight-ahead approximation is known to be less accurate. Within the development of 3D corrections, well-defined convergence criteria have been considered, allowing approximation errors at each stage in model development to be quantified. The present level of development assumes the neutron cross sections have an isotropic component treated within N explicit angular directions and a forward component represented by the straight-ahead approximation. The N = 1 solution refers to the straight-ahead treatment, while N = 2 represents the bi-directional model in current use for engineering design. The figure below shows neutrons, protons, and alphas for various values of N at locations in an aluminum sphere exposed to a solar particle event (SPE) spectrum. The neutron fluence converges quickly in simple geometry with N > 14 directions. The improved code, 3DHZETRN, transports neutrons, light ions, and heavy ions under space-like boundary conditions through general geometry while maintaining a high degree of computational efficiency. A brief overview of the 3D transport formalism for neutrons and light ions is given, and extensive benchmarking results with the Monte Carlo codes Geant4, FLUKA, and

Dissecting jets and missing energy searches using $n$-body extended simplified models

DOE PAGES

Cohen, Timothy; Dolan, Matthew J.; El Hedri, Sonia; ...

2016-08-04

Simplified Models are a useful way to characterize new physics scenarios for the LHC. Particle decays are often represented using non-renormalizable operators that involve the minimal number of fields required by symmetries. Generalizing to a wider class of decay operators allows one to model a variety of final states. This approach, which we dub the $n$-body extension of Simplified Models, provides a unifying treatment of the signal phase space resulting from a variety of signals. In this paper, we present the first application of this framework in the context of multijet plus missing energy searches. The main result of thismore » work is a global performance study with the goal of identifying which set of observables yields the best discriminating power against the largest Standard Model backgrounds for a wide range of signal jet multiplicities. Our analysis compares combinations of one, two and three variables, placing emphasis on the enhanced sensitivity gain resulting from non-trivial correlations. Utilizing boosted decision trees, we compare and classify the performance of missing energy, energy scale and energy structure observables. We demonstrate that including an observable from each of these three classes is required to achieve optimal performance. In conclusion, this work additionally serves to establish the utility of $n$-body extended Simplified Models as a diagnostic for unpacking the relative merits of different search strategies, thereby motivating their application to new physics signatures beyond jets and missing energy.« less

The FLUKA Code: An Overview

NASA Technical Reports Server (NTRS)

Ballarini, F.; Battistoni, G.; Campanella, M.; Carboni, M.; Cerutti, F.; Empl, A.; Fasso, A.; Ferrari, A.; Gadioli, E.; Garzelli, M. V.;

Considerations of MCNP Monte Carlo code to be used as a radiotherapy treatment planning tool.

PubMed

Juste, B; Miro, R; Gallardo, S; Verdu, G; Santos, A

2005-01-01

The present work has simulated the photon and electron transport in a Theratron 780® (MDS Nordion)⁶⁰Co radiotherapy unit, using the Monte Carlo transport code, MCNP (Monte Carlo N-Particle). This project explains mainly the different methodologies carried out to speedup calculations in order to apply this code efficiently in radiotherapy treatment planning.

Test Particle Simulations of Electron Injection by the Bursty Bulk Flows (BBFs) using High Resolution Lyon-Feddor-Mobarry (LFM) Code

NASA Astrophysics Data System (ADS)

Eshetu, W. W.; Lyon, J.; Wiltberger, M. J.; Hudson, M. K.

2017-12-01

Test particle simulations of electron injection by the bursty bulk flows (BBFs) have been done using a test particle tracer code [1], and the output fields of the Lyon-Feddor-Mobarry global magnetohydro- dynamics (MHD) code[2]. The MHD code was run with high resolu- tion (oct resolution), and with specified solar wind conditions so as to reproduce the observed qualitative picture of the BBFs [3]. Test par- ticles were injected so that they interact with earthward propagating BBFs. The result of the simulation shows that electrons are pushed ahead of the BBFs and accelerated into the inner magnetosphere. Once electrons are in the inner magnetosphere they are further energized by drift resonance with the azimuthal electric field. In addition pitch angle scattering of electrons resulting in the violation conservation of the first adiabatic invariant has been observed. The violation of the first adiabatic invariant occurs as electrons cross a weak magnetic field region with a strong gradient of the field perturbed by the BBFs. References 1. Kress, B. T., Hudson,M. K., Looper, M. D. , Albert, J., Lyon, J. G., and Goodrich, C. C. (2007), Global MHD test particle simulations of ¿ 10 MeV radiation belt electrons during storm sudden commencement, J. Geophys. Res., 112, A09215, doi:10.1029/2006JA012218. Lyon,J. G., Fedder, J. A., and Mobarry, C.M., The Lyon- Fedder-Mobarry (LFM) Global MHD Magnetospheric Simulation Code (2004), J. Atm. And Solar-Terrestrial Phys., 66, Issue 15-16, 1333- 1350,doi:10.1016/j.jastp. Wiltberger, Merkin, M., Lyon, J. G., and Ohtani, S. (2015), High-resolution global magnetohydrodynamic simulation of bursty bulk flows, J. Geophys. Res. Space Physics, 120, 45554566, doi:10.1002/2015JA021080.

Extended-release niacin treatment of the atherogenic lipid profile and lipoprotein(a) in diabetes.

PubMed

Pan, Jianqiu; Van, Joanne T; Chan, Eve; Kesala, Renata L; Lin, Michael; Charles, M Arthur

2002-09-01

We tested the hypotheses that extended-release niacin is effective for the separate treatments of abnormalities in low-density liprotein (LDL) size, high-density lipoprotein (HDL)-2, and lipoprotein(a) [Lp(a)] without potential negative effects on glycated hemoglobin levels. The lipids that constitute the atherogenic lipid profile (ALP), such as triglycerides, small, dense LDL-cholesterol particle concentration, LDL particle size, total HDL-cholesterol (HDLc), HDL-2, and HDL-2 cholesterol concentration, as well as total LDL-cholesterol (LDLc) and Lp(a), were measured in 36 diabetic patients with primary abnormalities of LDL particle size (n = 25), HDL-2 (n = 23), and/or Lp(a) (n = 12) before and after extended-release niacin treatment. LDL particle size and HDL-2 were measured using polyacrylamide gradient gel electrophoreses and Lp(a) was measured by enzyme-linked immunosorbent assay (ELISA). After extended-release niacin, LDL peak particle diameter increased from 25.2 +/- 0.6 nm to 26.1 +/- 0.7 nm (P <.0001); small, dense LDLc concentration decreased from 30 +/- 17 mg/dL to 17 +/- 10 mg/dL (P <.0001); total HDLc increased from 42 +/- 9 mg/dL to 57 +/- 16 mg/dL (P <.0001); HDL-2 as the percent of total HDLc mass increased from 34% +/- 10% to 51% +/- 17% (P <.0001); and Lp(a) decreased from 37 +/- 10 mg/dL to 23 +/- 10 mg/dL (P <.001). Mean hemoglobin A(1c) level was improved during treatment from 7.5% +/- 1.6% to 6.5% +/- 0.9% (P <.0001). A subset of patients who had no change in hemoglobin A(1c) levels before and after treatment (6.8% +/- 1% v 6.7% +/- 1%; not significant) showed identical lipid changes. Twenty-two percent of patients were unable to tolerate extended-release niacin due to reversible side effects. These data indicate that in diabetic patients, extended-release niacin (1) is effective for separately treating diabetic dyslipidemias associated with abnormal LDL size, HDL-2, and Lp(a) independently of glycated hemoglobin levels; (2) must be used with

Feasibility study for using an extended three-wave model to simulate plasma-based backward Raman amplification in one spatial dimension

NASA Astrophysics Data System (ADS)

Wang, T.-L.; Michta, D.; Lindberg, R. R.; Charman, A. E.; Martins, S. F.; Wurtele, J. S.

2009-12-01

Results are reported of a one-dimensional simulation study comparing the modeling capability of a recently formulated extended three-wave model [R. R. Lindberg, A. E. Charman, and J. S. Wurtele, Phys. Plasmas 14, 122103 (2007); Phys. Plasmas 15, 055911 (2008)] to that of a particle-in-cell (PIC) code, as well as to a more conventional three-wave model, in the context of the plasma-based backward Raman amplification (PBRA) [G. Shvets, N. J. Fisch, A. Pukhov et al., Phys. Rev. Lett. 81, 4879 (1998); V. M. Malkin, G. Shvets, and N. J. Fisch, Phys. Rev. Lett. 82, 4448 (1999); Phys. Rev. Lett. 84, 1208 (2000)]. The extended three-wave model performs essentially as well as or better than a conventional three-wave description in all temperature regimes tested, and significantly better at the higher temperatures studied, while the computational savings afforded by the extended three-wave model make it a potentially attractive tool that can be used prior to or in conjunction with PIC simulations to model the kinetic effects of PBRA for nonrelativistic laser pulses interacting with underdense thermal plasmas. Very fast but reasonably accurate at moderate plasma temperatures, this model may be used to perform wide-ranging parameter scans or other exploratory analyses quickly and efficiently, in order to guide subsequent simulation via more accurate if intensive PIC techniques or other algorithms approximating the full Vlasov-Maxwell equations.

Assessing the dietary bioavailability of metals associated with natural particles: Extending the use of the reverse labeling approach to zinc

USGS Publications Warehouse

Croteau, Marie-Noele; Cain, Daniel J.; Fuller, Christopher C.

2017-01-01

We extend the use of a novel tracing technique to quantify the bioavailability of zinc (Zn) associated with natural particles using snails enriched with a less common Zn stable isotope. Lymnaea stagnalis is a model species that has relatively fast Zn uptake rates from the dissolved phase, enabling their rapid enrichment in 67Zn during the initial phase of labeling. Isotopically enriched snails were subsequently exposed to algae mixed with increasing amounts of metal-rich particles collected from two acid mine drainage impacted rivers. Zinc bioavailability from the natural particles was inferred from calculations of 66Zn assimilation into the snail’s soft tissues. Zinc assimilation efficiency (AE) varied from 28% for the Animas River particles to 45% for the Snake River particles, indicating that particle-bound, or sorbed Zn, was bioavailable from acid mine drainage wastes. The relative binding strength of Zn sorption to the natural particles was inversely related to Zn bioavailability; a finding that would not have been possible without using the reverse labeling approach. Differences in the chemical composition of the particles suggest that their geochemical properties may influence the extent of Zn bioavailability.

Assessing the Dietary Bioavailability of Metals Associated with Natural Particles: Extending the Use of the Reverse Labeling Approach to Zinc.

PubMed

Croteau, Marie-Noële; Cain, Daniel J; Fuller, Christopher C

2017-03-07

We extend the use of a novel tracing technique to quantify the bioavailability of zinc (Zn) associated with natural particles using snails enriched with a less common Zn stable isotope. Lymnaea stagnalis is a model species that has relatively fast Zn uptake rates from the dissolved phase, enabling their rapid enrichment in 67 Zn during the initial phase of labeling. Isotopically enriched snails were subsequently exposed to algae mixed with increasing amounts of metal-rich particles collected from two acid mine drainage impacted rivers. Zinc bioavailability from the natural particles was inferred from calculations of 66 Zn assimilation into the snail's soft tissues. Zinc assimilation efficiency (AE) varied from 28% for the Animas River particles to 45% for the Snake River particles, indicating that particle-bound, or sorbed Zn, was bioavailable from acid mine drainage wastes. The relative binding strength of Zn sorption to the natural particles was inversely related to Zn bioavailability; a finding that would not have been possible without using the reverse labeling approach. Differences in the chemical composition of the particles suggest that their geochemical properties may influence the extent of Zn bioavailability.

Revised Extended Grid Library

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

Martz, Roger L.

The Revised Eolus Grid Library (REGL) is a mesh-tracking library that was developed for use with the MCNP6TM computer code so that (radiation) particles can track on an unstructured mesh. The unstructured mesh is a finite element representation of any geometric solid model created with a state-of-the-art CAE/CAD tool. The mesh-tracking library is written using modern Fortran and programming standards; the library is Fortran 2003 compliant. The library was created with a defined application programmer interface (API) so that it could easily integrate with other particle tracking/transport codes. The library does not handle parallel processing via the message passing interfacemore » (mpi), but has been used successfully where the host code handles the mpi calls. The library is thread-safe and supports the OpenMP paradigm. As a library, all features are available through the API and overall a tight coupling between it and the host code is required. Features of the library are summarized with the following list: Can accommodate first and second order 4, 5, and 6-sided polyhedra; any combination of element types may appear in a single geometry model; parts may not contain tetrahedra mixed with other element types; pentahedra and hexahedra can be together in the same part; robust handling of overlaps and gaps; tracks element-to-element to produce path length results at the element level; finds element numbers for a given mesh location; finds intersection points on element faces for the particle tracks; produce a data file for post processing results analysis; reads Abaqus .inp input (ASCII) files to obtain information for the global mesh-model; supports parallel input processing via mpi; and support parallel particle transport by both mpi and OpenMP.« less

Role of N-Methyl-D-Aspartate Receptors in Action-Based Predictive Coding Deficits in Schizophrenia.

PubMed

Kort, Naomi S; Ford, Judith M; Roach, Brian J; Gunduz-Bruce, Handan; Krystal, John H; Jaeger, Judith; Reinhart, Robert M G; Mathalon, Daniel H

2017-03-15

Recent theoretical models of schizophrenia posit that dysfunction of the neural mechanisms subserving predictive coding contributes to symptoms and cognitive deficits, and this dysfunction is further posited to result from N-methyl-D-aspartate glutamate receptor (NMDAR) hypofunction. Previously, by examining auditory cortical responses to self-generated speech sounds, we demonstrated that predictive coding during vocalization is disrupted in schizophrenia. To test the hypothesized contribution of NMDAR hypofunction to this disruption, we examined the effects of the NMDAR antagonist, ketamine, on predictive coding during vocalization in healthy volunteers and compared them with the effects of schizophrenia. In two separate studies, the N1 component of the event-related potential elicited by speech sounds during vocalization (talk) and passive playback (listen) were compared to assess the degree of N1 suppression during vocalization, a putative measure of auditory predictive coding. In the crossover study, 31 healthy volunteers completed two randomly ordered test days, a saline day and a ketamine day. Event-related potentials during the talk/listen task were obtained before infusion and during infusion on both days, and N1 amplitudes were compared across days. In the case-control study, N1 amplitudes from 34 schizophrenia patients and 33 healthy control volunteers were compared. N1 suppression to self-produced vocalizations was significantly and similarly diminished by ketamine (Cohen's d = 1.14) and schizophrenia (Cohen's d = .85). Disruption of NMDARs causes dysfunction in predictive coding during vocalization in a manner similar to the dysfunction observed in schizophrenia patients, consistent with the theorized contribution of NMDAR hypofunction to predictive coding deficits in schizophrenia. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Clinical code set engineering for reusing EHR data for research: A review.

PubMed

Williams, Richard; Kontopantelis, Evangelos; Buchan, Iain; Peek, Niels

2017-06-01

The construction of reliable, reusable clinical code sets is essential when re-using Electronic Health Record (EHR) data for research. Yet code set definitions are rarely transparent and their sharing is almost non-existent. There is a lack of methodological standards for the management (construction, sharing, revision and reuse) of clinical code sets which needs to be addressed to ensure the reliability and credibility of studies which use code sets. To review methodological literature on the management of sets of clinical codes used in research on clinical databases and to provide a list of best practice recommendations for future studies and software tools. We performed an exhaustive search for methodological papers about clinical code set engineering for re-using EHR data in research. This was supplemented with papers identified by snowball sampling. In addition, a list of e-phenotyping systems was constructed by merging references from several systematic reviews on this topic, and the processes adopted by those systems for code set management was reviewed. Thirty methodological papers were reviewed. Common approaches included: creating an initial list of synonyms for the condition of interest (n=20); making use of the hierarchical nature of coding terminologies during searching (n=23); reviewing sets with clinician input (n=20); and reusing and updating an existing code set (n=20). Several open source software tools (n=3) were discovered. There is a need for software tools that enable users to easily and quickly create, revise, extend, review and share code sets and we provide a list of recommendations for their design and implementation. Research re-using EHR data could be improved through the further development, more widespread use and routine reporting of the methods by which clinical codes were selected. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

TRAX-CHEM: A pre-chemical and chemical stage extension of the particle track structure code TRAX in water targets

NASA Astrophysics Data System (ADS)

Boscolo, D.; Krämer, M.; Durante, M.; Fuss, M. C.; Scifoni, E.

2018-04-01

The production, diffusion, and interaction of particle beam induced water-derived radicals is studied with the a pre-chemical and chemical module of the Monte Carlo particle track structure code TRAX, based on a step by step approach. After a description of the model implemented, the chemical evolution of the most important products of water radiolysis is studied for electron, proton, helium, and carbon ion radiation at different energies. The validity of the model is verified by comparing the calculated time and LET dependent yield with experimental data from literature and other simulation approaches.

PFMCal : Photonic force microscopy calibration extended for its application in high-frequency microrheology

NASA Astrophysics Data System (ADS)

Butykai, A.; Domínguez-García, P.; Mor, F. M.; Gaál, R.; Forró, L.; Jeney, S.

2017-11-01

automatic calibration process which requires only to write the input data in the main script. Additionally, we include a calibration method based on thermal noise statistics, which can be used with viscoelastic fluids if the trap stiffness is previously estimated. Reasons for the new version: This version extends the functionality of PFMCal for the particular case of spherical probes and unknown fluid viscosities. The extended code is automatic, works in different operating systems and it is compatible with GNU Octave. Summary of revisions: The original MatLab program in the previous version, which is executed by PFMCal.m, is not changed. Here, we have added two additional main archives named PFMCal_auto.m and PFMCal_histo.m, which implement automatic calculations of the calibration process and calibration through Boltzmann statistics, respectively. The process of calibration using this code for spherical beads is described in the README.pdf file provided in the new code submission. Here, we obtain different calibration factors, β (given in μm/V), according to [2], related to two statistical quantities: the mean-squared displacement (MSD), βMSD, and the velocity autocorrelation function (VAF), βVAF. Using that methodology, the trap stiffness, k, and the zero-shear viscosity of the fluid, η, can be calculated if the value of the particle's radius, a, is previously known. For comparison, we include in the extended code the method of calibration using the corner frequency of the power-spectral density (PSD) [5], providing a calibration factor βPSD. Besides, with the prior estimation of the trap stiffness, along with the known value of the particle's radius, we can use thermal noise statistics to obtain calibration factors, β, according to the quadratic form of the optical potential, βE, and related to the Gaussian distribution of the bead's positions, βσ2. This method has been demonstrated to be applicable to the calibration of optical tweezers when using non

Particle acceleration and transport at a 2D CME-driven shock using the HAFv3 and PATH Code

NASA Astrophysics Data System (ADS)

Li, G.; Ao, X.; Fry, C. D.; Verkhoglyadova, O. P.; Zank, G. P.

2012-12-01

We study particle acceleration at a 2D CME-driven shock and the subsequent transport in the inner heliosphere (up to 2 AU) by coupling the kinematic Hakamada-Akasofu-Fry version 3 (HAFv3) solar wind model (Hakamada and Akasofu, 1982, Fry et al. 2003) with the Particle Acceleration and Transport in the Heliosphere (PATH) model (Zank et al., 2000, Li et al., 2003, 2005, Verkhoglyadova et al. 2009). The HAFv3 provides the evolution of a two-dimensional shock geometry and other plasma parameters, which are fed into the PATH model to investigate the effect of a varying shock geometry on particle acceleration and transport. The transport module of the PATH model is parallelized and utilizes the state-of-the-art GPU computation technique to achieve a rapid physics-based numerical description of the interplanetary energetic particles. Together with a fast execution of the HAFv3 model, the coupled code gives us a possibility to nowcast/forecast the interplanetary radiation environment.

Extending R packages to support 64-bit compiled code: An illustration with spam64 and GIMMS NDVI3g data

NASA Astrophysics Data System (ADS)

Gerber, Florian; Mösinger, Kaspar; Furrer, Reinhard

2017-07-01

Software packages for spatial data often implement a hybrid approach of interpreted and compiled programming languages. The compiled parts are usually written in C, C++, or Fortran, and are efficient in terms of computational speed and memory usage. Conversely, the interpreted part serves as a convenient user-interface and calls the compiled code for computationally demanding operations. The price paid for the user friendliness of the interpreted component is-besides performance-the limited access to low level and optimized code. An example of such a restriction is the 64-bit vector support of the widely used statistical language R. On the R side, users do not need to change existing code and may not even notice the extension. On the other hand, interfacing 64-bit compiled code efficiently is challenging. Since many R packages for spatial data could benefit from 64-bit vectors, we investigate strategies to efficiently pass 64-bit vectors to compiled languages. More precisely, we show how to simply extend existing R packages using the foreign function interface to seamlessly support 64-bit vectors. This extension is shown with the sparse matrix algebra R package spam. The new capabilities are illustrated with an example of GIMMS NDVI3g data featuring a parametric modeling approach for a non-stationary covariance matrix.

Status report on the 'Merging' of the Electron-Cloud Code POSINST with the 3-D Accelerator PIC CODE WARP

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

Vay, J.-L.; Furman, M.A.; Azevedo, A.W.

2004-04-19

We have integrated the electron-cloud code POSINST [1] with WARP [2]--a 3-D parallel Particle-In-Cell accelerator code developed for Heavy Ion Inertial Fusion--so that the two can interoperate. Both codes are run in the same process, communicate through a Python interpreter (already used in WARP), and share certain key arrays (so far, particle positions and velocities). Currently, POSINST provides primary and secondary sources of electrons, beam bunch kicks, a particle mover, and diagnostics. WARP provides the field solvers and diagnostics. Secondary emission routines are provided by the Tech-X package CMEE.

Tristan code and its application

NASA Astrophysics Data System (ADS)

Nishikawa, K.-I.

Since TRISTAN: The 3-D Electromagnetic Particle Code was introduced in 1990, it has been used for many applications including the simulations of global solar windmagnetosphere interaction. The most essential ingridients of this code have been published in the ISSS-4 book. In this abstract we describe some of issues and an application of this code for the study of global solar wind-magnetosphere interaction including a substorm study. The basic code (tristan.f) for the global simulation and a local simulation of reconnection with a Harris model (issrec2.f) are available at http:/www.physics.rutger.edu/˜kenichi. For beginners the code (isssrc2.f) with simpler boundary conditions is suitable to start to run simulations. The future of global particle simulations for a global geospace general circulation (GGCM) model with predictive capability (for Space Weather Program) is discussed.

Smooth particle hydrodynamics: theory and application to the origin of the moon

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

Benz, W.

1986-01-01

The origin of the moon is modeled by the so-called smooth particle hydrodynamics (SPH) method (Lucy, 1977, Monaghan 1985) which substitutes to the fluid a finite set of extended particles, the hydrodynamics equations reduce to the equation of motion of individual particles. These equations of motion differ only from the standard gravitational N-body problem insofar that pressure gradients and viscosity terms have to be added to the gradient of the potential to derive the forces between the particles. The numerical tools developed for ''classical'' N-body problems can therefore be readily applied to solve 3 dimensional hydroynamical problems. 12 refs., 1more » fig.« less

New optimal asymmetric quantum codes constructed from constacyclic codes

NASA Astrophysics Data System (ADS)

Xu, Gen; Li, Ruihu; Guo, Luobin; Lü, Liangdong

2017-02-01

In this paper, we propose the construction of asymmetric quantum codes from two families of constacyclic codes over finite field 𝔽q2 of code length n, where for the first family, q is an odd prime power with the form 4t + 1 (t ≥ 1 is integer) or 4t - 1 (t ≥ 2 is integer) and n1 = q2+1 2; for the second family, q is an odd prime power with the form 10t + 3 or 10t + 7 (t ≥ 0 is integer) and n2 = q2+1 5. As a result, families of new asymmetric quantum codes [[n,k,dz/dx

Exclusion Bounds for Extended Anyons

NASA Astrophysics Data System (ADS)

Larson, Simon; Lundholm, Douglas

2018-01-01

We introduce a rigorous approach to the many-body spectral theory of extended anyons, that is quantum particles confined to two dimensions that interact via attached magnetic fluxes of finite extent. Our main results are many-body magnetic Hardy inequalities and local exclusion principles for these particles, leading to estimates for the ground-state energy of the anyon gas over the full range of the parameters. This brings out further non-trivial aspects in the dependence on the anyonic statistics parameter, and also gives improvements in the ideal (non-extended) case.

Convolutional encoding of self-dual codes

NASA Technical Reports Server (NTRS)

Solomon, G.

1994-01-01

There exist almost complete convolutional encodings of self-dual codes, i.e., block codes of rate 1/2 with weights w, w = 0 mod 4. The codes are of length 8m with the convolutional portion of length 8m-2 and the nonsystematic information of length 4m-1. The last two bits are parity checks on the two (4m-1) length parity sequences. The final information bit complements one of the extended parity sequences of length 4m. Solomon and van Tilborg have developed algorithms to generate these for the Quadratic Residue (QR) Codes of lengths 48 and beyond. For these codes and reasonable constraint lengths, there are sequential decodings for both hard and soft decisions. There are also possible Viterbi-type decodings that may be simple, as in a convolutional encoding/decoding of the extended Golay Code. In addition, the previously found constraint length K = 9 for the QR (48, 24;12) Code is lowered here to K = 8.

Implementation of the 3D edge plasma code EMC3-EIRENE on NSTX

DOE PAGES

Lore, J. D.; Canik, J. M.; Feng, Y.; ...

2012-05-09

The 3D edge transport code EMC3-EIRENE has been applied for the first time to the NSTX spherical tokamak. A new disconnected double null grid has been developed to allow the simulation of plasma where the radial separation of the inner and outer separatrix is less than characteristic widths (e.g. heat flux width) at the midplane. Modelling results are presented for both an axisymmetric case and a case where 3D magnetic field is applied in an n = 3 configuration. In the vacuum approximation, the perturbed field consists of a wide region of destroyed flux surfaces and helical lobes which aremore » a mixture of long and short connection length field lines formed by the separatrix manifolds. This structure is reflected in coupled 3D plasma fluid (EMC3) and kinetic neutral particle (EIRENE) simulations. The helical lobes extending inside of the unperturbed separatrix are filled in by hot plasma from the core. The intersection of the lobes with the divertor results in a striated flux footprint pattern on the target plates. As a result, profiles of divertor heat and particle fluxes are compared with experimental data, and possible sources of discrepancy are discussed.« less

Energetic-particle-modified global Alfvén eigenmodes

NASA Astrophysics Data System (ADS)

Lestz, J. B.; Belova, E. V.; Gorelenkov, N. N.

