High-Speed Particle-in-Cell Simulation Parallelized with Graphic Processing Units for Low Temperature Plasmas for Material Processing

NASA Astrophysics Data System (ADS)

Hur, Min Young; Verboncoeur, John; Lee, Hae June

2014-10-01

Particle-in-cell (PIC) simulations have high fidelity in the plasma device requiring transient kinetic modeling compared with fluid simulations. It uses less approximation on the plasma kinetics but requires many particles and grids to observe the semantic results. It means that the simulation spends lots of simulation time in proportion to the number of particles. Therefore, PIC simulation needs high performance computing. In this research, a graphic processing unit (GPU) is adopted for high performance computing of PIC simulation for low temperature discharge plasmas. GPUs have many-core processors and high memory bandwidth compared with a central processing unit (CPU). NVIDIA GeForce GPUs were used for the test with hundreds of cores which show cost-effective performance. PIC code algorithm is divided into two modules which are a field solver and a particle mover. The particle mover module is divided into four routines which are named move, boundary, Monte Carlo collision (MCC), and deposit. Overall, the GPU code solves particle motions as well as electrostatic potential in two-dimensional geometry almost 30 times faster than a single CPU code. This work was supported by the Korea Institute of Science Technology Information.

Antimicrobial activities, DNA interactions, spectroscopic (FT-IR and UV-Vis) characterizations, and DFT calculations for pyridine-2-carboxylic acid and its derivates

NASA Astrophysics Data System (ADS)

Tamer, Ömer; Tamer, Sevil Arabacı; İdil, Önder; Avcı, Davut; Vural, Hatice; Atalay, Yusuf

2018-01-01

In this paper, pyridine- 2- carboxylic acid, also known as picolinic acid (pic), and its two derivate, 4- methoxy-pyridine- 2- carboxylic acid (4-Mpic) and 4- chloro-pyridine- 2- carboxylic acid (4-Clpic) have been characterized by FT-IR and UV-Vis spectroscopy techniques as well as DFT calculations. B3LYP level of Density Functional Theory (DFT) method was used to obtain ground state geometries, vibration wavenumbers, first order hyperpolarizabilities and molecular electrostatic potential (MEP) surfaces for pic, 4Clpic and 4Mpic. The electronic absorption wavelengths and HOMO-LUMO energies were investigated by time dependent B3LYP (TD-B3LYP) level with the conductor-like polarizable continuum model (CPCM). The effects of Cl atom and OCH3 group on HOMO-LUMO energy gaps and first order hyperpolarizability parameters of pic, 4Clpic and 4Mpic molecules were examined. All molecules were screened for their antibacterial activities against Gram-positive and Gram-negative bacteria and for their antifungal activities against yeast strains by using minimal inhibitory concentration method (MIC). All compounds (pic, 4Mpic and 4Clpic) have been found to be very active against to the Gram (+) and Gram (-) bacteria. The DNA interactions of pic, 4Clpic and 4Mpic were analyzed by molecular docking simulations, and the interaction of the 4Mpic molecule with DNA is found to be higher than 4Clpic and pic.

A two-dimensional particle-in-cell model of a dusty plasma

NASA Technical Reports Server (NTRS)

Young, B.; Cravens, T. E.; Armstrong, T. P.; Friauf, R. J.

1994-01-01

Dusty plasmas are present in comets, in the ring systems of the outer planets, and in the interstellar medium. A two-dimensional particle-in-cell (PIC) model of a dusty plasma is presented in this paper. The PIC code is best suited for modeling the plasma-dust interaction for large grains, with diameters of the order of a centimeter. We have modeled the charging process for an individual dust grain and the associated potential pattern in the surrounding plasma. We have also considered the case of a large number of grains in a plasma, with intergrain separations of the order of the Debye length, and have shown that the plasma becomes depleted and the charge on a dust grain is reduced, as other workers in this field have predicted (cf. C. K. Goertz, 1989). We examine the electron and ion distribution functions in the vicinity of a charged grain and demonstrate that the ions near a grain have clearly been accelerated by the electrostatic potential.

Full PIC simulations of solar radio emission

NASA Astrophysics Data System (ADS)

Sgattoni, A.; Henri, P.; Briand, C.; Amiranoff, F.; Riconda, C.

2017-12-01

Solar radio emissions are electromagnetic (EM) waves emitted in the solar wind plasma as a consequence of electron beams accelerated during solar flares or interplanetary shocks such as ICMEs. To describe their origin, a multi-stage model has been proposed in the 60s which considers a succession of non-linear three-wave interaction processes. A good understanding of the process would allow to infer the kinetic energy transfered from the electron beam to EM waves, so that the radio waves recorded by spacecraft can be used as a diagnostic for the electron beam.Even if the electrostatic problem has been extensively studied, full electromagnetic simulations were attempted only recently. Our large scale 2D-3V electromagnetic PIC simulations allow to identify the generation of both electrostatic and EM waves originated by the succession of plasma instabilities. We tested several configurations varying the electron beam density and velocity considering a background plasma of uniform density. For all the tested configurations approximately 105 of the electron-beam kinetic energy is transfered into EM waves emitted in all direction nearly isotropically. With this work we aim to design experiments of laboratory astrophysics to reproduce the electromagnetic emission process and test its efficiency.

Study of discrete-particle effects in a one-dimensional plasma simulation with the Krook type collision model

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

Lai, Po-Yen; Chen, Liu; Institute for Fusion Theory and Simulation, Zhejiang University, 310027 Hangzhou

2015-09-15

The thermal relaxation time of a one-dimensional plasma has been demonstrated to scale with N{sub D}{sup 2} due to discrete particle effects by collisionless particle-in-cell (PIC) simulations, where N{sub D} is the particle number in a Debye length. The N{sub D}{sup 2} scaling is consistent with the theoretical analysis based on the Balescu-Lenard-Landau kinetic equation. However, it was found that the thermal relaxation time is anomalously shortened to scale with N{sub D} while externally introducing the Krook type collision model in the one-dimensional electrostatic PIC simulation. In order to understand the discrete particle effects enhanced by the Krook type collisionmore » model, the superposition principle of dressed test particles was applied to derive the modified Balescu-Lenard-Landau kinetic equation. The theoretical results are shown to be in good agreement with the simulation results when the collisional effects dominate the plasma system.« less

Steady-State Ion Beam Modeling with MICHELLE

NASA Astrophysics Data System (ADS)

Petillo, John

2003-10-01

There is a need to efficiently model ion beam physics for ion implantation, chemical vapor deposition, and ion thrusters. Common to all is the need for three-dimensional (3D) simulation of volumetric ion sources, ion acceleration, and optics, with the ability to model charge exchange of the ion beam with a background neutral gas. The two pieces of physics stand out as significant are the modeling of the volumetric source and charge exchange. In the MICHELLE code, the method for modeling the plasma sheath in ion sources assumes that the electron distribution function is a Maxwellian function of electrostatic potential over electron temperature. Charge exchange is the process by which a neutral background gas with a "fast" charged particle streaming through exchanges its electron with the charged particle. An efficient method for capturing this is essential, and the model presented is based on semi-empirical collision cross section functions. This appears to be the first steady-state 3D algorithm of its type to contain multiple generations of charge exchange, work with multiple species and multiple charge state beam/source particles simultaneously, take into account the self-consistent space charge effects, and track the subsequent fast neutral particles. The solution used by MICHELLE is to combine finite element analysis with particle-in-cell (PIC) methods. The basic physics model is based on the equilibrium steady-state application of the electrostatic particle-in-cell (PIC) approximation employing a conformal computational mesh. The foundation stems from the same basic model introduced in codes such as EGUN. Here, Poisson's equation is used to self-consistently include the effects of space charge on the fields, and the relativistic Lorentz equation is used to integrate the particle trajectories through those fields. The presentation will consider the complexity of modeling ion thrusters.

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

Fluid preconditioning for Newton–Krylov-based, fully implicit, electrostatic particle-in-cell simulations

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

Chen, G., E-mail: gchen@lanl.gov; Chacón, L.; Leibs, C.A.

2014-02-01

A recent proof-of-principle study proposes an energy- and charge-conserving, nonlinearly implicit electrostatic particle-in-cell (PIC) algorithm in one dimension [9]. The algorithm in the reference employs an unpreconditioned Jacobian-free Newton–Krylov method, which ensures nonlinear convergence at every timestep (resolving the dynamical timescale of interest). Kinetic enslavement, which is one key component of the algorithm, not only enables fully implicit PIC as a practical approach, but also allows preconditioning the kinetic solver with a fluid approximation. This study proposes such a preconditioner, in which the linearized moment equations are closed with moments computed from particles. Effective acceleration of the linear GMRES solvemore » is demonstrated, on both uniform and non-uniform meshes. The algorithm performance is largely insensitive to the electron–ion mass ratio. Numerical experiments are performed on a 1D multi-scale ion acoustic wave test problem.« less

Continuously differentiable PIC shape functions for triangular meshes

DOE PAGES

Barnes, D. C.

2018-03-21

In this study, a new class of continuously-differentiable shape functions is developed and applied to two-dimensional electrostatic PIC simulation on an unstructured simplex (triangle) mesh. It is shown that troublesome aliasing instabilities are avoided for cold plasma simulation in which the Debye length is as small as 0.01 cell sizes. These new shape functions satisfy all requirements for PIC particle shape. They are non-negative, have compact support, and partition unity. They are given explicitly by cubic expressions in the usual triangle logical (areal) coordinates. The shape functions are not finite elements because their structure depends on the topology of themore » mesh, in particular, the number of triangles neighboring each mesh vertex. Nevertheless, they may be useful as approximations to solution of other problems in which continuity of derivatives is required or desired.« less

Continuously differentiable PIC shape functions for triangular meshes

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

Barnes, D. C.

In this study, a new class of continuously-differentiable shape functions is developed and applied to two-dimensional electrostatic PIC simulation on an unstructured simplex (triangle) mesh. It is shown that troublesome aliasing instabilities are avoided for cold plasma simulation in which the Debye length is as small as 0.01 cell sizes. These new shape functions satisfy all requirements for PIC particle shape. They are non-negative, have compact support, and partition unity. They are given explicitly by cubic expressions in the usual triangle logical (areal) coordinates. The shape functions are not finite elements because their structure depends on the topology of themore » mesh, in particular, the number of triangles neighboring each mesh vertex. Nevertheless, they may be useful as approximations to solution of other problems in which continuity of derivatives is required or desired.« less

HESQ (Helical Electrostatic Quadrupole), a low energy beam transport for the SSC linac

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

Raparia, D.

A Helical Electrostatic Quadrupole (HESQ) is an option for the low energy beam transport (LEBT) of the SSC linac to transport and match a 35 keV H{sup {minus}} beam from a circular symmetric Magnetron ion source to a 428 MHz RFQ. Being an electrostatic focusing lens, the HESQ avoids neutralization of the H{sup {minus}} beam due to the background gas. The HESQ lenses provide stronger first-order focusing in contrast to weak second-order focusing of einzel lenses and is also stronger than alternating gradient focusing. In this paper, we will present a design and results of a PIC code simulation withmore » space charge.« less

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.

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.

3D electrostatic gyrokinetic electron and fully kinetic ion simulation of lower-hybrid drift instability of Harris current sheet

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

Wang, Zhenyu; Lin, Yu; Wang, Xueyi

The eigenmode stability properties of three-dimensional lower-hybrid-drift-instabilities (LHDI) in a Harris current sheet with a small but finite guide magnetic field have been systematically studied by employing the gyrokinetic electron and fully kinetic ion (GeFi) particle-in-cell (PIC) simulation model with a realistic ion-to-electron mass ratio m i/m e. In contrast to the fully kinetic PIC simulation scheme, the fast electron cyclotron motion and plasma oscillations are systematically removed in the GeFi model, and hence one can employ the realistic m i/m e. The GeFi simulations are benchmarked against and show excellent agreement with both the fully kinetic PIC simulation and the analytical eigenmode theory. Our studies indicate that, for small wavenumbers, ky, along the current direction, the most unstable eigenmodes are peaked at the location wheremore » $$\\vec{k}$$• $$\\vec{B}$$ =0, consistent with previous analytical and simulation studies. Here, $$\\vec{B}$$ is the equilibrium magnetic field and $$\\vec{k}$$ is the wavevector perpendicular to the nonuniformity direction. As ky increases, however, the most unstable eigenmodes are found to be peaked at $$\\vec{k}$$ •$$\\vec{B}$$ ≠0. Additionally, the simulation results indicate that varying m i/m e, the current sheet width, and the guide magnetic field can affect the stability of LHDI. Simulations with the varying mass ratio confirm the lower hybrid frequency and wave number scalings.« less

3D electrostatic gyrokinetic electron and fully kinetic ion simulation of lower-hybrid drift instability of Harris current sheet

DOE PAGES

Wang, Zhenyu; Lin, Yu; Wang, Xueyi; ...

2016-07-07

The eigenmode stability properties of three-dimensional lower-hybrid-drift-instabilities (LHDI) in a Harris current sheet with a small but finite guide magnetic field have been systematically studied by employing the gyrokinetic electron and fully kinetic ion (GeFi) particle-in-cell (PIC) simulation model with a realistic ion-to-electron mass ratio m i/m e. In contrast to the fully kinetic PIC simulation scheme, the fast electron cyclotron motion and plasma oscillations are systematically removed in the GeFi model, and hence one can employ the realistic m i/m e. The GeFi simulations are benchmarked against and show excellent agreement with both the fully kinetic PIC simulation and the analytical eigenmode theory. Our studies indicate that, for small wavenumbers, ky, along the current direction, the most unstable eigenmodes are peaked at the location wheremore » $$\\vec{k}$$• $$\\vec{B}$$ =0, consistent with previous analytical and simulation studies. Here, $$\\vec{B}$$ is the equilibrium magnetic field and $$\\vec{k}$$ is the wavevector perpendicular to the nonuniformity direction. As ky increases, however, the most unstable eigenmodes are found to be peaked at $$\\vec{k}$$ •$$\\vec{B}$$ ≠0. Additionally, the simulation results indicate that varying m i/m e, the current sheet width, and the guide magnetic field can affect the stability of LHDI. Simulations with the varying mass ratio confirm the lower hybrid frequency and wave number scalings.« less

Forced Reconnection in the Near Magnetotail: Onset and Energy Conversion in PIC and MHD Simulations

NASA Technical Reports Server (NTRS)

Birn, J.; Hesse, Michael

2014-01-01

Using two-dimensional particle-in-cell (PIC) together with magnetohydrodynamic (MHD) Q1 simulations of magnetotail dynamics, we investigate the evolution toward onset of reconnection and the subsequent energy transfer and conversion. In either case, reconnection onset is preceded by a driven phase, during which magnetic flux is added to the tail at the high-latitude boundaries, followed by a relaxation phase, during which the configuration continues to respond to the driving. The boundary deformation leads to the formation of thin embedded current sheets, which are bifurcated in the near tail, converging to a single sheet farther out in the MHD simulations. The thin current sheets in the PIC simulation are carried by electrons and are associated with a strong perpendicular electrostatic field, which may provide a connection to parallel potentials and auroral arcs and an ionospheric signal even prior to the onset of reconnection. The PIC simulation very well satisfies integral entropy conservation (intrinsic to ideal MHD) during this phase, supporting ideal ballooning stability. Eventually, the current intensification leads to the onset of reconnection, the formation and ejection of a plasmoid, and a collapse of the inner tail. The earthward flow shows the characteristics of a dipolarization front: enhancement of Bz, associated with a thin vertical electron current sheet in the PIC simulation. Both MHD and PIC simulations show a dominance of energy conversion from incoming Poynting flux to outgoing enthalpy flux, resulting in heating of the inner tail. Localized Joule dissipation plays only a minor role.

A Hamiltonian electromagnetic gyrofluid model

NASA Astrophysics Data System (ADS)

Waelbroeck, F. L.; Hazeltine, R. D.; Morrison, P. J.

2009-11-01

An isothermal truncation of the electromagnetic gyrofluid model of Snyder and Hammett [Phys. Plasmas 8, 3199 (2001)] is shown to be Hamiltonian. The corresponding noncanonical Lie-Poisson bracket and its Casimir invariants are presented. The model describes the evolution of the density, the electrostatic potential, and the component of the vector potential along a strong background field. This makes it suitable for describing such phenomena as the propagation of kinetic-Alfv'en modons, the nonlinear saturation of drift-tearing modes, and the diamagnetic stabilization of the internal kink. The invariants are used to obtain a set of coupled Grad-Shafranov equations describing equilibria and propagating coherent structures. They also lead to a Lagrangian formulation of the equations of motion that is well suited to solution with the PIC method.

Analytic model of a laser-accelerated composite plasma target and its stability

NASA Astrophysics Data System (ADS)

Khudik, Vladimir; Shvets, Gennady

2013-10-01

A self-consistent analytical model of monoenergetic acceleration of a one and two-species ultrathin target irradiated by a circularly polarized laser pulse is developed. In the accelerated reference frame, the bulk plasma in the target is neutral and its parameters are assumed to be stationary. It is found that the structure of the target depends strongly on the temperatures of electrons and ions, which are both strongly influenced by the laser pulse pedestal. When the electron temperature is large, the hot electrons bounce back and forth inside the potential well formed by ponderomotive and electrostatic potentials while the heavy and light ions are forced-balanced by the electrostatic and non-inertial fields forming two separated layers. In the opposite limiting case when the ion temperature is large, the hot ions are trapped in the potential well formed by the ion-sheath's electric and non-inertial potentials while the cold electrons are forced-balanced by the electrostatic and ponderomotive fields. Using PIC simulations we have determined which scenario is realized in practice depending on the initial target structure and laser intensity. Target stability with respect to Rayleigh-Taylor instability will also be discussed. This work is supported by the US DOE grants DE-FG02-04ER41321 and DE-FG02-07ER54945.

AP-Cloud: Adaptive particle-in-cloud method for optimal solutions to Vlasov–Poisson equation

DOE PAGES

Wang, Xingyu; Samulyak, Roman; Jiao, Xiangmin; ...

2016-04-19

We propose a new adaptive Particle-in-Cloud (AP-Cloud) method for obtaining optimal numerical solutions to the Vlasov–Poisson equation. Unlike the traditional particle-in-cell (PIC) method, which is commonly used for solving this problem, the AP-Cloud adaptively selects computational nodes or particles to deliver higher accuracy and efficiency when the particle distribution is highly non-uniform. Unlike other adaptive techniques for PIC, our method balances the errors in PDE discretization and Monte Carlo integration, and discretizes the differential operators using a generalized finite difference (GFD) method based on a weighted least square formulation. As a result, AP-Cloud is independent of the geometric shapes ofmore » computational domains and is free of artificial parameters. Efficient and robust implementation is achieved through an octree data structure with 2:1 balance. We analyze the accuracy and convergence order of AP-Cloud theoretically, and verify the method using an electrostatic problem of a particle beam with halo. Here, simulation results show that the AP-Cloud method is substantially more accurate and faster than the traditional PIC, and it is free of artificial forces that are typical for some adaptive PIC techniques.« less

AP-Cloud: Adaptive Particle-in-Cloud method for optimal solutions to Vlasov–Poisson equation

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

Wang, Xingyu; Samulyak, Roman, E-mail: roman.samulyak@stonybrook.edu; Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973

We propose a new adaptive Particle-in-Cloud (AP-Cloud) method for obtaining optimal numerical solutions to the Vlasov–Poisson equation. Unlike the traditional particle-in-cell (PIC) method, which is commonly used for solving this problem, the AP-Cloud adaptively selects computational nodes or particles to deliver higher accuracy and efficiency when the particle distribution is highly non-uniform. Unlike other adaptive techniques for PIC, our method balances the errors in PDE discretization and Monte Carlo integration, and discretizes the differential operators using a generalized finite difference (GFD) method based on a weighted least square formulation. As a result, AP-Cloud is independent of the geometric shapes ofmore » computational domains and is free of artificial parameters. Efficient and robust implementation is achieved through an octree data structure with 2:1 balance. We analyze the accuracy and convergence order of AP-Cloud theoretically, and verify the method using an electrostatic problem of a particle beam with halo. Simulation results show that the AP-Cloud method is substantially more accurate and faster than the traditional PIC, and it is free of artificial forces that are typical for some adaptive PIC techniques.« less

AP-Cloud: Adaptive particle-in-cloud method for optimal solutions to Vlasov–Poisson equation

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

Wang, Xingyu; Samulyak, Roman; Jiao, Xiangmin

We propose a new adaptive Particle-in-Cloud (AP-Cloud) method for obtaining optimal numerical solutions to the Vlasov–Poisson equation. Unlike the traditional particle-in-cell (PIC) method, which is commonly used for solving this problem, the AP-Cloud adaptively selects computational nodes or particles to deliver higher accuracy and efficiency when the particle distribution is highly non-uniform. Unlike other adaptive techniques for PIC, our method balances the errors in PDE discretization and Monte Carlo integration, and discretizes the differential operators using a generalized finite difference (GFD) method based on a weighted least square formulation. As a result, AP-Cloud is independent of the geometric shapes ofmore » computational domains and is free of artificial parameters. Efficient and robust implementation is achieved through an octree data structure with 2:1 balance. We analyze the accuracy and convergence order of AP-Cloud theoretically, and verify the method using an electrostatic problem of a particle beam with halo. Here, simulation results show that the AP-Cloud method is substantially more accurate and faster than the traditional PIC, and it is free of artificial forces that are typical for some adaptive PIC techniques.« less

Fluctuations, noise, and numerical methods in gyrokinetic particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas Grant

In this thesis, the role of the "marker weight" (or "particle weight") used in gyrokinetic particle-in-cell (PIC) simulations is explored. Following a review of the foundations and major developments of gyrokinetic theory, key concepts of the Monte Carlo methods which form the basis for PIC simulations are set forth. Consistent with these methods, a Klimontovich representation for the set of simulation markers is developed in the extended phase space {R, v||, v ⊥, W, P} (with the additional coordinates representing weight fields); clear distinctions are consequently established between the marker distribution function and various physical distribution functions (arising from diverse moments of the marker distribution). Equations describing transport in the simulation are shown to be easily derivable using the formalism. The necessity of a two-weight model for nonequilibrium simulations is demonstrated, and a simple method for calculating the second (background-related) weight is presented. Procedures for arbitrary marker loading schemes in gyrokinetic PIC simulations are outlined; various initialization methods for simulations are compared. Possible effects of inadequate velocity-space resolution in gyrokinetic continuum simulations are explored. The "partial-f" simulation method is developed and its limitations indicated. A quasilinear treatment of electrostatic drift waves is shown to correctly predict nonlinear saturation amplitudes, and the relevance of the gyrokinetic fluctuation-dissipation theorem in assessing the effects of discrete-marker-induced statistical noise on the resulting marginally stable states is demonstrated.

Formation of electrostatic structures by wakefield acceleration in ultrarelativistic plasma flows: Electron acceleration to cosmic ray energies

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

Dieckmann, M.E.; Shukla, P.K.; Eliasson, B.

2006-06-15

The ever increasing performance of supercomputers is now enabling kinetic simulations of extreme astrophysical and laser produced plasmas. Three-dimensional particle-in-cell (PIC) simulations of relativistic shocks have revealed highly filamented spatial structures and their ability to accelerate particles to ultrarelativistic speeds. However, these PIC simulations have not yet revealed mechanisms that could produce particles with tera-electron volt energies and beyond. In this work, PIC simulations in one dimension (1D) of the foreshock region of an internal shock in a gamma ray burst are performed to address this issue. The large spatiotemporal range accessible to a 1D simulation enables the self-consistent evolutionmore » of proton phase space structures that can accelerate particles to giga-electron volt energies in the jet frame of reference, and to tens of tera-electron volt in the Earth's frame of reference. One potential source of ultrahigh energy cosmic rays may thus be the thermalization of relativistically moving plasma.« less

Modeling of negative ion extraction from a magnetized plasma source: Derivation of scaling laws and description of the origins of aberrations in the ion beam

NASA Astrophysics Data System (ADS)

Fubiani, G.; Garrigues, L.; Boeuf, J. P.

2018-02-01

We model the extraction of negative ions from a high brightness high power magnetized negative ion source. The model is a Particle-In-Cell (PIC) algorithm with Monte-Carlo Collisions. The negative ions are generated only on the plasma grid surface (which separates the plasma from the electrostatic accelerator downstream). The scope of this work is to derive scaling laws for the negative ion beam properties versus the extraction voltage (potential of the first grid of the accelerator) and plasma density and investigate the origins of aberrations on the ion beam. We show that a given value of the negative ion beam perveance correlates rather well with the beam profile on the extraction grid independent of the simulated plasma density. Furthermore, the extracted beam current may be scaled to any value of the plasma density. The scaling factor must be derived numerically but the overall gain of computational cost compared to performing a PIC simulation at the real plasma density is significant. Aberrations appear for a meniscus curvature radius of the order of the radius of the grid aperture. These aberrations cannot be cancelled out by switching to a chamfered grid aperture (as in the case of positive ions).

Nonlinear Evolution of Counter-Propagating Whistler Mode Waves Excited by Anisotropic Electrons Within the Equatorial Source Region: 1-D PIC Simulations

NASA Astrophysics Data System (ADS)

Chen, Huayue; Gao, Xinliang; Lu, Quanming; Sun, Jicheng; Wang, Shui

2018-02-01

Nonlinear physical processes related to whistler mode waves are attracting more and more attention for their significant role in reshaping whistler mode spectra in the Earth's magnetosphere. Using a 1-D particle-in-cell simulation model, we have investigated the nonlinear evolution of parallel counter-propagating whistler mode waves excited by anisotropic electrons within the equatorial source region. In our simulations, after the linear phase of whistler mode instability, the strong electrostatic standing structures along the background magnetic field will be formed, resulting from the coupling between excited counter-propagating whistler mode waves. The wave numbers of electrostatic standing structures are about twice those of whistler mode waves generated by anisotropic hot electrons. Moreover, these electrostatic standing structures can further be coupled with either parallel or antiparallel propagating whistler mode waves to excite high-k modes in this plasma system. Compared with excited whistler mode waves, these high-k modes typically have 3 times wave number, same frequency, and about 2 orders of magnitude smaller amplitude. Our study may provide a fresh view on the evolution of whistler mode waves within their equatorial source regions in the Earth's magnetosphere.

Kinetic electron and ion instability of the lunar wake simulated at physical mass ratio

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

Haakonsen, Christian Bernt, E-mail: chaako@mit.edu; Hutchinson, Ian H., E-mail: ihutch@mit.edu; Zhou, Chuteng, E-mail: ctzhou@mit.edu

2015-03-15

The solar wind wake behind the moon is studied with 1D electrostatic particle-in-cell (PIC) simulations using a physical ion to electron mass ratio (unlike prior investigations); the simulations also apply more generally to supersonic flow of dense magnetized plasma past non-magnetic objects. A hybrid electrostatic Boltzmann electron treatment is first used to investigate the ion stability in the absence of kinetic electron effects, showing that the ions are two-stream unstable for downstream wake distances (in lunar radii) greater than about three times the solar wind Mach number. Simulations with PIC electrons are then used to show that kinetic electron effectsmore » can lead to disruption of the ion beams at least three times closer to the moon than in the hybrid simulations. This disruption occurs as the result of a novel wake phenomenon: the non-linear growth of electron holes spawned from a narrow dimple in the electron velocity distribution. Most of the holes arising from the dimple are small and quickly leave the wake, approximately following the unperturbed electron phase-space trajectories, but some holes originating near the center of the wake remain and grow large enough to trigger disruption of the ion beams. Non-linear kinetic-electron effects are therefore essential to a comprehensive understanding of the 1D electrostatic stability of such wakes, and possible observational signatures in ARTEMIS data from the lunar wake are discussed.« less

Recent advances in nonlinear implicit, electrostatic particle-in-cell (PIC) algorithms

NASA Astrophysics Data System (ADS)

Chen, Guangye; Chacón, Luis; Barnes, Daniel

2012-10-01

An implicit 1D electrostatic PIC algorithmfootnotetextChen, Chac'on, Barnes, J. Comput. Phys. 230 (2011) has been developed that satisfies exact energy and charge conservation. The algorithm employs a kinetic-enslaved Jacobian-free Newton-Krylov methodfootnotetextIbid. that ensures nonlinear convergence while taking timesteps comparable to the dynamical timescale of interest. Here we present two main improvements of the algorithm. The first is the formulation of a preconditioner based on linearized fluid equations, which are closed using available particle information. The computational benefit is that solving the fluid system is much cheaper than the kinetic one. The effectiveness of the preconditioner in accelerating nonlinear iterations on challenging problems will be demonstrated. A second improvement is the generalization of Ref. 1 to curvilinear meshes,footnotetextChac'on, Chen, Barnes, J. Comput. Phys. submitted (2012) with a hybrid particle update of positions and velocities in logical and physical space respectively.footnotetextSwift, J. Comp. Phys., 126 (1996) The curvilinear algorithm remains exactly charge and energy-conserving, and can be extended to multiple dimensions. We demonstrate the accuracy and efficiency of the algorithm with a 1D ion-acoustic shock wave simulation.

Simulation of electrostatic ion instabilities in the presence of parallel currents and transverse electric fields

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Ganguli, G.; Lee, Y. C.; Palmadesso, P. J.

1989-01-01

A spatially two-dimensional electrostatic PIC simulation code was used to study the stability of a plasma equilibrium characterized by a localized transverse dc electric field and a field-aligned drift for L is much less than Lx, where Lx is the simulation length in the x direction and L is the scale length associated with the dc electric field. It is found that the dc electric field and the field-aligned current can together play a synergistic role to enable the excitation of electrostatic waves even when the threshold values of the field aligned drift and the E x B drift are individually subcritical. The simulation results show that the growing ion waves are associated with small vortices in the linear stage, which evolve to the nonlinear stage dominated by larger vortices with lower frequencies.

Green Tea Catechin-Based Complex Micelles Combined with Doxorubicin to Overcome Cardiotoxicity and Multidrug Resistance

PubMed Central

Cheng, Tangjian; Liu, Jinjian; Ren, Jie; Huang, Fan; Ou, Hanlin; Ding, Yuxun; Zhang, Yumin; Ma, Rujiang; An, Yingli; Liu, Jianfeng; Shi, Linqi

2016-01-01

Chemotherapy for cancer treatment has been demonstrated to cause some side effects on healthy tissues and multidrug resistance of the tumor cells, which greatly limits therapeutic efficacy. To address these limitations and achieve better therapeutic efficacy, combination therapy based on nanoparticle platforms provides a promising approach through delivering different agents simultaneously to the same destination with synergistic effect. In this study, a novel green tea catechin-based polyion complex (PIC) micelle loaded with doxorubicin (DOX) and (-)-Epigallocatechin-3-O-gallate (EGCG) was constructed through electrostatic interaction and phenylboronic acid-catechol interaction between poly(ethylene glycol)-block-poly(lysine-co-lysine-phenylboronic acid) (PEG-PLys/PBA) and EGCG. DOX was co-loaded in the PIC micelles through π-π stacking interaction with EGCG. The phenylboronic acid-catechol interaction endowed the PIC micelles with high stability under physiological condition. Moreover, acid cleavability of phenylboronic acid-catechol interaction in the micelle core has significant benefits for delivering EGCG and DOX to same destination with synergistic effects. In addition, benefiting from the oxygen free radicals scavenging activity of EGCG, combination therapy with EGCG and DOX in the micelle core could protect the cardiomyocytes from DOX-mediated cardiotoxicity according to the histopathologic analysis of hearts. Attributed to modulation of EGCG on P-glycoprotein (P-gp) activity, this kind of PIC micelles could effectively reverse multidrug resistance of cancer cells. These results suggested that EGCG based PIC micelles could effectively overcome DOX induced cardiotoxicity and multidrug resistance. PMID:27375779

Green Tea Catechin-Based Complex Micelles Combined with Doxorubicin to Overcome Cardiotoxicity and Multidrug Resistance.

PubMed

Cheng, Tangjian; Liu, Jinjian; Ren, Jie; Huang, Fan; Ou, Hanlin; Ding, Yuxun; Zhang, Yumin; Ma, Rujiang; An, Yingli; Liu, Jianfeng; Shi, Linqi

2016-01-01

Chemotherapy for cancer treatment has been demonstrated to cause some side effects on healthy tissues and multidrug resistance of the tumor cells, which greatly limits therapeutic efficacy. To address these limitations and achieve better therapeutic efficacy, combination therapy based on nanoparticle platforms provides a promising approach through delivering different agents simultaneously to the same destination with synergistic effect. In this study, a novel green tea catechin-based polyion complex (PIC) micelle loaded with doxorubicin (DOX) and (-)-Epigallocatechin-3-O-gallate (EGCG) was constructed through electrostatic interaction and phenylboronic acid-catechol interaction between poly(ethylene glycol)-block-poly(lysine-co-lysine-phenylboronic acid) (PEG-PLys/PBA) and EGCG. DOX was co-loaded in the PIC micelles through π-π stacking interaction with EGCG. The phenylboronic acid-catechol interaction endowed the PIC micelles with high stability under physiological condition. Moreover, acid cleavability of phenylboronic acid-catechol interaction in the micelle core has significant benefits for delivering EGCG and DOX to same destination with synergistic effects. In addition, benefiting from the oxygen free radicals scavenging activity of EGCG, combination therapy with EGCG and DOX in the micelle core could protect the cardiomyocytes from DOX-mediated cardiotoxicity according to the histopathologic analysis of hearts. Attributed to modulation of EGCG on P-glycoprotein (P-gp) activity, this kind of PIC micelles could effectively reverse multidrug resistance of cancer cells. These results suggested that EGCG based PIC micelles could effectively overcome DOX induced cardiotoxicity and multidrug resistance.

Adjuvant-Loaded Spiky Gold Nanoparticles for Activation of Innate Immune Cells.

PubMed

Nam, Jutaek; Son, Sejin; Moon, James J

2017-10-01

Gold nanoparticles are versatile carriers for delivery of biomacromolecules. Here, we have developed spiky gold nanoparticles (SGNPs) that can efficiently deliver immunostimulatory agents. Our goal was to develop a platform technology for co-delivery of multiple adjuvant molecules for synergistic stimulation and maturation of innate immune cells. SGNPs were synthesized by a seed-mediated, surfactant-free synthesis method and incorporated with polyinosinic-polycytidylic acid (pIC) and DNA oligonucleotide containing unmethylated CpG motif (CpG) by an electrostatic layer-by-layer approach. Adjuvant-loaded SGNP nano-complexes were examined for their biophysical and biochemical properties and studied for immune activation using bone marrow-derived dendritic cells (BMDCs). We have synthesized SGNPs with branched nano-spikes layered with pIC and/or CpG. Adjuvant-loaded SGNP nano-complexes promoted cellular uptake of the adjuvants. Importantly, we achieved spatio-temporal control over co-delivery of pIC and CpG via SGNPs, which produced synergistic enhancement in cytokine release (IL-6, TNF-α) and upregulation of co-stimulatory markers (CD40, CD80, CD86) in BMDCs, compared with pIC, CpG, or their admixtures. SGNPs serve as a versatile delivery platform that allows flexible and on-demand cargo fabrication for strong activation of innate immune cells.

Monoenergetic ion acceleration and Rayleigh-Taylor instability of the composite target irradiated by the laser pulse

NASA Astrophysics Data System (ADS)

Khudik, Vladimir; Yi, S. Austin; Shvets, Gennady

2012-10-01

Acceleration of ions in the two-specie composite target irradiated by a circularly polarized laser pulse is studied analytically and via particle-in-cell (PIC) simulations. A self-consistent analytical model of the composite target is developed. In this model, target parameters are stationary in the center of mass of the system: heavy and light ions are completely separated from each other and form two layers, while electrons are bouncing in the potential well formed by the laser ponderomotive and electrostatic potentials. They are distributed in the direction of acceleration by the Boltzmann law and over velocities by the Maxwell-Juttner law. The laser pulse interacts directly only with electrons in a thin sheath layer, and these electrons transfer the laser pressure to the target ions. In the fluid approximation it is shown, the composite target is still susceptible to the Rayleigh-Taylor instability [1]. Using PIC simulations we found the growth rate of initially seeded perturbations as a function of their wavenumber for different composite target parameters and compare it with analytical results. Useful scaling laws between this rate and laser pulse pressure and target parameters are discussed.[4pt] [1] T.P. Yu, A. Pukhov, G. Shvets, M. Chen, T. H. Ratliff, S. A. Yi, and V. Khudik, Phys. Plasmas, 18, 043110 (2011).

A Variational Formulation of Macro-Particle Algorithms for Kinetic Plasma Simulations

NASA Astrophysics Data System (ADS)

Shadwick, B. A.

2013-10-01

Macro-particle based simulations methods are in widespread use in plasma physics; their computational efficiency and intuitive nature are largely responsible for their longevity. In the main, these algorithms are formulated by approximating the continuous equations of motion. For systems governed by a variational principle (such as collisionless plasmas), approximations of the equations of motion is known to introduce anomalous behavior, especially in system invariants. We present a variational formulation of particle algorithms for plasma simulation based on a reduction of the distribution function onto a finite collection of macro-particles. As in the usual Particle-In-Cell (PIC) formulation, these macro-particles have a definite momentum and are spatially extended. The primary advantage of this approach is the preservation of the link between symmetries and conservation laws. For example, nothing in the reduction introduces explicit time dependence to the system and, therefore, the continuous-time equations of motion exactly conserve energy; thus, these models are free of grid-heating. In addition, the variational formulation allows for constructing models of arbitrary spatial and temporal order. In contrast, the overall accuracy of the usual PIC algorithm is at most second due to the nature of the force interpolation between the gridded field quantities and the (continuous) particle position. Again in contrast to the usual PIC algorithm, here the macro-particle shape is arbitrary; the spatial extent is completely decoupled from both the grid-size and the ``smoothness'' of the shape; smoother particle shapes are not necessarily larger. For simplicity, we restrict our discussion to one-dimensional, non-relativistic, un-magnetized, electrostatic plasmas. We comment on the extension to the electromagnetic case. Supported by the US DoE under contract numbers DE-FG02-08ER55000 and DE-SC0008382.

The Electrostatic Instability for Realistic Pair Distributions in Blazar/EBL Cascades

NASA Astrophysics Data System (ADS)

Vafin, S.; Rafighi, I.; Pohl, M.; Niemiec, J.

2018-04-01

This work revisits the electrostatic instability for blazar-induced pair beams propagating through the intergalactic medium (IGM) using linear analysis and PIC simulations. We study the impact of the realistic distribution function of pairs resulting from the interaction of high-energy gamma-rays with the extragalactic background light. We present analytical and numerical calculations of the linear growth rate of the instability for the arbitrary orientation of wave vectors. Our results explicitly demonstrate that the finite angular spread of the beam dramatically affects the growth rate of the waves, leading to the fastest growth for wave vectors quasi-parallel to the beam direction and a growth rate at oblique directions that is only a factor of 2–4 smaller compared to the maximum. To study the nonlinear beam relaxation, we performed PIC simulations that take into account a realistic wide-energy distribution of beam particles. The parameters of the simulated beam-plasma system provide an adequate physical picture that can be extrapolated to realistic blazar-induced pairs. In our simulations, the beam looses only 1% of its energy, and we analytically estimate that the beam would lose its total energy over about 100 simulation times. An analytical scaling is then used to extrapolate the parameters of realistic blazar-induced pair beams. We find that they can dissipate their energy slightly faster by the electrostatic instability than through inverse-Compton scattering. The uncertainties arising from, e.g., details of the primary gamma-ray spectrum are too large to make firm statements for individual blazars, and an analysis based on their specific properties is required.

Electron Surfing Acceleration in High Mach Number Shocks

NASA Astrophysics Data System (ADS)

Hoshino, M.; Amano, T.; Matsumoto, Y.

2016-12-01

Many energetic events associated with shock waves have been argued in this context of the diffusive shock acceleration (DSA), and the origin of high-energy particles observed in astrophysical shocks are believed to be attributed to DSA. However, electron nonthermal acceleration still remains an unresolved issue of considerable interest. While cosmic rays of supernova remnant shocks with power-law spectra are believed to be produced by DSA, energetic electrons with a power-law energy spectrum are rarely ever observed at interplanetary shocks and at planetary bow shocks (e.g., Lario et al. 2003), and the diffusive-type acceleration seems to be necessarily malfunctioning in the heliosphere. The malfunctioning reason is thought to be a lack of pre-acceleration mechanism of supra-thermal electrons.In this presentation, we propose that the supra-thermal electrons can be generated by the mechanism of shock surfing acceleration (SSA) in a high Mach number magnetosonic shock. In the surfing mechanism, a series of large-amplitude electrostatic waves are excited by Buneman instability in the foot region under the interaction between the reflected ions and the incoming electrons, and it is argued that the electrons trapped in the electrostatic waves can be accelerated up to a relativistic energy (Hoshino and Shimada, 2002). Since the electron SSA has been studied based on one- or two-dimensional PIC simulations so far, SSA in three-dimensional system is questionable and remains an open question. We discuss based on our theoretical model and three-dimensional PIC simulation with a high-performance computing that the efficiency of SSA in three-dimensional system remains amazingly strong and plays an important role on the electron pre-acceleration/injection problem.

Dissemination and support of ARGUS for accelerator applications

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

Not Available

The ARGUS code is a three-dimensional code system for simulating for interactions between charged particles, electric and magnetic fields, and complex structure. It is a system of modules that share common utilities for grid and structure input, data handling, memory management, diagnostics, and other specialized functions. The code includes the fields due to the space charge and current density of the particles to achieve a self-consistent treatment of the particle dynamics. The physic modules in ARGUS include three-dimensional field solvers for electrostatics and electromagnetics, a three-dimensional electromagnetic frequency-domain module, a full particle-in-cell (PIC) simulation module, and a steady-state PIC model.more » These are described in the Appendix to this report. This project has a primary mission of developing the capabilities of ARGUS in accelerator modeling of release to the accelerator design community. Five major activities are being pursued in parallel during the first year of the project. To improve the code and/or add new modules that provide capabilities needed for accelerator design. To produce a User's Guide that documents the use of the code for all users. To release the code and the User's Guide to accelerator laboratories for their own use, and to obtain feed-back from the. To build an interactive user interface for setting up ARGUS calculations. To explore the use of ARGUS on high-power workstation platforms.« less

Observation of 1-D time dependent non-propagating laser plasma structures using fluid and PIC codes

NASA Astrophysics Data System (ADS)

Verma, Deepa; Bera, Ratan Kumar; Kumar, Atul; Patel, Bhavesh; Das, Amita

2017-12-01

The manuscript reports the observation of time dependent localized and non-propagating structures in the coupled laser plasma system through 1-D fluid and Particle-In-Cell (PIC) simulations. It is reported that such structures form spontaneously as a result of collision amongst certain exact solitonic solutions. They are seen to survive as coherent entities for a long time up to several hundreds of plasma periods. Furthermore, it is shown that such time dependence can also be artificially recreated by significantly disturbing the delicate balance between the radiation and the density fields required for the exact non-propagating solution obtained by Esirkepov et al., JETP 68(1), 36-41 (1998). The ensuing time evolution is an interesting interplay between kinetic and field energies of the system. The electrostatic plasma oscillations are coupled with oscillations in the electromagnetic field. The inhomogeneity of the background and the relativistic nature, however, invariably produces large amplitude density perturbations leading to its wave breaking. In the fluid simulations, the signature of wave breaking can be discerned by a drop in the total energy which evidently gets lost to the grid. The PIC simulations are observed to closely follow the fluid simulations till the point of wave breaking. However, the total energy in the case of PIC simulations is seen to remain conserved throughout the simulations. At the wave breaking, the particles are observed to acquire thermal kinetic energy in the case of PIC. Interestingly, even after wave breaking, compact coherent structures with trapped radiation inside high-density peaks continue to exist both in PIC and fluid simulations. Although the time evolution does not exactly match in the two simulations as it does prior to the process of wave breaking, the time-dependent features exhibited by the remnant structures are characteristically similar.

Issues and opportunities: beam simulations for heavy ion fusion

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

Friedman, A

1999-07-15

UCRL- JC- 134975 PREPRINT code offering 3- D, axisymmetric, and ''transverse slice'' (steady flow) geometries, with a hierarchy of models for the ''lattice'' of focusing, bending, and accelerating elements. Interactive and script- driven code steering is afforded through an interpreter interface. The code runs with good parallel scaling on the T3E. Detailed simulations of machine segments and of complete small experiments, as well as simplified full- system runs, have been carried out, partially benchmarking the code. A magnetoinductive model, with module impedance and multi- beam effects, is under study. experiments, including an injector scalable to multi- beam arrays, a high-more » current beam transport and acceleration experiment, and a scaled final- focusing experiment. These ''phase I'' projects are laying the groundwork for the next major step in HIF development, the Integrated Research Experiment (IRE). Simulations aimed directly at the IRE must enable us to: design a facility with maximum power on target at minimal cost; set requirements for hardware tolerances, beam steering, etc.; and evaluate proposed chamber propagation modes. Finally, simulations must enable us to study all issues which arise in the context of a fusion driver, and must facilitate the assessment of driver options. In all of this, maximum advantage must be taken of emerging terascale computer architectures, requiring an aggressive code development effort. An organizing principle should be pursuit of the goal of integrated and detailed source- to- target simulation. methods for analysis of the beam dynamics in the various machine concepts, using moment- based methods for purposes of design, waveform synthesis, steering algorithm synthesis, etc. Three classes of discrete- particle models should be coupled: (1) electrostatic/ magnetoinductive PIC simulations should track the beams from the source through the final- focusing optics, passing details of the time- dependent distribution function to (2) electromagnetic or magnetoinductive PIC or hybrid PIG/ fluid simulations in the fusion chamber (which would finally pass their particle trajectory information to the radiation- hydrodynamics codes used for target design); in parallel, (3) detailed PIC, delta- f, core/ test- particle, and perhaps continuum Vlasov codes should be used to study individual sections of the driver and chamber very carefully; consistency may be assured by linking data from the PIC sequence, and knowledge gained may feed back into that sequence.« less

Hot DA white dwarf model atmosphere calculations: including improved Ni PI cross-sections

NASA Astrophysics Data System (ADS)

Preval, S. P.; Barstow, M. A.; Badnell, N. R.; Hubeny, I.; Holberg, J. B.

2017-02-01

To calculate realistic models of objects with Ni in their atmospheres, accurate atomic data for the relevant ionization stages need to be included in model atmosphere calculations. In the context of white dwarf stars, we investigate the effect of changing the Ni IV-VI bound-bound and bound-free atomic data on model atmosphere calculations. Models including photoionization cross-section (PICS) calculated with AUTOSTRUCTURE show significant flux attenuation of up to ˜80 per cent shortward of 180 Å in the extreme ultraviolet (EUV) region compared to a model using hydrogenic PICS. Comparatively, models including a larger set of Ni transitions left the EUV, UV, and optical continua unaffected. We use models calculated with permutations of these atomic data to test for potential changes to measured metal abundances of the hot DA white dwarf G191-B2B. Models including AUTOSTRUCTURE PICS were found to change the abundances of N and O by as much as ˜22 per cent compared to models using hydrogenic PICS, but heavier species were relatively unaffected. Models including AUTOSTRUCTURE PICS caused the abundances of N/O IV and V to diverge. This is because the increased opacity in the AUTOSTRUCTURE PICS model causes these charge states to form higher in the atmosphere, more so for N/O V. Models using an extended line list caused significant changes to the Ni IV-V abundances. While both PICS and an extended line list cause changes in both synthetic spectra and measured abundances, the biggest changes are caused by using AUTOSTRUCTURE PICS for Ni.

In vitro and in vivo protein release and anti-ischemia/reperfusion injury properties of bone morphogenetic protein-2-loaded glycyrrhetinic acid-poly(ethylene glycol)-b-poly(l-lysine) nanoparticles

PubMed Central

Shan, Fang; Liu, YuJuan; Jiang, Haiying; Tong, Fei

2017-01-01

Here, we describe a bone morphogenetic protein-2 (BMP-2) nanocarrier based on glycyrrhetinic acid (GA)-poly(ethylene glycol) (PEG)-b-poly(l-lysine) (PLL). A protein nanocarrier was synthesized, characterized and evaluated as a BMP-2 delivery system. The designed nanocarrier was synthesized based on the ring-opening polymerization of amino acid N-carboxyanhydride. The final product was measured with 1H nuclear magnetic resonance. GA-PEG-b-PLL nanocarrier could combine with BMP-2 through electrostatic interaction to form polyion complex (PIC) micelles. BMP-2 could be rapidly and efficiently encapsulated through the GA-PEG-b-PLL nanocarrier under physiological conditions, exhibiting efficient encapsulation and sustained release. In addition, the GA-PEG-b-PLL-mediated BMP-2 delivery system could target the liver against hepatic diseases as it has GA-binding receptors. The anti-hepatic ischemia/reperfusion injury (anti-HI/RI) effect of BMP-2/GA-PEG-b-PLL PIC micelles was investigated in rats using free BMP-2 and BMP-2/PEG-b-PLL PIC micelles as controls, and the results showed that BMP-2/GA-PEG-b-PLL PIC micelles indicated significantly enhanced anti-HI/RI property compared to BMP-2 and BMP-2/PEG-b-PLL. All results suggested that GA-PEG-b-PLL could be used as a potential BMP-2 nanocarrier. PMID:29089759

UCLA Final Technical Report for the "Community Petascale Project for Accelerator Science and Simulation”.

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

Mori, Warren

The UCLA Plasma Simulation Group is a major partner of the “Community Petascale Project for Accelerator Science and Simulation”. This is the final technical report. We include an overall summary, a list of publications, progress for the most recent year, and individual progress reports for each year. We have made tremendous progress during the three years. SciDAC funds have contributed to the development of a large number of skeleton codes that illustrate how to write PIC codes with a hierarchy of parallelism. These codes cover 2D and 3D as well as electrostatic solvers (which are used in beam dynamics codesmore » and quasi-static codes) and electromagnetic solvers (which are used in plasma based accelerator codes). We also used these ideas to develop a GPU enabled version of OSIRIS. SciDAC funds were also contributed to the development of strategies to eliminate the Numerical Cerenkov Instability (NCI) which is an issue when carrying laser wakefield accelerator (LWFA) simulations in a boosted frame and when quantifying the emittance and energy spread of self-injected electron beams. This work included the development of a new code called UPIC-EMMA which is an FFT based electromagnetic PIC code and to new hybrid algorithms in OSIRIS. A new hybrid (PIC in r-z and gridless in φ) algorithm was implemented into OSIRIS. In this algorithm the fields and current are expanded into azimuthal harmonics and the complex amplitude for each harmonic is calculated separately. The contributions from each harmonic are summed and then used to push the particles. This algorithm permits modeling plasma based acceleration with some 3D effects but with the computational load of an 2D r-z PIC code. We developed a rigorously charge conserving current deposit for this algorithm. Very recently, we made progress in combining the speed up from the quasi-3D algorithm with that from the Lorentz boosted frame. SciDAC funds also contributed to the improvement and speed up of the quasi-static PIC code QuickPIC. We have also used our suite of PIC codes to make scientific discovery. Highlights include supporting FACET experiments which achieved the milestones of showing high beam loading and energy transfer efficiency from a drive electron beam to a witness electron beam and the discovery of a self-loading regime a for high gradient acceleration of a positron beam. Both of these experimental milestones were published in Nature together with supporting QuickPIC simulation results. Simulation results from QuickPIC were used on the cover of Nature in one case. We are also making progress on using highly resolved QuickPIC simulations to show that ion motion may not lead to catastrophic emittance growth for tightly focused electron bunches loaded into nonlinear wakefields. This could mean that fully self-consistent beam loading scenarios are possible. This work remains in progress. OSIRIS simulations were used to discover how 200 MeV electron rings are formed in LWFA experiments, on how to generate electrons that have a series of bunches on nanometer scale, and how to transport electron beams from (into) plasma sections into (from) conventional beam optic sections.« less

PIC Modeling of Argon Plasma Flow in MNX

NASA Astrophysics Data System (ADS)

Cohen, Samuel; Sefkow, Adam

2007-11-01

A linear helicon-heated plasma device - the Magnetic Nozzle Experiment (MNX) at the Princeton Plasma Physics Laboratory - is used for studies of the formation of strong electrostatic double layers near mechanical and magnetic apertures and the acceleration of plasma ions into supersonic directed beams. In order to characterize the role of the aperture and its involvement with ion acceleration, detailed particle-in-cell simulations are employed to study the effects of the surrounding boundary geometry on the plasma dynamics near the aperture region, within which the transition from a collisional to collisionless regime occurs. The presence of a small superthermal electron population is examined, and the model includes a background neutral population which can be ionized by energetic electrons. By self-consistently evaluating the temporal evolution of the plasma in the vicinity of the aperture, the formation mechanism of the double layer is investigated.

Neuromodulation impact on nonlinear firing behavior of a reduced model motoneuron with the active dendrite

PubMed Central

Kim, Hojeong; Heckman, C. J.

2014-01-01

Neuromodulatory inputs from brainstem systems modulate the normal function of spinal motoneurons by altering the activation properties of persistent inward currents (PICs) in their dendrites. However, the effect of the PIC on firing outputs also depends on its location in the dendritic tree. To investigate the interaction between PIC neuromodulation and PIC location dependence, we used a two-compartment model that was biologically realistic in that it retains directional and frequency-dependent electrical coupling between the soma and the dendrites, as seen in multi-compartment models based on full anatomical reconstructions of motoneurons. Our two-compartment approach allowed us to systematically vary the coupling parameters between the soma and the dendrite to accurately reproduce the effect of location of the dendritic PIC on the generation of nonlinear (hysteretic) motoneuron firing patterns. Our results show that as a single parameter value for PIC activation was either increased or decreased by 20% from its default value, the solution space of the coupling parameter values for nonlinear firing outputs was drastically reduced by approximately 80%. As a result, the model tended to fire only in a linear mode at the majority of dendritic PIC sites. The same results were obtained when all parameters for the PIC activation simultaneously changed only by approximately ±10%. Our results suggest the democratization effect of neuromodulation: the neuromodulation by the brainstem systems may play a role in switching the motoneurons with PICs at different dendritic locations to a similar mode of firing by reducing the effect of the dendritic location of PICs on the firing behavior. PMID:25309410

Pseudospectral Model for Hybrid PIC Hall-effect Thruster Simulation

DTIC Science & Technology

2015-07-01

and Fernandez6 (hybrid- PIC ). This work follows the example of Lam and Fernandez but substitutes a spectral description in the azimuthal direction to...Paper 3. DATES COVERED (From - To) July 2015-July 2015 4. TITLE AND SUBTITLE Pseudospectral model for hybrid PIC Hall-effect thruster simulationect...of a pseudospectral azimuthal-axial hybrid- PIC HET code which is designed to explicitly resolve and filter azimuthal fluctuations in the

The Heliopause Electrostatic Rapid Transit System (HERTS) Design, Trades, and Analyses Performed in the First Year of a Two Year Investigation

NASA Technical Reports Server (NTRS)

Wiegmann, Bruce M.

2016-01-01

The Heliopause Electrostatic Rapid Transit System (HERTS)1 was one of the seven total Phase II NASA Innovative Advanced Concepts (NIAC) that was down-selected in 2015 for continued funding and research. In Phase I we learned that a spacecraft propelled by an Electric Sail (E-Sail) can travel great astronomical distances, such as to the Heliopause region of the solar system (approx.100 to 120 AU) in approximately one quarter of the time (10 years) versus the time it took the Voyager spacecraft launched in 1977 (36 years). The current work within the Phase II NIAC effort builds upon the work that was done in the Phase I NIAC and is focused on: 1) Testing of plasma interaction with a charged wire in a unique MSFC test chamber, 2) Development of a Particle-in-Cell (PIC) models that are validated in the plasma testing and used to extrapolate to the E-Sail propulsion system design. 3) Further down select of a wire deployment and control approach from those narrowed down in the Phase I effort. This paper will document the findings to date (June, 2016) of the above focused areas.

The ZPIC educational code suite

NASA Astrophysics Data System (ADS)

Calado, R.; Pardal, M.; Ninhos, P.; Helm, A.; Mori, W. B.; Decyk, V. K.; Vieira, J.; Silva, L. O.; Fonseca, R. A.

2017-10-01

Particle-in-Cell (PIC) codes are used in almost all areas of plasma physics, such as fusion energy research, plasma accelerators, space physics, ion propulsion, and plasma processing, and many other areas. In this work, we present the ZPIC educational code suite, a new initiative to foster training in plasma physics using computer simulations. Leveraging on our expertise and experience from the development and use of the OSIRIS PIC code, we have developed a suite of 1D/2D fully relativistic electromagnetic PIC codes, as well as 1D electrostatic. These codes are self-contained and require only a standard laptop/desktop computer with a C compiler to be run. The output files are written in a new file format called ZDF that can be easily read using the supplied routines in a number of languages, such as Python, and IDL. The code suite also includes a number of example problems that can be used to illustrate several textbook and advanced plasma mechanisms, including instructions for parameter space exploration. We also invite contributions to this repository of test problems that will be made freely available to the community provided the input files comply with the format defined by the ZPIC team. The code suite is freely available and hosted on GitHub at https://github.com/zambzamb/zpic. Work partially supported by PICKSC.

Dissemination and support of ARGUS for accelerator applications. Technical progress report, April 24, 1991--January 20, 1992

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

Not Available

The ARGUS code is a three-dimensional code system for simulating for interactions between charged particles, electric and magnetic fields, and complex structure. It is a system of modules that share common utilities for grid and structure input, data handling, memory management, diagnostics, and other specialized functions. The code includes the fields due to the space charge and current density of the particles to achieve a self-consistent treatment of the particle dynamics. The physic modules in ARGUS include three-dimensional field solvers for electrostatics and electromagnetics, a three-dimensional electromagnetic frequency-domain module, a full particle-in-cell (PIC) simulation module, and a steady-state PIC model.more » These are described in the Appendix to this report. This project has a primary mission of developing the capabilities of ARGUS in accelerator modeling of release to the accelerator design community. Five major activities are being pursued in parallel during the first year of the project. To improve the code and/or add new modules that provide capabilities needed for accelerator design. To produce a User`s Guide that documents the use of the code for all users. To release the code and the User`s Guide to accelerator laboratories for their own use, and to obtain feed-back from the. To build an interactive user interface for setting up ARGUS calculations. To explore the use of ARGUS on high-power workstation platforms.« less

Molecular Dynamic 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

2010-11-01

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 (P^3M) code ddcMD to perform these simulations. As a starting point in our study, we examined the wake of a particle passing through a plasma. In this poster, we compare the wake observed in 3D ddcMD simulations with that predicted by Vlasov theory and those observed in the electrostatic PIC code BEPS where the cell size was reduced to .03λD.

Stable carbon isotope signals in particulate organic and inorganic carbon of coccolithophores - A numerical model study for Emiliania huxleyi.

PubMed

Holtz, Lena-Maria; Wolf-Gladrow, Dieter; Thoms, Silke

2017-05-07

A recent numerical cell model, which explains observed light and carbonate system effects on particulate organic and inorganic carbon (POC and PIC) production rates under the assumption of internal pH homeostasis, is extended for stable carbon isotopes ( 12 C, 13 C). Aim of the present study is to mechanistically understand the stable carbon isotopic fractionation signal (ε) in POC and PIC and furthermore the vital effect(s) included in measured ε PIC values. The virtual cell is divided into four compartments, for each of which the 12 C as well as the 13 C carbonate system kinetics are implemented. The compartments are connected to each other via trans-membrane fluxes. In contrast to existing carbon fractionation models, the presented model calculates the disequilibrium state for both carbonate systems and for each compartment. It furthermore calculates POC and PIC production rates as well as ε POC and ε PIC as a function of given light conditions and the compositions of the external carbonate system. Measured POC and PIC production rates as well as ε PIC values are reproduced well by the model (comparison with literature data). The observed light effect on ε POC (increase of ε POC with increasing light intensities), however, is not reproduced by the basic model set-up, which is solely based on RubisCO fractionation. When extending the latter set-up by assuming that biological fractionation includes further carbon fractionation steps besides the one of RubisCO, the observed light effect on ε POC is also reproduced. By means of the extended model version, four different vital effects that superimpose each other in a real cell can be detected. Finally, we discuss potential limitations of the ε PIC proxy. Copyright © 2017 Elsevier Ltd. All rights reserved.

AMBER: a PIC slice code for DARHT

NASA Astrophysics Data System (ADS)

Vay, Jean-Luc; Fawley, William

1999-11-01

The accelerator for the second axis of the Dual Axis Radiographic Hydrodynamic Test (DARHT) facility will produce a 4-kA, 20-MeV, 2-μ s output electron beam with a design goal of less than 1000 π mm-mrad normalized transverse emittance and less than 0.5-mm beam centroid motion. In order to study the beam dynamics throughout the accelerator, we have developed a slice Particle-In-Cell code named AMBER, in which the beam is modeled as a time-steady flow, subject to self, as well as external, electrostatic and magnetostatic fields. The code follows the evolution of a slice of the beam as it propagates through the DARHT accelerator lattice, modeled as an assembly of pipes, solenoids and gaps. In particular, we have paid careful attention to non-paraxial phenomena that can contribute to nonlinear forces and possible emittance growth. We will present the model and the numerical techniques implemented, as well as some test cases and some preliminary results obtained when studying emittance growth during the beam propagation.

eIF1 Loop 2 interactions with Met-tRNAi control the accuracy of start codon selection by the scanning preinitiation complex.

PubMed

Thakur, Anil; Hinnebusch, Alan G

2018-05-01

The eukaryotic 43S preinitiation complex (PIC), bearing initiator methionyl transfer RNA (Met-tRNA i ) in a ternary complex (TC) with eukaryotic initiation factor 2 (eIF2)-GTP, scans the mRNA leader for an AUG codon in favorable context. AUG recognition evokes rearrangement from an open PIC conformation with TC in a "P OUT " state to a closed conformation with TC more tightly bound in a "P IN " state. eIF1 binds to the 40S subunit and exerts a dual role of enhancing TC binding to the open PIC conformation while antagonizing the P IN state, necessitating eIF1 dissociation for start codon selection. Structures of reconstituted PICs reveal juxtaposition of eIF1 Loop 2 with the Met-tRNA i D loop in the P IN state and predict a distortion of Loop 2 from its conformation in the open complex to avoid a clash with Met-tRNA i We show that Ala substitutions in Loop 2 increase initiation at both near-cognate UUG codons and AUG codons in poor context. Consistently, the D71A-M74A double substitution stabilizes TC binding to 48S PICs reconstituted with mRNA harboring a UUG start codon, without affecting eIF1 affinity for 40S subunits. Relatively stronger effects were conferred by arginine substitutions; and no Loop 2 substitutions perturbed the rate of TC loading on scanning 40S subunits in vivo. Thus, Loop 2-D loop interactions specifically impede Met-tRNA i accommodation in the P IN state without influencing the P OUT mode of TC binding; and Arg substitutions convert the Loop 2-tRNA i clash to an electrostatic attraction that stabilizes P IN and enhances selection of poor start codons in vivo.

Theoretical analysis on lower band cascade as a mechanism for multiband chorus in the Earth's magnetosphere

NASA Astrophysics Data System (ADS)

Gao, Xinliang; Lu, Quanming; Wang, Shaojie; Wang, Shui

2018-05-01

Whistler-mode waves play a crucial role in controlling electron dynamics in the Earth's Van Allen radiation belt, which is increasingly important for spacecraft safety. Using THEMIS waveform data, Gao et al. [X. L. Gao, Q. Lu, J. Bortnik, W. Li, L. Chen, and S. Wang, Geophys. Res. Lett., 43, 2343-2350, 2016] have reported two multiband chorus events, wherein upper-band chorus appears at harmonics of lower-band chorus. They proposed that upper-band harmonic waves are excited through the nonlinear coupling between the electromagnetic and electrostatic components of lower-band chorus, a second-order effect called "lower band cascade". However, the theoretical explanation of lower band cascade was not thoroughly explained in the earlier work. In this paper, based on a cold plasma assumption, we have obtained the explicit nonlinear driven force of lower band cascade through a full nonlinear theoretical analysis, which includes both the ponderomotive force and coupling between electrostatic and electromagnetic components of the pump whistler wave. Moreover, we discover the existence of an efficient energy-transfer (E-t) channel from lower-band to upper-band whistler-mode waves during lower band cascade for the first time, which is also confirmed by PIC simulations. For lower-band whistler-mode waves with a small wave normal angle (WNA), the E-t channel is detected when the driven upper-band wave nearly satisfies the linear dispersion relation of whistler mode. While, for lower-band waves with a large WNA, the E-t channel is found when the lower-band wave is close to its resonant frequency, and the driven upper-band wave becomes quasi-electrostatic. Through this efficient channel, the harmonic upper band of whistler waves is generated through energy cascade from the lower band, and the two-band spectral structure of whistler waves is then formed. Both two types of banded whistler-mode spectrum have also been successfully reproduced by PIC simulations.

Australian Validation of the Hierarchical Personality Inventory for Children (HiPIC)

ERIC Educational Resources Information Center

Hopkinson, Laura; Watt, Dianne; Roodenburg, John

2014-01-01

The Hierarchical Personality Inventory for Children (HiPIC) is a developmentally appropriate parent-report measure of the Five Factor Model (FFM) that has been validated in several European languages but only recently in English. The English translation of the HiPIC was evaluated in an Australian context. Parent-rated HiPIC scores were obtained…

PIC code modeling of spacecraft charging potential during electron beam injection into a background of neutral gas and plasma, part 1

NASA Technical Reports Server (NTRS)

Koga, J. K.; Lin, C. S.; Winglee, R. M.

1989-01-01

Injections of nonrelativistic electron beams from an isolated equipotential conductor into a uniform background of plasma and neutral gas were simulated using a 2-D electrostatic particle code. The ionization effects on spacecraft charging are examined by including interactions of electrons with neutral gas. The simulations show that the conductor charging potential decreases with increasing neutral background density due to the production of secondary electrons near the conductor surface. In the spacecraft wake, the background electrons accelerated towards the charged spacecraft produce an enhancement of secondary electrons and ions. Simulations run for longer times indicate that the spacecraft potential is further reduced and short wavelength beam-plasma oscillations appear. The results are applied to explain the spacecraft charging potential measured during the SEPAC experiments from Spacelab 1.

The UPSF code: a metaprogramming-based high-performance automatically parallelized plasma simulation framework

NASA Astrophysics Data System (ADS)

Gao, Xiatian; Wang, Xiaogang; Jiang, Binhao

2017-10-01

UPSF (Universal Plasma Simulation Framework) is a new plasma simulation code designed for maximum flexibility by using edge-cutting techniques supported by C++17 standard. Through use of metaprogramming technique, UPSF provides arbitrary dimensional data structures and methods to support various kinds of plasma simulation models, like, Vlasov, particle in cell (PIC), fluid, Fokker-Planck, and their variants and hybrid methods. Through C++ metaprogramming technique, a single code can be used to arbitrary dimensional systems with no loss of performance. UPSF can also automatically parallelize the distributed data structure and accelerate matrix and tensor operations by BLAS. A three-dimensional particle in cell code is developed based on UPSF. Two test cases, Landau damping and Weibel instability for electrostatic and electromagnetic situation respectively, are presented to show the validation and performance of the UPSF code.

3D-QSAR and docking studies of flavonoids as potent Escherichia coli inhibitors

PubMed Central

Fang, Yajing; Lu, Yulin; Zang, Xixi; Wu, Ting; Qi, XiaoJuan; Pan, Siyi; Xu, Xiaoyun

2016-01-01

Flavonoids are potential antibacterial agents. However, key substituents and mechanism for their antibacterial activity have not been fully investigated. The quantitative structure-activity relationship (QSAR) and molecular docking of flavonoids relating to potent anti-Escherichia coli agents were investigated. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were developed by using the pIC50 values of flavonoids. The cross-validated coefficient (q2) values for CoMFA (0.743) and for CoMSIA (0.708) were achieved, illustrating high predictive capabilities. Selected descriptors for the CoMFA model were ClogP (logarithm of the octanol/water partition coefficient), steric and electrostatic fields, while, ClogP, electrostatic and hydrogen bond donor fields were used for the CoMSIA model. Molecular docking results confirmed that half of the tested flavonoids inhibited DNA gyrase B (GyrB) by interacting with adenosine-triphosphate (ATP) pocket in a same orientation. Polymethoxyl flavones, flavonoid glycosides, isoflavonoids changed their orientation, resulting in a decrease of inhibitory activity. Moreover, docking results showed that 3-hydroxyl, 5-hydroxyl, 7-hydroxyl and 4-carbonyl groups were found to be crucial active substituents of flavonoids by interacting with key residues of GyrB, which were in agreement with the QSAR study results. These results provide valuable information for structure requirements of flavonoids as antibacterial agents. PMID:27049530

Global linear gyrokinetic simulations for LHD including collisions

NASA Astrophysics Data System (ADS)

Kauffmann, K.; Kleiber, R.; Hatzky, R.; Borchardt, M.

2010-11-01

The code EUTERPE uses a Particle-In-Cell (PIC) method to solve the gyrokinetic equation globally (full radius, full flux surface) for three-dimensional equilibria calculated with VMEC. Recently this code has been extended to include multiple kinetic species and electromagnetic effects. Additionally, a pitch-angle scattering operator has been implemented in order to include collisional effects in the simulation of instabilities and to be able to simulate neoclassical transport. As a first application of this extended code we study the effects of collisions on electrostatic ion-temperature-gradient (ITG) instabilities in LHD.

Fully implicit Particle-in-cell algorithms for multiscale plasma simulation

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

Chacon, Luis

The outline of the paper is as follows: Particle-in-cell (PIC) methods for fully ionized collisionless plasmas, explicit vs. implicit PIC, 1D ES implicit PIC (charge and energy conservation, moment-based acceleration), and generalization to Multi-D EM PIC: Vlasov-Darwin model (review and motivation for Darwin model, conservation properties (energy, charge, and canonical momenta), and numerical benchmarks). The author demonstrates a fully implicit, fully nonlinear, multidimensional PIC formulation that features exact local charge conservation (via a novel particle mover strategy), exact global energy conservation (no particle self-heating or self-cooling), adaptive particle orbit integrator to control errors in momentum conservation, and canonical momenta (EM-PICmore » only, reduced dimensionality). The approach is free of numerical instabilities: ω peΔt >> 1, and Δx >> λ D. It requires many fewer dofs (vs. explicit PIC) for comparable accuracy in challenging problems. Significant CPU gains (vs explicit PIC) have been demonstrated. The method has much potential for efficiency gains vs. explicit in long-time-scale applications. Moment-based acceleration is effective in minimizing N FE, leading to an optimal algorithm.« less

Prediction impact curve is a new measure integrating intervention effects in the evaluation of risk models.

PubMed

Campbell, William; Ganna, Andrea; Ingelsson, Erik; Janssens, A Cecile J W

2016-01-01

We propose a new measure of assessing the performance of risk models, the area under the prediction impact curve (auPIC), which quantifies the performance of risk models in terms of their average health impact in the population. Using simulated data, we explain how the prediction impact curve (PIC) estimates the percentage of events prevented when a risk model is used to assign high-risk individuals to an intervention. We apply the PIC to the Atherosclerosis Risk in Communities (ARIC) Study to illustrate its application toward prevention of coronary heart disease. We estimated that if the ARIC cohort received statins at baseline, 5% of events would be prevented when the risk model was evaluated at a cutoff threshold of 20% predicted risk compared to 1% when individuals were assigned to the intervention without the use of a model. By calculating the auPIC, we estimated that an average of 15% of events would be prevented when considering performance across the entire interval. We conclude that the PIC is a clinically meaningful measure for quantifying the expected health impact of risk models that supplements existing measures of model performance. Copyright © 2016 Elsevier Inc. All rights reserved.

Status and future plans for open source QuickPIC

NASA Astrophysics Data System (ADS)

An, Weiming; Decyk, Viktor; Mori, Warren

2017-10-01

QuickPIC is a three dimensional (3D) quasi-static particle-in-cell (PIC) code developed based on the UPIC framework. It can be used for efficiently modeling plasma based accelerator (PBA) problems. With quasi-static approximation, QuickPIC can use different time scales for calculating the beam (or laser) evolution and the plasma response, and a 3D plasma wake field can be simulated using a two-dimensional (2D) PIC code where the time variable is ξ = ct - z and z is the beam propagation direction. QuickPIC can be thousand times faster than the normal PIC code when simulating the PBA. It uses an MPI/OpenMP hybrid parallel algorithm, which can be run on either a laptop or the largest supercomputer. The open source QuickPIC is an object-oriented program with high level classes written in Fortran 2003. It can be found at https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource.git

Constructing a short form of the hierarchical personality inventory for children (HiPIC): the HiPIC-30.

PubMed

Vollrath, Margarete E; Hampson, Sarah E; Torgersen, Svenn

2016-05-01

Children's personality traits are invaluable predictors of concurrent and later mental and physical health. Several validated longer inventories for assessing the widely recognized Five-Factor Model of personality in children are available, but short forms are scarce. This study aimed at constructing a 30-item form of the 144-item Hierarchical Personality Inventory for Children (HiPIC) (Mervielde & De Fruyt, ). Participants were 1543 children aged 6-12 years (sample 1) and 3895 children aged 8 years (sample 2). Sample 1 completed the full HiPIC, from which we constructed the HiPIC-30, and the Child Behaviour Checklist (Achenbach, ). Sample 2 completed the HiPIC-30. The HiPIC-30 personality domains correlated over r = .90 with the full HiPIC domains, had good Cronbach's alphas and correlated similarly with CBCL behaviour problems and gender as the full HiPIC. The factor structures of the HiPIC-30 were convergent across samples, but the imagination factor was not clear-cut. We conclude that the HiPIC-30 is a reliable and valid questionnaire for the Five-Factor personality traits in children. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Coupling MHD and PIC models in 2 dimensions

NASA Astrophysics Data System (ADS)

Daldorff, L.; Toth, G.; Sokolov, I.; Gombosi, T. I.; Lapenta, G.; Brackbill, J. U.; Markidis, S.; Amaya, J.

2013-12-01

Even for extended fluid plasma models, like Hall, anisotropic ion pressure and multi fluid MHD, there are still many plasma phenomena that are not well captured. For this reason, we have coupled the Implicit Particle-In-Cell (iPIC3D) code with the BATSRUS global MHD code. The PIC solver is applied in a part of the computational domain, for example, in the vicinity of reconnection sites, and overwrites the MHD solution. On the other hand, the fluid solver provides the boundary conditions for the PIC code. To demonstrate the use of the coupled codes for magnetospheric applications, we perform a 2D magnetosphere simulation, where BATSRUS solves for Hall MHD in the whole domain except for the tail reconnection region, which is handled by iPIC3D.

Absolute radiometric calibration of Landsat using a pseudo invariant calibration site

USGS Publications Warehouse

Helder, D.; Thome, K.J.; Mishra, N.; Chander, G.; Xiong, Xiaoxiong; Angal, A.; Choi, Tae-young

2013-01-01

Pseudo invariant calibration sites (PICS) have been used for on-orbit radiometric trending of optical satellite systems for more than 15 years. This approach to vicarious calibration has demonstrated a high degree of reliability and repeatability at the level of 1-3% depending on the site, spectral channel, and imaging geometries. A variety of sensors have used this approach for trending because it is broadly applicable and easy to implement. Models to describe the surface reflectance properties, as well as the intervening atmosphere have also been developed to improve the precision of the method. However, one limiting factor of using PICS is that an absolute calibration capability has not yet been fully developed. Because of this, PICS are primarily limited to providing only long term trending information for individual sensors or cross-calibration opportunities between two sensors. This paper builds an argument that PICS can be used more extensively for absolute calibration. To illustrate this, a simple empirical model is developed for the well-known Libya 4 PICS based on observations by Terra MODIS and EO-1 Hyperion. The model is validated by comparing model predicted top-of-atmosphere reflectance values to actual measurements made by the Landsat ETM+ sensor reflective bands. Following this, an outline is presented to develop a more comprehensive and accurate PICS absolute calibration model that can be Système international d'unités (SI) traceable. These initial concepts suggest that absolute calibration using PICS is possible on a broad scale and can lead to improved on-orbit calibration capabilities for optical satellite sensors.

Boltzmann Transport in Hybrid PIC HET Modeling

DTIC Science & Technology

2015-07-01

Paper 3. DATES COVERED (From - To) July 2015-July 2015 4. TITLE AND SUBTITLE Boltzmann transport in hybrid PIC HET modeling 5a. CONTRACT NUMBER In...reproduce experimentally observed mobility trends derived from HPHall, a workhorse hybrid- PIC HET simulation code. 15. SUBJECT TERMS 16. SECURITY...CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18 . NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON Justin Koo a. REPORT Unclassified b. ABSTRACT

Time-implicit fluid/particle hybrid simulations of the anode plasma dynamics in ion diodes

NASA Astrophysics Data System (ADS)

Pointon, T. D.; Boine-Frankenheim, O.; Mehlhorn, T. A.

1997-04-01

Applied-B ion diode experiments with Li+1 ion sources on the PBFA II and SABRE ion accelerators show that early in the pulse the beam is essentially pure Li+1, but is rapidly overwhelmed by impurity ions, called the `parasitic load'. Furthermore, the increasing parasitic current rapidly drops the diode voltage, limiting the accelerator power that can be coupled into the beam. This `impedance collapse' is believed to arise from the desorption of impurity neutrals from the anode surface. These neutrals charge-exchange with the ions, rapidly expanding into the anode-cathode gap where they are ionized by beam ions or secondary electrons. In order to model these processes we are developing a 1 1/2 D electrostatic multifluid/PIC (hybrid) code, designed to self-consistently simulate collisional plasma/neutral systems with an arbitrary number of interacting species, over greatly varying density regimes and together with applied electric and magnetic fields.

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 simulations. The other is that the level of electric field fluctuations scales as 1/ΛPIC ∝ p. We provide a corresponding exact expression, taking into account the finite superparticle size. We confirm both expectations with simulations. Fourth, we compare the Vlasov-Maxwell theory, often used for code benchmarking, to the PIC model. The former describes a phase-space fluid with Λ = + ∞ and no correlations, while the PIC plasma features a small Λ and a high level of correlations when compared to a real plasma. These differences have to be kept in mind when interpreting and validating PIC results against the Vlasov-Maxwell theory and when modeling real physical plasmas.

Chromium picolinate modulates serotonergic properties and carbohydrate metabolism in a rat model of diabetes.

PubMed

Komorowski, James R; Tuzcu, Mehmet; Sahin, Nurhan; Juturu, Vijaya; Orhan, Cemal; Ulas, Mustafa; Sahin, Kazim

2012-10-01

Chromium picolinate (CrPic) has shown both antidepressant and antidiabetic properties. In this study, the effects of CrPic on serotonergic properties and carbohydrate metabolism in diabetic rats were evaluated. Sixty male Sprague-Dawley rats were divided into four groups. (1) The control group received only standard diet (8 % fat). (2) The CrPic group was fed standard diet and CrPic (80 μg CrPic per kilogram body mass (b.m.)/day), for 10 weeks (microgram/kilogram b.m./day). (3) The HFD/STZ group fed a high-fat diet (HFD, 40 % fat) for 2 weeks and then received streptozotocin (STZ, 40 mg/kg, i.p.) (i.v.) HFD-STZ-CrPic group treated as the previous group and then were administered CrPic. CrPic administration to HFD/STZ-treated rats increased brain chromium levels and improved all measurements of carbohydrate metabolism and serotonergic properties (P<0.001). CrPic also significantly increased levels of insulin, tryptophan, and serotonin (P<0.001) in the serum and brain, and decreased cortisol levels in the serum (P<0.01). Except chromium levels, no significant effect of CrPic supplementation was detected on the overall measured parameters in the control group. CrPic administration was well tolerated without any adverse events. The results support the use of CrPic supplementation which improves serotonergic properties of brain in diabetes.

Calcium Carbonate Dissolution Above the Lysocline: Implications of Copepod Grazing on Coccolithophores

NASA Astrophysics Data System (ADS)

White, M. M.; Waller, J. D.; Lubelczyk, L.; Drapeau, D.; Bowler, B.; Wyeth, A.; Fields, D.; Balch, W. M.

2016-02-01

Copepod-coccolithophore predator-prey interactions are of great importance because they facilitate the export of particulate inorganic and organic carbon (PIC and POC) from the surface ocean. Coccolith dissolution in acidic copepod guts has been proposed as a possible explanation for the paradox of PIC dissolution above the lysocline, but warrants further investigation. Using a new application of the 14C-microdiffusion technique, we investigated the dissolution of coccoliths in copepod guts. We considered both an estuarine predator-prey model (Acartia tonsa and Pleurochrysis carterae) and an open ocean predator-prey model (Calanus finmarchicus and Emiliania huxleyi). Additionally, we considered the impacts of pCO2 on this process to advance our understanding of the effects of ocean acidification on trophic interactions. In the estuarine predator-prey model, fecal pellets produced immediately after previously-starved copepods grazed on P. carterae had PIC/POC ratios 27-40 % lower than that of the algae, indicating PIC dissolution within the copepod gut, with no impact of pCO2 on this dissolution. Subsequent fecal pellets showed increasing PIC/POC, suggesting that calcite dissolution decreases as the gut fills. The open ocean predator-prey model showed equivocal results, indicating high variability among individual grazing behavior, and therefore no consistent impact of copepod grazing on coccolith dissolution above the lysocline in the open ocean. We will further discuss the effects of fecal pellet PIC/POC ratios on sinking rate.

Three-Dimensional Simulations of Electron Beams Focused by Periodic Permanent Magnets

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1999-01-01

A fully three-dimensional (3D) model of an electron beam focused by a periodic permanent magnet (PPM) stack has been developed. First, the simulation code MAFIA was used to model a PPM stack using the magnetostatic solver. The exact geometry of the magnetic focusing structure was modeled; thus, no approximations were made regarding the off-axis fields. The fields from the static solver were loaded into the 3D particle-in-cell (PIC) solver of MAFIA where fully 3D behavior of the beam was simulated in the magnetic focusing field. The PIC solver computes the time-integration of electromagnetic fields simultaneously with the time integration of the equations of motion of charged particles that move under the influence of those fields. Fields caused by those moving charges are also taken into account; thus, effects like space charge and magnetic forces between particles are fully simulated. The electron beam is simulated by a number of macro-particles. These macro-particles represent a given charge Q amounting to that of several million electrons in order to conserve computational time and memory. Particle motion is unrestricted, so particle trajectories can cross paths and move in three dimensions under the influence of 3D electric and magnetic fields. Correspondingly, there is no limit on the initial current density distribution of the electron beam, nor its density distribution at any time during the simulation. Simulation results including beam current density, percent ripple and percent transmission will be presented, and the effects current, magnetic focusing strength and thermal velocities have on beam behavior will be demonstrated using 3D movies showing the evolution of beam characteristics in time and space. Unlike typical beam optics models, this 3D model allows simulation of asymmetric designs such as non- circularly symmetric electrostatic or magnetic focusing as well as the inclusion of input/output couplers.

Charged aerodynamics of a Low Earth Orbit cylinder

NASA Astrophysics Data System (ADS)

Capon, C. J.; Brown, M.; Boyce, R. R.

2016-11-01

This work investigates the charged aerodynamic interaction of a Low Earth Orbiting (LEO) cylinder with the ionosphere. The ratio of charge to neutral drag force on a 2D LEO cylinder with diffusely reflecting cool walls is derived analytically and compared against self-consistent electrostatic Particle-in-Cell (PIC) simulations. Analytical calculations predict that neglecting charged drag in an O+ dominated LEO plasma with a neutral to ion number density ratio of 102 will cause a 10% over-prediction of O density based on body accelerations when body potential (ɸB) is ≤ -390 V. Above 900 km altitude in LEO, where H+ becomes the dominant ion species, analytical predictions suggest charge drag becomes equivalent to neutral drag for ɸB ≤ -0.75 V. Comparing analytical predictions against PIC simulations in the range of 0 < - ɸB < 50 V found that analytical charged drag was under-estimated for all body potentials; the degree of under-estimation increasing with ɸB. Based on the -50 V PIC simulations, our in-house 6 degree of freedom orbital propagator saw a reduction in the semi-major axis of a 10 kg satellite at 700 km of 6.9 m/day and 0.98 m/day at 900 km compared that caused purely by neutral drag - 0.67 m/day and 0.056 m/day respectively. Hence, this work provides initial evidence that charged aerodynamics may become significant compared to neutral aerodynamics for high voltage LEO bodies.

Independent contrasts and PGLS regression estimators are equivalent.

PubMed

Blomberg, Simon P; Lefevre, James G; Wells, Jessie A; Waterhouse, Mary

2012-05-01

We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has several implications: 1. Understanding the structure of the linear model for GLS regression provides insight into when and why phylogeny is important in comparative studies. 2. The limitations of the PIC regression analysis are the same as the limitations of the GLS model. In particular, phylogenetic covariance applies only to the response variable in the regression and the explanatory variable should be regarded as fixed. Calculation of PICs for explanatory variables should be treated as a mathematical idiosyncrasy of the PIC regression algorithm. 3. Since the GLS estimator is the best linear unbiased estimator (BLUE), the slope parameter estimated using PICs is also BLUE. 4. If the slope is estimated using different branch lengths for the explanatory and response variables in the PIC algorithm, the estimator is no longer the BLUE, so this is not recommended. Finally, we discuss whether or not and how to accommodate phylogenetic covariance in regression analyses, particularly in relation to the problem of phylogenetic uncertainty. This discussion is from both frequentist and Bayesian perspectives.

The formation of relativistic plasma structures and their potential role in the generation of cosmic ray electrons

NASA Astrophysics Data System (ADS)

Dieckmann, M. E.

2008-11-01

Recent particle-in-cell (PIC) simulation studies have addressed particle acceleration and magnetic field generation in relativistic astrophysical flows by plasma phase space structures. We discuss the astrophysical environments such as the jets of compact objects, and we give an overview of the global PIC simulations of shocks. These reveal several types of phase space structures, which are relevant for the energy dissipation. These structures are typically coupled in shocks, but we choose to consider them here in an isolated form. Three structures are reviewed. (1) Simulations of interpenetrating or colliding plasma clouds can trigger filamentation instabilities, while simulations of thermally anisotropic plasmas observe the Weibel instability. Both transform a spatially uniform plasma into current filaments. These filament structures cause the growth of the magnetic fields. (2) The development of a modified two-stream instability is discussed. It saturates first by the formation of electron phase space holes. The relativistic electron clouds modulate the ion beam and a secondary, spatially localized electrostatic instability grows, which saturates by forming a relativistic ion phase space hole. It accelerates electrons to ultra-relativistic speeds. (3) A simulation is also revised, in which two clouds of an electron-ion plasma collide at the speed 0.9c. The inequal densities of both clouds and a magnetic field that is oblique to the collision velocity vector result in waves with a mixed electrostatic and electromagnetic polarity. The waves give rise to growing corkscrew distributions in the electrons and ions that establish an equipartition between the electron, the ion and the magnetic energy. The filament-, phase space hole- and corkscrew structures are discussed with respect to electron acceleration and magnetic field generation.

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.

Multiscale simulation of DC corona discharge and ozone generation from nanostructures

NASA Astrophysics Data System (ADS)

Wang, Pengxiang

Atmospheric direct current (dc) corona discharge from micro-sized objects has been widely used as an ion source in many devices, such as photocopiers, laser printers, and electronic air cleaners. Shrinking the size of the discharge electrode to the nanometer range (e.g., through the use of carbon nanotubes or CNTs) is expected to lead to a significant reduction in power consumption and detrimental ozone production in these devices. The objectives of this study are to unveil the fundamental physics of the nanoscale corona discharge and to evaluate its performance and ozone production through numerical models. The extremely small size of CNTs presents considerable complexity and challenges in modeling CNT corona discharges. A hybrid multiscale model, which combines a kinetic particle-in-cell plus Monte Carlo collision (PIC-MCC) model and a continuum model, is developed to simulate the corona discharge from nanostructures. The multiscale model is developed in several steps. First, a pure PIC-MCC model is developed and PIC-MCC simulations of corona plasma from micro-sized electrode with same boundary conditions as prior model are performed to validate the PIC-MCC scheme. The agreement between the PIC-MCC model and the prior continuum model indicates the validity of the PIC-MCC scheme. The validated PIC-MCC scheme is then coupled with a continuum model to simulate the corona discharge from a micro-sized electrode. Unlike the prior continuum model which only predicts the corona plasma region, the hybrid model successfully predicts the self-consistent discharge process in the entire corona discharge gap that includes both corona plasma region and unipolar ion region. The voltage-current density curves obtained by the hybrid model agree well with analytical prediction and experimental results. The hybrid modeling approach, which combines the accuracy of a kinetic model and the efficiency of a continuum model, is thus validated for modeling dc corona discharges. For simulation of corona discharges from nanostructures, a one-dimensional (1-D) multiscale model is used due to the prohibitive computational expense associated with two-dimensional (2-D) modeling. Near the nanoscale discharge electrode surface, a kinetic model based on PIC-MCC is used due to a relatively large Knudsen number in this region. Far away from the nanoscale discharge electrode, a continuum model is used since the Knudsen number is very small there. The multiscale modeling results are compared with experimental data. The quantitative agreement in positive discharges and qualitative agreement in negative discharges validate the modeling approach. The mechanism of sustaining the discharge process from nanostructures is revealed and is found to be different from that of discharge from micro- or macro-sized electrodes. Finally, the corona plasma model is combined with a plasma chemistry model and a transport model to predict the ozone production from the nanoscale corona. The dependence of ozone production on the applied potential and air velocity is studied. The electric field distribution in a 2-D multiscale domain (from nanoscale to microscale) is predicted by solving the Poisson's equation using a finite difference scheme. The discretized linear equations are solved using a multigrid method under the framework of PETSc on a paralleled supercomputer. Although the Poisson solver is able to resolve the multiscale field, the prohibitively long computation time limits the use of a 2-D solver in the current PIC-MCC scheme.

The Heliopause Electrostatic Rapid Transit System (HERTS) Design, Trades, and Analyses Performed in a Two Year NASA Investigation of Electric Sail Propulsion Systems

NASA Technical Reports Server (NTRS)

Wiegmann, Bruce M.

2017-01-01

The Heliopause Electrostatic Rapid Transit System (HERTS) was one of the seven total Phase II NASA Innovative Advanced Concepts (NIAC) that was down-selected in 2015 for continued funding and research. In Phase I our team learned that a spacecraft propelled by an Electric Sail (E-Sail) can travel great astronomical distances, such as to the Heliopause region of the solar system (approx. 100 to 120 AU) in approximately one quarter of the time (10 years) versus the time it took the Voyager spacecraft launched in 1977 (36 years). The completed work within the Phase II NIAC funded effort builds upon the work that was done in the Phase I NIAC and is focused on: 1) Testing of plasma interaction with a charged wire in a MSFC simulated solar environment vacuum test chamber. 2) Development of a Particle-in-Cell (PIC) models that are validated in the plasma testing and used to extrapolate to the E-Sail propulsion system design. 3) Conceptual design of a Technology Demonstration Mission (TDM) spacecraft developed to showcase E-Sail propulsion systems. 4) Down selection of both: a) Materials for a multi km length conductor and, b) Best configuration of the proposed conductor deployment subsystem. This paper will document the findings to date (June, 2017) of the above focused areas.

A Huygens immersed-finite-element particle-in-cell method for modeling plasma-surface interactions with moving interface

NASA Astrophysics Data System (ADS)

Cao, Huijun; Cao, Yong; Chu, Yuchuan; He, Xiaoming; Lin, Tao

2018-06-01

Surface evolution is an unavoidable issue in engineering plasma applications. In this article an iterative method for modeling plasma-surface interactions with moving interface is proposed and validated. In this method, the plasma dynamics is simulated by an immersed finite element particle-in-cell (IFE-PIC) method, and the surface evolution is modeled by the Huygens wavelet method which is coupled with the iteration of the IFE-PIC method. Numerical experiments, including prototypical engineering applications, such as the erosion of Hall thruster channel wall, are presented to demonstrate features of this Huygens IFE-PIC method for simulating the dynamic plasma-surface interactions.

Evaluating CoLiDeS + Pic: The Role of Relevance of Pictures in User Navigation Behaviour

ERIC Educational Resources Information Center

Karanam, Saraschandra; van Oostendorp, Herre; Indurkhya, Bipin

2012-01-01

CoLiDeS + Pic is a cognitive model of web-navigation that incorporates semantic information from pictures into CoLiDeS. In our earlier research, we have demonstrated that by incorporating semantic information from pictures, CoLiDeS + Pic can predict the hyperlinks on the shortest path more frequently, and also with greater information scent,…

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

Lange, R.; Dickerson, M.A.; Peterson, K.R.

Two numerical models for the calculation of air concentration and ground deposition of airborne effluent releases are compared. The Particle-in-Cell (PIC) model and the Straight-Line Airflow Gaussian model were used for the simulation. Two sites were selected for comparison: the Hudson River Valley, New York, and the area around the Savannah River Plant, South Carolina. Input for the models was synthesized from meteorological data gathered in previous studies by various investigators. It was found that the PIC model more closely simulated the three-dimensional effects of the meteorology and topography. Overall, the Gaussian model calculated higher concentrations under stable conditions withmore » better agreement between the two methods during neutral to unstable conditions. In addition, because of its consideration of exposure from the returning plume after flow reversal, the PIC model calculated air concentrations over larger areas than did the Gaussian model.« less

Biodistribution of charged F(ab')2 photoimmunoconjugates in a xenograft model of ovarian cancer.

PubMed

Duska, L R; Hamblin, M R; Bamberg, M P; Hasan, T

1997-01-01

The effect of charge modification of photoimmunoconjugates (PICs) on their biodistribution in a xenograft model of ovarian cancer was investigated. Chlorin(e6)c(e6) was attached site specifically to the F(ab')2 fragment of the murine monoclonal antibody OC125, directed against human ovarian cancer cells, via poly-1-lysine linkers carrying cationic or anionic charges. Preservation of immunoreactivity was checked by enzyme-linked immunosorbent assay (ELISA). PICs were radiolabelled with 125I and compared with non-specific rabbit IgG PICs after intraperitoneal (i.p.) injection into nude mice. Samples were taken from normal organs and tumour at 3 h and 24 h. Tumour to normal 125I ratios showed that the cationic OC125F(ab')2 PIC had the highest tumour selectivity. Ratios for c(e6) were uniformly higher than for 125I, indicating that c(e6) became separated from 125I. OC125F(ab')2 gave highest tissue values of 125I, followed by cationic OC125F(ab')2 PIC; other species were much lower. The amounts of c(e6) delivered per gram of tumour were much higher for cationic OC125F(ab')2 PIC than for other species. The results indicate that cationic charge stimulates the endocytosis and lysosomal degradation of the OC125F(ab')2-pl-c(e6) that has bound to the i.p. tumour. Positively charged PICs may have applications in the i.p. photoimmunotherapy of minimal residual ovarian cancer.

Insulin receptors and downstream substrates associate with membrane microdomains after treatment with insulin or chromium(III) picolinate.

PubMed

Al-Qatati, Abeer; Winter, Peter W; Wolf-Ringwall, Amber L; Chatterjee, Pabitra B; Van Orden, Alan K; Crans, Debbie C; Roess, Deborah A; Barisas, B George

2012-04-01

We have examined the association of insulin receptors (IR) and downstream signaling molecules with membrane microdomains in rat basophilic leukemia (RBL-2H3) cells following treatment with insulin or tris(2-pyridinecarbxylato)chromium(III) (Cr(pic)(3)). Single-particle tracking demonstrated that individual IR on these cells exhibited reduced lateral diffusion and increased confinement within 100 nm-scale membrane compartments after treatment with either 200 nM insulin or 10 μM Cr(pic)(3). These treatments also increased the association of native IR, phosphorylated insulin receptor substrate 1 and phosphorylated AKT with detergent-resistant membrane microdomains of characteristically high buoyancy. Confocal fluorescence microscopic imaging of Di-4-ANEPPDHQ labeled RBL-2H3 cells also showed that plasma membrane lipid order decreased following treatment with Cr(pic)(3) but was not altered by insulin treatment. Fluorescence correlation spectroscopy demonstrated that Cr(pic)(3) did not affect IR cell-surface density or compete with insulin for available binding sites. Finally, Fourier transform infrared spectroscopy indicated that Cr(pic)(3) likely associates with the lipid interface in reverse-micelle model membranes. Taken together, these results suggest that activation of IR signaling in a cellular model system by both insulin and Cr(pic)(3) involves retention of IR in specialized nanometer-scale membrane microdomains but that the insulin-like effects of Cr(pic)(3) are due to changes in membrane lipid order rather than to direct interactions with IR. © Springer Science+Business Media, LLC 2011

Modeling the interaction of seven bisphosphonates with the hydroxyapatite(100) face.

PubMed

Chen, Chunyu; Xia, Mingzhu; Wu, Lei; Zhou, Chao; Wang, Fengyun

2012-09-01

The interaction of seven pamidronate bisphosphonate (Pami-BPs) and its analogs with the hydroxyapatite (HAP) (100) surface was studied using density functional theory (DFT) and molecular dynamic (MD) methods. Partial Mulliken oxygen atomic charges in protonated structures were calculated at the level of B3LYP/6-31G*. The MD simulation was performed using the Discover module of Material Studio by compass force field. The results indicate the abilities of donating electrons of the oxygen atoms of the phosphate groups that are closely associated with the antiresorptive potency. The binding energies, including vdw and electrostatic, are used to discuss the mechanism of antiresorption. The results of calculations show that the strength of interaction of the HAP (100) face with the bisphosphonates is N(4) > N(6) > N(7) > N(5) > N(3) > N(2) > N(1) according to their experimental pIC(50) values.

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.

Particle-In-Cell simulations of electron beam microbunching instability in three dimensions

NASA Astrophysics Data System (ADS)

Huang, Chengkun; Zeng, Y.; Meyers, M. D.; Yi, S.; Albright, B. J.; Kwan, T. J. T.

2013-10-01

Microbunching instability due to Coherent Synchrotron Radiation (CSR) in a magnetic chicane is one of the major effects that can degrade the electron beam quality in an X-ray Free Electron Laser. Self-consistent simulation using the Particle-In-Cell (PIC) method for the CSR fields of the beam and their effects on beam dynamics have been elusive due to the excessive dispersion error on the grid. We have implemented a high-order finite-volume PIC scheme that models the propagation of the CSR fields accurately. This new scheme is characterized and optimized through a detailed dispersion analysis. The CSR fields from our improved PIC calculation are compared to the extended CSR numerical model based on the Lienard-Wiechert formula in 2D/3D. We also conduct beam dynamics simulation of the microbunching instability using our new PIC capability. Detailed self-consistent PIC simulations of the CSR fields and beam dynamics will be presented and discussed. Work supported by the U.S. Department of Energy through the LDRD program at Los Alamos National Laboratory.

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

Precise engineering of siRNA delivery vehicles to tumors using polyion complexes and gold nanoparticles.

PubMed

Kim, Hyun Jin; Takemoto, Hiroyasu; Yi, Yu; Zheng, Meng; Maeda, Yoshinori; Chaya, Hiroyuki; Hayashi, Kotaro; Mi, Peng; Pittella, Frederico; Christie, R James; Toh, Kazuko; Matsumoto, Yu; Nishiyama, Nobuhiro; Miyata, Kanjiro; Kataoka, Kazunori

2014-09-23

For systemic delivery of siRNA to solid tumors, a size-regulated and reversibly stabilized nanoarchitecture was constructed by using a 20 kDa siRNA-loaded unimer polyion complex (uPIC) and 20 nm gold nanoparticle (AuNP). The uPIC was selectively prepared by charge-matched polyionic complexation of a poly(ethylene glycol)-b-poly(L-lysine) (PEG-PLL) copolymer bearing ∼40 positive charges (and thiol group at the ω-end) with a single siRNA bearing 40 negative charges. The thiol group at the ω-end of PEG-PLL further enabled successful conjugation of the uPICs onto the single AuNP through coordinate bonding, generating a nanoarchitecture (uPIC-AuNP) with a size of 38 nm and a narrow size distribution. In contrast, mixing thiolated PEG-PLLs and AuNPs produced a large aggregate in the absence of siRNA, suggesting the essential role of the preformed uPIC in the formation of nanoarchitecture. The smart uPIC-AuNPs were stable in serum-containing media and more resistant against heparin-induced counter polyanion exchange, compared to uPICs alone. On the other hand, the treatment of uPIC-AuNPs with an intracellular concentration of glutathione substantially compromised their stability and triggered the release of siRNA, demonstrating the reversible stability of these nanoarchitectures relative to thiol exchange and negatively charged AuNP surface. The uPIC-AuNPs efficiently delivered siRNA into cultured cancer cells, facilitating significant sequence-specific gene silencing without cytotoxicity. Systemically administered uPIC-AuNPs showed appreciably longer blood circulation time compared to controls, i.e., bare AuNPs and uPICs, indicating that the conjugation of uPICs onto AuNP was crucial for enhancing blood circulation time. Finally, the uPIC-AuNPs efficiently accumulated in a subcutaneously inoculated luciferase-expressing cervical cancer (HeLa-Luc) model and achieved significant luciferase gene silencing in the tumor tissue. These results demonstrate the strong potential of uPIC-AuNP nanoarchitectures for systemic siRNA delivery to solid tumors.

A portable platform for accelerated PIC codes and its application to GPUs using OpenACC

NASA Astrophysics Data System (ADS)

Hariri, F.; Tran, T. M.; Jocksch, A.; Lanti, E.; Progsch, J.; Messmer, P.; Brunner, S.; Gheller, C.; Villard, L.

2016-10-01

We present a portable platform, called PIC_ENGINE, for accelerating Particle-In-Cell (PIC) codes on heterogeneous many-core architectures such as Graphic Processing Units (GPUs). The aim of this development is efficient simulations on future exascale systems by allowing different parallelization strategies depending on the application problem and the specific architecture. To this end, this platform contains the basic steps of the PIC algorithm and has been designed as a test bed for different algorithmic options and data structures. Among the architectures that this engine can explore, particular attention is given here to systems equipped with GPUs. The study demonstrates that our portable PIC implementation based on the OpenACC programming model can achieve performance closely matching theoretical predictions. Using the Cray XC30 system, Piz Daint, at the Swiss National Supercomputing Centre (CSCS), we show that PIC_ENGINE running on an NVIDIA Kepler K20X GPU can outperform the one on an Intel Sandy bridge 8-core CPU by a factor of 3.4.

Evaluation of possible antioxidant and anticonvulsant effects of the ethyl acetate fraction from Platonia insignis Mart. (Bacuri) on epilepsy models.

PubMed

Júnior, Joaquim Soares da Costa; de Almeida, Antonia Amanda C; Tomé, Adriana da Rocha; Citó, Antonia Maria das Graças Lopes; Saffi, Jenifer; de Freitas, Rivelilson Mendes

2011-12-01

The aim of present study was to examine the effects of the ethyl acetate fraction (EAF) from Platonia insignis on lipid peroxidation level, nitrite formation, and superoxide dismutase and catalase activities in rat striatum prior to pilocarpine-induced seizures as well as to explore its anticonvulsant activity in adult rats prior to pentylenetetrazole (PTZ)- and picrotoxin (PIC)-induced seizures. Wistar rats were treated with vehicle, atropine (25mg/kg), EAF (0.1, 1, and 10mg/kg), pilocarpine (400mg/kg, P400 group), PTZ (60 mg/kg, PTZ group), PIC (8 mg/kg, PIC group), atropine+P400, EAF+P400, EAF+PTZ, or EAF+PIC. Significant decreases in number of crossings and rearings were observed in the P400 group. The EAF 10+P400 group also had significant increases in these parameters. In addition, in rats treated with P400, there were significant increases in lipid peroxidation and nitrite levels; however, there were no alterations in SOD and catalase activities. In the EAF 10+P400 group, lipid peroxidation and nitrite levels significantly decreased and SOD and catalase activities significantly increased after pilocarpine-induced seizures. Additionally, effects of the EAF were evaluated in PTZ and PIC models. EAF did not increase the latency to development of convulsions induced with PTZ and PIC at the doses tested. Our findings strongly support the hypothesis that EAF does not have anticonvulsant activity in the different models of epilepsy studied. Our results indicate that in the in vivo model of pilocarpine-induced seizures, EAF has antioxidant activity, but not anticonvulsant properties at the doses tested. Copyright © 2011. Published by Elsevier Inc.

Laser-plasma interactions with a Fourier-Bessel particle-in-cell method

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

Andriyash, Igor A., E-mail: igor.andriyash@gmail.com; LOA, ENSTA ParisTech, CNRS, Ecole polytechnique, Université Paris-Saclay, 828 bd des Maréchaux, 91762 Palaiseau cedex; Lehe, Remi

A new spectral particle-in-cell (PIC) method for plasma modeling is presented and discussed. In the proposed scheme, the Fourier-Bessel transform is used to translate the Maxwell equations to the quasi-cylindrical spectral domain. In this domain, the equations are solved analytically in time, and the spatial derivatives are approximated with high accuracy. In contrast to the finite-difference time domain (FDTD) methods, that are used commonly in PIC, the developed method does not produce numerical dispersion and does not involve grid staggering for the electric and magnetic fields. These features are especially valuable in modeling the wakefield acceleration of particles in plasmas.more » The proposed algorithm is implemented in the code PLARES-PIC, and the test simulations of laser plasma interactions are compared to the ones done with the quasi-cylindrical FDTD PIC code CALDER-CIRC.« less

Biodistribution of charged F(ab')2 photoimmunoconjugates in a xenograft model of ovarian cancer.

PubMed Central

Duska, L. R.; Hamblin, M. R.; Bamberg, M. P.; Hasan, T.

1997-01-01

The effect of charge modification of photoimmunoconjugates (PICs) on their biodistribution in a xenograft model of ovarian cancer was investigated. Chlorin(e6)c(e6) was attached site specifically to the F(ab')2 fragment of the murine monoclonal antibody OC125, directed against human ovarian cancer cells, via poly-1-lysine linkers carrying cationic or anionic charges. Preservation of immunoreactivity was checked by enzyme-linked immunosorbent assay (ELISA). PICs were radiolabelled with 125I and compared with non-specific rabbit IgG PICs after intraperitoneal (i.p.) injection into nude mice. Samples were taken from normal organs and tumour at 3 h and 24 h. Tumour to normal 125I ratios showed that the cationic OC125F(ab')2 PIC had the highest tumour selectivity. Ratios for c(e6) were uniformly higher than for 125I, indicating that c(e6) became separated from 125I. OC125F(ab')2 gave highest tissue values of 125I, followed by cationic OC125F(ab')2 PIC; other species were much lower. The amounts of c(e6) delivered per gram of tumour were much higher for cationic OC125F(ab')2 PIC than for other species. The results indicate that cationic charge stimulates the endocytosis and lysosomal degradation of the OC125F(ab')2-pl-c(e6) that has bound to the i.p. tumour. Positively charged PICs may have applications in the i.p. photoimmunotherapy of minimal residual ovarian cancer. PMID:9062404

Efficient Modeling of Laser-Plasma Accelerators with INF&RNO

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

Benedetti, C.; Schroeder, C. B.; Esarey, E.

2010-06-01

The numerical modeling code INF&RNO (INtegrated Fluid& paRticle simulatioN cOde, pronounced"inferno") is presented. INF&RNO is an efficient 2D cylindrical code to model the interaction of a short laser pulse with an underdense plasma. The code is based on an envelope model for the laser while either a PIC or a fluid description can be used for the plasma. The effect of the laser pulse on the plasma is modeled with the time-averaged poderomotive force. These and other features allow for a speedup of 2-4 orders of magnitude compared to standard full PIC simulations while still retaining physical fidelity. The codemore » has been benchmarked against analytical solutions and 3D PIC simulations and here a set of validation tests together with a discussion of the performances are presented.« less

Efficient Modeling of Laser-Plasma Accelerators with INF&RNO

NASA Astrophysics Data System (ADS)

Benedetti, C.; Schroeder, C. B.; Esarey, E.; Geddes, C. G. R.; Leemans, W. P.

2010-11-01

The numerical modeling code INF&RNO (INtegrated Fluid & paRticle simulatioN cOde, pronounced "inferno") is presented. INF&RNO is an efficient 2D cylindrical code to model the interaction of a short laser pulse with an underdense plasma. The code is based on an envelope model for the laser while either a PIC or a fluid description can be used for the plasma. The effect of the laser pulse on the plasma is modeled with the time-averaged poderomotive force. These and other features allow for a speedup of 2-4 orders of magnitude compared to standard full PIC simulations while still retaining physical fidelity. The code has been benchmarked against analytical solutions and 3D PIC simulations and here a set of validation tests together with a discussion of the performances are presented.

Seagrass meadows as a globally significant carbonate reservoir

NASA Astrophysics Data System (ADS)

Mazarrasa, I.; Marbà, N.; Lovelock, C. E.; Serrano, O.; Lavery, P. S.; Fourqurean, J. W.; Kennedy, H.; Mateo, M. A.; Krause-Jensen, D.; Steven, A. D. L.; Duarte, C. M.

2015-08-01

There has been growing interest in quantifying the capacity of seagrass ecosystems to act as carbon sinks as a natural way of offsetting anthropogenic carbon emissions to the atmosphere. However, most of the efforts have focused on the particulate organic carbon (POC) stocks and accumulation rates and ignored the particulate inorganic carbon (PIC) fraction, despite important carbonate pools associated with calcifying organisms inhabiting the meadows, such as epiphytes and benthic invertebrates, and despite the relevance that carbonate precipitation and dissolution processes have in the global carbon cycle. This study offers the first assessment of the global PIC stocks in seagrass sediments using a synthesis of published and unpublished data on sediment carbonate concentration from 403 vegetated and 34 adjacent un-vegetated sites. PIC stocks in the top 1 m of sediment ranged between 3 and 1660 Mg PIC ha-1, with an average of 654 ± 24 Mg PIC ha-1, exceeding those of POC reported in previous studies by about a factor of 5. Sedimentary carbonate stocks varied across seagrass communities, with meadows dominated by Halodule, Thalassia or Cymodocea supporting the highest PIC stocks, and tended to decrease polewards at a rate of -8 ± 2 Mg PIC ha-1 per degree of latitude (general linear model, GLM; p < 0.0003). Using PIC concentrations and estimates of sediment accretion in seagrass meadows, the mean PIC accumulation rate in seagrass sediments is found to be 126.3 ± 31.05 g PIC m-2 yr-1. Based on the global extent of seagrass meadows (177 000 to 600 000 km2), these ecosystems globally store between 11 and 39 Pg of PIC in the top metre of sediment and accumulate between 22 and 75 Tg PIC yr-1, representing a significant contribution to the carbonate dynamics of coastal areas. Despite the fact that these high rates of carbonate accumulation imply CO2 emissions from precipitation, seagrass meadows are still strong CO2 sinks as demonstrated by the comparison of carbon (PIC and POC) stocks between vegetated and adjacent un-vegetated sediments.

Contribution of intrinsic properties and synaptic inputs to motoneuron discharge patterns: a simulation study

PubMed Central

ElBasiouny, Sherif M.; Rymer, W. Zev; Heckman, C. J.

2012-01-01

Motoneuron discharge patterns reflect the interaction of synaptic inputs with intrinsic conductances. Recent work has focused on the contribution of conductances mediating persistent inward currents (PICs), which amplify and prolong the effects of synaptic inputs on motoneuron discharge. Certain features of human motor unit discharge are thought to reflect a relatively stereotyped activation of PICs by excitatory synaptic inputs; these features include rate saturation and de-recruitment at a lower level of net excitation than that required for recruitment. However, PIC activation is also influenced by the pattern and spatial distribution of inhibitory inputs that are activated concurrently with excitatory inputs. To estimate the potential contributions of PIC activation and synaptic input patterns to motor unit discharge patterns, we examined the responses of a set of cable motoneuron models to different patterns of excitatory and inhibitory inputs. The models were first tuned to approximate the current- and voltage-clamp responses of low- and medium-threshold spinal motoneurons studied in decerebrate cats and then driven with different patterns of excitatory and inhibitory inputs. The responses of the models to excitatory inputs reproduced a number of features of human motor unit discharge. However, the pattern of rate modulation was strongly influenced by the temporal and spatial pattern of concurrent inhibitory inputs. Thus, even though PIC activation is likely to exert a strong influence on firing rate modulation, PIC activation in combination with different patterns of excitatory and inhibitory synaptic inputs can produce a wide variety of motor unit discharge patterns. PMID:22031773

Rapamycin treatment benefits glucose metabolism in mouse models of type 2 diabetes.

PubMed

Reifsnyder, Peter C; Flurkey, Kevin; Te, Austen; Harrison, David E

2016-11-30

Numerous studies suggest that rapamycin treatment promotes insulin resistance, implying that rapamycin could have negative effects on patients with, or at risk for, type 2 diabetes (T2D). New evidence, however, indicates that rapamycin treatment produces some benefits to energy metabolism, even in the context of T2D. Here, we survey 5 mouse models of T2D (KK, KK-Ay, NONcNZO10, BKS- db/db , TALLYHO) to quantify effects of rapamycin on well-recognized markers of glucose homeostasis within a wide range of T2D environments. Interestingly, dietary rapamycin treatment did not exacerbate impaired glucose or insulin tolerance, or elevate circulating lipids as T2D progressed. In fact, rapamycin increased insulin sensitivity and reduced weight gain in 3 models, and decreased hyperinsulinemia in 2 models. A key covariate of this genetically-based, differential response was pancreatic insulin content (PIC): Models with low PIC exhibited more beneficial effects than models with high PIC. However, a minimal PIC threshold may exist, below which hypoinsulinemic hyperglycemia develops, as it did in TALLYHO. Our results, along with other studies, indicate that beneficial or detrimental metabolic effects of rapamycin treatment, in a diabetic or pre-diabetic context, are driven by the interaction of rapamycin with the individual model's pancreatic physiology.

Regulation of organic nucleic acids and serum biochemistry parameters by dietary chromium picolinate supplementation in swine model.

PubMed

Jiajun, Yang; Aiyun, Han; Shanshan, Zheng; Minhong, Zhang

2011-04-01

The relationships between chromium and metabolism are sophisticated. Organic nucleic acids and serum biochemistry parameters are affected by dietary chromium levels. The objective of this work was to study the effect of chromium picolinate (CrPic) supplementation on total DNA and RNA contents, the ratio of RNA/DNA in muscle and in pancreatic tissue, the level of insulin receptor (IR) mRNA and some serum biochemistry parameters in a porcine model. Young animals (48) were assigned randomly into three groups of 16 piglets, fed with three different dietary levels of Cr (common basal feedstuff alone or supplemented with CrPic at a dose of 1.61 μg/g or 3.22 μg/g, which corresponds to 0.2 μg/g and 0.4 μg/g Cr). After 80 days, the animals were sacrificed and skeletal muscle and pancreatic tissues were analyzed to detect differences caused by different levels of dietary Cr. The total content of RNA in muscle was increased significantly (P<0.05) in the CrPic supplemented groups. There was no significant difference between groups in the concentrations of total RNA in the pancreas or DNA in the muscle and pancreatic tissues. The RNA/DNA ratio in pancreas showed no significant change but the ratio was increased significantly (P<0.05) in muscle. There was a slight increase of the mRNA level of IR but there was no significant difference between groups. The content of serum cholesterol and insulin were reduced significantly (P<0.05) in the CrPic-supplemented groups and the content of high-density lipoprotein cholesterol (HDLC) was increased significantly (P<0.05) as the CrPic dose increased. There was a slight (non-significant) reduction of the concentrations of serum triglyceride and low-density lipoprotein cholesterol (LDLC) in the CrPic supplementation groups. Supplementary CrPic caused no significant change of muscular mRNA level of IR in healthy animals. An increased content of RNA in muscle, improved cholesterol metabolism and improved insulin sensitivity were found in these CrPic-treated groups in the porcine model. Copyright © 2011 Elsevier GmbH. All rights reserved.

Influence of picolinic acid on seizure susceptibility in mice.

PubMed

Cioczek-Czuczwar, Anna; Czuczwar, Piotr; Turski, Waldemar Andrzej; Parada-Turska, Jolanta

2017-02-01

The mechanism of drug resistance in epilepsy remains unknown. Picolinic acid (PIC) is an endogenous metabolite of the kynurenine pathway and a chelating agent added to dietary supplements. Both inhibitory and excitatory properties of PIC were reported. The aim of this study was to determine the influence of exogenously applied PIC upon the electroconvulsive threshold and the activity of chemical convulsants in eight models of epilepsy in mice. All experiments were performed on adult male Swiss albino mice. Electroconvulsions were induced through ear clip electrodes. The electroconvulsive threshold (current strength necessary to induce tonic seizures in 50% of the tested group - CS 50 ) was estimated for control animals and animals pretreated with PIC. To determine the possible convulsant activity of PIC, it was administered subcutaneously or intracerebroventricularly in increasing doses to calculate the CD 50 values (doses of convulsants necessary to produce seizures in 50% of the animals). Chemical convulsions were induced by challenging the animals with increasing doses of convulsant to calculate the CD 50 values. The following convulsants were used: 4-aminopyridine, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, bicuculline, N-methyl-d-aspartate, nicotine, pentylenetrazole, pilocarpine hydrochloride and strychnine nitrate. PIC significantly decreased the electroconvulsive threshold and, after intracerebroventricular injection, but not subcutaneous, produced convulsions. Of the studied convulsants, only the activity of pilocarpine hydrochloride was significantly enhanced by PIC. PIC enhances seizure activity and potentially may play a role in the pathogenesis of drug resistant epilepsy. Future studies should focus on the interactions between PIC and antiepileptic drugs. Copyright © 2016. Published by Elsevier Urban & Partner Sp. z o.o.

Electron-beam-ion-source (EBIS) modeling progress at FAR-TECH, Inc

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

Kim, J. S., E-mail: kim@far-tech.com; Zhao, L., E-mail: kim@far-tech.com; Spencer, J. A., E-mail: kim@far-tech.com

FAR-TECH, Inc. has been developing a numerical modeling tool for Electron-Beam-Ion-Sources (EBISs). The tool consists of two codes. One is the Particle-Beam-Gun-Simulation (PBGUNS) code to simulate a steady state electron beam and the other is the EBIS-Particle-In-Cell (EBIS-PIC) code to simulate ion charge breeding with the electron beam. PBGUNS, a 2D (r,z) electron gun and ion source simulation code, has been extended for efficient modeling of EBISs and the work was presented previously. EBIS-PIC is a space charge self-consistent PIC code and is written to simulate charge breeding in an axisymmetric 2D (r,z) device allowing for full three-dimensional ion dynamics.more » This 2D code has been successfully benchmarked with Test-EBIS measurements at Brookhaven National Laboratory. For long timescale (< tens of ms) ion charge breeding, the 2D EBIS-PIC simulations take a long computational time making the simulation less practical. Most of the EBIS charge breeding, however, may be modeled in 1D (r) as the axial dependence of the ion dynamics may be ignored in the trap. Where 1D approximations are valid, simulations of charge breeding in an EBIS over long time scales become possible, using EBIS-PIC together with PBGUNS. Initial 1D results are presented. The significance of the magnetic field to ion dynamics, ion cooling effects due to collisions with neutral gas, and the role of Coulomb collisions are presented.« less

Mutual reinforcement of pathophysiological host-microbe interactions in intestinal stasis models

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

Touw, Ketrija; Ringus, Daina L.; Hubert, Nathaniel

Chronic diseases arise when there is mutual reinforcement of pathophysiological processes that cause an aberrant steady state. Such a sequence of events may underlie chronic constipation, which has been associated with dysbiosis of the gut. In this study we hypothesized that assemblage of microbial communities, directed by slow gastrointestinal transit, affects host function in a way that reinforces constipation and further maintains selection on microbial communities. In our study, we used two models – an opioid-induced consti- pation model in mice, and a humanized mouse model where germ-free mice were colonized with stool from a patient with constipation-predominant irritable bowelmore » syndrome (IBS-C) in humans. We examined the impact of pharmacologically (loperamide)-induced constipation (PIC) and IBS-C on the structural and functional profile of the gut microbiota. Germ-free (GF) mice were colonized with microbiota from PIC donor mice and IBS-C patients to determine how the microbiota affects the host. PIC and IBS-C promoted changes in the gut microbiota, characterized by increased relative abundance of Bacteroides ovatus and Parabacteroides distasonis in both models. PIC mice exhibited decreased luminal concentrations of butyrate in the cecum and altered metabolic profiles of the gut microbiota. Colonization of GF mice with PIC-associated mice cecal or human IBS-C fecal microbiota significantly increased GI transit time when compared to control microbiota recipients. IBS-C-associated gut microbiota also impacted colonic contractile properties. Lastly, our findings support the concept that constipation is characterized by dis- ease-associated steady states caused by reinforcement of pathophysiological factors in host-microbe interactions.« less

Mutual reinforcement of pathophysiological host-microbe interactions in intestinal stasis models

DOE PAGES

Touw, Ketrija; Ringus, Daina L.; Hubert, Nathaniel; ...