2018-04-01

Fully self-consistent hybrid MHD/particle simulations reveal strong energetic particle modifications to sub-cyclotron global Alfvén eigenmodes (GAEs) in low-aspect ratio, NSTX-like conditions. Key parameters defining the fast ion distribution function—the normalized injection velocity v0/vA and central pitch—are varied in order to study their influence on the characteristics of the excited modes. It is found that the frequency of the most unstable mode changes significantly and continuously with beam parameters, in accordance with the Doppler-shifted cyclotron resonances which drive the modes, and depending most substantially on v0/vA . This unexpected result is present for both counter-propagating GAEs, which are routinely excited in NSTX, and high frequency co-GAEs, which have not been previously studied. Large changes in frequency without clear corresponding changes in the mode structure are signatures of an energetic particle mode, referred to here as an energetic-particle-modified GAE. Additional simulations conducted for a fixed MHD equilibrium demonstrate that the GAE frequency shift cannot be explained by the equilibrium changes due to energetic particle effects.

One-dimensional energetic particle quasilinear diffusion for realistic TAE instabilities

NASA Astrophysics Data System (ADS)

Duarte, Vinicius; Ghantous, Katy; Berk, Herbert; Gorelenkov, Nikolai

2014-10-01

Owing to the proximity of the characteristic phase (Alfvén) velocity and typical energetic particle (EP) superthermal velocities, toroidicity-induced Alfvén eigenmodes (TAEs) can be resonantly destabilized endangering the plasma performance. Thus, it is of ultimate importance to understand the deleterious effects on the confinement resulting from fast ion driven instabilities expected in fusion-grade plasmas. We propose to study the interaction of EPs and TAEs using a line broadened quasilinear model, which captures the interaction in both regimes of isolated and overlapping modes. The resonance particles diffuse in the phase space where the problem essentially reduces to one dimension with constant kinetic energy and the diffusion mainly along the canonical toroidal angular momentum. Mode structure and wave particle resonances are computed by the NOVA code and are used in a quasilinear diffusion code that is being written to study the evolution of the distribution function, under the assumption that they can be considered virtually unalterable during the diffusion. A new scheme for the resonant particle diffusion is being proposed that builds on the 1-D nature of the diffusion from a single mode, which leads to a momentum conserving difference scheme even when there is mode overlap.

PoMiN: A Post-Minkowskian N-Body Solver

NASA Astrophysics Data System (ADS)

Feng, Justin; Baumann, Mark; Hall, Bryton; Doss, Joel; Spencer, Lucas; Matzner, Richard

2018-05-01

PoMiN is a lightweight N-body code based on the Post-Minkowskian N-body Hamiltonian of Ledvinka, Schafer, and Bicak, which includes General Relativistic effects up to first order in Newton's constant G, and all orders in the speed of light c. PoMiN is a single file written in C and uses a fourth-order Runge-Kutta integration scheme. PoMiN has also been written to handle an arbitrary number of particles (both massive and massless) with a computational complexity that scales as O(N^2).

Common Eigenvectors of N Particles' Compatible Observables and its Squeezing Operator

NASA Astrophysics Data System (ADS)

Xu, Shi-Min; Xu, Xing-Lei; Li, Hong-Qi

We construct 2N operators for a N-particle system, namely one center-of-mass coordinate operator, N-1 relative coordinate operators, one total momentum operator and N-1 mass-weighted relative momentum operators, and give common eigenvectors of N compatible observables \\{∑ Ni=1hat {p}i,hat {x}1-hat {x}2,hat {x}2-hat {x}3,hat {x}3-hat {x}4,...; ,hat {x}N-1-hat {x}N\\}, which are composed of N particles' coordinate hat {x}i and momentum hat {p}i. By compatible, we mean such observables can be simultaneously determined. Using the technique of integration within an ordered product of operators (IWOP), we prove that the common eigenvectors are complete and orthonormal, and hereby qualified for making up a representation. This new representation can be applied to solving some dynamic problems in quantum mechanics.

Hawking Radiation of the Charged Particles via Tunneling from the ( n+2)-Dimensional Topological Reissner-Nordström-de Sitter Black Hole

NASA Astrophysics Data System (ADS)

Yan, Han

2012-08-01

Extending Parikh-Wilczek's semi-classical tunneling method, we discuss the Hawking radiation of the charged massive particles via tunneling from the cosmological horizon of ( n+2)-dimensional Topological Reissner-Nordström-de Sitter black hole.The result shows that, when energy conservation and electric charge conservation are taken into account, the derived spectrum deviates from the pure thermal one, but satisfies the unitary theory, which provides a probability for the solution of the information loss paradox.

The Splashback Radius of Halos from Particle Dynamics. I. The SPARTA Algorithm

NASA Astrophysics Data System (ADS)

Diemer, Benedikt

2017-07-01

Motivated by the recent proposal of the splashback radius as a physical boundary of dark-matter halos, we present a parallel computer code for Subhalo and PARticle Trajectory Analysis (SPARTA). The code analyzes the orbits of all simulation particles in all host halos, billions of orbits in the case of typical cosmological N-body simulations. Within this general framework, we develop an algorithm that accurately extracts the location of the first apocenter of particles after infall into a halo, or splashback. We define the splashback radius of a halo as the smoothed average of the apocenter radii of individual particles. This definition allows us to reliably measure the splashback radii of 95% of host halos above a resolution limit of 1000 particles. We show that, on average, the splashback radius and mass are converged to better than 5% accuracy with respect to mass resolution, snapshot spacing, and all free parameters of the method.

Biological dose estimation for charged-particle therapy using an improved PHITS code coupled with a microdosimetric kinetic model.

PubMed

Sato, Tatsuhiko; Kase, Yuki; Watanabe, Ritsuko; Niita, Koji; Sihver, Lembit

2009-01-01

Microdosimetric quantities such as lineal energy, y, are better indexes for expressing the RBE of HZE particles in comparison to LET. However, the use of microdosimetric quantities in computational dosimetry is severely limited because of the difficulty in calculating their probability densities in macroscopic matter. We therefore improved the particle transport simulation code PHITS, providing it with the capability of estimating the microdosimetric probability densities in a macroscopic framework by incorporating a mathematical function that can instantaneously calculate the probability densities around the trajectory of HZE particles with a precision equivalent to that of a microscopic track-structure simulation. A new method for estimating biological dose, the product of physical dose and RBE, from charged-particle therapy was established using the improved PHITS coupled with a microdosimetric kinetic model. The accuracy of the biological dose estimated by this method was tested by comparing the calculated physical doses and RBE values with the corresponding data measured in a slab phantom irradiated with several kinds of HZE particles. The simulation technique established in this study will help to optimize the treatment planning of charged-particle therapy, thereby maximizing the therapeutic effect on tumors while minimizing unintended harmful effects on surrounding normal tissues.

Modeling Cell and Tumor-Metastasis Dosimetry with the Particle and Heavy Ion Transport Code System (PHITS) Software for Targeted Alpha-Particle Radionuclide Therapy.

PubMed

Lee, Dongyoul; Li, Mengshi; Bednarz, Bryan; Schultz, Michael K

2018-06-26

The use of targeted radionuclide therapy for cancer is on the rise. While beta-particle-emitting radionuclides have been extensively explored for targeted radionuclide therapy, alpha-particle-emitting radionuclides are emerging as effective alternatives. In this context, fundamental understanding of the interactions and dosimetry of these emitted particles with cells in the tumor microenvironment is critical to ascertaining the potential of alpha-particle-emitting radionuclides. One important parameter that can be used to assess these metrics is the S-value. In this study, we characterized several alpha-particle-emitting radionuclides (and their associated radionuclide progeny) regarding S-values in the cellular and tumor-metastasis environments. The Particle and Heavy Ion Transport code System (PHITS) was used to obtain S-values via Monte Carlo simulation for cell and tumor metastasis resulting from interactions with the alpha-particle-emitting radionuclides, lead-212 ( 212 Pb), actinium-225 ( 225 Ac) and bismuth-213 ( 213 Bi); these values were compared to the beta-particle-emitting radionuclides yttrium-90 ( 90 Y) and lutetium-177 ( 177 Lu) and an Auger-electron-emitting radionuclide indium-111 ( 111 In). The effect of cellular internalization on S-value was explored at increasing degree of internalization for each radionuclide. This aspect of S-value determination was further explored in a cell line-specific fashion for six different cancer cell lines based on the cell dimensions obtained by confocal microscopy. S-values from PHITS were in good agreement with MIRDcell S-values (cellular S-values) and the values found by Hindié et al. (tumor S-values). In the cellular model, 212 Pb and 213 Bi decay series produced S-values that were 50- to 120-fold higher than 177 Lu, while 225 Ac decay series analysis suggested S-values that were 240- to 520-fold higher than 177 Lu. S-values arising with 100% cellular internalization were two- to sixfold higher for the nucleus

New syndrome decoder for (n, 1) convolutional codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1983-01-01

The letter presents a new syndrome decoding algorithm for the (n, 1) convolutional codes (CC) that is different and simpler than the previous syndrome decoding algorithm of Schalkwijk and Vinck. The new technique uses the general solution of the polynomial linear Diophantine equation for the error polynomial vector E(D). A recursive, Viterbi-like, algorithm is developed to find the minimum weight error vector E(D). An example is given for the binary nonsystematic (2, 1) CC.

An adaptive extended finite element method for the analysis of agglomeration of colloidal particles in a flowing fluid

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

Choi, Young Joon; Jorshari, Razzi Movassaghi; Djilali, Ned

2015-03-10

Direct numerical simulations of the flow-nanoparticle interaction in a colloidal suspension are presented using an extended finite element method (XFEM) in which the dynamics of the nanoparticles is solved in a fully-coupled manner with the flow. The method is capable of accurately describing solid-fluid interfaces without the need of boundary-fitted meshes to investigate the dynamics of particles in complex flows. In order to accurately compute the high interparticle shear stresses and pressures while minimizing computing costs, an adaptive meshing technique is incorporated with the fluid-structure interaction algorithm. The particle-particle interaction at the microscopic level is modeled using the Lennard-Jones (LJ)more » potential and the corresponding potential parameters are determined by a scaling procedure. The study is relevant to the preparation of inks used in the fabrication of catalyst layers for fuel cells. In this paper, we are particularly interested in investigating agglomeration of the nanoparticles under external shear flow in a sliding bi-periodic Lees-Edwards frame. The results indicate that the external shear has a crucial impact on the structure formation of colloidal particles in a suspension.« less

Physics of Alfvén waves and energetic particles in burning plasmas

NASA Astrophysics Data System (ADS)

Chen, Liu; Zonca, Fulvio

2016-01-01

Dynamics of shear Alfvén waves and energetic particles are crucial to the performance of burning fusion plasmas. This article reviews linear as well as nonlinear physics of shear Alfvén waves and their self-consistent interaction with energetic particles in tokamak fusion devices. More specifically, the review on the linear physics deals with wave spectral properties and collective excitations by energetic particles via wave-particle resonances. The nonlinear physics deals with nonlinear wave-wave interactions as well as nonlinear wave-energetic particle interactions. Both linear as well as nonlinear physics demonstrate the qualitatively important roles played by realistic equilibrium nonuniformities, magnetic field geometries, and the specific radial mode structures in determining the instability evolution, saturation, and, ultimately, energetic-particle transport. These topics are presented within a single unified theoretical framework, where experimental observations and numerical simulation results are referred to elucidate concepts and physics processes.

Monte Carlo N-Particle Tracking of Ultrafine Particle Flow in Bent Micro-Tubes

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

Casella, Andrew M.; Loyalka, Sudarsham K.

2016-02-16

The problem of large pressure-differential driven laminar convective-diffusive ultrafine aerosol flow through bent micro-tubes is of interest in several contemporary research areas including; release of contents from pressurized containment vessels, aerosol sampling equipment, advanced scientific instruments, gas-phase micro-heat exchangers, and microfluidic devices. In each of these areas, the predominant problem is the determination of the fraction of particles entering the micro-tube that is deposited within the tube and the fraction that is transmitted through. Due to the extensive parameter restrictions of this class of problems, a Lagrangian particle tracking method making use of the coupling of the analytical stream linemore » solutions of Dean and the simplified Langevin equation is quite a useful tool in problem characterization. This method is a direct analog to the Monte Carlo N-Particle method of particle transport extensively used in nuclear physics and engineering. In this work, 10 nm diameter particles with a density of 1 g/cm3 are tracked within micro-tubes with toroidal bends with pressure differentials ranging between 0.2175 and 0.87 atmospheres. The tubes have radii of 25 microns and 50 microns and the radius of curvature is between 1 m and 0.3183 cm. The carrier gas is helium, and temperatures of 298 K and 558 K are considered. Numerical convergence is considered as a function of time step size and of the number of particles per simulation. Particle transmission rates and deposition patterns within the bent micro-tubes are calculated.« less

Unified Models of Turbulence and Nonlinear Wave Evolution in the Extended Solar Corona and Solar Wind

NASA Technical Reports Server (NTRS)

Cranmer, Steven R.; Wagner, William (Technical Monitor)

2004-01-01

The PI (Cranmer) and Co-I (A. van Ballegooijen) made substantial progress toward the goal of producing a unified model of the basic physical processes responsible for solar wind acceleration. The approach outlined in the original proposal comprised two complementary pieces: (1) to further investigate individual physical processes under realistic coronal and solar wind conditions, and (2) to extract the dominant physical effects from simulations and apply them to a 1D model of plasma heating and acceleration. The accomplishments in Year 2 are divided into these two categories: 1a. Focused Study of Kinetic Magnetohydrodynamic (MHD) Turbulence. lb. Focused Study of Non - WKB Alfven Wave Rejection. and 2. The Unified Model Code. We have continued the development of the computational model of a time-study open flux tube in the extended corona. The proton-electron Monte Carlo model is being tested, and collisionless wave-particle interactions are being included. In order to better understand how to easily incorporate various kinds of wave-particle processes into the code, the PI performed a detailed study of the so-called "Ito Calculus", i.e., the mathematical theory of how to update the positions of particles in a probabilistic manner when their motions are governed by diffusion in velocity space.

Preliminary Assessment of Turbomachinery Codes

NASA Technical Reports Server (NTRS)

Mazumder, Quamrul H.

2007-01-01

This report assesses different CFD codes developed and currently being used at Glenn Research Center to predict turbomachinery fluid flow and heat transfer behavior. This report will consider the following codes: APNASA, TURBO, GlennHT, H3D, and SWIFT. Each code will be described separately in the following section with their current modeling capabilities, level of validation, pre/post processing, and future development and validation requirements. This report addresses only previously published and validations of the codes. However, the codes have been further developed to extend the capabilities of the codes.

Consumer acceptance of a quick response (QR) code for the food traceability system: Application of an extended technology acceptance model (TAM).

PubMed

Kim, Yeong Gug; Woo, Eunju

2016-07-01

The objectives of this study are to apply the TAM using the addition of perceived information to individuals' behavioral intention to use the QR code for the food traceability system; and to determine the moderating effects of food involvement on the relationship between perceived information and perceived usefulness. Results from a survey of 420 respondents are analyzed using structural equation modeling. The study findings reveal that the extended TAM has a satisfactory fit to the data and that the underlying dimensions have a significant effect on consumers' intention to use the QR code for the food traceability system. In addition, food involvement plays a significant moderating function in the relationship between perceived information and perceived usefulness. The implications of this study for future research are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Adamek, Julian; Daverio, David; Durrer, Ruth

We present a new N-body code, gevolution , for the evolution of large scale structure in the Universe. Our code is based on a weak field expansion of General Relativity and calculates all six metric degrees of freedom in Poisson gauge. N-body particles are evolved by solving the geodesic equation which we write in terms of a canonical momentum such that it remains valid also for relativistic particles. We validate the code by considering the Schwarzschild solution and, in the Newtonian limit, by comparing with the Newtonian N-body codes Gadget-2 and RAMSES . We then proceed with a simulation ofmore » large scale structure in a Universe with massive neutrinos where we study the gravitational slip induced by the neutrino shear stress. The code can be extended to include different kinds of dark energy or modified gravity models and going beyond the usually adopted quasi-static approximation. Our code is publicly available.« less

Numerical investigation of non-perturbative kinetic effects of energetic particles on toroidicity-induced Alfvén eigenmodes in tokamaks and stellarators

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

Slaby, Christoph; Könies, Axel; Kleiber, Ralf

2016-09-15

The resonant interaction of shear Alfvén waves with energetic particles is investigated numerically in tokamak and stellarator geometry using a non-perturbative MHD-kinetic hybrid approach. The focus lies on toroidicity-induced Alfvén eigenmodes (TAEs), which are most easily destabilized by a fast-particle population in fusion plasmas. While the background plasma is treated within the framework of an ideal-MHD theory, the drive of the fast particles, as well as Landau damping of the background plasma, is modelled using the drift-kinetic Vlasov equation without collisions. Building on analytical theory, a fast numerical tool, STAE-K, has been developed to solve the resulting eigenvalue problem usingmore » a Riccati shooting method. The code, which can be used for parameter scans, is applied to tokamaks and the stellarator Wendelstein 7-X. High energetic-ion pressure leads to large growth rates of the TAEs and to their conversion into kinetically modified TAEs and kinetic Alfvén waves via continuum interaction. To better understand the physics of this conversion mechanism, the connections between TAEs and the shear Alfvén wave continuum are examined. It is shown that, when energetic particles are present, the continuum deforms substantially and the TAE frequency can leave the continuum gap. The interaction of the TAE with the continuum leads to singularities in the eigenfunctions. To further advance the physical model and also to eliminate the MHD continuum together with the singularities in the eigenfunctions, a fourth-order term connected to radiative damping has been included. The radiative damping term is connected to non-ideal effects of the bulk plasma and introduces higher-order derivatives to the model. Thus, it has the potential to substantially change the nature of the solution. For the first time, the fast-particle drive, Landau damping, continuum damping, and radiative damping have been modelled together in tokamak- as well as in stellarator

Some Colleges Extend Their Codes of Conduct to Off-Campus Behavior.

ERIC Educational Resources Information Center

Gose, Ben

1998-01-01

Protesters at the University of California at Berkeley are calling for the expulsion of a sophomore who failed to report a murder. However, the student's behavior does not violate the university's code of conduct, which is restricted to campus behavior. Some institutions are expanding the geographic reach of their codes to discipline students for…

Extending ALE3D, an Arbitrarily Connected hexahedral 3D Code, to Very Large Problem Size (U)

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

Nichols, A L

2010-12-15

As the number of compute units increases on the ASC computers, the prospect of running previously unimaginably large problems is becoming a reality. In an arbitrarily connected 3D finite element code, like ALE3D, one must provide a unique identification number for every node, element, face, and edge. This is required for a number of reasons, including defining the global connectivity array required for domain decomposition, identifying appropriate communication patterns after domain decomposition, and determining the appropriate load locations for implicit solvers, for example. In most codes, the unique identification number is defined as a 32-bit integer. Thus the maximum valuemore » available is 231, or roughly 2.1 billion. For a 3D geometry consisting of arbitrarily connected hexahedral elements, there are approximately 3 faces for every element, and 3 edges for every node. Since the nodes and faces need id numbers, using 32-bit integers puts a hard limit on the number of elements in a problem at roughly 700 million. The first solution to this problem would be to replace 32-bit signed integers with 32-bit unsigned integers. This would increase the maximum size of a problem by a factor of 2. This provides some head room, but almost certainly not one that will last long. Another solution would be to replace all 32-bit int declarations with 64-bit long long declarations. (long is either a 32-bit or a 64-bit integer, depending on the OS). The problem with this approach is that there are only a few arrays that actually need to extended size, and thus this would increase the size of the problem unnecessarily. In a future computing environment where CPUs are abundant but memory relatively scarce, this is probably the wrong approach. Based on these considerations, we have chosen to replace only the global identifiers with the appropriate 64-bit integer. The problem with this approach is finding all the places where data that is specified as a 32-bit integer needs to

Beam-dynamics codes used at DARHT

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

Ekdahl, Jr., Carl August

Several beam simulation codes are used to help gain a better understanding of beam dynamics in the DARHT LIAs. The most notable of these fall into the following categories: for beam production – Tricomp Trak orbit tracking code, LSP Particle in cell (PIC) code, for beam transport and acceleration – XTR static envelope and centroid code, LAMDA time-resolved envelope and centroid code, LSP-Slice PIC code, for coasting-beam transport to target – LAMDA time-resolved envelope code, LSP-Slice PIC code. These codes are also being used to inform the design of Scorpius.

An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins.

PubMed

Yusufi, Faraaz Noor Khan; Park, Wonjun; Lee, May May; Lee, Dong-Yup

2009-01-01

Advances in high-throughput techniques have led to the creation of increasing amounts of glycome data. The storage and analysis of this data would benefit greatly from a compact notation for describing glycan structures that can be easily stored and interpreted by computers. Towards this end, we propose a fixed-length alpha-numeric code for representing N-linked glycan structures commonly found in secreted glycoproteins from mammalian cell cultures. This code, GlycoDigit, employs a pre-assigned alpha-numeric index to represent the monosaccharides attached in different branches to the core glycan structure. The present branch-centric representation allows us to visualize the structure while the numerical nature of the code makes it machine readable. In addition, a difference operator can be defined to quantitatively differentiate between glycan structures for further analysis. The usefulness and applicability of GlycoDigit were demonstrated by constructing and visualizing an N-linked glycosylation network.

Expanding the genetic code for site-specific labelling of tobacco mosaic virus coat protein and building biotin-functionalized virus-like particles.

PubMed

Wu, F C; Zhang, H; Zhou, Q; Wu, M; Ballard, Z; Tian, Y; Wang, J Y; Niu, Z W; Huang, Y

2014-04-18

A method for site-specific and high yield modification of tobacco mosaic virus coat protein (TMVCP) utilizing a genetic code expanding technology and copper free cycloaddition reaction has been established, and biotin-functionalized virus-like particles were built by the self-assembly of the protein monomers.

Extended Plate and Beam Wall System

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

Gunderson, Patti

Home Innovation Research Labs studied the extended plate and beam wall (EP&B) system during a two-year period from mid-2015 to mid-2017 to determine the wall’s structural performance, moisture durability, constructability, and costeffectiveness for use as a high-R enclosure system for energy code minimum and above-code performance in climate zones 4–8.

NIMROD Modeling of Sawtooth Modes Using Hot-Particle Closures

NASA Astrophysics Data System (ADS)

Kruger, Scott; Jenkins, T. G.; Held, E. D.; King, J. R.

2015-11-01

In DIII-D shot 96043, RF heating gives rise to an energetic ion population that alters the sawtooth stability boundary, replacing conventional sawtooth cycles by longer-period, larger-amplitude `giant sawtooth' oscillations. We explore the use of particle-in-cell closures within the NIMROD code to numerically represent the RF-induced hot-particle distribution, and investigate the role of this distribution in determining the altered mode onset threshold and subsequent nonlinear evolution. Equilibrium reconstructions from the experimental data are used to enable these detailed validation studies. Effects of other parameters on the sawtooth behavior, such as the plasma Lundquist number and hot-particle beta-fraction, are also considered. The fast energetic particles present many challenges for the PIC closure. We review new algorithm and performance improvements to address these challenges, and provide a preliminary assessment of the efficacy of the PIC closure versus a continuum model for energetic particle modeling. We also compare our results with those of, and discuss plans for a more complete validation campaign for this discharge. Supported by US Department of Energy via the SciDAC Center for Extended MHD Modeling (CEMM).

Chemically Reacting One-Dimensional Gas-Particle Flows

NASA Technical Reports Server (NTRS)

Tevepaugh, J. A.; Penny, M. M.

1975-01-01

The governing equations for the one-dimensional flow of a gas-particle system are discussed. Gas-particle effects are coupled via the system momentum and energy equations with the gas assumed to be chemically frozen or in chemical equilibrium. A computer code for calculating the one-dimensional flow of a gas-particle system is discussed and a user's input guide presented. The computer code provides for the expansion of the gas-particle system from a specified starting velocity and nozzle inlet geometry. Though general in nature, the final output of the code is a startline for initiating the solution of a supersonic gas-particle system in rocket nozzles. The startline includes gasdynamic data defining gaseous startline points from the nozzle centerline to the nozzle wall and particle properties at points along the gaseous startline.

Spatial separation and entanglement of identical particles

NASA Astrophysics Data System (ADS)

Cunden, Fabio Deelan; di Martino, Sara; Facchi, Paolo; Florio, Giuseppe

2014-04-01

We reconsider the effect of indistinguishability on the reduced density operator of the internal degrees of freedom (tracing out the spatial degrees of freedom) for a quantum system composed of identical particles located in different spatial regions. We explicitly show that if the spin measurements are performed in disjoint spatial regions then there are no constraints on the structure of the reduced state of the system. This implies that the statistics of identical particles has no role from the point of view of separability and entanglement when the measurements are spatially separated. We extend the treatment to the case of n particles and show the connection with some recent criteria for separability based on subalgebras of observables.

Linear calculations of edge current driven kink modes with BOUT++ code

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

Li, G. Q., E-mail: ligq@ipp.ac.cn; Xia, T. Y.; Lawrence Livermore National Laboratory, Livermore, California 94550

This work extends previous BOUT++ work to systematically study the impact of edge current density on edge localized modes, and to benchmark with the GATO and ELITE codes. Using the CORSICA code, a set of equilibria was generated with different edge current densities by keeping total current and pressure profile fixed. Based on these equilibria, the effects of the edge current density on the MHD instabilities were studied with the 3-field BOUT++ code. For the linear calculations, with increasing edge current density, the dominant modes are changed from intermediate-n and high-n ballooning modes to low-n kink modes, and the linearmore » growth rate becomes smaller. The edge current provides stabilizing effects on ballooning modes due to the increase of local shear at the outer mid-plane with the edge current. For edge kink modes, however, the edge current does not always provide a destabilizing effect; with increasing edge current, the linear growth rate first increases, and then decreases. In benchmark calculations for BOUT++ against the linear results with the GATO and ELITE codes, the vacuum model has important effects on the edge kink mode calculations. By setting a realistic density profile and Spitzer resistivity profile in the vacuum region, the resistivity was found to have a destabilizing effect on both the kink mode and on the ballooning mode. With diamagnetic effects included, the intermediate-n and high-n ballooning modes can be totally stabilized for finite edge current density.« less

Destabilization of low-n peeling modes by trapped energetic particles

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

Hao, G. Z.; Wang, A. K.; Mou, Z. Z.

2013-06-15

The kinetic effect of trapped energetic particles (EPs), arising from perpendicular neutral beam injection, on the stable low-n peeling modes in tokamak plasmas is investigated, through numerical solution of the mode's dispersion relation derived from an energy principle. A resistive-wall peeling mode with m/n=6/1, with m and n being the poloidal and toroidal mode numbers, respectively, is destabilized by trapped EPs as the EPs' pressure exceeds a critical value β{sub c}{sup *}, which is sensitive to the pitch angle of trapped EPs. The dependence of β{sub c}{sup *} on the particle pitch angle is eventually determined by the bounce averagemore » of the mode eigenfunction. Peeling modes with higher m and n numbers can also be destabilized by trapped EPs. Depending on the wall distance, either a resistive-wall peeling mode or an ideal-kink peeling mode can be destabilized by EPs.« less

Synthesis of poly(N-isopropylacrylamide) particles for metal affinity binding of peptides

PubMed Central

Tsai, Hsin-Yi; Lee, Alexander; Peng, Wei; Yates, Matthew Z.

2013-01-01

Temperature-sensitive poly(N-isopropylacrylamide) (PNIPAM) microgel particles with metal affinity ligands were prepared for selective binding of peptides containing the His6-tag (six consecutive histidine residues). The PNIPAM particles were copolymerized with the functional ligand vinylbenzyl iminodiacetic acid (VBIDA) through a two-stage dispersion polymerization using poly(N-vinyl pyrrolidone) (PVP) as a steric stabilizer. The resulting particles were monodisperse in size and colloidally stable over a wide range of temperature and ionic strength due to chemically grafted PVP chains. The particle size was also found to be sensitive to ionic strength and pH of the aqueous environment, likely due to the electrostatic repulsion between ionized VBIDA groups. Divalent nickel ions were chelated to the VBIDA groups, allowing selective metal affinity attachment of a His6-Cys peptide. The peptide was released upon the addition of the competitive ligand imidazole, demonstrating that the peptide attachment to the particles is reversible and selective. PMID:24176889

Implementation of a Post-Code Pause: Extending Post-Event Debriefing to Include Silence.

PubMed

Copeland, Darcy; Liska, Heather

2016-01-01

This project arose out of a need to address two issues at our hospital: we lacked a formal debriefing process for code/trauma events and the emergency department wanted to address the psychological and spiritual needs of code/trauma responders. We developed a debriefing process for code/trauma events that intentionally included mechanisms to facilitate recognition, acknowledgment, and, when needed, responses to the psychological and spiritual needs of responders. A post-code pause process was implemented in the emergency department with the aims of standardizing a debriefing process, encouraging a supportive team-based culture, improving transition back to "normal" activities after responding to code/trauma events, and providing responders an opportunity to express reverence for patients involved in code/trauma events. The post-code pause process incorporates a moment of silence and the addition of two simple questions to a traditional operational debrief. Implementation of post-code pauses was feasible despite the fast paced nature of the department. At the end of the 1-year pilot period, staff members reported increases in feeling supported by peers and leaders, their ability to pay homage to patients, and having time to regroup prior to returning to their assignment. There was a decrease in the number of respondents reporting having thoughts or feelings associated with the event within 24 hr. The pauses create a mechanism for operational team debriefing, provide an opportunity for staff members to honor their work and their patients, and support an environment in which the psychological and spiritual effects of responding to code/trauma events can be acknowledged.

Investigation of energetic particle induced geodesic acoustic mode

NASA Astrophysics Data System (ADS)

Schneller, Mirjam; Fu, Guoyong; Chavdarovski, Ilija; Wang, Weixing; Lauber, Philipp; Lu, Zhixin

2017-10-01

Energetic particles are ubiquitous in present and future tokamaks due to heating systems and fusion reactions. Anisotropy in the distribution function of the energetic particle population is able to excite oscillations from the continuous spectrum of geodesic acoustic modes (GAMs), which cannot be driven by plasma pressure gradients due to their toroidally and nearly poloidally symmetric structures. These oscillations are known as energetic particle-induced geodesic acoustic modes (EGAMs) [G.Y. Fu'08] and have been observed in recent experiments [R. Nazikian'08]. EGAMs are particularly attractive in the framework of turbulence regulation, since they lead to an oscillatory radial electric shear which can potentially saturate the turbulence. For the presented work, the nonlinear gyrokinetic, electrostatic, particle-in-cell code GTS [W.X. Wang'06] has been extended to include an energetic particle population following either bump-on-tail Maxwellian or slowing-down [Stix'76] distribution function. With this new tool, we study growth rate, frequency and mode structure of the EGAM in an ASDEX Upgrade-like scenario. A detailed understanding of EGAM excitation reveals essential for future studies of EGAM interaction with micro-turbulence. Funded by the Max Planck Princeton Research Center. Computational resources of MPCDF and NERSC are greatefully acknowledged.

An extended validation of the last generation of particle finite element method for free surface flows

NASA Astrophysics Data System (ADS)

Gimenez, Juan M.; González, Leo M.

2015-03-01

In this paper, a new generation of the particle method known as Particle Finite Element Method (PFEM), which combines convective particle movement and a fixed mesh resolution, is applied to free surface flows. This interesting variant, previously described in the literature as PFEM-2, is able to use larger time steps when compared to other similar numerical tools which implies shorter computational times while maintaining the accuracy of the computation. PFEM-2 has already been extended to free surface problems, being the main topic of this paper a deep validation of this methodology for a wider range of flows. To accomplish this task, different improved versions of discontinuous and continuous enriched basis functions for the pressure field have been developed to capture the free surface dynamics without artificial diffusion or undesired numerical effects when different density ratios are involved. A collection of problems has been carefully selected such that a wide variety of Froude numbers, density ratios and dominant dissipative cases are reported with the intention of presenting a general methodology, not restricted to a particular range of parameters, and capable of using large time-steps. The results of the different free-surface problems solved, which include: Rayleigh-Taylor instability, sloshing problems, viscous standing waves and the dam break problem, are compared to well validated numerical alternatives or experimental measurements obtaining accurate approximations for such complex flows.

Assessment of Microphysical Models in the National Combustion Code (NCC) for Aircraft Particulate Emissions: Particle Loss in Sampling Lines

NASA Technical Reports Server (NTRS)

Wey, Thomas; Liu, Nan-Suey

2008-01-01

This paper at first describes the fluid network approach recently implemented into the National Combustion Code (NCC) for the simulation of transport of aerosols (volatile particles and soot) in the particulate sampling systems. This network-based approach complements the other two approaches already in the NCC, namely, the lower-order temporal approach and the CFD-based approach. The accuracy and the computational costs of these three approaches are then investigated in terms of their application to the prediction of particle losses through sample transmission and distribution lines. Their predictive capabilities are assessed by comparing the computed results with the experimental data. The present work will help establish standard methodologies for measuring the size and concentration of particles in high-temperature, high-velocity jet engine exhaust. Furthermore, the present work also represents the first step of a long term effort of validating physics-based tools for the prediction of aircraft particulate emissions.

Capture of 0.1-μm aerosol particles containing viable H1N1 influenza virus by N95 filtering facepiece respirators.

PubMed

Harnish, Delbert A; Heimbuch, Brian K; Balzli, Charles; Choe, Melanie; Lumley, April E; Shaffer, Ronald E; Wander, Joseph D

2016-01-01

Nosocomial infections pose an escalating threat to both patients and healthcare workers (HCWs). A widely recommended device for individual respiratory protection, the N95 filtering facepiece respirator (FFR) has been shown to provide efficient filtration of inert particles larger and smaller than the nominal most-penetrating particle size (MPPS) range, 0.03-0.3 μm. Humans generate respiratory aerosols in the MPPS range, suggesting that short-range disease transmission could occur via small infectious particles. Data presented here show that the N95 FFR will afford a significant measure of protection against infectious particles as small as a bare H1N1 influenza virion, and that the capture mechanism does not discriminate in favor of, or against, biological particles.

Performance analysis of parallel gravitational N-body codes on large GPU clusters

NASA Astrophysics Data System (ADS)

Huang, Si-Yi; Spurzem, Rainer; Berczik, Peter

2016-01-01

We compare the performance of two very different parallel gravitational N-body codes for astrophysical simulations on large Graphics Processing Unit (GPU) clusters, both of which are pioneers in their own fields as well as on certain mutual scales - NBODY6++ and Bonsai. We carry out benchmarks of the two codes by analyzing their performance, accuracy and efficiency through the modeling of structure decomposition and timing measurements. We find that both codes are heavily optimized to leverage the computational potential of GPUs as their performance has approached half of the maximum single precision performance of the underlying GPU cards. With such performance we predict that a speed-up of 200 - 300 can be achieved when up to 1k processors and GPUs are employed simultaneously. We discuss the quantitative information about comparisons of the two codes, finding that in the same cases Bonsai adopts larger time steps as well as larger relative energy errors than NBODY6++, typically ranging from 10 - 50 times larger, depending on the chosen parameters of the codes. Although the two codes are built for different astrophysical applications, in specified conditions they may overlap in performance at certain physical scales, thus allowing the user to choose either one by fine-tuning parameters accordingly.

Multi-Sensor Detection with Particle Swarm Optimization for Time-Frequency Coded Cooperative WSNs Based on MC-CDMA for Underground Coal Mines

PubMed Central

Xu, Jingjing; Yang, Wei; Zhang, Linyuan; Han, Ruisong; Shao, Xiaotao

2015-01-01

In this paper, a wireless sensor network (WSN) technology adapted to underground channel conditions is developed, which has important theoretical and practical value for safety monitoring in underground coal mines. According to the characteristics that the space, time and frequency resources of underground tunnel are open, it is proposed to constitute wireless sensor nodes based on multicarrier code division multiple access (MC-CDMA) to make full use of these resources. To improve the wireless transmission performance of source sensor nodes, it is also proposed to utilize cooperative sensors with good channel conditions from the sink node to assist source sensors with poor channel conditions. Moreover, the total power of the source sensor and its cooperative sensors is allocated on the basis of their channel conditions to increase the energy efficiency of the WSN. To solve the problem that multiple access interference (MAI) arises when multiple source sensors transmit monitoring information simultaneously, a kind of multi-sensor detection (MSD) algorithm with particle swarm optimization (PSO), namely D-PSO, is proposed for the time-frequency coded cooperative MC-CDMA WSN. Simulation results show that the average bit error rate (BER) performance of the proposed WSN in an underground coal mine is improved significantly by using wireless sensor nodes based on MC-CDMA, adopting time-frequency coded cooperative transmission and D-PSO algorithm with particle swarm optimization. PMID:26343660

Multi-Sensor Detection with Particle Swarm Optimization for Time-Frequency Coded Cooperative WSNs Based on MC-CDMA for Underground Coal Mines.

PubMed

Xu, Jingjing; Yang, Wei; Zhang, Linyuan; Han, Ruisong; Shao, Xiaotao

2015-08-27

In this paper, a wireless sensor network (WSN) technology adapted to underground channel conditions is developed, which has important theoretical and practical value for safety monitoring in underground coal mines. According to the characteristics that the space, time and frequency resources of underground tunnel are open, it is proposed to constitute wireless sensor nodes based on multicarrier code division multiple access (MC-CDMA) to make full use of these resources. To improve the wireless transmission performance of source sensor nodes, it is also proposed to utilize cooperative sensors with good channel conditions from the sink node to assist source sensors with poor channel conditions. Moreover, the total power of the source sensor and its cooperative sensors is allocated on the basis of their channel conditions to increase the energy efficiency of the WSN. To solve the problem that multiple access interference (MAI) arises when multiple source sensors transmit monitoring information simultaneously, a kind of multi-sensor detection (MSD) algorithm with particle swarm optimization (PSO), namely D-PSO, is proposed for the time-frequency coded cooperative MC-CDMA WSN. Simulation results show that the average bit error rate (BER) performance of the proposed WSN in an underground coal mine is improved significantly by using wireless sensor nodes based on MC-CDMA, adopting time-frequency coded cooperative transmission and D-PSO algorithm with particle swarm optimization.

Evaluation of a low-cost optical particle counter (Alphasense OPC-N2) for ambient air monitoring

NASA Astrophysics Data System (ADS)

Crilley, Leigh R.; Shaw, Marvin; Pound, Ryan; Kramer, Louisa J.; Price, Robin; Young, Stuart; Lewis, Alastair C.; Pope, Francis D.

2018-02-01

A fast-growing area of research is the development of low-cost sensors for measuring air pollutants. The affordability and size of low-cost particle sensors makes them an attractive option for use in experiments requiring a number of instruments such as high-density spatial mapping. However, for these low-cost sensors to be useful for these types of studies their accuracy and precision need to be quantified. We evaluated the Alphasense OPC-N2, a promising low-cost miniature optical particle counter, for monitoring ambient airborne particles at typical urban background sites in the UK. The precision of the OPC-N2 was assessed by co-locating 14 instruments at a site to investigate the variation in measured concentrations. Comparison to two different reference optical particle counters as well as a TEOM-FDMS enabled the accuracy of the OPC-N2 to be evaluated. Comparison of the OPC-N2 to the reference optical instruments shows some limitations for measuring mass concentrations of PM1, PM2.5 and PM10. The OPC-N2 demonstrated a significant positive artefact in measured particle mass during times of high ambient RH (> 85 %) and a calibration factor was developed based upon κ-Köhler theory, using average bulk particle aerosol hygroscopicity. Application of this RH correction factor resulted in the OPC-N2 measurements being within 33 % of the TEOM-FDMS, comparable to the agreement between a reference optical particle counter and the TEOM-FDMS (20 %). Inter-unit precision for the 14 OPC-N2 sensors of 22 ± 13 % for PM10 mass concentrations was observed. Overall, the OPC-N2 was found to accurately measure ambient airborne particle mass concentration provided they are (i) correctly calibrated and (ii) corrected for ambient RH. The level of precision demonstrated between multiple OPC-N2s suggests that they would be suitable devices for applications where the spatial variability in particle concentration was to be determined.

Simplified Syndrome Decoding of (n, 1) Convolutional Codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1983-01-01

A new syndrome decoding algorithm for the (n, 1) convolutional codes (CC) that is different and simpler than the previous syndrome decoding algorithm of Schalkwijk and Vinck is presented. The new algorithm uses the general solution of the polynomial linear Diophantine equation for the error polynomial vector E(D). This set of Diophantine solutions is a coset of the CC space. A recursive or Viterbi-like algorithm is developed to find the minimum weight error vector cirumflex E(D) in this error coset. An example illustrating the new decoding algorithm is given for the binary nonsymmetric (2,1)CC.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.

PubMed

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin

2014-10-14

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Multidimensional Multiphysics Simulation of TRISO Particle Fuel

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

J. D. Hales; R. L. Williamson; S. R. Novascone

2013-11-01

Multidimensional multiphysics analysis of TRISO-coated particle fuel using the BISON finite-element based nuclear fuels code is described. The governing equations and material models applicable to particle fuel and implemented in BISON are outlined. Code verification based on a recent IAEA benchmarking exercise is described, and excellant comparisons are reported. Multiple TRISO-coated particles of increasing geometric complexity are considered. It is shown that the code's ability to perform large-scale parallel computations permits application to complex 3D phenomena while very efficient solutions for either 1D spherically symmetric or 2D axisymmetric geometries are straightforward. Additionally, the flexibility to easily include new physical andmore » material models and uncomplicated ability to couple to lower length scale simulations makes BISON a powerful tool for simulation of coated-particle fuel. Future code development activities and potential applications are identified.« less

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

NASA Astrophysics Data System (ADS)

Vincenti, H.; Lobet, M.; Lehe, R.; Sasanka, R.; Vay, J.-L.

2017-01-01

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈ 20 pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD register length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scatter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of × 2 to × 2.5 speed-up in double precision for particle shape factor of orders 1- 3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles).

Studies of Planet Formation Using a Hybrid N-Body + Planetesimal Code

NASA Technical Reports Server (NTRS)

Kenyon, Scott J.

2004-01-01

The goal of our proposal was to use a hybrid multi-annulus planetesimal/n-body code to examine the planetesimal theory, one of the two main theories of planet formation. We developed this code to follow the evolution of numerous 1 m to 1 km planetesimals as they collide, merge, and grow into full-fledged planets. Our goal was to apply the code to several well-posed, topical problems in planet formation and to derive observational consequences of the models. We planned to construct detailed models to address two fundamental issues: (1) icy planets: models for icy planet formation will demonstrate how the physical properties of debris disks - including the Kuiper Belt in our solar system - depend on initial conditions and input physics; and (2) terrestrial planets: calculations following the evolution of 1-10 km planetesimals into Earth-mass planets and rings of dust will provide a better understanding of how terrestrial planets form and interact with their environment.

An Extended Duopoly Game.

ERIC Educational Resources Information Center

Eckalbar, John C.

2002-01-01

Illustrates how principles and intermediate microeconomic students can gain an understanding for strategic price setting by playing a relatively large oligopoly game. Explains that the game extends to a continuous price space and outlines appropriate applications. Offers the Mathematica code to instructors so that the assumptions of the game can…

An N-body Integrator for Planetary Rings

NASA Astrophysics Data System (ADS)

Hahn, Joseph M.

2011-04-01

A planetary ring that is disturbed by a satellite's resonant perturbation can respond in an organized way. When the resonance lies in the ring's interior, the ring responds via an m-armed spiral wave, while a ring whose edge is confined by the resonance exhibits an m-lobed scalloping along the ring-edge. The amplitude of these disturbances are sensitive to ring surface density and viscosity, so modelling these phenomena can provide estimates of the ring's properties. However a brute force attempt to simulate a ring's full azimuthal extent with an N-body code will likely fail because of the large number of particles needed to resolve the ring's behavior. Another impediment is the gravitational stirring that occurs among the simulated particles, which can wash out the ring's organized response. However it is possible to adapt an N-body integrator so that it can simulate a ring's collective response to resonant perturbations. The code developed here uses a few thousand massless particles to trace streamlines within the ring. Particles are close in a radial sense to these streamlines, which allows streamlines to be treated as straight wires of constant linear density. Consequently, gravity due to these streamline is a simple function of the particle's radial distance to all streamlines. And because particles are responding to smooth gravitating streamlines, rather than discrete particles, this method eliminates the stirring that ordinarily occurs in brute force N-body calculations. Note also that ring surface density is now a simple function of streamline separations, so effects due to ring pressure and viscosity are easily accounted for, too. A poster will describe this N-body method in greater detail. Simulations of spiral density waves and scalloped ring-edges are executed in typically ten minutes on a desktop PC, and results for Saturn's A and B rings will be presented at conference time.

Submillimeter-Wave Observations of C_3N^- in AN Extended Negative Glow Discharge

NASA Astrophysics Data System (ADS)

Amano, T.

2009-06-01

Extended negative glow and hollow anode discharges are found to be good sources of negative ions, such as CN^-, C_2H^-, and C_4H^-, for observations of pure rotational lines in the submillimeter-wave region. Thaddeus et al. detected C_3N^- in a glow discharge in HC_3N diluted in Ar buffer gas, and its rotational lines up to 378 GHz (J=39-38) were measured. In the present investigation, this anion has been observed in an extended negative glow discharge in a gas mixture of C_2N_2 (˜ 2 mTorr) and C_2H_2 (˜ 3 mTorr) in Ar buffer gas of ˜ 15 mTorr at the cell wall temperature of 230 K. The optimum discharge current was 2-4 mA with 250 Gauss longitudinal magnetic field. The rotational lines of up to J=51-50 in the 495 GHz region have been measured, and the improved rotational and centrifugal distortion constants are obtained. In the discharge optimum for production of C_3N^-, neither CN nor C_3N was detected with a similar signal accumulation time used for observations of the anion. However, this reaction has been found to be an excellent source for HC_3N, and the dominant formation mechanism of C_3N^- is likely to be the dissociative electron attachment to HC_3N. The radiative association of C_3N with electrons seems to be unlikely at least for the extended negative glow discharge. Apparently HC_3N is synthesized by a fast neutral and neutral reaction (C_2{H}_2 + CN → HC_3{N} + {H} It is interesting to see that an isomer, HCCNC, is also detected in the discharge, although the number density of this species is found to be about two orders of magnitude smaller than that of HC_3N. Another isomer, HNCCC, has also been observed with much weaker signal intensity. This species might have been produced by the dissociative recombination reaction of HC_3NH^+ with electrons, although the detection of this cation has not been successful in this type of discharge. T. Amano, J. Chem. Phys., 129, 244305 (2008). P. Thaddeus et al.,Astrophys. J., 677,1132-1139 (2008) K. Graupner

A fully-implicit Particle-In-Cell Monte Carlo Collision code for the simulation of inductively coupled plasmas

NASA Astrophysics Data System (ADS)

Mattei, S.; Nishida, K.; Onai, M.; Lettry, J.; Tran, M. Q.; Hatayama, A.

2017-12-01

We present a fully-implicit electromagnetic Particle-In-Cell Monte Carlo collision code, called NINJA, written for the simulation of inductively coupled plasmas. NINJA employs a kinetic enslaved Jacobian-Free Newton Krylov method to solve self-consistently the interaction between the electromagnetic field generated by the radio-frequency coil and the plasma response. The simulated plasma includes a kinetic description of charged and neutral species as well as the collision processes between them. The algorithm allows simulations with cell sizes much larger than the Debye length and time steps in excess of the Courant-Friedrichs-Lewy condition whilst preserving the conservation of the total energy. The code is applied to the simulation of the plasma discharge of the Linac4 H- ion source at CERN. Simulation results of plasma density, temperature and EEDF are discussed and compared with optical emission spectroscopy measurements. A systematic study of the energy conservation as a function of the numerical parameters is presented.

REBOUND-ing Off Asteroids: An N-body Particle Model for Ejecta Dynamics on Small Bodies

NASA Astrophysics Data System (ADS)

Larson, Jennifer; Sarid, Gal

2017-10-01

Here we describe our numerical approach to model the evolution of ejecta clouds. Modeling with an N-body particle method enables us to study the micro-dynamics while varying the particle size distribution. A hydrodynamic approach loses many of the fine particle-particle interactions included in the N-body particle approach (Artemieva 2008).We use REBOUND, an N-body integration package (Rein et al. 2012) developed to model various dynamical systems (planetary orbits, ring systems, etc.) with high resolution calculations at a lower performance cost than other N-body integrators (Rein & Tamayo 2017). It offers both symplectic (WHFast) and non-symplectic (IAS15) methods (Rein & Spiegel 2014, Rein & Tamayo 2015). We primarily use the IAS15 integrator due to its robustness and accuracy with short interaction distances and non-conservative forces. We implemented a wrapper (developed in Python) to handle changes in time step and integrator at different stages of ejecta particle evolution.To set up the system, each particle is given a velocity away from the target body’s surface at a given angle within a defined ejecta cone. We study the ejecta cloud evolution beginning immediately after an impact rather than the actual impact itself. This model considers effects such as varying particle size distribution, radiation pressure, perturbations from a binary component, particle-particle collisions and non-axisymmetric gravity of the target body. Restrictions on the boundaries of the target body’s surface define the physical shape and help count the number of particles that land on the target body. Later, we will build the central body from individual particles to allow for a wider variety of target body shapes and topographies.With our particle modeling approach, individual particle trajectories are tracked and predicted on short, medium and long timescales. Our approach will be applied to modeling of the ejecta cloud produced during the Double Asteroid Redirection Test

Modeling anomalous radial transport in kinetic transport codes

NASA Astrophysics Data System (ADS)

Bodi, K.; Krasheninnikov, S. I.; Cohen, R. H.; Rognlien, T. D.

2009-11-01

Anomalous transport is typically the dominant component of the radial transport in magnetically confined plasmas, where the physical origin of this transport is believed to be plasma turbulence. A model is presented for anomalous transport that can be used in continuum kinetic edge codes like TEMPEST, NEO and the next-generation code being developed by the Edge Simulation Laboratory. The model can also be adapted to particle-based codes. It is demonstrated that the model with a velocity-dependent diffusion and convection terms can match a diagonal gradient-driven transport matrix as found in contemporary fluid codes, but can also include off-diagonal effects. The anomalous transport model is also combined with particle drifts and a particle/energy-conserving Krook collision operator to study possible synergistic effects with neoclassical transport. For the latter study, a velocity-independent anomalous diffusion coefficient is used to mimic the effect of long-wavelength ExB turbulence.

New quantum codes derived from a family of antiprimitive BCH codes

NASA Astrophysics Data System (ADS)

Liu, Yang; Li, Ruihu; Lü, Liangdong; Guo, Luobin

The Bose-Chaudhuri-Hocquenghem (BCH) codes have been studied for more than 57 years and have found wide application in classical communication system and quantum information theory. In this paper, we study the construction of quantum codes from a family of q2-ary BCH codes with length n=q2m+1 (also called antiprimitive BCH codes in the literature), where q≥4 is a power of 2 and m≥2. By a detailed analysis of some useful properties about q2-ary cyclotomic cosets modulo n, Hermitian dual-containing conditions for a family of non-narrow-sense antiprimitive BCH codes are presented, which are similar to those of q2-ary primitive BCH codes. Consequently, via Hermitian Construction, a family of new quantum codes can be derived from these dual-containing BCH codes. Some of these new antiprimitive quantum BCH codes are comparable with those derived from primitive BCH codes.

Heterogeneous reaction of N2O5 with airborne TiO2 particles and its implication for stratospheric particle injection

NASA Astrophysics Data System (ADS)

Tang, M. J.; Telford, P. J.; Pope, F. D.; Rkiouak, L.; Abraham, N. L.; Archibald, A. T.; Braesicke, P.; Pyle, J. A.; McGregor, J.; Watson, I. M.; Cox, R. A.; Kalberer, M.

2014-06-01

Injection of aerosol particles (or their precursors) into the stratosphere to scatter solar radiation back into space has been suggested as a solar-radiation management scheme for the mitigation of global warming. TiO2 has recently been highlighted as a possible candidate particle because of its high refractive index, but its impact on stratospheric chemistry via heterogeneous reactions is as yet unknown. In this work the heterogeneous reaction of airborne sub-micrometre TiO2 particles with N2O5 has been investigated for the first time, at room temperature and different relative humidities (RH), using an atmospheric pressure aerosol flow tube. The uptake coefficient of N2O5 onto TiO2, γ(N2O5), was determined to be ~1.0 × 10-3 at low RH, increasing to ~3 × 10-3 at 60% RH. The uptake of N2O5 onto TiO2 is then included in the UKCA chemistry-climate model to assess the impact of this reaction on stratospheric chemistry. While the impact of TiO2 on the scattering of solar radiation is chosen to be similar to the aerosol from the Mt Pinatubo eruption, the impact of TiO2 injection on stratospheric N2O5 is much smaller.

EMPIRE: A Reaction Model Code for Nuclear Astrophysics

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

Palumbo, A., E-mail: apalumbo@bnl.gov; Herman, M.; Capote, R.

The correct modeling of abundances requires knowledge of nuclear cross sections for a variety of neutron, charged particle and γ induced reactions. These involve targets far from stability and are therefore difficult (or currently impossible) to measure. Nuclear reaction theory provides the only way to estimate values of such cross sections. In this paper we present application of the EMPIRE reaction code to nuclear astrophysics. Recent measurements are compared to the calculated cross sections showing consistent agreement for n-, p- and α-induced reactions of strophysical relevance.