2017-03-20

Chronic diseases arise when there is mutual reinforcement of pathophysiological processes that cause an aberrant steady state. Such a sequence of events may underlie chronic constipation, which has been associated with dysbiosis of the gut. In this study we hypothesized that assemblage of microbial communities, directed by slow gastrointestinal transit, affects host function in a way that reinforces constipation and further maintains selection on microbial communities. In our study, we used two models – an opioid-induced consti- pation model in mice, and a humanized mouse model where germ-free mice were colonized with stool from a patient with constipation-predominant irritable bowelmore » syndrome (IBS-C) in humans. We examined the impact of pharmacologically (loperamide)-induced constipation (PIC) and IBS-C on the structural and functional profile of the gut microbiota. Germ-free (GF) mice were colonized with microbiota from PIC donor mice and IBS-C patients to determine how the microbiota affects the host. PIC and IBS-C promoted changes in the gut microbiota, characterized by increased relative abundance of Bacteroides ovatus and Parabacteroides distasonis in both models. PIC mice exhibited decreased luminal concentrations of butyrate in the cecum and altered metabolic profiles of the gut microbiota. Colonization of GF mice with PIC-associated mice cecal or human IBS-C fecal microbiota significantly increased GI transit time when compared to control microbiota recipients. IBS-C-associated gut microbiota also impacted colonic contractile properties. Lastly, our findings support the concept that constipation is characterized by dis- ease-associated steady states caused by reinforcement of pathophysiological factors in host-microbe interactions.« less

Efficient Modeling of Laser-Plasma Accelerators with INF and RNO

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

Benedetti, C.; Schroeder, C. B.; Esarey, E.

2010-11-04

The numerical modeling code INF and RNO (INtegrated Fluid and paRticle simulatioN cOde, pronounced 'inferno') is presented. INF and RNO is an efficient 2D cylindrical code to model the interaction of a short laser pulse with an underdense plasma. The code is based on an envelope model for the laser while either a PIC or a fluid description can be used for the plasma. The effect of the laser pulse on the plasma is modeled with the time-averaged poderomotive force. These and other features allow for a speedup of 2-4 orders of magnitude compared to standard full PIC simulations whilemore » still retaining physical fidelity. The code has been benchmarked against analytical solutions and 3D PIC simulations and here a set of validation tests together with a discussion of the performances are presented.« less

A PIC-MCC code RFdinity1d for simulation of discharge initiation by ICRF antenna

NASA Astrophysics Data System (ADS)

Tripský, M.; Wauters, T.; Lyssoivan, A.; Bobkov, V.; Schneider, P. A.; Stepanov, I.; Douai, D.; Van Eester, D.; Noterdaeme, J.-M.; Van Schoor, M.; ASDEX Upgrade Team; EUROfusion MST1 Team

2017-12-01

Discharges produced and sustained by ion cyclotron range of frequency (ICRF) waves in absence of plasma current will be used on ITER for (ion cyclotron-) wall conditioning (ICWC, Te = 3{-}5 eV, ne < 1018 m-3 ). In this paper, we present the 1D particle-in-cell Monte Carlo collision (PIC-MCC) RFdinity1d for the study the breakdown phase of ICRF discharges, and its dependency on the RF discharge parameters (i) antenna input power P i , (ii) RF frequency f, (iii) shape of the electric field and (iv) the neutral gas pressure pH_2 . The code traces the motion of both electrons and ions in a narrow bundle of magnetic field lines close to the antenna straps. The charged particles are accelerated in the parallel direction with respect to the magnetic field B T by two electric fields: (i) the vacuum RF field of the ICRF antenna E_z^RF and (ii) the electrostatic field E_zP determined by the solution of Poisson’s equation. The electron density evolution in simulations follows exponential increase, {\\dot{n_e} ∼ ν_ion t } . The ionization rate varies with increasing electron density as different mechanisms become important. The charged particles are affected solely by the antenna RF field E_z^RF at low electron density ({ne < 1011} m-3 , {≤ft \\vert E_z^RF \\right \\vert \\gg ≤ft \\vert E_zP \\right \\vert } ). At higher densities, when the electrostatic field E_zP is comparable to the antenna RF field E_z^RF , the ionization frequency reaches the maximum. Plasma oscillations propagating toroidally away from the antenna are observed. The simulated energy distributions of ions and electrons at {ne ∼ 1015} m-3 correspond a power-law Kappa energy distribution. This energy distribution was also observed in NPA measurements at ASDEX Upgrade in ICWC experiments.

Core Mediator structure at 3.4 Å extends model of transcription initiation complex.

PubMed

Nozawa, Kayo; Schneider, Thomas R; Cramer, Patrick

2017-05-11

Mediator is a multiprotein co-activator that binds the transcription pre-initiation complex (PIC) and regulates RNA polymerase (Pol) II. The Mediator head and middle modules form the essential core Mediator (cMed), whereas the tail and kinase modules play regulatory roles. The architecture of Mediator and its position on the PIC are known, but atomic details are limited to Mediator subcomplexes. Here we report the crystal structure of the 15-subunit cMed from Schizosaccharomyces pombe at 3.4 Å resolution. The structure shows an unaltered head module, and reveals the intricate middle module, which we show is globally required for transcription. Sites of known Mediator mutations cluster at the interface between the head and middle modules, and in terminal regions of the head subunits Med6 (ref. 16) and Med17 (ref. 17) that tether the middle module. The structure led to a model for Saccharomyces cerevisiae cMed that could be combined with the 3.6 Å cryo-electron microscopy structure of the core PIC (cPIC). The resulting atomic model of the cPIC-cMed complex informs on interactions of the submodules forming the middle module, called beam, knob, plank, connector, and hook. The hook is flexibly linked to Mediator by a conserved hinge and contacts the transcription initiation factor IIH (TFIIH) kinase that phosphorylates the carboxy (C)-terminal domain (CTD) of Pol II and was recently positioned on the PIC. The hook also contains residues that crosslink to the CTD and reside in a previously described cradle. These results provide a framework for understanding Mediator function, including its role in stimulating CTD phosphorylation by TFIIH.

Two-way coupling of magnetohydrodynamic simulations with embedded particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Makwana, K. D.; Keppens, R.; Lapenta, G.

2017-12-01

We describe a method for coupling an embedded domain in a magnetohydrodynamic (MHD) simulation with a particle-in-cell (PIC) method. In this two-way coupling we follow the work of Daldorff et al. (2014) [19] in which the PIC domain receives its initial and boundary conditions from MHD variables (MHD to PIC coupling) while the MHD simulation is updated based on the PIC variables (PIC to MHD coupling). This method can be useful for simulating large plasma systems, where kinetic effects captured by particle-in-cell simulations are localized but affect global dynamics. We describe the numerical implementation of this coupling, its time-stepping algorithm, and its parallelization strategy, emphasizing the novel aspects of it. We test the stability and energy/momentum conservation of this method by simulating a steady-state plasma. We test the dynamics of this coupling by propagating plasma waves through the embedded PIC domain. Coupling with MHD shows satisfactory results for the fast magnetosonic wave, but significant distortion for the circularly polarized Alfvén wave. Coupling with Hall-MHD shows excellent coupling for the whistler wave. We also apply this methodology to simulate a Geospace Environmental Modeling (GEM) challenge type of reconnection with the diffusion region simulated by PIC coupled to larger scales with MHD and Hall-MHD. In both these cases we see the expected signatures of kinetic reconnection in the PIC domain, implying that this method can be used for reconnection studies.

Polarization-dependent imaging contrast in abalone shells

NASA Astrophysics Data System (ADS)

Metzler, Rebecca A.; Zhou, Dong; Abrecht, Mike; Chiou, Jau-Wern; Guo, Jinghua; Ariosa, Daniel; Coppersmith, Susan N.; Gilbert, P. U. P. A.

2008-02-01

Many biominerals contain micro- or nanocrystalline mineral components, organized accurately into architectures that confer the material with improved mechanical performance at the macroscopic scale. We present here an effect which enables us to observe the relative orientation of individual crystals at the submicron scale. We call it polarization-dependent imaging contrast (PIC), as it is an imaging development of the well-known x-ray linear dichroism. Most importantly, PIC is obtained in situ, in biominerals. We present here PIC in the prismatic and nacreous layers of Haliotis rufescens (red abalone), confirm it in geologic calcite and aragonite, and corroborate the experimental data with theoretical simulated spectra. PIC reveals different and unexpected aspects of nacre architecture that have inspired theoretical models for nacre formation.

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

Program Package for 3d PIC Model of Plasma Fiber

NASA Astrophysics Data System (ADS)

Kulhánek, Petr; Břeň, David

2007-08-01

A fully three dimensional Particle in Cell model of the plasma fiber had been developed. The code is written in FORTRAN 95, implementation CVF (Compaq Visual Fortran) under Microsoft Visual Studio user interface. Five particle solvers and two field solvers are included in the model. The solvers have relativistic and non-relativistic variants. The model can deal both with periodical and non-periodical boundary conditions. The mechanism of the surface turbulences generation in the plasma fiber was successfully simulated with the PIC program package.

Variables that influence energy partition in asymmetric reconnection

NASA Astrophysics Data System (ADS)

Wang, S.; Chen, L. J.; Bessho, N.; Hesse, M.; Yamada, M.; Yoo, J.

2017-12-01

The energy conversion in the diffusion region during asymmetric reconnection is studied using particle-in-cell (PIC) simulations and measurements from the Magnetospheric Multiscale (MMS) spacecraft. The simulation analysis shows that the energy partition is highly region-dependent and varies with the guide field strength. Without a guide field, within the central electron diffusion region, the input magnetic energy is mostly converted to the electron thermal energies; half of the magnetic energy input to the region extending from the X-line to a few ion inertial lengths downstream where the ion outflow peaks is converted to the plasma energy gain, with approximately equal partition between ions and electrons, similar to the laboratory results from the Magnetic Reconnection Experiment (MRX); over the entire ion diffusion region, about half of the energy goes to ions, and 20% goes to electrons. Electrons obtain energies mainly from the reconnection electric field (Er). For the ion total energy gain in the diffusion region, about 2/3 comes from the in-plane electrostatic field Ein and 1/3 comes from Er. Adding a guide field tends to reduce the plasma energy gain through reducing the contribution from Ein, even though the reconnection rates are similar. The energy partition in the diffusion region observed by MMS is estimated and compared with the results from PIC simulations and MRX experiments.

Assessment of the anticonvulsant potency of various benzylamide derivatives in the mouse maximal electroshock-induced seizure threshold model.

PubMed

Świąder, Mariusz J; Paruszewski, Ryszard; Łuszczki, Jarogniew J

2016-04-01

The aim of this study was to assess the anticonvulsant potency of 6 various benzylamide derivatives [i.e., nicotinic acid benzylamide (Nic-BZA), picolinic acid 2-fluoro-benzylamide (2F-Pic-BZA), picolinic acid benzylamide (Pic-BZA), (RS)-methyl-alanine-benzylamide (Me-Ala-BZA), isonicotinic acid benzylamide (Iso-Nic-BZA), and (R)-N-methyl-proline-benzylamide (Me-Pro-BZA)] in the threshold for maximal electroshock (MEST)-induced seizures in mice. Electroconvulsions (seizure activity) were produced in mice by means of a current (sine-wave, 50Hz, 500V, strength from 4 to 18mA, ear-clip electrodes, 0.2-s stimulus duration, tonic hindlimb extension taken as the endpoint). Nic-BZA, 2F-Pic-BZA, Pic-BZA, Me-Ala-BZA, Iso-Nic-BZA, and Me-Pro-BZA administered systemically (ip) in a dose-dependent manner increase the threshold for maximal electroconvulsions in mice. Linear regression analysis of Nic-BZA, 2F-Pic-BZA, Pic-BZA, MeAla-BZA, IsoNic-BZA, and Me-Pro-BZA doses and their corresponding threshold increases allowed determining threshold increasing doses by 20% (TID20 values) that elevate the threshold in drug-treated animals over the threshold in control animals. The experimentally derived TID20 values in the MEST test for Nic-BZA, 2F-Pic-BZA, Pic-BZA, Me-Ala-BZA, Iso-Nic-BZA, and Me-Pro-BZA were 7.45mg/kg, 7.72mg/kg, 8.74mg/kg, 15.11mg/kg, 21.95mg/kg and 28.06mg/kg, respectively. The studied benzylamide derivatives can be arranged with respect to their anticonvulsant potency in the MEST test as follows: Nic-BZA>2F-Pic-BZA>Pic-BZA>Me-Ala-BZA>Iso-Nic-BZA>Me-Pro-BZA. Copyright © 2015 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Adaptive and Personalized Plasma Insulin Concentration Estimation for Artificial Pancreas Systems.

PubMed

Hajizadeh, Iman; Rashid, Mudassir; Samadi, Sediqeh; Feng, Jianyuan; Sevil, Mert; Hobbs, Nicole; Lazaro, Caterina; Maloney, Zacharie; Brandt, Rachel; Yu, Xia; Turksoy, Kamuran; Littlejohn, Elizabeth; Cengiz, Eda; Cinar, Ali

2018-05-01

The artificial pancreas (AP) system, a technology that automatically administers exogenous insulin in people with type 1 diabetes mellitus (T1DM) to regulate their blood glucose concentrations, necessitates the estimation of the amount of active insulin already present in the body to avoid overdosing. An adaptive and personalized plasma insulin concentration (PIC) estimator is designed in this work to accurately quantify the insulin present in the bloodstream. The proposed PIC estimation approach incorporates Hovorka's glucose-insulin model with the unscented Kalman filtering algorithm. Methods for the personalized initialization of the time-varying model parameters to individual patients for improved estimator convergence are developed. Data from 20 three-days-long closed-loop clinical experiments conducted involving subjects with T1DM are used to evaluate the proposed PIC estimation approach. The proposed methods are applied to the clinical data containing significant disturbances, such as unannounced meals and exercise, and the results demonstrate the accurate real-time estimation of the PIC with the root mean square error of 7.15 and 9.25 mU/L for the optimization-based fitted parameters and partial least squares regression-based testing parameters, respectively. The accurate real-time estimation of PIC will benefit the AP systems by preventing overdelivery of insulin when significant insulin is present in the bloodstream.

MP-Pic simulation of CFB riser with EMMS-based drag model

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

Li, F.; Song, F.; Benyahia, S.

2012-01-01

MP-PIC (multi-phase particle in cell) method combined with the EMMS (energy minimization multi- scale) drag force model was implemented with the open source program MFIX to simulate the gas–solid flows in CFB (circulatingfluidizedbed) risers. Calculated solid flux by the EMMS drag agrees well with the experimental value; while the traditional homogeneous drag over-predicts this value. EMMS drag force model can also predict the macro-and meso-scale structures. Quantitative comparison of the results by the EMMS drag force model and the experimental measurements show high accuracy of the model. The effects of the number of particles per parcel and wall conditions onmore » the simulation results have also been investigated in the paper. This work proved that MP-PIC combined with the EMMS drag model can successfully simulate the fluidized flows in CFB risers and it serves as a candidate to realize real-time simulation of industrial processes in the future.« less

A particle-in-cell method for the simulation of plasmas based on an unconditionally stable field solver

DOE PAGES

Wolf, Eric M.; Causley, Matthew; Christlieb, Andrew; ...

2016-08-09

Here, we propose a new particle-in-cell (PIC) method for the simulation of plasmas based on a recently developed, unconditionally stable solver for the wave equation. This method is not subject to a CFL restriction, limiting the ratio of the time step size to the spatial step size, typical of explicit methods, while maintaining computational cost and code complexity comparable to such explicit schemes. We describe the implementation in one and two dimensions for both electrostatic and electromagnetic cases, and present the results of several standard test problems, showing good agreement with theory with time step sizes much larger than allowedmore » by typical CFL restrictions.« less

The HIBEAM Manual

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

Fawley, William M.

2000-02-01

HIBEAM is a 2 1/2D particle-in-cell (PIC) simulation code developed in the late 1990's in the Heavy-Ion Fusion research program at Lawrence Berkeley National Laboratory. The major purpose of HIBEAM is to simulate the transverse (i.e., X-Y) dynamics of a space-charge-dominated, non-relativistic heavy-ion beam being transported in a static accelerator focusing lattice. HIBEAM has been used to study beam combining systems, effective dynamic apertures in electrostatic quadrupole lattices, and emittance growth due to transverse misalignments. At present, HIBEAM runs on the CRAY vector machines (C90 and J90's) at NERSC, although it would be relatively simple to port the code tomore » UNIX workstations so long as IMSL math routines were available.« less

Temporal Evolution of the Plasma Sheath Surrounding Solar Cells in Low Earth Orbit

NASA Technical Reports Server (NTRS)

Willis, Emily M.; Pour, Maria Z. A.

2017-01-01

Initial results from the PIC simulation and the LEM simulation have been presented. The PIC simulation results show that more detailed study is required to refine the ISS solar array current collection model and to understand the development of the current collection in time. The initial results from the LEM demonstrate that is it possible the transients are caused by solar array interaction with the environment, but there are presently too many assumptions in the model to be certain. Continued work on the PIC simulation will provide valuable information on the development of the barrier potential, which will allow refinement the LEM simulation and a better understanding of the causes and effects of the transients.

Proceedings of the 14th International Conference on the Numerical Simulation of Plasmas

NASA Astrophysics Data System (ADS)

Partial Contents are as follows: Numerical Simulations of the Vlasov-Maxwell Equations by Coupled Particle-Finite Element Methods on Unstructured Meshes; Electromagnetic PIC Simulations Using Finite Elements on Unstructured Grids; Modelling Travelling Wave Output Structures with the Particle-in-Cell Code CONDOR; SST--A Single-Slice Particle Simulation Code; Graphical Display and Animation of Data Produced by Electromagnetic, Particle-in-Cell Codes; A Post-Processor for the PEST Code; Gray Scale Rendering of Beam Profile Data; A 2D Electromagnetic PIC Code for Distributed Memory Parallel Computers; 3-D Electromagnetic PIC Simulation on the NRL Connection Machine; Plasma PIC Simulations on MIMD Computers; Vlasov-Maxwell Algorithm for Electromagnetic Plasma Simulation on Distributed Architectures; MHD Boundary Layer Calculation Using the Vortex Method; and Eulerian Codes for Plasma Simulations.

Reflected Charged Particle Populations around Dipolar Lunar Magnetic Anomalies

NASA Astrophysics Data System (ADS)

Deca, Jan; Divin, Andrey

2016-10-01

In this work we analyze and compare the reflected particle populations for both a horizontal and a vertical dipole model embedded in the lunar surface, representing the solar wind interaction with two different lunar magnetic anomaly (LMA) structures. Using the 3D full-kinetic electromagnetic code iPic3D, in combination with a test-particle approach to generate particle trajectories, we focus on the ion and electron dynamics. Whereas the vertical model electrostatically reflects ions upward under both near-parallel and near-perpendicular angles with respect to the lunar surface, the horizontal model only has a significant shallow component. Characterizing the electron dynamics, we find that the interplay of the mini-magnetosphere electric and magnetic fields is capable of temporarily trapping low-energy electrons and possibly ejecting them upstream. Our results are in agreement with recent high-resolution observations. Low- to medium-altitude ion and electron observations might be excellent indicators to complement orbital magnetic field measurements and better uncover the underlying magnetic field structure. The latter is of particular importance in defining the correlation between LMAs and lunar swirls, and further testing the solar wind shielding hypothesis for albedo markings due to space weathering. Observing more reflected ions does not necessarily point to the existence of a mini-magnetosphere.

REFLECTED CHARGED PARTICLE POPULATIONS AROUND DIPOLAR LUNAR MAGNETIC ANOMALIES

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

Deca, Jan; Divin, Andrey

2016-10-01

In this work we analyze and compare the reflected particle populations for both a horizontal and a vertical dipole model embedded in the lunar surface, representing the solar wind interaction with two different lunar magnetic anomaly (LMA) structures. Using the 3D full-kinetic electromagnetic code iPic3D, in combination with a test-particle approach to generate particle trajectories, we focus on the ion and electron dynamics. Whereas the vertical model electrostatically reflects ions upward under both near-parallel and near-perpendicular angles with respect to the lunar surface, the horizontal model only has a significant shallow component. Characterizing the electron dynamics, we find that themore » interplay of the mini-magnetosphere electric and magnetic fields is capable of temporarily trapping low-energy electrons and possibly ejecting them upstream. Our results are in agreement with recent high-resolution observations. Low- to medium-altitude ion and electron observations might be excellent indicators to complement orbital magnetic field measurements and better uncover the underlying magnetic field structure. The latter is of particular importance in defining the correlation between LMAs and lunar swirls, and further testing the solar wind shielding hypothesis for albedo markings due to space weathering. Observing more reflected ions does not necessarily point to the existence of a mini-magnetosphere.« less

A multi-dimensional, energy- and charge-conserving, nonlinearly implicit, electromagnetic Vlasov–Darwin particle-in-cell algorithm

DOE PAGES

Chen, G.; Chacón, L.

2015-08-11

For decades, the Vlasov–Darwin model has been recognized to be attractive for particle-in-cell (PIC) kinetic plasma simulations in non-radiative electromagnetic regimes, to avoid radiative noise issues and gain computational efficiency. However, the Darwin model results in an elliptic set of field equations that renders conventional explicit time integration unconditionally unstable. We explore a fully implicit PIC algorithm for the Vlasov–Darwin model in multiple dimensions, which overcomes many difficulties of traditional semi-implicit Darwin PIC algorithms. The finite-difference scheme for Darwin field equations and particle equations of motion is space–time-centered, employing particle sub-cycling and orbit-averaging. This algorithm conserves total energy, local charge,more » canonical-momentum in the ignorable direction, and preserves the Coulomb gauge exactly. An asymptotically well-posed fluid preconditioner allows efficient use of large cell sizes, which are determined by accuracy considerations, not stability, and can be orders of magnitude larger than required in a standard explicit electromagnetic PIC simulation. Finally, we demonstrate the accuracy and efficiency properties of the algorithm with various numerical experiments in 2D–3V.« less

Developing Chemistry and Kinetic Modeling Tools for Low-Temperature Plasma Simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas; Beckwith, Kris; Davidson, Bradley; Kruger, Scott; Pankin, Alexei; Roark, Christine; Stoltz, Peter

2015-09-01

We discuss the use of proper orthogonal decomposition (POD) methods in VSim, a FDTD plasma simulation code capable of both PIC/MCC and fluid modeling. POD methods efficiently generate smooth representations of noisy self-consistent or test-particle PIC data, and are thus advantageous in computing macroscopic fluid quantities from large PIC datasets (e.g. for particle-based closure computations) and in constructing optimal visual representations of the underlying physics. They may also confer performance advantages for massively parallel simulations, due to the significant reduction in dataset sizes conferred by truncated singular-value decompositions of the PIC data. We also demonstrate how complex LTP chemistry scenarios can be modeled in VSim via an interface with MUNCHKIN, a developing standalone python/C++/SQL code that identifies reaction paths for given input species, solves 1D rate equations for the time-dependent chemical evolution of the system, and generates corresponding VSim input blocks with appropriate cross-sections/reaction rates. MUNCHKIN also computes reaction rates from user-specified distribution functions, and conducts principal path analyses to reduce the number of simulated chemical reactions. Supported by U.S. Department of Energy SBIR program, Award DE-SC0009501.

Comparison of Hall Thruster Plume Expansion Model with Experimental Data

DTIC Science & Technology

2006-05-23

focus of this study, is a hybrid particle- in-cell ( PIC ) model that tracks particles along an unstructured tetrahedral mesh. * Research Engineer...measurements of the ion current density profile, ion energy distributions, and ion species fraction distributions using a nude Faraday probe, retarding...Vol.37 No.1. 6 Oh, D. and Hastings, D., “Three Dimensional PIC -DSMC Simulations of Hall Thruster Plumes and Analysis for Realistic Spacecraft

Muscle length-dependent contribution of motoneuron Cav1.3 channels to force production in model slow motor unit.

PubMed

Kim, Hojeong

2017-07-01

Persistent inward current (PIC)-generating Ca v 1.3 channels in spinal motoneuron dendrites are thought to be actively recruited during normal behaviors. However, whether and how the activation of PIC channels influences force output of motor unit remains elusive. Here, building a physiologically realistic model of slow motor unit I demonstrated that force production induced by the PIC activation is much smaller for short than lengthened muscles during the regular firing of the motoneuron that transitions from the quiescent state by either a brief current pulse at the soma or a brief synaptic excitation at the dendrites. By contrast, the PIC-induced force potentiation was maximal for short muscles when the motoneuron switched from a stable low-frequency firing state to a stable high-frequency firing state by the current pulse at the soma. Under the synaptic excitation at the dendrites, however, the force could not be potentiated by the transitioning of the motoneuron from a low- to a high-frequency firing state due to the simultaneous onset of PIC at the dendrites and firing at the soma. The strong dependency of the input-output relationship of the motor unit on the neuromodulation and Ia afferent inputs for the PIC channels was further shown under static variations in muscle length. Taken together, these findings suggest that the PIC activation in the motoneuron dendrites may differentially affect the force production of the motor unit, depending not only on the firing state history of the motoneuron and the variation in muscle length but also on the mode of motor activity. NEW & NOTEWORTHY Ca v 1.3 channels in motoneuron dendrites are actively involved during normal motor activities. To investigate the effects of the activation of motoneuron Ca v 1.3 channels on force production, a model motor unit was built based on best-available data. The simulation results suggest that force potentiation induced by Ca v 1.3 channel activation is strongly modulated not only by firing history of the motoneuron but also by length variation of the muscle as well as neuromodulation inputs from the brainstem. Copyright © 2017 the American Physiological Society.

Particle-in-cell simulations of bounded plasma discharges applied to low pressure high density sources and positive columns

NASA Astrophysics Data System (ADS)

Kawamura, Emi

Particle-in-cell (PIC) simulations of bounded plasma discharges are attractive because the fields and the particle motion can be obtained self-consistently from first principles. Thus, we can accurately model a wide range of nonlocal and kinetic behavior. The only disadvantage is that PIC may be computationally expensive compared to other methods. Fluid codes, for example, may run faster but make assumptions about the bulk plasma velocity distributions and ignore kinetic effects. In Chapter 1, we demonstrate methods of accelerating PIC simulations of bounded plasma discharges. We find that a combination of physical and numerical methods makes run-times for PIC codes much more competitive with other types of codes. In processing plasmas, the ion energy distributions (IEDs) arriving at the wafer target are crucial in determining ion anisotropy and etch rates. The current trend for plasma reactors is towards lower gas pressure and higher plasma density. In Chapter 2, we review and analyze IEDs arriving at the target of low pressure high density rf plasma reactors. In these reactors, the sheath is typically collisionless. We then perform PIC simulations of collisionless rf sheaths and find that the key parameter governing the shape of the TED at the wafer is the ratio of the ion transit time across the sheath over the rf period. Positive columns are the source of illumination in fluorescent mercury-argon lamps. The efficiency of light production increases with decreasing gas pressure and decreasing discharge radius. Most current lamp software is based on the local concept even though low pressure lighting discharges tend to be nonlocal. In Chapter 3, we demonstrate a 1d3v radial PIC model to conduct nonlocal kinetic simulations of low pressure, small radius positive columns. When compared to other available codes, we find that our PIC code makes the least approximations and assumptions and is accurate and stable over a wider parameter range. We analyze the PIC simulation results in detail and find that the radial electron heat flow, which is neglected in local models, plays a major role in maintaining the global power balance. In Chapter 2, we focused on the sheaths of low pressure high density plasma reactors. In Chapter 4, we extend our study to the bulk and presheaths. Typical industrial plasma reactors often use gases with complex chemistries which tend to generate discharges containing negative ions. For high density electronegative plasmas with low gas pressure, we expect Coulomb collisions between positive and negative ions to dominate over collisions between ions and neutrals. We incorporate a Coulomb collision model into our PIC code to study the effect of this ion-ion Coulomb scattering. We find that the Coulomb collisions between the positive and negative ions significantly modify the negative ion flux, density and kinetic energy profiles.

Comparison of Hall Thruster Plume Expansion Model with Experimental Data (Preprint)

DTIC Science & Technology

2006-07-01

Cartesian mesh. AQUILA, the focus of this study, is a hybrid PIC model that tracks particles along an unstructured tetrahedral mesh. COLISEUM is capable...measurements of the ion current density profile, ion energy distributions, and ion species fraction distributions using a nude Faraday probe...Spacecraft and Rockets, Vol.37 No.1. 6 Oh, D. and Hastings, D., “Three Dimensional PIC -DSMC Simulations of Hall Thruster Plumes and Analysis for

Particle Acceleration in Pulsar Wind Nebulae: PIC Modelling

NASA Astrophysics Data System (ADS)

Sironi, Lorenzo; Cerutti, Benoît

We discuss the role of PIC simulations in unveiling the origin of the emitting particles in PWNe. After describing the basics of the PIC technique, we summarize its implications for the quiescent and the flaring emission of the Crab Nebula, as a prototype of PWNe. A consensus seems to be emerging that, in addition to the standard scenario of particle acceleration via the Fermi process at the termination shock of the pulsar wind, magnetic reconnection in the wind, at the termination shock and in the Nebula plays a major role in powering the multi-wavelength signatures of PWNe.

Study of Ion Beam Forming Process in Electric Thruster Using 3D FEM Simulation

NASA Astrophysics Data System (ADS)

Huang, Tao; Jin, Xiaolin; Hu, Quan; Li, Bin; Yang, Zhonghai

2015-11-01

There are two algorithms to simulate the process of ion beam forming in electric thruster. The one is electrostatic steady state algorithm. Firstly, an assumptive surface, which is enough far from the accelerator grids, launches the ion beam. Then the current density is calculated by theory formula. Secondly these particles are advanced one by one according to the equations of the motions of ions until they are out of the computational region. Thirdly, the electrostatic potential is recalculated and updated by solving Poisson Equation. At the end, the convergence is tested to determine whether the calculation should continue. The entire process will be repeated until the convergence is reached. Another one is time-depended PIC algorithm. In a global time step, we assumed that some new particles would be produced in the simulation domain and its distribution of position and velocity were certain. All of the particles that are still in the system will be advanced every local time steps. Typically, we set the local time step low enough so that the particle needs to be advanced about five times to move the distance of the edge of the element in which the particle is located.

Magnetospheric Reconnection in Modified Current-Sheet Equilibria

NASA Astrophysics Data System (ADS)

Newman, D. L.; Goldman, M. V.; Lapenta, G.; Markidis, S.

2012-10-01

Particle simulations of magnetic reconnection in Earth's magnetosphere are frequently initialized with a current-carrying Harris equilibrium superposed on a current-free uniform background plasma. The Harris equilibrium satisfies local charge neutrality, but requires that the sheet current be dominated by the hotter species -- often the ions in Earth's magnetosphere. This constraint is not necessarily consistent with observations. A modified kinetic equilibrium that relaxes this constraint on the currents was proposed by Yamada et al. [Phys. Plasmas., 7, 1781 (2000)] with no background population. These modified equilibria were characterized by an asymptotic converging or diverging electrostatic field normal to the current sheet. By reintroducing the background plasma, we have developed new families of equilibria where the asymptotic fields are suppressed by Debye shielding. Because the electrostatic potential profiles of these new equilibria contain wells and/or barriers capable of spatially isolating different populations of electrons and/or ions, these solutions can be further generalized to include classes of asymmetric kinetic equilibria. Examples of both symmetric and asymmetric equilibria will be presented. The dynamical evolution of these equilibria, when perturbed, will be further explored by means of implicit 2D PIC reconnection simulations, including comparisons with simulations employing standard Harris-equilibrium initializations.

Development of a local anesthetic lidocaine-loaded redox-active injectable gel for postoperative pain management.

PubMed

Nagasaki, Yukio; Mizukoshi, Yutaro; Gao, Zhenyu; Feliciano, Chitho P; Chang, Kyungho; Sekiyama, Hiroshi; Kimura, Hiroyuki

2017-07-15

Although local anesthesia is commonly applied for pain relief, there are several issues such as its short duration of action and low effectiveness at the areas of inflammation due to the acidic pH. The presence of excessive amount of reactive oxygen species (ROS) is known to induce inflammation and aggravate pain. To resolve these issues, we developed a redox-active injectable gel (RIG) with ROS-scavenging activity. RIG was prepared by mixing polyamine-b-poly(ethylene glycol)-b-polyamine with nitroxide radical moieties as side chains on the polyamine segments (PMNT-b-PEG-b-PMNT) with a polyanion, which formed a flower-type micelle via electrostatic complexation. Lidocaine could be stably incorporated in its core. When the temperature of the solution was increased to 37°C, the PIC-type flower micelle transformed to gel. The continuous release of lidocaine from the gel was observed for more than three days, without remarkable initial burst, which is probably owing to the stable entrapment of lidocaine in the PIC core of the gel. We evaluated the analgesic effect of RIG in carrageenan-induced arthritis mouse model. Results showed that lidocaine-loaded RIG has stronger and longer analgesic effect when administered in inflamed areas. In contrast, while the use of non-complexed lidocaine did not show analgesic effect one day after its administration. Note that no effect was observed when PIC-type flower micelle without ROS-scavenging ability was used. These findings suggest that local anesthetic-loaded RIG can effectively reduce the number of injection times and limit the side effects associated with the use of anti-inflammatory drugs for postoperative pain management. 1. We have been working on nanomaterials, which effectively eliminate ROS, avoiding dysfunction of mitochondria in healthy cells. 2. We designed redox injectable gel using polyion complexed flower type micelle, which can eliminates ROS locally. 3. We could prepare local anesthesia-loaded redox injectable gel (lido@RIG). 4. Drug release could be extended by local administration of lido@RIG. 5. Deprotonation of lidocaine improved anesthetic effect because ROS were eliminated locally by RIG. 6. Local inflammation could be also suppressed by lido@RIG. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Estimates of the location of L-type Ca2+ channels in motoneurons of different sizes: a computational study.

PubMed

Grande, Giovanbattista; Bui, Tuan V; Rose, P Ken

2007-06-01

In the presence of monoamines, L-type Ca(2+) channels on the dendrites of motoneurons contribute to persistent inward currents (PICs) that can amplify synaptic inputs two- to sixfold. However, the exact location of the L-type Ca(2+) channels is controversial, and the importance of the location as a means of regulating the input-output properties of motoneurons is unknown. In this study, we used a computational strategy developed previously to estimate the dendritic location of the L-type Ca(2+) channels and test the hypothesis that the location of L-type Ca(2+) channels varies as a function of motoneuron size. Compartmental models were constructed based on dendritic trees of five motoneurons that ranged in size from small to large. These models were constrained by known differences in PIC activation reported for low- and high-conductance motoneurons and the relationship between somatic PIC threshold and the presence or absence of tonic excitatory or inhibitory synaptic activity. Our simulations suggest that L-type Ca(2+) channels are concentrated in hotspots whose distance from the soma increases with the size of the dendritic tree. Moving the hotspots away from these sites (e.g., using the hotspot locations from large motoneurons on intermediate-sized motoneurons) fails to replicate the shifts in PIC threshold that occur experimentally during tonic excitatory or inhibitory synaptic activity. In models equipped with a size-dependent distribution of L-type Ca(2+) channels, the amplification of synaptic current by PICs depends on motoneuron size and the location of the synaptic input on the dendritic tree.

Numerical heating in Particle-In-Cell simulations with Monte Carlo binary collisions

NASA Astrophysics Data System (ADS)

Alves, E. Paulo; Mori, Warren; Fiuza, Frederico

2017-10-01

The binary Monte Carlo collision (BMCC) algorithm is a robust and popular method to include Coulomb collision effects in Particle-in-Cell (PIC) simulations of plasmas. While a number of works have focused on extending the validity of the model to different physical regimes of temperature and density, little attention has been given to the fundamental coupling between PIC and BMCC algorithms. Here, we show that the coupling between PIC and BMCC algorithms can give rise to (nonphysical) numerical heating of the system, that can be far greater than that observed when these algorithms operate independently. This deleterious numerical heating effect can significantly impact the evolution of the simulated system particularly for long simulation times. In this work, we describe the source of this numerical heating, and derive scaling laws for the numerical heating rates based on the numerical parameters of PIC-BMCC simulations. We compare our theoretical scalings with PIC-BMCC numerical experiments, and discuss strategies to minimize this parasitic effect. This work is supported by DOE FES under FWP 100237 and 100182.

Foundry fabricated photonic integrated circuit optical phase lock loop.

PubMed

Bałakier, Katarzyna; Fice, Martyn J; Ponnampalam, Lalitha; Graham, Chris S; Wonfor, Adrian; Seeds, Alwyn J; Renaud, Cyril C

2017-07-24

This paper describes the first foundry-based InP photonic integrated circuit (PIC) designed to work within a heterodyne optical phase locked loop (OPLL). The PIC and an external electronic circuit were used to phase-lock a single-line semiconductor laser diode to an incoming reference laser, with tuneable frequency offset from 4 GHz to 12 GHz. The PIC contains 33 active and passive components monolithically integrated on a single chip, fully demonstrating the capability of a generic foundry PIC fabrication model. The electronic part of the OPLL consists of commercially available RF components. This semi-packaged system stabilizes the phase and frequency of the integrated laser so that an absolute frequency, high-purity heterodyne signal can be generated when the OPLL is in operation, with phase noise lower than -100 dBc/Hz at 10 kHz offset from the carrier. This is the lowest phase noise level ever demonstrated by monolithically integrated OPLLs.

Plasma particle simulation of electrostatic ion thrusters

NASA Technical Reports Server (NTRS)

Peng, Xiaohang; Keefer, Dennis; Ruyten, Wilhelmus

1990-01-01

Charge exchange collisons between beam ions and neutral propellant gas can result in erosion of the accelerator grid surfaces of an ion engine. A particle in cell (PIC) is developed along with a Monte Carlo method to simulate the ion dynamics and charge exchange processes in the grid region of an ion thruster. The simulation is two-dimensional axisymmetric and uses three velocity components (2d3v) to investigate the influence of charge exchange collisions on the ion sputtering of the accelerator grid surfaces. An example calculation has been performed for an ion thruster operated on xenon propellant. The simulation shows that the greatest sputtering occurs on the downstream surface of the grid, but some sputtering can also occur on the upstream surface as well as on the interior of the grid aperture.

Ion acceleration by laser hole-boring into plasmas

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

Pogorelsky, I. V.; Dover, N. P.; Babzien, M.

By experiment and simulations, we study the interaction of an intense CO{sub 2} laser pulse with slightly overcritical plasmas of fully ionized helium gas. Transverse optical probing is used to show a recession of the front plasma surface with an initial velocity >10{sup 6} m/s driven by hole-boring by the laser pulse and the resulting radiation pressure driven electrostatic shocks. The collisionless shock propagates through the plasma, dissipates into an ion-acoustic solitary wave, and eventually becomes collisional as it slows further. These observations are supported by PIC simulations which prove the conclusion that monoenergetic protons observed in our earlier reportedmore » experiment with a hydrogen jet result from ion trapping and reflection from a shock wave driven through the plasma.« less

Revisiting linear plasma waves for finite value of the plasma parameter

NASA Astrophysics Data System (ADS)

Grismayer, Thomas; Fahlen, Jay; Decyk, Viktor; Mori, Warren

2010-11-01

We investigate through theory and PIC simulations the Landau-damping of plasma waves with finite plasma parameter. We concentrate on the linear regime, γφB, where the waves are typically small and below the thermal noise. We simulate these condition using 1,2,3D electrostatic PIC codes (BEPS), noting that modern computers now allow us to simulate cases where (nλD^3 = [1e2;1e6]). We study these waves by using a subtraction technique in which two simulations are carried out. In the first, a small wave is initialized or driven, in the second no wave is excited. The results are subtracted to provide a clean signal that can be studied. As nλD^3 is decreased, the number of resonant electrons can be small for linear waves. We show how the damping changes as a result of having few resonant particles. We also find that for small nλD^3 fluctuations can cause the electrons to undergo collisions that eventually destroy the initial wave. A quantity of interest is the the life time of a particular mode which depends on the plasma parameter and the wave number. The life time is estimated and then compared with the numerical results. A surprising result is that even for large values of nλD^3 some non-Vlasov discreteness effects appear to be important.

Time-domain simulation of nonlinear radiofrequency phenomena

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

Jenkins, Thomas G.; Austin, Travis M.; Smithe, David N.

Nonlinear effects associated with the physics of radiofrequency wave propagation through a plasma are investigated numerically in the time domain, using both fluid and particle-in-cell (PIC) methods. We find favorable comparisons between parametric decay instability scenarios observed on the Alcator C-MOD experiment [J. C. Rost, M. Porkolab, and R. L. Boivin, Phys. Plasmas 9, 1262 (2002)] and PIC models. The capability of fluid models to capture important nonlinear effects characteristic of wave-plasma interaction (frequency doubling, cyclotron resonant absorption) is also demonstrated.

Time-domain simulation of nonlinear radiofrequency phenomena

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Austin, Travis M.; Smithe, David N.; Loverich, John; Hakim, Ammar H.

2013-01-01

Nonlinear effects associated with the physics of radiofrequency wave propagation through a plasma are investigated numerically in the time domain, using both fluid and particle-in-cell (PIC) methods. We find favorable comparisons between parametric decay instability scenarios observed on the Alcator C-MOD experiment [J. C. Rost, M. Porkolab, and R. L. Boivin, Phys. Plasmas 9, 1262 (2002)] and PIC models. The capability of fluid models to capture important nonlinear effects characteristic of wave-plasma interaction (frequency doubling, cyclotron resonant absorption) is also demonstrated.

Experimental verification of layout physical verification of silicon photonics

NASA Astrophysics Data System (ADS)

El Shamy, Raghi S.; Swillam, Mohamed A.

2018-02-01

Silicon photonics have been approved as one of the best platforms for dense integration of photonic integrated circuits (PICs) due to the high refractive index contrast among its materials. Silicon on insulator (SOI) is a widespread photonics technology, which support a variety of devices for lots of applications. As the photonics market is growing, the number of components in the PICs increases which increase the need for an automated physical verification (PV) process. This PV process will assure reliable fabrication of the PICs as it will check both the manufacturability and the reliability of the circuit. However, PV process is challenging in the case of PICs as it requires running an exhaustive electromagnetic (EM) simulations. Our group have recently proposed an empirical closed form models for the directional coupler and the waveguide bends based on the SOI technology. The models have shown a very good agreement with both finite element method (FEM) and finite difference time domain (FDTD) solvers. These models save the huge time of the 3D EM simulations and can be easily included in any electronic design automation (EDA) flow as the equations parameters can be easily extracted from the layout. In this paper we present experimental verification for our previously proposed models. SOI directional couplers with different dimensions have been fabricated using electron beam lithography and measured. The results from the measurements of the fabricate devices have been compared to the derived models and show a very good agreement. Also the matching can reach 100% by calibrating certain parameter in the model.

Extended Magnetohydrodynamics with Embedded Particle-in-Cell Simulation of Ganymede's Magnetosphere

NASA Technical Reports Server (NTRS)

Toth, Gabor; Jia, Xianzhe; Markidis, Stefano; Peng, Ivy Bo; Chen, Yuxi; Daldorff, Lars K. S.; Tenishev, Valeriy M.; Borovikov, Dmitry; Haiducek, John D.; Gombosi, Tamas I.;

Reduced 3d modeling on injection schemes for laser wakefield acceleration at plasma scale lengths

NASA Astrophysics Data System (ADS)

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

2017-10-01

Current modelling techniques for laser wakefield acceleration (LWFA) are based on particle-in-cell (PIC) codes which are computationally demanding. In PIC simulations the laser wavelength λ0, in μm-range, has to be resolved over the acceleration lengths in meter-range. A promising approach is the ponderomotive guiding center solver (PGC) by only considering the laser envelope for laser pulse propagation. Therefore only the plasma skin depth λp has to be resolved, leading to speedups of (λp /λ0) 2. This allows to perform a wide-range of parameter studies and use it for λ0 <<λp studies. We present the 3d version of a PGC solver in the massively parallel, fully relativistic PIC code OSIRIS. Further, a discussion and characterization of the validity of the PGC solver for injection schemes on the plasma scale lengths, such as down-ramp injection, magnetic injection and ionization injection, through parametric studies, full PIC simulations and theoretical scaling, is presented. This work was partially supported by Fundacao para a Ciencia e Tecnologia (FCT), Portugal, through Grant No. PTDC/FIS-PLA/2940/2014 and PD/BD/105882/2014.

On-chip immobilization of planarians for in vivo imaging.

PubMed

Dexter, Joseph P; Tamme, Mary B; Lind, Christine H; Collins, Eva-Maria S

2014-09-17

Planarians are an important model organism for regeneration and stem cell research. A complete understanding of stem cell and regeneration dynamics in these animals requires time-lapse imaging in vivo, which has been difficult to achieve due to a lack of tissue-specific markers and the strong negative phototaxis of planarians. We have developed the Planarian Immobilization Chip (PIC) for rapid, stable immobilization of planarians for in vivo imaging without injury or biochemical alteration. The chip is easy and inexpensive to fabricate, and worms can be mounted for and removed after imaging within minutes. We show that the PIC enables significantly higher-stability immobilization than can be achieved with standard techniques, allowing for imaging of planarians at sub-cellular resolution in vivo using brightfield and fluorescence microscopy. We validate the performance of the PIC by performing time-lapse imaging of planarian wound closure and sequential imaging over days of head regeneration. We further show that the device can be used to immobilize Hydra, another photophobic regenerative model organism. The simple fabrication, low cost, ease of use, and enhanced specimen stability of the PIC should enable its broad application to in vivo studies of stem cell and regeneration dynamics in planarians and Hydra.

On-chip immobilization of planarians for in vivo imaging

PubMed Central

Dexter, Joseph P.; Tamme, Mary B.; Lind, Christine H.; Collins, Eva-Maria S.

2014-01-01

Planarians are an important model organism for regeneration and stem cell research. A complete understanding of stem cell and regeneration dynamics in these animals requires time-lapse imaging in vivo, which has been difficult to achieve due to a lack of tissue-specific markers and the strong negative phototaxis of planarians. We have developed the Planarian Immobilization Chip (PIC) for rapid, stable immobilization of planarians for in vivo imaging without injury or biochemical alteration. The chip is easy and inexpensive to fabricate, and worms can be mounted for and removed after imaging within minutes. We show that the PIC enables significantly higher-stability immobilization than can be achieved with standard techniques, allowing for imaging of planarians at sub-cellular resolution in vivo using brightfield and fluorescence microscopy. We validate the performance of the PIC by performing time-lapse imaging of planarian wound closure and sequential imaging over days of head regeneration. We further show that the device can be used to immobilize Hydra, another photophobic regenerative model organism. The simple fabrication, low cost, ease of use, and enhanced specimen stability of the PIC should enable its broad application to in vivo studies of stem cell and regeneration dynamics in planarians and Hydra. PMID:25227263

Hall-MHD and PIC Modeling of the Conduction-to-Opening Transition in a Plasma Opening Switch

NASA Astrophysics Data System (ADS)

Schumer, J. W.; SwanekampDdagger, S. B.; Ottinger, P. F.; Commisso, R. J.; Weber, B. V.

1998-11-01

Utilizing the fast opening characteristics of a plasma opening switch (POS), inductive energy storage devices can generate short-duration high-power pulses (<0.1 μ s, >1 TW) with current rise-times on the order of 10 ns. Plasma redistribution and thinning during the POS conduction phase can be modeled adequately with MHD methods. By including the Hall term in Ohm's Law, MHD methods can simulate plasmas with density gradient scale lengths between c/ω_pe < Ln < c/ω_pi. However, the neglect of electron inertia (c/ω_pe) and space-charge separation (λ_De) by single-fluid theory eventually becomes invalid in small gap regions that form during POS opening. PIC methods are well-suited for low-density plasmas, but are numerically taxed by high-density POS regions. An interface converts MHD (Mach2) output into PIC (Magic) input suitable for validating various transition criteria through comparison of current and density distributions from both methods. We will discuss recent progress in interfacing Hall-MHD and PIC simulations. Work supported by Defense Special Weapons Agency. ^ NRL-NRC Research Associate. hspace0.25in ^ JAYCOR, Vienna, VA 22102.

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

Plasma non-uniformity in a symmetric radiofrequency capacitively-coupled reactor with dielectric side-wall: a two dimensional particle-in-cell/Monte Carlo collision simulation

NASA Astrophysics Data System (ADS)

Liu, Yue; Booth, Jean-Paul; Chabert, Pascal

2018-02-01

A Cartesian-coordinate two-dimensional electrostatic particle-in-cell/Monte Carlo collision (PIC/MCC) plasma simulation code is presented, including a new treatment of charge balance at dielectric boundaries. It is used to simulate an Ar plasma in a symmetric radiofrequency capacitively-coupled parallel-plate reactor with a thick (3.5 cm) dielectric side-wall. The reactor size (12 cm electrode width, 2.5 cm electrode spacing) and frequency (15 MHz) are such that electromagnetic effects can be ignored. The dielectric side-wall effectively shields the plasma from the enhanced electric field at the powered-grounded electrode junction, which has previously been shown to produce locally enhanced plasma density (Dalvie et al 1993 Appl. Phys. Lett. 62 3207-9 Overzet and Hopkins 1993 Appl. Phys. Lett. 63 2484-6 Boeuf and Pitchford 1995 Phys. Rev. E 51 1376-90). Nevertheless, enhanced electron heating is observed in a region adjacent to the dielectric boundary, leading to maxima in ionization rate, plasma density and ion flux to the electrodes in this region, and not at the reactor centre as would otherwise be expected. The axially-integrated electron power deposition peaks closer to the dielectric edge than the electron density. The electron heating components are derived from the PIC/MCC simulations and show that this enhanced electron heating results from increased Ohmic heating in the axial direction as the electron density decreases towards the side-wall. We investigated the validity of different analytical formulas to estimate the Ohmic heating by comparing them to the PIC results. The widespread assumption that a time-averaged momentum transfer frequency, v m , can be used to estimate the momentum change can cause large errors, since it neglects both phase and amplitude information. Furthermore, the classical relationship between the total electron current and the electric field must be used with caution, particularly close to the dielectric edge where the (neglected) pressure gradient term becomes significant.

[Accession to the PIC/S and pharmaceutical quality system in Japan].

PubMed

Katori, Noriko

2014-01-01

In March, 2012, Japan made the application for membership of the Pharmaceutical Inspection convention and Pharmaceutical Inspection Co-operation scheme (PIC/S) which is an international body of a GMP inspection. The globalization of pharmaceutical manufacturing and sales has been a driving force behind the decision to become a PIC/S member. For the application for membership, Japan's GMP inspectorate needs to fulfill PIC/S requirements, for example, the inspection organization has to have a quality system as a global standard. One of the other requirements is that the GMP inspectorate can access Official Medicines Control Laboratories (OMCL) having high analytical skills and also have a quality system based on ISO 17025. I would like to describe the process to make up a quality system in the National Institute of Health Sciences and also the circumstances around the PIC/S application in Japan.

First PIC simulations modeling the interaction of ultra-intense lasers with sub-micron, liquid crystal targets

NASA Astrophysics Data System (ADS)

McMahon, Matthew; Poole, Patrick; Willis, Christopher; Andereck, David; Schumacher, Douglass

2014-10-01

We recently introduced liquid crystal films as on-demand, variable thickness (50-5000 nanometers), low cost targets for intense laser experiments. Here we present the first particle-in-cell (PIC) simulations of short pulse laser excitation of liquid crystal targets treating Scarlet (OSU) class lasers using the PIC code LSP. In order to accurately model the target evolution, a low starting temperature and field ionization model are employed. This is essential as large starting temperatures, often used to achieve large Debye lengths, lead to expansion of the target causing significant reduction of the target density before the laser pulse can interact. We also present an investigation of the modification of laser pulses by very thin targets. This work was supported by the DARPA PULSE program through a grant from ARMDEC, by the US Department of Energy under Contract No. DE-NA0001976, and allocations of computing time from the Ohio Supercomputing Center.

Characterizing a New Candidate Benchmark Brown Dwarf Companion in the β Pic Moving Group

NASA Astrophysics Data System (ADS)

Phillips, Caprice; Bowler, Brendan; Liu, Michael C.; Mace, Gregory N.; Sokal, Kimberly R.

2018-01-01

Benchmark brown dwarfs are objects that have at least two measured fundamental quantities such as luminosity and age, and therefore can be used to test substellar atmospheric and evolutionary models. Nearby, young, loose associations such as the β Pic moving group represent some of the best regions in which to identify intermediate-age benchmark brown dwarfs due to their well-constrained ages and metallicities. We present a spectroscopic study of a new companion at the hydrogen-burning limit orbiting a low-mass star at a separation of 9″ (650 AU) in the 23 Myr old β Pic moving group. The medium-resolution near-infrared spectrum of this companion from IRTF/SpeX shows clear signs of low surface gravity and yields an index-based spectral type of M6±1 with a VL-G gravity on the Allers & Liu classification system. Currently, there are four known brown dwarf and giant planet companions in the β Pic moving group: HR 7329 B, PZ Tel B, β Pic b, and 51 Eri b. Depending on its exact age and accretion history, this new object may represent the third brown dwarf companion and fifth substellar companion in this association.

Enhanced quasi-static particle-in-cell simulation of electron cloud instabilities in circular accelerators

NASA Astrophysics Data System (ADS)

Feng, Bing

Electron cloud instabilities have been observed in many circular accelerators around the world and raised concerns of future accelerators and possible upgrades. In this thesis, the electron cloud instabilities are studied with the quasi-static particle-in-cell (PIC) code QuickPIC. Modeling in three-dimensions the long timescale propagation of beam in electron clouds in circular accelerators requires faster and more efficient simulation codes. Thousands of processors are easily available for parallel computations. However, it is not straightforward to increase the effective speed of the simulation by running the same problem size on an increasingly number of processors because there is a limit to domain size in the decomposition of the two-dimensional part of the code. A pipelining algorithm applied on the fully parallelized particle-in-cell code QuickPIC is implemented to overcome this limit. The pipelining algorithm uses multiple groups of processors and optimizes the job allocation on the processors in parallel computing. With this novel algorithm, it is possible to use on the order of 102 processors, and to expand the scale and the speed of the simulation with QuickPIC by a similar factor. In addition to the efficiency improvement with the pipelining algorithm, the fidelity of QuickPIC is enhanced by adding two physics models, the beam space charge effect and the dispersion effect. Simulation of two specific circular machines is performed with the enhanced QuickPIC. First, the proposed upgrade to the Fermilab Main Injector is studied with an eye upon guiding the design of the upgrade and code validation. Moderate emittance growth is observed for the upgrade of increasing the bunch population by 5 times. But the simulation also shows that increasing the beam energy from 8GeV to 20GeV or above can effectively limit the emittance growth. Then the enhanced QuickPIC is used to simulate the electron cloud effect on electron beam in the Cornell Energy Recovery Linac (ERL) due to extremely small emittance and high peak currents anticipated in the machine. A tune shift is discovered from the simulation; however, emittance growth of the electron beam in electron cloud is not observed for ERL parameters.

Fast 2D Fluid-Analytical Simulation of IEDs and Plasma Uniformity in Multi-frequency CCPs

NASA Astrophysics Data System (ADS)

Kawamura, E.; Lieberman, M. A.; Graves, D. B.

2014-10-01

A fast 2D axisymmetric fluid-analytical model using the finite elements tool COMSOL is interfaced with a 1D particle-in-cell (PIC) code to study ion energy distributions (IEDs) in multi-frequency argon capacitively coupled plasmas (CCPs). A bulk fluid plasma model which solves the time-dependent plasma fluid equations is coupled with an analytical sheath model which solves for the sheath parameters. The fluid-analytical results are used as input to a PIC simulation of the sheath region of the discharge to obtain the IEDs at the wafer electrode. Each fluid-analytical-PIC simulation on a moderate 2.2 GHz CPU workstation with 8 GB of memory took about 15-20 minutes. The 2D multi-frequency fluid-analytical model was compared to 1D PIC simulations of a symmetric parallel plate discharge, showing good agreement. Fluid-analytical simulations of a 2/60/162 MHz argon CCP with a typical asymmetric reactor geometry were also conducted. The low 2 MHz frequency controlled the sheath width and voltage while the higher frequencies controlled the plasma production. A standing wave was observable at the highest frequency of 162 MHz. Adding 2 MHz power to a 60 MHz discharge or 162 MHz to a dual frequency 2 MHz/60 MHz discharge enhanced the plasma uniformity. This work was supported by the Department of Energy Office of Fusion Energy Science Contract DE-SC000193, and in part by gifts from Lam Research Corporation and Micron Corporation.

Computational Modeling of Ultrafast Pulse Propagation in Nonlinear Optical Materials

NASA Technical Reports Server (NTRS)

Goorjian, Peter M.; Agrawal, Govind P.; Kwak, Dochan (Technical Monitor)

1996-01-01

There is an emerging technology of photonic (or optoelectronic) integrated circuits (PICs or OEICs). In PICs, optical and electronic components are grown together on the same chip. rib build such devices and subsystems, one needs to model the entire chip. Accurate computer modeling of electromagnetic wave propagation in semiconductors is necessary for the successful development of PICs. More specifically, these computer codes would enable the modeling of such devices, including their subsystems, such as semiconductor lasers and semiconductor amplifiers in which there is femtosecond pulse propagation. Here, the computer simulations are made by solving the full vector, nonlinear, Maxwell's equations, coupled with the semiconductor Bloch equations, without any approximations. The carrier is retained in the description of the optical pulse, (i.e. the envelope approximation is not made in the Maxwell's equations), and the rotating wave approximation is not made in the Bloch equations. These coupled equations are solved to simulate the propagation of femtosecond optical pulses in semiconductor materials. The simulations describe the dynamics of the optical pulses, as well as the interband and intraband.

The Effects of Insulator Wall Material on Hall Thruster Discharges: A Numerical Study

DTIC Science & Technology

2001-01-03

An investigation was undertaken to determine how the choice of insulator wall material inside a Hall thruster discharge channel might affect thruster operation. In order to study this, an evolved hybrid particle-in-cell (PIC) numerical Hall thruster model, HPHall, was used. HPHall solves a set of quasi-one-dimensional fluid equations for electrons and tracks heavy particles using a PIC method.

Resolving the Kinetic Reconnection Length Scale in Global Magnetospheric Simulations with MHD-EPIC

NASA Astrophysics Data System (ADS)

Toth, G.; Chen, Y.; Cassak, P.; Jordanova, V.; Peng, B.; Markidis, S.; Gombosi, T. I.

2016-12-01

We have recently developed a new modeling capability: the Magnetohydrodynamics with Embedded Particle-in-Cell (MHD-EPIC) algorithm with support from Los Alamos SHIELDS and NSF INSPIRE grants. We have implemented MHD-EPIC into the Space Weather Modeling Framework (SWMF) using the implicit Particle-in-Cell (iPIC3D) and the BATS-R-US extended magnetohydrodynamic codes. The MHD-EPIC model allows two-way coupled simulations in two and three dimensions with multiple embedded PIC regions. Both BATS-R-US and iPIC3D are massively parallel codes. The MHD-EPIC approach allows global magnetosphere simulations with embedded kinetic simulations. For small magnetospheres, like Ganymede or Mercury, we can easily resolve the ion scales around the reconnection sites. Modeling the Earth magnetosphere is very challenging even with our efficient MHD-EPIC model due to the large separation between the global and ion scales. On the other hand the large separation of scales may be exploited: the solution may not be sensitive to the ion inertial length as long as it is small relative to the global scales. The ion inertial length can be varied by changing the ion mass while keeping the MHD mass density, the velocity, and pressure the same for the initial and boundary conditions. Our two-dimensional MHD-EPIC simulations for the dayside reconnection region show in fact, that the overall solution is not sensitive to ion inertial length. The shape, size and frequency of flux transfer events are very similar for a wide range of ion masses. Our results mean that 3D MHD-EPIC simulations for the Earth and other large magnetospheres can be made computationally affordable by artificially increasing the ion mass: the required grid resolution and time step in the PIC model are proportional to the ion inertial length. Changing the ion mass by a factor of 4, for example, speeds up the PIC code by a factor of 256. In fact, this approach allowed us to perform an hour-long 3D MHD-EPIC simulations for the Earth magnetosphere.

Wave-Kinetic Simulations of the Nonlinear Generation of Electromagnetic VLF Waves through Velocity Ring Instabilities

NASA Astrophysics Data System (ADS)

Ganguli, G.; Crabtree, C. E.; Rudakov, L.; Mithaiwala, M.

2014-12-01

Velocity ring instabilities are a common naturally occuring magnetospheric phenomenon that can also be generated by man made ionospheric experiments. These instabilities are known to generate lower-hybrid waves, which generally cannot propagte out of the source region. However, nonlinear wave physics can convert these linearly driven electrostatic lower-hybrid waves into electromagnetic waves that can escape the source region. These nonlinearly generated waves can be an important source of VLF turbulence that controls the trapped electron lifetime in the radiation belts. We develop numerical solutions to the wave-kinetic equation in a periodic box including the effects of nonlinear (NL) scattering (nonlinear Landau damping) of Lower-hybrid waves giving the evolution of the wave-spectra in wavenumber space. Simultaneously we solve the particle diffusion equation of both the background plasma particles and the ring ions, due to both linear and nonlinear Landau resonances. At initial times for cold ring ions, an electrostatic beam mode is excited, while the kinetic mode is stable. As the instability progresses the ring ions heat, the beam mode is stabilized, and the kinetic mode destabilizes. When the amplitude of the waves becomes sufficient the lower-hybrid waves are scattered (by either nearly unmagnetized ions or magnetized electrons) into electromagnetic magnetosonic waves [Ganguli et al 2010]. The effect of NL scattering is to limit the amplitude of the waves, slowing down the quasilinear relaxation time and ultimately allowing more energy from the ring to be liberated into waves [Mithaiwala et al. 2011]. The effects of convection out of the instability region are modeled, additionally limiting the amplitude of the waves, allowing further energy to be liberated from the ring [Scales et al., 2012]. Results are compared to recent 3D PIC simulations [Winske and Duaghton 2012].

A curvilinear, fully implicit, conservative electromagnetic PIC algorithm in multiple dimensions

DOE PAGES

Chacon, L.; Chen, G.

2016-04-19

Here, we extend a recently proposed fully implicit PIC algorithm for the Vlasov–Darwin model in multiple dimensions (Chen and Chacón (2015) [1]) to curvilinear geometry. As in the Cartesian case, the approach is based on a potential formulation (Φ, A), and overcomes many difficulties of traditional semi-implicit Darwin PIC algorithms. Conservation theorems for local charge and global energy are derived in curvilinear representation, and then enforced discretely by a careful choice of the discretization of field and particle equations. Additionally, the algorithm conserves canonical-momentum in any ignorable direction, and preserves the Coulomb gauge ∇ • A = 0 exactly. Anmore » asymptotically well-posed fluid preconditioner allows efficient use of large cell sizes, which are determined by accuracy considerations, not stability, and can be orders of magnitude larger than required in a standard explicit electromagnetic PIC simulation. We demonstrate the accuracy and efficiency properties of the algorithm with numerical experiments in mapped meshes in 1D-3V and 2D-3V.« less

A curvilinear, fully implicit, conservative electromagnetic PIC algorithm in multiple dimensions

NASA Astrophysics Data System (ADS)

Chacón, L.; Chen, G.

2016-07-01

We extend a recently proposed fully implicit PIC algorithm for the Vlasov-Darwin model in multiple dimensions (Chen and Chacón (2015) [1]) to curvilinear geometry. As in the Cartesian case, the approach is based on a potential formulation (ϕ, A), and overcomes many difficulties of traditional semi-implicit Darwin PIC algorithms. Conservation theorems for local charge and global energy are derived in curvilinear representation, and then enforced discretely by a careful choice of the discretization of field and particle equations. Additionally, the algorithm conserves canonical-momentum in any ignorable direction, and preserves the Coulomb gauge ∇ ṡ A = 0 exactly. An asymptotically well-posed fluid preconditioner allows efficient use of large cell sizes, which are determined by accuracy considerations, not stability, and can be orders of magnitude larger than required in a standard explicit electromagnetic PIC simulation. We demonstrate the accuracy and efficiency properties of the algorithm with numerical experiments in mapped meshes in 1D-3V and 2D-3V.

A curvilinear, fully implicit, conservative electromagnetic PIC algorithm in multiple dimensions

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

Chacon, L.; Chen, G.

Here, we extend a recently proposed fully implicit PIC algorithm for the Vlasov–Darwin model in multiple dimensions (Chen and Chacón (2015) [1]) to curvilinear geometry. As in the Cartesian case, the approach is based on a potential formulation (Φ, A), and overcomes many difficulties of traditional semi-implicit Darwin PIC algorithms. Conservation theorems for local charge and global energy are derived in curvilinear representation, and then enforced discretely by a careful choice of the discretization of field and particle equations. Additionally, the algorithm conserves canonical-momentum in any ignorable direction, and preserves the Coulomb gauge ∇ • A = 0 exactly. Anmore » asymptotically well-posed fluid preconditioner allows efficient use of large cell sizes, which are determined by accuracy considerations, not stability, and can be orders of magnitude larger than required in a standard explicit electromagnetic PIC simulation. We demonstrate the accuracy and efficiency properties of the algorithm with numerical experiments in mapped meshes in 1D-3V and 2D-3V.« less

Fast 2D fluid-analytical simulation of ion energy distributions and electromagnetic effects in multi-frequency capacitive discharges

NASA Astrophysics Data System (ADS)

Kawamura, E.; Lieberman, M. A.; Graves, D. B.

2014-12-01

A fast 2D axisymmetric fluid-analytical plasma reactor model using the finite elements simulation tool COMSOL is interfaced with a 1D particle-in-cell (PIC) code to study ion energy distributions (IEDs) in multi-frequency capacitive argon discharges. A bulk fluid plasma model, which solves the time-dependent plasma fluid equations for the ion continuity and electron energy balance, is coupled with an analytical sheath model, which solves for the sheath parameters. The time-independent Helmholtz equation is used to solve for the fields and a gas flow model solves for the steady-state pressure, temperature and velocity of the neutrals. The results of the fluid-analytical model are used as inputs to a PIC simulation of the sheath region of the discharge to obtain the IEDs at the target electrode. Each 2D fluid-analytical-PIC simulation on a moderate 2.2 GHz CPU workstation with 8 GB of memory took about 15-20 min. The multi-frequency 2D fluid-analytical model was compared to 1D PIC simulations of a symmetric parallel-plate discharge, showing good agreement. We also conducted fluid-analytical simulations of a multi-frequency argon capacitively coupled plasma (CCP) with a typical asymmetric reactor geometry at 2/60/162 MHz. The low frequency 2 MHz power controlled the sheath width and sheath voltage while the high frequencies controlled the plasma production. A standing wave was observable at the highest frequency of 162 MHz. We noticed that adding 2 MHz power to a 60 MHz discharge or 162 MHz to a dual frequency 2 MHz/60 MHz discharge can enhance the plasma uniformity. We found that multiple frequencies were not only useful for controlling IEDs but also plasma uniformity in CCP reactors.

Gyrokinetic and kinetic particle-in-cell simulations of guide-field reconnection. I. Macroscopic effects of the electron flows

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

Muñoz, P. A., E-mail: munozp@mps.mpg.de; Kilian, P.; Büchner, J.

In this work, we compare gyrokinetic (GK) with fully kinetic Particle-in-Cell (PIC) simulations of magnetic reconnection in the limit of strong guide field. In particular, we analyze the limits of applicability of the GK plasma model compared to a fully kinetic description of force free current sheets for finite guide fields (b{sub g}). Here, we report the first part of an extended comparison, focusing on the macroscopic effects of the electron flows. For a low beta plasma (β{sub i} = 0.01), it is shown that both plasma models develop magnetic reconnection with similar features in the secondary magnetic islands if a sufficientlymore » high guide field (b{sub g} ≳ 30) is imposed in the kinetic PIC simulations. Outside of these regions, in the separatrices close to the X points, the convergence between both plasma descriptions is less restrictive (b{sub g} ≳ 5). Kinetic PIC simulations using guide fields b{sub g} ≲ 30 reveal secondary magnetic islands with a core magnetic field and less energetic flows inside of them in comparison to the GK or kinetic PIC runs with stronger guide fields. We find that these processes are mostly due to an initial shear flow absent in the GK initialization and negligible in the kinetic PIC high guide field regime, in addition to fast outflows on the order of the ion thermal speed that violate the GK ordering. Since secondary magnetic islands appear after the reconnection peak time, a kinetic PIC/GK comparison is more accurate in the linear phase of magnetic reconnection. For a high beta plasma (β{sub i} = 1.0) where reconnection rates and fluctuations levels are reduced, similar processes happen in the secondary magnetic islands in the fully kinetic description, but requiring much lower guide fields (b{sub g} ≲ 3)« less

Research on ponderomotive driven Vlasov–Poisson system in electron acoustic wave parametric region

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

Xiao, C. Z.; Huang, T. W.; Liu, Z. J.

2014-03-15

Theoretical analysis and corresponding 1D Particle-in-Cell (PIC) simulations of ponderomotive driven Vlasov–Poisson system in electron acoustic wave (EAW) parametric region are demonstrated. Theoretical analysis identifies that under the resonant condition, a monochromatic EAW can be excited when the wave number of the drive ponderomotive force satisfies 0.26≲k{sub d}λ{sub D}≲0.53. If k{sub d}λ{sub D}≲0.26, nonlinear superposition of harmonic waves can be resonantly excited, called kinetic electrostatic electron nonlinear waves. Numerical simulations have demonstrated these wave excitation and evolution dynamics, in consistence with the theoretical predictions. The physical nature of these two waves is supposed to be interaction of harmonic waves, andmore » their similar phase space properties are also discussed.« less

NASA's Electric Sail Propulsion System Investigations over the Past Three Years

NASA Technical Reports Server (NTRS)

Wiegmann, Bruce M.

2017-01-01

Personnel from NASA's MSFC have been investigating the feasibility of an advanced propulsion system known as the Electric Sail for future scientific missions of exploration. This team initially won a NASA Space Technology Mission Directorate (STMD) Phase I NASA Innovative Advanced Concept (NIAC) award and then a two year follow-on Phase II NIAC award. This paper documents the findings from this three year investigation. An Electric sail propulsion system is a propellant-less and extremely fast propulsion system that takes advantage of the ions that are present in the solar wind to provide very rapid transit speeds whether to deep space or to the inner solar system. Scientific spacecraft could arrive to Pluto in 5 years, to the boundary of the solar system in ten to twelve years vs. thirty five plus years it took the Voyager spacecraft. The team's recent focused activities are: 1) Developing a Particle in Cell (PIC) numeric engineering model from the experimental data collected at MSFC's Solar Wind Facility on the interaction between simulated solar wind interaction with a charged bare wire that can be applied to a variety of missions, 2) The development of the necessary tether deployers/tethers to enable successful deployment of multiple, multi km length bare tethers, 3) Determining the different missions that can be captured from this revolutionary propulsion system 4) Conceptual designs of spacecraft to reach various destinations whether to the edge of the solar system, or as Heliophysics sentinels around the sun, or to trips to examine a multitude of asteroids These above activities, once demonstrated analytically, will require a technology demonstration mission (2021 to 2023) to demonstrate that all systems work together seamlessly before a Heliophysics Electrostatic Rapid Transit System (HERTS) could be given the go-ahead. The proposed demonstration mission will require that a small spacecraft must first travel to cis-lunar space as the Electric Sail must be outside of Earth's Magnetic fields to produce thrust. The paper will outline what was done over the past three years from performing various plasma chamber tests to obtain data for the PIC model development, investigation of tether material trades, and conceptual designs of proposed spacecraft.

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.

Anomalous electron transport in Hall-effect thrusters: Comparison between quasi-linear kinetic theory and particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Lafleur, T.; Martorelli, R.; Chabert, P.; Bourdon, A.

2018-06-01

Kinetic drift instabilities have been implicated as a possible mechanism leading to anomalous electron cross-field transport in E × B discharges, such as Hall-effect thrusters. Such instabilities, which are driven by the large disparity in electron and ion drift velocities, present a significant challenge to modelling efforts without resorting to time-consuming particle-in-cell (PIC) simulations. Here, we test aspects of quasi-linear kinetic theory with 2D PIC simulations with the aim of developing a self-consistent treatment of these instabilities. The specific quantities of interest are the instability growth rate (which determines the spatial and temporal evolution of the instability amplitude), and the instability-enhanced electron-ion friction force (which leads to "anomalous" electron transport). By using the self-consistently obtained electron distribution functions from the PIC simulations (which are in general non-Maxwellian), we find that the predictions of the quasi-linear kinetic theory are in good agreement with the simulation results. By contrast, the use of Maxwellian distributions leads to a growth rate and electron-ion friction force that is around 2-4 times higher, and consequently significantly overestimates the electron transport. A possible method for self-consistently modelling the distribution functions without requiring PIC simulations is discussed.

A new hybrid code (CHIEF) implementing the inertial electron fluid equation without approximation

NASA Astrophysics Data System (ADS)

Muñoz, P. A.; Jain, N.; Kilian, P.; Büchner, J.

2018-03-01

We present a new hybrid algorithm implemented in the code CHIEF (Code Hybrid with Inertial Electron Fluid) for simulations of electron-ion plasmas. The algorithm treats the ions kinetically, modeled by the Particle-in-Cell (PiC) method, and electrons as an inertial fluid, modeled by electron fluid equations without any of the approximations used in most of the other hybrid codes with an inertial electron fluid. This kind of code is appropriate to model a large variety of quasineutral plasma phenomena where the electron inertia and/or ion kinetic effects are relevant. We present here the governing equations of the model, how these are discretized and implemented numerically, as well as six test problems to validate our numerical approach. Our chosen test problems, where the electron inertia and ion kinetic effects play the essential role, are: 0) Excitation of parallel eigenmodes to check numerical convergence and stability, 1) parallel (to a background magnetic field) propagating electromagnetic waves, 2) perpendicular propagating electrostatic waves (ion Bernstein modes), 3) ion beam right-hand instability (resonant and non-resonant), 4) ion Landau damping, 5) ion firehose instability, and 6) 2D oblique ion firehose instability. Our results reproduce successfully the predictions of linear and non-linear theory for all these problems, validating our code. All properties of this hybrid code make it ideal to study multi-scale phenomena between electron and ion scales such as collisionless shocks, magnetic reconnection and kinetic plasma turbulence in the dissipation range above the electron scales.

A novel type of cellular senescence that can be enhanced in mouse models and human tumor xenografts to suppress prostate tumorigenesis

PubMed Central

Alimonti, Andrea; Nardella, Caterina; Chen, Zhenbang; Clohessy, John G.; Carracedo, Arkaitz; Trotman, Lloyd C.; Cheng, Ke; Varmeh, Shohreh; Kozma, Sara C.; Thomas, George; Rosivatz, Erika; Woscholski, Rudiger; Cognetti, Francesco; Scher, Howard I.; Pandolfi, Pier Paolo

2010-01-01

Irreversible cell growth arrest, a process termed cellular senescence, is emerging as an intrinsic tumor suppressive mechanism. Oncogene-induced senescence is thought to be invariably preceded by hyperproliferation, aberrant replication, and activation of a DNA damage checkpoint response (DDR), rendering therapeutic enhancement of this process unsuitable for cancer treatment. We previously demonstrated in a mouse model of prostate cancer that inactivation of the tumor suppressor phosphatase and tensin homolog deleted on chromosome 10 (Pten) elicits a senescence response that opposes tumorigenesis. Here, we show that Pten-loss–induced cellular senescence (PICS) represents a senescence response that is distinct from oncogene-induced senescence and can be targeted for cancer therapy. Using mouse embryonic fibroblasts, we determined that PICS occurs rapidly after Pten inactivation, in the absence of cellular proliferation and DDR. Further, we found that PICS is associated with enhanced p53 translation. Consistent with these data, we showed that in mice p53-stabilizing drugs potentiated PICS and its tumor suppressive potential. Importantly, we demonstrated that pharmacological inhibition of PTEN drives senescence and inhibits tumorigenesis in vivo in a human xenograft model of prostate cancer. Taken together, our data identify a type of cellular senescence that can be triggered in nonproliferating cells in the absence of DNA damage, which we believe will be useful for developing a “pro-senescence” approach for cancer prevention and therapy. PMID:20197621

Cost-effective treatment of low-risk carcinoma not invading bladder muscle.

PubMed

Green, David A; Rink, Michael; Cha, Eugene K; Xylinas, Evanguelos; Chughtai, Bilal; Scherr, Douglas S; Shariat, Shahrokh F; Lee, Richard K

2013-03-01

Study Type - Therapy (cost effectiveness analysis) Level of Evidence 2a What's known on the subject? and What does the study add? Bladder cancer is one of the costliest malignancies to treat throughout the life of a patient. The most cost-effective management for low-risk non-muscle-invasive bladder cancer is not known. The current study shows that employing cystoscopic office fulguration for low-risk appearing bladder cancer recurrences can materially impact the cost-effectiveness of therapy. In a follow-up protocol where office fulguration is routinely employed for low-risk bladder cancers, peri-operative intravesical chemotherapy may not provide any additional cost-effectiveness benefit. To examine the cost-effectiveness of fulguration vs transurethral resection of bladder tumour (TURBT) with and without perioperative intravesical chemotherapy (PIC) for managing low-risk carcinoma not invading bladder muscle (NMIBC). Low-risk NMIBC carries a low progression rate, lending support to the use of office-based fulguration for small recurrences rather than traditional TURBT. A Markov state transition model was created to simulate treatment of NMIBC with vs without PIC, with recurrence treated by formal TURBT vs treatment with fulguration. Costing data were obtained from the Medicare Resource Based Relative Value Scale. Data regarding the success of PIC were obtained from the peer-reviewed literature, as were corresponding utilities for bladder cancer-related procedures. Sensitivity analyses were performed. At 5-year follow-up, a strategy of fulguration without PIC was the most cost-effective (mean cost-effectiveness = US $654.8/quality-adjusted life year), despite a lower recurrence rate with PIC. Both fulguration strategies dominated each TURBT strategy. Sensitivity analysis showed that fulguration without PIC dominated all other strategies when the recurrence rate after PIC was increased to ≥14.2% per year. Similarly, the cost-effectiveness of TURBT becomes more competitive with fulguration when the total cost of TURBT declines < US $1175. The present study shows that fulguration without PIC was the most cost-effective strategy for treating low-risk NMIBC. The effectiveness of PIC and the cost of TURBT can materially impact the cost-effectiveness of the different management strategies. These results should be considered in treatment decisions in the context of preserving oncological control. © 2012 BJU INTERNATIONAL.

Testing COBOL Programs by Mutation. Volume I. Introduction to the CMS.1 System.

DTIC Science & Technology

1980-02-01

ALTER-OCCURS><SYMBOL TABLE location><code><x> where code = 0 means "add 1 to occurs", = 1 means "subtract 1 from occurs". 4 Insert a filler ( PIC X) in...REC. 31 01 OLD-REC. 32 03 FILLER PIC X. 33 03 OLD-KEY PIC X(12). 34 03 FILLER PIC X(67). 35S to NEdETF 36 RECORD CONTATS 90 CHARACTERS 37 LABEL RECORDS...ARE STANDARD 3S DATA RECORD IS NEd-REC. 39 01 NEd-REC. AO 03 FILLER PIC 1. Al 03 NEW-(FY PIC X(12). A2 03 FILLER PIC 1(6?). 43 ED PMTHR 44 RECORD

Molecular analysis of hprt mutations induced by chromium picolinate in CHO AA8 cells.

PubMed

Coryell, Virginia H; Stearns, Diane M

2006-11-07

Chromium picolinate (CrPic) is a popular dietary supplement, marketed to the public for weight loss, bodybuilding, and control of blood sugar. Recommendations for long-term use at high dosages have led to questions regarding its safety. Previous studies have reported that CrPic can cause chromosomal aberrations and mutations. The purpose of the current work was to compare the mutagenicity of CrPic as a suspension in acetone versus a solution in DMSO, and to characterize the hprt mutations induced by CrPic in CHO AA8 cells. Treatments of 2% acetone or 2% DMSO alone produced no significant increase in 6-thioguanine (6-TG)-resistant mutants after 48 h exposures. Mutants resistant to 6-TG were generated by exposing cells for 48 h to 80 microg/cm(2) CrPic in acetone or to 1.0mM CrPic in DMSO. CrPic in acetone produced an average induced mutation frequency (MF) of 56 per 10(6) surviving cells relative to acetone solvent. CrPic in acetone was 3.5-fold more mutagenic than CrPic in DMSO, which produced an MF of 16.2. Characterization of 61 total mutations in 48 mutants generated from exposure to CrPic in acetone showed that base substitutions comprised 33% of the mutations, with transversions being predominant; deletions made up 62% of the mutations, with one-exon deletions predominating; and 1-4 bp insertions made up 5% of the characterized mutations. CrPic induced a statistically greater number of deletions and a statistically smaller number of base substitutions than have been measured in spontaneously generated mutants. These data confirm previous studies showing that CrPic is mutagenic, and support the contention that further study is needed to verify the safety of CrPic for human consumption.

Large Scale Earth's Bow Shock with Northern IMF as Simulated by PIC Code in Parallel with MHD Model

NASA Astrophysics Data System (ADS)

Baraka, Suleiman

2016-06-01

In this paper, we propose a 3D kinetic model (particle-in-cell, PIC) for the description of the large scale Earth's bow shock. The proposed version is stable and does not require huge or extensive computer resources. Because PIC simulations work with scaled plasma and field parameters, we also propose to validate our code by comparing its results with the available MHD simulations under same scaled solar wind (SW) and (IMF) conditions. We report new results from the two models. In both codes the Earth's bow shock position is found to be ≈14.8 R E along the Sun-Earth line, and ≈29 R E on the dusk side. Those findings are consistent with past in situ observations. Both simulations reproduce the theoretical jump conditions at the shock. However, the PIC code density and temperature distributions are inflated and slightly shifted sunward when compared to the MHD results. Kinetic electron motions and reflected ions upstream may cause this sunward shift. Species distributions in the foreshock region are depicted within the transition of the shock (measured ≈2 c/ ω pi for Θ Bn = 90° and M MS = 4.7) and in the downstream. The size of the foot jump in the magnetic field at the shock is measured to be (1.7 c/ ω pi ). In the foreshocked region, the thermal velocity is found equal to 213 km s-1 at 15 R E and is equal to 63 km s -1 at 12 R E (magnetosheath region). Despite the large cell size of the current version of the PIC code, it is powerful to retain macrostructure of planets magnetospheres in very short time, thus it can be used for pedagogical test purposes. It is also likely complementary with MHD to deepen our understanding of the large scale magnetosphere.

GPU acceleration of particle-in-cell methods

NASA Astrophysics Data System (ADS)

Cowan, Benjamin; Cary, John; Meiser, Dominic

2015-11-01

Graphics processing units (GPUs) have become key components in many supercomputing systems, as they can provide more computations relative to their cost and power consumption than conventional processors. However, to take full advantage of this capability, they require a strict programming model which involves single-instruction multiple-data execution as well as significant constraints on memory accesses. To bring the full power of GPUs to bear on plasma physics problems, we must adapt the computational methods to this new programming model. We have developed a GPU implementation of the particle-in-cell (PIC) method, one of the mainstays of plasma physics simulation. This framework is highly general and enables advanced PIC features such as high order particles and absorbing boundary conditions. The main elements of the PIC loop, including field interpolation and particle deposition, are designed to optimize memory access. We describe the performance of these algorithms and discuss some of the methods used. Work supported by DARPA contract W31P4Q-15-C-0061 (SBIR).

Rise time of proton cut-off energy in 2D and 3D PIC simulations

NASA Astrophysics Data System (ADS)

Babaei, J.; Gizzi, L. A.; Londrillo, P.; Mirzanejad, S.; Rovelli, T.; Sinigardi, S.; Turchetti, G.

2017-04-01

The Target Normal Sheath Acceleration regime for proton acceleration by laser pulses is experimentally consolidated and fairly well understood. However, uncertainties remain in the analysis of particle-in-cell simulation results. The energy spectrum is exponential with a cut-off, but the maximum energy depends on the simulation time, following different laws in two and three dimensional (2D, 3D) PIC simulations so that the determination of an asymptotic value has some arbitrariness. We propose two empirical laws for the rise time of the cut-off energy in 2D and 3D PIC simulations, suggested by a model in which the proton acceleration is due to a surface charge distribution on the target rear side. The kinetic energy of the protons that we obtain follows two distinct laws, which appear to be nicely satisfied by PIC simulations, for a model target given by a uniform foil plus a contaminant layer that is hydrogen-rich. The laws depend on two parameters: the scaling time, at which the energy starts to rise, and the asymptotic cut-off energy. The values of the cut-off energy, obtained by fitting 2D and 3D simulations for the same target and laser pulse configuration, are comparable. This suggests that parametric scans can be performed with 2D simulations since 3D ones are computationally very expensive, delegating their role only to a correspondence check. In this paper, the simulations are carried out with the PIC code ALaDyn by changing the target thickness L and the incidence angle α, with a fixed a0 = 3. A monotonic dependence, on L for normal incidence and on α for fixed L, is found, as in the experimental results for high temporal contrast pulses.

Speed-limited particle-in-cell (SLPIC) simulation

NASA Astrophysics Data System (ADS)

Werner, Gregory; Cary, John; Jenkins, Thomas

2016-10-01

Speed-limited particle-in-cell (SLPIC) simulation is a new method for particle-based plasma simulation that allows increased timesteps in cases where the timestep is determined (e.g., in standard PIC) not by the smallest timescale of interest, but rather by an even smaller physical timescale that affects numerical stability. For example, SLPIC need not resolve the plasma frequency if plasma oscillations do not play a significant role in the simulation; in contrast, standard PIC must usually resolve the plasma frequency to avoid instability. Unlike fluid approaches, SLPIC retains a fully-kinetic description of plasma particles and includes all the same physical phenomena as PIC; in fact, if SLPIC is run with a PIC-compatible timestep, it is identical to PIC. However, unlike PIC, SLPIC can run stably with larger timesteps. SLPIC has been shown to be effective for finding steady-state solutions for 1D collisionless sheath problems, greatly speeding up computation despite a large ion/electron mass ratio. SLPIC is a relatively small modification of standard PIC, with no complexities that might degrade parallel efficiency (compared to PIC), and is similarly compatible with PIC field solvers and boundary conditions.

Simulation of stimulated Brillouin scattering and stimulated Raman scattering in shock ignition

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

Hao, L.; Li, J.; Liu, W. D.

2016-04-15

We study stimulated Brillouin scattering (SBS) and stimulated Raman scattering (SRS) in shock ignition by comparing fluid and particle-in-cell (PIC) simulations. Under typical parameters for the OMEGA experiments [Theobald et al., Phys. Plasmas 19, 102706 (2012)], a series of 1D fluid simulations with laser intensities ranging between 2 × 10{sup 15} and 2 × 10{sup 16 }W/cm{sup 2} finds that SBS is the dominant instability, which increases significantly with the incident intensity. Strong pump depletion caused by SBS and SRS limits the transmitted intensity at the 0.17n{sub c} to be less than 3.5 × 10{sup 15 }W/cm{sup 2}. The PIC simulations show similar physics but with higher saturationmore » levels for SBS and SRS convective modes and stronger pump depletion due to higher seed levels for the electromagnetic fields in PIC codes. Plasma flow profiles are found to be important in proper modeling of SBS and limiting its reflectivity in both the fluid and PIC simulations.« less

Image annotation based on positive-negative instances learning

NASA Astrophysics Data System (ADS)

Zhang, Kai; Hu, Jiwei; Liu, Quan; Lou, Ping

2017-07-01

Automatic image annotation is now a tough task in computer vision, the main sense of this tech is to deal with managing the massive image on the Internet and assisting intelligent retrieval. This paper designs a new image annotation model based on visual bag of words, using the low level features like color and texture information as well as mid-level feature as SIFT, and mixture the pic2pic, label2pic and label2label correlation to measure the correlation degree of labels and images. We aim to prune the specific features for each single label and formalize the annotation task as a learning process base on Positive-Negative Instances Learning. Experiments are performed using the Corel5K Dataset, and provide a quite promising result when comparing with other existing methods.

Relativistically induced transparency acceleration of light ions by an ultrashort laser pulse interacting with a heavy-ion-plasma density gradient.

PubMed

Sahai, Aakash A; Tsung, Frank S; Tableman, Adam R; Mori, Warren B; Katsouleas, Thomas C

2013-10-01

The relativistically induced transparency acceleration (RITA) scheme of proton and ion acceleration using laser-plasma interactions is introduced, modeled, and compared to the existing schemes. Protons are accelerated with femtosecond relativistic pulses to produce quasimonoenergetic bunches with controllable peak energy. The RITA scheme works by a relativistic laser inducing transparency [Akhiezer and Polovin, Zh. Eksp. Teor. Fiz 30, 915 (1956); Kaw and Dawson, Phys. Fluids 13, 472 (1970); Max and Perkins, Phys. Rev. Lett. 27, 1342 (1971)] to densities higher than the cold-electron critical density, while the background heavy ions are stationary. The rising laser pulse creates a traveling acceleration structure at the relativistic critical density by ponderomotively [Lindl and Kaw, Phys. Fluids 14, 371 (1971); Silva et al., Phys. Rev. E 59, 2273 (1999)] driving a local electron density inflation, creating an electron snowplow and a co-propagating electrostatic potential. The snowplow advances with a velocity determined by the rate of the rise of the laser's intensity envelope and the heavy-ion-plasma density gradient scale length. The rising laser is incrementally rendered transparent to higher densities such that the relativistic-electron plasma frequency is resonant with the laser frequency. In the snowplow frame, trace density protons reflect off the electrostatic potential and get snowplowed, while the heavier background ions are relatively unperturbed. Quasimonoenergetic bunches of velocity equal to twice the snowplow velocity can be obtained and tuned by controlling the snowplow velocity using laser-plasma parameters. An analytical model for the proton energy as a function of laser intensity, rise time, and plasma density gradient is developed and compared to 1D and 2D PIC OSIRIS [Fonseca et al., Lect. Note Comput. Sci. 2331, 342 (2002)] simulations. We model the acceleration of protons to GeV energies with tens-of-femtoseconds laser pulses of a few petawatts. The scaling of proton energy with laser power compares favorably to other mechanisms for ultrashort pulses [Schreiber et al., Phys. Rev. Lett. 97, 045005 (2006); Esirkepov et al., Phys. Rev. Lett. 92, 175003 (2004); Silva et al., Phys. Rev. Lett. 92, 015002 (2004); Fiuza et al., Phys. Rev. Lett. 109, 215001 (2012)].

Ion and Electron Energization in Guide Field Reconnection Outflows with Kinetic Riemann Simulations and Parallel Shock Simulations

NASA Astrophysics Data System (ADS)

Zhang, Q.; Drake, J. F.; Swisdak, M.

2017-12-01

How ions and electrons are energized in magnetic reconnection outflows is an essential topic throughout the heliosphere. Here we carry out guide field PIC Riemann simulations to explore the ion and electron energization mechanisms far downstream of the x-line. Riemann simulations, with their simple magnetic geometry, facilitate the study of the reconnection outflow far downstream of the x-line in much more detail than is possible with conventional reconnection simulations. We find that the ions get accelerated at rotational discontinuities, counter stream, and give rise to two slow shocks. We demonstrate that the energization mechanism at the slow shocks is essentially the same as that of parallel electrostatic shocks. Also, the electron confining electric potential at the slow shocks is driven by the counterstreaming beams, which tend to break the quasi-neutrality. Based on this picture, we build a kinetic model to self consistently predict the downstream ion and electron temperatures. Additional explorations using parallel shock simulations also imply that in a very low beta(0.001 0.01 for a modest guide field) regime, electron energization will be insignificant compared to the ion energization. Our model and the parallel shock simulations might be used as simple tools to understand and estimate the energization of ions and electrons and the energy partition far downstream of the x-line.

Numerical fatigue analysis of premolars restored by CAD/CAM ceramic crowns.

PubMed

Homaei, Ehsan; Jin, Xiao-Zhuang; Pow, Edmond Ho Nang; Matinlinna, Jukka Pekka; Tsoi, James Kit-Hon; Farhangdoost, Khalil

2018-04-10

The purpose of this study was to estimate the fatigue life of premolars restored with two dental ceramics, lithium disilicate (LD) and polymer infiltrated ceramic (PIC) using the numerical method and compare it with the published in vitro data. A premolar restored with full-coverage crown was digitized. The volumetric shape of tooth tissues and crowns were created in Mimics ® . They were transferred to IA-FEMesh for mesh generation and the model was analyzed with Abaqus. By combining the stress distribution results with fatigue stress-life (S-N) approach, the lifetime of restored premolars was predicted. The predicted lifetime was 1,231,318 cycles for LD with fatigue load of 1400N, while the one for PIC was 475,063 cycles with the load of 870N. The peak value of maximum principal stress occurred at the contact area (LD: 172MPa and PIC: 96MPa) and central fossa (LD: 100MPa and PIC: 64MPa) for both ceramics which were the most seen failure areas in the experiment. In the adhesive layer, the maximum shear stress was observed at the shoulder area (LD: 53.6MPa and PIC: 29MPa). The fatigue life and failure modes of all-ceramic crown determined by the numerical method seem to correlate well with the previous experimental study. Copyright © 2018 The Academy of Dental Materials. Published by Elsevier Inc. All rights reserved.

Protective effects of resveratrol and its analogs on age-related macular degeneration in vitro.

PubMed

Kang, Jung-Hwan; Choung, Se-Young

2016-12-01

Damage of retinal pigment epithelial (RPE) cells by A2E may be critical for age-related macular degeneration (AMD) management. Accumulation and photooxidation of A2E are known to be one of the critical causes in AMD. Here, we evaluated the protective effect of resveratrol (RES), piceatannol (PIC) and RES glycones on blue-light-induced RPE cell death caused by A2E photooxidation. A2E treatment followed by blue light exposure caused significant damages on human RPE cells (ARPE-19). But the damages were attenuated by post- and pre-treatment of RES and PIC in our in vitro models. The results of cell free system and FAB-MS analysis clearly showed that the reduction of A2E by blue light exposure was significantly rescued, and that oxidized forms of A2E were significantly reduced by RES or PIC treatment. Besides, RES or PIC inhibited the intracellular accumulation of A2E. Not only RES and PIC but RES glycones showed protection of ARPE-19 cells against A2E and blue-light-induced photo-damage. These findings demonstrate that RES and its analogs may have protective effects against A2E and blue-light-induced ARPE-19 cell death through regulation of A2E accumulation as well as photooxidation of A2E. Thus RES and its analogs may be beneficial for AMD treatment.

Plasmon-induced charge separation: chemistry and wide applications.

PubMed

Tatsuma, Tetsu; Nishi, Hiroyasu; Ishida, Takuya

2017-05-01

Recent development of nanoplasmonics has stimulated chemists to utilize plasmonic nanomaterials for efficient and distinctive photochemical applications, and physicists to boldly go inside the "wet" chemistry world. The discovery of plasmon-induced charge separation (PICS) has even accelerated these trends. On the other hand, some confusion is found in discussions about PICS. In this perspective, we focus on differences between PICS and some other phenomena such as co-catalysis effect and plasmonic nanoantenna effect. In addition, materials and nanostructures suitable for PICS are shown, and characteristics and features unique to PICS are documented. Although it is well known that PICS has been applied to photovoltaics and photocatalysis, here light is shed on other applications that take better advantage of PICS, such as chemical sensing and biosensing, various photochromisms, photoswitchable functionalities and nanoscale photofabrication.

The use of polyion complex micelles to enhance the oral delivery of salmon calcitonin and transport mechanism across the intestinal epithelial barrier.

PubMed

Li, Na; Li, Xin-Ru; Zhou, Yan-Xia; Li, Wen-Jing; Zhao, Yong; Ma, Shu-Jin; Li, Jin-Wen; Gao, Ya-Jie; Liu, Yan; Wang, Xing-Lin; Yin, Dong-Dong

2012-12-01

The objective of the present study was to demonstrate the effect of polyanionic copolymer mPEG-grafted-alginic acid (mPEG-g-AA)-based polyion complex (PIC) micelles on enhancing the oral absorption of salmon calcitonin (sCT) in vivo and in vitro and identify the transepithelial transport mechanism of PIC micelles across the intestinal barrier. mPEG-g-AA was first successfully synthesized and characterized in cytotoxicity. The PIC micelles were approximately of 72 nm in diameter with a narrow distribution. The extremely significant enhancement of hypocalcemia efficacy of sCT-loaded PIC micelles in rats was evidenced by intraduodenal administration in comparison with sCT solution. The presence of mPEG-grafted-chitosan in PIC micelles had no favorable effect on this action in the referred content. In the Caco-2 transport studies, PIC micelles could significantly increase the permeability of sCT across Caco-2 monolayers without significantly affecting transepithelial electrical resistance values during the transport study. No evident alterations in the F-actin cytoskeleton were detected by confocal microscope observation following treatment of the cell monolayers with PIC micelles, which further certified the incapacity of PIC micelles to open the intercellular tight junctions. In addition, TEM observations showed that the intact PIC micelles were transported across the everted gut sac. These suggested that the transport of PIC micelles across Caco-2 cell monolayers involve a predominant transcytosis mechanism via endocytosis rather than paracellular pathway. Furthermore, PIC micelles were localized in both the cytoplasm and the nuclei observed by CLSM. Therefore, PIC micelles might be a potentially applicable tool for enhancing the oral absorption of cationic peptide and protein drugs. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

Shoup, R.W.; Long, F.; Martin, T.H.

Sandia is developing PBFA-Z, a 20-MA driver for z-pinch experiments by replacing the water lines, insulator stack, and MITLs on PBFA II with new hardware. The design of the vacuum insulator stack was dictated by the drive voltage, the electric field stress and grading requirements, the water line and MITL interface requirements, and the machine operations and maintenance requirements. The insulator stack will consist of four separate modules, each of a different design because of different voltage drive and hardware interface requirements. The shape of the components in each module, i.e., grading rings, insulator rings, flux excluders, anode and cathodemore » conductors, and the design of the water line and MITL interfaces, were optimized by using the electrostatic analysis codes, ELECTRO and JASON. The time dependent performance of the insulator stack was evaluated using IVORY, a 2-D PIC code. This paper will describe the insulator stack design and present the results of the ELECTRO and IVORY analyses.« less

KEEN Wave Simulations: Comparing various PIC to various fixed grid Vlasov to Phase-Space Adaptive Sparse Tiling & Effective Lagrangian (PASTEL) Techniques

NASA Astrophysics Data System (ADS)

Afeyan, Bedros; Larson, David; Shadwick, Bradley; Sydora, Richard

2017-10-01

We compare various ways of solving the Vlasov-Poisson and Vlasov-Maxwell equations on rather demanding nonlinear kinetic phenomena associated with KEEN and KEEPN waves. KEEN stands for Kinetic, Electrostatic, Electron Nonlinear, and KEEPN, for electron-positron or pair plasmas analogs. Because these self-organized phase space structures are not steady-state, or single mode, or fluid or low order moment equation limited, typical techniques with low resolution or too much noise will distort the answer too much, too soon, and fail. This will be shown via Penrose criteria triggers for instability at the formation stage as well as particle orbit statistics in fully formed KEEN waves and KEEN-KEEN and KEEN-EPW interacting states. We will argue that PASTEL is a viable alternative to traditional methods with reasonable chances of success in higher dimensions. Work supported by a Grant from AFOSR PEEP.

Self-consistent simulation of radio frequency multipactor on micro-grooved dielectric surface

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

Cai, Libing; Wang, Jianguo, E-mail: wanguiuc@mail.xjtu.edu.cn; Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024

2015-02-07

The multipactor plays a key role in the surface breakdown on the feed dielectric window irradiated by high power microwave. To study the suppression of multipactor, a 2D electrostatic PIC-MCC simulation code was developed. The space charge field, including surface deposited charge and multipactor electron charge field, is obtained by solving 2D Poisson's equation in time. Therefore, the simulation is self-consistent and does not require presetting a fixed space charge field. By using this code, the self-consistent simulation of the RF multipactor on the periodic micro-grooved dielectric surface is realized. The 2D space distributions of the multipactor electrons and spacemore » charge field are presented. From the simulation results, it can be found that only half slopes have multipactor discharge when the slope angle exceeds a certain value, and the groove presents a pronounced suppression effect on the multipactor.« less

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

Sengupta, M.; Ganesh, R.

The dynamics of cylindrically trapped electron plasma has been investigated using a newly developed 2D Electrostatic PIC code that uses unapproximated, mass-included equations of motion for simulation. Exhaustive simulations, covering the entire range of Brillouin ratio, were performed for uniformly filled circular profiles in rigid rotor equilibrium. The same profiles were then loaded away from equilibrium with an initial value of rigid rotation frequency different from that required for radial force balance. Both these sets of simulations were performed for an initial zero-temperature or cold load of the plasma with no spread in either angular velocity or radial velocity. Themore » evolution of the off-equilibrium initial conditions to a steady state involve radial breathing of the profile that scales in amplitude and algebraic growth with Brillouin fraction. For higher Brillouin fractions, the growth of the breathing mode is followed by complex dynamics of spontaneous hollow density structures, excitation of poloidal modes, leading to a monotonically falling density profile.« less

ESCAP/POPIN Expert Working Group on Development of Population Information Centres and Networks, 20-23 June 1984, Bangkok, Thailand.

PubMed

1984-07-01

An overview of current population information programs at the regional, national, and global level was presented at a meeting of the Expert Working Group on Development of Population Information Centres and Networks. On the global level, the decentralized Population Information Network (POPIN) was established, consisting of population libraries, clearinghouses, information systems, and documentation centers. The Economic and Social Commission for Asia and the Pacific (ESCAP) Regional Population Information Centre (PIC) has actively promoted the standardization of methodologies for the collection and processing of data, the use of compatible terminology, adoption of classification systems, computer-assisted data and information handling, and improved programs of publication and infomration dissemination, within and among national centers. Among the national PICs, 83% are attached to the primary national family planning/fertility control unit and 17% are attached to demographic data, research, and analysis units. Lack of access to specialized information handling equipment such as microcomputers, word processors, and computer terminals remains a problem for PICs. Recommendations were made by the Expert Working Group to improve the functions of PICs: 1) the mandate and resoponsibilities of the PIC should be explicilty stated; 2) PICs should collect, process, and disseminate population information in the most effective format to workers in the population feild; 3) PICs should be given flexibility in the performance of activitites by their governing bodies; 4) short-term training should be provided in computerization and dissemination of information; 5) research and evaluation mechanisms for PIC activities should be developed; 6) PIC staff should prepare policy briefs for decision makers; 7) access to parent organizations should be given to nongovernment PICs; 8) study tours to foreign PICs should be organized for PIC staff; and 9) on-the-job training in indexing and abstracting should be provided. Networking among PICs can be further facilitated by written acquisition policies, automation of bibliographic information, common classification systems, and exchange of ideas and experience between various systems.

Comparison of Children With and Without ADHD on a New Pictorial Self-Assessment of Executive Functions.

PubMed

Bar-Ilan, Ruthie Traub; Cohen, Noa; Maeir, Adina

We examined the Pictorial Interview of Children's Metacognition and Executive Functions' (PIC-ME's) reliability and validity, targeting children's appraisal of their executive function (EF) in daily life. One hundred children with attention deficit hyperactivity disorder (ADHD) and 44 typically developing children (ages 5-10 yr) completed the PIC-ME. Parents completed the PIC-ME and Behavior Rating Inventory of Executive Function (BRIEF). Cronbach's α for the child PIC-ME was .914. A high correlation was found between the parent PIC-ME total and the BRIEF (r = .724). Comparisons between groups revealed significant differences on the parent PIC-ME (p < .0001) but none on the child PIC-ME. Children with ADHD identified a median of eight EF challenges they wanted to set as treatment goals. Results support the PIC-ME's initial reliability and validity among children with ADHD. Children were able to identify several EF challenges and engage in goal setting. Copyright © 2018 by the American Occupational Therapy Association, Inc.

3D Hall MHD-EPIC Simulations of Ganymede's Magnetosphere

NASA Astrophysics Data System (ADS)

Zhou, H.; Toth, G.; Jia, X.

2017-12-01

Fully kinetic modeling of a complete 3D magnetosphere is still computationally expensive and not feasible on current computers. While magnetohydrodynamic (MHD) models have been successfully applied to a wide range of plasma simulation, they cannot capture some important kinetic effects. We have recently developed a new modeling tool to embed the implicit particle-in-cell (PIC) model iPIC3D into the Block-Adaptive-Tree-Solarwind-Roe-Upwind-Scheme (BATS-R-US) magnetohydrodynamic model. This results in a kinetic model of the regions where kinetic effects are important. In addition to the MHD-EPIC modeling of the magnetosphere, the improved model presented here is now able to represent the moon as a resistive body. We use a stretched spherical grid with adaptive mesh refinement (AMR) to capture the resistive body and its boundary. A semi-implicit scheme is employed for solving the magnetic induction equation to allow time steps that are not limited by the resistivity. We have applied the model to Ganymede, the only moon in the solar system known to possess a strong intrinsic magnetic field, and included finite resistivity beneath the moon`s surface to model the electrical properties of the interior in a self-consistent manner. The kinetic effects of electrons and ions on the dayside magnetopause and tail current sheet are captured with iPIC3D. Magnetic reconnections under different upstream background conditions of several Galileo flybys are simulated to study the global reconnection rate and the magnetospheric dynamics

Study on the After Cavity Interaction in a 140 GHz Gyrotron Using 3D CFDTD PIC Simulations

NASA Astrophysics Data System (ADS)

Lin, M. C.; Illy, S.; Avramidis, K.; Thumm, M.; Jelonnek, J.

2016-10-01

A computational study on after cavity interaction (ACI) in a 140 GHz gryotron for fusion research has been performed using a 3-D conformal finite-difference time-domain (CFDTD) particle-in-cell (PIC) method. The ACI, i.e. beam wave interaction in the non-linear uptaper after the cavity has attracted a lot of attention and been widely investigated in recent years. In a dynamic ACI, a TE mode is excited by the electron beam at the same frequency as in the cavity, and the same mode is also interacting with the spent electron beam at a different frequency in the non-linear uptaper after the cavity while in a static ACI, a mode interacts with the beam both at the cavity and at the uptaper, but at the same frequency. A previous study on the dynamic ACI on a 140 GHz gyrotron has concluded that more advanced numerical simulations such as particle-in-cell (PIC) modeling should be employed to study or confirm the dynamic ACI in addition to using trajectory codes. In this work, we use a 3-D full wave time domain simulation based on the CFDTD PIC method to include the rippled-wall launcher of the quasi-optical output coupler into the simulations which breaks the axial symmetry of the original model employing a symmetric one. A preliminary simulation result has confirmed the dynamic ACI effect in this 140 GHz gyrotron in good agreement with the former study. A realistic launcher will be included in the model for studying the dynamic ACI and compared with the homogenous one.

Chromium picolinate enhances skeletal muscle cellular insulin signaling in vivo in obese, insulin-resistant JCR:LA-cp rats.

PubMed

Wang, Zhong Q; Zhang, Xian H; Russell, James C; Hulver, Matthew; Cefalu, William T

2006-02-01

Chromium is one of the few trace minerals for which a specific cellular mechanism of action has not been identified. Recent in vitro studies suggest that chromium supplementation may improve insulin sensitivity by enhancing insulin receptor signaling, but this has not been demonstrated in vivo. We investigated the effect of chromium supplementation on insulin receptor signaling in an insulin-resistant rat model, the JCR:LA-corpulent rat. Male JCR:LA-cp rats (4 mo of age) were randomly assigned to receive chromium picolinate (CrPic) (obese n=6, lean n=5) or vehicle (obese n=5, lean n=5) for 3 mo. The CrPic was provided in the water, and based on calculated water intake, rats randomized to CrPic received 80 microg/(kg.d). At the end of the study, skeletal muscle (vastus lateralis) biopsies were obtained at baseline and at 5, 15, and 30 min postinsulin stimulation to assess insulin signaling. Obese rats treated with CrPic had significantly improved glucose disposal rates and demonstrated a significant increase in insulin-stimulated phosphorylation of insulin receptor substrate (IRS)-1 and phosphatidylinositol (PI)-3 kinase activity in skeletal muscle compared with obese controls. The increase in cellular signaling was not associated with increased protein levels of the IRS proteins, PI-3 kinase or Akt. However, protein tyrosine phosphatase 1B (PTP1B) levels were significantly lower in obese rats administered CrPic than obese controls. When corrected for protein content, PTP1B activity was also significantly lower in obese rats administered CrPic than obese controls. Our data suggest that chromium supplementation of obese, insulin-resistant rats may improve insulin action by enhancing intracellular signaling.

Effects of chromium(III) picolinate on cortisol and DHEAs secretion in H295R human adrenocortical cells.

PubMed

Kim, Beob G; Adams, Julye M; Jackson, Brian A; Lindemann, Merlin D

2010-02-01

Dietary chromium(III) picolinate (CrPic) effects on circulating steroid hormones have been reported in various experimental animals. However, direct effects of CrPic on adrenocortical steroidogenesis are uncertain. Therefore, the objective was to determine the effects of CrPic on cortisol and dehydroepiandrosterone sulfate (DHEAs) secretion from H295R cells. In experiment 1, a 24-h exposure to CrPic (0 to 200 microM) had both linear (p < 0.001) and quadratic (p < 0.001) effects on cortisol secretion from forskolin-stimulated cells with the highest cortisol secretion at 0.1 microM of CrPic and the lowest at 200 microM of CrPic. In experiment 2, a 48-h exposure to CrPic (200 microM) decreased cortisol (p < 0.07) release from forskolin-stimulated cells during a 24-h collection period. In experiment 3, a 48-h exposure to CrPic (100 microM) decreased cortisol (p < 0.05) and DHEAs (p < 0.01) from forskolin-stimulated cells during a 24-h sampling period. In experiment 4, a 24-h exposure to forskolin followed by a 24-h exposure to both forskolin and CrPic (100 and 200 microM) decreased both cortisol and DHEAs secretion (p < 0.01). This study suggests that at high concentrations, CrPic inhibits aspects of steroidogenesis in agonist-stimulated adrenocortical cells.

PIC Activation through Functional Interplay between Mediator and TFIIH.

PubMed

Malik, Sohail; Molina, Henrik; Xue, Zhu

2017-01-06

The multiprotein Mediator coactivator complex functions in large part by controlling the formation and function of the promoter-bound preinitiation complex (PIC), which consists of RNA polymerase II and general transcription factors. However, precisely how Mediator impacts the PIC, especially post-recruitment, has remained unclear. Here, we have studied Mediator effects on basal transcription in an in vitro transcription system reconstituted from purified components. Our results reveal a close functional interplay between Mediator and TFIIH in the early stages of PIC development. We find that under conditions when TFIIH is not normally required for transcription, Mediator actually represses transcription. TFIIH, whose recruitment to the PIC is known to be facilitated by the Mediator, then acts to relieve Mediator-induced repression to generate an active form of the PIC. Gel mobility shift analyses of PICs and characterization of TFIIH preparations carrying mutant XPB translocase subunit further indicate that this relief of repression is achieved through expending energy via ATP hydrolysis, suggesting that it is coupled to TFIIH's established promoter melting activity. Our interpretation of these results is that Mediator functions as an assembly factor that facilitates PIC maturation through its various stages. Whereas the overall effect of the Mediator is to stimulate basal transcription, its initial engagement with the PIC generates a transcriptionally inert PIC intermediate, which necessitates energy expenditure to complete the process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Prevalence and characteristics of plateau iris configuration among American Caucasian, American Chinese and mainland Chinese subjects.

PubMed

Li, Yingjie; Wang, Ye Elaine; Huang, Guofu; Wang, Dandan; He, Mingguang; Qiu, Mary; Lin, Shan

2014-04-01

To investigate the prevalence, risk factors and characteristics of plateau iris configuration (PIC) among American Caucasian, American Chinese and mainland Chinese. This multicentre, cross-sectional study of non-glaucomatous subjects (40-80 years) included 111 American Caucasian, 116 American Chinese and 110 mainland Chinese. Prevalence of PIC based on ultrasound biomicroscopy imaging was compared among the different ethnic groups. Risk factors and anterior segment optical coherence tomography-measured iris and angle parameters in eyes with PIC were compared. The prevalence of PIC was 25.2% in American Caucasian, 24.1% in American Chinese and 20.9% in mainland Chinese (p=0.73). The presence of PIC was associated with more positive spherical equivalence (OR=1.31, p=0.002) and shorter axial length (OR=0.75, p=0.04). There were significant differences in angle recess area (ARA) (p=0.04), IT750 (p=0.007) and IT2000 (p<0.001) between Chinese and Caucasians who have PIC. The prevalence of PIC did not differ among American Caucasian, American Chinese and mainland Chinese. PIC was associated with non-myopia and shorter axial length. Chinese eyes with PIC had smaller ARA and thicker irides than Caucasian ones. PIC might be a physiological variation of the iris and ciliary body that exists in normal eyes, both in Chinese and Caucasians.

Plasmon-induced charge separation: chemistry and wide applications

PubMed Central

Nishi, Hiroyasu; Ishida, Takuya

2017-01-01

Recent development of nanoplasmonics has stimulated chemists to utilize plasmonic nanomaterials for efficient and distinctive photochemical applications, and physicists to boldly go inside the “wet” chemistry world. The discovery of plasmon-induced charge separation (PICS) has even accelerated these trends. On the other hand, some confusion is found in discussions about PICS. In this perspective, we focus on differences between PICS and some other phenomena such as co-catalysis effect and plasmonic nanoantenna effect. In addition, materials and nanostructures suitable for PICS are shown, and characteristics and features unique to PICS are documented. Although it is well known that PICS has been applied to photovoltaics and photocatalysis, here light is shed on other applications that take better advantage of PICS, such as chemical sensing and biosensing, various photochromisms, photoswitchable functionalities and nanoscale photofabrication. PMID:28507702

A Combined Very Large Telescope and Gemini Study of the Atmosphere of the Directly Imaged Planet, Beta Pictoris b

NASA Technical Reports Server (NTRS)

Currie, Thayne; Burrows, Adam; Madhusudhan, Nikku; Fukagawa, Misato; Girard, Julien H.; Dawson, Rebekah; Murray-Clay, Ruth; Kenyon, Scott; Kuchner, Marc J.; Matsumura, Soko;

A COMBINED VERY LARGE TELESCOPE AND GEMINI STUDY OF THE ATMOSPHERE OF THE DIRECTLY IMAGED PLANET, β PICTORIS b

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

Currie, Thayne; Jayawardhana, Ray; Burrows, Adam

We analyze new/archival VLT/NaCo and Gemini/NICI high-contrast imaging of the young, self-luminous planet β Pictoris b in seven near-to-mid IR photometric filters, using advanced image processing methods to achieve high signal-to-noise, high precision measurements. While β Pic b's near-IR colors mimic those of a standard, cloudy early-to-mid L dwarf, it is overluminous in the mid-infrared compared to the field L/T dwarf sequence. Few substellar/planet-mass objects—i.e., κ And b and 1RXJ 1609B—match β Pic b's JHK{sub s}L' photometry and its 3.1 μm and 5 μm photometry are particularly difficult to reproduce. Atmosphere models adopting cloud prescriptions and large (∼60 μm) dustmore » grains fail to reproduce the β Pic b spectrum. However, models incorporating thick clouds similar to those found for HR 8799 bcde, but also with small (a few microns) modal particle sizes, yield fits consistent with the data within the uncertainties. Assuming solar abundance models, thick clouds, and small dust particles ((a) = 4 μm), we derive atmosphere parameters of log (g) = 3.8 ± 0.2 and T{sub eff} = 1575-1650 K, an inferred mass of 7{sup +4}{sub -3} M{sub J} , and a luminosity of log(L/L{sub ☉}) ∼–3.80 ± 0.02. The best-estimated planet radius, ≈1.65 ± 0.06 R{sub J} , is near the upper end of allowable planet radii for hot-start models given the host star's age and likely reflects challenges constructing accurate atmospheric models. Alternatively, these radii are comfortably consistent with hot-start model predictions if β Pic b is younger than ≈7 Myr, consistent with a late formation well after its host star's birth ∼12{sup +8}{sub -4} Myr ago.« less

A Combined Very Large Telescope and Gemini Study of the Atmosphere of the Directly Imaged Planet, β Pictoris b

NASA Astrophysics Data System (ADS)

Currie, Thayne; Burrows, Adam; Madhusudhan, Nikku; Fukagawa, Misato; Girard, Julien H.; Dawson, Rebekah; Murray-Clay, Ruth; Kenyon, Scott; Kuchner, Marc; Matsumura, Soko; Jayawardhana, Ray; Chambers, John; Bromley, Ben

2013-10-01

We analyze new/archival VLT/NaCo and Gemini/NICI high-contrast imaging of the young, self-luminous planet β Pictoris b in seven near-to-mid IR photometric filters, using advanced image processing methods to achieve high signal-to-noise, high precision measurements. While β Pic b's near-IR colors mimic those of a standard, cloudy early-to-mid L dwarf, it is overluminous in the mid-infrared compared to the field L/T dwarf sequence. Few substellar/planet-mass objects—i.e., κ And b and 1RXJ 1609B—match β Pic b's JHKsL' photometry and its 3.1 μm and 5 μm photometry are particularly difficult to reproduce. Atmosphere models adopting cloud prescriptions and large (~60 μm) dust grains fail to reproduce the β Pic b spectrum. However, models incorporating thick clouds similar to those found for HR 8799 bcde, but also with small (a few microns) modal particle sizes, yield fits consistent with the data within the uncertainties. Assuming solar abundance models, thick clouds, and small dust particles (langarang = 4 μm), we derive atmosphere parameters of log (g) = 3.8 ± 0.2 and T eff = 1575-1650 K, an inferred mass of 7^{+4}_{-3} MJ , and a luminosity of log(L/L ⊙) ~-3.80 ± 0.02. The best-estimated planet radius, ≈1.65 ± 0.06 RJ , is near the upper end of allowable planet radii for hot-start models given the host star's age and likely reflects challenges constructing accurate atmospheric models. Alternatively, these radii are comfortably consistent with hot-start model predictions if β Pic b is younger than ≈7 Myr, consistent with a late formation well after its host star's birth ~12^{+8}_{-4} Myr ago.

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

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

NASA Astrophysics Data System (ADS)

Zoete, V.; Michielin, O.; Karplus, M.

2003-12-01

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SAS bur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, ΔGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC 50 without reparametrization.

Relativistic extension of a charge-conservative finite element solver for time-dependent Maxwell-Vlasov equations

NASA Astrophysics Data System (ADS)

Na, D.-Y.; Moon, H.; Omelchenko, Y. A.; Teixeira, F. L.

2018-01-01

Accurate modeling of relativistic particle motion is essential for physical predictions in many problems involving vacuum electronic devices, particle accelerators, and relativistic plasmas. A local, explicit, and charge-conserving finite-element time-domain (FETD) particle-in-cell (PIC) algorithm for time-dependent (non-relativistic) Maxwell-Vlasov equations on irregular (unstructured) meshes was recently developed by Moon et al. [Comput. Phys. Commun. 194, 43 (2015); IEEE Trans. Plasma Sci. 44, 1353 (2016)]. Here, we extend this FETD-PIC algorithm to the relativistic regime by implementing and comparing three relativistic particle-pushers: (relativistic) Boris, Vay, and Higuera-Cary. We illustrate the application of the proposed relativistic FETD-PIC algorithm for the analysis of particle cyclotron motion at relativistic speeds, harmonic particle oscillation in the Lorentz-boosted frame, and relativistic Bernstein modes in magnetized charge-neutral (pair) plasmas.

Study of plasma meniscus formation and beam halo in negative ion source using the 3D3VPIC model

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

Nishioka, S.; Goto, I.; Hatayama, A.

2015-04-08

In this paper, the effect of the electron confinement time on the plasma meniscus and the fraction of the beam halo is investigated by 3D3V-PIC (three dimension in real space and three dimension in velocity space) (Particle in Cell) simulation in the extraction region of negative ion source. The electron confinement time depends on the characteristic time of electron escape along the magnetic field as well as the characteristic time of diffusion across the magnetic field. Our 3D3V-PIC results support the previous result by 2D3V-PIC results i.e., it is confirmed that the penetration of the plasma meniscus becomes deep intomore » the source plasma region when the effective confinement time is short.« less

Tuning the Size of Nanoassembles: A Hierarchical Transfer of Information from Dendrimers to Polyion Complexes.