Charge Injection Capacity of TiN Electrodes for an Extended Voltage Range

PubMed Central

Patan, Mustafa; Shah, Tosha; Sahin, Mesut

2011-01-01

Many applications of neural stimulation demand a high current density from the electrodes used for stimulus delivery. New materials have been searched that can provide such large current and charge densities where the traditional noble metal and capacitor electrodes are inadequate. Titanium nitride, which has been used in cardiac pacemaker leads for many years, is one of these materials recently considered for neural stimulation. In this short report, we investigated the charge injection capacity of TiN electrodes for an extended range of cathodic voltages. The injected charge increased first slowly as a function of the electrode voltage, and then at a faster rate beyond −1.6 V. The maximum charge was 4.45 mC/cm2 (n=6) for a cathodic voltage peak of −3.0 V and a bias voltage of −0.8 V. There was no evidence of bubble generation under microscopic observation. The unrecoverable charges remained under 7% of the total injected charge for the largest cathodic voltage tested. These large values of charge injection capacity and relatively small unrecoverable charges warrant further investigation of the charge injection mechanism in TiN interfaces at this extended range of electrode voltages. PMID:17946870

Microdosimetric evaluation of the neutron field for BNCT at Kyoto University reactor by using the PHITS code.

PubMed

Baba, H; Onizuka, Y; Nakao, M; Fukahori, M; Sato, T; Sakurai, Y; Tanaka, H; Endo, S

2011-02-01

In this study, microdosimetric energy distributions of secondary charged particles from the (10)B(n,α)(7)Li reaction in boron-neutron capture therapy (BNCT) field were calculated using the Particle and Heavy Ion Transport code System (PHITS). The PHITS simulation was performed to reproduce the geometrical set-up of an experiment that measured the microdosimetric energy distributions at the Kyoto University Reactor where two types of tissue-equivalent proportional counters were used, one with A-150 wall alone and another with a 50-ppm-boron-loaded A-150 wall. It was found that the PHITS code is a useful tool for the simulation of the energy deposited in tissue in BNCT based on the comparisons with experimental results.

Role of small-norm components in extended random-phase approximation

NASA Astrophysics Data System (ADS)

Tohyama, Mitsuru

2017-09-01

The role of the small-norm amplitudes in extended random-phase approximation (RPA) theories such as the particle-particle and hole-hole components of one-body amplitudes and the two-body amplitudes other than two-particle/two-hole components are investigated for the one-dimensional Hubbard model using an extended RPA derived from the time-dependent density matrix theory. It is found that these amplitudes cannot be neglected in strongly interacting regions where the effects of ground-state correlations are significant.

Sparse Coding for N-Gram Feature Extraction and Training for File Fragment Classification

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

Wang, Felix; Quach, Tu-Thach; Wheeler, Jason

File fragment classification is an important step in the task of file carving in digital forensics. In file carving, files must be reconstructed based on their content as a result of their fragmented storage on disk or in memory. Existing methods for classification of file fragments typically use hand-engineered features such as byte histograms or entropy measures. In this paper, we propose an approach using sparse coding that enables automated feature extraction. Sparse coding, or sparse dictionary learning, is an unsupervised learning algorithm, and is capable of extracting features based simply on how well those features can be used tomore » reconstruct the original data. With respect to file fragments, we learn sparse dictionaries for n-grams, continuous sequences of bytes, of different sizes. These dictionaries may then be used to estimate n-gram frequencies for a given file fragment, but for significantly larger n-gram sizes than are typically found in existing methods which suffer from combinatorial explosion. To demonstrate the capability of our sparse coding approach, we used the resulting features to train standard classifiers such as support vector machines (SVMs) over multiple file types. Experimentally, we achieved significantly better classification results with respect to existing methods, especially when the features were used in supplement to existing hand-engineered features.« less

Sparse Coding for N-Gram Feature Extraction and Training for File Fragment Classification

DOE PAGES

Wang, Felix; Quach, Tu-Thach; Wheeler, Jason; ...

2018-04-05

File fragment classification is an important step in the task of file carving in digital forensics. In file carving, files must be reconstructed based on their content as a result of their fragmented storage on disk or in memory. Existing methods for classification of file fragments typically use hand-engineered features such as byte histograms or entropy measures. In this paper, we propose an approach using sparse coding that enables automated feature extraction. Sparse coding, or sparse dictionary learning, is an unsupervised learning algorithm, and is capable of extracting features based simply on how well those features can be used tomore » reconstruct the original data. With respect to file fragments, we learn sparse dictionaries for n-grams, continuous sequences of bytes, of different sizes. These dictionaries may then be used to estimate n-gram frequencies for a given file fragment, but for significantly larger n-gram sizes than are typically found in existing methods which suffer from combinatorial explosion. To demonstrate the capability of our sparse coding approach, we used the resulting features to train standard classifiers such as support vector machines (SVMs) over multiple file types. Experimentally, we achieved significantly better classification results with respect to existing methods, especially when the features were used in supplement to existing hand-engineered features.« less

Agile deployment and code coverage testing metrics of the boot software on-board Solar Orbiter's Energetic Particle Detector

NASA Astrophysics Data System (ADS)

Parra, Pablo; da Silva, Antonio; Polo, Óscar R.; Sánchez, Sebastián

2018-02-01

In this day and age, successful embedded critical software needs agile and continuous development and testing procedures. This paper presents the overall testing and code coverage metrics obtained during the unit testing procedure carried out to verify the correctness of the boot software that will run in the Instrument Control Unit (ICU) of the Energetic Particle Detector (EPD) on-board Solar Orbiter. The ICU boot software is a critical part of the project so its verification should be addressed at an early development stage, so any test case missed in this process may affect the quality of the overall on-board software. According to the European Cooperation for Space Standardization ESA standards, testing this kind of critical software must cover 100% of the source code statement and decision paths. This leads to the complete testing of fault tolerance and recovery mechanisms that have to resolve every possible memory corruption or communication error brought about by the space environment. The introduced procedure enables fault injection from the beginning of the development process and enables to fulfill the exigent code coverage demands on the boot software.

New syndrome decoding techniques for the (n, k) convolutional codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1984-01-01

This paper presents a new syndrome decoding algorithm for the (n, k) convolutional codes (CC) which differs completely from an earlier syndrome decoding algorithm of Schalkwijk and Vinck. The new algorithm is based on the general solution of the syndrome equation, a linear Diophantine equation for the error polynomial vector E(D). The set of Diophantine solutions is a coset of the CC. In this error coset a recursive, Viterbi-like algorithm is developed to find the minimum weight error vector (circumflex)E(D). An example, illustrating the new decoding algorithm, is given for the binary nonsystemmatic (3, 1)CC. Previously announced in STAR as N83-34964

Elementary particles, dark matter candidate and new extended standard model

NASA Astrophysics Data System (ADS)

Hwang, Jaekwang

2017-01-01

Elementary particle decays and reactions are discussed in terms of the three-dimensional quantized space model beyond the standard model. Three generations of the leptons and quarks correspond to the lepton charges. Three heavy leptons and three heavy quarks are introduced. And the bastons (new particles) are proposed as the possible candidate of the dark matters. Dark matter force, weak force and strong force are explained consistently. Possible rest masses of the new particles are, tentatively, proposed for the experimental searches. For more details, see the conference paper at https://www.researchgate.net/publication/308723916.

Smoothed Particle Hydrodynamic Simulator

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

2016-10-05

This code is a highly modular framework for developing smoothed particle hydrodynamic (SPH) simulations running on parallel platforms. The compartmentalization of the code allows for rapid development of new SPH applications and modifications of existing algorithms. The compartmentalization also allows changes in one part of the code used by many applications to instantly be made available to all applications.

A three-dimensional spacecraft-charging computer code

NASA Technical Reports Server (NTRS)

Rubin, A. G.; Katz, I.; Mandell, M.; Schnuelle, G.; Steen, P.; Parks, D.; Cassidy, J.; Roche, J.

1980-01-01

A computer code is described which simulates the interaction of the space environment with a satellite at geosynchronous altitude. Employing finite elements, a three-dimensional satellite model has been constructed with more than 1000 surface cells and 15 different surface materials. Free space around the satellite is modeled by nesting grids within grids. Applications of this NASA Spacecraft Charging Analyzer Program (NASCAP) code to the study of a satellite photosheath and the differential charging of the SCATHA (satellite charging at high altitudes) satellite in eclipse and in sunlight are discussed. In order to understand detector response when the satellite is charged, the code is used to trace the trajectories of particles reaching the SCATHA detectors. Particle trajectories from positive and negative emitters on SCATHA also are traced to determine the location of returning particles, to estimate the escaping flux, and to simulate active control of satellite potentials.

Swelling of two-dimensional polymer rings by trapped particles.

PubMed

Haleva, E; Diamant, H

2006-09-01

The mean area of a two-dimensional Gaussian ring of N monomers is known to diverge when the ring is subject to a critical pressure differential, p c ~ N -1. In a recent publication (Eur. Phys. J. E 19, 461 (2006)) we have shown that for an inextensible freely jointed ring this divergence turns into a second-order transition from a crumpled state, where the mean area scales as [A]~N-1, to a smooth state with [A]~N(2). In the current work we extend these two models to the case where the swelling of the ring is caused by trapped ideal-gas particles. The Gaussian model is solved exactly, and the freely jointed one is treated using a Flory argument, mean-field theory, and Monte Carlo simulations. For a fixed number Q of trapped particles the criticality disappears in both models through an unusual mechanism, arising from the absence of an area constraint. In the Gaussian case the ring swells to such a mean area, [A]~ NQ, that the pressure exerted by the particles is at p c for any Q. In the freely jointed model the mean area is such that the particle pressure is always higher than p c, and [A] consequently follows a single scaling law, [A]~N(2) f (Q/N), for any Q. By contrast, when the particles are in contact with a reservoir of fixed chemical potential, the criticality is retained. Thus, the two ensembles are manifestly inequivalent in these systems.

Simulation of halo particles with Simpsons

NASA Astrophysics Data System (ADS)

Machida, Shinji

2003-12-01

Recent code improvements and some simulation results of halo particles with Simpsons will be presented. We tried to identify resonance behavior of halo particles by looking at tune evolution of individual macro particle.

Energetic particle modes of q = 1 high-order harmonics in tokamak plasmas with monotonic weak magnetic shear

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

Ren, Zhen-Zhen; Wang, Feng; Fu, G. Y.

Linear and nonlinear simulations of high-order harmonics q=1 energetic particle modes excited by trapped energetic particles in tokamaks are carried out using kinetic/magnetohydrodynamic hybrid code M3D-K. It is found that with a flat safety factor profile in the core region, the linear growth rate of high-order harmonics (m=n>1) driven by energetic trapped particles can be higher than the m/n=1/1 component. The high m=n>1 modes become more unstable when the pressure of energetic particles becomes higher. Moreover, it is shown that there exist multiple resonant locations satisfying different resonant conditions in the phase space of energetic particles for the high-order harmonicsmore » modes, whereas there is only one precessional resonance for the m/n=1/1 harmonics. The fluid nonlinearity reduces the saturation level of the n=1 component, while it hardly affects those of the high n components, especially the modes with m=n=3,4. The frequency of these modes does not chirp significantly, which is different with the typical fishbone driven by trapped particles. Lastly, in addition, the flattening region of energetic particle distribution due to high-order harmonics excitation is wider than that due to m/n=1/1 component, although the m/n=1/1 component has a higher saturation amplitude.« less

Energetic particle modes of q = 1 high-order harmonics in tokamak plasmas with monotonic weak magnetic shear

DOE PAGES

Ren, Zhen-Zhen; Wang, Feng; Fu, G. Y.; ...

2017-04-24

Linear and nonlinear simulations of high-order harmonics q=1 energetic particle modes excited by trapped energetic particles in tokamaks are carried out using kinetic/magnetohydrodynamic hybrid code M3D-K. It is found that with a flat safety factor profile in the core region, the linear growth rate of high-order harmonics (m=n>1) driven by energetic trapped particles can be higher than the m/n=1/1 component. The high m=n>1 modes become more unstable when the pressure of energetic particles becomes higher. Moreover, it is shown that there exist multiple resonant locations satisfying different resonant conditions in the phase space of energetic particles for the high-order harmonicsmore » modes, whereas there is only one precessional resonance for the m/n=1/1 harmonics. The fluid nonlinearity reduces the saturation level of the n=1 component, while it hardly affects those of the high n components, especially the modes with m=n=3,4. The frequency of these modes does not chirp significantly, which is different with the typical fishbone driven by trapped particles. Lastly, in addition, the flattening region of energetic particle distribution due to high-order harmonics excitation is wider than that due to m/n=1/1 component, although the m/n=1/1 component has a higher saturation amplitude.« less

Calculating the n-point correlation function with general and efficient python code

NASA Astrophysics Data System (ADS)

Genier, Fred; Bellis, Matthew

2018-01-01

There are multiple approaches to understanding the evolution of large-scale structure in our universe and with it the role of baryonic matter, dark matter, and dark energy at different points in history. One approach is to calculate the n-point correlation function estimator for galaxy distributions, sometimes choosing a particular type of galaxy, such as luminous red galaxies. The standard way to calculate these estimators is with pair counts (for the 2-point correlation function) and with triplet counts (for the 3-point correlation function). These are O(n2) and O(n3) problems, respectively and with the number of galaxies that will be characterized in future surveys, having efficient and general code will be of increasing importance. Here we show a proof-of-principle approach to the 2-point correlation function that relies on pre-calculating galaxy locations in coarse “voxels”, thereby reducing the total number of necessary calculations. The code is written in python, making it easily accessible and extensible and is open-sourced to the community. Basic results and performance tests using SDSS/BOSS data will be shown and we discuss the application of this approach to the 3-point correlation function.

A (72, 36; 15) box code

NASA Technical Reports Server (NTRS)

Solomon, G.

1993-01-01

A (72,36;15) box code is constructed as a 9 x 8 matrix whose columns add to form an extended BCH-Hamming (8,4;4) code and whose rows sum to odd or even parity. The newly constructed code, due to its matrix form, is easily decodable for all seven-error and many eight-error patterns. The code comes from a slight modification in the parity (eighth) dimension of the Reed-Solomon (8,4;5) code over GF(512). Error correction uses the row sum parity information to detect errors, which then become erasures in a Reed-Solomon correction algorithm.

High-fidelity plasma codes for burn physics

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

Cooley, James; Graziani, Frank; Marinak, Marty

Accurate predictions of equation of state (EOS), ionic and electronic transport properties are of critical importance for high-energy-density plasma science. Transport coefficients inform radiation-hydrodynamic codes and impact diagnostic interpretation, which in turn impacts our understanding of the development of instabilities, the overall energy balance of burning plasmas, and the efficacy of self-heating from charged-particle stopping. Important processes include thermal and electrical conduction, electron-ion coupling, inter-diffusion, ion viscosity, and charged particle stopping. However, uncertainties in these coefficients are not well established. Fundamental plasma science codes, also called high-fidelity plasma codes, are a relatively recent computational tool that augments both experimental datamore » and theoretical foundations of transport coefficients. This paper addresses the current status of HFPC codes and their future development, and the potential impact they play in improving the predictive capability of the multi-physics hydrodynamic codes used in HED design.« less

Nonlinear dynamics of toroidal Alfvén eigenmodes in presence of tearing modes

NASA Astrophysics Data System (ADS)

Zhu, Jia; Ma, Zhiwei; Wang, Sheng; Zhang, Wei

2016-10-01

A new hybrid kinetic-MHD code CLT-K is developed to study nonlinear dynamics of n =1 toroidal Alfvén eigenmodes (TAEs) with the m/n =2/1 tearing mode. It is found that the n =1 TAE is first excited by isotropic energetic particles in the earlier stage and reaches the steady state due to wave-particle interaction. After the saturation of the n =1 TAE, the tearing mode intervenes and triggers the second growth of the mode. The modes goes into the second steady state due to multiple tearing mode-mode nonlinear coupling. Both wave-particle and wave-wave interactions are observed in our hybrid simulation.

Development of a model and computer code to describe solar grade silicon production processes

NASA Technical Reports Server (NTRS)

Gould, R. K.; Srivastava, R.

1979-01-01

Two computer codes were developed for describing flow reactors in which high purity, solar grade silicon is produced via reduction of gaseous silicon halides. The first is the CHEMPART code, an axisymmetric, marching code which treats two phase flows with models describing detailed gas-phase chemical kinetics, particle formation, and particle growth. It can be used to described flow reactors in which reactants, mix, react, and form a particulate phase. Detailed radial gas-phase composition, temperature, velocity, and particle size distribution profiles are computed. Also, deposition of heat, momentum, and mass (either particulate or vapor) on reactor walls is described. The second code is a modified version of the GENMIX boundary layer code which is used to compute rates of heat, momentum, and mass transfer to the reactor walls. This code lacks the detailed chemical kinetics and particle handling features of the CHEMPART code but has the virtue of running much more rapidly than CHEMPART, while treating the phenomena occurring in the boundary layer in more detail.

ME(SSY)**2: Monte Carlo Code for Star Cluster Simulations

NASA Astrophysics Data System (ADS)

Freitag, Marc Dewi

2013-02-01

ME(SSY)**2 stands for “Monte-carlo Experiments with Spherically SYmmetric Stellar SYstems." This code simulates the long term evolution of spherical clusters of stars; it was devised specifically to treat dense galactic nuclei. It is based on the pioneering Monte Carlo scheme proposed by Hénon in the 70's and includes all relevant physical ingredients (2-body relaxation, stellar mass spectrum, collisions, tidal disruption, ldots). It is basically a Monte Carlo resolution of the Fokker-Planck equation. It can cope with any stellar mass spectrum or velocity distribution. Being a particle-based method, it also allows one to take stellar collisions into account in a very realistic way. This unique code, featuring most important physical processes, allows million particle simulations, spanning a Hubble time, in a few CPU days on standard personal computers and provides a wealth of data only rivalized by N-body simulations. The current version of the software requires the use of routines from the "Numerical Recipes in Fortran 77" (http://www.nrbook.com/a/bookfpdf.php).

Particle production of a graphite target system for the intensity frontier

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

Ding, X.; Kirk, H.; McDonald, K. T.

2015-05-03

A solid graphite target system is considered for an intense muon and/or neutrino source in support of physics at the intensity frontier. We previously optimized the geometric parameters of the beam and target to maximize particle production at low energies by incoming protons with kinetic energy of 6.75 GeV and an rms geometric emittance of 5 mm-mrad using the MARS15(2014) code. In this study, we ran MARS15 with ROOT-based geometry and also considered a mercury-jet target as an upgrade option. The optimization was extended to focused proton beams with transverse emittances from 5 to 50 mm-mrad, showing that the particlemore » production decreases slowly with increasing emittance. We also studied beam-dump configurations to suppress the rate of undesirable high-energy secondary particles in the beam.« less

Saturation of Alfvén modes in tokamaks

DOE PAGES

White, Roscoe; Gorelenkov, Nikolai; Gorelenkova, Marina; ...

2016-09-20

Here, the growth of Alfvén modes driven unstable by a distribution of high energy particles up to saturation is investigated with a guiding center code, using numerical eigenfunctions produced by linear theory and a numerical high energy particle distribution, in order to make detailed comparison with experiment and with models for saturation amplitudes and the modification of beam profiles. Two innovations are introduced. First, a very noise free means of obtaining the mode-particle energy and momentum transfer is introduced, and secondly, a spline representation of the actual beam particle distribution is used.

Saturation of Alfvén modes in tokamaks

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

White, Roscoe; Gorelenkov, Nikolai; Gorelenkova, Marina

Here, the growth of Alfvén modes driven unstable by a distribution of high energy particles up to saturation is investigated with a guiding center code, using numerical eigenfunctions produced by linear theory and a numerical high energy particle distribution, in order to make detailed comparison with experiment and with models for saturation amplitudes and the modification of beam profiles. Two innovations are introduced. First, a very noise free means of obtaining the mode-particle energy and momentum transfer is introduced, and secondly, a spline representation of the actual beam particle distribution is used.

SciDAC Center for Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasmas

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

Lin, Zhihong

2013-12-18

During the first year of the SciDAC gyrokinetic particle simulation (GPS) project, the GPS team (Zhihong Lin, Liu Chen, Yasutaro Nishimura, and Igor Holod) at the University of California, Irvine (UCI) studied the tokamak electron transport driven by electron temperature gradient (ETG) turbulence, and by trapped electron mode (TEM) turbulence and ion temperature gradient (ITG) turbulence with kinetic electron effects, extended our studies of ITG turbulence spreading to core-edge coupling. We have developed and optimized an elliptic solver using finite element method (FEM), which enables the implementation of advanced kinetic electron models (split-weight scheme and hybrid model) in the SciDACmore » GPS production code GTC. The GTC code has been ported and optimized on both scalar and vector parallel computer architectures, and is being transformed into objected-oriented style to facilitate collaborative code development. During this period, the UCI team members presented 11 invited talks at major national and international conferences, published 22 papers in peer-reviewed journals and 10 papers in conference proceedings. The UCI hosted the annual SciDAC Workshop on Plasma Turbulence sponsored by the GPS Center, 2005-2007. The workshop was attended by about fifties US and foreign researchers and financially sponsored several gradual students from MIT, Princeton University, Germany, Switzerland, and Finland. A new SciDAC postdoc, Igor Holod, has arrived at UCI to initiate global particle simulation of magnetohydrodynamics turbulence driven by energetic particle modes. The PI, Z. Lin, has been promoted to the Associate Professor with tenure at UCI.« less

The STAGS computer code

NASA Technical Reports Server (NTRS)

Almroth, B. O.; Brogan, F. A.

1978-01-01

Basic information about the computer code STAGS (Structural Analysis of General Shells) is presented to describe to potential users the scope of the code and the solution procedures that are incorporated. Primarily, STAGS is intended for analysis of shell structures, although it has been extended to more complex shell configurations through the inclusion of springs and beam elements. The formulation is based on a variational approach in combination with local two dimensional power series representations of the displacement components. The computer code includes options for analysis of linear or nonlinear static stress, stability, vibrations, and transient response. Material as well as geometric nonlinearities are included. A few examples of applications of the code are presented for further illustration of its scope.

A 2D electrostatic PIC code for the Mark III Hypercube

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

Ferraro, R.D.; Liewer, P.C.; Decyk, V.K.

We have implemented a 2D electrostastic plasma particle in cell (PIC) simulation code on the Caltech/JPL Mark IIIfp Hypercube. The code simulates plasma effects by evolving in time the trajectories of thousands to millions of charged particles subject to their self-consistent fields. Each particle`s position and velocity is advanced in time using a leap frog method for integrating Newton`s equations of motion in electric and magnetic fields. The electric field due to these moving charged particles is calculated on a spatial grid at each time by solving Poisson`s equation in Fourier space. These two tasks represent the largest part ofmore » the computation. To obtain efficient operation on a distributed memory parallel computer, we are using the General Concurrent PIC (GCPIC) algorithm previously developed for a 1D parallel PIC code.« less

Unified Models of Turbulence and Nonlinear Wave Evolution in the Extended Solar Corona and Solar Wind

NASA Technical Reports Server (NTRS)

Cranmer, Steven R.; Wagner, William (Technical Monitor)

2003-01-01

) which are an alternate means of heating protons via stochastic interactions similar to particle-particle collisions. 1b. Focused Study of the Multi-Mode Detailed Balance Formalism. The PI began to explore the feasibility of using the "weak turbulence," or detailed-balance theory of Tsytovich, Melrose, and others to encompass the relevant physics of the solar wind. This study did not go far, however, because if the "strong" MHD turbulence discussed above is a dominant player in the wind's acceleration region, this formalism is inherently not applicable to the corona. We will continue to study the various published approaches to the weak turbulence formalism, especially with an eye on ways to parameterize nonlinear wave reflection rates. 2. Building the Unified Model Code Architecture. We have begun developing the computational model of a time-steady open flux tube in the extended corona. The model will be "unified" in the sense that it will include (simultaneously for the first time) as many of the various proposed physical processes as possible, all on equal footing. To retain this generality, we have formulated the problem in two interconnected parts: a completely kinetic model for the particles, using the Monte Carlo approach, and a finite-difference approach for the self-consistent fluctuation spectra. The two codes are run sequentially and iteratively until complete consistency is achieved. The current version of the Monte Carlo code incorporates gravity, the zero-current electric field, magnetic mirroring, and collisions. The fluctuation code incorporates WKJ3 wave action conservation and the cascade/dissipation processes discussed above. The codes are being run for various test problems with known solutions. Planned additions to the codes include prescriptions for nonlinear wave steepening, kinetic velocity-space diffusion, and multi-mode coupling (including reflection and refraction).

Comparisons of time explicit hybrid kinetic-fluid code Architect for Plasma Wakefield Acceleration with a full PIC code

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

Massimo, F., E-mail: francesco.massimo@ensta-paristech.fr; Dipartimento SBAI, Università di Roma “La Sapienza“, Via A. Scarpa 14, 00161 Roma; Atzeni, S.

Architect, a time explicit hybrid code designed to perform quick simulations for electron driven plasma wakefield acceleration, is described. In order to obtain beam quality acceptable for applications, control of the beam-plasma-dynamics is necessary. Particle in Cell (PIC) codes represent the state-of-the-art technique to investigate the underlying physics and possible experimental scenarios; however PIC codes demand the necessity of heavy computational resources. Architect code substantially reduces the need for computational resources by using a hybrid approach: relativistic electron bunches are treated kinetically as in a PIC code and the background plasma as a fluid. Cylindrical symmetry is assumed for themore » solution of the electromagnetic fields and fluid equations. In this paper both the underlying algorithms as well as a comparison with a fully three dimensional particle in cell code are reported. The comparison highlights the good agreement between the two models up to the weakly non-linear regimes. In highly non-linear regimes the two models only disagree in a localized region, where the plasma electrons expelled by the bunch close up at the end of the first plasma oscillation.« less

Formation of cage-like particles by poly(amino acid)-based block copolymers in aqueous solution.

PubMed Central

Cudd, A; Bhogal, M; O'Mullane, J; Goddard, P

1991-01-01

When dissolved in N,N-dimethylformamide and then dialyzed against phosphate-buffered saline, A-B-A block copolymers composed of poly [N5-(2-hydroxyethyl)-L-glutamine]-block-poly(gamma-benzyl-L-glutamate)- block-poly [N5-(2-hydroxyethyl)-L-glutamine] form particles. The particles are cage-like structures with average diameters of 300 nm (average polydispersity, 0.3-0.5). They are stable in aqueous solution at 4 degrees C for up to 3 weeks, at which time flocculation becomes apparent. Negative staining and freeze-fracture electron microscopy suggest that cage-like particles are formed by selective association of segregated micelle populations. A model of particle formation is presented in which B blocks form micelles in dimethylformamide. On dialysis against an aqueous solution, the extended A blocks then associate intermolecularly to form rod-shaped micelles, which connect the B block micelles. The result is a meshed cage-like particle. The implications of these observations on the aggregation behavior of polymeric surfactants in dilute solution are discussed. Images PMID:11607245

High dynamic range coding imaging system

NASA Astrophysics Data System (ADS)

Wu, Renfan; Huang, Yifan; Hou, Guangqi

2014-10-01

We present a high dynamic range (HDR) imaging system design scheme based on coded aperture technique. This scheme can help us obtain HDR images which have extended depth of field. We adopt Sparse coding algorithm to design coded patterns. Then we utilize the sensor unit to acquire coded images under different exposure settings. With the guide of the multiple exposure parameters, a series of low dynamic range (LDR) coded images are reconstructed. We use some existing algorithms to fuse and display a HDR image by those LDR images. We build an optical simulation model and get some simulation images to verify the novel system.