PubMed

Amaral, Sandra P; Tawara, Maun H; Fernandez-Villamarin, Marcos; Borrajo, Erea; Martínez-Costas, José; Vidal, Anxo; Riguera, Ricardo; Fernandez-Megia, Eduardo

2018-05-04

The generation of dendrimers is a powerful tool in the control of the size and biodistribution of polyion complexes (PIC). Using a combinatorial screening of six dendrimers (18-243 terminal groups) and five oppositely charged PEGylated copolymers, a dendrimer-to-PIC hierarchical transfer of structural information was revealed with PIC diameters that increased from 80 to 500 nm on decreasing the dendrimer generation. This rise in size, which was also accompanied by a micelle-to-vesicle transition, is interpreted according to a cone- to rod-shaped progression in the architecture of the unit PIC (uPIC). This precise size tuning enabled dendritic PICs to act as nanorulers for controlled biodistribution. Overall, a domino-like control of the size and biological properties of PIC that is not attainable with linear polymers is feasible through dendrimer generation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inter-annual Variability in Global Suspended Particulate Inorganic Carbon Inventory Using Space-based Measurements

NASA Astrophysics Data System (ADS)

Hopkins, J.; Balch, W. M.; Henson, S.; Poulton, A. J.; Drapeau, D.; Bowler, B.; Lubelczyk, L.

2016-02-01

Coccolithophores, the single celled phytoplankton that produce an outer covering of calcium carbonate coccoliths, are considered to be the greatest contributors to the global oceanic particulate inorganic carbon (PIC) pool. The reflective coccoliths scatter light back out from the ocean surface, enabling PIC concentration to be quantitatively estimated from ocean color satellites. Here we use datasets of AQUA MODIS PIC concentration from 2003-2014 (using the recently-revised PIC algorithm), as well as statistics on coccolithophore vertical distribution derived from cruises throughout the world ocean, to estimate the average global (surface and integrated) PIC standing stock and its associated inter-annual variability. In addition, we divide the global ocean into Longhurst biogeochemical provinces, update the PIC biomass statistics and identify those regions that have the greatest inter-annual variability and thus may exert the greatest influence on global PIC standing stock and the alkalinity pump.

Electrostatic potential map modelling with COSY Infinity

NASA Astrophysics Data System (ADS)

Maloney, J. A.; Baartman, R.; Planche, T.; Saminathan, S.

2016-06-01

COSY Infinity (Makino and Berz, 2005) is a differential-algebra based simulation code which allows accurate calculation of transfer maps to arbitrary order. COSY's existing internal procedures were modified to allow electrostatic elements to be specified using an array of field potential data from the midplane. Additionally, a new procedure was created allowing electrostatic elements and their fringe fields to be specified by an analytic function. This allows greater flexibility in accurately modelling electrostatic elements and their fringe fields. Applied examples of these new procedures are presented including the modelling of a shunted electrostatic multipole designed with OPERA, a spherical electrostatic bender, and the effects of different shaped apertures in an electrostatic beam line.

46 CFR 13.301 - Original application for “Tankerman-PIC (Barge)” endorsement.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 1 2010-10-01 2010-10-01 false Original application for âTankerman-PIC (Barge)â endorsement. 13.301 Section 13.301 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MERCHANT MARINE....301 Original application for “Tankerman-PIC (Barge)” endorsement. Each applicant for a “Tankerman-PIC...

Peroxydisulfate activation by [RuII(tpy)(pic)(H2O)]+. Kinetic, mechanistic and anti-microbial activity studies.

PubMed

Chatterjee, Debabrata; Banerjee, Priyabrata; Bose, Jagadeesh C K; Mukhopadhyay, Sudit

2012-03-07

The oxidation of [Ru(II)(tpy)(pic)H(2)O](+) (tpy = 2,2',6',2''-terpyridine; pic(-) = picolinate) by peroxidisulfate (S(2)O(8)(2-)) as precursor oxidant has been investigated kinetically by UV-VIS, IR and EPR spectroscopy. The overall oxidation of Ru(II)- to Ru(IV)-species takes place in a consecutive manner involving oxidation of [Ru(II)(tpy)(pic)H(2)O](+) to [Ru(III)(tpy)(pic)(OH)](+), and its further oxidation of to the ultimate product [Ru(IV)(tpy)(pic)(O)](+) complex. The time course of the reaction was followed as a function of [S(2)O(8)(2-)], ionic strength (I) and temperature. Kinetic data and activation parameters are interpreted in terms of an outer-sphere electron transfer mechanism. Anti-microbial activity of Ru(II)(tpy)(pic)H(2)O](+) complex by inhibiting the growth of Escherichia coli DH5α in presence of peroxydisulfate has been explored, and the results of the biological studies have been discussed in terms of the [Ru(IV)(tpy)(pic)(O)](+) mediated cleavage of chromosomal DNA of the bacteria.

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.

The microscopic Z-pinch process of current-carrying rarefied deuterium plasma shell

NASA Astrophysics Data System (ADS)

Ning, Cheng; Feng, Zhixing; Xue, Chuang; Li, Baiwen

2015-02-01

For insight into the microscopic mechanism of Z-pinch dynamic processes, a code of two-dimensional particle-in-cell (PIC) simulation has been developed in cylindrical coordinates. In principle, the Z-pinch of current-carrying rarefied deuterium plasma shell has been simulated by means of this code. Many results related to the microscopic processes of the Z-pinch are obtained. They include the spatio-temporal distributions of electromagnetic field, current density, forces experienced by the ions and electrons, positions and energy distributions of particles, and trailing mass and current. In radial direction, the electric and magnetic forces exerted on the electrons are comparable in magnitude, while the forces exerted on the ions are mainly the electric forces. So in the Z-pinch process, the electrons are first accelerated in Z direction and get higher velocities; then, they are driven inwards to the axis at the same time by the radial magnetic forces (i.e., Lorentz forces) of them. That causes the separations between the electrons and ions because the ion mass is much larger than the electron's, and in turn a strong electrostatic field is produced. The produced electrostatic field attracts the ions to move towards the electrons. When the electrons are driven along the radial direction to arrive at the axis, they shortly move inversely due to the static repellency among them and their tiny mass, while the ions continue to move inertially inwards, and later get into stagnation, and finally scatter outwards. Near the stagnation, the energies of the deuterium ions mostly range from 0.3 to 6 keV, while the electron energies are mostly from 5 to 35 keV. The radial components, which can contribute to the pinched plasma temperature, of the most probable energies of electron and ion at the stagnation are comparable to the Bennett equilibrium temperature (about 1 keV), and also to the highest temperatures of electron and ion obtained in one dimensional radiation magnetohydrodynamic simulation of the plasma shell Z-pinch. The trailing mass is about 20% of the total mass of the shell, and the maximum trailing current is about 7% of the driven current under our trailing definition. Our PIC simulation also demonstrates that the plasma shell first experiences a snow-plow like implosion process, which is relatively stable.

Development of the micro pixel chamber based on MEMS technology

NASA Astrophysics Data System (ADS)

Takemura, T.; Takada, A.; Kishimoto, T.; Komura, S.; Kubo, H.; Matsuoka, Y.; Miuchi, K.; Miyamoto, S.; Mizumoto, T.; Mizumura, Y.; Motomura, T.; Nakamasu, Y.; Nakamura, K.; Oda, M.; Ohta, K.; Parker, J. D.; Sawano, T.; Sonoda, S.; Tanimori, T.; Tomono, D.; Yoshikawa, K.

2018-02-01

Micro pixel chambers (μ-PIC) are gaseous two-dimensional imaging detectors originally manufactured using printed circuit board (PCB) technology. They are used in MeV gamma-ray astronomy, medicalimaging, neutron imaging, the search for dark matter, and dose monitoring. The position resolution of the present μ-PIC is approximately 120 μm (RMS), however some applications require a fine position resolution of less than 100 μm. To this end, we have started to develop a μ-PIC based on micro electro mechanical system (MEMS) technology, which provides better manufacturing accuracy than PCB technology. Our simulation predicted the gains of MEMS μ-PICs to be twice those of PCB μ-PICs at the same anode voltage. We manufactured two MEMS μ-PICs and tested them to study their behavior. In these experiments, we successfully operated the fabricatedMEMS μ-PICs and we achieved a maximum gain of approximately 7×103 and collected their energy spectra under irradiation of X-rays from 55Fe. However, the measured gains of the MEMS μ-PICs were less than half of the values predicted in the simulations. We postulated that the gains of the MEMS μ-PICs are diminished by the effect of the silicon used as a semiconducting substrate.

Storage of Maize in Purdue Improved Crop Storage (PICS) Bags

PubMed Central

2017-01-01

Interest in using hermetic technologies as a pest management solution for stored grain has risen in recent years. One hermetic approach, Purdue Improved Crop Storage (PICS) bags, has proven successful in controlling the postharvest pests of cowpea. This success encouraged farmers to use of PICS bags for storing other crops including maize. To assess whether maize can be safely stored in PICS bags without loss of quality, we carried out laboratory studies of maize grain infested with Sitophilus zeamais (Motshulsky) and stored in PICS triple bags or in woven polypropylene bags. Over an eight month observation period, temperatures in the bags correlated with ambient temperature for all treatments. Relative humidity inside PICS bags remained constant over this period despite the large changes that occurred in the surrounding environment. Relative humidity in the woven bags followed ambient humidity closely. PICS bags containing S. zeamais-infested grain saw a significant decline in oxygen compared to the other treatments. Grain moisture content declined in woven bags, but remained high in PICS bags. Seed germination was not significantly affected over the first six months in all treatments, but declined after eight months of storage when infested grain was held in woven bags. Relative damage was low across treatments and not significantly different between treatments. Overall, maize showed no signs of deterioration in PICS bags versus the woven bags and PICS bags were superior to woven bags in terms of specific metrics of grain quality. PMID:28072835

Smart Power: New power integrated circuit technologies and their applications

NASA Astrophysics Data System (ADS)

Kuivalainen, Pekka; Pohjonen, Helena; Yli-Pietilae, Timo; Lenkkeri, Jaakko

1992-05-01

Power Integrated Circuits (PIC) is one of the most rapidly growing branches of the semiconductor technology. The PIC markets has been forecast to grow from 660 million dollars in 1990 to 1658 million dollars in 1994. It has even been forecast that at the end of the 1990's the PIC markets would correspond to the value of the whole semiconductor production in 1990. Automotive electronics will play the leading role in the development of the standard PIC's. Integrated motor drivers (36 V/4 A), smart integrated switches (60 V/30 A), solenoid drivers, integrated switch-mode power supplies and regulators are the latest standard devices of the PIC manufactures. ASIC (Application Specific Integrated Circuits) PIC solutions are needed for the same reasons as other ASIC devices: there are no proper standard devices, a company has a lot of application knowhow, which should be kept inside the company, the size of the product must be reduced, and assembly costs are wished to be reduced by decreasing the number of discrete devices. During the next few years the most probable ASIC PIC applications in Finland will be integrated solenoid and motor drivers, an integrated electronic lamp ballast circuit and various sensor interface circuits. Application of the PIC technologies to machines and actuators will strongly be increased all over the world. This means that various PIC's, either standard PIC's or full custom ASIC circuits, will appear in many products which compete with the corresponding Finnish products. Therefore the development of the PIC technologies must be followed carefully in order to immediately be able to apply the latest development in the smart power technologies and their design methods.

Seagrass meadows as a globally significant carbonate reservoir

NASA Astrophysics Data System (ADS)

Mazarrasa, I.; Marbà, N.; Lovelock, C. E.; Serrano, O.; Lavery, P. S.; Fourqurean, J. W.; Kennedy, H.; Mateo, M. A.; Krause-Jensen, D.; Steven, A. D. L.; Duarte, C. M.

2015-03-01

There has been a growing interest in quantifying the capacity of seagrass ecosystems to act as carbon sinks as a natural way of offsetting anthropogenic carbon emissions to the atmosphere. However, most of the efforts have focused on the organic carbon (POC) stocks and accumulation rates and ignored the inorganic carbon (PIC) fraction, despite important carbonate pools associated with calcifying organisms inhabiting the meadows, such as epiphytes and benthic invertebrates, and despite the relevance that carbonate precipitation and dissolution processes have in the global carbon cycle. This study offers the first assessment of the global PIC stocks in seagrass sediments using a synthesis of published and unpublished data on sediment carbonate concentration from 402 vegetated and 34 adjacent un-vegetated sites. PIC stocks in the top 1 m sediments ranged between 3 and 1660 Mg PIC ha-1, with an average of 654 ± 24 Mg PIC ha-1, exceeding about 5 fold those of POC reported in previous studies. Sedimentary carbonate stocks varied across seagrass communities, with meadows dominated by Halodule, Thalassia or Cymodocea supporting the highest PIC stocks, and tended to decrease polewards at a rate of -8 ± 2 Mg PIC ha-1 degree-1 of latitude (GLM, p < 0.0003). Using PIC concentration and estimates of sediment accretion in seagrass meadows, mean PIC accumulation rates in seagrass sediments is 126.3 ± 0.7 g PIC m-2 y-1. Based on the global extent of seagrass meadows (177 000 to 600 000 km2), these ecosystems globally store between 11 and 39 Pg of PIC in the top meter of sediment and accumulate between 22 and 76 Tg PIC y-1, representing a significant contribution to the carbonate dynamics of coastal areas. Despite that these high rates of carbonate accumulation imply CO2 emissions from precipitation, seagrass meadows are still strong CO2 sinks as demonstrates the comparison of carbon (POC and POC) stocks between vegetated and adjacent un-vegetated sediments.

Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules--applications in biotechnology.

PubMed

Neves-Petersen, Maria Teresa; Petersen, Steffen B

2003-01-01

The molecular understanding of the initial interaction between a protein and, e.g., its substrate, a surface or an inhibitor is essentially an understanding of the role of electrostatics in intermolecular interactions. When studying biomolecules it is becoming increasingly evident that electrostatic interactions play a role in folding, conformational stability, enzyme activity and binding energies as well as in protein-protein interactions. In this chapter we present the key basic equations of electrostatics necessary to derive the equations used to model electrostatic interactions in biomolecules. We will also address how to solve such equations. This chapter is divided into two major sections. In the first part we will review the basic Maxwell equations of electrostatics equations called the Laws of Electrostatics that combined will result in the Poisson equation. This equation is the starting point of the Poisson-Boltzmann (PB) equation used to model electrostatic interactions in biomolecules. Concepts as electric field lines, equipotential surfaces, electrostatic energy and when can electrostatics be applied to study interactions between charges will be addressed. In the second part we will arrive at the electrostatic equations for dielectric media such as a protein. We will address the theory of dielectrics and arrive at the Poisson equation for dielectric media and at the PB equation, the main equation used to model electrostatic interactions in biomolecules (e.g., proteins, DNA). It will be shown how to compute forces and potentials in a dielectric medium. In order to solve the PB equation we will present the continuum electrostatic models, namely the Tanford-Kirkwood and the modified Tandord-Kirkwood methods. Priority will be given to finding the protonation state of proteins prior to solving the PB equation. We also present some methods that can be used to map and study the electrostatic potential distribution on the molecular surface of proteins. The combination of graphical visualisation of the electrostatic fields combined with knowledge about the location of key residues on the protein surface allows us to envision atomic models for enzyme function. Finally, we exemplify the use of some of these methods on the enzymes of the lipase family.

VizieR Online Data Catalog: A dust model for bet Pic from 0.58 to 870um (Ballering+, 2016)

NASA Astrophysics Data System (ADS)

Ballering, N. P.; Su, K. Y. L.; Rieke, G. H.; Gaspar, A.

2016-08-01

β Pic was imaged with the HST/STIS CCD in coronagraphic (50CORON) mode under program GO-12551 (PI: Apai), and the results of these observations were published in Apai et al. (2015ApJ...800..136A). The instrument bandpass is set by the response of the CCD and centered at 0.58um. We searched the HST archive and found previously unpublished observations of β Pic with the WFC3 instrument in the IR channel (filter F110W at ~1.16um) from program GO-11150 (PI: Graham). The Spitzer/MIPS observations of β Pic were taken under the Spitzer Guaranteed Time Observing Program 90 (PI: M. Werner). The data at all three bands (24, 70, and 160um) are published here for the first time. Two sets of 24um observations were obtained. The first set was obtained on 2004 March 20, the second set of data was obtained on 2004 April 11. Two sets of 70um observations were obtained. The first set was obtained on 2004 April 12. The second set was obtained on 2005 April 4. Herschel/PACS 70um scan map observations of β Pic (PI G. Olofsson, observation IDs 1342186612 and 1342186613) were published by Vandenbussche et al. (2010A&A...518L.133V). We used the ALMA 870um continuum image previously published by Dent et al. (2014Sci...343.1490D). (1 data file).

A detailed investigation of light-harvesting efficiency of blue color emitting divergent iridium dendrimers with peripheral phenylcarbazole units.

PubMed

Cho, Yang-Jin; Wee, Kyung-Ryang; Son, Ho-Jin; Cho, Dae Won; Kang, Sang Ook

2014-03-14

The increase in phosphorescence efficiency was estimated by the energy transfer mechanism for divergent iridium dendrimers with peripheral phenylcarbazole units. A series of Ir-core/phenylcarbazole-end dendrons of the type, Ir(dfppy)2(pic-Czn) (Gn, n = 0, 1, 2, and 3), was synthesized, where dfppy, pic, and Czn (n = 2, 4, and 8) are 2-(4,6-difluorophenyl)pyridine, picolinate substituted with Czn at the 3-position, and 4-(9-carbazolyl)phenyldendrons connected with 3,5-di(methyleneoxy)benzyloxy branches, respectively. Selective excitation of the Czn units of G1–G3 resulted in >90% quenching of the Cz fluorescence accompanied by the growth of phosphorescence from the Ir(dfppy)2(pic) core as a consequence of energy transfer from the excited-singlet Czn chromophore to the core. The rate constants of energy transfer were determined by steady-state and transient spectroscopic measurements to be 4.32 × 10(9) s(−1) (G1), 2.37 × 10(9) s(−1) (G2), and 1.46 × 10(9) s(−1) (G3), which were in good agreement with those calculated using the Förster model. The phosphorescence enhancements were 157 (G1), 213 (G2), and 264% (G3) when compared to the phosphorescence of the core Ir(dfppy)2(pic-Ph2) (G0), in which pic-Ph2 is 3-(3,5-dibenzyloxybenzyl)picolinate.

Damping of Bernstein-Greene-Kruskal modes in collisional plasmas

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

Valentini, Francesco

2008-02-15

In this paper, the effect of Coulomb collisions on the stability of Bernstein-Greene-Kruskal (BGK) modes [I. B. Bernstein, J. M. Greene, and M. D. Krukal, Phys. Rev. 108, 546 (1957)] is analyzed by comparing the numerical results of collisional particle-in-cell (PIC) simulations with the theoretical predictions by Zakharov and Karpman [V. E. Zakharov and V. I. Karpman, Sov. Phys. JETP 16, 351 (1963)], for the collisional damping of nonlinear plasma waves. In the absence of collisions, BGK modes are undamped nonlinear electrostatic oscillations, solutions of the Vlasov-Poisson equations; in these structures nonlinearity manifests as the formation of a plateau inmore » the resonant region of the particle distribution function, due to trapping of resonant particles, thus preventing linear Landau damping. When particle-particle Coulomb collisions are effective, this plateau is smoothed out since collisions drive the velocity distribution towards the Maxwellian shape, thus destroying the BGK structure. As shown by Zakharov and Karpman in 1963, under certain assumptions, an exponential time decay with constant damping rate is predicted for the electric field amplitude and a linear dependence of the damping rate on the collision frequency is found. In this paper, the theory by Zakharov and Karpman is revisited and the effects of collisions on the stability of BGK modes and on the long time evolution of nonlinear Landau damping are numerically investigated. The numerical results are obtained through a collisional PIC code that reproduces a physical phenomenology also observed in recent experiments with trapped pure electron plasmas.« less

High-performance modeling of plasma-based acceleration and laser-plasma interactions

NASA Astrophysics Data System (ADS)

Vay, Jean-Luc; Blaclard, Guillaume; Godfrey, Brendan; Kirchen, Manuel; Lee, Patrick; Lehe, Remi; Lobet, Mathieu; Vincenti, Henri

2016-10-01

Large-scale numerical simulations are essential to the design of plasma-based accelerators and laser-plasma interations for ultra-high intensity (UHI) physics. The electromagnetic Particle-In-Cell (PIC) approach is the method of choice for self-consistent simulations, as it is based on first principles, and captures all kinetic effects, and also scale favorably to many cores on supercomputers. The standard PIC algorithm relies on second-order finite-difference discretization of the Maxwell and Newton-Lorentz equations. We present here novel formulations, based on very high-order pseudo-spectral Maxwell solvers, which enable near-total elimination of the numerical Cherenkov instability and increased accuracy over the standard PIC method for standard laboratory frame and Lorentz boosted frame simulations. We also present the latest implementations in the PIC modules Warp-PICSAR and FBPIC on the Intel Xeon Phi and GPU architectures. Examples of applications will be given on the simulation of laser-plasma accelerators and high-harmonic generation with plasma mirrors. Work supported by US-DOE Contracts DE-AC02-05CH11231 and by the European Commission through the Marie Slowdoska-Curie fellowship PICSSAR Grant Number 624543. Used resources of NERSC.

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

Shoup, R.W.; Long, F.; Martin, T.H.

Sandia has developed PBFA-Z, a 20-MA driver for z-pinch experiments by replacing the water lines, insulator stack. and MITLs on PBFA II with hardware of a new design. The PBFA-Z accelerator was designed to deliver 20 MA to a 15-mg z-pinch load in 100 ns. The accelerator was modeled using circuit codes to determine the time-dependent voltage and current waveforms at the input and output of the water lines, the insulator stack, and the MITLs. The design of the vacuum insulator stack was dictated by the drive voltage, the electric field stress and grading requirements, the water line and MITLmore » interface requirements, and the machine operations and maintenance requirements. The insulator stack consists of four separate modules, each of a different design because of different voltage drive and hardware interface requirements. The shape of the components in each module, i.e., grading rings, insulator rings, flux excluders, anode and cathode conductors, and the design of the water line and MITL interfaces, were optimized by using the electrostatic analysis codes, ELECTRO and JASON. The time-dependent performance of the insulator stacks was evaluated using IVORY, a 2-D PIC code. This paper will describe the insulator stack design, present the results of the ELECTRO and IVORY analyses, and show the results of the stack measurements.« less

Sirepo - Warp

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

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

The Heliopause Electrostatic Rapid Transit System (HERTS) - Design, Trades, and Analyses Performed in a Two Year NASA Investigation of Electric Sail Propulsion Systems

NASA Technical Reports Server (NTRS)

Wiegmann, Bruce M.; Scheider, Todd; Heaton, Andrew; Vaughn, Jason; Stone, Nobie; Wright, Ken

2017-01-01

Personnel from NASA's MSFC have been investigating the feasibility of an advanced propulsion system known as the Electric Sail (E-Sail) for future scientific exploration missions. This team initially won a NASA Space Technology Mission Directorate (STMD) Phase I NASA Innovative Advanced Concept (NIAC) award and then a two-year follow-on Phase II NIAC award in October 2015. This paper documents the findings from this three-year investigation. An Electric sail, a propellant-less propulsion system, uses solar wind ions to rapidly travel either to deep space or the inner solar system. Scientific spacecraft could reach Pluto in 5 years, or the boundary of the solar system in ten to twelve years compared to the thirty-five plus years the Voyager spacecraft took. The team's recent focuses have been: 1) Developing a Particle in Cell (PIC) numeric engineering model from MSFC's experimental data on the interaction between simulated solar wind and a charged bare wire that can be applied to a variety of missions, 2) Determining what missions could benefit from this revolutionary propulsion system, 3) Conceptualizing spacecraft designs for various tasks: to reach the solar system's edge, to orbit the sun as Heliophysics sentinels, or to examine a multitude of asteroids.

Spectral and Temporal Characteristics of LS PEG and TW PIC Using XMM-NEWTON Data

NASA Astrophysics Data System (ADS)

Talebpour Sheshvan, Nasrin; Balman, Solen

2016-07-01

We report the analysis of archival XMM-Newton X-ray observations of LS Peg and TW Pic. These are Cataclysmic Variables (CVs) suggested as Intermediate Polars (IPs), but unconfirmed in the X-rays. Identification of several periodic oscillations in the optical band hint them as IPs. Unlike the previous spectral analysis on the EPIC-MOS data by fitting a hot optically thin plasma emission model with a single temperature for LS Peg, we simultaneously fitted all EPIC spectrum (pn+MOS) using a composite model of absorption for interstellar medium (tbabs) with two different partial covering absorbers (pcfabs) including a multitemperature plasma emission component (cevmkl) and a Gaussian emission line at 6.4 keV. TW Pic is best modeled in a similar manner with only one partial covering absorber and an extra Gaussian emission line at 6.7 keV. LS Peg has a maximum plasma temperature of ˜14.8 keV with an X-ray luminosity of ˜5×10^{32}ergs ^{-1} translating to an accretion rate of ˜1.27×10^{-10}M _{⊙}yr ^{-1}. TW Pic shows kT _{max} ˜38.7 keV with an X-ray luminosity around 1.6×10^{33}ergs ^{-1} at an accretion rate of ˜4×10^{-10}M _{⊙}yr ^{-1}. In addition, we discuss orbital modulations in the X-rays and power spectral analysis, and derive the EPIC pn spectra for orbital minimum and orbital maximum phases for both sources. We elaborate on the geometry of accretion and absorption in the X-ray emitting regions of both sources with articulation on the magnetic nature.

The long-term quality of life in patients with persistent inflammation-immunosuppression and catabolism syndrome after severe acute pancreatitis: A retrospective cohort study.

PubMed

Yang, Na; Li, Baiqiang; Ye, Bo; Ke, Lu; Chen, Faxi; Lu, Guotao; Jiang, Fangfang; Tong, Zhihui; Li, Jieshou; Li, Weiqin

2017-12-01

To explore clinical characteristics and long-term quality of life (QOL) in severe acute pancreatitis (SAP) patients with persistent inflammation-immunosuppression and catabolism syndrome (PICS). SAP patients admitted to ICU were eligible for the retrospective cohort study if they needed prolonged intensive care (>14days). Post-ICU QOL was assessed by a questionnaire, including 36-item Short Form Health Survey (SF-36) and record of re-work in a long-term follow-up. 214 SAP patients were enrolled, in which 149 (69.6%) patients met the criteria of PICS. PICS patients had more complications and ICU days compared to non-PICS patients (P<0.001), and their post-ICU mortality was higher (P=0.046). When adjusted for confounders, PICS was independently associated with higher post-ICU mortality (hazard ratio 4.5; 95% CI, 1.2 to 16.3; P=0.024). The 36-item Short Form Health Survey (SF-36) score was lower for PICS group in six subscales (P<0.001). Only 28.8% patients in the PICS group returned to work compared to 60% patients in the non-PICS group (P=0.001) CONCLUSIONS: SAP patients with prolonged ICU stay had a high morbidity of PICS, which was a risk factor for the post-ICU mortality and poor long-term QOL. Copyright © 2017 Elsevier Inc. All rights reserved.

Traveling-Wave Tube Amplifier Model to Predict High-Order Modulation Intersymbol Interference

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Andro, Monty; Williams, W. D. (Technical Monitor)

2001-01-01

Demands for increased data rates in satellite communications necessitate higher order modulation schemes, larger system bandwidth, and minimum distortion of the modulated signal as it is passed through the traveling wave tube amplifier (TWTA). One type of distortion that the TWTA contributes to is intersymbol interference (ISI), and this becomes particularly disruptive with wide-band, complex modulation schemes. It is suspected that in addition to the dispersion of the TWT, frequency dependent reflections due to mismatches within the TWT are a significant contributor to ISI. To experimentally investigate the effect of these mismatches within the physical TWT on ISI would be prohibitively expensive, as it would require manufacturing numerous amplifiers in addition to the acquisition of the required digital hardware. In an attempt to develop a more accurate model to correlate IS1 with the TWTA and the operational signal, a fully three-dimensional (3D), time-dependent, TWT interaction model has been developed using the electromagnetic particle-in-cell (PIC) code MAFIA (solution of Maxwell's equations by the Finite-Integration-Algorithm). The model includes a user defined slow-wave circuit with a spatially tapered region of loss to implement a sever, and spatially varied geometry (such as helical pitch) to implement a phase velocity taper. The model also includes user defined input/output coupling and an electron beam contained by solenoidal, electrostatic, or periodic permanent magnet (PPM) focusing allowing standard or novel TWTs to be investigated. This model comprehensively takes into account the effects of frequency dependent nonlinear distortions (MAM and AMPM); gain ripple due to frequency dependent reflections at the input/output coupling, severs, and mismatches from dynamic pitch variations; drive induced oscillations; harmonic generation; intermodulation products; and backward waves.

OSIRIS - an object-oriented parallel 3D PIC code for modeling laser and particle beam-plasma interaction

NASA Astrophysics Data System (ADS)

Hemker, Roy

1999-11-01

The advances in computational speed make it now possible to do full 3D PIC simulations of laser plasma and beam plasma interactions, but at the same time the increased complexity of these problems makes it necessary to apply modern approaches like object oriented programming to the development of simulation codes. We report here on our progress in developing an object oriented parallel 3D PIC code using Fortran 90. In its current state the code contains algorithms for 1D, 2D, and 3D simulations in cartesian coordinates and for 2D cylindrically-symmetric geometry. For all of these algorithms the code allows for a moving simulation window and arbitrary domain decomposition for any number of dimensions. Recent 3D simulation results on the propagation of intense laser and electron beams through plasmas will be presented.

Anomalous photo-ionization of 4d shell in medium-Z ionized atoms

NASA Astrophysics Data System (ADS)

Klapisch, M.; Busquet, M.

2013-09-01

Photoionization (PI) cross sections (PICS) are necessary for the simulation of astrophysical and ICF plasmas. In order to be used in plasma modeling, the PICS are usually fit to simple analytical formulas. We observed an unusual spectral shape of the PICS of the 4d shell of ionized Xe and other elements, computed with different codes: a local minimum occurs around twice the threshold energy. We explain this phenomenon as interference between the bound 4d wavefunction and the free electron wavefunction, which is similar to the Cooper minima for neutral atoms. Consequently, the usual fitting formulas, which consist of a combination of inverse powers of the frequency beyond threshold, may yield rates for PI and radiative recombination (RR) that are incorrect by orders of magnitude. A new fitting algorithm is proposed and is included in the latest version of HULLAC.v9.5.

Exploring Ultrahigh-Intensity Laser-Plasma Interaction Physics with QED Particle-in-Cell Simulations

NASA Astrophysics Data System (ADS)

Luedtke, S. V.; Yin, L.; Labun, L. A.; Albright, B. J.; Stark, D. J.; Bird, R. F.; Nystrom, W. D.; Hegelich, B. M.

2017-10-01

Next generation high-intensity lasers are reaching intensity regimes where new physics-quantum electrodynamics (QED) corrections to otherwise classical plasma dynamics-becomes important. Modeling laser-plasma interactions in these extreme settings presents a challenge to traditional particle-in-cell (PIC) codes, which either do not have radiation reaction or include only classical radiation reaction. We discuss a semi-classical approach to adding quantum radiation reaction and photon production to the PIC code VPIC. We explore these intensity regimes with VPIC, compare with results from the PIC code PSC, and report on ongoing work to expand the capability of VPIC in these regimes. This work was supported by the U.S. DOE, Los Alamos National Laboratory Science program, LDRD program, NNSA (DE-NA0002008), and AFOSR (FA9550-14-1-0045). HPC resources provided by TACC, XSEDE, and LANL Institutional Computing.

Recent advances in the modeling of plasmas with the Particle-In-Cell methods

NASA Astrophysics Data System (ADS)

Vay, Jean-Luc; Lehe, Remi; Vincenti, Henri; Godfrey, Brendan; Lee, Patrick; Haber, Irv

2015-11-01

The Particle-In-Cell (PIC) approach is the method of choice for self-consistent simulations of plasmas from first principles. The fundamentals of the PIC method were established decades ago but improvements or variations are continuously being proposed. We report on several recent advances in PIC related algorithms, including: (a) detailed analysis of the numerical Cherenkov instability and its remediation, (b) analytic pseudo-spectral electromagnetic solvers in Cartesian and cylindrical (with azimuthal modes decomposition) geometries, (c) arbitrary-order finite-difference and generalized pseudo-spectral Maxwell solvers, (d) novel analysis of Maxwell's solvers' stencil variation and truncation, in application to domain decomposition strategies and implementation of Perfectly Matched Layers in high-order and pseudo-spectral solvers. Work supported by US-DOE Contracts DE-AC02-05CH11231 and the US-DOE SciDAC program ComPASS. Used resources of NERSC, supported by US-DOE Contract DE-AC02-05CH11231.

Polygonal Impact Craters on selected Minor Bodies: Rhea, Dione, Tethys, Ceres, and Vesta

NASA Astrophysics Data System (ADS)

Neidhart, Tanja; Leitner, Johannes; Firneis, Maria

2017-04-01

A polygonal impact crater (PIC) is a crater that does not have a full circular shape in plane view but consists of straight crater rim segments. PICs are common on all objects in our solar system that show a cratered surface. Previous studies showed that PICs make up about 10-25% of craters on Mercury, Venus, Mars, and the Moon [1, 2, 3, 4]. Although there have been several studies on PICs on the terrestrial planets, and the Moon there are only very few investigations on PICs on minor bodies, even though there exist surface maps of Rhea, Tethys, Dione, Ceres, and Vesta that have an appropriate resolution. The aim of this study is to get more information about the abundance and characteristics of PICs on these objects. We analysed all approved craters on Rhea, Dione, Tethys, Ceres, and Vesta using images provided by the IAU/NASA/USGS Planetary Database [5]. For the classification of PICs the definition by [2] was used which states that a crater is polygonal if it consists of at least two straight crater rim segments having a discernable angle. In total 417 impact craters were examined and 227 of them were classified as polygonal. On Rhea about 48% of the approved craters are PICs, on Dione 59%, on Tethys 34%, on Ceres 74%, and on Vesta 56%. The comparison with studies on PICs on terrestrial planets, and the Moon conducted by [1, 2, 3, 4] showed that the percentage of PICs found in this study is much higher. Most of the PICs have two or three straight rim segments and only few PICs are hexagonal or pentagonal. The mean angle between the straight rims yields 121° for Rhea, 124° for Dione, 123° for Tethys, 133° for Ceres, and 134° for Vesta. These angles are well in accordance to an average angle of 112° on Mercury [1]. Also the size distribution of PICs is in accordance to results by [4] who proved that PICs seem to favor small to middle size diameters. The largest diameters of non-polygonal craters on Vesta range from 0.6 km to 450 km while the diameters of PICs only range from 3.1 km to 53.2 km [5]. The study proves that a large number of polygonal impact craters on Rhea, Dione, Tethys, Ceres, and Vesta exist but it is still unclear why the fraction of PICs on these bodies is much higher than for terrestrial planets and the Moon. One possible solution could be the different composition of the surfaces of these bodies in comparison to the terrestrial planets but for definite answers to this question further understanding of the formation process of PICs, which is still unclear, is necessary. References: [1] Weihs G. T. et al. (2015) Planet. Space Sci., 111, 77-82. [2] Aittola M. et al. (2010) Icarus, 205, 356-363. [3] Öhman et al. (2008) Meteoritics & Planet. Sci., 43, 1605-1628. [4] Öhman et al. (2010) Geol. Soc. Spec. Pap., 465, 51-65. [5] IAU/NASA/USGS Planetary Database. (2016), http://planetarynames.wr.usgs.gov/.

FAST TRACK COMMUNICATION: The origin of Bohm diffusion, investigated by a comparison of different modelling methods

NASA Astrophysics Data System (ADS)

Bultinck, E.; Mahieu, S.; Depla, D.; Bogaerts, A.

2010-07-01

'Bohm diffusion' causes the electrons to diffuse perpendicularly to the magnetic field lines. However, its origin is not yet completely understood: low and high frequency electric field fluctuations are both named to cause Bohm diffusion. The importance of including this process in a Monte Carlo (MC) model is demonstrated by comparing calculated ionization rates with particle-in-cell/Monte Carlo collisions (PIC/MCC) simulations. A good agreement is found with a Bohm diffusion parameter of 0.05, which corresponds well to experiments. Since the PIC/MCC method accounts for fast electric field fluctuations, we conclude that Bohm diffusion is caused by fast electric field phenomena.

A Database Design for the Brazilian Air Force Military Personnel Control System.

DTIC Science & Technology

1987-06-01

GIVEN A RECNum GET MOVING HISTORICAL". 77 SEL4 PlC X(70) VALUE ". 4. GIVEN A RECNUM GET NOMINATION HISTORICAL". 77 SEL5 PIC X(70) VALUE it 5. GIVEN A...WHERE - "°RECNUM = :RECNUM". 77 SQL-SEL3-LENGTH PIC S9999 VALUE 150 COMP. 77 SQL- SEL4 PIC X(150) VALUE "SELECT ABBREV,DTNOM,DTEXO,SITN FROM...NOMINATION WHERE RECNUM 77 SQL- SEL4 -LENGTH PIC S9999 VALUE 150 COMP. 77 SQL-SEL5 PIC X(150) VALUE "SELECT ABBREVDTDES,DTWAIVER,SITD FROM DESIG WHERE RECNUM It

Accurate modeling of plasma acceleration with arbitrary order pseudo-spectral particle-in-cell methods

DOE PAGES

Jalas, S.; Dornmair, I.; Lehe, R.; ...

2017-03-20

Particle in Cell (PIC) simulations are a widely used tool for the investigation of both laser- and beam-driven plasma acceleration. It is a known issue that the beam quality can be artificially degraded by numerical Cherenkov radiation (NCR) resulting primarily from an incorrectly modeled dispersion relation. Pseudo-spectral solvers featuring infinite order stencils can strongly reduce NCR - or even suppress it - and are therefore well suited to correctly model the beam properties. For efficient parallelization of the PIC algorithm, however, localized solvers are inevitable. Arbitrary order pseudo-spectral methods provide this needed locality. Yet, these methods can again be pronemore » to NCR. Here in this paper, we show that acceptably low solver orders are sufficient to correctly model the physics of interest, while allowing for parallel computation by domain decomposition.« less

p-( sup 125 I)iodoclonidine is a partial agonist at the alpha 2-adrenergic receptor

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

Gerhardt, M.A.; Wade, S.M.; Neubig, R.R.

1990-08-01

The binding properties of p-(125I)iodoclonidine (( 125I)PIC) to human platelet membranes and the functional characteristics of PIC are reported. (125I)PIC bound rapidly and reversibly to platelet membranes, with a first-order association rate constant (kon) at room temperature of 8.0 +/- 2.7 x 10(6) M-1 sec-1 and a dissociation rate constant (koff) of 2.0 +/- 0.8 x 10(-3) sec-1. Scatchard plots of specific (125I)PIC binding (0.1-5 nM) were linear, with a Kd of 1.2 +/- 0.1 nM. (125I)PIC bound to the same number of high affinity sites as the alpha 2-adrenergic receptor (alpha 2-AR) full agonist (3H) bromoxidine (UK14,304), which representedmore » approximately 40% of the sites bound by the antagonist (3H)yohimbine. Guanosine 5'-(beta, gamma-imido)triphosphate greatly reduced the amount of (125I)PIC bound (greater than 80%), without changing the Kd of the residual binding. In competition experiments, the alpha 2-AR-selective ligands yohimbine, bromoxidine, oxymetazoline, clonidine, p-aminoclonidine, (-)-epinephrine, and idazoxan all had Ki values in the low nanomolar range, whereas prazosin, propranolol, and serotonin yielded Ki values in the micromolar range. Epinephrine competition for (125I)PIC binding was stereoselective. Competition for (3H)bromoxidine binding by PIC gave a Ki of 1.0 nM (nH = 1.0), whereas competition for (3H)yohimbine could be resolved into high and low affinity components, with Ki values of 3.7 and 84 nM, respectively. PIC had minimal agonist activity in inhibiting adenylate cyclase in platelet membranes, but it potentiated platelet aggregation induced by ADP with an EC50 of 1.5 microM. PIC also inhibited epinephrine-induced aggregation, with an IC50 of 5.1 microM. Thus, PIC behaves as a partial agonist in a human platelet aggregation assay. (125I)PIC binds to the alpha 2B-AR in NG-10815 cell membranes with a Kd of 0.5 +/- 0.1 nM.« less

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

Jalas, S.; Dornmair, I.; Lehe, R.

Particle in Cell (PIC) simulations are a widely used tool for the investigation of both laser- and beam-driven plasma acceleration. It is a known issue that the beam quality can be artificially degraded by numerical Cherenkov radiation (NCR) resulting primarily from an incorrectly modeled dispersion relation. Pseudo-spectral solvers featuring infinite order stencils can strongly reduce NCR - or even suppress it - and are therefore well suited to correctly model the beam properties. For efficient parallelization of the PIC algorithm, however, localized solvers are inevitable. Arbitrary order pseudo-spectral methods provide this needed locality. Yet, these methods can again be pronemore » to NCR. Here in this paper, we show that acceptably low solver orders are sufficient to correctly model the physics of interest, while allowing for parallel computation by domain decomposition.« less

Effects of supplemental nanoparticle trivalent chromium on the nutrient utilization, growth performance and serum traits of broilers.

PubMed

Lin, Y C; Huang, J T; Li, M Z; Cheng, C Y; Lien, T F

2015-02-01

The aim of this study was to investigate the effect of dietary supplementation of nanoparticle trivalent chromium on nutrient utilization, growth performance and serum traits of broilers. This study included two trials. In trial 1, 32 three-week-old broilers were divided into four groups: the control, chromium chloride (CrCl3), chromium picolinate (CrPic) and nanoparticle chromium picolinate (NanoCrPic). Chromium was added at a 1200 μg/kg level to evaluate the nutrient and chromium utilization. In trial 2, 160 one-day-old broilers were randomly divided into four groups as in trial 1, with four replicates. The results of trial 1 indicated that the chromium utilization is as follows: NanoCrPic > CrPic > CrCl3 and control groups, with significant differences between groups (p < 0.05). Crude fat utilization in CrCl3 group was lower than in that the control group (p < 0.05). The results of trial 2 indicated that feed intake of 4-5 weeks showed better result in the CrCl3 group than that in the CrPic group (p < 0.05). The results of serum traits indicated that the LDL-cholesterol in the NanoCrPic groups was lower than that in the CrPic group (p < 0.05). The NanoCrpic and CrPic groups showed significantly increased serum chromium concentration when compared with the control and CrCl3 groups; the triglyceride level in the CrCl3 group was lower than that in the CrPic group (p < 0.05). This study concluded that compared with CrPic, NanoCrpic supplementation could increase chromium utilization and lower the serum LDL-cholesterol of broilers. Journal of Animal Physiology and Animal Nutrition © 2014 Blackwell Verlag GmbH.

Positioning irrigation of contrast cystography for diagnosis of occult vesicoureteric reflux: association with technetium-99m dimercaptosuccinic acid scans.

PubMed

Berger, Christoph; Becker, Tanja; Koen, Mark; Zeino, Mazen; Fitz, Friedrich; Beheshti, Mohsen; Wolf-Kohlmeier, Iris; Haim, Silke; Riccabona, Marcus

2013-12-01

Positioning irrigation of contrast (PIC) cystography identifies occult or PIC vesicoureteral reflux (PIC-VUR) in children with recurrent febrile urinary tract infections (UTI) but no vesicoureteric reflux (VUR) on standard voiding cystourethrogram (VCUG). We sought to identify the relationship between PIC-VUR and renal scarring in technetium-99m dimercaptosuccinic acid (DMSA) scans. We retrospectively analysed PIC cystograms and DMSA scans for 154 kidneys in 81 children (65 girls; 16 boys; median age, 4.7 years; range, 0.9-15.2). Renal scarring was graded on a scale of 0-3. DMSA scans were pathologic in 66 patients (81%). Children had experienced mean 3.8 febrile UTI (range 1-25). Forty-seven (58%) children had a history of reflux, including 15 (19%) with previous anti-reflux operations. Indications for PIC cystography were recurrence of febrile UTI after either bilateral negative VCUG (66 children) or unilateral VUR (15 children) with contralateral/bilateral scarring or reflux that had changed sides in subsequent VCUGs. PIC-VUR was bilateral in 63, unilateral in 12, and absent in 6 children. Statistically significant associations between PIC-VUR grade and severity of renal scarring were identified in inter-individual (n = 77, p = 0.017) and intra-individual (refluxing vs. nonrefluxing kidney; n = 12, p = 0.008) analyses. After excluding patients with history of VUR, statistical significance was maintained in inter-individual analysis (n = 49; p = 0.018). The data suggest an association between PIC-VUR and severity of renal scarring, and legitimise the use of PIC cystography in children with renal scarring due to recurrent febrile UTI but negative findings on VCUG. Copyright © 2012 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

Quantification of Poly(I:C)-Mediated Protection against Genital Herpes Simplex Virus Type 2 Infection

PubMed Central

Herbst-Kralovetz, Melissa M.; Pyles, Richard B.

2006-01-01

Alternative strategies for controlling the growing herpes simplex virus type 2 (HSV-2) epidemic are needed. A novel class of immunomodulatory microbicides has shown promise as antiherpetics, including intravaginally applied CpG-containing oligodeoxynucleotides that stimulate toll-like receptor 9 (TLR9). In the current study, we quantified protection against experimental genital HSV-2 infection provided by an alternative nucleic acid-based TLR agonist, polyinosine-poly(C) (PIC) (TLR3 agonist). Using a protection quantification paradigm, groups of mice were PIC treated and then subdivided into groups challenged with escalating doses of HSV-2. Using this paradigm, a temporal window of PIC efficacy for single applications was defined as 1 day prior to (prophylactic) through 4 h after (therapeutic) viral challenge. PIC treatment within this window protected against 10-fold-higher HSV-2 challenges, as indicated by increased 50% infectious dose values relative to those for vehicle-treated controls. Disease resolution and survival were significantly enhanced by repetitive PIC doses. Using optimal PIC regimens, cytokine induction was evaluated in murine vaginal lavages and in human vaginal epithelial cells. Similar induction patterns were observed, with kinetics that explained the limited durability of PIC-afforded protection. Daily PIC delivery courses did not generate sustained cytokine levels in murine vaginal fluids that would be indicative of local immunotoxicity. No evidence of immunotoxicity was observed in selected organs that were analyzed following repetitive vaginal PIC doses. Animal and in vitro data indicate that PIC may prove to be a valuable preventative microbicide and/or therapeutic agent against genital herpes by increasing resistance to HSV-2 and enhancing disease resolution following a failure of prevention. PMID:17005677

Stapes Displacement and Intracochlear Pressure in Response to Very High Level, Low Frequency Sounds

PubMed Central

Greene, Nathaniel T.; Jenkins, Herman A.; Tollin, Daniel J.; Easter, James R.

2018-01-01

The stapes is held in the oval window by the stapedial annular ligament (SAL), which restricts total peak-to-peak displacement of the stapes. Previous studies have suggested that for moderate (< 130 dB SPL) sound levels intracochlear pressure (PIC), measured at the base of the cochlea far from the basilar membrane, increases directly proportionally with stapes displacement (DStap), thus a current model of impulse noise exposure (the Auditory Hazard Assessment Algorithm for Humans, or AHAAH) predicts that peak PIC will vary linearly with DStap up to some saturation point. However, no direct tests of DStap, or of the relationship with PIC during such motion, have been performed during acoustic stimulation of the human ear. In order to examine the relationship between DStap and PIC to very high level sounds, measurements of DStap and PIC were made in cadaveric human temporal bones. Specimens were prepared by mastoidectomy and extended facial recess to expose the ossicular chain. Measurements of PIC were made in scala vestibuli (PSV) and scala tympani (PST), along with the SPL in the external auditory canal (PEAC), concurrently with laser Doppler vibrometry (LDV) measurements of stapes velocity (VStap). Stimuli were moderate (~100 dB SPL) to very high level (up to ~170 dB SPL), low frequency tones (20–2560 Hz). Both DStap and PSV increased proportionally with sound pressure level in the ear canal up to approximately ~150 dB SPL, above which both DStap and PSV showed a distinct deviation from proportionality with PEAC. Both DStap and PSV approached saturation: DStap at a value exceeding 150 μm, which is substantially higher than has been reported for small mammals, while PSV showed substantial frequency dependence in the saturation point. The relationship between PSV and DStap remained constant, and cochlear input impedance did not vary across the levels tested, consistent with prior measurements at lower sound levels. These results suggest that PSV sound pressure holds constant relationship with DStap, described by the cochlear input impedance, at these, but perhaps not higher, stimulation levels. Additionally, these results indicate that the AHAAH model, which was developed using results from small animals, underestimates the sound pressure levels in the cochlea in response to high level sound stimulation, and must be revised. PMID:28189837

The Danish version of the questionnaire on pain communication: preliminary validation in cancer patients.

PubMed

Jacobsen, R; Møldrup, C; Christrup, L; Sjøgren, P; Hansen, O B

2009-07-01

The modified version of the patients' Perceived Involvement in Care Scale (M-PICS) is a tool designed to assess cancer patients' perceptions of patient-health care provider pain communication process. The objective of this study was to examine the psychometric properties of the shortened Danish version of the M-PICS (SDM-PICS). The validated English version of the M-PICS was translated into Danish following the repeated back-translation procedure. Cancer patients were recruited for the study from specialized pain management facilities. Thirty-three patients responded to the SDM-PICS, Danish Barriers Questionnaire II, Hospital Anxiety and Depression Scale, and Brief Pain Inventory Pain Severity Scale. A factor analysis of the SDM-PICS resulted in two factors: Factor one, patient information, consisted of four items assessing the extent to which the patient shared information with his/her health care provider, and Factor two, health care provider information, consisted of four items measuring the degree to which a health care provider was perceived as the one who shares information. Two separate items addressed the perceived level of information exchange between the patient and the health care provider. The SDM-PICS total had an internal consistency of 0.88. The SDM-PICS scores were positively related to pain relief and inversely related to the measures of cognitive pain management barriers, anxiety, and reported pain levels. The SDM-PICS seems to be a reliable and valid measure of perceived patient-health care provider communication in the context of cancer pain.

Investigation of plasma-surface interaction effects on pulsed electrostatic manipulation for reentry blackout alleviation

NASA Astrophysics Data System (ADS)

Krishnamoorthy, S.; Close, S.

2017-03-01

The reentry blackout phenomenon affects most spacecraft entering a dense planetary atmosphere from space, due to the presence of a plasma layer that surrounds the spacecraft. This plasma layer is created by ionization of ambient air due to shock and frictional heating, and in some cases is further enhanced due to contamination by ablation products. This layer causes a strong attenuation of incoming and outgoing electromagnetic waves including those used for command and control, communication and telemetry over a period referred to as the ‘blackout period’. The blackout period may last up to several minutes and is a major contributor to the landing error ellipse at best, and a serious safety hazard in the worst case, especially in the context of human spaceflight. In this work, we present a possible method for alleviation of reentry blackout using electronegative DC pulses applied from insulated electrodes on the reentry vehicle’s surface. We study the reentry plasma’s interaction with a DC pulse using a particle-in-cell (PIC) model. Detailed models of plasma-insulator interaction are included in our simulations. The absorption and scattering of ions and electrons at the plasma-dielectric interface are taken into account. Secondary emission from the insulating surface is also considered, and its implications on various design issues is studied. Furthermore, we explore the effect of changing the applied voltage and the impact of surface physics on the creation and stabilization of communication windows. The primary aim of this analysis is to examine the possibility of restoring L- and S-band communication from the spacecraft to a ground station. Our results provide insight into the effect of key design variables on the response of the plasma to the applied voltage pulse. Simulations show the creation of pockets where electron density in the plasma layer is reduced three orders of magnitude or more in the vicinity of the electrodes. These pockets extend to distances up to three times the electrode length normal to the vehicle surface. Based on our results, we postulate that pulsed electrostatic manipulation (PEM) may be a viable candidate for reentry blackout alleviation in the future.

Simulations of Solar Wind Plasma Flow Around a Simple Solar Sail

NASA Technical Reports Server (NTRS)

Garrett, Henry B.; Wang, Joseph

2004-01-01

In recent years, a number of solar sail missions of various designs and sizes have been proposed (e.g., Geostorm). Of importance to these missions is the interaction between the ambient solar wind plasma environment and the sail. Assuming a typical 1 AU solar wind environment of 400 km/s velocity, 3.5 cu cm density, ion temperature of approx.10 eV, electron temperature of 40 eV, and an ambient magnetic field strength of 10(exp -4) G, a first order estimate of the plasma interaction with square solar sails on the order of the sizes being considered for a Geostorm mission (50 m x 50 m and 75 m x 75 m corresponding to approx.2 and approx.3 times the Debye length in the plasma) is carried out. First, a crude current balance for the sail surface immersed in the plasma environment and in sunlight was used to estimate the surface potential of the model sails. This gave surface potentials of approx.10 V positive relative to the solar wind plasma. A 3-D, Electrostatic Particle-in-Cell (PIC) code was then used to simulate the solar wind flowing around the solar sail. It is assumed in the code that the solar wind protons can be treated as particles while the electrons follow a Boltzmann distribution. Next, the electric field and particle trajectories are solved self-consistently to give the proton flow field, the electrostatic field around the sail, and the plasma density in 3-D. The model sail was found to be surrounded by a plasma sheath within which the potential is positive compared to the ambient plasma and followed by a separate plasma wake which is negative relative to the plasma. This structure departs dramatically from a negatively charged plate such as might be found in the Earth s ionosphere on the night side where both the plate and its negative wake are contiguous. The implications of these findings are discussed as they apply to the proposed Geostorm solar sail mission.

Electrostatic solitary waves in current layers: from Cluster observations during a super-substorm to beam experiments at the LAPD

NASA Astrophysics Data System (ADS)

Pickett, J. S.; Chen, L.-J.; Santolík, O.; Grimald, S.; Lavraud, B.; Verkhoglyadova, O. P.; Tsurutani, B. T.; Lefebvre, B.; Fazakerley, A.; Lakhina, G. S.; Ghosh, S. S.; Grison, B.; Décréau, P. M. E.; Gurnett, D. A.; Torbert, R.; Cornilleau-Wehrlin, N.; Dandouras, I.; Lucek, E.

2009-06-01

Electrostatic Solitary Waves (ESWs) have been observed by several spacecraft in the current layers of Earth's magnetosphere since 1982. ESWs are manifested as isolated pulses (one wave period) in the high time resolution waveform data obtained on these spacecraft. They are thus nonlinear structures generated out of nonlinear instabilities and processes. We report the first observations of ESWs associated with the onset of a super-substorm that occurred on 24 August 2005 while the Cluster spacecraft were located in the magnetotail at around 18-19 RE and moving northward from the plasma sheet to the lobes. These ESWs were detected in the waveform data of the WBD plasma wave receiver on three of the Cluster spacecraft. The majority of the ESWs were detected about 5 min after the super-substorm onset during which time 1) the PEACE electron instrument detected significant field-aligned electron fluxes from a few 100 eV to 3.5 keV, 2) the EDI instrument detected bursts of field-aligned electron currents, 3) the FGM instrument detected substantial magnetic fluctuations and the presence of Alfvén waves, 4) the STAFF experiment detected broadband electric and magnetic waves, ion cyclotron waves and whistler mode waves, and 5) CIS detected nearly comparable densities of H+ and O+ ions and a large tailward H+ velocity. We compare the characteristics of the ESWs observed during this event to those created in the laboratory at the University of California-Los Angeles Plasma Device (LAPD) with an electron beam. We find that the time durations of both space and LAPD ESWs are only slightly larger than the respective local electron plasma periods, indicating that electron, and not ion, dynamics are responsible for generation of the ESWs. We have discussed possible mechanisms for generating the ESWs in space, including the beam and kinetic Buneman type instabilities and the acoustic instabilities. Future studies will examine these mechanisms in more detail using the space measurements as inputs to models, and better relate the ESW space measurements to the laboratory through PIC code models.

Influence of RNA Strand Rigidity on Polyion Complex Formation with Block Catiomers.

PubMed

Hayashi, Kotaro; Chaya, Hiroyuki; Fukushima, Shigeto; Watanabe, Sumiyo; Takemoto, Hiroyasu; Osada, Kensuke; Nishiyama, Nobuhiro; Miyata, Kanjiro; Kataoka, Kazunori

2016-03-01

Polyion complexes (b-PICs) are prepared by mixing single- or double-stranded oligo RNA (aniomer) with poly(ethylene glycol)-b-poly(L-lysine) (PEG-PLL) (block catiomer) to clarify the effect of aniomer chain rigidity on association behaviors at varying concentrations. Here, a 21-mer single-stranded RNA (ssRNA) (persistence length: 1.0 nm) and a 21-mer double-stranded RNA (small interfering RNA, siRNA) (persistence length: 62 nm) are compared. Both oligo RNAs form a minimal charge-neutralized ionomer pair with a single PEG-PLL chain, termed unit b-PIC (uPIC), at low concentrations (<≈ 0.01 mg mL(-1)). Above the critical association concentration (≈ 0.01 mg mL(-1)), ssRNA b-PICs form secondary associates, PIC micelles, with sizes up to 30-70 nm, while no such multimolecular assembly is observed for siRNA b-PICs. The entropy gain associated with the formation of a segregated PIC phase in the multimolecular PIC micelles may not be large enough for rigid siRNA strands to compensate with appreciably high steric repulsion derived from PEG chains. Chain rigidity appears to be a critical parameter in polyion complex association. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Restoration of Akt activity by the bisperoxovanadium compound bpV(pic) attenuates hippocampal apoptosis in experimental neonatal pneumococcal meningitis

PubMed Central

Sury, Matthias D; Vorlet-Fawer, Lorianne; Agarinis, Claudia; Yousefi, Shida; Grandgirard, Denis; Leib, Stephen L; Christen, Stephan

2010-01-01

Pneumococcal meningitis causes apoptosis of developing neurons in the dentate gyrus of the hippocampus. The death of these cells is accompanied with long-term learning and memory deficits in meningitis survivors. Here, we studied the role of the PI3K/Akt (protein kinase B) survival pathway in hippocampal apoptosis in a well-characterized infant rat model of pneumococcal meningitis. Meningitis was accompanied by a significant decrease of the PI3K product phosphatidylinositol 3,4,5-triphosphate (PIP3) and of phosphorylated (i.e., activated) Akt in the hippocampus. At the cellular level, phosphorylated Akt was decreased in both the granular layer and the subgranular zone of the dentate gyrus, the region where the developing neurons undergo apoptosis. Protein levels and activity of PTEN, the major antagonist of PI3K, were unaltered by infection, suggesting that the observed decrease in PIP3 and Akt phosphorylation is a result of decreased PI3K signaling. Treatment with the PTEN inhibitor bpV(pic) restored Akt activity and significantly attenuated hippocampal apoptosis. Co-treatment with the specific PI3K inhibitor LY294002 reversed restoration of Akt activity and attenuation of hippocampal apoptosis, while it had no significant effect on these parameters on its own. These results indicate that the inhibitory effect of bpV(pic) on apoptosis was mediated by PI3K-dependent activation of Akt, strongly suggesting that bpV(pic) acted on PTEN. Treatment with bpV(pic) also partially inhibited the concentration of bacteria and cytokines in the CSF, but this effect was not reversed by LY294002, indicating that the effect of bpV(pic) on apoptosis was independent of its effect on CSF bacterial burden and cytokine levels. These results indicate that the PI3K/Akt pathway plays an important role in the death and survival of developing hippocampal neurons during the acute phase of pneumococcal meningitis. PMID:20875857

ACTIVATION OF COMMON ANTIVIRAL PATHWAYS CAN POTENTIATE INFLAMMATORY RESPONSES TO SEPTIC SHOCK

PubMed Central

Doughty, Lesley A.; Carlton, Stacey; Galen, Benjamin; Cooma-Ramberan, Indranie; Chung, Chung-Shiang; Ayala, Alfred

2006-01-01

Induction of the antiviral cytokine interferon α/β (IFN-α/β) is common in many viral infections. The impact of ongoing antiviral responses on subsequent bacterial infection is not well understood. In human disease, bacterial superinfection complicating a viral infection can result in significant morbidity and mortality. We injected mice with polyinosinic-polycytidylic (PIC) acid, a TLR3 ligand and known IFN-α/β inducer as well as nuclear factor κB (NF-κB) activator to simulate very early antiviral pathways. We then challenged mice with an in vivo septic shock model characterized by slowly evolving bacterial infection to simulate bacterial superinfection early during a viral infection. Our data demonstrated robust induction of IFN-α in serum within 24 h of PIC injection with IFN-α/β–dependent major histocompatibility antigen class II up-regulation on peritoneal macrophages. PIC pretreatment before septic shock resulted in augmented tumor necrosis factor alpha and interleukins 6 and 10 and heightened lethality compared with septic shock alone. Intact IFN-α/β signaling was necessary for augmentation of the inflammatory response to in vivo septic shock and to both TLR2 and TLR4 agonists in vitro. To assess the NF-κB contribution to PIC-modulated inflammatory responses to septic shock, we treated with parthenolide an NF-κB inhibitor before PIC and septic shock. Parthenolide did not inhibit IFN-α induction by PIC. Inhibition of NF-κB by parthenolide did reduce IFN-α–mediated potentiation of the cytokine response and lethality from septic shock. Our data demonstrate that pathways activated early during many viral infections can have a detrimental impact on the outcome of subsequent bacterial infection. These pathways may be critical to understanding the heightened morbidity and mortality from bacterial superinfection after viral infection in human disease. PMID:16878028

On newly and recently recorded species of the genus Lema Fabricius (Coleoptera, Chrysomelidae, Criocerinae) from Taiwan

PubMed Central

Lee, Chi-Feng; Matsumura, Yoko

2013-01-01

Abstract New records of four species (Lema lacertosa Lacordaire, 1845, Lema diversipes Pic, 1921, Lema cyanella (Linnaeus, 1758), Lema trivittata trivittata Say, 1824 and additional information on one recently recorded species (Lema solani Fabricius, 1798) are reported for Taiwan. Lema diversipes Pic, 1921 is removed from synonymy with Lema lacertosa Lacordaire, 1845; both species are redescribed. A lectotype is designated for Lema phungi Pic, 1924. The synonymies of Lema phungi Pic, 1924 and Lema jeanvoinei Pic, 1932 with Lema lacertosa Lacordaire, 1845 are supported. A revised key to the known species in Taiwan is provided. PMID:23653513

Innate Immunity in the Persistent Inflammation, Immunosuppression, and Catabolism Syndrome and Its Implications for Therapy

PubMed Central

Horiguchi, Hiroyuki; Loftus, Tyler J.; Hawkins, Russell B.; Raymond, Steven L.; Stortz, Julie A.; Hollen, McKenzie K.; Weiss, Brett P.; Miller, Elizabeth S.; Bihorac, Azra; Larson, Shawn D.; Mohr, Alicia M.; Brakenridge, Scott C.; Tsujimoto, Hironori; Ueno, Hideki; Moore, Frederick A.; Moldawer, Lyle L.; Efron, Philip A.