Code subspaces for LLM geometries

NASA Astrophysics Data System (ADS)

Berenstein, David; Miller, Alexandra

2018-03-01

We consider effective field theory around classical background geometries with a gauge theory dual, specifically those in the class of LLM geometries. These are dual to half-BPS states of N= 4 SYM. We find that the language of code subspaces is natural for discussing the set of nearby states, which are built by acting with effective fields on these backgrounds. This work extends our previous work by going beyond the strict infinite N limit. We further discuss how one can extract the topology of the state beyond N→∞ and find that, as before, uncertainty and entanglement entropy calculations provide a useful tool to do so. Finally, we discuss obstructions to writing down a globally defined metric operator. We find that the answer depends on the choice of reference state that one starts with. Therefore, within this setup, there is ambiguity in trying to write an operator that describes the metric globally.

Comparison of a 3D multi‐group SN particle transport code with Monte Carlo for intercavitary brachytherapy of the cervix uteri

PubMed Central

Wareing, Todd A.; Failla, Gregory; Horton, John L.; Eifel, Patricia J.; Mourtada, Firas

2009-01-01

A patient dose distribution was calculated by a 3D multi‐group SN particle transport code for intracavitary brachytherapy of the cervix uteri and compared to previously published Monte Carlo results. A Cs‐137 LDR intracavitary brachytherapy CT data set was chosen from our clinical database. MCNPX version 2.5.c, was used to calculate the dose distribution. A 3D multi‐group SN particle transport code, Attila version 6.1.1 was used to simulate the same patient. Each patient applicator was built in SolidWorks, a mechanical design package, and then assembled with a coordinate transformation and rotation for the patient. The SolidWorks exported applicator geometry was imported into Attila for calculation. Dose matrices were overlaid on the patient CT data set. Dose volume histograms and point doses were compared. The MCNPX calculation required 14.8 hours, whereas the Attila calculation required 22.2 minutes on a 1.8 GHz AMD Opteron CPU. Agreement between Attila and MCNPX dose calculations at the ICRU 38 points was within ±3%. Calculated doses to the 2 cc and 5 cc volumes of highest dose differed by not more than ±1.1% between the two codes. Dose and DVH overlays agreed well qualitatively. Attila can calculate dose accurately and efficiently for this Cs‐137 CT‐based patient geometry. Our data showed that a three‐group cross‐section set is adequate for Cs‐137 computations. Future work is aimed at implementing an optimized version of Attila for radiotherapy calculations. PACS number: 87.53.Jw

Single-particle cryo-EM-Improved ab initio 3D reconstruction with SIMPLE/PRIME.

PubMed

Reboul, Cyril F; Eager, Michael; Elmlund, Dominika; Elmlund, Hans

2018-01-01

Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over-the-counter laptops and CPU workstations is demonstrated. © 2017 The Protein Society.

TOPAS Tool for Particle Simulation

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

Perl, Joseph

2013-05-30

TOPAS lets users simulate the passage of subatomic particles moving through any kind of radiation therapy treatment system, can import a patient geometry, can record dose and other quantities, has advanced graphics, and is fully four-dimensional (3D plus time) to handle the most challenging time-dependent aspects of modern cancer treatments.TOPAS unlocks the power of the most accurate particle transport simulation technique, the Monte Carlo (MC) method, while removing the painstaking coding work such methods used to require. Research physicists can use TOPAS to improve delivery systems towards safer and more effective radiation therapy treatments, easily setting up and running complexmore » simulations that previously used to take months of preparation. Clinical physicists can use TOPAS to increase accuracy while reducing side effects, simulating patient-specific treatment plans at the touch of a button. TOPAS is designed as a “user code” layered on top of the Geant4 Simulation Toolkit. TOPAS includes the standard Geant4 toolkit, plus additional code to make Geant4 easier to control and to extend Geant4 functionality. TOPAS aims to make proton simulation both “reliable” and “repeatable.” “Reliable” means both accurate physics and a high likelihood to simulate precisely what the user intended to simulate, reducing issues of wrong units, wrong materials, wrong scoring locations, etc. “Repeatable” means not just getting the same result from one simulation to another, but being able to easily restore a previously used setup and reducing sources of error when a setup is passed from one user to another. TOPAS control system incorporates key lessons from safety management, proactively removing possible sources of user error such as line-ordering mistakes In control files. TOPAS has been used to model proton therapy treatment examples including the UCSF eye treatment head, the MGH stereotactic alignment in radiosurgery treatment head and the MGH gantry

GPUs, a New Tool of Acceleration in CFD: Efficiency and Reliability on Smoothed Particle Hydrodynamics Methods

PubMed Central

Crespo, Alejandro C.; Dominguez, Jose M.; Barreiro, Anxo; Gómez-Gesteira, Moncho; Rogers, Benedict D.

2011-01-01

Smoothed Particle Hydrodynamics (SPH) is a numerical method commonly used in Computational Fluid Dynamics (CFD) to simulate complex free-surface flows. Simulations with this mesh-free particle method far exceed the capacity of a single processor. In this paper, as part of a dual-functioning code for either central processing units (CPUs) or Graphics Processor Units (GPUs), a parallelisation using GPUs is presented. The GPU parallelisation technique uses the Compute Unified Device Architecture (CUDA) of nVidia devices. Simulations with more than one million particles on a single GPU card exhibit speedups of up to two orders of magnitude over using a single-core CPU. It is demonstrated that the code achieves different speedups with different CUDA-enabled GPUs. The numerical behaviour of the SPH code is validated with a standard benchmark test case of dam break flow impacting on an obstacle where good agreement with the experimental results is observed. Both the achieved speed-ups and the quantitative agreement with experiments suggest that CUDA-based GPU programming can be used in SPH methods with efficiency and reliability. PMID:21695185

The Deceptively Simple N170 Reflects Network Information Processing Mechanisms Involving Visual Feature Coding and Transfer Across Hemispheres.

PubMed

Ince, Robin A A; Jaworska, Katarzyna; Gross, Joachim; Panzeri, Stefano; van Rijsbergen, Nicola J; Rousselet, Guillaume A; Schyns, Philippe G

2016-08-22

A key to understanding visual cognition is to determine "where", "when", and "how" brain responses reflect the processing of the specific visual features that modulate categorization behavior-the "what". The N170 is the earliest Event-Related Potential (ERP) that preferentially responds to faces. Here, we demonstrate that a paradigmatic shift is necessary to interpret the N170 as the product of an information processing network that dynamically codes and transfers face features across hemispheres, rather than as a local stimulus-driven event. Reverse-correlation methods coupled with information-theoretic analyses revealed that visibility of the eyes influences face detection behavior. The N170 initially reflects coding of the behaviorally relevant eye contralateral to the sensor, followed by a causal communication of the other eye from the other hemisphere. These findings demonstrate that the deceptively simple N170 ERP hides a complex network information processing mechanism involving initial coding and subsequent cross-hemispheric transfer of visual features. © The Author 2016. Published by Oxford University Press.

The Deceptively Simple N170 Reflects Network Information Processing Mechanisms Involving Visual Feature Coding and Transfer Across Hemispheres

PubMed Central

Ince, Robin A. A.; Jaworska, Katarzyna; Gross, Joachim; Panzeri, Stefano; van Rijsbergen, Nicola J.; Rousselet, Guillaume A.; Schyns, Philippe G.

2016-01-01

A key to understanding visual cognition is to determine “where”, “when”, and “how” brain responses reflect the processing of the specific visual features that modulate categorization behavior—the “what”. The N170 is the earliest Event-Related Potential (ERP) that preferentially responds to faces. Here, we demonstrate that a paradigmatic shift is necessary to interpret the N170 as the product of an information processing network that dynamically codes and transfers face features across hemispheres, rather than as a local stimulus-driven event. Reverse-correlation methods coupled with information-theoretic analyses revealed that visibility of the eyes influences face detection behavior. The N170 initially reflects coding of the behaviorally relevant eye contralateral to the sensor, followed by a causal communication of the other eye from the other hemisphere. These findings demonstrate that the deceptively simple N170 ERP hides a complex network information processing mechanism involving initial coding and subsequent cross-hemispheric transfer of visual features. PMID:27550865

Porting plasma physics simulation codes to modern computing architectures using the libmrc framework

NASA Astrophysics Data System (ADS)

Germaschewski, Kai; Abbott, Stephen

2015-11-01

Available computing power has continued to grow exponentially even after single-core performance satured in the last decade. The increase has since been driven by more parallelism, both using more cores and having more parallelism in each core, e.g. in GPUs and Intel Xeon Phi. Adapting existing plasma physics codes is challenging, in particular as there is no single programming model that covers current and future architectures. We will introduce the open-source libmrc framework that has been used to modularize and port three plasma physics codes: The extended MHD code MRCv3 with implicit time integration and curvilinear grids; the OpenGGCM global magnetosphere model; and the particle-in-cell code PSC. libmrc consolidates basic functionality needed for simulations based on structured grids (I/O, load balancing, time integrators), and also introduces a parallel object model that makes it possible to maintain multiple implementations of computational kernels, on e.g. conventional processors and GPUs. It handles data layout conversions and enables us to port performance-critical parts of a code to a new architecture step-by-step, while the rest of the code can remain unchanged. We will show examples of the performance gains and some physics applications.

Studies of Planet Formation using a Hybrid N-body + Planetesimal Code

NASA Technical Reports Server (NTRS)

Kenyon, Scott J.; Bromley, Benjamin C.; Salamon, Michael (Technical Monitor)

2005-01-01

The goal of our proposal was to use a hybrid multi-annulus planetesimal/n-body code to examine the planetesimal theory, one of the two main theories of planet formation. We developed this code to follow the evolution of numerous 1 m to 1 km planetesimals as they collide, merge, and grow into full-fledged planets. Our goal was to apply the code to several well-posed, topical problems in planet formation and to derive observational consequences of the models. We planned to construct detailed models to address two fundamental issues: 1) icy planets - models for icy planet formation will demonstrate how the physical properties of debris disks, including the Kuiper Belt in our solar system, depend on initial conditions and input physics; and 2) terrestrial planets - calculations following the evolution of 1-10 km planetesimals into Earth-mass planets and rings of dust will provide a better understanding of how terrestrial planets form and interact with their environment. During the past year, we made progress on each issue. Papers published in 2004 are summarized. Summaries of work to be completed during the first half of 2005 and work planned for the second half of 2005 are included.

Implementing displacement damage calculations for electrons and gamma rays in the Particle and Heavy-Ion Transport code System

NASA Astrophysics Data System (ADS)

Iwamoto, Yosuke

2018-03-01

In this study, the Monte Carlo displacement damage calculation method in the Particle and Heavy-Ion Transport code System (PHITS) was improved to calculate displacements per atom (DPA) values due to irradiation by electrons (or positrons) and gamma rays. For the damage due to electrons and gamma rays, PHITS simulates electromagnetic cascades using the Electron Gamma Shower version 5 (EGS5) algorithm and calculates DPA values using the recoil energies and the McKinley-Feshbach cross section. A comparison of DPA values calculated by PHITS and the Monte Carlo assisted Classical Method (MCCM) reveals that they were in good agreement for gamma-ray irradiations of silicon and iron at energies that were less than 10 MeV. Above 10 MeV, PHITS can calculate DPA values not only for electrons but also for charged particles produced by photonuclear reactions. In DPA depth distributions under electron and gamma-ray irradiations, build-up effects can be observed near the target's surface. For irradiation of 90-cm-thick carbon by protons with energies of more than 30 GeV, the ratio of the secondary electron DPA values to the total DPA values is more than 10% and increases with an increase in incident energy. In summary, PHITS can calculate DPA values for all particles and materials over a wide energy range between 1 keV and 1 TeV for electrons, gamma rays, and charged particles and between 10-5 eV and 1 TeV for neutrons.

Extended Thomas-Fermi density functional for the unitary Fermi gas

NASA Astrophysics Data System (ADS)

Salasnich, Luca; Toigo, Flavio

2008-11-01

We determine the energy density ξ(3/5)nɛF and the gradient correction λℏ2(∇n)2/(8mn) of the extended Thomas-Fermi (ETF) density functional, where n is the number density and ɛF is the Fermi energy, for a trapped two-component Fermi gas with infinite scattering length (unitary Fermi gas) on the basis of recent diffusion Monte Carlo (DMC) calculations [Phys. Rev. Lett. 99, 233201 (2007)]. In particular we find that ξ=0.455 and λ=0.13 give the best fit of the DMC data with an even number N of particles. We also study the odd-even splitting γN1/9ℏω of the ground-state energy for the unitary gas in a harmonic trap of frequency ω determining the constant γ . Finally we investigate the effect of the gradient term in the time-dependent ETF model by introducing generalized Galilei-invariant hydrodynamics equations.

The FLUKA code for space applications: recent developments

NASA Technical Reports Server (NTRS)

Andersen, V.; Ballarini, F.; Battistoni, G.; Campanella, M.; Carboni, M.; Cerutti, F.; Empl, A.; Fasso, A.; Ferrari, A.; Gadioli, E.;

Particle size reduction of Si3N4 with Si3N4 milling hardware

NASA Technical Reports Server (NTRS)

Herbell, T. P.; Freedman, M. R.; Kiser, J. D.

1986-01-01

The grinding of Si3N4 powder using reaction bonded Si3N4 attrition, vibratory, and ball mills with Si3N4 media was examined. The rate of particle size reduction and the change in the chemical composition of the powder were determined in order to compare the grinding efficiency and the increase in impurity content resulting from mill and media wear for each technique. Attrition and vibratory milling exhibited rates of specific surface area increase that were approximately eight times that observed in ball milling. Vibratory milling introduced the greatest impurity pickup.

Arene-Inserted Extended Germa[n]pericyclynes: Synthesis, Structure, and Phosphorescence Properties.

PubMed

Tanimoto, Hiroki; Mori, Junta; Ito, Shunichiro; Nishiyama, Yasuhiro; Morimoto, Tsumoru; Tanaka, Kazuo; Chujo, Yoshiki; Kakiuchi, Kiyomi

2017-07-26

This report describes the synthesis and characterization of arene-inserted extended (ArEx) germa[n]pericyclynes composed of germanium and 1,4-diethynylbenzene units. These novel cyclic germanium-π unit materials were synthesized with diethynylbenzene and germanium dichloride. X-ray crystallographic analysis revealed their structures, and the planar conformation of ArEx germa[4]pericyclyne along with the regular aromatic rings. UV/Vis absorption spectra and fluorescence emission spectra showed considerably unique and highly improved character compared to previously reported germa[n]pericyclynes. Even in the absence of transition metal components, phosphorescence emissions were observed, and the emission lifetimes were dramatically improved. ArEx germa[n]pericyclynes showed high photoluminescence quantum yields, whereas low photoluminescence quantum yields were observed for acyclic compounds. Density functional theory calculations show delocalized orbitals between skipped alkyne units through a germanium tether, and an increase in the HOMO energy level, leading to a small HOMO-LUMO energy gap. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multitasking the three-dimensional transport code TORT on CRAY platforms

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

Azmy, Y.Y.; Barnett, D.A.; Burre, C.A.

1996-04-01

The multitasking options in the three-dimensional neutral particle transport code TORT originally implemented for Cray`s CTSS operating system are revived and extended to run on Cray Y/MP and C90 computers using the UNICOS operating system. These include two coarse-grained domain decompositions; across octants, and across directions within an octant, termed Octant Parallel (OP), and Direction Parallel (DP), respectively. Parallel performance of the DP is significantly enhanced by increasing the task grain size and reducing load imbalance via dynamic scheduling of the discrete angles among the participating tasks. Substantial Wall Clock speedup factors, approaching 4.5 using 8 tasks, have been measuredmore » in a time-sharing environment, and generally depend on the test problem specifications, number of tasks, and machine loading during execution.« less

The Magnetic Reconnection Code: an AMR-based fully implicit simulation suite

NASA Astrophysics Data System (ADS)

Germaschewski, K.; Bhattacharjee, A.; Ng, C.-S.

2006-12-01

Extended MHD models, which incorporate two-fluid effects, are promising candidates to enhance understanding of collisionless reconnection phenomena in laboratory, space and astrophysical plasma physics. In this paper, we introduce two simulation codes in the Magnetic Reconnection Code suite which integrate reduced and full extended MHD models. Numerical integration of these models comes with two challenges: Small-scale spatial structures, e.g. thin current sheets, develop and must be well resolved by the code. Adaptive mesh refinement (AMR) is employed to provide high resolution where needed while maintaining good performance. Secondly, the two-fluid effects in extended MHD give rise to dispersive waves, which lead to a very stringent CFL condition for explicit codes, while reconnection happens on a much slower time scale. We use a fully implicit Crank--Nicholson time stepping algorithm. Since no efficient preconditioners are available for our system of equations, we instead use a direct solver to handle the inner linear solves. This requires us to actually compute the Jacobian matrix, which is handled by a code generator that calculates the derivative symbolically and then outputs code to calculate it.

Evaluation of the accuracy of mono-energetic electron and beta-emitting isotope dose-point kernels using particle and heavy ion transport code system: PHITS.

PubMed

Shiiba, Takuro; Kuga, Naoya; Kuroiwa, Yasuyoshi; Sato, Tatsuhiko

2017-10-01

We assessed the accuracy of mono-energetic electron and beta-emitting isotope dose-point kernels (DPKs) calculated using the particle and heavy ion transport code system (PHITS) for patient-specific dosimetry in targeted radionuclide treatment (TRT) and compared our data with published data. All mono-energetic and beta-emitting isotope DPKs calculated using PHITS, both in water and compact bone, were in good agreement with those in literature using other MC codes. PHITS provided reliable mono-energetic electron and beta-emitting isotope scaled DPKs for patient-specific dosimetry. Copyright © 2017 Elsevier Ltd. All rights reserved.

Computed secondary-particle energy spectra following nonelastic neutron interactions with C-12 for E(n) between 15 and 60 MeV: Comparisons of results from two calculational methods

NASA Astrophysics Data System (ADS)

Dickens, J. K.

1991-04-01

The organic scintillation detector response code SCINFUL has been used to compute secondary-particle energy spectra, d(sigma)/dE, following nonelastic neutron interactions with C-12 for incident neutron energies between 15 and 60 MeV. The resulting spectra are compared with published similar spectra computed by Brenner and Prael who used an intranuclear cascade code, including alpha clustering, a particle pickup mechanism, and a theoretical approach to sequential decay via intermediate particle-unstable states. The similarities of and the differences between the results of the two approaches are discussed.

Low Density Parity Check Codes: Bandwidth Efficient Channel Coding

NASA Technical Reports Server (NTRS)

Fong, Wai; Lin, Shu; Maki, Gary; Yeh, Pen-Shu

2003-01-01

Low Density Parity Check (LDPC) Codes provide near-Shannon Capacity performance for NASA Missions. These codes have high coding rates R=0.82 and 0.875 with moderate code lengths, n=4096 and 8176. Their decoders have inherently parallel structures which allows for high-speed implementation. Two codes based on Euclidean Geometry (EG) were selected for flight ASIC implementation. These codes are cyclic and quasi-cyclic in nature and therefore have a simple encoder structure. This results in power and size benefits. These codes also have a large minimum distance as much as d,,, = 65 giving them powerful error correcting capabilities and error floors less than lo- BER. This paper will present development of the LDPC flight encoder and decoder, its applications and status.

Sonocatalytic degradation of humic acid by N-doped TiO2 nano-particle in aqueous solution.

PubMed

Kamani, Hossein; Nasseri, Simin; Khoobi, Mehdi; Nabizadeh Nodehi, Ramin; Mahvi, Amir Hossein

2016-01-01

Un-doped and N-doped TiO2 nano-particles with different nitrogen contents were successfully synthesized by a simple sol-gel method, and were characterized by X-ray diffraction, field emission scanning electron microscopy, Energy dispersive X-ray analysis and UV-visible diffuse reflectance spectra techniques. Then enhancement of sonocatalytic degradation of humic acid by un-doped and N-doped TiO2 nano-particles in aqueous environment was investigated. The effects of various parameters such as initial concentration of humic acid, N-doping, and the degradation kinetics were investigated. The results of characterization techniques affirmed that the synthesis of un-doped and N-doped TiO2 nano-particles was successful. Degradation of humic acid by using different nano-particles obeyed the first-order kinetic. Among various nano-particles, N-doped TiO2 with molar doping ratio of 6 % and band gap of 2.92 eV, exhibited the highest sonocatalytic degradation with an apparent-first-order rate constant of 1.56 × 10(-2) min(-1). The high degradation rate was associated with the lower band gap energy and well-formed anatase phase. The addition of nano-catalysts could enhance the degradation efficiency of humic acid as well as N-doped TiO2 with a molar ratio of 6 %N/Ti was found the best nano-catalyst among the investigated catalysts. The sonocatalytic degradation with nitrogen doped semiconductors could be a suitable oxidation process for removal of refractory pollutants such as humic acid from aqueous solution.

Metabolically Generated Stable Isotope-Labeled Deoxynucleoside Code for Tracing DNA N6-Methyladenine in Human Cells.

PubMed

Liu, Baodong; Liu, Xiaoling; Lai, Weiyi; Wang, Hailin

2017-06-06

DNA N 6 -methyl-2'-deoxyadenosine (6mdA) is an epigenetic modification in both eukaryotes and bacteria. Here we exploited stable isotope-labeled deoxynucleoside [ 15 N 5 ]-2'-deoxyadenosine ([ 15 N 5 ]-dA) as an initiation tracer and for the first time developed a metabolically differential tracing code for monitoring DNA 6mdA in human cells. We demonstrate that the initiation tracer [ 15 N 5 ]-dA undergoes a specific and efficient adenine deamination reaction leading to the loss the exocyclic amine 15 N, and further utilizes the purine salvage pathway to generate mainly both [ 15 N 4 ]-dA and [ 15 N 4 ]-2'-deoxyguanosine ([ 15 N 4 ]-dG) in mammalian genomes. However, [ 15 N 5 ]-dA is largely retained in the genomes of mycoplasmas, which are often found in cultured cells and experimental animals. Consequently, the methylation of dA generates 6mdA with a consistent coding pattern, with a predominance of [ 15 N 4 ]-6mdA. Therefore, mammalian DNA 6mdA can be potentially discriminated from that generated by infecting mycoplasmas. Collectively, we show a promising approach for identification of authentic DNA 6mdA in human cells and determine if the human cells are contaminated with mycoplasmas.

Wave-particle energy exchange directly observed in a kinetic Alfvén-branch wave

PubMed Central

Gershman, Daniel J.; F-Viñas, Adolfo; Dorelli, John C.; Boardsen, Scott A.; Avanov, Levon A.; Bellan, Paul M.; Schwartz, Steven J.; Lavraud, Benoit; Coffey, Victoria N.; Chandler, Michael O.; Saito, Yoshifumi; Paterson, William R.; Fuselier, Stephen A.; Ergun, Robert E.; Strangeway, Robert J.; Russell, Christopher T.; Giles, Barbara L.; Pollock, Craig J.; Torbert, Roy B.; Burch, James L.

2017-01-01

Alfvén waves are fundamental plasma wave modes that permeate the universe. At small kinetic scales, they provide a critical mechanism for the transfer of energy between electromagnetic fields and charged particles. These waves are important not only in planetary magnetospheres, heliospheres and astrophysical systems but also in laboratory plasma experiments and fusion reactors. Through measurement of charged particles and electromagnetic fields with NASA's Magnetospheric Multiscale (MMS) mission, we utilize Earth's magnetosphere as a plasma physics laboratory. Here we confirm the conservative energy exchange between the electromagnetic field fluctuations and the charged particles that comprise an undamped kinetic Alfvén wave. Electrons confined between adjacent wave peaks may have contributed to saturation of damping effects via nonlinear particle trapping. The investigation of these detailed wave dynamics has been unexplored territory in experimental plasma physics and is only recently enabled by high-resolution MMS observations. PMID:28361881

Wave-particle energy exchange directly observed in a kinetic Alfvén-branch wave.

PubMed

Gershman, Daniel J; F-Viñas, Adolfo; Dorelli, John C; Boardsen, Scott A; Avanov, Levon A; Bellan, Paul M; Schwartz, Steven J; Lavraud, Benoit; Coffey, Victoria N; Chandler, Michael O; Saito, Yoshifumi; Paterson, William R; Fuselier, Stephen A; Ergun, Robert E; Strangeway, Robert J; Russell, Christopher T; Giles, Barbara L; Pollock, Craig J; Torbert, Roy B; Burch, James L

2017-03-31

Alfvén waves are fundamental plasma wave modes that permeate the universe. At small kinetic scales, they provide a critical mechanism for the transfer of energy between electromagnetic fields and charged particles. These waves are important not only in planetary magnetospheres, heliospheres and astrophysical systems but also in laboratory plasma experiments and fusion reactors. Through measurement of charged particles and electromagnetic fields with NASA's Magnetospheric Multiscale (MMS) mission, we utilize Earth's magnetosphere as a plasma physics laboratory. Here we confirm the conservative energy exchange between the electromagnetic field fluctuations and the charged particles that comprise an undamped kinetic Alfvén wave. Electrons confined between adjacent wave peaks may have contributed to saturation of damping effects via nonlinear particle trapping. The investigation of these detailed wave dynamics has been unexplored territory in experimental plasma physics and is only recently enabled by high-resolution MMS observations.

Microgels for long-term storage of vitamins for extended spaceflight

NASA Astrophysics Data System (ADS)

Schroeder, R.

2018-02-01

Biocompatible materials that can encapsulate large amounts of nutrients while protecting them from degrading environmental influences are highly desired for extended manned spaceflight. In this study, alkaline-degradable microgels based on poly(N-vinylcaprolactam) (PVCL) were prepared and analysed with their regard to stabilise retinol which acts as a model vitamin (vitamin A1). It was investigated whether the secondary crosslinking of the particles with a polyphenol can prevent the isomerisation of biologically active all-trans retinol to biologically inactive cis-trans retinol. Both loading with retinol and secondary crosslinking of the particles was performed at room temperature to prevent an early degradation of the vitamin. This study showed that PVCL microgels drastically improve the water solubility of hydrophobic retinol. Additionally, it is demonstrated that the highly crosslinked microgel particles in aqueous solution can be utilised to greatly retard the light- and temperature-induced isomerisation process of retinol by a factor of almost 100 compared to pure retinol stored in ethanol. The use of microgels offers various advantages over other drug delivery systems as they exhibit enhanced biocompatibility and superior aqueous solubility.

Extended hierarchical solvent perturbations from curved surfaces of mesoporous silica particles in a deep eutectic solvent.

PubMed

Hammons, Joshua A; Zhang, Fan; Ilavsky, Jan

2018-06-15

Many applications of deep eutectic solvents (DES) rely on exploitation of their unique yet complex liquid structures. Due to the ionic nature of the DES components, their diffuse structures are perturbed in the presence of a charged surface. We hypothesize that it is possible to perturb the bulk DES structure far (>100 nm) from a curved, charged surface with mesoscopic dimensions. We performed in situ, synchrotron-based ultra-small angle X-ray scattering (USAXS) experiments to study the solvent distribution near the surface of charged mesoporous silica particles (MPS) (≈0.5 µm in diameter) suspended in both water and a common type of DES (1:2 choline Cl-:ethylene glycol). A careful USAXS analysis reveals that the perturbation of electron density distribution within the DES extends ≈1 μm beyond the particle surface, and that this perturbation can be manipulated by the addition of salt ions (AgCl). The concentration of the pore-filling fluid is greatly reduced in the DES. Notably, we extracted the real-space structures of these fluctuations from the USAXS data using a simulated annealing approach that does not require a priori knowledge about the scattering form factor, and can be generalized to a wide range of complex small-angle scattering problems. Copyright © 2018 Elsevier Inc. All rights reserved.

Defect annealing of alpha-particle irradiated n-GaAs

NASA Astrophysics Data System (ADS)

Goodman, S. A.; Auret, F. D.; Myburg, G.

1994-09-01

The annealing behaviour of irradiation induced defects in n-type GaAs irradiated at 300 K with 5.4 MeV alpha-particles from an americium-241 (Am-241) radio nuclide have been investigated. The annealing kinetics are presented for the alpha-particle induced defects Eα1 Eα5 detected in Organo-Metallic Vapor Phase Epitaxially (OMVPE) grown n-GaAs doped with silicon to 1.2×1016 cm-3, these kinetics are compared to those obtained for similar defects (E1 E5) detected after electron irradiation. While defects Pα1 and Pα2 were detected after removal of the electron defects Eα4 and Eα5, respectively, a new defect labelled Pα0, located 0.152 eV below the conduction band, was introduced by annealing. The thermal behaviour and trap characteristics of these three defects (Pα0 Pα2) are presented. In an attempt to further characterise defects Pα0 and Pα1 a preiliminary study investigating the emission rate field dependence of these defects was conducted, it was observed that defect Pα0 exhibited a fairly strong field dependence while Pα1 exhibited a much weaker dependence.

Analysis of Alfvén eigenmode destabilization by energetic particles in Large Helical Device using a Landau-closure model

DOE PAGES

Varela, Jacobo Rodriguez; Spong, D. A.; Garcia, L.

2017-03-06

Here, energetic particle populations in nuclear fusion experiments can destabilize the Alfvén Eigenmodes through inverse Landau damping and couplings with gap modes in the shear Alfvén continua. We use the reduced MHD equations to describe the linear evolution of the poloidal flux and the toroidal component of the vorticity in a full 3D system, coupled with equations of density and parallel velocity moments for the energetic particles. We add the Landau damping and resonant destabilization effects using a closure relation. We apply the model to study the Alfvén mode stability in the inward-shifted configurations of the Large Helical Device (LHD), performing a parametric analysis of the energetic particle β (more » $${{\\beta}_{f}}$$ ) in a range of realistic values, the ratios of the energetic particle thermal/Alfvén velocities ($${{V}_{\\text{th}}}/{{V}_{A0}}$$ ), the magnetic Lundquist numbers (S) and the toroidal modes (n). The n = 1 and n = 2 TAEs are destabilized, although the n = 3 and n = 4 TAEs are weakly perturbed. The most unstable configurations are associated with the density gradients of energetic particles in the plasma core: the TAEs are destabilized, even for small energetic particle populations, if their thermal velocity is lower than 0.4 times the Alfvén velocity. The frequency range of MHD bursts measured in the LHD are 50–70 kHz for the n = 1 and 60–80 kHz for the n = 2 TAE, which is consistent with the model predictions.« less

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Monte Carlo Particle Lists: MCPL

NASA Astrophysics Data System (ADS)

Kittelmann, T.; Klinkby, E.; Knudsen, E. B.; Willendrup, P.; Cai, X. X.; Kanaki, K.

2017-09-01

A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community, along with converters and plugins for several popular simulation packages.

Monitoring Cosmic Radiation Risk: Comparisons between Observations and Predictive Codes for Naval Aviation

DTIC Science & Technology

2009-01-01

proton PARMA PHITS -based Analytical Radiation Model in the Atmosphere PCAIRE Predictive Code for Aircrew Radiation Exposure PHITS Particle and...radiation transport code utilized is called PARMA ( PHITS based Analytical Radiation Model in the Atmosphere) [36]. The particle fluxes calculated from the...same dose equivalent coefficient regulations from the ICRP-60 regulations. As a result, the transport codes utilized by EXPACS ( PHITS ) and CARI-6

Monitoring Cosmic Radiation Risk: Comparisons Between Observations and Predictive Codes for Naval Aviation

DTIC Science & Technology

2009-07-05

proton PARMA PHITS -based Analytical Radiation Model in the Atmosphere PCAIRE Predictive Code for Aircrew Radiation Exposure PHITS Particle and Heavy...transport code utilized is called PARMA ( PHITS based Analytical Radiation Model in the Atmosphere) [36]. The particle fluxes calculated from the input...dose equivalent coefficient regulations from the ICRP-60 regulations. As a result, the transport codes utilized by EXPACS ( PHITS ) and CARI-6 (PARMA

Extended Policies case

EIA Publications

2016-01-01

The Annual Energy Outlook 2016 (AEO2016) Extended Policies case includes selected policies that go beyond current laws and regulations. Existing tax credits that have scheduled reductions and sunset dates are assumed to remain unchanged through 2040. Other efficiency policies, including corporate average fuel economy standards, appliance standards, and building codes, are expanded beyond current provisions; and the U.S. Environmental Protection Agency (EPA) Clean Power Plan (CPP) regulations that reduce carbon dioxide emissions from electric power generation are tightened after 2030.

Development of high performance particle in cell code for the exascale age

NASA Astrophysics Data System (ADS)

Lapenta, Giovanni; Amaya, Jorge; Gonzalez, Diego; Deep-Est H2020 Consortium Collaboration

2017-10-01

Magnetized plasmas are most effectively described by magneto-hydrodynamics, MHD, a fluid theory based on describing some fields defined in space: electromagnetic fields, density, velocity and temperature of the plasma. However, microphysics processes need kinetic theory, where statistical distributions of particles are governed by the Boltzmann equation. While fluid models are based on the ordinary space and time, kinetic models require a six dimensional space, called phase space, besides time. The two methods are not separated but rather interact to determine the system evolution. Arriving at a single self-consistent model is the goal of our research. We present a new approach developed with the goal of extending the reach of kinetic models to the fluid scales. Kinetic models are a higher order description and all fluid effects are included in them. However, the cost in terms of computing power is much higher and it has been so far prohibitively expensive to treat space weather events fully kinetically. We have now designed a new method capable of reducing that cost by several orders of magnitude making it possible for kinetic models to study macroscopic systems. H2020 Deep-EST consortium (European Commission).

Studies of particle wake potentials in plasmas

NASA Astrophysics Data System (ADS)

Ellis, Ian N.; Graziani, Frank R.; Glosli, James N.; Strozzi, David J.; Surh, Michael P.; Richards, David F.; Decyk, Viktor K.; Mori, Warren B.

2011-09-01

A detailed understanding of electron stopping and scattering in plasmas with variable values for the number of particles within a Debye sphere is still not at hand. Presently, there is some disagreement in the literature concerning the proper description of these processes. Theoretical models assume electrostatic (Coulomb force) interactions between particles and neglect magnetic effects. Developing and validating proper descriptions requires studying the processes using first-principle plasma simulations. We are using the particle-particle particle-mesh (PPPM) code ddcMD and the particle-in-cell (PIC) code BEPS to perform these simulations. As a starting point in our study, we examine the wake of a particle passing through a plasma in 3D electrostatic simulations performed with ddcMD and BEPS. In this paper, we compare the wakes observed in these simulations with each other and predictions from collisionless kinetic theory. The relevance of the work to Fast Ignition is discussed.

Code Development in Coupled PARCS/RELAP5 for Supercritical Water Reactor

DOE PAGES

Hu, Po; Wilson, Paul

2014-01-01

The new capability is added to the existing coupled code package PARCS/RELAP5, in order to analyze SCWR design under supercritical pressure with the separated water coolant and moderator channels. This expansion is carried out on both codes. In PARCS, modification is focused on extending the water property tables to supercritical pressure, modifying the variable mapping input file and related code module for processing thermal-hydraulic information from separated coolant/moderator channels, and modifying neutronics feedback module to deal with the separated coolant/moderator channels. In RELAP5, modification is focused on incorporating more accurate water properties near SCWR operation/transient pressure and temperature in themore » code. Confirming tests of the modifications is presented and the major analyzing results from the extended codes package are summarized.« less

Importance biasing scheme implemented in the PRIZMA code

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

Kandiev, I.Z.; Malyshkin, G.N.

1997-12-31

PRIZMA code is intended for Monte Carlo calculations of linear radiation transport problems. The code has wide capabilities to describe geometry, sources, material composition, and to obtain parameters specified by user. There is a capability to calculate path of particle cascade (including neutrons, photons, electrons, positrons and heavy charged particles) taking into account possible transmutations. Importance biasing scheme was implemented to solve the problems which require calculation of functionals related to small probabilities (for example, problems of protection against radiation, problems of detection, etc.). The scheme enables to adapt trajectory building algorithm to problem peculiarities.

Wave-particle energy exchange directly observed in a kinetic Alfvén-branch wave

DOE PAGES

Gershman, Daniel J.; F-Viñas, Adolfo; Dorelli, John C.; ...

2017-03-31

Alfvén waves are fundamental plasma wave modes that permeate the universe. At small kinetic scales, they provide a critical mechanism for the transfer of energy between electromagnetic fields and charged particles. These waves are important not only in planetary magnetospheres, heliospheres and astrophysical systems but also in laboratory plasma experiments and fusion reactors. Through measurement of charged particles and electromagnetic fields with NASA’s Magnetospheric Multiscale (MMS) mission, we utilize Earth’s magnetosphere as a plasma physics laboratory. Here we confirm the conservative energy exchange between the electromagnetic field fluctuations and the charged particles that comprise an undamped kinetic Alfvén wave. Electronsmore » confined between adjacent wave peaks may have contributed to saturation of damping effects via nonlinear particle trapping. As a result, the investigation of these detailed wave dynamics has been unexplored territory in experimental plasma physics and is only recently enabled by high-resolution MMS observations.« less

Wave-particle energy exchange directly observed in a kinetic Alfvén-branch wave

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

Gershman, Daniel J.; F-Viñas, Adolfo; Dorelli, John C.

Alfvén waves are fundamental plasma wave modes that permeate the universe. At small kinetic scales, they provide a critical mechanism for the transfer of energy between electromagnetic fields and charged particles. These waves are important not only in planetary magnetospheres, heliospheres and astrophysical systems but also in laboratory plasma experiments and fusion reactors. Through measurement of charged particles and electromagnetic fields with NASA’s Magnetospheric Multiscale (MMS) mission, we utilize Earth’s magnetosphere as a plasma physics laboratory. Here we confirm the conservative energy exchange between the electromagnetic field fluctuations and the charged particles that comprise an undamped kinetic Alfvén wave. Electronsmore » confined between adjacent wave peaks may have contributed to saturation of damping effects via nonlinear particle trapping. As a result, the investigation of these detailed wave dynamics has been unexplored territory in experimental plasma physics and is only recently enabled by high-resolution MMS observations.« less

Radiation Protection Studies for Medical Particle Accelerators using Fluka Monte Carlo Code.

PubMed

Infantino, Angelo; Cicoria, Gianfranco; Lucconi, Giulia; Pancaldi, Davide; Vichi, Sara; Zagni, Federico; Mostacci, Domiziano; Marengo, Mario

2017-04-01

Radiation protection (RP) in the use of medical cyclotrons involves many aspects both in the routine use and for the decommissioning of a site. Guidelines for site planning and installation, as well as for RP assessment, are given in international documents; however, the latter typically offer analytic methods of calculation of shielding and materials activation, in approximate or idealised geometry set-ups. The availability of Monte Carlo (MC) codes with accurate up-to-date libraries for transport and interaction of neutrons and charged particles at energies below 250 MeV, together with the continuously increasing power of modern computers, makes the systematic use of simulations with realistic geometries possible, yielding equipment and site-specific evaluation of the source terms, shielding requirements and all quantities relevant to RP at the same time. In this work, the well-known FLUKA MC code was used to simulate different aspects of RP in the use of biomedical accelerators, particularly for the production of medical radioisotopes. In the context of the Young Professionals Award, held at the IRPA 14 conference, only a part of the complete work is presented. In particular, the simulation of the GE PETtrace cyclotron (16.5 MeV) installed at S. Orsola-Malpighi University Hospital evaluated the effective dose distribution around the equipment; the effective number of neutrons produced per incident proton and their spectral distribution; the activation of the structure of the cyclotron and the vault walls; the activation of the ambient air, in particular the production of 41Ar. The simulations were validated, in terms of physical and transport parameters to be used at the energy range of interest, through an extensive measurement campaign of the neutron environmental dose equivalent using a rem-counter and TLD dosemeters. The validated model was then used in the design and the licensing request of a new Positron Emission Tomography facility. © The Author 2016

PDT - PARTICLE DISPLACEMENT TRACKING SOFTWARE

NASA Technical Reports Server (NTRS)

Wernet, M. P.

1994-01-01

Particle Imaging Velocimetry (PIV) is a quantitative velocity measurement technique for measuring instantaneous planar cross sections of a flow field. The technique offers very high precision (1%) directionally resolved velocity vector estimates, but its use has been limited by high equipment costs and complexity of operation. Particle Displacement Tracking (PDT) is an all-electronic PIV data acquisition and reduction procedure which is simple, fast, and easily implemented. The procedure uses a low power, continuous wave laser and a Charged Coupled Device (CCD) camera to electronically record the particle images. A frame grabber board in a PC is used for data acquisition and reduction processing. PDT eliminates the need for photographic processing, system costs are moderately low, and reduced data are available within seconds of acquisition. The technique results in velocity estimate accuracies on the order of 5%. The software is fully menu-driven from the acquisition to the reduction and analysis of the data. Options are available to acquire a single image or 5- or 25-field series of images separated in time by multiples of 1/60 second. The user may process each image, specifying its boundaries to remove unwanted glare from the periphery and adjusting its background level to clearly resolve the particle images. Data reduction routines determine the particle image centroids and create time history files. PDT then identifies the velocity vectors which describe the particle movement in the flow field. Graphical data analysis routines are included which allow the user to graph the time history files and display the velocity vector maps, interpolated velocity vector grids, iso-velocity vector contours, and flow streamlines. The PDT data processing software is written in FORTRAN 77 and the data acquisition routine is written in C-Language for 80386-based IBM PC compatibles running MS-DOS v3.0 or higher. Machine requirements include 4 MB RAM (3 MB Extended), a single or

Extending software repository hosting to code review and testing

NASA Astrophysics Data System (ADS)

Gonzalez Alvarez, A.; Aparicio Cotarelo, B.; Lossent, A.; Andersen, T.; Trzcinska, A.; Asbury, D.; Hłimyr, N.; Meinhard, H.

2015-12-01

We will describe how CERN's services around Issue Tracking and Version Control have evolved, and what the plans for the future are. We will describe the services main design, integration and structure, giving special attention to the new requirements from the community of users in terms of collaboration and integration tools and how we address this challenge when defining new services based on GitLab for collaboration to replace our current Gitolite service and Code Review and Jenkins for Continuous Integration. These new services complement the existing ones to create a new global "development tool stack" where each working group can place its particular development work-flow.

Long distance quantum communication with quantum Reed-Solomon codes

NASA Astrophysics Data System (ADS)

Muralidharan, Sreraman; Zou, Chang-Ling; Li, Linshu; Jiang, Liang; Jianggroup Team

We study the construction of quantum Reed Solomon codes from classical Reed Solomon codes and show that they achieve the capacity of quantum erasure channel for multi-level quantum systems. We extend the application of quantum Reed Solomon codes to long distance quantum communication, investigate the local resource overhead needed for the functioning of one-way quantum repeaters with these codes, and numerically identify the parameter regime where these codes perform better than the known quantum polynomial codes and quantum parity codes . Finally, we discuss the implementation of these codes into time-bin photonic states of qubits and qudits respectively, and optimize the performance for one-way quantum repeaters.

Hybrid-view programming of nuclear fusion simulation code in the PGAS parallel programming language XcalableMP

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

Tsugane, Keisuke; Boku, Taisuke; Murai, Hitoshi

Recently, the Partitioned Global Address Space (PGAS) parallel programming model has emerged as a usable distributed memory programming model. XcalableMP (XMP) is a PGAS parallel programming language that extends base languages such as C and Fortran with directives in OpenMP-like style. XMP supports a global-view model that allows programmers to define global data and to map them to a set of processors, which execute the distributed global data as a single thread. In XMP, the concept of a coarray is also employed for local-view programming. In this study, we port Gyrokinetic Toroidal Code - Princeton (GTC-P), which is a three-dimensionalmore » gyrokinetic PIC code developed at Princeton University to study the microturbulence phenomenon in magnetically confined fusion plasmas, to XMP as an example of hybrid memory model coding with the global-view and local-view programming models. In local-view programming, the coarray notation is simple and intuitive compared with Message Passing Interface (MPI) programming while the performance is comparable to that of the MPI version. Thus, because the global-view programming model is suitable for expressing the data parallelism for a field of grid space data, we implement a hybrid-view version using a global-view programming model to compute the field and a local-view programming model to compute the movement of particles. Finally, the performance is degraded by 20% compared with the original MPI version, but the hybrid-view version facilitates more natural data expression for static grid space data (in the global-view model) and dynamic particle data (in the local-view model), and it also increases the readability of the code for higher productivity.« less

Hybrid-view programming of nuclear fusion simulation code in the PGAS parallel programming language XcalableMP

DOE PAGES

Tsugane, Keisuke; Boku, Taisuke; Murai, Hitoshi; ...

2016-06-01

Recently, the Partitioned Global Address Space (PGAS) parallel programming model has emerged as a usable distributed memory programming model. XcalableMP (XMP) is a PGAS parallel programming language that extends base languages such as C and Fortran with directives in OpenMP-like style. XMP supports a global-view model that allows programmers to define global data and to map them to a set of processors, which execute the distributed global data as a single thread. In XMP, the concept of a coarray is also employed for local-view programming. In this study, we port Gyrokinetic Toroidal Code - Princeton (GTC-P), which is a three-dimensionalmore » gyrokinetic PIC code developed at Princeton University to study the microturbulence phenomenon in magnetically confined fusion plasmas, to XMP as an example of hybrid memory model coding with the global-view and local-view programming models. In local-view programming, the coarray notation is simple and intuitive compared with Message Passing Interface (MPI) programming while the performance is comparable to that of the MPI version. Thus, because the global-view programming model is suitable for expressing the data parallelism for a field of grid space data, we implement a hybrid-view version using a global-view programming model to compute the field and a local-view programming model to compute the movement of particles. Finally, the performance is degraded by 20% compared with the original MPI version, but the hybrid-view version facilitates more natural data expression for static grid space data (in the global-view model) and dynamic particle data (in the local-view model), and it also increases the readability of the code for higher productivity.« less

Load management strategy for Particle-In-Cell simulations in high energy particle acceleration

NASA Astrophysics Data System (ADS)

Beck, A.; Frederiksen, J. T.; Dérouillat, J.

2016-09-01

In the wake of the intense effort made for the experimental CILEX project, numerical simulation campaigns have been carried out in order to finalize the design of the facility and to identify optimal laser and plasma parameters. These simulations bring, of course, important insight into the fundamental physics at play. As a by-product, they also characterize the quality of our theoretical and numerical models. In this paper, we compare the results given by different codes and point out algorithmic limitations both in terms of physical accuracy and computational performances. These limitations are illustrated in the context of electron laser wakefield acceleration (LWFA). The main limitation we identify in state-of-the-art Particle-In-Cell (PIC) codes is computational load imbalance. We propose an innovative algorithm to deal with this specific issue as well as milestones towards a modern, accurate high-performance PIC code for high energy particle acceleration.

Center for Extended Magnetohydrodynamics Modeling - Final Technical Report

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

Parker, Scott

This project funding supported approximately 74 percent of a Ph.D. graduate student, not including costs of travel and supplies. We had a highly successful research project including the development of a second-order implicit electromagnetic kinetic ion hybrid model [Cheng 2013, Sturdevant 2016], direct comparisons with the extended MHD NIMROD code and kinetic simulation [Schnack 2013], modeling of slab tearing modes using the fully kinetic ion hybrid model and finally, modeling global tearing modes in cylindrical geometry using gyrokinetic simulation [Chen 2015, Chen 2016]. We developed an electromagnetic second-order implicit kinetic ion fluid electron hybrid model [Cheng 2013]. As a firstmore » step, we assumed isothermal electrons, but have included drift-kinetic electrons in similar models [Chen 2011]. We used this simulation to study the nonlinear evolution of the tearing mode in slab geometry, including nonlinear evolution and saturation [Cheng 2013]. Later, we compared this model directly to extended MHD calculations using the NIMROD code [Schnack 2013]. In this study, we investigated the ion-temperature-gradient instability with an extended MHD code for the first time and got reasonable agreement with the kinetic calculation in terms of linear frequency, growth rate and mode structure. We then extended this model to include orbit averaging and sub-cycling of the ions and compared directly to gyrokinetic theory [Sturdevant 2016]. This work was highlighted in an Invited Talk at the International Conference on the Numerical Simulation of Plasmas in 2015. The orbit averaging sub-cycling multi-scale algorithm is amenable to hybrid architectures with GPUS or math co-processors. Additionally, our participation in the Center for Extend Magnetohydrodynamics motivated our research on developing the capability for gyrokinetic simulation to model a global tearing mode. We did this in cylindrical geometry where the results could be benchmarked with existing eigenmode

Measurement of the elliptic anisotropy of charged particles produced in PbPb collisions at s N N = 2.76 TeV

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

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.

Tmore » he anisotropy of the azimuthal distributions of charged particles produced in s N N = 2.76 eV PbPb collisions is studied with the CMS experiment at the LHC. he elliptic anisotropy parameter, v 2, defined as the second coefficient in a Fourier expansion of the particle invariant yields, is extracted using the event-plane method, two- and four-particle cumulants, and Lee-Yang zeros. he anisotropy is presented as a function of transverse momentum (p), pseudorapidity (η) over a broad kinematic range, 0.3<20 GeV/c, |η|<2.4, and in 12 classes of collision centrality from 0 to 80%. he results are compared to those obtained at lower center-of-mass energies, and various scaling behaviors are examined. When scaled by the geometric eccentricity of the collision zone, the elliptic anisotropy is found to obey a universal scaling with the transverse particle density for different collision systems and center-of-mass energies.« less

Measurement of the elliptic anisotropy of charged particles produced in PbPb collisions at s N N = 2.76 TeV

DOE PAGES

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; ...

2013-01-07

Tmore » he anisotropy of the azimuthal distributions of charged particles produced in s N N = 2.76 eV PbPb collisions is studied with the CMS experiment at the LHC. he elliptic anisotropy parameter, v 2, defined as the second coefficient in a Fourier expansion of the particle invariant yields, is extracted using the event-plane method, two- and four-particle cumulants, and Lee-Yang zeros. he anisotropy is presented as a function of transverse momentum (p), pseudorapidity (η) over a broad kinematic range, 0.3<20 GeV/c, |η|<2.4, and in 12 classes of collision centrality from 0 to 80%. he results are compared to those obtained at lower center-of-mass energies, and various scaling behaviors are examined. When scaled by the geometric eccentricity of the collision zone, the elliptic anisotropy is found to obey a universal scaling with the transverse particle density for different collision systems and center-of-mass energies.« less

Particle-size reduction of Si3N4 powder with Si3N4 milling hardware

NASA Technical Reports Server (NTRS)

Herbell, T. P.; Freedman, M. R.; Kiser, J. D.

1986-01-01

The grinding of Si3N4 powder using reaction bonded Si3N4 attrition, vibratory, and ball mills with Si3N4 media was examined. The rate of particle size reduction and the change in the chemical composition of the powder were determined in order to compare the grinding efficiency and the increase in impurity content resulting from mill and media wear for each technique. Attrition and vibratory milling exhibited rates of specific surface area increase that were approximately eight times that observed in ball milling. Vibratory milling introduced the greatest impurity pickup.

Sandia Simple Particle Tracking (Sandia SPT) v. 1.0

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

Anthony, Stephen M.

2015-06-15

Sandia SPT is designed as software to accompany a book chapter being published a methods chapter which provides an introduction on how to label and track individual proteins. The Sandia Simple Particle Tracking code uses techniques common to the image processing community, where its value is that it facilitates implementing the methods described in the book chapter by providing the necessary open-source code. The code performs single particle spot detection (or segmentation and localization) followed by tracking (or connecting the detected particles into trajectories). The book chapter, which along with the headers in each file, constitutes the documentation for themore » code is: Anthony, S.M.; Carroll-Portillo, A.; Timlon, J.A., Dynamics and Interactions of Individual Proteins in the Membrane of Living Cells. In Anup K. Singh (Ed.) Single Cell Protein Analysis Methods in Molecular Biology. Springer« less

NRMC - A GPU code for N-Reverse Monte Carlo modeling of fluids in confined media

NASA Astrophysics Data System (ADS)

Sánchez-Gil, Vicente; Noya, Eva G.; Lomba, Enrique

2017-08-01

NRMC is a parallel code for performing N-Reverse Monte Carlo modeling of fluids in confined media [V. Sánchez-Gil, E.G. Noya, E. Lomba, J. Chem. Phys. 140 (2014) 024504]. This method is an extension of the usual Reverse Monte Carlo method to obtain structural models of confined fluids compatible with experimental diffraction patterns, specifically designed to overcome the problem of slow diffusion that can appear under conditions of tight confinement. Most of the computational time in N-Reverse Monte Carlo modeling is spent in the evaluation of the structure factor for each trial configuration, a calculation that can be easily parallelized. Implementation of the structure factor evaluation in NVIDIA® CUDA so that the code can be run on GPUs leads to a speed up of up to two orders of magnitude.

On the numerical dispersion of electromagnetic particle-in-cell code: Finite grid instability

NASA Astrophysics Data System (ADS)

Meyers, M. D.; Huang, C.-K.; Zeng, Y.; Yi, S. A.; Albright, B. J.