2018-01-01

Clinical and technological advances promoting early hemorrhage control and physiologic resuscitation as well as early diagnosis and optimal treatment of sepsis have significantly decreased in-hospital mortality for many critically ill patient populations. However, a substantial proportion of severe trauma and sepsis survivors will develop protracted organ dysfunction termed chronic critical illness (CCI), defined as ≥14 days requiring intensive care unit (ICU) resources with ongoing organ dysfunction. A subset of CCI patients will develop the persistent inflammation, immunosuppression, and catabolism syndrome (PICS), and these individuals are predisposed to a poor quality of life and indolent death. We propose that CCI and PICS after trauma or sepsis are the result of an inappropriate bone marrow response characterized by the generation of dysfunctional myeloid populations at the expense of lympho- and erythropoiesis. This review describes similarities among CCI/PICS phenotypes in sepsis, cancer, and aging and reviews the role of aberrant myelopoiesis in the pathophysiology of CCI and PICS. In addition, we characterize pathogen recognition, the interface between innate and adaptive immune systems, and therapeutic approaches including immune modulators, gut microbiota support, and nutritional and exercise therapy. Finally, we discuss the future of diagnostic and prognostic approaches guided by machine and deep-learning models trained and validated on big data to identify patients for whom these approaches will yield the greatest benefits. A deeper understanding of the pathophysiology of CCI and PICS and continued investigation into novel therapies harbor the potential to improve the current dismal long-term outcomes for critically ill post-injury and post-infection patients. PMID:29670613

Design new P-glycoprotein modulators based on molecular docking and CoMFA study of α, β-unsaturated carbonyl-based compounds and oxime analogs as anticancer agents

NASA Astrophysics Data System (ADS)

Sepehri, Bakhtyar; Ghavami, Raouf

2017-02-01

In this research, molecular docking and CoMFA were used to determine interactions of α, β-unsaturated carbonyl-based compounds and oxime analogs with P-glycoprotein and prediction of their activity. Molecular docking study shown these molecules establish strong Van der Waals interactions with side chain of PHE-332, PHE-728 and PHE-974. Based on the effect of component numbers on squared correlation coefficient for cross validation tests (including leave-one-out and leave-many-out), CoMFA models with five components were built to predict pIC50 of molecules in seven cancer cell lines (including Panc-1 (pancreas cancer cell line), PaCa-2 (pancreatic carcinoma cell line), MCF-7 (breast cancer cell line), A-549 (epithelial), HT-29 (colon cancer cell line), H-460 (lung cancer cell line), PC-3 (prostate cancer cell line)). R2 values for training and test sets were in the range of 0.94-0.97 and 0.84 to 0.92, respectively, and for LOO and LMO cross validation test, q2 values were in the range of 0.75-0.82 and 0.65 to 0.73, respectively. Based on molecular docking results and extracted steric and electrostatic contour maps for CoMFA models, four new molecules with higher activity with respect to the most active compound in data set were designed.

High fidelity 3-dimensional models of beam-electron cloud interactions in circular accelerators

NASA Astrophysics Data System (ADS)

Feiz Zarrin Ghalam, Ali

Electron cloud is a low-density electron profile created inside the vacuum chamber of circular machines with positively charged beams. Electron cloud limits the peak current of the beam and degrades the beams' quality through luminosity degradation, emittance growth and head to tail or bunch to bunch instability. The adverse effects of electron cloud on long-term beam dynamics becomes more and more important as the beams go to higher and higher energies. This problem has become a major concern in many future circular machines design like the Large Hadron Collider (LHC) under construction at European Center for Nuclear Research (CERN). Due to the importance of the problem several simulation models have been developed to model long-term beam-electron cloud interaction. These models are based on "single kick approximation" where the electron cloud is assumed to be concentrated at one thin slab around the ring. While this model is efficient in terms of computational costs, it does not reflect the real physical situation as the forces from electron cloud to the beam are non-linear contrary to this model's assumption. To address the existing codes limitation, in this thesis a new model is developed to continuously model the beam-electron cloud interaction. The code is derived from a 3-D parallel Particle-In-Cell (PIC) model (QuickPIC) originally used for plasma wakefield acceleration research. To make the original model fit into circular machines environment, betatron and synchrotron equations of motions have been added to the code, also the effect of chromaticity, lattice structure have been included. QuickPIC is then benchmarked against one of the codes developed based on single kick approximation (HEAD-TAIL) for the transverse spot size of the beam in CERN-LHC. The growth predicted by QuickPIC is less than the one predicted by HEAD-TAIL. The code is then used to investigate the effect of electron cloud image charges on the long-term beam dynamics, particularly on the transverse tune shift of the beam at CERN Super Proton Synchrotron (SPS) ring. The force from the electron cloud image charges on the beam cancels the force due to cloud compression formed on the beam axis and therefore the tune shift is mainly due to the uniform electron cloud density. (Abstract shortened by UMI.)

Particle-in-cell and global simulations of α to γ transition in atmospheric pressure Penning-dominated capacitive discharges

NASA Astrophysics Data System (ADS)

Kawamura, E.; Lieberman, M. A.; Lichtenberg, A. J.; Chabert, P.; Lazzaroni, C.

2014-06-01

Atmospheric pressure radio-frequency (rf) capacitive micro-discharges are of interest due to emerging applications, especially in the bio-medical field. A previous global model did not consider high-power phenomena such as sheath multiplication, thus limiting its applicability to the lower power range. To overcome this, we use one-dimensional particle-in-cell (PIC) simulations of atmospheric He/0.1% N2 capacitive discharges over a wide range of currents and frequencies to guide the development of a more general global model which is also valid at higher powers. The new model includes sheath multiplication and two classes of electrons: the higher temperature ‘hot’ electrons associated with the sheaths, and the cooler ‘warm’ electrons associated with the bulk. The electric field and the electron power balance are solved analytically to determine the time-varying hot and warm temperatures and the effective rate coefficients. The particle balance equations are integrated numerically to determine the species densities. The model and PIC results are compared, showing reasonable agreement over the range of currents and frequencies studied. They indicate a transition from an α mode at low power characterized by relatively high electron temperature Te with a near uniform profile to a γ mode at high power with a Te profile strongly depressed in the bulk plasma. The transition is accompanied by an increase in density and a decrease in sheath widths. The current and frequency scalings of the model are confirmed by the PIC simulations.

Particle-In-Cell Modeling For MJ Dense Plasma Focus with Varied Anode Shape

NASA Astrophysics Data System (ADS)

Link, A.; Halvorson, C.; Schmidt, A.; Hagen, E. C.; Rose, D.; Welch, D.

2014-10-01

Megajoule scale dense plasma focus (DPF) Z-pinches with deuterium gas fill are compact devices capable of producing 1012 neutrons per shot but past predictive models of large-scale DPF have not included kinetic effects such as ion beam formation or anomalous resistivity. We report on progress of developing a predictive DPF model by extending our 2D axisymmetric collisional kinetic particle-in-cell (PIC) simulations to the 1 MJ, 2 MA Gemini DPF using the PIC code LSP. These new simulations incorporate electrodes, an external pulsed-power driver circuit, and model the plasma from insulator lift-off through the pinch phase. The simulations were performed using a new hybrid fluid-to-kinetic model transitioning from a fluid description to a fully kinetic PIC description during the run-in phase. Simulations are advanced through the final pinch phase using an adaptive variable time-step to capture the fs and sub-mm scales of the kinetic instabilities involved in the ion beam formation and neutron production. Results will be present on the predicted effects of different anode configurations. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory (LLNL) under Contract DE-AC52-07NA27344 and supported by the Laboratory Directed Research and Development Program (11-ERD-063) and the Computing Grand Challenge program at LLNL. This work supported by Office of Defense Nuclear Nonproliferation Research and Development within U.S. Department of Energy's National Nuclear Security Administration.

Measuring Stability and Security in Iraq

DTIC Science & Technology

2008-12-01

majority of the country. On September 1, 2008, Anbar Province, once an AQI stronghold, transferred to Provincial Iraqi Control ( PIC ). With the...transfer of Babil and Wasit Provinces to PIC in October 2008, the ISF is now in charge of security operations in the majority of Iraq’s 18 provinces... PIC ). Security responsibility for Babil Province was handed over to the GoI on October 23, 2008, and Wasit Province transitioned to PIC on October

Intracellular pressure is a motive force for cell motion in Amoeba proteus.

PubMed

Yanai, M; Kenyon, C M; Butler, J P; Macklem, P T; Kelly, S M

1996-01-01

The cortical filament layer of free-living amoebae contains concentrated actomyosin, suggesting that it can contract and produce an internal hydrostatic pressure. We report here on direct and dynamic intracellular pressure (P(ic)) measurements in Amoeba proteus made using the servo-null technique. In resting apolar A. proteus, P(ic) increased while the cells remained immobile and at apparently constant volume. P(ic) then decreased approximately coincident with pseudopod formation. There was a positive correlation between P(ic) at the onset of movement and the rate of pseudopod formation. These results are the first direct evidence that hydrostatic pressure may be a motive force for cell motion. We postulate that contractile elements in the amoeba's cortical layer contract and increase P(ic) and that this P(ic) is utilized to overcome the viscous flow resistance of the intracellular contents during pseudopod formation.

Plasma sheet low-entropy flow channels and dipolarization fronts from macro to micro scales: Global MHD and PIC simulations

NASA Astrophysics Data System (ADS)

Merkin, V. G.; Wiltberger, M. J.; Sitnov, M. I.; Lyon, J.

2016-12-01

Observations show that much of plasma and magnetic flux transport in the magnetotail occurs in the form of discrete activations such as bursty bulk flows (BBFs). These flow structures are typically associated with strong peaks of the Z-component of the magnetic field normal to the magnetotail current sheet (dipolarization fronts, DFs), as well as density and flux tube entropy depletions also called plasma bubbles. Extensive observational analysis of these structures has been carried out using data from Geotail spacecraft and more recently from Cluster, THEMIS, and MMS multi-probe missions. Global magnetohydrodynamic (MHD) simulations of the magnetosphere reveal similar plasma sheet flow bursts, in agreement with regional MHD and particle-in-cell (PIC) models. We present results of high-resolution simulations using the Lyon-Fedder-Mobarry (LFM) global MHD model and analyze the properties of the bursty flows including their structure and evolution as they propagate from the mid-tail region into the inner magnetosphere. We highlight similarities and differences with the corresponding observations and discuss comparative properties of plasma bubbles and DFs in our global MHD simulations with their counterparts in 3D PIC simulations.

Psychophysical experiments on the PicHunter image retrieval system

NASA Astrophysics Data System (ADS)

Papathomas, Thomas V.; Cox, Ingemar J.; Yianilos, Peter N.; Miller, Matt L.; Minka, Thomas P.; Conway, Tiffany E.; Ghosn, Joumana

2001-01-01

Psychophysical experiments were conducted on PicHunter, a content-based image retrieval (CBIR) experimental prototype with the following properties: (1) Based on a model of how users respond, it uses Bayes's rule to predict what target users want, given their actions. (2) It possesses an extremely simple user interface. (3) It employs an entropy- based scheme to improve convergence. (4) It introduces a paradigm for assessing the performance of CBIR systems. Experiments 1-3 studied human judgment of image similarity to obtain data for the model. Experiment 4 studied the importance of using: (a) semantic information, (b) memory of earlier input, and (c) relative and absolute judgments of similarity. Experiment 5 tested an approach that we propose for comparing performances of CBIR systems objectively. Finally, experiment 6 evaluated the most informative display-updating scheme that is based on entropy minimization, and confirmed earlier simulation results. These experiments represent one of the first attempts to quantify CBIR performance based on psychophysical studies, and they provide valuable data for improving CBIR algorithms. Even though they were designed with PicHunter in mind, their results can be applied to any CBIR system and, more generally, to any system that involves judgment of image similarity by humans.

Temporal dynamics of sand dune bidirectional reflectance characteristics for absolute radiometric calibration of optical remote sensing data

NASA Astrophysics Data System (ADS)

Coburn, Craig A.; Logie, Gordon S. J.

2018-01-01

Attempts to use pseudoinvariant calibration sites (PICS) for establishing absolute radiometric calibration of Earth observation (EO) satellites requires high-quality information about the nature of the bidirectional reflectance distribution function (BRDF) of the surfaces used for these calibrations. Past studies have shown that the PICS method is useful for evaluating the trend of sensors over time or for the intercalibration of sensors. The PICS method was not considered until recently for deriving absolute radiometric calibration. This paper presents BRDF data collected by a high-performance portable goniometer system to develop a temporal BRDF model for the Algodones Dunes in California. By sampling the BRDF of the sand surface at similar solar zenith angles to those normally encountered by EO satellites, additional information on the changing nature of the surface can improve models used to provide absolute radiometric correction. The results demonstrated that the BRDF of a reasonably simple sand surface was complex with changes in anisotropy taking place in response to changing solar zenith angles. For the majority of observation and illumination angles, the spectral reflectance anisotropy observed varied between 1% and 5% in patterns that repeat around solar noon.

An alternative model to distribute VO software to WLCG sites based on CernVM-FS: a prototype at PIC Tier1

NASA Astrophysics Data System (ADS)

Lanciotti, E.; Merino, G.; Bria, A.; Blomer, J.

2011-12-01

In a distributed computing model as WLCG the software of experiment specific application software has to be efficiently distributed to any site of the Grid. Application software is currently installed in a shared area of the site visible for all Worker Nodes (WNs) of the site through some protocol (NFS, AFS or other). The software is installed at the site by jobs which run on a privileged node of the computing farm where the shared area is mounted in write mode. This model presents several drawbacks which cause a non-negligible rate of job failure. An alternative model for software distribution based on the CERN Virtual Machine File System (CernVM-FS) has been tried at PIC, the Spanish Tierl site of WLCG. The test bed used and the results are presented in this paper.

Integrated Work Management: PIC, Course 31884

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

Simpson, Lewis Edward

The person-in-charge (PIC) plays a key role in the integrated work management (IWM) process at Los Alamos National Laboratory (LANL, or the Laboratory) because the PIC is assigned responsibility and authority by the responsible line manager (RLM) for the overall validation, coordination, release, execution, and closeout of a work activity in accordance with IWM. This course, Integrated Work Management: PIC (Course 31884), describes the PIC’s IWM roles and responsibilities. This course also discusses IWM requirements that the PIC must meet. For a general overview of the IWM process, see self-study Course 31881, Integrated Work Management: Overview. For instruction on themore » preparer’s role, see self-study Course 31883, Integrated Work Management: Preparer.« less

An energy- and charge-conserving, nonlinearly implicit, electromagnetic 1D-3V Vlasov-Darwin particle-in-cell algorithm

NASA Astrophysics Data System (ADS)

Chen, G.; Chacón, L.

2014-10-01

A recent proof-of-principle study proposes a nonlinear electrostatic implicit particle-in-cell (PIC) algorithm in one dimension (Chen et al., 2011). The algorithm employs a kinetically enslaved Jacobian-free Newton-Krylov (JFNK) method, and conserves energy and charge to numerical round-off. In this study, we generalize the method to electromagnetic simulations in 1D using the Darwin approximation to Maxwell's equations, which avoids radiative noise issues by ordering out the light wave. An implicit, orbit-averaged, time-space-centered finite difference scheme is employed in both the 1D Darwin field equations (in potential form) and the 1D-3V particle orbit equations to produce a discrete system that remains exactly charge- and energy-conserving. Furthermore, enabled by the implicit Darwin equations, exact conservation of the canonical momentum per particle in any ignorable direction is enforced via a suitable scattering rule for the magnetic field. We have developed a simple preconditioner that targets electrostatic waves and skin currents, and allows us to employ time steps O(√{mi /me } c /veT) larger than the explicit CFL. Several 1D numerical experiments demonstrate the accuracy, performance, and conservation properties of the algorithm. In particular, the scheme is shown to be second-order accurate, and CPU speedups of more than three orders of magnitude vs. an explicit Vlasov-Maxwell solver are demonstrated in the "cold" plasma regime (where kλD ≪ 1).

Limiting assumptions in molecular modeling: electrostatics.

PubMed

Marshall, Garland R

2013-02-01

Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

2009-03-14

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.; Knepley, Matthew G.; Anitescu, Mihai

2009-03-01

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

PubMed Central

Zhou, Y. C.; Holst, Michael; McCammon, J. Andrew

2008-01-01

In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods. PMID:19461946

Effects of chromium picolinate on glucose uptake in insulin-resistant 3T3-L1 adipocytes involve activation of p38 MAPK.

PubMed

Wang, Yi-qun; Yao, Ming-hui

2009-12-01

Chromium picolinate (CrPic) has been discovered as a supplemental or alternative medication for type 2 diabetes, but its mechanism of action is not well understood. The purpose of this study was to explore the possible anti-diabetic mechanisms of CrPic in insulin-resistant 3T3-L1 adipocytes; the insulin resistance was induced by treatment with high glucose and insulin for 24 h. The effects of CrPic on glucose metabolism and the glucose uptake-inducing activity of CrPic were investigated. Meanwhile, the effects of CrPic on glucose transporter 4 (GLUT4) translocation were visualized by immonofluorescence microscopy. In addition, its effects on insulin signaling pathways and mitogen-activated protein kinase (MAPK) signaling cascades were assessed by immunoblotting analysis and real-time PCR. The results showed that CrPic induced glucose metabolism and uptake, as well as GLUT4 translocation to plasma membrane (PM) in both control and insulin-resistant 3T3-L1 adipocytes without any changes in insulin receptor beta (IR-beta), protein kinase B (AKt), c-Cbl, extracellular signal-regulated kinase (ERK), c-Jun phosphorylation and c-Cbl-associated protein (CAP) mRNA levels. Interestingly, CrPic was able to increase the basal and insulin-stimulated levels of p38 MAPK activation in the control and insulin-resistant cells. Pretreatment with the specific p38 MAPK inhibitor SB203580 partially inhibited the CrPic-induced glucose transport, but CrPic-activated translocation of GLUT4 was not inhibited by SB203580. This study provides an experimental evidence of the effects of CrPic on glucose uptake through the activation of p38 MAPK and it is independent of the effect on GLUT4 translocation. The findings also suggest exciting new insights into the role of p38 MAPK in glucose uptake and GLUT4 translocation.

Clinical studies on chromium picolinate supplementation in diabetes mellitus--a review.

PubMed

Broadhurst, C Leigh; Domenico, Philip

2006-12-01

Chromium (Cr) picolinate (CrPic) is a widely used nutritional supplement for optimal insulin function. A relationship among Cr status, diabetes, and associated pathologies has been established. Virtually all trials using CrPic supplementation for subjects with diabetes have demonstrated beneficial effects. Thirteen of 15 clinical studies (including 11 randomized, controlled studies) involving a total of 1,690 subjects (1,505 in CrPic group) reported significant improvement in at least one outcome of glycemic control. All 15 studies showed salutary effects in at least one parameter of diabetes management, including dyslipidemia. Positive outcomes from CrPic supplementation included reduced blood glucose, insulin, cholesterol, and triglyceride levels and reduced requirements for hypoglycemic medication. The greater bioavailability of CrPic compared with other forms of Cr (e.g., niacin-bound Cr or CrCl(3)) may explain its comparatively superior efficacy in glycemic and lipidemic control. The pooled data from studies using CrPic supplementation for type 2 diabetes mellitus subjects show substantial reductions in hyperglycemia and hyperinsulinemia, which equate to a reduced risk for disease complications. Collectively, the data support the safety and therapeutic value of CrPic for the management of cholesterolemia and hyperglycemia in subjects with diabetes.

Ion Thermalization and Electron Heating across Quasi-Perpendicular Shocks Observed by the MMS Mission

NASA Astrophysics Data System (ADS)

Chen, L.-J.; Wilson, L. B., III; Wang, S.; Bessho, N.; Viñas, A. F.-; Lai, H.; Russell, C. T.; Schwartz, S. J.; Hesse, M.; Moore, T. E.; Burch, J. L.; Gershman, D. J.; Giles, B. L.; Torbert, R. B.; Ergun, R. E.; Dorelli, J.; Strangeway, R. J.; Paterson, W. R.; Lavraud, B.; Khotyaintsev, Yu. V.

2017-12-01

Collisionless shocks often involve intense plasma heating in space and astrophysical systems. Despite decades of research, a number of key questions concerning electron and ion heating across collisionless shocks remain unanswered. We 'image' 20 supercritical quasi-perpendicular bow shocks encountered by the Magnetospheric Multiscale (MMS) spacecraft with electron and ion distribution functions to address how ions are thermalized and how electrons are heated. The continuous burst measurements of 3D plasma distribution functions from MMS reveal that the primary thermalization phase of ions occurs concurrently with the main temperature increase of electrons as well as large-amplitude wave fluctuations. Approaching the shock from upstream, the ion temperature (Ti) increases due to the reflected ions joining the incoming solar wind population, as recognized by prior studies, and the increase of Ti precedes that of the electrons. Thermalization in the form of merging between the decelerated solar wind ions and the reflected component often results in a decrease in Ti. In most cases, the Ti decrease is followed by a gradual increase further downstream. Anisotropic, energy-dependent, and/or nongyrotropic electron energization are observed in association with large electric field fluctuations in the main electron temperature (Te) gradient, motivating a renewed scrutiny of the effects from the electrostatic cross-shock potential and wave fluctuations on electron heating. Particle-in-cell (PIC) simulations are carried out to assist interpretations of the MMS observations. We assess the roles of instabilities and the cross-shock potential in thermalizing ions and heating electrons based on the MMS measurements and PIC simulation results. Challenges will be posted for future computational studies and laboratory experiments on collisionless shocks.

Ion Thermalization and Electron Heating across Quasi-Perpendicular Shocks Observed by the MMS Mission

NASA Astrophysics Data System (ADS)

Chen, L. J.; Wilson, L. B., III; Wang, S.; Bessho, N.; Figueroa-Vinas, A.; Lai, H.; Russell, C. T.; Schwartz, S. J.; Hesse, M.; Moore, T. E.; Burch, J.; Gershman, D. J.; Giles, B. L.; Torbert, R. B.; Ergun, R.; Dorelli, J.; Strangeway, R. J.; Paterson, W. R.; Lavraud, B.; Khotyaintsev, Y. V.

2017-12-01

Collisionless shocks often involve intense plasma heating in space and astrophysical systems. Despite decades of research, a number of key questions concerning electron and ion heating across collisionless shocks remain unanswered. We `image' 20 supercritical quasi-perpendicular bow shocks encountered by the Magnetospheric Multiscale (MMS) spacecraft with electron and ion distribution functions to address how ions are thermalized and how electrons are heated. The continuous burst measurements of 3D plasma distribution functions from MMS reveal that the primary thermalization phase of ions occurs concurrently with the main temperature increase of electrons as well as large-amplitude wave fluctuations. Approaching the shock from upstream, the ion temperature (Ti) increases due to the reflected ions joining the incoming solar wind population, as recognized by prior studies, and the increase of Ti precedes that of the electrons. Thermalization in the form of merging between the decelerated solar wind ions and the reflected component often results in a decrease in Ti. In most cases, the Ti decrease is followed by a gradual increase further downstream. Anisotropic, energy-dependent, and/or nongyrotropic electron energization are observed in association with large electric field fluctuations in the main electron temperature (Te) gradient, motivating a renewed scrutiny of the effects from the electrostatic cross-shock potential and wave fluctuations on electron heating. Particle-in-cell (PIC) simulations are carried out to assist interpretations of the MMS observations. We assess the roles of instabilities and the cross-shock potential in thermalizing ions and heating electrons based on the MMS measurements and PIC simulation results. Challenges will be posted for future computational studies and laboratory experiments on collisionless shocks.

Quasi-monoenergetic proton beam from a proton-layer embedded metal foil irradiated by an intense laser pulse

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

Kim, Kyung Nam; Lee, Kitae, E-mail: klee@kaeri.re.kr; Kumar, Manoj

A target structure, ion-layer embedded foil (ILEF) is proposed for producing a quasi-monoenergetic proton beam by utilizing a bulk electrostatic field, which is generated by irradiating the target with an ultra-intense laser pulse, inside the plasma. Compared with the case of a single metal foil in which the proton layer is initially present on the surface, in the ILEF target, the proton layer is initially located inside a metal foil. A two-dimensional particle-in-cell (PIC) simulation shows that the target generates a proton beam with a narrow energy spread. With a laser intensity of 2 × 10{sup 19 }W/cm{sup 2}, a 22-MeV proton beammore » with an energy spread of 8% at the full-width-half-maximum (FWHM) is obtained when the proton layer is located at 0.4 μm inside the rear surface of a 2.4 μm-thick copper foil. When the proton layer moves toward the front side, a proton beam with a flat-top energy distribution ranging from 15 MeV to 35 MeV is obtained. Further, with a higher laser intensity of 10{sup 21 }W/cm{sup 2}, a proton beam with the maximum energy of 345 MeV and FWHM energy spread of 7.2% is obtained. The analysis of the PIC simulation with an aid of a fluid analysis shows that the spectrum is affected by the initial position of the proton layer, its initial spread during the formation of the sheath field, and the space charge effect.« less

Laser-driven relativistic electron beam interaction with solid dielectric

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

Sarkisov, G. S.; Ivanov, V. V.; Leblanc, P.

2012-07-30

The multi-frames shadowgraphy, interferometry and polarimetry diagnostics with sub-ps time resolution were used for an investigation of ionization wave dynamics inside a glass target induced by laser-driven relativistic electron beam. Experiments were done using the 50 TW Leopard laser at the UNR. For a laser flux of {approx}2 Multiplication-Sign 10{sup 18}W/cm{sup 2} a hemispherical ionization wave propagates at c/3. The maximum of the electron density inside the glass target is {approx}2 Multiplication-Sign 10{sup 19}cm{sup -3}. Magnetic and electric fields are less than {approx}15 kG and {approx}1 MV/cm, respectively. The electron temperature has a maximum of {approx}0.5 eV. 2D interference phasemore » shift shows the 'fountain effect' of electron beam. The very low ionization inside glass target {approx}0.1% suggests a fast recombination at the sub-ps time scale. 2D PIC-simulations demonstrate radial spreading of fast electrons by self-consistent electrostatic fields.« less

Multiparticle collision simulations of two-dimensional one-component plasmas: Anomalous transport and dimensional crossovers

NASA Astrophysics Data System (ADS)

Di Cintio, Pierfrancesco; Livi, Roberto; Lepri, Stefano; Ciraolo, Guido

2017-04-01

By means of hybrid multiparticle collsion-particle-in-cell (MPC-PIC) simulations we study the dynamical scaling of energy and density correlations at equilibrium in moderately coupled two-dimensional (2D) and quasi-one-dimensional (1D) plasmas. We find that the predictions of nonlinear fluctuating hydrodynamics for the structure factors of density and energy fluctuations in 1D systems with three global conservation laws hold true also for 2D systems that are more extended along one of the two spatial dimensions. Moreover, from the analysis of the equilibrium energy correlators and density structure factors of both 1D and 2D neutral plasmas, we find that neglecting the contribution of the fluctuations of the vanishing self-consistent electrostatic fields overestimates the interval of frequencies over which the anomalous transport is observed. Such violations of the expected scaling in the currents correlation are found in different regimes, hindering the observation of the asymptotic scaling predicted by the theory.

A probabilistic assessment of calcium carbonate export and dissolution in the modern ocean

NASA Astrophysics Data System (ADS)

Battaglia, G.; Steinacher, M.; Joos, F.

2015-12-01

The marine cycle of calcium carbonate (CaCO3) is an important element of the carbon cycle and co-governs the distribution of carbon and alkalinity within the ocean. However, CaCO3 fluxes and mechanisms governing CaCO3 dissolution are highly uncertain. We present an observationally-constrained, probabilistic assessment of the global and regional CaCO3 budgets. Parameters governing pelagic CaCO3 export fluxes and dissolution rates are sampled using a Latin-Hypercube scheme to construct a 1000 member ensemble with the Bern3D ocean model. Ensemble results are constrained by comparing simulated and observation-based fields of excess dissolved calcium carbonate (TA*). The minerals calcite and aragonite are modelled explicitly and ocean-sediment fluxes are considered. For local dissolution rates either a strong, a weak or no dependency on CaCO3 saturation is assumed. Median (68 % confidence interval) global CaCO3 export is 0.82 (0.67-0.98) Gt PIC yr-1, within the lower half of previously published estimates (0.4-1.8 Gt PIC yr-1). The spatial pattern of CaCO3 export is broadly consistent with earlier assessments. Export is large in the Southern Ocean, the tropical Indo-Pacific, the northern Pacific and relatively small in the Atlantic. Dissolution within the 200 to 1500 m depth range (0.33; 0.26-0.40 Gt PIC yr-1) is substantially lower than inferred from the TA*-CFC age method (1 ± 0.5 Gt PIC yr-1). The latter estimate is likely biased high as the TA*-CFC method neglects transport. The constrained results are robust across a range of diapycnal mixing coefficients and, thus, ocean circulation strengths. Modelled ocean circulation and transport time scales for the different setups were further evaluated with CFC11 and radiocarbon observations. Parameters and mechanisms governing dissolution are hardly constrained by either the TA* data or the current compilation of CaCO3 flux measurements such that model realisations with and without saturation-dependent dissolution achieve skill. We suggest to apply saturation-independent dissolution rates in Earth System Models to minimise computational costs.

Effects of dietary chromium picolinate and peppermint essential oil on growth performance and blood biochemical parameters of broiler chicks reared under heat stress conditions

NASA Astrophysics Data System (ADS)

Akbari, Mohsen; Torki, Mehran

2014-08-01

A study was conducted using 240 female day-old broiler chicks to evaluate the effects of dietary chromium picolinate (CrPic), peppermint essential oil (P.mint), or their combination on growth performance and blood biochemical parameters of female broiler chicks raised under heat stress conditions (HS, 23.9 to 38 °C cycling). Average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR) were obtained from 1 to 42 days of age. Furthermore, at the end of the experiment (day 42), birds were bled to determine some blood biochemical parameters and weighed for final body weight (BW). ADFI, ADG, and BW were not influenced significantly by dietary CrPic and P.mint ( P > 0.05). A significant interaction between dietary CrPic and P.mint on FCR ( P = 0.012) was detected. FCR significantly decreased in chicks fed the diet including both CrPic and P.mint compared with the CrPic group. Significant interaction between dietary P.mint and CrPic on serum concentrations of triglycerides, glucose, and albumin were observed ( P < 0.05), but the other measured blood biochemical parameters were not statistically affected by dietary treatments ( P > 0.05). The serum concentrations of glucose, triglycerides were decreased ( P < 0.05) in broilers fed the diet including both CrPic and P.mint. Plasma chromium (Cr) content increased significantly ( P < 0.05) in birds fed the CrPic-included diet compared with the control group ( P < 0.05). From the results of the present experiment it can be concluded that dietary supplementation with combined P.mint and CrPic could have beneficial effects on some blood biochemical parameters of female chicks reared under heat stress conditions.

Effects of dietary chromium picolinate and peppermint essential oil on growth performance and blood biochemical parameters of broiler chicks reared under heat stress conditions.

PubMed

Akbari, Mohsen; Torki, Mehran

2014-08-01

A study was conducted using 240 female day-old broiler chicks to evaluate the effects of dietary chromium picolinate (CrPic), peppermint essential oil (P.mint), or their combination on growth performance and blood biochemical parameters of female broiler chicks raised under heat stress conditions (HS, 23.9 to 38 °C cycling). Average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR) were obtained from 1 to 42 days of age. Furthermore, at the end of the experiment (day 42), birds were bled to determine some blood biochemical parameters and weighed for final body weight (BW). ADFI, ADG, and BW were not influenced significantly by dietary CrPic and P.mint (P>0.05). A significant interaction between dietary CrPic and P.mint on FCR (P=0.012) was detected. FCR significantly decreased in chicks fed the diet including both CrPic and P.mint compared with the CrPic group. Significant interaction between dietary P.mint and CrPic on serum concentrations of triglycerides, glucose, and albumin were observed (P<0.05), but the other measured blood biochemical parameters were not statistically affected by dietary treatments (P>0.05). The serum concentrations of glucose, triglycerides were decreased (P<0.05) in broilers fed the diet including both CrPic and P.mint. Plasma chromium (Cr) content increased significantly (P<0.05) in birds fed the CrPic-included diet compared with the control group (P<0.05). From the results of the present experiment it can be concluded that dietary supplementation with combined P.mint and CrPic could have beneficial effects on some blood biochemical parameters of female chicks reared under heat stress conditions.

Neolinoptes gen. n., a replacement name for the net-winged beetle genus Linoptes Gorham, 1884 and a new species of Lycomorphon from Guyana (Coleoptera: Lycidae).

PubMed

Nascimento, Elynton Alves DO; Bocakova, Milada

2017-01-09

Neolinoptes gen. n. is erected to replace Linoptes Gorham, 1884, preoccupied by Linoptes Menge, 1854 (Arachnida: Araneae). Consequently, Neolinoptes imbrex (Gorham, 1884) comb. n., N. amazonicus (Pic, 1923) comb. n., N. atronotatus (Pic, 1922) comb. n., N. atripennis (Pic, 1932) comb. n. are proposed. Calocladon rubidum Gorham, 1884 is transferred to Neolinoptes. Lycomorphon iwokrama sp. n. is proposed as new to science and the genus is recorded from Guyana for the first time. Additionally, Falsocaenia irregularis var. germaini Pic, 1931 is elevated to species rank and past confusion on F. irregularis discussed. New data on geographical distribution of Falsocaenia paranana (Pic, 1922) are presented.

Anti-diabetic activity of chromium picolinate and biotin in rats with type 2 diabetes induced by high-fat diet and streptozotocin.

PubMed

Sahin, Kazim; Tuzcu, Mehmet; Orhan, Cemal; Sahin, Nurhan; Kucuk, Osman; Ozercan, Ibrahim H; Juturu, Vijaya; Komorowski, James R

2013-07-28

The objective of the present study was to evaluate anti-diabetic effects of chromium picolinate (CrPic) and biotin supplementations in type 2 diabetic rats. The type 2 diabetic rat model was induced by high-fat diet (HFD) and low-dose streptozotocin. The rats were divided into five groups as follows: (1) non-diabetic rats fed a regular diet; (2) diabetic rats fed a HFD; (3) diabetic rats fed a HFD and supplemented with CrPic (80 μg/kg body weight (BW) per d); (4) diabetic rats fed a HFD and supplemented with biotin (300 μg/kg BW per d); (5) diabetic rats fed a HFD and supplemented with both CrPic and biotin. Circulating glucose, cortisol, total cholesterol, TAG, NEFA and malondialdehyde concentrations decreased (P< 0·05), but serum insulin concentrations increased (P< 0·05) in diabetic rats treated with biotin and CrPic, particularly with a combination of the supplements. Feeding a HFD to diabetic rats decreased PPAR-γ expression in adipose tissue and phosphorylated insulin receptor substrate 1 (p-IRS-1) expression of liver, kidney and muscle tissues, while the supplements increased (P< 0·001) PPAR-γ and p-IRS-1 expressions in relevant tissues. Expression of NF-κB in the liver and kidney was greater in diabetic rats fed a HFD, as compared with rats fed a regular diet (P< 0·01). The supplements decreased the expression of NF-κB in diabetic rats (P< 0·05). Results of the present study revealed that supplementing CrPic and biotin alone or in a combination exerts anti-diabetic activities, probably through modulation of PPAR-γ, IRS-1 and NF-κB proteins.

Magnetohydrodynamics with Embedded Particle-in-Cell Simulation of Mercury's Magnetosphere

NASA Astrophysics Data System (ADS)

Chen, Y.; Toth, G.; Jia, X.; Gombosi, T. I.; Markidis, S.

2015-12-01

Mercury's magnetosphere is much more dynamic than other planetary magnetospheres because of Mercury's weak intrinsic magnetic field and its proximity to the Sun. Magnetic reconnection and Kelvin-Helmholtz phenomena occur in Mercury's magnetopause and magnetotail at higher frequencies than in other planetary magnetosphere. For instance, chains of flux transfer events (FTEs) on the magnetopause, have been frequentlyobserved by the the MErcury Surface, Space ENvironment, GEochemistry and Ranging (MESSENGER) spacecraft (Slavin et al., 2012). Because ion Larmor radius is comparable to typical spatial scales in Mercury's magnetosphere, finite Larmor radius effects need to be accounted for. In addition, it is important to take in account non-ideal dissipation mechanisms to accurately describe magnetic reconnection. A kinetic approach allows us to model these phenomena accurately. However, kinetic global simulations, even for small-size magnetospheres like Mercury's, are currently unfeasible because of the high computational cost. In this work, we carry out global simulations of Mercury's magnetosphere with the recently developed MHD-EPIC model, which is a two-way coupling of the extended magnetohydrodynamic (XMHD) code BATS-R-US with the implicit Particle-in-Cell (PIC) model iPIC3D. The PIC model can cover the regions where kinetic effects are most important, such as reconnection sites. The BATS-R-US code, on the other hand, can efficiently handle the rest of the computational domain where the MHD or Hall MHD description is sufficient. We will present our preliminary results and comparison with MESSENGER observations.

Searching for Short GRBs in Soft Gamma Rays with INTEGRAL/PICsIT

NASA Astrophysics Data System (ADS)

Rodi, James; Bazzano, Angela; Ubertini, Pietro; Natalucci, Lorenzo; Savchenko, V.; Kuulkers, E.; Ferrigno, Carlo; Bozzo, Enrico; Brandt, Soren; Chenevez, Jerome; Courvoisier, T. J.-L.; Diehl, R.; Domingo, A.; Hanlon, L.; Jourdain, E.; von Kienlin, A.; Laurent, P.; Lebrun, F.; Lutovinov, A.; Martin-Carrillo, A.; Mereghetti, S.; Roques, J.-P.; Sunyaev, R.

2018-01-01

With gravitational wave (GW) detections by the LIGO/Virgo collaboration over the past several years, there is heightened interest in gamma-ray bursts (GRBs), especially “short” GRBs (T90 <2s). The high-energy PICsIT detector (~0.2 – 10 MeV) on-board the INTErnational Gamma-Ray Astrophysics Laboratory (INTEGRAL) is able to observe sources out to approximately 70° off-axis, making it essentially a soft gamma-ray, all-sky monitor for impulsive events, such as SGRBs. Because SGRBs typically have hard spectra with peak energies of a few hundred keV, PICsIT with its ~ 3000 cm2 collecting area is able to provide spectral information about these sources at soft gamma-ray energies.We have begun a study of PICsIT data for faint SGRBs similar to the one associated with the binary neutron star (BNS) merger GW 170817, and also are preparing for future GW triggers by developing a real-time burst analysis for PICsIT. Searching the PICsIT data for significant excesses during ~30 min-long pointings containing times of SGRBs, we have been able to differentiate between SGRBs and spurious events. Also, this work allows us to assess what fraction of reported SGRBs have been detected by PICsIT, which can be used to provide an estimate of the number of GW BNS events seen by PICsIT during the next LIGO/Virgo observing run starting in Fall 2018.

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 magnetosphere to the ionosphere [2]. [1] G.L. Delzanno, E. Camporeale, "CPIC: a new Particle-in-Cell code for plasma-material interaction studies", in preparation (2012). [2] J.E. Borovsky, D.J. McComas, M.F. Thomsen, J.L. Burch, J. Cravens, C.J. Pollock, T.E. Moore, and S.B. Mende, "Magnetosphere-Ionosphere Observatory (MIO): A multisatellite mission designed to solve the problem of what generates auroral arcs," Eos. Trans. Amer. Geophys. Union 79 (45), F744 (2000).

Effect of the ordered interfacial water layer in protein complex formation: A nonlocal electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, A.; Sabirianov, R. F.; Mei, W. N.; Namavar, F.; Khoynezhad, A.

2010-08-01

Using a nonlocal electrostatic approach that incorporates the short-range structure of the contacting media, we evaluated the electrostatic contribution to the energy of the complex formation of two model proteins. In this study, we have demonstrated that the existence of an ordered interfacial water layer at the protein-solvent interface reduces the charging energy of the proteins in the aqueous solvent, and consequently increases the electrostatic contribution to the protein binding (change in free energy upon the complex formation of two proteins). This is in contrast with the finding of the continuum electrostatic model, which suggests that electrostatic interactions are not strong enough to compensate for the unfavorable desolvation effects.

Effect of the ordered interfacial water layer in protein complex formation: A nonlocal electrostatic approach.

PubMed

Rubinstein, A; Sabirianov, R F; Mei, W N; Namavar, F; Khoynezhad, A

2010-08-01

Using a nonlocal electrostatic approach that incorporates the short-range structure of the contacting media, we evaluated the electrostatic contribution to the energy of the complex formation of two model proteins. In this study, we have demonstrated that the existence of an ordered interfacial water layer at the protein-solvent interface reduces the charging energy of the proteins in the aqueous solvent, and consequently increases the electrostatic contribution to the protein binding (change in free energy upon the complex formation of two proteins). This is in contrast with the finding of the continuum electrostatic model, which suggests that electrostatic interactions are not strong enough to compensate for the unfavorable desolvation effects.

An incompressible two-dimensional multiphase particle-in-cell model for dense particle flows

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

Snider, D.M.; O`Rourke, P.J.; Andrews, M.J.

1997-06-01

A two-dimensional, incompressible, multiphase particle-in-cell (MP-PIC) method is presented for dense particle flows. The numerical technique solves the governing equations of the fluid phase using a continuum model and those of the particle phase using a Lagrangian model. Difficulties associated with calculating interparticle interactions for dense particle flows with volume fractions above 5% have been eliminated by mapping particle properties to a Eulerian grid and then mapping back computed stress tensors to particle positions. This approach utilizes the best of Eulerian/Eulerian continuum models and Eulerian/Lagrangian discrete models. The solution scheme allows for distributions of types, sizes, and density of particles,more » with no numerical diffusion from the Lagrangian particle calculations. The computational method is implicit with respect to pressure, velocity, and volume fraction in the continuum solution thus avoiding courant limits on computational time advancement. MP-PIC simulations are compared with one-dimensional problems that have analytical solutions and with two-dimensional problems for which there are experimental data.« less

Effect of electron Monte Carlo collisions on a hybrid simulation of a low-pressure capacitively coupled plasma

NASA Astrophysics Data System (ADS)

Hwang, Seok Won; Lee, Ho-Jun; Lee, Hae June

2014-12-01

Fluid models have been widely used and conducted successfully in high pressure plasma simulations where the drift-diffusion and the local-field approximation are valid. However, fluid models are not able to demonstrate non-local effects related to large electron energy relaxation mean free path in low pressure plasmas. To overcome this weakness, a hybrid model coupling electron Monte Carlo collision (EMCC) method with the fluid model is introduced to obtain precise electron energy distribution functions using pseudo-particles. Steady state simulation results by a one-dimensional hybrid model which includes EMCC method for the collisional reactions but uses drift-diffusion approximation for electron transport in a fluid model are compared with those of a conventional particle-in-cell (PIC) and a fluid model for low pressure capacitively coupled plasmas. At a wide range of pressure, the hybrid model agrees well with the PIC simulation with a reduced calculation time while the fluid model shows discrepancy in the results of the plasma density and the electron temperature.

Modeling and simulations of the double-probe electric field instrument in tenuous and cold streaming plasmas

NASA Astrophysics Data System (ADS)

Miyake, Y.; Cully, C. M.; Usui, H.; Nakashima, H.

2013-12-01

In order to increase accuracy and reliability of in-situ measurements made by scientific spacecraft, it is imperative to develop comprehensive understanding of spacecraft-plasma interactions. In space environments, not only the spacecraft charging but also surrounding plasma disturbances such as caused by the wake formation may interfere directly with in-situ measurements. The self-consistent solutions of such phenomena are necessary to assess their effects on scientific spacecraft systems. As our recent activity, we work on the modeling and simulations of Cluster double-probe instrument in tenuous and cold streaming plasmas [1]. Double-probe electric field sensors are often deployed using wire booms with radii much less than typical Debye lengths of magnetospheric plasmas (millimeters compared to tens of meters). However, in tenuous and cold streaming plasmas seen in the polar cap and lobe regions, the wire booms have a high positive potential due to photoelectron emission and can strongly scatter approaching ions. Consequently, an electrostatic wake formed behind the spacecraft is further enhanced by the presence of the wire booms. We reproduce this process for the case of the Cluster satellite by performing plasma particle-in-cell (PIC) simulations [2], which include the effects of both the spacecraft body and the wire booms in a simultaneous manner, on modern supercomputers. The simulations reveal that the effective thickness of the booms for the Cluster Electric Field and Wave (EFW) instrument is magnified from its real thickness (2.2 millimeters) to several meters, when the spacecraft potential is at 30-40 volts. Such booms enhance the wake electric field magnitude by a factor of about 2 depending on the spacecraft potential, and play a principal role in explaining the in situ Cluster EFW data showing sinusoidal spurious electric fields of about 10 mV/m amplitudes. The boom effects are quantified by comparing PIC simulations with and without wire booms. The paper also reports some recent progress of ongoing PIC simulation research that focuses on spurious electric field generation in subsonic ion flows. Our preliminary simulation results revealed that; (1) there is no apparent wake signature behind the spacecraft in such a condition, but (2) spurious electric field over 1 mV/m amplitude is observed in the direction of the flow vector. The observed field amplitude is sometimes comparable to the convection electric field (a few mV/m) associated with the flow. Our analysis also confirmed that the spurious field is caused by a weakly-asymmetric potential pattern created by the ion flow. We will present the parametric study of such spurious fields for various conditions of plasma flows. [References] [1] Miyake, Y., C. M. Cully, H. Usui, and H. Nakashima (2013), Plasma particle simulations of wake formation behind a spacecraft with thin wire booms, submitted to J. Geophys. Res. [2] Miyake, Y., and H. Usui (2009), New electromagnetic particle simulation code for the analysis of spacecraft-plasma interactions, Phys. Plasmas, 16, 062904, doi:10.1063/1.3147922.

Coupled particle-in-cell and Monte Carlo transport modeling of intense radiographic sources

NASA Astrophysics Data System (ADS)

Rose, D. V.; Welch, D. R.; Oliver, B. V.; Clark, R. E.; Johnson, D. L.; Maenchen, J. E.; Menge, P. R.; Olson, C. L.; Rovang, D. C.

2002-03-01

Dose-rate calculations for intense electron-beam diodes using particle-in-cell (PIC) simulations along with Monte Carlo electron/photon transport calculations are presented. The electromagnetic PIC simulations are used to model the dynamic operation of the rod-pinch and immersed-B diodes. These simulations include algorithms for tracking electron scattering and energy loss in dense materials. The positions and momenta of photons created in these materials are recorded and separate Monte Carlo calculations are used to transport the photons to determine the dose in far-field detectors. These combined calculations are used to determine radiographer equations (dose scaling as a function of diode current and voltage) that are compared directly with measured dose rates obtained on the SABRE generator at Sandia National Laboratories.

Efficient modeling of laser-plasma accelerator staging experiments using INF&RNO

NASA Astrophysics Data System (ADS)

Benedetti, C.; Schroeder, C. B.; Geddes, C. G. R.; Esarey, E.; Leemans, W. P.

2017-03-01

The computational framework INF&RNO (INtegrated Fluid & paRticle simulatioN cOde) allows for fast and accurate modeling, in 2D cylindrical geometry, of several aspects of laser-plasma accelerator physics. In this paper, we present some of the new features of the code, including the quasistatic Particle-In-Cell (PIC)/fluid modality, and describe using different computational grids and time steps for the laser envelope and the plasma wake. These and other features allow for a speedup of several orders of magnitude compared to standard full 3D PIC simulations while still retaining physical fidelity. INF&RNO is used to support the experimental activity at the BELLA Center, and we will present an example of the application of the code to the laser-plasma accelerator staging experiment.

Leveraging social media in the stem cell sector: exploring Twitter's potential as a vehicle for public information campaigns.

PubMed

McNutt, Kathleen; Zarzeczny, Amy

2017-10-01

Our aim in this project was to explore Twitter's potential as a vehicle for an online public information campaign (PIC) focused on providing evidence-based information about stem cell therapies and the market for unproven stem cell-based interventions. We designed an online, Twitter-based PIC using classic design principles and identified a set of target intermediaries (organizations with online influence) using a network governance approach. We tracked the PIC's dissemination over a 2-month period, and evaluated it using metrics from the #SMMStandards Conclave. Participation was limited but the PIC achieved some reach and engagement. Social media based online PICs appear to have potential but also face challenges. Future research is required to better understand how to most effectively maximize their strengths.

Geometric and electrostatic modeling using molecular rigidity functions

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

Mu, Lin; Xia, Kelin; Wei, Guowei

Geometric and electrostatic modeling is an essential component in computational biophysics and molecular biology. Commonly used geometric representations admit geometric singularities such as cusps, tips and self-intersecting facets that lead to computational instabilities in the molecular modeling. Our present work explores the use of flexibility and rigidity index (FRI), which has a proved superiority in protein B-factor prediction, for biomolecular geometric representation and associated electrostatic analysis. FRI rigidity surfaces are free of geometric singularities. We propose a rigidity based Poisson–Boltzmann equation for biomolecular electrostatic analysis. These approaches to surface and electrostatic modeling are validated by a set of 21 proteins.more » Our results are compared with those of established methods. Finally, being smooth and analytically differentiable, FRI rigidity functions offer excellent curvature analysis, which characterizes concave and convex regions on protein surfaces. Polarized curvatures constructed by using the product of minimum curvature and electrostatic potential is shown to predict potential protein–ligand binding sites.« less

Geometric and electrostatic modeling using molecular rigidity functions

DOE PAGES

Mu, Lin; Xia, Kelin; Wei, Guowei

2017-03-01

Geometric and electrostatic modeling is an essential component in computational biophysics and molecular biology. Commonly used geometric representations admit geometric singularities such as cusps, tips and self-intersecting facets that lead to computational instabilities in the molecular modeling. Our present work explores the use of flexibility and rigidity index (FRI), which has a proved superiority in protein B-factor prediction, for biomolecular geometric representation and associated electrostatic analysis. FRI rigidity surfaces are free of geometric singularities. We propose a rigidity based Poisson–Boltzmann equation for biomolecular electrostatic analysis. These approaches to surface and electrostatic modeling are validated by a set of 21 proteins.more » Our results are compared with those of established methods. Finally, being smooth and analytically differentiable, FRI rigidity functions offer excellent curvature analysis, which characterizes concave and convex regions on protein surfaces. Polarized curvatures constructed by using the product of minimum curvature and electrostatic potential is shown to predict potential protein–ligand binding sites.« less

Electron Heating and Acceleration in a Reconnecting Magnetotail

NASA Astrophysics Data System (ADS)

El-Alaoui, M.; Zhou, M.; Lapenta, G.; Berchem, J.; Richard, R. L.; Schriver, D.; Walker, R. J.

2017-12-01

Electron heating and acceleration in the magnetotail have been investigated intensively. A major site for this process is the reconnection region. However, where and how the electrons are accelerated in a realistic three-dimensional X-line geometry is not fully understood. In this study, we employed a three-dimensional implicit particle-in-cell (iPIC3D) simulation and large-scale kinetic (LSK) simulation to address these problems. We modeled a magnetotail reconnection event observed by THEMIS in an iPIC3D simulation with initial and boundary conditions given by a global magnetohydrodynamic (MHD) simulation of Earth's magnetosphere. The iPIC3D simulation system includes the region of fast outflow emanating from the reconnection site that drives dipolarization fronts. We found that current sheet electrons exhibit elongated (cigar-shaped) velocity distributions with a higher parallel temperature. Using LSK we then followed millions of test electrons using the electromagnetic fields from iPIC3D. We found that magnetotail reconnection can generate power law spectra around the near-Earth X-line. A significant number of electrons with energies higher than 50 keV are produced. We identified several acceleration mechanisms at different locations that were responsible for energizing these electrons: non-adiabatic cross-tail drift, betatron and Fermi acceleration. Relative contributions to the energy gain of these high energy electrons from the different mechanisms will be discussed.

Model and particle-in-cell simulation of ion energy distribution in collisionless sheath

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

Zhou, Zhuwen, E-mail: zzwwdxy@gznc.edu.cn; Key Laboratory of Photoelectron Materials Design and Simulation in Guizhou Province, Guiyang 550018; Scientific Research Innovation Team in Plasma and Functional Thin Film Materials in Guizhou Province, Guiyang 550018

2015-06-15

In this paper, we propose a self-consistent theoretical model, which is described by the ion energy distributions (IEDs) in collisionless sheaths, and the analytical results for different combined dc/radio frequency (rf) capacitive coupled plasma discharge cases, including sheath voltage errors analysis, are compared with the results of numerical simulations using a one-dimensional plane-parallel particle-in-cell (PIC) simulation. The IEDs in collisionless sheaths are performed on combination of dc/rf voltage sources electrodes discharge using argon as the process gas. The incident ions on the grounded electrode are separated, according to their different radio frequencies, and dc voltages on a separated electrode, themore » IEDs, and widths of energy in sheath and the plasma sheath thickness are discussed. The IEDs, the IED widths, and sheath voltages by the theoretical model are investigated and show good agreement with PIC simulations.« less

Grand challenge problems in environmental modeling and remediation: groundwater contaminant transport

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

Todd Arbogast; Steve Bryant; Clint N. Dawson

1998-08-31

This report describes briefly the work of the Center for Subsurface Modeling (CSM) of the University of Texas at Austin (and Rice University prior to September 1995) on the Partnership in Computational Sciences Consortium (PICS) project entitled Grand Challenge Problems in Environmental Modeling and Remediation: Groundwater Contaminant Transport.

Three dimensional particle-in-cell simulations of electron beams created via reflection of intense laser light from a water target

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

Ngirmang, Gregory K., E-mail: ngirmang.1@osu.edu; Orban, Chris; Feister, Scott

We present 3D Particle-in-Cell (PIC) modeling of an ultra-intense laser experiment by the Extreme Light group at the Air Force Research Laboratory using the Large Scale Plasma (LSP) PIC code. This is the first time PIC simulations have been performed in 3D for this experiment which involves an ultra-intense, short-pulse (30 fs) laser interacting with a water jet target at normal incidence. The laser-energy-to-ejected-electron-energy conversion efficiency observed in 2D(3v) simulations were comparable to the conversion efficiencies seen in the 3D simulations, but the angular distribution of ejected electrons in the 2D(3v) simulations displayed interesting differences with the 3D simulations' angular distribution;more » the observed differences between the 2D(3v) and 3D simulations were more noticeable for the simulations with higher intensity laser pulses. An analytic plane-wave model is discussed which provides some explanation for the angular distribution and energies of ejected electrons in the 2D(3v) simulations. We also performed a 3D simulation with circularly polarized light and found a significantly higher conversion efficiency and peak electron energy, which is promising for future experiments.« less

Estimating Particulate Inorganic Carbon Concentrations of the Global Ocean From Ocean Color Measurements Using a Reflectance Difference Approach

NASA Astrophysics Data System (ADS)

Mitchell, C.; Hu, C.; Bowler, B.; Drapeau, D.; Balch, W. M.

2017-11-01

A new algorithm for estimating particulate inorganic carbon (PIC) concentrations from ocean color measurements is presented. PIC plays an important role in the global carbon cycle through the oceanic carbonate pump, therefore accurate estimations of PIC concentrations from satellite remote sensing are crucial for observing changes on a global scale. An extensive global data set was created from field and satellite observations for investigating the relationship between PIC concentrations and differences in the remote sensing reflectance (Rrs) at green, red, and near-infrared (NIR) wavebands. Three color indices were defined: two as the relative height of Rrs(667) above a baseline running between Rrs(547) and an Rrs in the NIR (either 748 or 869 nm), and one as the difference between Rrs(547) and Rrs(667). All three color indices were found to explain over 90% of the variance in field-measured PIC. But, due to the lack of availability of Rrs(NIR) in the standard ocean color data products, most of the further analysis presented here was done using the color index determined from only two bands. The new two-band color index algorithm was found to retrieve PIC concentrations more accurately than the current standard algorithm used in generating global PIC data products. Application of the new algorithm to satellite imagery showed patterns on the global scale as revealed from field measurements. The new algorithm was more resistant to atmospheric correction errors and residual errors in sun glint corrections, as seen by a reduction in the speckling and patchiness in the satellite-derived PIC images.

Effects of Chromium Picolinate on Food Intake and Satiety

PubMed Central

Morrison, Christopher D.; Cefalu, William T.; Martin, Corby K.; Coulon, Sandra; Geiselman, Paula; Han, Hongmei; White, Christy L.; Williamson, Donald A.