2015-09-01

The Particle-In-Cell (PIC) method is widely used in relativistic particle beam and laser plasma modeling. However, the PIC method exhibits numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We review the numerical dispersion relation of the Electromagnetic PIC model. We rigorously derive the faithful 3-D numerical dispersion relation of the PIC model, for a simple, direct current deposition scheme, which does not conserve electric charge exactly. We then specialize to the Yee FDTD scheme. In particular, we clarify the presence of alias modes in an eigenmode analysis of the PIC model, which combines both discrete and continuous variables. The manner in which the PIC model updates and samples the fields and distribution function, together with the temporal and spatial phase factors from solving Maxwell's equations on the Yee grid with the leapfrog scheme, is explicitly accounted for. Numerical solutions to the electrostatic-like modes in the 1-D dispersion relation for a cold drifting plasma are obtained for parameters of interest. In the succeeding analysis, we investigate how the finite grid instability arises from the interaction of the numerical modes admitted in the system and their aliases. The most significant interaction is due critically to the correct representation of the operators in the dispersion relation. We obtain a simple analytic expression for the peak growth rate due to this interaction, which is then verified by simulation. We demonstrate that our analysis is readily extendable to charge conserving models.

On the numerical dispersion of electromagnetic particle-in-cell code: Finite grid instability

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

Meyers, M.D., E-mail: mdmeyers@physics.ucla.edu; Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095; Huang, C.-K., E-mail: huangck@lanl.gov

The Particle-In-Cell (PIC) method is widely used in relativistic particle beam and laser plasma modeling. However, the PIC method exhibits numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We review the numerical dispersion relation of the Electromagnetic PIC model. We rigorously derive the faithful 3-D numerical dispersion relation of the PIC model, for a simple, direct current deposition scheme, which does not conserve electric charge exactly. We then specialize to the Yee FDTDmore » scheme. In particular, we clarify the presence of alias modes in an eigenmode analysis of the PIC model, which combines both discrete and continuous variables. The manner in which the PIC model updates and samples the fields and distribution function, together with the temporal and spatial phase factors from solving Maxwell's equations on the Yee grid with the leapfrog scheme, is explicitly accounted for. Numerical solutions to the electrostatic-like modes in the 1-D dispersion relation for a cold drifting plasma are obtained for parameters of interest. In the succeeding analysis, we investigate how the finite grid instability arises from the interaction of the numerical modes admitted in the system and their aliases. The most significant interaction is due critically to the correct representation of the operators in the dispersion relation. We obtain a simple analytic expression for the peak growth rate due to this interaction, which is then verified by simulation. We demonstrate that our analysis is readily extendable to charge conserving models.« less

Primer development to obtain complete coding sequence of HA and NA genes of influenza A/H3N2 virus.

PubMed

Agustiningsih, Agustiningsih; Trimarsanto, Hidayat; Setiawaty, Vivi; Artika, I Made; Muljono, David Handojo

2016-08-30

Influenza is an acute respiratory illness and has become a serious public health problem worldwide. The need to study the HA and NA genes in influenza A virus is essential since these genes frequently undergo mutations. This study describes the development of primer sets for RT-PCR to obtain complete coding sequence of Hemagglutinin (HA) and Neuraminidase (NA) genes of influenza A/H3N2 virus from Indonesia. The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009. An optimum RT-PCR condition was acquired for all HA and NA fragments designed to cover complete coding sequence of HA and NA genes. A total of 71 samples were successfully sequenced for complete coding sequence both of HA and NA genes out of 145 samples of influenza A/H3N2 tested. The developed primer sets were suitable for obtaining complete coding sequences of HA and NA genes of Indonesian samples from 2008 to 2009.

An extended micromechanics method for probing interphase properties in polymer nanocomposites [An extended micromechanics method for overlapping geometries with application to polymer nanocomposites

DOE PAGES

Liu, Zeliang; Moore, John A.; Liu, Wing Kam

2016-05-03

Inclusions comprised on filler particles and interphase regions commonly form complex morphologies in polymer nanocomposites. Addressing these morphologies as systems of overlapping simple shapes allows for the study of dilute particles, clustered particles, and interacting interphases all in one general modeling framework. To account for the material properties in these overlapping geometries, weighted-mean and additive overlapping conditions are introduced and the corresponding inclusion-wise integral equations are formulated. An extended micromechanics method based on these overlapping conditions for linear elastic and viscoelastic heterogeneous material is then developed. An important feature of the proposed approach is that the effect of both themore » geometric overlapping (clustered particles) and physical overlapping (interacting interphases) on the effective properties can be distinguished. Lastly, we apply the extended micromechanics method to a viscoelastic polymer nanocomposite with interphase regions, and estimate the properties and thickness of the interphase region based on experimental data for carbon-black filled styrene butadiene rubbers.« less

An extended micromechanics method for probing interphase properties in polymer nanocomposites [An extended micromechanics method for overlapping geometries with application to polymer nanocomposites

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

Liu, Zeliang; Moore, John A.; Liu, Wing Kam

Inclusions comprised on filler particles and interphase regions commonly form complex morphologies in polymer nanocomposites. Addressing these morphologies as systems of overlapping simple shapes allows for the study of dilute particles, clustered particles, and interacting interphases all in one general modeling framework. To account for the material properties in these overlapping geometries, weighted-mean and additive overlapping conditions are introduced and the corresponding inclusion-wise integral equations are formulated. An extended micromechanics method based on these overlapping conditions for linear elastic and viscoelastic heterogeneous material is then developed. An important feature of the proposed approach is that the effect of both themore » geometric overlapping (clustered particles) and physical overlapping (interacting interphases) on the effective properties can be distinguished. Lastly, we apply the extended micromechanics method to a viscoelastic polymer nanocomposite with interphase regions, and estimate the properties and thickness of the interphase region based on experimental data for carbon-black filled styrene butadiene rubbers.« less

Spacecraft Solar Particle Event (SPE) Shielding: Shielding Effectiveness as a Function of SPE model as Determined with the FLUKA Radiation Transport Code

NASA Technical Reports Server (NTRS)

Koontz, Steve; Atwell, William; Reddell, Brandon; Rojdev, Kristina

2010-01-01

Analysis of both satellite and surface neutron monitor data demonstrate that the widely utilized Exponential model of solar particle event (SPE) proton kinetic energy spectra can seriously underestimate SPE proton flux, especially at the highest kinetic energies. The more recently developed Band model produces better agreement with neutron monitor data ground level events (GLEs) and is believed to be considerably more accurate at high kinetic energies. Here, we report the results of modeling and simulation studies in which the radiation transport code FLUKA (FLUktuierende KAskade) is used to determine the changes in total ionizing dose (TID) and single-event environments (SEE) behind aluminum, polyethylene, carbon, and titanium shielding masses when the assumed form (i. e., Band or Exponential) of the solar particle event (SPE) kinetic energy spectra is changed. FLUKA simulations have fully three dimensions with an isotropic particle flux incident on a concentric spherical shell shielding mass and detector structure. The effects are reported for both energetic primary protons penetrating the shield mass and secondary particle showers caused by energetic primary protons colliding with shielding mass nuclei. Our results, in agreement with previous studies, show that use of the Exponential form of the event

Comparative study of Monte Carlo particle transport code PHITS and nuclear data processing code NJOY for recoil cross section spectra under neutron irradiation

NASA Astrophysics Data System (ADS)

Iwamoto, Yosuke; Ogawa, Tatsuhiko

2017-04-01

Because primary knock-on atoms (PKAs) create point defects and clusters in materials that are irradiated with neutrons, it is important to validate the calculations of recoil cross section spectra that are used to estimate radiation damage in materials. Here, the recoil cross section spectra of fission- and fusion-relevant materials were calculated using the Event Generator Mode (EGM) of the Particle and Heavy Ion Transport code System (PHITS) and also using the data processing code NJOY2012 with the nuclear data libraries TENDL2015, ENDF/BVII.1, and JEFF3.2. The heating number, which is the integral of the recoil cross section spectra, was also calculated using PHITS-EGM and compared with data extracted from the ACE files of TENDL2015, ENDF/BVII.1, and JENDL4.0. In general, only a small difference was found between the PKA spectra of PHITS + TENDL2015 and NJOY + TENDL2015. From analyzing the recoil cross section spectra extracted from the nuclear data libraries using NJOY2012, we found that the recoil cross section spectra were incorrect for 72Ge, 75As, 89Y, and 109Ag in the ENDF/B-VII.1 library, and for 90Zr and 55Mn in the JEFF3.2 library. From analyzing the heating number, we found that the data extracted from the ACE file of TENDL2015 for all nuclides were problematic in the neutron capture region because of incorrect data regarding the emitted gamma energy. However, PHITS + TENDL2015 can calculate PKA spectra and heating numbers correctly.

New Syndrome Decoding Techniques for the (n, K) Convolutional Codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1983-01-01

This paper presents a new syndrome decoding algorithm for the (n,k) convolutional codes (CC) which differs completely from an earlier syndrome decoding algorithm of Schalkwijk and Vinck. The new algorithm is based on the general solution of the syndrome equation, a linear Diophantine equation for the error polynomial vector E(D). The set of Diophantine solutions is a coset of the CC. In this error coset a recursive, Viterbi-like algorithm is developed to find the minimum weight error vector (circumflex)E(D). An example, illustrating the new decoding algorithm, is given for the binary nonsystemmatic (3,1)CC.

Error Correcting Codes and Related Designs

DTIC Science & Technology

1990-09-30

Theory, IT-37 (1991), 1222-1224. 6. Codes and designs, existence and uniqueness, Discrete Math ., to appear. 7. (with R. Brualdi and N. Cai), Orphan...structure of the first order Reed-Muller codes, Discrete Math ., to appear. 8. (with J. H. Conway and N.J.A. Sloane), The binary self-dual codes of length up...18, 1988. 4. "Codes and Designs," Mathematics Colloquium, Technion, Haifa, Israel, March 6, 1989. 5. "On the Covering Radius of Codes," Discrete Math . Group

Studies of Particle Wake Potentials in Plasmas

NASA Astrophysics Data System (ADS)

Ellis, Ian; Graziani, Frank; Glosli, James; Strozzi, David; Surh, Michael; Richards, David; Decyk, Viktor; Mori, Warren

2011-10-01

Fast Ignition studies require a detailed understanding of electron scattering, stopping, and energy deposition in plasmas with variable values for the number of particles within a Debye sphere. Presently there is disagreement in the literature concerning the proper description of these processes. Developing and validating proper descriptions requires studying the processes using first-principle electrostatic simulations and possibly including magnetic fields. We are using the particle-particle particle-mesh (PPPM) code ddcMD and the particle-in-cell (PIC) code BEPS to perform these simulations. As a starting point in our study, we examine the wake of a particle passing through a plasma in 3D electrostatic simulations performed with ddcMD and with BEPS using various cell sizes. In this poster, we compare the wakes we observe in these simulations with each other and predictions from Vlasov theory. Prepared by LLNL under Contract DE-AC52-07NA27344 and by UCLA under Grant DE-FG52-09NA29552.

Optical network security using unipolar Walsh code

NASA Astrophysics Data System (ADS)

Sikder, Somali; Sarkar, Madhumita; Ghosh, Shila

2018-04-01

Optical code-division multiple-access (OCDMA) is considered as a good technique to provide optical layer security. Many research works have been published to enhance optical network security by using optical signal processing. The paper, demonstrates the design of the AWG (arrayed waveguide grating) router-based optical network for spectral-amplitude-coding (SAC) OCDMA networks with Walsh Code to design a reconfigurable network codec by changing signature codes to against eavesdropping. In this paper we proposed a code reconfiguration scheme to improve the network access confidentiality changing the signature codes by cyclic rotations, for OCDMA system. Each of the OCDMA network users is assigned a unique signature code to transmit the information and at the receiving end each receiver correlates its own signature pattern a(n) with the receiving pattern s(n). The signal arriving at proper destination leads to s(n)=a(n).

Extension of analog network coding in wireless information exchange

NASA Astrophysics Data System (ADS)

Chen, Cheng; Huang, Jiaqing

2012-01-01

Ever since the concept of analog network coding(ANC) was put forward by S.Katti, much attention has been focused on how to utilize analog network coding to take advantage of wireless interference, which used to be considered generally harmful, to improve throughput performance. Previously, only the case of two nodes that need to exchange information has been fully discussed while the issue of extending analog network coding to more than three nodes remains undeveloped. In this paper, we propose a practical transmission scheme to extend analog network coding to more than two nodes that need to exchange information among themselves. We start with the case of three nodes that need to exchange information and demonstrate that through utilizing our algorithm, the throughput can achieve 33% and 20% increase compared with that of traditional transmission scheduling and digital network coding, respectively. Then, we generalize the algorithm so that it can fit for occasions with any number of nodes. We also discuss some technical issues and throughput analysis as well as the bit error rate.

SU-E-T-590: Optimizing Magnetic Field Strengths with Matlab for An Ion-Optic System in Particle Therapy Consisting of Two Quadrupole Magnets for Subsequent Simulations with the Monte-Carlo Code FLUKA

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

Baumann, K; Weber, U; Simeonov, Y

Purpose: Aim of this study was to optimize the magnetic field strengths of two quadrupole magnets in a particle therapy facility in order to obtain a beam quality suitable for spot beam scanning. Methods: The particle transport through an ion-optic system of a particle therapy facility consisting of the beam tube, two quadrupole magnets and a beam monitor system was calculated with the help of Matlab by using matrices that solve the equation of motion of a charged particle in a magnetic field and field-free region, respectively. The magnetic field strengths were optimized in order to obtain a circular andmore » thin beam spot at the iso-center of the therapy facility. These optimized field strengths were subsequently transferred to the Monte-Carlo code FLUKA and the transport of 80 MeV/u C12-ions through this ion-optic system was calculated by using a user-routine to implement magnetic fields. The fluence along the beam-axis and at the iso-center was evaluated. Results: The magnetic field strengths could be optimized by using Matlab and transferred to the Monte-Carlo code FLUKA. The implementation via a user-routine was successful. Analyzing the fluence-pattern along the beam-axis the characteristic focusing and de-focusing effects of the quadrupole magnets could be reproduced. Furthermore the beam spot at the iso-center was circular and significantly thinner compared to an unfocused beam. Conclusion: In this study a Matlab tool was developed to optimize magnetic field strengths for an ion-optic system consisting of two quadrupole magnets as part of a particle therapy facility. These magnetic field strengths could subsequently be transferred to and implemented in the Monte-Carlo code FLUKA to simulate the particle transport through this optimized ion-optic system.« less

Nonlinear verification of a linear critical gradient model for energetic particle transport by Alfven eigenmodes

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

Bass, Eric M.; Waltz, R. E.

Here, a “stiff transport” critical gradient model of energetic particle (EP) transport by EPdriven Alfven eigenmodes (AEs) is verified against local nonlinear gyrokinetic simulations of a well-studied beam-heated DIII-D discharge 146102. A greatly simplifying linear “recipe” for the limiting EP-density gradient (critical gradient) is considered here. In this recipe, the critical gradient occurs when the AE linear growth rate, driven mainly by the EP gradient, exceeds the ion temperature gradient (ITG) or trapped electron mode (TEM) growth rate, driven by the thermal plasma gradient, at the same toroidal mode number (n) as the AE peak growth, well below the ITG/TEMmore » peak n. This linear recipe for the critical gradient is validated against the critical gradient determined from far more expensive local nonlinear simulations in the gyrokinetic code GYRO, as identified by the point of transport runaway when all driving gradients are held fixed. The reduced linear model is extended to include the stabilization from equilibrium E×B velocity shear. The nonlinear verification unambiguously endorses one of two alternative recipes proposed in Ref. 1: the EP-driven AE growth rate should be determined with rather than without added thermal plasma drive.« less

Nonlinear verification of a linear critical gradient model for energetic particle transport by Alfven eigenmodes

DOE PAGES

Bass, Eric M.; Waltz, R. E.

2017-12-08

Here, a “stiff transport” critical gradient model of energetic particle (EP) transport by EPdriven Alfven eigenmodes (AEs) is verified against local nonlinear gyrokinetic simulations of a well-studied beam-heated DIII-D discharge 146102. A greatly simplifying linear “recipe” for the limiting EP-density gradient (critical gradient) is considered here. In this recipe, the critical gradient occurs when the AE linear growth rate, driven mainly by the EP gradient, exceeds the ion temperature gradient (ITG) or trapped electron mode (TEM) growth rate, driven by the thermal plasma gradient, at the same toroidal mode number (n) as the AE peak growth, well below the ITG/TEMmore » peak n. This linear recipe for the critical gradient is validated against the critical gradient determined from far more expensive local nonlinear simulations in the gyrokinetic code GYRO, as identified by the point of transport runaway when all driving gradients are held fixed. The reduced linear model is extended to include the stabilization from equilibrium E×B velocity shear. The nonlinear verification unambiguously endorses one of two alternative recipes proposed in Ref. 1: the EP-driven AE growth rate should be determined with rather than without added thermal plasma drive.« less

ORBIT modelling of fast particle redistribution induced by sawtooth instability

NASA Astrophysics Data System (ADS)

Kim, Doohyun; Podestà, Mario; Poli, Francesca; Princeton Plasma Physics Laboratory Team

2017-10-01

Initial tests on NSTX-U show that introducing energy selectivity for sawtooth (ST) induced fast ion redistribution improves the agreement between experimental and simulated quantities, e.g. neutron rate. Thus, it is expected that a proper description of the fast particle redistribution due to ST can improve the modelling of ST instability and interpretation of experiments using a transport code. In this work, we use ORBIT code to characterise the redistribution of fast particles. In order to simulate a ST crash, a spatial and temporal displacement is implemented as ξ (ρ , t , θ , ϕ) = ∑ξmn (ρ , t) cos (mθ + nϕ) to produce perturbed magnetic fields from the equilibrium field B-> , δB-> = ∇ × (ξ-> × B->) , which affect the fast particle distribution. From ORBIT simulations, we find suitable amplitudes of ξ for each ST crash to reproduce the experimental results. The comparison of the simulation and the experimental results will be discussed as well as the dependence of fast ion redistribution on fast ion phase space variables (i.e. energy, magnetic moment and toroidal angular momentum). Work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences under Contract Number DE-AC02-09CH11466.

A coded tracking telemetry system

USGS Publications Warehouse

Howey, P.W.; Seegar, W.S.; Fuller, M.R.; Titus, K.; Amlaner, Charles J.

1989-01-01

We describe the general characteristics of an automated radio telemetry system designed to operate for prolonged periods on a single frequency. Each transmitter sends a unique coded signal to a receiving system that encodes and records only the appropriater, pre-programmed codes. A record of the time of each reception is stored on diskettes in a micro-computer. This system enables continuous monitoring of infrequent signals (e.g. one per minute or one per hour), thus extending operation life or allowing size reduction of the transmitter, compared to conventional wildlife telemetry. Furthermore, when using unique codes transmitted on a single frequency, biologists can monitor many individuals without exceeding the radio frequency allocations for wildlife.

Extended endoscopic transsphenoidal approach infrachiasmatic corridor.

PubMed

Ceylan, Savas; Anik, Ihsan; Koc, Kenan; Cabuk, Burak

2015-01-01

An extended endoscopic transsphenoidal approach is required for skull base lesions extending to the suprasellar area. Inferior approach using the infrachiasmatic corridor allows access to the lesions through the tumor growth that is favorable for the extended transsphenoidal approaches. Infrachiasmatic corridor is a safer route for the inferior approaches that is made up by basal arachnoid membrane and Liliequist's membrane with its leaves (diencephalic and mesencephalic leaf). This area extends from the optic canal and tuberculum sella to the corpus mamillare. We performed extended endoscopic approach using the infrachiasmatic corridor in 52 cases, including tuberculum sella meningiomas (n:23), craniopharyngiomas (n:16), suprasellar Rathke's cleft cyst (n:6), pituitary adenoma (n:2), fibrous dysplasia (n:1), infundibular granulosa cell tumor (n:2), and epidermoid tumor (n:2). Total resection was achieved in 17 of 23 (74%) with tuberculum sellae meningioma using infrachiasmatic approach. Twenty patients presented with visual disorders and 14 of them improved. There were two postoperative cerebrospinal fluid (CSF) leakages and one transient diabetes insipidus and one permanent diabetes insipidus. Sixteen patients were operated on by the infrachiasmatic approach for craniopharyngiomas. Improvement was reached in seven of eight patients presented with visual disorders. Complete tumor resection was performed in 10 of 16 cases and cyst aspiration in 4 cases, and there were remnants in two cases. Postoperative CSF leakage was seen in two patients. Infrachiasmatic corridor provides an easier and safer inferior route for the removal of middle midline skull base lesions in selected cases.

Extended maximum likelihood halo-independent analysis of dark matter direct detection data

DOE PAGES

Gelmini, Graciela B.; Georgescu, Andreea; Gondolo, Paolo; ...

2015-11-24

We extend and correct a recently proposed maximum-likelihood halo-independent method to analyze unbinned direct dark matter detection data. Instead of the recoil energy as independent variable we use the minimum speed a dark matter particle must have to impart a given recoil energy to a nucleus. This has the advantage of allowing us to apply the method to any type of target composition and interaction, e.g. with general momentum and velocity dependence, and with elastic or inelastic scattering. We prove the method and provide a rigorous statistical interpretation of the results. As first applications, we find that for dark mattermore » particles with elastic spin-independent interactions and neutron to proton coupling ratio f n/f p=-0.7, the WIMP interpretation of the signal observed by CDMS-II-Si is compatible with the constraints imposed by all other experiments with null results. We also find a similar compatibility for exothermic inelastic spin-independent interactions with f n/f p=-0.8.« less

Particle Hydrodynamics with Material Strength for Multi-Layer Orbital Debris Shield Design

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.

1999-01-01

Three dimensional simulation of oblique hypervelocity impact on orbital debris shielding places extreme demands on computer resources. Research to date has shown that particle models provide the most accurate and efficient means for computer simulation of shield design problems. In order to employ a particle based modeling approach to the wall plate impact portion of the shield design problem, it is essential that particle codes be augmented to represent strength effects. This report describes augmentation of a Lagrangian particle hydrodynamics code developed by the principal investigator, to include strength effects, allowing for the entire shield impact problem to be represented using a single computer code.

Monte Carlo parametric studies of neutron interrogation with the Associated Particle Technique for cargo container inspections

NASA Astrophysics Data System (ADS)

Deyglun, Clément; Carasco, Cédric; Pérot, Bertrand

2014-06-01

The detection of Special Nuclear Materials (SNM) by neutron interrogation is extensively studied by Monte Carlo simulation at the Nuclear Measurement Laboratory of CEA Cadarache (French Alternative Energies and Atomic Energy Commission). The active inspection system is based on the Associated Particle Technique (APT). Fissions induced by tagged neutrons (i.e. correlated to an alpha particle in the DT neutron generator) in SNM produce high multiplicity coincidences which are detected with fast plastic scintillators. At least three particles are detected in a short time window following the alpha detection, whereas nonnuclear materials mainly produce single events, or pairs due to (n,2n) and (n,n'γ) reactions. To study the performances of an industrial cargo container inspection system, Monte Carlo simulations are performed with the MCNP-PoliMi transport code, which records for each neutron history the relevant information: reaction types, position and time of interactions, energy deposits, secondary particles, etc. The output files are post-processed with a specific tool developed with ROOT data analysis software. Particles not correlated with an alpha particle (random background), counting statistics, and time-energy resolutions of the data acquisition system are taken into account in the numerical model. Various matrix compositions, suspicious items, SNM shielding and positions inside the container, are simulated to assess the performances and limitations of an industrial system.

On the Formation of Extended Galactic Disks by Tidally Disrupted Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Peñarrubia, Jorge; McConnachie, Alan; Babul, Arif

2006-10-01

We explore the possibility that extended disks, such as that recently discovered in M31, are the result of a single dwarf (109-1010 Msolar) satellite merger. We conduct N-body simulations of dwarf NFW halos with embedded spheroidal stellar components on coplanar, prograde orbits in an M31-like host galaxy. As the orbit decays due to dynamical friction and the system is disrupted, the stellar particles relax to form an extended, exponential-disk-like structure that spans the radial range 30-200 kpc. The disk scale length Rd correlates with the initial extent of the stellar component within the satellite halo: the more embedded the stars, the smaller the resulting disk scale length. If the progenitors start on circular orbits, the kinematics of the stars that make up the extended disk have an average rotational motion that is 30-50 km s-1 lower than the host's circular velocity. For dwarf galaxies moving on highly eccentric orbits (e~=0.7), the stellar debris exhibits a much lower rotational velocity. Our results imply that extended galactic disks might be a generic feature of the hierarchical formation of spiral galaxies such as M31 and the Milky Way.

Energetic Particle Loss Estimates in W7-X

NASA Astrophysics Data System (ADS)

Lazerson, Samuel; Akaslompolo, Simppa; Drevlak, Micheal; Wolf, Robert; Darrow, Douglass; Gates, David; W7-X Team

2017-10-01

The collisionless loss of high energy H+ and D+ ions in the W7-X device are examined using the BEAMS3D code. Simulations of collisionless losses are performed for a large ensemble of particles distributed over various flux surfaces. A clear loss cone of particles is present in the distribution for all particles. These simulations are compared against slowing down simulations in which electron impact, ion impact, and pitch angle scattering are considered. Full device simulations allow tracing of particle trajectories to the first wall components. These simulations provide estimates for placement of a novel set of energetic particle detectors. Recent performance upgrades to the code are allowing simulations with > 1000 processors providing high fidelity simulations. Speedup and future works are discussed. DE-AC02-09CH11466.

Hydrodynamic simulations with the Godunov smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Murante, G.; Borgani, S.; Brunino, R.; Cha, S.-H.

2011-10-01

We present results based on an implementation of the Godunov smoothed particle hydrodynamics (GSPH), originally developed by Inutsuka, in the GADGET-3 hydrodynamic code. We first review the derivation of the GSPH discretization of the equations of moment and energy conservation, starting from the convolution of these equations with the interpolating kernel. The two most important aspects of the numerical implementation of these equations are (a) the appearance of fluid velocity and pressure obtained from the solution of the Riemann problem between each pair of particles, and (b) the absence of an artificial viscosity term. We carry out three different controlled hydrodynamical three-dimensional tests, namely the Sod shock tube, the development of Kelvin-Helmholtz instabilities in a shear-flow test and the 'blob' test describing the evolution of a cold cloud moving against a hot wind. The results of our tests confirm and extend in a number of aspects those recently obtained by Cha, Inutsuka & Nayakshin: (i) GSPH provides a much improved description of contact discontinuities, with respect to smoothed particle hydrodynamics (SPH), thus avoiding the appearance of spurious pressure forces; (ii) GSPH is able to follow the development of gas-dynamical instabilities, such as the Kevin-Helmholtz and the Rayleigh-Taylor ones; (iii) as a result, GSPH describes the development of curl structures in the shear-flow test and the dissolution of the cold cloud in the 'blob' test. Besides comparing the results of GSPH with those from standard SPH implementations, we also discuss in detail the effect on the performances of GSPH of changing different aspects of its implementation: choice of the number of neighbours, accuracy of the interpolation procedure to locate the interface between two fluid elements (particles) for the solution of the Riemann problem, order of the reconstruction for the assignment of variables at the interface, choice of the limiter to prevent oscillations of

Cosmology in one dimension: Vlasov dynamics.