2008-01-01

Abstract Background Chromium picolinate (CrPic) has been shown to attenuate weight gain, but the mechanism underlying this effect is unknown. Methods We assessed the effect of CrPic in modulating food intake in healthy, overweight, adult women who reported craving carbohydrates (Study 1) and performed confirmatory studies in Sprague-Dawley rats (Study 2). Study 1 utilized a double-blind placebo-controlled design and randomly assigned 42 overweight adult women with carbohydrate cravings to receive 1,000 μg of chromium as CrPic or placebo for 8 weeks. Food intake at breakfast, lunch, and dinner was directly measured at baseline, week 1, and week 8. For Study 2, Sprague-Dawley rats were fasted for 24 h and subsequently injected intraperitoneally with 0, 1, 10, or 50 μg/kg CrPic. Subsequently, rats were implanted with an indwelling third ventricular cannula. Following recovery, 0, 0.4, 4, or 40 ng of CrPic was injected directly into the brain via the intracerebroventricular cannula, and spontaneous 24-h food intake was measured. Results Study 1 demonstrated that CrPic, as compared to placebo, reduced food intake (P < 0.0001), hunger levels (P < 0.05), and fat cravings (P < 0.0001) and tended to decrease body weight (P = 0.08). In study 2, intraperitoneal administration resulted in a subtle decrease in food intake at only the highest dose (P = 0.03). However, when administered centrally, CrPic dose-dependently decreased food intake (P < 0.05). Conclusions These data suggest CrPic has a role in food intake regulation, which may be mediated by a direct effect on the brain. PMID:18715218

Review on the Modeling of Electrostatic MEMS

PubMed Central

Chuang, Wan-Chun; Lee, Hsin-Li; Chang, Pei-Zen; Hu, Yuh-Chung

2010-01-01

Electrostatic-driven microelectromechanical systems devices, in most cases, consist of couplings of such energy domains as electromechanics, optical electricity, thermoelectricity, and electromagnetism. Their nonlinear working state makes their analysis complex and complicated. This article introduces the physical model of pull-in voltage, dynamic characteristic analysis, air damping effect, reliability, numerical modeling method, and application of electrostatic-driven MEMS devices. PMID:22219707

46 CFR 13.309 - Eligibility: Cargo course.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Eligibility: Cargo course. 13.309 Section 13.309... TANKERMEN Requirements for âTankerman-PIC (Barge)â Endorsement § 13.309 Eligibility: Cargo course. Each... a course in DL or LG appropriate for tank barges and for Tankerman-PIC or Tankerman-PIC (Barge), and...

46 CFR 13.309 - Eligibility: Cargo course.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 1 2012-10-01 2012-10-01 false Eligibility: Cargo course. 13.309 Section 13.309... TANKERMEN Requirements for âTankerman-PIC (Barge)â Endorsement § 13.309 Eligibility: Cargo course. Each... a course in DL or LG appropriate for tank barges and for Tankerman-PIC or Tankerman-PIC (Barge), and...

46 CFR 13.309 - Eligibility: Cargo course.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 1 2010-10-01 2010-10-01 false Eligibility: Cargo course. 13.309 Section 13.309... TANKERMEN Requirements for âTankerman-PIC (Barge)â Endorsement § 13.309 Eligibility: Cargo course. Each... a course in DL or LG appropriate for tank barges and for Tankerman-PIC or Tankerman-PIC (Barge), and...

46 CFR 13.309 - Eligibility: Cargo course.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 1 2011-10-01 2011-10-01 false Eligibility: Cargo course. 13.309 Section 13.309... TANKERMEN Requirements for âTankerman-PIC (Barge)â Endorsement § 13.309 Eligibility: Cargo course. Each... a course in DL or LG appropriate for tank barges and for Tankerman-PIC or Tankerman-PIC (Barge), and...

Chemical properties and biotoxicity of several chromium picolinate derivatives.

PubMed

Liu, Bin; Liu, Yanfei; Chai, Jie; Hu, Xiangquan; Wu, Duoming; Yang, Binsheng

2016-11-01

As a man-made additive, chromium picolinate Cr(pic) 3 has become a popular dietary supplement worldwide. In this paper Cr(pic) 3 and its new derivatives Cr(6-CH 3 -pic) 3 (1), [Cr(6-NH 2 -pic) 2 (H 2 O) 2 ]NO 3 (2) and Cr(3-NH 2 -pic) 3 (3) were synthesized, and complexes 1 and 2 were characterized by X-ray crystal structure (where pic=2-carboxypyridine). The relationship between the chemical properties and biotoxicity of these complexes was fully discussed: (1) The dynamics stability of chromium picolinate complexes mainly depends on the CrN bonds length. (2) There is a positive correlation between the dynamics stability, electrochemical potentials and generation of reactive oxygen species through Fenton-like reaction. (3) However, no biological toxicity was observed through MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and sub-chronic oral toxicity study for these chromium picolinate compounds. Together, our findings establish a framework for understanding the structure-property-toxicity relationships of the chromium picolinate complexes. Copyright © 2016 Elsevier Inc. All rights reserved.

Effects of chromium picolinate on the viability of chick embryo fibroblast.

PubMed

Bai, Y; Zhao, X; Qi, C; Wang, L; Cheng, Z; Liu, M; Liu, J; Yang, D; Wang, S; Chai, T

2014-04-01

Chromium picolinate (CrPic), which is used as a nutritional supplement and to treat type 2 diabetes, has gained much attention because of its cytotoxicity. This study evaluated the effects of CrPic on the viability of the chick embryo fibroblast (CEF) using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, morphological detection, and flow cytometry. The results show that lower concentrations of CrPic (8 and 16 μM) did not damage CEF viability (p > 0.05). However, higher CrPic concentrations (400 and 600 μM) indicated a highly significant effect on the production of intracellular reactive oxygen species, alteration of mitochondrial membrane potential, intracellular calcium ion concentration, and the apoptosis rate (p < 0.01), contrary to lower CrPic concentrations (8 and 16 μM) and control group. Moreover, apoptotic morphological changes induced by these processes in CEF were confirmed using Hoechst 33258 staining. Cell death induced by higher concentrations of CrPic was caused by an apoptotic and a necrotic mechanism, whereas the main mechanism of oxidative stress-induced mitochondrial dysfunction was apoptotic death.

Nonlinear behaviour of cantilevered carbon nanotube resonators based on a new nonlinear electrostatic load model

NASA Astrophysics Data System (ADS)

Farokhi, Hamed; Païdoussis, Michael P.; Misra, Arun K.

2018-04-01

The present study examines the nonlinear behaviour of a cantilevered carbon nanotube (CNT) resonator and its mass detection sensitivity, employing a new nonlinear electrostatic load model. More specifically, a 3D finite element model is developed in order to obtain the electrostatic load distribution on cantilevered CNT resonators. A new nonlinear electrostatic load model is then proposed accounting for the end effects due to finite length. Additionally, a new nonlinear size-dependent continuum model is developed for the cantilevered CNT resonator, employing the modified couple stress theory (to account for size-effects) together with the Kelvin-Voigt model (to account for nonlinear damping); the size-dependent model takes into account all sources of nonlinearity, i.e. geometrical and inertial nonlinearities as well as nonlinearities associated with damping, small-scale, and electrostatic load. The nonlinear equation of motion of the cantilevered CNT resonator is obtained based on the new models developed for the CNT resonator and the electrostatic load. The Galerkin method is then applied to the nonlinear equation of motion, resulting in a set of nonlinear ordinary differential equations, consisting of geometrical, inertial, electrical, damping, and size-dependent nonlinear terms. This high-dimensional nonlinear discretized model is solved numerically utilizing the pseudo-arclength continuation technique. The nonlinear static and dynamic responses of the system are examined for various cases, investigating the effect of DC and AC voltages, length-scale parameter, nonlinear damping, and electrostatic load. Moreover, the mass detection sensitivity of the system is examined for possible application of the CNT resonator as a nanosensor.

Assessment of Different Discrete Particle Methods Ability To Predict Gas-Particle Flow in a Small-Scale Fluidized Bed

DOE PAGES

Lu, Liqiang; Gopalan, Balaji; Benyahia, Sofiane

2017-06-21

Several discrete particle methods exist in the open literature to simulate fluidized bed systems, such as discrete element method (DEM), time driven hard sphere (TDHS), coarse-grained particle method (CGPM), coarse grained hard sphere (CGHS), and multi-phase particle-in-cell (MP-PIC). These different approaches usually solve the fluid phase in a Eulerian fixed frame of reference and the particle phase using the Lagrangian method. The first difference between these models lies in tracking either real particles or lumped parcels. The second difference is in the treatment of particle-particle interactions: by calculating collision forces (DEM and CGPM), using momentum conservation laws (TDHS and CGHS),more » or based on particle stress model (MP-PIC). These major model differences lead to a wide range of results accuracy and computation speed. However, these models have never been compared directly using the same experimental dataset. In this research, a small-scale fluidized bed is simulated with these methods using the same open-source code MFIX. The results indicate that modeling the particle-particle collision by TDHS increases the computation speed while maintaining good accuracy. Also, lumping few particles in a parcel increases the computation speed with little loss in accuracy. However, modeling particle-particle interactions with solids stress leads to a big loss in accuracy with a little increase in computation speed. The MP-PIC method predicts an unphysical particle-particle overlap, which results in incorrect voidage distribution and incorrect overall bed hydrodynamics. Based on this study, we recommend using the CGHS method for fluidized bed simulations due to its computational speed that rivals that of MPPIC while maintaining a much better accuracy.« less

Assessment of Different Discrete Particle Methods Ability To Predict Gas-Particle Flow in a Small-Scale Fluidized Bed

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

Lu, Liqiang; Gopalan, Balaji; Benyahia, Sofiane

Several discrete particle methods exist in the open literature to simulate fluidized bed systems, such as discrete element method (DEM), time driven hard sphere (TDHS), coarse-grained particle method (CGPM), coarse grained hard sphere (CGHS), and multi-phase particle-in-cell (MP-PIC). These different approaches usually solve the fluid phase in a Eulerian fixed frame of reference and the particle phase using the Lagrangian method. The first difference between these models lies in tracking either real particles or lumped parcels. The second difference is in the treatment of particle-particle interactions: by calculating collision forces (DEM and CGPM), using momentum conservation laws (TDHS and CGHS),more » or based on particle stress model (MP-PIC). These major model differences lead to a wide range of results accuracy and computation speed. However, these models have never been compared directly using the same experimental dataset. In this research, a small-scale fluidized bed is simulated with these methods using the same open-source code MFIX. The results indicate that modeling the particle-particle collision by TDHS increases the computation speed while maintaining good accuracy. Also, lumping few particles in a parcel increases the computation speed with little loss in accuracy. However, modeling particle-particle interactions with solids stress leads to a big loss in accuracy with a little increase in computation speed. The MP-PIC method predicts an unphysical particle-particle overlap, which results in incorrect voidage distribution and incorrect overall bed hydrodynamics. Based on this study, we recommend using the CGHS method for fluidized bed simulations due to its computational speed that rivals that of MPPIC while maintaining a much better accuracy.« less

Effect of the ordered interfacial water layer in protein complex formation: a non-local electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, Alexander; Sabirianov, Renat

2011-03-01

Using a non-local electrostatic approach that incorporates the short-range structure of the contacting media, we evaluated the electrostatic contribution to the energy of the complex formation of two model proteins. In this study, we have demonstrated that the existence of an low-dielectric interfacial water layer at the protein-solvent interface reduces the charging energy of the proteins in the aqueous solvent, and consequently increases the electrostatic contribution to the protein binding (change in free energy upon the complex formation of two proteins). This is in contrast with the finding of the continuum electrostatic model, which suggests that electrostatic interactions are not strong enough to compensate for the unfavorable desolvation effects.

Spacecraft-environment interaction model cross comparison applied to Solar Probe Plus

NASA Astrophysics Data System (ADS)

Lapenta, G.; Deca, J.; Markidis, S.; Marchand, R.; Guillemant, S.; Matéo Vélez, J.; Miyake, Y.; Usui, H.; Ergun, R.; Sturner, A. P.

2013-12-01

Given that our society becomes increasingly dependent on space technology, it is imperative to develop a good understanding of spacecraft-plasma interactions. Two main issues are important. First, one needs to be able to design a reliable spacecraft that can survive in the harsh solar wind conditions, and second a very good knowledge of the behaviour and plasma structure around the spacecraft is required to be able to interpret and correct measurements from onboard instruments and science experiments. In this work we present the results of a cross-comparison study between five spacecraft-plasma models (EMSES, iPic3D, LASP, PTetra, SPIS) used to simulate the interaction of the Solar Probe Plus (SPP) satellite with the space environment under representative solar wind conditions near perihelion. The purpose of this cross-comparison is to assess the consistency and validity of the different numerical approaches from the similarities and differences of their predictions under well defined conditions, with attention to the implicit PIC code iPic3D, which has never been used for spacecraft-environment interaction studies before. The physical effects considered are spacecraft charging, photoelectron and secondary electron emission, the presence of a background magnetic field and density variations. The latter of which can cause the floating potential of SPP to go from negative to positive or visa versa, depending on the solar wind conditions, and spacecraft material properties. Simulation results are presented and compared with increasing levels of complexity in the physics to evaluate the sensitivity of the model predictions to certain physical effects. The comparisons focus particularly on spacecraft floating potential, detailed contributions to the currents collected and emitted by the spacecraft, and on the potential and density spatial profiles near the satellite. Model predictions obtained with our different computational approaches are found to be in good agreement when the physical processes are treated similarly. The comparisons considered here indicate that, with the correct parameterization of important physical effects such as photoemission and secondary electron emission, our simulation models should have the required skill to predict details of satellite-plasma interaction physics with a high level of confidence. This work was supported by the International Space Science Institute in Bern Switzerland. The potential profile around the Solar Probe Plus spacecraft in orbital flow, from the iPic3D code. The physical model includes photo- and secondary electrons and a static magnetic field.

Parametric Model Based On Imputations Techniques for Partly Interval Censored Data

NASA Astrophysics Data System (ADS)

Zyoud, Abdallah; Elfaki, F. A. M.; Hrairi, Meftah

2017-12-01

The term ‘survival analysis’ has been used in a broad sense to describe collection of statistical procedures for data analysis. In this case, outcome variable of interest is time until an event occurs where the time to failure of a specific experimental unit might be censored which can be right, left, interval, and Partly Interval Censored data (PIC). In this paper, analysis of this model was conducted based on parametric Cox model via PIC data. Moreover, several imputation techniques were used, which are: midpoint, left & right point, random, mean, and median. Maximum likelihood estimate was considered to obtain the estimated survival function. These estimations were then compared with the existing model, such as: Turnbull and Cox model based on clinical trial data (breast cancer data), for which it showed the validity of the proposed model. Result of data set indicated that the parametric of Cox model proved to be more superior in terms of estimation of survival functions, likelihood ratio tests, and their P-values. Moreover, based on imputation techniques; the midpoint, random, mean, and median showed better results with respect to the estimation of survival function.

PCE: web tools to compute protein continuum electrostatics

PubMed Central

Miteva, Maria A.; Tufféry, Pierre; Villoutreix, Bruno O.

2005-01-01

PCE (protein continuum electrostatics) is an online service for protein electrostatic computations presently based on the MEAD (macroscopic electrostatics with atomic detail) package initially developed by D. Bashford [(2004) Front Biosci., 9, 1082–1099]. This computer method uses a macroscopic electrostatic model for the calculation of protein electrostatic properties, such as pKa values of titratable groups and electrostatic potentials. The MEAD package generates electrostatic energies via finite difference solution to the Poisson–Boltzmann equation. Users submit a PDB file and PCE returns potentials and pKa values as well as color (static or animated) figures displaying electrostatic potentials mapped on the molecular surface. This service is intended to facilitate electrostatics analyses of proteins and thereby broaden the accessibility to continuum electrostatics to the biological community. PCE can be accessed at . PMID:15980492

Role of liver fatty acid binding protein in hepatocellular injury: effect of CrPic treatment.

PubMed

Fan, Weijiang; Chen, Kun; Zheng, Guoqiang; Wang, Wenhang; Teng, Anguo; Liu, Anjun; Ming, Dongfeng; Yan, Peng

2013-07-01

This study was designed to investigate the molecular mechanisms of chromium picolinate (CrPic, Fig. 1) hepatoprotective activity from alloxan-induced hepatic injury. Diabetes is induced by alloxan-treatment concurrently with the hepatic injury in mice. In this study, we investigate the protective effect of CrPic treatment in hepatic injury and the signal role of liver fatty acid binding protein in early hepatocellular injury diagnostics. In this study, alanine aminotransferase (ALT; EC 2.6.1.2) and aspartate aminotransferase (AST; EC 2.6.1.1) levels in the alloxan group were higher 71% and 50%, respectively, than those of the control group (ALT: 14.51±0.74; AST: 22.60±0.69). The AST and ALT levels in CrPic group were of minimal difference compared to the control groups. Here, CrPic exhibited amelioration alloxan induced oxidative stress in mouse livers. A significant increase in liver fatty acid-binding protein (L-FABP) was observed, which indicates increased fatty acid utilization in liver tissue [1]. In this study, the mRNA levels of L-FABP increased in both the control (1.1 fold) and CrPic (0.78 fold) groups compared the alloxan group. These findings suggest that hepatic injury may be prevented by CrPic, and is a potential target for use in the treatment of early hepatic injury. Copyright © 2013 Elsevier Inc. All rights reserved.

Role of positive ions on the surface production of negative ions in a fusion plasma reactor type negative ion source--Insights from a three dimensional particle-in-cell Monte Carlo collisions model

NASA Astrophysics Data System (ADS)

Fubiani, G.; Boeuf, J. P.

2013-11-01

Results from a 3D self-consistent Particle-In-Cell Monte Carlo Collisions (PIC MCC) model of a high power fusion-type negative ion source are presented for the first time. The model is used to calculate the plasma characteristics of the ITER prototype BATMAN ion source developed in Garching. Special emphasis is put on the production of negative ions on the plasma grid surface. The question of the relative roles of the impact of neutral hydrogen atoms and positive ions on the cesiated grid surface has attracted much attention recently and the 3D PIC MCC model is used to address this question. The results show that the production of negative ions by positive ion impact on the plasma grid is small with respect to the production by atomic hydrogen or deuterium bombardment (less than 10%).

Evaluation of the Parent-Implemented Communication Strategies (PiCS) Project Using the Multiattribute Utility (MAU) Approach

ERIC Educational Resources Information Center

Stoner, Julia B.; Meadan, Hedda; Angell, Maureen E.; Daczewitz, Marcus

2012-01-01

We conducted a multiattribute utility (MAU) evaluation to assess the Parent-Implemented Communication Strategies (PiCS) project which was funded by the Institute of Education Sciences (IES). In the PiCS project parents of young children with developmental disabilities are trained and coached in their homes on naturalistic and visual teaching…

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

Water column profiles of particulate inorganic carbon in the northeast subarctic Pacific Ocean

NASA Astrophysics Data System (ADS)

Sutton, J. N.; Bishop, J. K.; Martinez, E. J.; Weiss, G. A.; Weiss, A.; Derr, A.; Strubhar, W.; Robert, M.; Wood, T.

2013-12-01

High resolution and real-time measurement of particulate inorganic carbon (PIC) content in seawater is necessary to improve our spatial and temporal understanding of marine carbon flux and the possible effects of ocean acidification on the biological pump. On four occasions since August 2012, we have mapped PIC distribution from surface to bottom at 26 stations along the IOS-Canada Line P transect from western Vancouver Island, BC, Canada to Ocean Station PAPA, 50N 145W using a prototype (PIC001) and a near-commercial quality (PIC008) optical birefringence sensor. The sensors are highly modified 6000m-rated WETLabs C-star transmissometers, which use a polarized laser beam and a cross-polarized receiver to measure photons emitted after passing through birefringent solids. At major stations along Line P (P2, P4, P8, P12, P16, P20, P26), one-liter rosette-collected calibration water samples were filtered through 0.45 μm Supor filters using a small-volume direct filtration system. These samples were analysed for acid-leachable particulate elements (with emphasis on Ca, Na, and Mg) by inductively coupled plasma mass spectrometry (ICPMS). ICPMS PIC was calculated as residual Ca after correction for seawater Ca using Na data. Here we report results for late summer (Aug. 2012) and winter (Feb. 2013). As expected, high levels of PIC (> 100 nmol L-1 to > 2000 nmol L-1) were found in surface waters but rapidly declined at depths greater than 200m and increased again in the nepheloid layer (>50 nmol L-1). Striking seasonal differences in PIC content and PIC profile shape were observed particularly at near shore stations P2, P4, P8 and P12. The results from this research, including sensor evolution and calibration performance, will be presented.

Effects of Chromium Picolinate on Vascular Reactivity and Cardiac Ischemia Reperfusion Injury in Spontaneously Hypertensive Rats

PubMed Central

Abebe, Worku; Liu, Jun Yao; Wimborne, Hereward; Mozaffari, Mahmood S.

2013-01-01

Chromium picolinate [Cr(pic)3] is a nutritional supplement widely promoted to exert beneficial metabolic effects in patients with type 2 diabetes/impaired glucose tolerance. Frequent comorbidities in these individuals include systemic hypertension, abnormal vascular function and ischemic heart disease but information on effects of the supplement on these aspects is sparse. Utilizing male spontaneously hypertensive rats (SHR), we examined potential impact of Cr(pic)3 on blood pressure, vascular reactivity and myocardial ischemia reperfusion injury (IRI). Dietary Cr(pic)3 supplementation (as 10 mg chromium/kg diet for 6 weeks) did not affect blood pressure of the SHR. Also, neither norepinephrine (NE) and potassium chloride (KCl)-induced contractility nor sodium nitroprusside (SNP)-induced relaxation of aortic smooth muscle from the SHR was altered by Cr(pic)3 treatment. However, Cr(pic)3 augmented endothelium-dependent relaxation of aortas, produced by acetylcholine (ACh), and this effect was abolished by N-nitro-L-arginine methyl ester (L-NAME) suggesting induction of nitric oxide (NO) production/release. Treatment with Cr(pic)3 did not affect baseline coronary flow rate and rate-pressure-product (RPP) or infarct size following regional IRI. Nonetheless, Cr(pic)3 treatment was associated with improved coronary flow and recovery of myocardial contractility and relaxation following ischemia reperfusion insult. In conclusion, dietary Cr(pic)3 treatment of SHR neither alters blood pressure nor vascular smooth muscle reactivity, but causes enhancement of endothelium-dependent vasorelaxation associated with NO production/release. Additionally, while the treatment does not affect infarct size, it improves functional recovery of the viable portion of the myocardium following IRI. PMID:20885007

Effects of chromium picolinate on vascular reactivity and cardiac ischemia-reperfusion injury in spontaneously hypertensive rats.

PubMed

Abebe, Worku; Liu, Jun Yao; Wimborne, Hereward; Mozaffari, Mahmood S

2010-01-01

Chromium picolinate [Cr(pic)(3)] is a nutritional supplement widely promoted to exert beneficial metabolic effects in patients with type 2 diabetes/impaired glucose tolerance. Frequent comorbidities in these individuals include systemic hypertension, abnormal vascular function and ischemic heart disease, but information on the effects of the supplement on these aspects is sparse. Utilizing male spontaneously hypertensive rats (SHR), we examined the potential impact of Cr(pic)(3) on blood pressure, vascular reactivity and myocardial ischemia-reperfusion injury (IRI). Dietary Cr(pic)(3) supplementation (as 10 mg chromium/kg diet for six weeks) did not affect blood pressure of the SHR. Also, neither norepinephrine (NE) and potassium chloride (KCl)-induced contractility nor sodium nitroprusside (SNP)-induced relaxation of aortic smooth muscle from the SHR was altered by Cr(pic)(3) treatment. However, Cr(pic)(3) augmented endothelium-dependent relaxation of aortas, produced by acetylcholine (ACh), and this effect was abolished by N-nitro-L-arginine methyl ester (L-NAME), suggesting induction of nitric oxide (NO) production/release. Treatment with Cr(pic)(3) did not affect baseline coronary flow rate and rate-pressure-product (RPP) or infarct size following regional IRI. Nonetheless, Cr(pic)(3) treatment was associated with improved coronary flow and recovery of myocardial contractility and relaxation following ischemia-reperfusion insult. In conclusion, dietary Cr(pic)(3) treatment of SHR alters neither blood pressure nor vascular smooth muscle reactivity but causes enhancement of endothelium-dependent vasorelaxation associated with NO production/release. Additionally, while the treatment does not affect infarct size, it improves functional recovery of the viable portion of the myocardium following IRI.

Freeing data through The Polar Information Commons

NASA Astrophysics Data System (ADS)

de Bruin, T.; Chen, R. S.; Parsons, M. A.; Carlson, D. J.; Cass, K.; Finney, K.; Wilbanks, J.; Jochum, K.

2010-12-01

The polar regions are changing rapidly with dramatic global effect. Wise management of resources, improved decision support, and effective international cooperation on resource and geopolitical issues require deeper understanding and better prediction of these changes. Unfortunately, polar data and information remain scattered, scarce, and sporadic. Inspired by the Antarctic Treaty of 1959 that established the Antarctic as a global commons to be used only for peaceful purposes and scientific research, we assert that data and information about the polar regions are themselves “public goods” that should be shared ethically and with minimal constraint. ICSU’s Committee on Data (CODATA) therefore started the Polar Information Commons (PIC) as an open, virtual repository for vital scientific data and information. The PIC provides a shared, community-based cyber-infrastructure fostering innovation, improving scientific efficiency, and encouraging participation in polar research, education, planning, and management. The PIC builds on the legacy of the International Polar Year (IPY), providing a long-term framework for access to and preservation of both existing and future data and information about the polar regions. Rapid change demands rapid data access. The PIC system enables scientists to quickly expose their data to the world and share them through open protocols on the Internet. A PIC digital label will alert users and data centers to new polar data and ensure that usage rights are clear. The PIC utilizes the Science Commons Protocol for Implementing Open Access Data, which promotes open data access through the public domain coupled with community norms of practice to ensure use of data in a fair and equitable manner. A set of PIC norms has been developed in consultation with key polar data organizations and other stakeholders. We welcome inputs from the broad science community as we further develop and refine the PIC approach and move ahead with implementation.

On the Impact of Electrostatic Correlations on the Double-Layer Polarization of a Spherical Particle in an Alternating Current Field.

PubMed

Alidoosti, Elaheh; Zhao, Hui

2018-05-15

At concentrated electrolytes, the ion-ion electrostatic correlation effect is considered an important factor in electrokinetics. In this paper, we compute, in theory and simulation, the dipole moment for a spherical particle (charged, dielectric) under the action of an alternating electric field using the modified continuum Poisson-Nernst-Planck (PNP) model by Bazant et al. [ Double Layer in Ionic Liquids: Overscreening Versus Crowding . Phys. Rev. Lett. 2011 , 106 , 046102 ] We investigate the dependency of the dipole moment in terms of frequency and its variation with such quantities like ζ-potential, electrostatic correlation length, and double-layer thickness. With thin electric double layers, we develop simple models through performing an asymptotic analysis of the modified PNP model. We also present numerical results for an arbitrary Debye screening length and electrostatic correlation length. From the results, we find a complicated impact of electrostatic correlations on the dipole moment. For instance, with increasing the electrostatic correlation length, the dipole moment decreases and reaches a minimum and then it goes up. This is because of initially decreasing of surface conduction and finally increasing due to the impact of ion-ion electrostatic correlations on ion's convection and migration. Also, we show that in contrast to the standard PNP model, the modified PNP model can qualitatively explain the data from the experimental results in multivalent electrolytes.

Study of negative hydrogen ion beam optics using the 3D3V PIC model

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

Miyamoto, K., E-mail: kmiyamot@naruto-u.ac.jp; Nishioka, S.; Goto, I.

The mechanism of negative ion extraction under real conditions with the complex magnetic field is studied by using the 3D PIC simulation code. The extraction region of the negative ion source for the negative ion based neutral beam injection system in fusion reactors is modelled. It is shown that the E x B drift of electrons is caused by the magnetic filter and the electron suppression magnetic field, and the resultant asymmetry of the plasma meniscus. Furthermore, it is indicated that that the asymmetry of the plasma meniscus results in the asymmetry of negative ion beam profile including the beammore » halo. It could be demonstrated theoretically that the E x B drift is not significantly weakened by the elastic collisions of the electrons with neutral particles.« less

Copper Import into the Mitochondrial Matrix in Saccharomyces cerevisiae Is Mediated by Pic2, a Mitochondrial Carrier Family Protein*

PubMed Central

Vest, Katherine E.; Leary, Scot C.; Winge, Dennis R.; Cobine, Paul A.

2013-01-01

Saccharomyces cerevisiae must import copper into the mitochondrial matrix for eventual assembly of cytochrome c oxidase. This copper is bound to an anionic fluorescent molecule known as the copper ligand (CuL). Here, we identify for the first time a mitochondrial carrier family protein capable of importing copper into the matrix. In vitro transport of the CuL into the mitochondrial matrix was saturable and temperature-dependent. Strains with a deletion of PIC2 grew poorly on copper-deficient non-fermentable medium supplemented with silver and under respiratory conditions when challenged with a matrix-targeted copper competitor. Mitochondria from pic2Δ cells had lower total mitochondrial copper and exhibited a decreased capacity for copper uptake. Heterologous expression of Pic2 in Lactococcus lactis significantly enhanced CuL transport into these cells. Therefore, we propose a novel role for Pic2 in copper import into mitochondria. PMID:23846699

Copper import into the mitochondrial matrix in Saccharomyces cerevisiae is mediated by Pic2, a mitochondrial carrier family protein.

PubMed

Vest, Katherine E; Leary, Scot C; Winge, Dennis R; Cobine, Paul A

2013-08-16

Saccharomyces cerevisiae must import copper into the mitochondrial matrix for eventual assembly of cytochrome c oxidase. This copper is bound to an anionic fluorescent molecule known as the copper ligand (CuL). Here, we identify for the first time a mitochondrial carrier family protein capable of importing copper into the matrix. In vitro transport of the CuL into the mitochondrial matrix was saturable and temperature-dependent. Strains with a deletion of PIC2 grew poorly on copper-deficient non-fermentable medium supplemented with silver and under respiratory conditions when challenged with a matrix-targeted copper competitor. Mitochondria from pic2Δ cells had lower total mitochondrial copper and exhibited a decreased capacity for copper uptake. Heterologous expression of Pic2 in Lactococcus lactis significantly enhanced CuL transport into these cells. Therefore, we propose a novel role for Pic2 in copper import into mitochondria.

Multirate Particle-in-Cell Time Integration Techniques of Vlasov-Maxwell Equations for Collisionless Kinetic Plasma Simulations

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

Chen, Guangye; Chacon, Luis; Knoll, Dana Alan

2015-07-31

A multi-rate PIC formulation was developed that employs large timesteps for slow field evolution, and small (adaptive) timesteps for particle orbit integrations. Implementation is based on a JFNK solver with nonlinear elimination and moment preconditioning. The approach is free of numerical instabilities (ω peΔt >>1, and Δx >> λ D), and requires many fewer dofs (vs. explicit PIC) for comparable accuracy in challenging problems. Significant gains (vs. conventional explicit PIC) may be possible for large scale simulations. The paper is organized as follows: Vlasov-Maxwell Particle-in-cell (PIC) methods for plasmas; Explicit, semi-implicit, and implicit time integrations; Implicit PIC formulation (Jacobian-Free Newton-Krylovmore » (JFNK) with nonlinear elimination allows different treatments of disparate scales, discrete conservation properties (energy, charge, canonical momentum, etc.)); Some numerical examples; and Summary.« less

Interferometric imaging using Si3N4 photonic integrated circuits for a SPIDER imager.

PubMed

Su, Tiehui; Liu, Guangyao; Badham, Katherine E; Thurman, Samuel T; Kendrick, Richard L; Duncan, Alan; Wuchenich, Danielle; Ogden, Chad; Chriqui, Guy; Feng, Shaoqi; Chun, Jaeyi; Lai, Weicheng; Yoo, S J B

2018-05-14

This paper reports design, fabrication, and experimental demonstration of a silicon nitride photonic integrated circuit (PIC). The PIC is capable of conducting one-dimensional interferometric imaging with twelve baselines near λ = 1100-1600 nm. The PIC consists of twelve waveguide pairs, each leading to a multi-mode interferometer (MMI) that forms broadband interference fringes or each corresponding pair of the waveguides. Then an 18 channel arrayed waveguide grating (AWG) separates the combined signal into 18 signals of different wavelengths. A total of 103 sets of fringes are collected by the detector array at the output of the PIC. We keep the optical path difference (OPD) of each interferometer baseline to within 1 µm to maximize the visibility of the interference measurement. We also constructed a testbed to utilize the PIC for two-dimension complex visibility measurement with various targets. The experiment shows reconstructed images in good agreement with theoretical predictions.

Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture

PubMed Central

Eychenne, Thomas; Novikova, Elizaveta; Barrault, Marie-Bénédicte; Alibert, Olivier; Boschiero, Claire; Peixeiro, Nuno; Cornu, David; Redeker, Virginie; Kuras, Laurent; Nicolas, Pierre; Werner, Michel; Soutourina, Julie

2016-01-01

Mediator is a large coregulator complex conserved from yeast to humans and involved in many human diseases, including cancers. Together with general transcription factors, it stimulates preinitiation complex (PIC) formation and activates RNA polymerase II (Pol II) transcription. In this study, we analyzed how Mediator acts in PIC assembly using in vivo, in vitro, and in silico approaches. We revealed an essential function of the Mediator middle module exerted through its Med10 subunit, implicating a key interaction between Mediator and TFIIB. We showed that this Mediator–TFIIB link has a global role on PIC assembly genome-wide. Moreover, the amplitude of Mediator's effect on PIC formation is gene-dependent and is related to the promoter architecture in terms of TATA elements, nucleosome occupancy, and dynamics. This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts. PMID:27688401

Magnetosphere Modeling: From Cartoons to Simulations

NASA Astrophysics Data System (ADS)

Gombosi, T. I.

2017-12-01

Over the last half a century physics-based global computer simulations became a bridge between experiment and basic theory and now it represents the "third pillar" of geospace research. Today, many of our scientific publications utilize large-scale simulations to interpret observations, test new ideas, plan campaigns, or design new instruments. Realistic simulations of the complex Sun-Earth system have been made possible by the dramatically increased power of both computing hardware and numerical algorithms. Early magnetosphere models were based on simple E&M concepts (like the Chapman-Ferraro cavity) and hydrodynamic analogies (bow shock). At the beginning of the space age current system models were developed culminating in the sophisticated Tsyganenko-type description of the magnetic configuration. The first 3D MHD simulations of the magnetosphere were published in the early 1980s. A decade later there were several competing global models that were able to reproduce many fundamental properties of the magnetosphere. The leading models included the impact of the ionosphere by using a height-integrated electric potential description. Dynamic coupling of global and regional models started in the early 2000s by integrating a ring current and a global magnetosphere model. It has been recognized for quite some time that plasma kinetic effects play an important role. Presently, global hybrid simulations of the dynamic magnetosphere are expected to be possible on exascale supercomputers, while fully kinetic simulations with realistic mass ratios are still decades away. In the 2010s several groups started to experiment with PIC simulations embedded in large-scale 3D MHD models. Presently this integrated MHD-PIC approach is at the forefront of magnetosphere simulations and this technique is expected to lead to some important advances in our understanding of magnetosheric physics. This talk will review the evolution of magnetosphere modeling from cartoons to current systems, to global MHD to MHD-PIC and discuss the role of state-of-the-art models in forecasting space weather.

Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1

PubMed Central

Chu, Wen-Ting; Clarke, Jane; Shammas, Sarah L.; Wang, Jin

2017-01-01

PUMA, which belongs to the BH3-only protein family, is an intrinsically disordered protein (IDP). It binds to its cellular partner Mcl-1 through its BH3 motif, which folds upon binding into an α helix. We have applied a structure-based coarse-grained model, with an explicit Debye—Hückel charge model, to probe the importance of electrostatic interactions both in the early and the later stages of this model coupled folding and binding process. This model was carefully calibrated with the experimental data on helical content and affinity, and shown to be consistent with previously published experimental data on binding rate changes with respect to ionic strength. We find that intramolecular electrostatic interactions influence the unbound states of PUMA only marginally. Our results further suggest that intermolecular electrostatic interactions, and in particular non-native electrostatic interactions, are involved in formation of the initial encounter complex. We are able to reveal the binding mechanism in more detail than is possible using experimental data alone however, and in particular we uncover the role of non-native electrostatic interactions. We highlight the potential importance of such electrostatic interactions for describing the binding reactions of IDPs. Such approaches could be used to provide predictions for the results of mutational studies. PMID:28369057

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.

Particle-in-cell modeling for MJ scale dense plasma focus with varied anode shape

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

Link, A., E-mail: link6@llnl.gov; Halvorson, C., E-mail: link6@llnl.gov; Schmidt, A.

2014-12-15

Megajoule scale dense plasma focus (DPF) Z-pinches with deuterium gas fill are compact devices capable of producing 10{sup 12} neutrons per shot but past predictive models of large-scale DPF have not included kinetic effects such as ion beam formation or anomalous resistivity. We report on progress of developing a predictive DPF model by extending our 2D axisymmetric collisional kinetic particle-in-cell (PIC) simulations from the 4 kJ, 200 kA LLNL DPF to 1 MJ, 2 MA Gemini DPF using the PIC code LSP. These new simulations incorporate electrodes, an external pulsed-power driver circuit, and model the plasma from insulator lift-off throughmore » the pinch phase. To accommodate the vast range of relevant spatial and temporal scales involved in the Gemini DPF within the available computational resources, the simulations were performed using a new hybrid fluid-to-kinetic model. This new approach allows single simulations to begin in an electron/ion fluid mode from insulator lift-off through the 5-6 μs run-down of the 50+ cm anode, then transition to a fully kinetic PIC description during the run-in phase, when the current sheath is 2-3 mm from the central axis of the anode. Simulations are advanced through the final pinch phase using an adaptive variable time-step to capture the fs and sub-mm scales of the kinetic instabilities involved in the ion beam formation and neutron production. Validation assessments are being performed using a variety of different anode shapes, comparing against experimental measurements of neutron yield, neutron anisotropy and ion beam production.« less

Planning, Management and Evaluation: Realizing PIC Potential. Private Industry Council Guide. Working Draft.

ERIC Educational Resources Information Center

National Alliance of Business, Inc., Washington, DC.

This Planning, Management, and Evaluation (PME) guide was developed by the National Alliance of Business as part of its program of management assistance for Private Industry Councils (PICs). The guide is a tool which PICs can use to improve their capability to plan, manage, and evaluate the programs which they administer, and to establish locally…

PICs, TECs and LECs: Lessons to Be Learnt from the Differences between the USA Private Industry Councils and Britain's Training and Enterprise Councils.

ERIC Educational Resources Information Center

Bennett, Robert J.

1994-01-01

Comparison of Britain's Training and Enterprise Councils/Local Enterprise Companies with the United States' Private Industry Councils (PICs) shows common problems: inadequate financing, labor market fragmentation, staff turnover, and lack of national strategy. PICs have a clearer mission and greater success in developing partnerships with local…

Private Industry Councils: Examining Their Mission under the Job Training Partnership Act. Special Report Number 35.

ERIC Educational Resources Information Center

National Commission for Employment Policy (DOL), Washington, DC.

A number of findings and recommendations regarding the mission of Private Industry Councils (PICs) under the Job Training Partnership ACT (JTPA) were developed based on information collected in several ways: a focus group of PICs, roundtable discussions held nationwide with staff from nearly 100 PICs in 45 states, and canvasses of more than 200…

A spectral, quasi-cylindrical and dispersion-free Particle-In-Cell algorithm

DOE PAGES

Lehe, Remi; Kirchen, Manuel; Andriyash, Igor A.; ...

2016-02-17

We propose a spectral Particle-In-Cell (PIC) algorithm that is based on the combination of a Hankel transform and a Fourier transform. For physical problems that have close-to-cylindrical symmetry, this algorithm can be much faster than full 3D PIC algorithms. In addition, unlike standard finite-difference PIC codes, the proposed algorithm is free of spurious numerical dispersion, in vacuum. This algorithm is benchmarked in several situations that are of interest for laser-plasma interactions. These benchmarks show that it avoids a number of numerical artifacts, that would otherwise affect the physics in a standard PIC algorithm - including the zero-order numerical Cherenkov effect.

Library services and user satisfaction in developing countries: a case study.

PubMed

Mairaj, Muhammad Ijaz; Naseer, Mirza Muhammad

2013-12-01

Punjab Institute of Cardiology (PIC) is a recognised teaching hospital for cardiac care in the Punjab province of Pakistan. PIC has established a library to fulfil the research and information needs of health care professionals. This study aims to evaluate the satisfaction of users with the services of PIC library. A purposive sample of 15 health care professionals was selected. A semistructured interview technique based on an interview guide was used for collection of data. The data were qualitatively analysed using a thematic approach. Users of PIC library were satisfied with the library collection, organisation, reference and circulation services, staff attitudes, cooling and heating. They were concerned about library space, hours, furniture and environment, and suggested more availability of electronic library services, newer collections, better Internet access and comfortable furniture. The study proved useful to investigate users' satisfaction with the services of PIC library. It concludes that the PIC library should maintain and strengthen the services with which users are satisfied, and improve those about which they are concerned. The study will be useful to libraries in other developing countries for improvement in their services. © 2013 The authors. Health Information and Libraries Journal © 2013 Health Libraries Group.

Chromium picolinate supplementation in women: effects on body weight, composition, and iron status.

PubMed

Lukaski, Henry C; Siders, William A; Penland, James G

2007-03-01

This study tested the hypothesis that supplementation of chromium picolinate (CrPic), 200 microg Cr/d, compared with an equivalent amount of picolinic acid (1720 microg) in CrPic and placebo, decreases body weight, alters body composition, and reduces iron status of women fed diets of constant energy and nutrients. We fed 83 women nutritionally balanced diets, used anthropometry and dual x-ray absorptiometry to assess body composition, and measured serum and urinary Cr and biochemical indicators of iron status before and serially every 4 wk for 12 wk in a double-blind, randomized trial. CrPic supplementation increased (P < 0.0001) serum Cr concentration and urinary Cr excretion compared with picolinic acid and placebo. CrPic did not affect body weight or fat, although all groups lost (P < 0.05) weight and fat; it did not affect fat-free, mineral-free mass or measurements of iron status. Under conditions of controlled energy intake, CrPic supplementation of women did not independently influence body weight or composition or iron status. Thus, claims that supplementation of 200 microg of Cr as CrPic promotes weight loss and body composition changes are not supported.

Chromium picolinate induced apoptosis of lymphocytes and the signaling mechanisms thereof

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

Jana, Mahadevan; Rajaram, Anantanarayanan; Rajaram, Rama

2009-06-15

Cr(III)(picolinate){sub 3} [Cr(III)(pic){sub 3}] is currently used as a nutritional supplement and for treating Type-2 diabetes. The effect of Cr(III)(pic){sub 3} uptake in peripheral blood lymphocytes is investigated in this study. From the cytotoxicity data, DNA fragmentation pattern, Annexin V staining, TUNEL positivity and the ultrastructural characteristics such as chromatin condensation and formation of apoptotic bodies, it is clear that Cr(III)(pic){sub 3} induces a concentration dependent apoptosis. It is shown that reactive oxygen species (ROS) produced by treatment with Cr(III)(pic){sub 3} leads to apoptosis, since we find that pretreatment with N-acetyl cysteine inhibits the process. Using Western blotting technique andmore » fluorescence measurements, the downstream signaling molecules have also been identified. Cr(III)(pic){sub 3} treatment leads to collapse of the mitochondrial membrane potential, Bax expression, increase in cytosolic cytochrome c content and active caspase-3 and DNA fragmentation and all these manifestations are reduced by pretreating the lymphocytes with N-acetyl cysteine. Thus, it is shown that Cr(III)(pic){sub 3} is cytotoxic to lymphocytes with ROS and mitochondrial events playing a role in bringing about apoptosis.« less

Parallel Higher-order Finite Element Method for Accurate Field Computations in Wakefield and PIC Simulations

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

Candel, A.; Kabel, A.; Lee, L.

Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell)more » approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.« less

Characterization of punctate inner choroidopathy using enhanced depth imaging optical coherence tomography.

PubMed

Zarranz-Ventura, Javier; Sim, Dawn A; Keane, Pearse A; Patel, Praveen J; Westcott, Mark C; Lee, Richard W; Tufail, Adnan; Pavesio, Carlos E

2014-09-01

To perform qualitative and quantitative analyses of retinal and choroidal morphology in patients with punctate inner choroidopathy (PIC) using enhanced depth imaging optical coherence tomography (EDI-OCT). Cross-sectional, consecutive series. A total of 2242 patients attending 2 tertiary referral uveitis clinics at Moorfields Eye Hospital were screened; 46 patients with PIC diagnosis were identified, and 35 eyes (35 patients) had clinically inactive PIC had EDI-OCT images that met the inclusion criteria. Punctate inner choroidopathy lesions were qualitatively assessed for retinal features, such as (1) focal elevation of the retinal pigment epithelium (RPE), (2) focal atrophy of the outer retina/RPE, and (3) presence of sub-RPE hyperreflective deposits and choroidal features: (a) presence of focal hyperreflective dots in the inner choroid and (b) focal thinning of the choroid adjacent to PIC lesions. Quantitative analyses of the retina, choroid, and choroidal sublayers were performed, and associations with clinical and demographic data were examined. Prevalence of each lesion pattern and thickness of retinal and choroidal layers. A total of 90 discrete PIC lesions were captured; 46.6% of PIC lesions consisted of focal atrophy of the outer retina and RPE; 34.4% consisted of sub-RPE hyperreflective deposits; and 18.8% consisted of localized RPE elevation with underlying hyporeflective space. Focal hyperreflective dots were seen in the inner choroid of 68.5% of patients, with 17.1% of eyes presenting focal choroidal thinning underlying PIC lesions. By excluding high myopes, patients with "atypical" PIC had reduced retinal thickness compared with patients with "typical" PIC (246.65±30.2 vs. 270.05±24.6 μm; P = 0.04), and greater disease duration was associated with decreases in retinal thickness (r = -0.53; P = 0.01). A significant correlation was observed between best-corrected visual acuity and foveal retinal thickness (r = -0.40; P = 0.03). In a large series of patients with clinically inactive PIC, one fifth of the lesions analyzed revealed RPE elevation with underlying hyporeflective space, described before as a sign of activity and suggesting subclinical inflammation. Retinal thickness seems to be associated with disease type and duration of disease in non-highly myopic eyes. Improved visualization of the inner choroid using EDI-OCT may allow noninvasive assessment of inflammatory status. Copyright © 2014 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Body mass index is a practical preoperative nutritional index for postoperative infectious complications after intestinal resection in patients with Crohn's disease

PubMed Central

Zhu, Yibin; Zhou, Wei; Qi, Weilin; Liu, Wei; Chen, Mingyu; Zhu, Hepan; Xiang, Jianjian; Xie, Qingwen; Chen, Pengpeng

2017-01-01

Abstract The patients with Crohn's disease (CD) are often accompanied with nutritional deficiencies. Compared with other intestinal benign disease, patients with CD have the higher risk of developing postoperative complications following intestinal resection. The aim of this study was to investigate the risk factors for postoperative infectious complications (PICs) after intestinal resection for CD, as well as search a practical preoperative nutritional index for PICs in patients with CD. A total of 122 patients who underwent intestinal resection for CD during 2011 to 2015 were retrospectively analyzed. After operation, 28 (22.95%) patients experienced PICs. Compared with the non-PICs group, the patients with PICs have the lower preoperative body mass index (BMI) (16.96 ± 2.33 vs 19.53 ± 2.49 kg/m2, P < .001), lower albumin (ALB) (33.64 ± 5.58 vs 36.55 ± 5.69 g/L, P = .013), higher C-reactive protein (CRP) level (30.44 ± 37.06 vs 15.99 ± 33.30 mg/L, P = .052), and longer hospital stay (22.64 ± 9.93 vs 8.90 ± 4.32 days, P < .001). By analyzing the receiver-operating characteristic (ROC) curve, BMI have better value in predicting the occurrence of PICs than ALB. The areas under the ROC curves of BMI for PICs was 0.784 (95% confidence interval 0.690–0.878, P < .001) with an optimal diagnostic cut-off value of 17.5 kg/m2. In the univariate and multivariate analysis, BMI < 17.5 kg/m2 (P = .001), ALB < 33.6 g/L (P = .024), CRP ≥ 10 mg/L (P = .026) were risk factors for PICs. Patients with a lower preoperative BMI (BMI < 17.5 kg/m2) had a 7.35 times greater risk of PICs. Therefore, preoperative BMI could be regarded as a practical preoperative nutritional index for evaluating the nutritional preparation sufficiency before CD operations. Preoperative treatment with the aim of reducing CRP level and improving the patient's nutritional status may be helpful to reduce the rate of PICs. PMID:28591060

Impact of the Quality of Bowel Cleansing on the Efficacy of Colonic Cancer Screening: A Prospective, Randomized, Blinded Study

PubMed Central

2015-01-01

Objectives Efficacy of two low volume bowel cleansing preparations, polyethylene glycol plus ascorbate (PEG+Asc) and sodium picosulfate/magnesium citrate (NaPic/MgCit), were compared for polyp and adenoma detection rate (PDR and ADR) and overall cleansing ability. Primary endpoint was PDR (the number of patients with ≥1 polypoid or flat lesion recorded by the colonoscopist). Methods Diagnostic, surveillance or screening colonoscopy patients were enrolled into this investigator-blinded, multi-center Phase IV study and randomized 1:1 to receive PEG+Asc (administered the evening before and the morning of colonoscopy, per label) or NaPic/MgCit (administered in the morning and afternoon the day before colonoscopy, per label). The blinded colonoscopist documented any lesion and assessed cleansing quality (Harefield Cleansing Scale). Results Of 394 patients who completed the study, 393 (PEG+Asc, N=200; NaPic/MgCit, N=193) had a colonoscopy. Overall PDR for PEG+Asc versus NaPic/MgCit was 51.5% versus 44.0%, p=0.139. PDR and ADR on the right side of the bowel were significantly higher with PEG+Asc versus NaPic/MgCit (PDR: 56[28.0%] versus 32[16.6%], p=0.007; ADR: 42[21.0%] versus 23[11.9%], p=0.015), as was detection of flat lesions (43[21.5%] versus 25[13.0%], p=0.025). Cleansing quality was better with PEG+Asc than NaPic/MgCit (98.5% versus 57.5% considered successful cleansing). Overall, there were 132 treatment-emergent adverse events (93 versus 39 for PEG+Asc and NaPic/MgCit, respectively). These were mainly mild abdominal symptoms, all of which were reported for higher proportions of patients in the PEG+Asc than NaPic/MgCit group. Twice as many patients in the NaPic/MgCit versus the PEG+Asc group reported tolerance of cleansing solution as ‘very good’. Conclusions Compared with NaPic/MgCit, PEG+Asc may be more efficacious for overall cleansing ability, and subsequent detection of right-sided and flat lesions. This is likely attributable to the different administration schedules of the two bowel cleansing preparations, which may positively impact the detection and prevention of colorectal cancer, thereby improving mortality rates. Trial Registration ClinicalTrials.gov NCT01689792. PMID:25950434

Dust environment of an airless object: A phase space study with kinetic models

NASA Astrophysics Data System (ADS)

Kallio, E.; Dyadechkin, S.; Fatemi, S.; Holmström, M.; Futaana, Y.; Wurz, P.; Fernandes, V. A.; Álvarez, F.; Heilimo, J.; Jarvinen, R.; Schmidt, W.; Harri, A.-M.; Barabash, S.; Mäkelä, J.; Porjo, N.; Alho, M.

2016-01-01

The study of dust above the lunar surface is important for both science and technology. Dust particles are electrically charged due to impact of the solar radiation and the solar wind plasma and, therefore, they affect the plasma above the lunar surface. Dust is also a health hazard for crewed missions because micron and sub-micron sized dust particles can be toxic and harmful to the human body. Dust also causes malfunctions in mechanical devices and is therefore a risk for spacecraft and instruments on the lunar surface. Properties of dust particles above the lunar surface are not fully known. However, it can be stated that their large surface area to volume ratio due to their irregular shape, broken chemical bonds on the surface of each dust particle, together with the reduced lunar environment cause the dust particles to be chemically very reactive. One critical unknown factor is the electric field and the electric potential near the lunar surface. We have developed a modelling suite, Dusty Plasma Environments: near-surface characterisation and Modelling (DPEM), to study globally and locally dust environments of the Moon and other airless bodies. The DPEM model combines three independent kinetic models: (1) a 3D hybrid model, where ions are modelled as particles and electrons are modelled as a charged neutralising fluid, (2) a 2D electrostatic Particle-in-Cell (PIC) model where both ions and electrons are treated as particles, and (3) a 3D Monte Carlo (MC) model where dust particles are modelled as test particles. The three models are linked to each other unidirectionally; the hybrid model provides upstream plasma parameters to be used as boundary conditions for the PIC model which generates the surface potential for the MC model. We have used the DPEM model to study properties of dust particles injected from the surface of airless objects such as the Moon, the Martian moon Phobos and the asteroid RQ36. We have performed a (v0, m/q)-phase space study where the property of dust particles at different initial velocity (v0) and initial mass per charge (m/q) ratio were analysed. The study especially identifies regions in the phase space where the electric field within a non-quasineutral plasma region above the surface of the object, the Debye layer, becomes important compared with the gravitational force. Properties of the dust particles in the phase space region where the electric field plays an important role are studied by a 3D Monte Carlo model. The current DPEM modelling suite does not include models of how dust particles are initially injected from the surface. Therefore, the presented phase space study cannot give absolute 3D dust density distributions around the analysed airless objects. For that, an additional emission model is necessary, which determines how many dust particles are emitted at various places on the analysed (v0, m/q)-phase space. However, this study identifies phase space regions where the electric field within the Debye layer plays an important role for dust particles. Overall, the initial results indicate that when a realistic dust emission model is available, the unified lunar based DPEM modelling suite is a powerful tool to study globally and locally the dust environments of airless bodies such as planetary moons, Mercury, asteroids and non-active comets far from the Sun.

The Effect of Chromium Picolinate Supplementation on the Pancreas and Macroangiopathy in Type II Diabetes Mellitus Rats

PubMed Central

Huang, Shan; Peng, Wenfang; Jiang, Xiaohong; Shao, Kan; Xia, Lili; Tang, Yubin; Qiu, Jiayin

2014-01-01

Purpose. The aim was to explore the effect of the chromium picolinate (CrPic) administration on the pancreas and macroangiopathy of type II diabetes mellitus rats. Methods. The type II diabetes mellitus (T2DM) rat model was induced by low-dose streptozotocin (STZ). The rats were randomly divided into 5 groups (ten rats in each group). After supplementing CrPic for 15 weeks, the histopathological examination was performed by hematoxylin-eosin (HE) staining. Serum insulin and NO level were determined by radioimmunoassay and colorimetry, respectively. Serum glycosylated hemoglobin (HbA1C), adiponectin (APN), advanced glycation end products (AGES), and apelin were measured by ELISA. Real-time reverse transcription polymerase chain reaction (RT-PCR) was applied for detecting the mRNA expression of APN and apelin. Results. After CrPic treatment, compared with the T2DM control group (group 2), pancreas sections stained with HE showed the completed pancreatic cells structure and no inflammatory infiltration in groups 4 and 5. In addition, the levels of serum NO and insulin were significantly increased and the serum levels of HbA1C, AGES, APN, and apelin were significantly decreased in groups 4 and 5 compared with group 2. The mRNA expression of APN and apelin in groups 4 and 5 was also recovered to the normal level. Conclusion. CrPic can recover the function of Β-cells and alleviate macroangiopathy in STZ-induced T2DM rats. PMID:25054160

The effect of chromium picolinate supplementation on the pancreas and macroangiopathy in type II diabetes mellitus rats.

PubMed

Huang, Shan; Peng, Wenfang; Jiang, Xiaohong; Shao, Kan; Xia, Lili; Tang, Yubin; Qiu, Jiayin

2014-01-01

The aim was to explore the effect of the chromium picolinate (CrPic) administration on the pancreas and macroangiopathy of type II diabetes mellitus rats. The type II diabetes mellitus (T2DM) rat model was induced by low-dose streptozotocin (STZ). The rats were randomly divided into 5 groups (ten rats in each group). After supplementing CrPic for 15 weeks, the histopathological examination was performed by hematoxylin-eosin (HE) staining. Serum insulin and NO level were determined by radioimmunoassay and colorimetry, respectively. Serum glycosylated hemoglobin (HbA1C), adiponectin (APN), advanced glycation end products (AGES), and apelin were measured by ELISA. Real-time reverse transcription polymerase chain reaction (RT-PCR) was applied for detecting the mRNA expression of APN and apelin. After CrPic treatment, compared with the T2DM control group (group 2), pancreas sections stained with HE showed the completed pancreatic cells structure and no inflammatory infiltration in groups 4 and 5. In addition, the levels of serum NO and insulin were significantly increased and the serum levels of HbA1C, AGES, APN, and apelin were significantly decreased in groups 4 and 5 compared with group 2. The mRNA expression of APN and apelin in groups 4 and 5 was also recovered to the normal level. CrPic can recover the function of Β-cells and alleviate macroangiopathy in STZ-induced T2DM rats.

Operator-related aspects in endodontic malpractice claims in Finland.

PubMed

Vehkalahti, Miira M; Swanljung, Outi

2017-04-01

We analyzed operator-related differences in endodontic malpractice claims in Finland. Data comprised the endodontic malpractice claims handled at the Patient Insurance Centre (PIC) in 2002-2006 and 2011-2013. Two dental advisors at the PIC scrutinized the original documents of the cases (n = 1271). The case-related information included patient's age and gender, type of tooth, presence of radiographs, and methods of instrumentation and apex location. As injuries, we recorded broken instrument, perforation, injuries due to root canal irrigants/medicaments, and miscellaneous injuries. We categorized the injuries according to the PIC decisions as avoidable, unavoidable, or no injury. Operator-related information included dentist's age, gender, specialization, and service sector. We assessed level of patient documentation as adequate, moderate, or poor. Chi-squared tests, t-tests, and logistic regression modelling served in statistical analyses. Patients' mean age was 44.7 (range 8-85) years, and 71% were women. The private sector constituted 54% of claim cases. Younger patients, female dentists, and general practitioners predominated in the public sector. We found no sector differences in patients' gender, dentists' age, or type of injured tooth. PIC advisors confirmed no injury in 24% of claim cases; the advisors considered 65% of injury cases (n = 970) as avoidable and 35% as unavoidable. We found no operator-related differences in these figures. Working methods differed by operator's age and gender. Adequate patient documentation predominated in the public sector and among female, younger, or specialized dentists. Operator-related factors had no impact on endodontic malpractice claims.

Chromium picolinate inhibits resistin secretion in insulin-resistant 3T3-L1 adipocytes via activation of amp-activated protein kinase.

PubMed

Wang, Yi-Qun; Dong, Yi; Yao, Ming-Hui

2009-08-01

1. Chromium picolinate (CrPic) has been recommended as an alternative therapeutic regimen for Type 2 diabetes mellitus (T2DM). However, the molecular mechanism underlying the action of CrPic is poorly understood. 2. Using normal and insulin-resistant 3T3-L1 adipocytes, we examined the effects of CrPic on the gene transcription and secretion of adiponectin and resistin. In addition, using immunoblotting, ELISA and real-time reverse transcription-polymerase chain reaction (RT-PCR), we investigated the effects of 10 nmol/L CrPic for 24 h on AMP-activated protein kinase (AMPK) to determine whether this pathway contributed to the regulation of adiponectin and resistin expression and secretion. 3. Chromium picolinate did not modulate the expression of adiponectin and resistin; however, it did significantly inhibit the secretion of resistin, but not adiponectin, by normal and insulin-resistant 3T3-L1 adipocytes in vitro. Furthermore, although CrPic markedly elevated levels of phosphorylated AMPK and acetyl CoA carboxylase in 3T3-L1 adipocytes, it had no effect on the levels of AMPK alpha-1 and alpha-2 mRNA transcripts. Importantly, inhibition of AMPK by 2 h pretreatment of cells with 20 micromol/L compound C completely abolished the CrPic-induced suppression of resistin secretion. 4. In conclusion, the data suggest that CrPic inhibits resistin secretion via activation of AMPK in normal and insulin-resistant 3T3-L1 adipocytes.

Skeletal muscle-derived interstitial progenitor cells (PICs) display stem cell properties, being clonogenic, self-renewing, and multi-potent in vitro and in vivo.

PubMed

Cottle, Beverley J; Lewis, Fiona C; Shone, Victoria; Ellison-Hughes, Georgina M

2017-07-04

The development of cellular therapies to treat muscle wastage with disease or age is paramount. Resident muscle satellite cells are not currently regarded as a viable cell source due to their limited migration and growth capability ex vivo. This study investigated the potential of muscle-derived PW1 + /Pax7 - interstitial progenitor cells (PICs) as a source of tissue-specific stem/progenitor cells with stem cell properties and multipotency. Sca-1 + /PW1 + PICs were identified on tissue sections from hind limb muscle of 21-day-old mice, isolated by magnetic-activated cell sorting (MACS) technology and their phenotype and characteristics assessed over time in culture. Green fluorescent protein (GFP)-labelled PICs were used to determine multipotency in vivo in a tumour formation assay. Isolated PICs expressed markers of pluripotency (Oct3/4, Sox2, and Nanog), were clonogenic, and self-renewing with >60 population doublings, and a population doubling time of 15.8 ± 2.9 h. PICs demonstrated an ability to generate both striated and smooth muscle, whilst also displaying the potential to differentiate into cell types of the three germ layers both in vitro and in vivo. Moreover, PICs did not form tumours in vivo. These findings open new avenues for a variety of solid tissue engineering and regeneration approaches, utilising a single multipotent stem cell type isolated from an easily accessible source such as skeletal muscle.