PubMed

Manfredi, Giovanni; Rouet, Jean-Louis; Miller, Bruce; Shiozawa, Yui

2016-04-01

Numerical simulations of self-gravitating systems are generally based on N-body codes, which solve the equations of motion of a large number of interacting particles. This approach suffers from poor statistical sampling in regions of low density. In contrast, Vlasov codes, by meshing the entire phase space, can reach higher accuracy irrespective of the density. Here, we perform one-dimensional Vlasov simulations of a long-standing cosmological problem, namely, the fractal properties of an expanding Einstein-de Sitter universe in Newtonian gravity. The N-body results are confirmed for high-density regions and extended to regions of low matter density, where the N-body approach usually fails.

Efficient full wave code for the coupling of large multirow multijunction LH grills

NASA Astrophysics Data System (ADS)

Preinhaelter, Josef; Hillairet, Julien; Milanesio, Daniele; Maggiora, Riccardo; Urban, Jakub; Vahala, Linda; Vahala, George

2017-11-01

The full wave code OLGA, for determining the coupling of a single row lower hybrid launcher (waveguide grills) to the plasma, is extended to handle multirow multijunction active passive structures (like the C3 and C4 launchers on TORE SUPRA) by implementing the scattering matrix formalism. The extended code is still computationally fast because of the use of (i) 2D splines of the plasma surface admittance in the accessibility region of the k-space, (ii) high order Gaussian quadrature rules for the integration of the coupling elements and (iii) utilizing the symmetries of the coupling elements in the multiperiodic structures. The extended OLGA code is benchmarked against the ALOHA-1D, ALOHA-2D and TOPLHA codes for the coupling of the C3 and C4 TORE SUPRA launchers for several plasma configurations derived from reflectometry and interferometery. Unlike nearly all codes (except the ALOHA-1D code), OLGA does not require large computational resources and can be used for everyday usage in planning experimental runs. In particular, it is shown that the OLGA code correctly handles the coupling of the C3 and C4 launchers over a very wide range of plasma densities in front of the grill.

Toroidal Alfvén eigenmode triggered by trapped anisotropic energetic particles in a toroidal resistive plasma with free boundary

NASA Astrophysics Data System (ADS)

Yang, S. X.; Hao, G. Z.; Liu, Y. Q.; Wang, Z. X.; Hu, Y. J.; Zhu, J. X.; He, H. D.; Wang, A. K.

2018-04-01

The toroidal Alfvén eigenmode (TAE), excited by trapped energetic particles (EPs), is numerically investigated in a tokamak plasma, using the non-perturbative magnetohydrodynamic-kinetic hybrid formulation based MARS-K code (Liu et al 2008 Phys. Plasmas 15 112503). Compared with the fixed boundary condition at the plasma edge, a free boundary enhances the critical value of the EPs kinetic contribution for driving the TAE. Free boundary also induces finite perturbations at the plasma edge as expected. An anisotropic distribution of EPs, in the particle pitch angle space, strongly enhances the instability and results in a more global mode structure, compared with the isotropic case. The plasma resistivity is also found to play a role in the EPs-destabilized TAE. In particular, the mode stability domain is mapped out, in the 2D parameter space of the plasma resistivity and a quantity defining the width of the particle distribution in pitch angle (for anisotropic distribution). A resonance layer in the poloidal mode structure, with the layer width increasing with the plasma resistivity, appears at the large width of the particle distribution in pitch angle space. A mode conversion, from the modified ideal kink by the EPs kinetic effect to the TAE, is also observed while increasing the birth energy of EPs. Computational results suggest that the TAE mode structure can be modified by certain key plasma parameters, such as the EPs kinetic contribution, the equilibrium pressure, the plasma resistivity, the distribution of EPs, as well as the birth energy of EPs. Such modification of the eigenmode structure can only be obtained following the non-perturbative hybrid approach (Wang et al 2013 Phys. Rev. Lett. 111 145003, Wang et al 2015 Phys. Plasmas 22 022509), as adopted in this study. More importantly, numerical results show that near the marginal stability point, the dominant poloidal harmonics of the TAE overlap with each other, and are localized at the tip positions of

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

Microgels for long-term storage of vitamins for extended spaceflight.

PubMed

Schroeder, R

2018-02-01

Biocompatible materials that can encapsulate large amounts of nutrients while protecting them from degrading environmental influences are highly desired for extended manned spaceflight. In this study, alkaline-degradable microgels based on poly(N-vinylcaprolactam) (PVCL) were prepared and analysed with their regard to stabilise retinol which acts as a model vitamin (vitamin A 1 ). It was investigated whether the secondary crosslinking of the particles with a polyphenol can prevent the isomerisation of biologically active all-trans retinol to biologically inactive cis-trans retinol. Both loading with retinol and secondary crosslinking of the particles was performed at room temperature to prevent an early degradation of the vitamin. This study showed that PVCL microgels drastically improve the water solubility of hydrophobic retinol. Additionally, it is demonstrated that the highly crosslinked microgel particles in aqueous solution can be utilised to greatly retard the light- and temperature-induced isomerisation process of retinol by a factor of almost 100 compared to pure retinol stored in ethanol. The use of microgels offers various advantages over other drug delivery systems as they exhibit enhanced biocompatibility and superior aqueous solubility. Copyright © 2017 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Physics in ordered and disordered colloidal matter composed of poly(N-isopropylacrylamide) microgel particles.

PubMed

Yunker, Peter J; Chen, Ke; Gratale, Matthew D; Lohr, Matthew A; Still, Tim; Yodh, A G

2014-05-01

This review collects and describes experiments that employ colloidal suspensions to probe physics in ordered and disordered solids and related complex fluids. The unifying feature of this body of work is its clever usage of poly(N-isopropylacrylamide) (PNIPAM) microgel particles. These temperature-sensitive colloidal particles provide experimenters with a 'knob' for in situ control of particle size, particle interaction and particle packing fraction that, in turn, influence the structural and dynamical behavior of the complex fluids and solids. A brief summary of PNIPAM particle synthesis and properties is given, followed by a synopsis of current activity in the field. The latter discussion describes a variety of soft matter investigations including those that explore formation and melting of crystals and clusters, and those that probe structure, rearrangement and rheology of disordered (jammed/glassy) and partially ordered matter. The review, therefore, provides a snapshot of a broad range of physics phenomenology which benefits from the unique properties of responsive microgel particles.

Computed secondary-particle energy spectra following nonelastic neutron interactions with sup 12 C for E sub n between 15 and 60 MeV: Comparisons of results from two calculational methods

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

Dickens, J.K.

1991-04-01

The organic scintillation detector response code SCINFUL has been used to compute secondary-particle energy spectra, d{sigma}/dE, following nonelastic neutron interactions with {sup 12}C for incident neutron energies between 15 and 60 MeV. The resulting spectra are compared with published similar spectra computed by Brenner and Prael who used an intranuclear cascade code, including alpha clustering, a particle pickup mechanism, and a theoretical approach to sequential decay via intermediate particle-unstable states. The similarities of and the differences between the results of the two approaches are discussed. 16 refs., 44 figs., 2 tabs.

Shaped nanocrystal particles and methods for making the same

DOEpatents

Alivisatos, A Paul [Oakland, CA; Scher, Erik C [Menlo Park, CA; Manna, Liberato [Berkeley, CA

2011-11-22

Shaped nanocrystal particles and methods for making shaped nanocrystal particles are disclosed. One embodiment includes a method for forming a branched, nanocrystal particle. It includes (a) forming a core having a first crystal structure in a solution, (b) forming a first arm extending from the core having a second crystal structure in the solution, and (c) forming a second arm extending from the core having the second crystal structure in the solution.

Shaped nanocrystal particles and methods for making the same

DOEpatents

Alivisatos, A. Paul; Scher, Erik C; Manna, Liberato

2013-12-17

Shaped nanocrystal particles and methods for making shaped nanocrystal particles are disclosed. One embodiment includes a method for forming a branched, nanocrystal particle. It includes (a) forming a core having a first crystal structure in a solution, (b) forming a first arm extending from the core having a second crystal structure in the solution, and (c) forming a second arm extending from the core having the second crystal structure in the solution.

Shaped nanocrystal particles and methods for working the same

DOEpatents

Alivisatos, A. Paul; Sher, Eric C.; Manna, Liberato

2007-12-25

Shaped nanocrystal particles and methods for making shaped nanocrystal particles are disclosed. One embodiment includes a method for forming a branched, nanocrystal particle. It includes (a) forming a core having a first crystal structure in a solution, (b) forming a first arm extending from the core having a second crystal structure in the solution, and (c) forming a second arm extending from the core having the second crystal structure in the solution.

Shaped Nonocrystal Particles And Methods For Making The Same

DOEpatents

Alivisatos, A. Paul; Scher, Erik C.; Manna, Liberato

2005-02-15

Shaped nanocrystal particles and methods for making shaped nanocrystal particles are disclosed. One embodiment includes a method for forming a branched, nanocrystal particle. It includes (a) forming a core having a first crystal structure in a solution, (b) forming a first arm extending from the core having a second crystal structure in the solution, and (c) forming a second arm extending from the core having the second crystal structure in the solution.

Particle sorting in Filter Porous Media and in Sediment Transport: A Numerical and Experimental Study

NASA Astrophysics Data System (ADS)

Glascoe, L. G.; Ezzedine, S. M.; Kanarska, Y.; Lomov, I. N.; Antoun, T.; Smith, J.; Hall, R.; Woodson, S.

2014-12-01

Understanding the flow of fines, particulate sorting in porous media and fractured media during sediment transport is significant for industrial, environmental, geotechnical and petroleum technologies to name a few. For example, the safety of dam structures requires the characterization of the granular filter ability to capture fine-soil particles and prevent erosion failure in the event of an interfacial dislocation. Granular filters are one of the most important protective design elements of large embankment dams. In case of cracking and erosion, if the filter is capable of retaining the eroded fine particles, then the crack will seal and the dam safety will be ensured. Here we develop and apply a numerical tool to thoroughly investigate the migration of fines in granular filters at the grain scale. The numerical code solves the incompressible Navier-Stokes equations and uses a Lagrange multiplier technique. The numerical code is validated to experiments conducted at the USACE and ERDC. These laboratory experiments on soil transport and trapping in granular media are performed in constant-head flow chamber filled with the filter media. Numerical solutions are compared to experimentally measured flow rates, pressure changes and base particle distributions in the filter layer and show good qualitative and quantitative agreement. To further the understanding of the soil transport in granular filters, we investigated the sensitivity of the particle clogging mechanism to various parameters such as particle size ratio, the magnitude of hydraulic gradient, particle concentration, and grain-to-grain contact properties. We found that for intermediate particle size ratios, the high flow rates and low friction lead to deeper intrusion (or erosion) depths. We also found that the damage tends to be shallower and less severe with decreasing flow rate, increasing friction and concentration of suspended particles. We have extended these results to more realistic heterogeneous

Determination of the δ15N of nitrate in solids; RSIL lab code 2894

USGS Publications Warehouse

Coplen, Tyler B.; Qi, Haiping; Revesz, Kinga; Casciotti, Karen; Hannon, Janet E.

2007-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 2894 is to determine the δ15N of nitrate (NO3-) in solids. The nitrate fraction of the nitrogen species is dissolved by water (called leaching) and can be analyzed by the bacterial method covered in RSIL lab code 2899. After leaching, the δ15N of the dissolved NO3- is analyzed by conversion of the NO3- to nitrous oxide (N2O), which serves as the analyte for mass spectrometry. A culture of denitrifying bacteria is used in the enzymatic conversion of NO3- to N2O, which follows the pathway shown in equation 1: NO3- → NO2- → NO → 1/2 N2O (1) Because the bacteria Pseudomonas aureofaciens lack N2O reductive activity, the reaction stops at N2O, unlike the typical denitrification reaction that goes to N2. After several hours, the conversion is complete, and the N2O is extracted from the vial, separated from volatile organic vapor and water vapor by an automated -65 °C isopropanol-slush trap, a Nafion drier, a CO2 and water removal unit (Costech #021020 carbon dioxide absorbent with Mg(ClO4)2), and trapped in a small-volume trap immersed in liquid nitrogen with a modified Finnigan MAT (now Thermo Scientific) GasBench 2 introduction system. After the N2O is released, it is further purified by gas chromatography before introduction to the isotope-ratio mass spectrometer (IRMS). The IRMS is a Thermo Scientific Delta V Plus continuous flow IRMS (CF-IRMS). It has a universal triple collector, consisting of two wide cups with a narrow cup in the middle; it is capable of simultaneously measuring mass/charge (m/z) of the N2O molecule 44, 45, and 46. The ion beams from these m/z values are as follows: m/z = 44 = N2O = 14N14N16O; m/z = 45 = N2O = 14N15N16O or 14N14N17O; m/z = 46 = N2O = 14N14N18O. The 17O contributions to the m/z 44 and m/z 45 ion beams are accounted for before δ15N values are reported.

Effect of alpha-particle irradiation on the electrical properties of n-type Ge

NASA Astrophysics Data System (ADS)

Roro, K. T.; Janse van Rensburg, P. J.; Auret, F. D.; Coelho, S.

2009-12-01

Deep-level transient spectroscopy was used to investigate the effect of alpha particle irradiation on the electrical properties of n-type Ge. The samples were irradiated with alpha particles at room temperature using an americium-241 (Am-241) radionuclide source. The main defects introduced were found to be electron traps with energy levels at EC-0.38, EC-0.21, EC-0.20, EC-0.15, and EC-0.10 eV, respectively. The main defects in alpha particle irradiation are similar to those introduced by MeV electron irradiation, where the main defect is the E-center. A quadratic increase in concentration as a function of dose is observed.

Progressive video coding for noisy channels

NASA Astrophysics Data System (ADS)

Kim, Beong-Jo; Xiong, Zixiang; Pearlman, William A.

1998-10-01

We extend the work of Sherwood and Zeger to progressive video coding for noisy channels. By utilizing a 3D extension of the set partitioning in hierarchical trees (SPIHT) algorithm, we cascade the resulting 3D SPIHT video coder with a rate-compatible punctured convolutional channel coder for transmission of video over a binary symmetric channel. Progressive coding is achieved by increasing the target rate of the 3D embedded SPIHT video coder as the channel condition improves. The performance of our proposed coding system is acceptable at low transmission rate and bad channel conditions. Its low complexity makes it suitable for emerging applications such as video over wireless channels.

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes

PubMed Central

José, Marco V.; Govezensky, Tzipe; García, José A.; Bobadilla, Juan R.

2009-01-01

Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10−10 per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC. PMID:19183813

Fusion PIC code performance analysis on the Cori KNL system

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

Koskela, Tuomas S.; Deslippe, Jack; Friesen, Brian

We study the attainable performance of Particle-In-Cell codes on the Cori KNL system by analyzing a miniature particle push application based on the fusion PIC code XGC1. We start from the most basic building blocks of a PIC code and build up the complexity to identify the kernels that cost the most in performance and focus optimization efforts there. Particle push kernels operate at high AI and are not likely to be memory bandwidth or even cache bandwidth bound on KNL. Therefore, we see only minor benefits from the high bandwidth memory available on KNL, and achieving good vectorization ismore » shown to be the most beneficial optimization path with theoretical yield of up to 8x speedup on KNL. In practice we are able to obtain up to a 4x gain from vectorization due to limitations set by the data layout and memory latency.« less

Modeling Particle Acceleration and Transport at a 2-D CME-Driven Shock

NASA Astrophysics Data System (ADS)

Hu, Junxiang; Li, Gang; Ao, Xianzhi; Zank, Gary P.; Verkhoglyadova, Olga

2017-11-01

We extend our earlier Particle Acceleration and Transport in the Heliosphere (PATH) model to study particle acceleration and transport at a coronal mass ejection (CME)-driven shock. We model the propagation of a CME-driven shock in the ecliptic plane using the ZEUS-3D code from 20 solar radii to 2 AU. As in the previous PATH model, the initiation of the CME-driven shock is simplified and modeled as a disturbance at the inner boundary. Different from the earlier PATH model, the disturbance is now longitudinally dependent. Particles are accelerated at the 2-D shock via the diffusive shock acceleration mechanism. The acceleration depends on both the parallel and perpendicular diffusion coefficients κ|| and κ⊥ and is therefore shock-obliquity dependent. Following the procedure used in Li, Shalchi, et al. (k href="#jgra53857-bib-0045"/>), we obtain the particle injection energy, the maximum energy, and the accelerated particle spectra at the shock front. Once accelerated, particles diffuse and convect in the shock complex. The diffusion and convection of these particles are treated using a refined 2-D shell model in an approach similar to Zank et al. (k href="#jgra53857-bib-0089"/>). When particles escape from the shock, they propagate along and across the interplanetary magnetic field. The propagation is modeled using a focused transport equation with the addition of perpendicular diffusion. We solve the transport equation using a backward stochastic differential equation method where adiabatic cooling, focusing, pitch angle scattering, and cross-field diffusion effects are all included. Time intensity profiles and instantaneous particle spectra as well as particle pitch angle distributions are shown for two example CME shocks.

Code Modernization of VPIC

NASA Astrophysics Data System (ADS)

Bird, Robert; Nystrom, David; Albright, Brian

2017-10-01

The ability of scientific simulations to effectively deliver performant computation is increasingly being challenged by successive generations of high-performance computing architectures. Code development to support efficient computation on these modern architectures is both expensive, and highly complex; if it is approached without due care, it may also not be directly transferable between subsequent hardware generations. Previous works have discussed techniques to support the process of adapting a legacy code for modern hardware generations, but despite the breakthroughs in the areas of mini-app development, portable-performance, and cache oblivious algorithms the problem still remains largely unsolved. In this work we demonstrate how a focus on platform agnostic modern code-development can be applied to Particle-in-Cell (PIC) simulations to facilitate effective scientific delivery. This work builds directly on our previous work optimizing VPIC, in which we replaced intrinsic based vectorisation with compile generated auto-vectorization to improve the performance and portability of VPIC. In this work we present the use of a specialized SIMD queue for processing some particle operations, and also preview a GPU capable OpenMP variant of VPIC. Finally we include a lessons learnt. Work performed under the auspices of the U.S. Dept. of Energy by the Los Alamos National Security, LLC Los Alamos National Laboratory under contract DE-AC52-06NA25396 and supported by the LANL LDRD program.

Center for Extended Magnetohydrodynamics Modeling

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

Ramos, Jesus

This researcher participated in the DOE-funded Center for Extended Magnetohydrodynamics Modeling (CEMM), a multi-institutional collaboration led by the Princeton Plasma Physics Laboratory with Dr. Stephen Jardin as the overall Principal Investigator. This project developed advanced simulation tools to study the non-linear macroscopic dynamics of magnetically confined plasmas. The collaborative effort focused on the development of two large numerical simulation codes, M3D-C1 and NIMROD, and their application to a wide variety of problems. Dr. Ramos was responsible for theoretical aspects of the project, deriving consistent sets of model equations applicable to weakly collisional plasmas and devising test problems for verification ofmore » the numerical codes. This activity was funded for twelve years.« less

Development of the Small Package Single Particle Soot Photometer with extended range (SP2-XR) and black carbon detection efficiency compared to its predecessor, the SP2

NASA Astrophysics Data System (ADS)

Schulz, H.; Kok, G. L.; Zanatta, M.; Schwarz, J. P.; Herber, A. B.

2016-12-01

Black carbon (BC) aerosol is an important contributor to climate change due to its ability to very efficiently absorb solar radiation. The Single Particle Soot Photometer (SP2) is an instrument that quantifies the refractory mass of individual BC-containing particles with a laser-induced incandescence method. The SP2 has been deployed on ships, at ground based sites, and on research aircraft to quantify BC's mass loadings and microphysical properties. However, the SP2's particle detection range is generally limited to 70-700 nm volume-equivalent diameter for ambient BC. Ambient air typically contains substantial number concentrations below and mass concentrations above the limits of this range. To account for the unquantified particles, it is common to fit a log-normal distribution to the measured size distributions — an approach that leaves the BC community with uncertain results, and a need to learn about the occurrence of very small particles or very large BC aggregates. The SP2 is also large and heavy enough to limit its usability for aircraft and unmanned or towed airborne vehicles. We have developed a miniaturized SP2 to dramatically extend the range of applications for which the SP2 technique can be used. This new instrument, with the additional target of an extended measurement range, has been named the SP2-XR, and incorporates a newly designed optical block with updated electronics for signal recording and on-the-fly processing (gain stitching and peak analysis). The optical block improves the light-collection of both scattered and incandescent light from sampled particles. The target measurement range is 40-1000 nm. At the same time, the SP2-XR weighs less than half of an SP2 (15 kg for the complete system), and about 1/4 the volume ( 20 cm x 20 cm x 40 cm). The instrument software is designed to produce ready to use particle mass and binned size distributions or full particle trace records, according to different scientific needs. Thus, an SP2-XR may

Motion of dust particles in nonuniform magnetic field and applicability of smoothed particle hydrodynamics simulation

NASA Astrophysics Data System (ADS)

Saitou, Y.

2018-01-01

An SPH (Smoothed Particle Hydrodynamics) simulation code is developed to reproduce our findings on behavior of dust particles, which were obtained in our previous experiments (Phys. Plasmas, 23, 013709 (2016) and Abst. 18th Intern. Cong. Plasma Phys. (Kaohsiung, 2016)). Usually, in an SPH simulation, a smoothed particle is interpreted as a discretized fluid element. Here we regard the particles as dust particles because it is known that behavior of dust particles in complex plasmas can be described using fluid dynamics equations in many cases. Various rotation velocities that are difficult to achieve in the experiment are given to particles at boundaries in the newly developed simulation and motion of particles is investigated. Preliminary results obtained by the simulation are shown.

On complexity of trellis structure of linear block codes

NASA Technical Reports Server (NTRS)

Lin, Shu

1990-01-01

The trellis structure of linear block codes (LBCs) is discussed. The state and branch complexities of a trellis diagram (TD) for a LBC is investigated. The TD with the minimum number of states is said to be minimal. The branch complexity of a minimal TD for a LBC is expressed in terms of the dimensions of specific subcodes of the given code. Then upper and lower bounds are derived on the number of states of a minimal TD for a LBC, and it is shown that a cyclic (or shortened cyclic) code is the worst in terms of the state complexity among the LBCs of the same length and dimension. Furthermore, it is shown that the structural complexity of a minimal TD for a LBC depends on the order of its bit positions. This fact suggests that an appropriate permutation of the bit positions of a code may result in an equivalent code with a much simpler minimal TD. Boolean polynomial representation of codewords of a LBC is also considered. This representation helps in study of the trellis structure of the code. Boolean polynomial representation of a code is applied to construct its minimal TD. Particularly, the construction of minimal trellises for Reed-Muller codes and the extended and permuted binary primitive BCH codes which contain Reed-Muller as subcodes is emphasized. Finally, the structural complexity of minimal trellises for the extended and permuted, and double-error-correcting BCH codes is analyzed and presented. It is shown that these codes have relatively simple trellis structure and hence can be decoded with the Viterbi decoding algorithm.

A Very Efficient Transfer Function Bounding Technique on Bit Error Rate for Viterbi Decoded, Rate 1/N Convolutional Codes

NASA Technical Reports Server (NTRS)

Lee, P. J.

1984-01-01

For rate 1/N convolutional codes, a recursive algorithm for finding the transfer function bound on bit error rate (BER) at the output of a Viterbi decoder is described. This technique is very fast and requires very little storage since all the unnecessary operations are eliminated. Using this technique, we find and plot bounds on the BER performance of known codes of rate 1/2 with K 18, rate 1/3 with K 14. When more than one reported code with the same parameter is known, we select the code that minimizes the required signal to noise ratio for a desired bit error rate of 0.000001. This criterion of determining goodness of a code had previously been found to be more useful than the maximum free distance criterion and was used in the code search procedures of very short constraint length codes. This very efficient technique can also be used for searches of longer constraint length codes.

An implementation of a tree code on a SIMD, parallel computer

NASA Technical Reports Server (NTRS)

Olson, Kevin M.; Dorband, John E.

1994-01-01

We describe a fast tree algorithm for gravitational N-body simulation on SIMD parallel computers. The tree construction uses fast, parallel sorts. The sorted lists are recursively divided along their x, y and z coordinates. This data structure is a completely balanced tree (i.e., each particle is paired with exactly one other particle) and maintains good spatial locality. An implementation of this tree-building algorithm on a 16k processor Maspar MP-1 performs well and constitutes only a small fraction (approximately 15%) of the entire cycle of finding the accelerations. Each node in the tree is treated as a monopole. The tree search and the summation of accelerations also perform well. During the tree search, node data that is needed from another processor is simply fetched. Roughly 55% of the tree search time is spent in communications between processors. We apply the code to two problems of astrophysical interest. The first is a simulation of the close passage of two gravitationally, interacting, disk galaxies using 65,636 particles. We also simulate the formation of structure in an expanding, model universe using 1,048,576 particles. Our code attains speeds comparable to one head of a Cray Y-MP, so single instruction, multiple data (SIMD) type computers can be used for these simulations. The cost/performance ratio for SIMD machines like the Maspar MP-1 make them an extremely attractive alternative to either vector processors or large multiple instruction, multiple data (MIMD) type parallel computers. With further optimizations (e.g., more careful load balancing), speeds in excess of today's vector processing computers should be possible.

A Design for Composing and Extending Vehicle Models

NASA Technical Reports Server (NTRS)

Madden, Michael M.; Neuhaus, Jason R.

2003-01-01

The Systems Development Branch (SDB) at NASA Langley Research Center (LaRC) creates simulation software products for research. Each product consists of an aircraft model with experiment extensions. SDB treats its aircraft models as reusable components, upon which experiments can be built. SDB has evolved aircraft model design with the following goals: 1. Avoid polluting the aircraft model with experiment code. 2. Discourage the copy and tailor method of reuse. The current evolution of that architecture accomplishes these goals by reducing experiment creation to extend and compose. The architecture mechanizes the operational concerns of the model's subsystems and encapsulates them in an interface inherited by all subsystems. Generic operational code exercises the subsystems through the shared interface. An experiment is thus defined by the collection of subsystems that it creates ("compose"). Teams can modify the aircraft subsystems for the experiment using inheritance and polymorphism to create variants ("extend").

Modified NASA-Lewis chemical equilibrium code for MHD applications

NASA Technical Reports Server (NTRS)

Sacks, R. A.; Geyer, H. K.; Grammel, S. J.; Doss, E. D.

1979-01-01

A substantially modified version of the NASA-Lewis Chemical Equilibrium Code was recently developed. The modifications were designed to extend the power and convenience of the Code as a tool for performing combustor analysis for MHD systems studies. The effect of the programming details is described from a user point of view.

Code C# for chaos analysis of relativistic many-body systems with reactions