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes.

PubMed

Balasubramaniam, Muthukumar; Davids, Benem; Addai, Amma B; Pandhare, Jui; Dash, Chandravanu

2017-02-22

HIV-1 envelope proteins engage cognate receptors on the target cell surface, which leads to viral-cell membrane fusion followed by the release of the viral capsid (CA) core into the cytoplasm. Subsequently, the viral Reverse Transcriptase (RT), as part of a namesake nucleoprotein complex termed the Reverse Transcription Complex (RTC), converts the viral single-stranded RNA genome into a double-stranded DNA copy (vDNA). This leads to the biogenesis of another nucleoprotein complex, termed the pre-integration complex (PIC), composed of the vDNA and associated virus proteins and host factors. The PIC-associated viral integrase (IN) orchestrates the integration of the vDNA into the host chromosomal DNA in a temporally and spatially regulated two-step process. First, the IN processes the 3' ends of the vDNA in the cytoplasm and, second, after the PIC traffics to the nucleus, it mediates integration of the processed vDNA into the chromosomal DNA. The PICs isolated from target cells acutely infected with HIV-1 are functional in vitro, as they are competent to integrate the associated vDNA into an exogenously added heterologous target DNA. Such PIC-based in vitro integration assays have significantly contributed to delineating the mechanistic details of retroviral integration and to discovering IN inhibitors. In this report, we elaborate upon an updated HIV-1 PIC assay that employs a nested real-time quantitative Polymerase Chain Reaction (qPCR)-based strategy for measuring the in vitro integration activity of isolated native PICs.

Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: exact results for spherical inclusions.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G

2011-09-28

We analyze the mathematically rigorous BIBEE (boundary-integral based electrostatics estimation) approximation of the mixed-dielectric continuum model of molecular electrostatics, using the analytically solvable case of a spherical solute containing an arbitrary charge distribution. Our analysis, which builds on Kirkwood's solution using spherical harmonics, clarifies important aspects of the approximation and its relationship to generalized Born models. First, our results suggest a new perspective for analyzing fast electrostatic models: the separation of variables between material properties (the dielectric constants) and geometry (the solute dielectric boundary and charge distribution). Second, we find that the eigenfunctions of the reaction-potential operator are exactly preserved in the BIBEE model for the sphere, which supports the use of this approximation for analyzing charge-charge interactions in molecular binding. Third, a comparison of BIBEE to the recent GBε theory suggests a modified BIBEE model capable of predicting electrostatic solvation free energies to within 4% of a full numerical Poisson calculation. This modified model leads to a projection-framework understanding of BIBEE and suggests opportunities for future improvements. © 2011 American Institute of Physics

Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

1992-01-01

The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.

Computation of Static Shapes and Voltages for Micromachined Deformable Mirrors with Nonlinear Electrostatic Actuators

NASA Technical Reports Server (NTRS)

Wang, P. K. C.; Hadaegh, F. Y.

1996-01-01

In modeling micromachined deformable mirrors with electrostatic actuators whose gap spacings are of the same order of magnitude as those of the surface deformations, it is necessary to use nonlinear models for the actuators. In this paper, we consider micromachined deformable mirrors modeled by a membrane or plate equation with nonlinear electrostatic actuator characteristics. Numerical methods for computing the mirror deformation due to given actuator voltages and the actuator voltages required for producing the desired deformations at the actuator locations are presented. The application of the proposed methods to circular deformable mirrors whose surfaces are modeled by elastic membranes is discussed in detail. Numerical results are obtained for a typical circular micromachined mirror with electrostatic actuators.

Flying mirror model for interaction of a super-intense laser pulse with a thin plasma layer: Transparency and shaping of linearly polarized laser pulses

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

Kulagin, Victor V.; Cherepenin, Vladimir A.; Hur, Min Sup

2007-11-15

A self-consistent one-dimensional (1D) flying mirror model is developed for description of an interaction of an ultra-intense laser pulse with a thin plasma layer (foil). In this model, electrons of the foil can have large longitudinal displacements and relativistic longitudinal momenta. An approximate analytical solution for a transmitted field is derived. Transmittance of the foil shows not only a nonlinear dependence on the amplitude of the incident laser pulse, but also time dependence and shape dependence in the high-transparency regime. The results are compared with particle-in-cell (PIC) simulations and a good agreement is ascertained. Shaping of incident laser pulses usingmore » the flying mirror model is also considered. It can be used either for removing a prepulse or for reducing the length of a short laser pulse. The parameters of the system for effective shaping are specified. Predictions of the flying mirror model for shaping are compared with the 1D PIC simulations, showing good agreement.« less

Hybrid 3D model for the interaction of plasma thruster plumes with nearby objects

NASA Astrophysics Data System (ADS)

Cichocki, Filippo; Domínguez-Vázquez, Adrián; Merino, Mario; Ahedo, Eduardo

2017-12-01

This paper presents a hybrid particle-in-cell (PIC) fluid approach to model the interaction of a plasma plume with a spacecraft and/or any nearby object. Ions and neutrals are modeled with a PIC approach, while electrons are treated as a fluid. After a first iteration of the code, the domain is split into quasineutral and non-neutral regions, based on non-neutrality criteria, such as the relative charge density and the Debye length-to-cell size ratio. At the material boundaries of the former quasineutral region, a dedicated algorithm ensures that the Bohm condition is met. In the latter non-neutral regions, the electron density and electric potential are obtained by solving the coupled electron momentum balance and Poisson equations. Boundary conditions for both the electric current and potential are finally obtained with a plasma sheath sub-code and an equivalent circuit model. The hybrid code is validated by applying it to a typical plasma plume-spacecraft interaction scenario, and the physics and capabilities of the model are finally discussed.

Chromium nanoparticle exhibits higher absorption efficiency than chromium picolinate and chromium chloride in Caco-2 cell monolayers.

PubMed

Zha, L-Y; Xu, Z-R; Wang, M-Q; Gu, L-Y

2008-04-01

This study was conducted to determine whether chromium nanoparticle (CrNano) exhibited higher absorption efficiency and possessed unique absorption mechanism in comparison to chromium picolinate (CrPic) and chromium chloride (CrCl(3)), as was postulated by previous reports. Twenty-one-day-old Caco-2 cell monolayers grown on semipermeable membranes in Snapwell tissue culture bichambers were incubated with CrNano, CrPic or CrCl(3) to examine their transport and uptake respectively. In the concentration range of 0.2-20 micromol/l, transport of CrNano, CrPic and CrCl(3) across Caco-2 monolayers both in apical-to-basolateral and basolateral-to-apical direction was concentration-, and time-dependent, and temperature independent. The apparent permeability coefficient (P(app)) of CrNano was between 5.89 and 7.92 x 10(-6) cm/s and that of CrPic and CrCl(3) was between 3.52 and 5.31 x 10(-6) cm/s and between 0.97 and 1.37 x 10(-6) cm/s respectively. Uptake of CrNano, CrPic and CrCl(3) by both apical and basolateral membranes was concentration- and time-dependent. Uptake of CrNano by apical membrane was significantly (p < 0.05) decreased when the incubation temperature was reduced from 37 degrees C to 4 degrees C. The transport efficiency of CrNano, CrPic and CrCl(3) after incubation for 120 min at 37 degrees C was 15.83% +/- 0.76%, 9.08% +/- 0.25% and 2.11% +/- 0.53% respectively. The uptake efficiency of CrNano, CrPic and CrCl(3) was 10.08% +/- 0.76%, 4.73% +/- 0.60% and 0.88% +/- 0.08% respectively. It was concluded that the epithelial transport of CrNano, CrPic and CrCl(3) across the Caco-2 cell monolayers was mainly via passive transport pathways. In addition, CrNano exhibited considerably higher absorption efficiency than both CrPic and CrCl(3) in Caco-2 cell monolayers.

Temperature affects the morphology and calcification of Emiliania huxleyi strains

NASA Astrophysics Data System (ADS)

Rosas-Navarro, Anaid; Langer, Gerald; Ziveri, Patrizia

2016-05-01

The global warming debate has sparked an unprecedented interest in temperature effects on coccolithophores. The calcification response to temperature changes reported in the literature, however, is ambiguous. The two main sources of this ambiguity are putatively differences in experimental setup and strain specificity. In this study we therefore compare three strains isolated in the North Pacific under identical experimental conditions. Three strains of Emiliania huxleyi type A were grown under non-limiting nutrient and light conditions, at 10, 15, 20 and 25 °C. All three strains displayed similar growth rate versus temperature relationships, with an optimum at 20-25 °C. Elemental production (particulate inorganic carbon (PIC), particulate organic carbon (POC), total particulate nitrogen (TPN)), coccolith mass, coccolith size, and width of the tube element cycle were positively correlated with temperature over the sub-optimum to optimum temperature range. The correlation between PIC production and coccolith mass/size supports the notion that coccolith mass can be used as a proxy for PIC production in sediment samples. Increasing PIC production was significantly positively correlated with the percentage of incomplete coccoliths in one strain only. Generally, coccoliths were heavier when PIC production was higher. This shows that incompleteness of coccoliths is not due to time shortage at high PIC production. Sub-optimal growth temperatures lead to an increase in the percentage of malformed coccoliths in a strain-specific fashion. Since in total only six strains have been tested thus far, it is presently difficult to say whether sub-optimal temperature is an important factor causing malformations in the field. The most important parameter in biogeochemical terms, the PIC : POC ratio, shows a minimum at optimum growth temperature in all investigated strains. This clarifies the ambiguous picture featuring in the literature, i.e. discrepancies between PIC : POC-temperature relationships reported in different studies using different strains and different experimental setups. In summary, global warming might cause a decline in coccolithophore's PIC contribution to the rain ratio, as well as improved fitness in some genotypes due to fewer coccolith malformations.

A New Kinetic Simulation Model with Self-Consistent Calculation of Regolith Layer Charging for Moon-Plasma Interactions

NASA Astrophysics Data System (ADS)

Han, D.; Wang, J.

2015-12-01

The moon-plasma interactions and the resulting surface charging have been subjects of extensive recent investigations. While many particle-in-cell (PIC) based simulation models have been developed, all existing PIC simulation models treat the surface of the Moon as a boundary condition to the plasma flow. In such models, the surface of the Moon is typically limited to simple geometry configurations, the surface floating potential is calculated from a simplified current balance condition, and the electric field inside the regolith layer cannot be resolved. This paper presents a new full particle PIC model to simulate local scale plasma flow and surface charging. A major feature of this new model is that the surface is treated as an "interface" between two mediums rather than a boundary, and the simulation domain includes not only the plasma but also the regolith layer and the bedrock underneath it. There are no limitations on the surface shape. An immersed-finite-element field solver is applied which calculates the regolith surface floating potential and the electric field inside the regolith layer directly from local charge deposition. The material property of the regolith layer is also explicitly included in simulation. This new model is capable of providing a self-consistent solution to the plasma flow field, lunar surface charging, the electric field inside the regolith layer and the bedrock for realistic surface terrain. This new model is applied to simulate lunar surface-plasma interactions and surface charging under various ambient plasma conditions. The focus is on the lunar terminator region, where the combined effects from the low sun elevation angle and the localized plasma wake generated by plasma flow over a rugged terrain can generate strongly differentially charged surfaces and complex dust dynamics. We discuss the effects of the regolith properties and regolith layer charging on the plasma flow field, dust levitation, and dust transport.

Hybrid-PIC Computer Simulation of the Plasma and Erosion Processes in Hall Thrusters

NASA Technical Reports Server (NTRS)

Hofer, Richard R.; Katz, Ira; Mikellides, Ioannis G.; Gamero-Castano, Manuel

2010-01-01

HPHall software simulates and tracks the time-dependent evolution of the plasma and erosion processes in the discharge chamber and near-field plume of Hall thrusters. HPHall is an axisymmetric solver that employs a hybrid fluid/particle-in-cell (Hybrid-PIC) numerical approach. HPHall, originally developed by MIT in 1998, was upgraded to HPHall-2 by the Polytechnic University of Madrid in 2006. The Jet Propulsion Laboratory has continued the development of HPHall-2 through upgrades to the physical models employed in the code, and the addition of entirely new ones. Primary among these are the inclusion of a three-region electron mobility model that more accurately depicts the cross-field electron transport, and the development of an erosion sub-model that allows for the tracking of the erosion of the discharge chamber wall. The code is being developed to provide NASA science missions with a predictive tool of Hall thruster performance and lifetime that can be used to validate Hall thrusters for missions.

Ultrahigh-order Maxwell solver with extreme scalability for electromagnetic PIC simulations of plasmas

NASA Astrophysics Data System (ADS)

Vincenti, Henri; Vay, Jean-Luc

2018-07-01

The advent of massively parallel supercomputers, with their distributed-memory technology using many processing units, has favored the development of highly-scalable local low-order solvers at the expense of harder-to-scale global very high-order spectral methods. Indeed, FFT-based methods, which were very popular on shared memory computers, have been largely replaced by finite-difference (FD) methods for the solution of many problems, including plasmas simulations with electromagnetic Particle-In-Cell methods. For some problems, such as the modeling of so-called "plasma mirrors" for the generation of high-energy particles and ultra-short radiations, we have shown that the inaccuracies of standard FD-based PIC methods prevent the modeling on present supercomputers at sufficient accuracy. We demonstrate here that a new method, based on the use of local FFTs, enables ultrahigh-order accuracy with unprecedented scalability, and thus for the first time the accurate modeling of plasma mirrors in 3D.

Distribution of planktonic biogenic carbonate organisms in the Southern Ocean south of Australia: a baseline for ocean acidification impact assessment

NASA Astrophysics Data System (ADS)

Trull, Thomas W.; Passmore, Abraham; Davies, Diana M.; Smit, Tim; Berry, Kate; Tilbrook, Bronte

2018-01-01

The Southern Ocean provides a vital service by absorbing about one-sixth of humankind's annual emissions of CO2. This comes with a cost - an increase in ocean acidity that is expected to have negative impacts on ocean ecosystems. The reduced ability of phytoplankton and zooplankton to precipitate carbonate shells is a clearly identified risk. The impact depends on the significance of these organisms in Southern Ocean ecosystems, but there is very little information on their abundance or distribution. To quantify their presence, we used coulometric measurement of particulate inorganic carbonate (PIC) on particles filtered from surface seawater into two size fractions: 50-1000 µm to capture foraminifera (the most important biogenic carbonate-forming zooplankton) and 1-50 µm to capture coccolithophores (the most important biogenic carbonate-forming phytoplankton). Ancillary measurements of biogenic silica (BSi) and particulate organic carbon (POC) provided context, as estimates of the biomass of diatoms (the highest biomass phytoplankton in polar waters) and total microbial biomass, respectively. Results for nine transects from Australia to Antarctica in 2008-2015 showed low levels of PIC compared to Northern Hemisphere polar waters. Coccolithophores slightly exceeded the biomass of diatoms in subantarctic waters, but their abundance decreased more than 30-fold poleward, while diatom abundances increased, so that on a molar basis PIC was only 1 % of BSi in Antarctic waters. This limited importance of coccolithophores in the Southern Ocean is further emphasized in terms of their associated POC, representing less than 1 % of total POC in Antarctic waters and less than 10 % in subantarctic waters. NASA satellite ocean-colour-based PIC estimates were in reasonable agreement with the shipboard results in subantarctic waters but greatly overestimated PIC in Antarctic waters. Contrastingly, the NASA Ocean Biogeochemical Model (NOBM) shows coccolithophores as overly restricted to subtropical and northern subantarctic waters. The cause of the strong southward decrease in PIC abundance in the Southern Ocean is not yet clear. The poleward decrease in pH is small, and while calcite saturation decreases strongly southward, it remains well above saturation ( > 2). Nitrate and phosphate variations would predict a poleward increase. Temperature and competition with diatoms for limiting iron appear likely to be important. While the future trajectory of coccolithophore distributions remains uncertain, their current low abundances suggest small impacts on overall Southern Ocean pelagic ecology.

β Pictoris' inner disk in polarized light and new orbital parameters for β Pictoris b

DOE PAGES

Millar-Blanchaer, Maxwell A.; Graham, James R.; Pueyo, Laurent; ...

2015-09-16

Here, we present H-band observations of β Pic with the Gemini Planet Imager's (GPI's) polarimetry mode that reveal the debris disk between ~0farcs3 (6 AU) and ~1farcs7 (33 AU), while simultaneously detecting β Pic b. The polarized disk image was fit with a dust density model combined with a Henyey–Greenstein scattering phase function. The best-fit model indicates a disk inclined to the line of sight (more » $$\\phi =85\\buildrel{\\circ}\\over{.} {27}_{-0.19}^{+0.26}$$) with a position angle (PA) $${\\theta }_{\\mathrm{PA}}=30\\buildrel{\\circ}\\over{.} {35}_{-0.28}^{+0.29}$$ (slightly offset from the main outer disk, $${\\theta }_{\\mathrm{PA}}\\approx 29^\\circ $$), that extends from an inner disk radius of $${23.6}_{-0.6}^{+0.9}\\;\\mathrm{AU}$$ to well outside GPI's field of view.« less

An Efficient Randomized Algorithm for Real-Time Process Scheduling in PicOS Operating System

NASA Astrophysics Data System (ADS)

Helmy*, Tarek; Fatai, Anifowose; Sallam, El-Sayed

PicOS is an event-driven operating environment designed for use with embedded networked sensors. More specifically, it is designed to support the concurrency in intensive operations required by networked sensors with minimal hardware requirements. Existing process scheduling algorithms of PicOS; a commercial tiny, low-footprint, real-time operating system; have their associated drawbacks. An efficient, alternative algorithm, based on a randomized selection policy, has been proposed, demonstrated, confirmed for efficiency and fairness, on the average, and has been recommended for implementation in PicOS. Simulations were carried out and performance measures such as Average Waiting Time (AWT) and Average Turn-around Time (ATT) were used to assess the efficiency of the proposed randomized version over the existing ones. The results prove that Randomized algorithm is the best and most attractive for implementation in PicOS, since it is most fair and has the least AWT and ATT on average over the other non-preemptive scheduling algorithms implemented in this paper.

Metabolic stability of new anticonvulsants in body fluids and organ homogenates.

PubMed

Marszałek, Dorota; Goldnik, Anna; Pluciński, Franciszek; Mazurek, Aleksander P; Jakubiak, Anna; Lis, Ewa; Tazbir, Piotr; Koziorowska, Agnieszka

2012-01-01

The stability as a function of time of compounds with established anticonvulsant activity: picolinic acid benzylamide (Pic-BZA), picolinic acid 2-fluorobenzylamide (Pic-2-F-BZA), picolinic acid 3-fluorobenzylamide (Pic-3-F-BZA), picolinic acid 4-fluorobenzylamide (Pic-4-F-BZA) and picolinic acid 2-methylbenzylamide (Pic-2-Me-BZA) in body fluids and homogenates of body organs were determined after incubation. It was found that they decompose relatively rapidly in liver and kidney and are stable against enzymes present in body fluids and some organs. These results are consistent with the bond strength expressed as total energy of amide bonds (calculated by quantum chemical methods) in the studied anticonvulsants. The calculated values of the amide bond energy are: 199.4 kcal/mol, 200.2 kcal/mol, 207.5 kcal/mol, 208.4 kcal/mol and 198.2 kcal/mol, respectively. The strength of the amide bonds in the studied anticonvulsants correctly reflects their stability in liver or kidney.

Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture.

PubMed

Eychenne, Thomas; Novikova, Elizaveta; Barrault, Marie-Bénédicte; Alibert, Olivier; Boschiero, Claire; Peixeiro, Nuno; Cornu, David; Redeker, Virginie; Kuras, Laurent; Nicolas, Pierre; Werner, Michel; Soutourina, Julie

2016-09-15

Mediator is a large coregulator complex conserved from yeast to humans and involved in many human diseases, including cancers. Together with general transcription factors, it stimulates preinitiation complex (PIC) formation and activates RNA polymerase II (Pol II) transcription. In this study, we analyzed how Mediator acts in PIC assembly using in vivo, in vitro, and in silico approaches. We revealed an essential function of the Mediator middle module exerted through its Med10 subunit, implicating a key interaction between Mediator and TFIIB. We showed that this Mediator-TFIIB link has a global role on PIC assembly genome-wide. Moreover, the amplitude of Mediator's effect on PIC formation is gene-dependent and is related to the promoter architecture in terms of TATA elements, nucleosome occupancy, and dynamics. This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts. © 2016 Eychenne et al.; Published by Cold Spring Harbor Laboratory Press.

DoD Personnel Security Program

DTIC Science & Technology

1987-01-01

Baltimore, Maryland 21203 Message Address: DIS PIC BALTIMORE MD/ /D0640 The request will include subject’s name, grade, social security number, date and...requests for initial investigations will be submitted to PIC regardless of their urgency. If, however, there is an urgent need for a postadjudication...investigation, or the mailing of a request to PIC for initia- tion of a postadjudication case would prejudice timely pursuit of investigative action, the

iVPIC: A low-­dispersion, energy-­conserving relativistic PIC solver for LPI simulations

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

Chacon, Luis

We have developed a novel low-­dispersion, exactly energy-­conserving PIC algorithm for the relativistic Vlasov-­Maxwell system. The approach features an exact energy conservation theorem while preserving the favorable performance and numerical dispersion properties of explicit PIC. The new algorithm has the potential to enable much longer laser-­plasma-­interaction (LPI) simulations than are currently possible.

Measurement of greenhouse gas emissions from agricultural sites using open-path optical remote sensing method.

PubMed

Ro, Kyoung S; Johnson, Melvin H; Varma, Ravi M; Hashmonay, Ram A; Hunt, Patrick

2009-08-01

Improved characterization of distributed emission sources of greenhouse gases such as methane from concentrated animal feeding operations require more accurate methods. One promising method is recently used by the USEPA. It employs a vertical radial plume mapping (VRPM) algorithm using optical remote sensing techniques. We evaluated this method to estimate emission rates from simulated distributed methane sources. A scanning open-path tunable diode laser was used to collect path-integrated concentrations (PICs) along different optical paths on a vertical plane downwind of controlled methane releases. Each cycle consists of 3 ground-level PICs and 2 above ground PICs. Three- to 10-cycle moving averages were used to reconstruct mass equivalent concentration plum maps on the vertical plane. The VRPM algorithm estimated emission rates of methane along with meteorological and PIC data collected concomitantly under different atmospheric stability conditions. The derived emission rates compared well with actual released rates irrespective of atmospheric stability conditions. The maximum error was 22 percent when 3-cycle moving average PICs were used; however, it decreased to 11% when 10-cycle moving average PICs were used. Our validation results suggest that this new VRPM method may be used for improved estimations of greenhouse gas emission from a variety of agricultural sources.

Simultaneous analysis of Cr(III), Cr(VI), and chromium picolinate in foods using capillary electrophoresis-inductively coupled plasma mass spectrometry.

PubMed

Chen, YiQuan; Chen, JinFa; Xi, Zhiming; Yang, Guidi; Wu, Zujian; Li, JianRong; Fu, FengFu

2015-05-01

We herein reported a method for the simultaneous detection of trace Cr(VI), Cr(III), and chromium(III) picolinate (CrPic) in foods using CE-ICP-MS together with ultrasonic-assisted extraction. The Cr(III) (Cr(3+) ) was chelated with trans-1,2-diaminocyclohexane-N,N,N´,N´-tetraacetic acid (DCTA) to form a single charged Cr-DCTA(-) complex. Then, Cr(VI) (CrO4 (2-) ), Cr-DCTA(-) , and CrPic were separated by CE within 8 min under a separation voltage of -13 KV followed by their monitoring with ICP mass spectrometer (ICP-MS). The proposed method is simple, effective, and sensitive. It has an instrument detection limit of 0.10, 0.18, and 0.20 ngCr/mL for Cr(VI), Cr(III), and CrPic, respectively. With the help of the methods, we have successfully determined Cr(VI), Cr(III), and CrPic in nutritional supplement (CrPic yeast tablet) with an RSD (n = 5) <6% and a recovery of 93-103%. The experimental results showed that CrPic was the main speciation of chromium in the nutritional supplement, with a concentration of 1514.6 μg Cr/g. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PIC1, an Ancient Permease in Arabidopsis Chloroplasts, Mediates Iron Transport[W

PubMed Central

Duy, Daniela; Wanner, Gerhard; Meda, Anderson R.; von Wirén, Nicolaus; Soll, Jürgen; Philippar, Katrin

2007-01-01

In chloroplasts, the transition metals iron and copper play an essential role in photosynthetic electron transport and act as cofactors for superoxide dismutases. Iron is essential for chlorophyll biosynthesis, and ferritin clusters in plastids store iron during germination, development, and iron stress. Thus, plastidic homeostasis of transition metals, in particular of iron, is crucial for chloroplast as well as plant development. However, very little is known about iron uptake by chloroplasts. Arabidopsis thaliana PERMEASE IN CHLOROPLASTS1 (PIC1), identified in a screen for metal transporters in plastids, contains four predicted α-helices, is targeted to the inner envelope, and displays homology with cyanobacterial permease-like proteins. Knockout mutants of PIC1 grew only heterotrophically and were characterized by a chlorotic and dwarfish phenotype reminiscent of iron-deficient plants. Ultrastructural analysis of plastids revealed severely impaired chloroplast development and a striking increase in ferritin clusters. Besides upregulation of ferritin, pic1 mutants showed differential regulation of genes and proteins related to iron stress or transport, photosynthesis, and Fe-S cluster biogenesis. Furthermore, PIC1 and its cyanobacterial homolog mediated iron accumulation in an iron uptake–defective yeast mutant. These observations suggest that PIC1 functions in iron transport across the inner envelope of chloroplasts and hence in cellular metal homeostasis. PMID:17337631

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.

PubMed

Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D; Schafer, Nicholas P; Kim, Bobby L; Cheung, Margaret S; Wolynes, Peter G

2016-01-01

While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes. © 2015 The Protein Society.

The interaction of extreme waves with hull elements

NASA Astrophysics Data System (ADS)

Galiev, Shamil; Flay, Richard

2010-05-01

The problem of the impact of a rogue wave onto a deformable marine structure is formulated in a few publications (see, for example, a short review in http://researchspace.auckland.ac.nz/handle/2292/4474). In this paper the results from numerical and experimental investigations of the effect of cavitation on the deformation of a hull element, loaded by a wall of water, generated by an extreme ocean surface wave are considered. The hull element is modelled as a circular metal plate with the edge of the plate rigidly clamped. The plate surface is much smaller than the surface of the wave front, so that at the initial moment of the interaction, the pressure is constant on the plate surface. At the next instant, because of the plate deformation, axisymmetric loading of the plate occurs. The influences of membrane forces and plastic deformations are ignored, and therefore, the equation of plate motion has the following classical form Eh3(wrrrr+2r -1wrrrr- r-2wrr+r-3wr) = - 121- ν2)[ρhwtt+ δ(r,t)(p+ ρ0a0wt)]. Here w is the plate displacement, subscripts t and rindicate derivatives with respect to time and the radial coordinate, PIC is the plate material density, his the plate thickness, Eis Young's modulus, PIC is Poisson's ratio and p is the pressure of the incident surface wave measured on the wall, PIC is the water density, PIC is the speed of sound in water, and PIC is the normal velocity of the plate. The term PIC takes into account the effect of the deformability of the plate. Obviously, the hull of a vessel is not rigid like a solid wall, but starts to deform and to move. This motion produces a reflected pressure wave, which travels from the hull into the water wave with a magnitude equal to PIC . The normal velocity is positive so the reflected pressure PIC is negative (tensile wave). If the fluid pressure drops below some critical value pk, the wet plate surface separates from the water, and cavitation may be generated. The function δ(r,t) takes into account the effect of the hull cavitation. The function PIC or 0, and is determined during the numerical calculations. Case PIC is valid for the case with no cavitation, and the case δ(r,t) = 0 corresponds to the case with hull cavitation. The results from these calculations allow us to draw the following conclusions. 1) The pressures generated depend greatly on the irregularity of waves. In particular, the shock pressures are affected by this irregularity, making the prediction of their magnitude almost impossible. 2) In the majority of cases, the elastic deformation of thin hull elements by a short duration water wave pressure pulse is accompanied by hull cavitation. The effect of cavitation may be important, provided that the time of loading by the water wall pressure is less than the period of the fundamental frequency of the hull element oscillations. 3) The cavitation zones can enclose practically the whole wet surface and thus completely change the water loading onto the hull element, compared to the pressures that would be developed in the absence of cavitation. 4) The hull element deformation generates surface pressure and cavitation waves. 5) Cavitation interaction of extreme water waves with structures, and hull response, are complex topics, which are not well understood and are expected to be important in the design of advanced ships in the future. 6) The existence of rogue waves makes it important to re-examine some of the ideas developed earlier which are fundamental to merchant ship design.

Collisionless spectral-kinetic Simulation of the Multipole Resonance Probe

NASA Astrophysics Data System (ADS)

Dobrygin, Wladislaw; Szeremley, Daniel; Schilling, Christian; Oberrath, Jens; Eremin, Denis; Mussenbrock, Thomas; Brinkmann, Ralf Peter

2012-10-01

Plasma resonance spectroscopy is a well established plasma diagnostic method realized in several designs. One of these designs is the multipole resonance probe (MRP). In its idealized - geometrically simplified - version it consists of two dielectrically shielded, hemispherical electrodes to which an RF signal is applied. A numerical tool is under development, which is capable of simulating the dynamics of the plasma surrounding the MRP in electrostatic approximation. In the simulation the potential is separeted in an inner and a vacuum potential. The inner potential is influenced by the charged partilces and is calculated by a specialized Poisson solver. The vacuum potential fulfills Laplace's equetion and consists of the applied voltage of the probe as boundary condition. Both potentials are expanded in spherical harmonics. For a practical particle pusher implementation, the expansion must be appropriately truncated. Compared to a PIC simulation a grid is unnecessary to calculate the force on the particles. This work purpose is a collisionless kinetic simulation, which can be used to investigate kinetic effects on the resonance behavior of the MRP.[4pt] [1] M. Lapke et al., Appl. Phys. Lett. 93, 2008, 051502.

Exposure of pregnant mice to chromium picolinate results in skeletal defects in their offspring.

PubMed

Bailey, M M; Boohaker, J G; Sawyer, R D; Behling, J E; Rasco, J F; Jernigan, J J; Hood, R D; Vincent, J B

2006-06-01

Chromium(III) picolinate, [Cr(pic)(3)], is a widely marketed dietary supplement. However, Cr(pic)(3) has been associated with oxidative damage to DNA in rats and mutations and DNA fragmentation in cell cultures. In isolated case reports, Cr(pic)(3) supplementation has been said to cause adverse effects, such as anemia, renal failure, liver dysfunction, and neuronal impairment. To date, no studies have been published regarding the safety of chromium picolinate supplementation to a developing fetus, although Cr(pic)(3) has been recommended for pregnant women who are diagnosed with gestational diabetes. From gestation days (GD) 6-17, pregnant CD-1 mice were fed diets containing either 200 mg/kg Cr(pic)(3), 200 mg/kg CrCl(3), 174 mg/kg picolinic acid, or the diet only to determine if Cr(pic)(3), CrCl(3), or picolinic acid could cause developmental toxicity. Dams were sacrificed on GD 17, and their litters were examined for adverse effects. The incidence of bifurcated cervical arches was significantly increased in fetuses from the Cr(pic)(3) group as compared to the diet-only group. Fetuses in the picolinic acid-treated group had an incidence double that of the control group; however, this increase was not statistically significant. Fetuses in the CrCl(3) group did not differ from the controls in any variable examined. No maternal toxicity was observed in any of the treatment groups. High maternal oral exposures to chromium picolinate can cause morphological defects in developing offspring of mice.

Accidental pharmacological poisonings in young children: population-based study in three settings.

PubMed

Bell, Jane C; Bentley, Jason P; Downie, Catriona; Cairns, Rose; Buckley, Nicholas A; Katelaris, Annette; Pearson, Sallie-Anne; Nassar, Natasha

2018-01-15

Pharmacological poisonings in young children are avoidable. Previous studies report calls to poisons centres, presentations to emergency departments (ED) or hospital admissions. There are limited data assessing concurrent management of poisonings across all three settings. We aimed to describe accidental pharmacological poisonings in young children across our Poisons Information Centre (PIC), EDs and hospitals. A population-based study in New South Wales, Australia, of PIC calls, ED presentations and hospital admissions for accidental pharmacological poisoning in children aged <5 years, 2007-2013. We examined trends, medicines responsible and subsequent management. Medicines were coded using ICD10-AM diagnosis codes (T36-50). Over 2007-2013, pharmacological poisonings accounted for 67,816 PIC calls, 7739 ED presentations and 2082 admissions. Rates (per 10,000 children) of PIC calls declined from 220 to 178; ED presentations were stable (∼22-24), with a decrease in emergency cases offset by an increase in semi- or non-urgent presentations; hospital admissions declined (8-5). Most PIC calls related to "non-opioid analgesics" (25%), and "topical agents" (18%). Nearly every day, one child aged <5 years was admitted to hospital for poisoning. "Benzodiazepines", "other and unspecified antidepressants", "uncategorised antihypertensives", and "4-aminophenol derivatives" accounted for over one-third of all admissions. Most PIC calls (90%) were advised to stay home, 6% referred to hospital. One-quarter of ED presentations resulted in admission. Poisonings reported to PIC and hospitals declined, however, non-urgent ED presentations increased. Strategies to reduce therapeutic errors and access to medicines, and education campaigns to improve Poisons Centre call rates to prevent unnecessary ED presentations are needed.

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements.

PubMed

Korsch, Michael; Marten, Silke-Mareike; Dötsch, Andreas; Jáuregui, Ruy; Pieper, Dietmar H; Obst, Ursula

2016-12-01

Cementing dental restorations on implants poses the risk of undetected excess cement. Such cement remnants may favor the development of inflammation in the peri-implant tissue. The effect of excess cement on the bacterial community is not yet known. The aim of this study was to analyze the effect of two different dental cements on the composition of the microbial peri-implant community. In a cohort of 38 patients, samples of the peri-implant tissue were taken with paper points from one implant per patient. In 15 patients, the suprastructure had been cemented with a zinc oxide-eugenol cement (Temp Bond, TB) and in 23 patients with a methacrylate cement (Premier Implant Cement, PIC). The excess cement found as well as suppuration was documented. Subgingival samples of all patients were analyzed for taxonomic composition by means of 16S amplicon sequencing. None of the TB-cemented implants had excess cement or suppuration. In 14 (61%) of the PIC, excess cement was found. Suppuration was detected in 33% of the PIC implants without excess cement and in 100% of the PIC implants with excess cement. The taxonomic analysis of the microbial samples revealed an accumulation of oral pathogens in the PIC patients independent of the presence of excess cement. Significantly fewer oral pathogens occurred in patients with TB compared to patients with PIC. Compared with TB, PIC favors the development of suppuration and the growth of periodontal pathogens. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Double-Stranded RNA-Dependent Protein Kinase Regulates the Motility of Breast Cancer Cells

PubMed Central

Xu, Mei; Chen, Gang; Wang, Siying; Liao, Mingjun; Frank, Jacqueline A.; Bower, Kimberly A.; Zhang, Zhuo; Shi, Xianglin; Luo, Jia

2012-01-01

Double-stranded RNA (dsRNA)-dependent protein kinase (PKR) is an interferon-induced protein kinase that plays a central role in the anti-viral process. Due to its pro-apoptotic and anti-proliferative action, there is an increased interest in PKR modulation as an anti-tumor strategy. PKR is overexpressed in breast cancer cells; however, the role of PKR in breast cancer cells is unclear. The expression/activity of PKR appears inversely related to the aggressiveness of breast cancer cells. The current study investigated the role of PKR in the motility/migration of breast cancer cells. The activation of PKR by a synthesized dsRNA (PIC) significantly decreased the motility of several breast cancer cell lines (BT474, MDA-MB231 and SKBR3). PIC inhibited cell migration and blocked cell membrane ruffling without affecting cell viability. PIC also induced the reorganization of the actin cytoskeleton and impaired the formation of lamellipodia. These effects of PIC were reversed by the pretreatment of a selective PKR inhibitor. PIC also activated p38 mitogen-activated protein kinase (MAPK) and its downstream MAPK-activated protein kinase 2 (MK2). PIC-induced activation of p38 MAPK and MK2 was attenuated by the PKR inhibitor and the PKR siRNA, but a selective p38 MAPK inhibitor (SB203580) or other MAPK inhibitors did not affect PKR activity, indicating that PKR is upstream of p38 MAPK/MK2. Cofilin is an actin severing protein and regulates membrane ruffling, lamellipodia formation and cell migration. PIC inhibited cofilin activity by enhancing its phosphorylation at Ser3. PIC activated LIM kinase 1 (LIMK1), an upstream kinase of cofilin in a p38 MAPK-dependent manner. We concluded that the activation of PKR suppressed cell motility by regulating the p38 MAPK/MK2/LIMK/cofilin pathway. PMID:23112838

Identification of amino acid residues of mammalian mitochondrial phosphate carrier important for its functional expression in yeast cells, as achieved by PCR-mediated random mutation and gap-repair cloning.

PubMed

Yamagoshi, Ryohei; Yamamoto, Takenori; Hashimoto, Mitsuru; Sugahara, Ryohei; Shiotsuki, Takahiro; Miyoshi, Hideto; Terada, Hiroshi; Shinohara, Yasuo

2017-01-01

The mitochondrial phosphate carrier (PiC) of mammals, but not the yeast one, is synthesized with a presequence. The deletion of this presequence of the mammalian PiC was reported to facilitate the import of the carrier into yeast mitochondria, but the question as to whether or not mammalian PiC could be functionally expressed in yeast mitochondria was not addressed. In the present study, we first examined whether the defective growth on a glycerol plate of yeast cells lacking the yeast PiC gene could be reversed by the introduction of expression vectors of rat PiCs. The introduction of expression vectors encoding full-length rat PiC (rPiC) or rPiC lacking the presequence (ΔNrPiC) was ineffective in restoring growth on the glycerol plates. When we examined the expression levels of individual rPiCs in yeast mitochondria, ΔNrPiC was expressed at a level similar to that of yeast PiC, but that of rPiC was very low. These results indicated that ΔNrPiC expressed in yeast mitochondria is inert. Next, we sought to isolate "revertants" viable on the glycerol plate by expressing randomly mutated ΔNrPiC, and obtained two clones. These clones carried either of two mutations, F267S or F282S; and these mutations restored the transport function of ΔNrPiC in yeast mitochondria. These two Phe residues were conserved in human carrier (hPiC), and the transport function of ΔNhPiC expressed in yeast mitochondria was also markedly improved by their substitutions. Thus, substitution of F267S or F282S was concluded to be important for functional expression of mammalian PiCs in yeast mitochondria. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Electrostatic Estimation of Intercalant Jump-Diffusion Barriers Using Finite-Size Ion Models.

PubMed

Zimmermann, Nils E R; Hannah, Daniel C; Rong, Ziqin; Liu, Miao; Ceder, Gerbrand; Haranczyk, Maciej; Persson, Kristin A

2018-02-01

We report on a scheme for estimating intercalant jump-diffusion barriers that are typically obtained from demanding density functional theory-nudged elastic band calculations. The key idea is to relax a chain of states in the field of the electrostatic potential that is averaged over a spherical volume using different finite-size ion models. For magnesium migrating in typical intercalation materials such as transition-metal oxides, we find that the optimal model is a relatively large shell. This data-driven result parallels typical assumptions made in models based on Onsager's reaction field theory to quantitatively estimate electrostatic solvent effects. Because of its efficiency, our potential of electrostatics-finite ion size (PfEFIS) barrier estimation scheme will enable rapid identification of materials with good ionic mobility.

Theory of the electron sheath and presheath

DOE PAGES

Scheiner, Brett; Baalrud, Scott D.; Yee, Benjamin T.; ...

2015-12-30

Here, electron sheaths are commonly found near Langmuir probes collecting the electron saturation current. The common assumption is that the probe collects the random flux of electrons incident on the sheath, which tacitly implies that there is no electron presheath and that the flux collected is due to a velocity space truncation of the electron velocity distribution function (EVDF). This work provides a dedicated theory of electron sheaths, which suggests that they are not so simple. Motivated by EVDFs observed in particle-in-cell(PIC) simulations, a 1D model for the electron sheath and presheath is developed. In the model, under low temperaturemore » plasma conditions (T e >> T i), an electron pressure gradient accelerates electrons in the presheath to a flow velocity that exceeds the electron thermal speed at the sheath edge. This pressure gradient generates large flow velocities compared to what would be generated by ballistic motion in response to the electric field. It is found that in many situations, under common plasma conditions, the electron presheath extends much further into the plasma than an analogous ion presheath. PIC simulations reveal that the ion density in the electron presheath is determined by a flow around the electron sheath and that this flow is due to 2D aspects of the sheath geometry. Simulations also indicate the presence of ion acoustic instabilities excited by the differential flow between electrons and ions in the presheath, which result in sheath edge fluctuations. The 1D model and time averaged PIC simulations are compared and it is shown that the model provides a good description of the electron sheath and presheath.« less

Simulation services and analysis tools at the CCMC to study multi-scale structure and dynamics of Earth's magnetopause

NASA Astrophysics Data System (ADS)

Kuznetsova, M. M.; Liu, Y. H.; Rastaetter, L.; Pembroke, A. D.; Chen, L. J.; Hesse, M.; Glocer, A.; Komar, C. M.; Dorelli, J.; Roytershteyn, V.

2016-12-01

The presentation will provide overview of new tools, services and models implemented at the Community Coordinated Modeling Center (CCMC) to facilitate MMS dayside results analysis. We will provide updates on implementation of Particle-in-Cell (PIC) simulations at the CCMC and opportunities for on-line visualization and analysis of results of PIC simulations of asymmetric magnetic reconnection for different guide fields and boundary conditions. Fields, plasma parameters, particle distribution moments as well as particle distribution functions calculated in selected regions of the vicinity of reconnection sites can be analyzed through the web-based interactive visualization system. In addition there are options to request distribution functions in user selected regions of interest and to fly through simulated magnetic reconnection configurations and a map of distributions to facilitate comparisons with observations. A broad collection of global magnetosphere models hosted at the CCMC provide opportunity to put MMS observations and local PIC simulations into global context. We recently implemented the RECON-X post processing tool (Glocer et al, 2016) which allows users to determine the location of separator surface around closed field lines and between open field lines and solar wind field lines. The tool also finds the separatrix line where the two surfaces touch and positions of magnetic nulls. The surfaces and the separatrix line can be visualized relative to satellite positions in the dayside magnetosphere using an interactive HTML-5 visualization for each time step processed. To validate global magnetosphere models' capability to simulate locations of dayside magnetosphere boundaries we will analyze the proximity of MMS to simulated separatrix locations for a set of MMS diffusion region crossing events.

Electromagnetic plasma simulation in realistic geometries

NASA Astrophysics Data System (ADS)

Brandon, S.; Ambrosiano, J. J.; Nielsen, D.

1991-08-01

Particle-in-Cell (PIC) calculations have become an indispensable tool to model the nonlinear collective behavior of charged particle species in electromagnetic fields. Traditional finite difference codes, such as CONDOR (2-D) and ARGUS (3-D), are used extensively to design experiments and develop new concepts. A wide variety of physical processes can be modeled simply and efficiently by these codes. However, experiments have become more complex. Geometrical shapes and length scales are becoming increasingly more difficult to model. Spatial resolution requirements for the electromagnetic calculation force large grids and small time steps. Many hours of CRAY YMP time may be required to complete 2-D calculation -- many more for 3-D calculations. In principle, the number of mesh points and particles need only to be increased until all relevant physical processes are resolved. In practice, the size of a calculation is limited by the computer budget. As a result, experimental design is being limited by the ability to calculate, not by the experimenters ingenuity or understanding of the physical processes involved. Several approaches to meet these computational demands are being pursued. Traditional PIC codes continue to be the major design tools. These codes are being actively maintained, optimized, and extended to handle large and more complex problems. Two new formulations are being explored to relax the geometrical constraints of the finite difference codes. A modified finite volume test code, TALUS, uses a data structure compatible with that of standard finite difference meshes. This allows a basic conformal boundary/variable grid capability to be retrofitted to CONDOR. We are also pursuing an unstructured grid finite element code, MadMax. The unstructured mesh approach provides maximum flexibility in the geometrical model while also allowing local mesh refinement.

Review of particle-in-cell modeling for the extraction region of large negative hydrogen ion sources for fusion

NASA Astrophysics Data System (ADS)

Wünderlich, D.; Mochalskyy, S.; Montellano, I. M.; Revel, A.

2018-05-01

Particle-in-cell (PIC) codes are used since the early 1960s for calculating self-consistently the motion of charged particles in plasmas, taking into account external electric and magnetic fields as well as the fields created by the particles itself. Due to the used very small time steps (in the order of the inverse plasma frequency) and mesh size, the computational requirements can be very high and they drastically increase with increasing plasma density and size of the calculation domain. Thus, usually small computational domains and/or reduced dimensionality are used. In the last years, the available central processing unit (CPU) power strongly increased. Together with a massive parallelization of the codes, it is now possible to describe in 3D the extraction of charged particles from a plasma, using calculation domains with an edge length of several centimeters, consisting of one extraction aperture, the plasma in direct vicinity of the aperture, and a part of the extraction system. Large negative hydrogen or deuterium ion sources are essential parts of the neutral beam injection (NBI) system in future fusion devices like the international fusion experiment ITER and the demonstration reactor (DEMO). For ITER NBI RF driven sources with a source area of 0.9 × 1.9 m2 and 1280 extraction apertures will be used. The extraction of negative ions is accompanied by the co-extraction of electrons which are deflected onto an electron dump. Typically, the maximum negative extracted ion current is limited by the amount and the temporal instability of the co-extracted electrons, especially for operation in deuterium. Different PIC codes are available for the extraction region of large driven negative ion sources for fusion. Additionally, some effort is ongoing in developing codes that describe in a simplified manner (coarser mesh or reduced dimensionality) the plasma of the whole ion source. The presentation first gives a brief overview of the current status of the ion source development for ITER NBI and of the PIC method. Different PIC codes for the extraction region are introduced as well as the coupling to codes describing the whole source (PIC codes or fluid codes). Presented and discussed are different physical and numerical aspects of applying PIC codes to negative hydrogen ion sources for fusion as well as selected code results. The main focus of future calculations will be the meniscus formation and identifying measures for reducing the co-extracted electrons, in particular for deuterium operation. The recent results of the 3D PIC code ONIX (calculation domain: one extraction aperture and its vicinity) for the ITER prototype source (1/8 size of the ITER NBI source) are presented.

Variability of western Amazon dry-season precipitation extremes: importance of decadal fluctuations and implications for predictability

NASA Astrophysics Data System (ADS)

Fernandes, K.; Baethgen, W.; Verchot, L. V.; Giannini, A.; Pinedo-Vasquez, M.

2014-12-01

A complete assessment of climate change projections requires understanding the combined effects of decadal variability and long-term trends and evaluating the ability of models to simulate them. The western Amazon severe droughts of the 2000s were the result of a modest drying trend enhanced by reduced moisture transport from the tropical Atlantic. Most of the WA dry-season precipitation decadal variability is attributable to decadal fluctuations of the north-south gradient (NSG) in Atlantic sea surface temperature (SST). The observed WA and NSG decadal co-variability is well reproduced in Global Climate Models (GCMs) pre-industrial control (PIC) and historical (HIST) experiments that were part of the Intergovernmental Panel on Climate Change fifth assessment report (IPCC-AR5). This suggests that unforced or natural climate variability, characteristic of the PIC simulations, determines the nature of this coupling, as the results from HIST simulations (forced with greenhouse gases (GHG) and natural and anthropogenic aerosols) are comparable in magnitude and spatial distribution. Decadal fluctuation in the NSG also determines shifts in the probability of repeated droughts and pluvials in WA, as there is a 65% chance of 3 or more years of droughts per decade when NSG>0 compared to 18% when NSG<0. The HIST and PIC model simulations also reproduce the observed shifts in probability distribution of droughts and pluvials as a function of the NSG decadal phase, suggesting there is great potential for decadal predictability based on GCMs. Persistence of the current NSG positive phase may lead to continuing above normal frequencies of western Amazon dry-season droughts.

Modeling Transport of Relativistic Electrons through Warm-Dense Matter Using Collisional PIC

NASA Astrophysics Data System (ADS)

May, J.; McGuffey, C.; Yabuuchi, T.; Wei, Ms; Beg, F.; Mori, Wb

2017-10-01

In electron transport experiments performed on the OMEGA EP laser system, a relativistic electron beam was created by focusing a high intensity (eA /me c > 1) laser onto a gold (Au) foil. Behind the Au foil was a layer of plastic (CH) foam, with an initial density of 200mg /cm3 . Before the high intensity laser was switched on, this foam was either left unperturbed; or it was shocked using a lower intensity laser (eA /me c 10-4) with beam path perpendicular to the high intensity laser, which left the CH layer in a warm dense matter (WDM) state with temperature of 40 eV and density of 30mg /cm3 . The electron beam was imaged by observing the k- α signal from a copper foil on the far side from the Au. The result was that transport was decreased by an order of magnitude in the WDM compared to the cold foam. We have modeled this experiment using the PIC code OSIRIS, with also a Monte Carlo Coulomb collision package. Our simulations indicate that the main cause of the differences in transport is a collimating magnetic field in the higher density, cold foam, created by collisional resistivity. The plasma density of the Au layer, difficult to model fully in PIC, appears to effect the heat capacity and therefore temperature and resistivity of the target. The authors acknowledge the support of the Department of Energy under contract DE-NA 0001833 and the National Science Foundation under contract ACI 1339893.

[PICS: pharmaceutical inspection cooperation scheme].

PubMed

Morénas, J

2009-01-01

The pharmaceutical inspection cooperation scheme (PICS) is a structure containing 34 participating authorities located worldwide (October 2008). It has been created in 1995 on the basis of the pharmaceutical inspection convention (PIC) settled by the European free trade association (EFTA) in1970. This scheme has different goals as to be an international recognised body in the field of good manufacturing practices (GMP), for training inspectors (by the way of an annual seminar and experts circles related notably to active pharmaceutical ingredients [API], quality risk management, computerized systems, useful for the writing of inspection's aide-memoires). PICS is also leading to high standards for GMP inspectorates (through regular crossed audits) and being a room for exchanges on technical matters between inspectors but also between inspectors and pharmaceutical industry.

Measurements of total production cross sections for $$\\pi^{+}$$+C, $$\\pi^{+}$$+Al, $$K^{+}$$+C, and $$K^{+}$$+Al at 60 GeV/c and $$\\pi^{+}$$+C and $$\\pi^{+}$$+Al at 31 GeV/c

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

Aduszkiewicz, A.; et al.

This paper presents several measurements of total production cross sections and total inelastic cross sections for the following reactions:more » $$\\pi^{+}$$+C, $$\\pi^{+}$$+Al, $$K^{+}$$+C, $$K^{+}$$+Al at 60 GeV/c, $$\\pi^{+}$$+C and $$\\pi^{+}$$+Al at 31 GeV/c . The measurements were made using the NA61/SHINE spectrometer at the CERN SPS. Comparisons with previous measurements are given and good agreement is seen. These interaction cross sections measurements are a key ingredient for neutrino flux prediction from the reinteractions of secondary hadrons in current and future accelerator-based long-baseline neutrino experiments.« less

NASA Numerical and Experimental Evaluation of UTRC Low Emissions Injector

NASA Technical Reports Server (NTRS)

Hicks, Yolanda R.; Tedder, Sarah A.; Anderson, Robert C.; Iannetti, Anthony C.; Smith, Lance L.; Dai, Zhongtao

2014-01-01

Computational and experimental analyses of a PICS-Pilot-In-Can-Swirler technology injector, developed by United Technologies Research Center (UTRC) are presented. NASA has defined technology targets for near term (called "N+1", circa 2015), midterm ("N+2", circa 2020) and far term ("N+3", circa 2030) that specify realistic emissions and fuel efficiency goals for commercial aircraft. This injector has potential for application in an engine to meet the Pratt & Whitney N+3 supersonic cycle goals, or the subsonic N+2 engine cycle goals. Experimental methods were employed to investigate supersonic cruise points as well as select points of the subsonic cycle engine; cruise, approach, and idle with a slightly elevated inlet pressure. Experiments at NASA employed gas analysis and a suite of laser-based measurement techniques to characterize the combustor flow downstream from the PICS dump plane. Optical diagnostics employed for this work included Planar Laser-Induced Fluorescence of fuel for injector spray pattern and Spontaneous Raman Spectroscopy for relative species concentration of fuel and CO2. The work reported here used unheated (liquid) Jet-A fuel for all fuel circuits and cycle conditions. The initial tests performed by UTRC used vaporized Jet-A to simulate the expected supersonic cruise condition, which anticipated using fuel as a heat sink. Using the National Combustion Code a PICS-based combustor was modeled with liquid fuel at the supersonic cruise condition. All CFD models used a cubic non-linear k-epsilon turbulence wall functions model, and a semi-detailed Jet-A kinetic mechanism based on a surrogate fuel mixture. Two initial spray droplet size distribution and spray cone conditions were used: 1) an initial condition (Lefebvre) with an assumed Rosin-Rammler distribution, and 7 degree Solid Spray Cone; and 2) the Boundary Layer Stripping (BLS) primary atomization model giving the spray size distribution and directional properties. Contour and line plots are shown in comparison with experimental data (where this data is available) for flow velocities, fuel, and temperature distribution. The CFD results are consistent with experimental observations for fuel distribution and vaporization. Analysis of gas sample results, using a previously-developed NASA NOx correlation, indicates that for sea-level takeoff, the PICS configuration is predicted to deliver an EINOx value of about 3 for the targeted supersonic aircraft. Emissions results at supersonic cruise conditions show potential for meeting the NASA goals with liquid fuel.

NASA Numerical and Experimental Evaluation of UTRC Low Emissions Injector

NASA Technical Reports Server (NTRS)

Hicks, Yolanda R.; Tedder, Sarah A.; Anderson, Robert C.; Iannetti, Anthony C.; Smith, Lance L.; Dai, Zhongtao

2014-01-01

Computational and experimental analyses of a PICS-Pilot-In-Can-Swirler technology injector, developed by United Technologies Research Center (UTRC) are presented. NASA has defined technology targets for near term (called "N+1", circa 2015), midterm ("N+2", circa 2020) and far term ("N+3", circa 2030) that specify realistic emissions and fuel efficiency goals for commercial aircraft. This injector has potential for application in an engine to meet the Pratt & Whitney N+3 supersonic cycle goals, or the subsonic N+2 engine cycle goals. Experimental methods were employed to investigate supersonic cruise points as well as select points of the subsonic cycle engine; cruise, approach, and idle with a slightly elevated inlet pressure. Experiments at NASA employed gas analysis and a suite of laser-based measurement techniques to characterize the combustor flow downstream from the PICS dump plane. Optical diagnostics employed for this work included Planar Laser-Induced Fluorescence of fuel for injector spray pattern and Spontaneous Raman Spectroscopy for relative species concentration of fuel and CO2. The work reported here used unheated (liquid) Jet-A fuel for all fuel circuits and cycle conditions. The initial tests performed by UTRC used vaporized Jet-A to simulate the expected supersonic cruise condition, which anticipated using fuel as a heat sink. Using the National Combustion Code a PICS-based combustor was modeled with liquid fuel at the supersonic cruise condition. All CFD models used a cubic non-linear k-epsilon turbulence wall functions model, and a semi-detailed Jet-A kinetic mechanism based on a surrogate fuel mixture. Two initial spray droplet size distribution and spray cone conditions were used: (1) an initial condition (Lefebvre) with an assumed Rosin-Rammler distribution, and 7 degree Solid Spray Cone; and (2) the Boundary Layer Stripping (BLS) primary atomization model giving the spray size distribution and directional properties. Contour and line plots are shown in comparison with experimental data (where this data is available) for flow velocities, fuel, and temperature distribution. The CFD results are consistent with experimental observations for fuel distribution and vaporization. Analysis of gas sample results, using a previously-developed NASA NOx correlation, indicates that for sea-level takeoff, the PICS configuration is predicted to deliver an EINOx value of about three for the targeted supersonic aircraft. Emissions results at supersonic cruise conditions show potential for meeting the NASA goals with liquid fuel.

Overcoming Challenges in Kinetic Modeling of Magnetized Plasmas and Vacuum Electronic Devices

NASA Astrophysics Data System (ADS)

Omelchenko, Yuri; Na, Dong-Yeop; Teixeira, Fernando

2017-10-01

We transform the state-of-the art of plasma modeling by taking advantage of novel computational techniques for fast and robust integration of multiscale hybrid (full particle ions, fluid electrons, no displacement current) and full-PIC models. These models are implemented in 3D HYPERS and axisymmetric full-PIC CONPIC codes. HYPERS is a massively parallel, asynchronous code. The HYPERS solver does not step fields and particles synchronously in time but instead executes local variable updates (events) at their self-adaptive rates while preserving fundamental conservation laws. The charge-conserving CONPIC code has a matrix-free explicit finite-element (FE) solver based on a sparse-approximate inverse (SPAI) algorithm. This explicit solver approximates the inverse FE system matrix (``mass'' matrix) using successive sparsity pattern orders of the original matrix. It does not reduce the set of Maxwell's equations to a vector-wave (curl-curl) equation of second order but instead utilizes the standard coupled first-order Maxwell's system. We discuss the ability of our codes to accurately and efficiently account for multiscale physical phenomena in 3D magnetized space and laboratory plasmas and axisymmetric vacuum electronic devices.

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).

Use of Molecular Dynamics for the Refinement of an Electrostatic Model for the In Silico Design of a Polymer Antidote for the Anticoagulant Fondaparinux

PubMed Central

Kwok, Ezra; Gopaluni, Bhushan; Kizhakkedathu, Jayachandran N.

2013-01-01

Molecular dynamics (MD) simulations results are herein incorporated into an electrostatic model used to determine the structure of an effective polymer-based antidote to the anticoagulant fondaparinux. In silico data for the polymer or its cationic binding groups has not, up to now, been available, and experimental data on the structure of the polymer-fondaparinux complex is extremely limited. Consequently, the task of optimizing the polymer structure is a daunting challenge. MD simulations provided a means to gain microscopic information on the interactions of the binding groups and fondaparinux that would have otherwise been inaccessible. This was used to refine the electrostatic model and improve the quantitative model predictions of binding affinity. Once refined, the model provided guidelines to improve electrostatic forces between candidate polymers and fondaparinux in order to increase association rate constants. PMID:27006916

Relativistically induced transparency acceleration of light ions by an ultrashort laser pulse interacting with a heavy-ion-plasma density gradient

NASA Astrophysics Data System (ADS)

Sahai, Aakash A.; Tsung, Frank S.; Tableman, Adam R.; Mori, Warren B.; Katsouleas, Thomas C.

2013-10-01

The relativistically induced transparency acceleration (RITA) scheme of proton and ion acceleration using laser-plasma interactions is introduced, modeled, and compared to the existing schemes. Protons are accelerated with femtosecond relativistic pulses to produce quasimonoenergetic bunches with controllable peak energy. The RITA scheme works by a relativistic laser inducing transparency [Akhiezer and Polovin, Zh. Eksp. Teor. Fiz 30, 915 (1956); Kaw and Dawson, Phys. FluidsPFLDAS0031-917110.1063/1.1692942 13, 472 (1970); Max and Perkins, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.27.1342 27, 1342 (1971)] to densities higher than the cold-electron critical density, while the background heavy ions are stationary. The rising laser pulse creates a traveling acceleration structure at the relativistic critical density by ponderomotively [Lindl and Kaw, Phys. FluidsPFLDAS0031-917110.1063/1.1693437 14, 371 (1971); Silva , Phys. Rev. E1063-651X10.1103/PhysRevE.59.2273 59, 2273 (1999)] driving a local electron density inflation, creating an electron snowplow and a co-propagating electrostatic potential. The snowplow advances with a velocity determined by the rate of the rise of the laser's intensity envelope and the heavy-ion-plasma density gradient scale length. The rising laser is incrementally rendered transparent to higher densities such that the relativistic-electron plasma frequency is resonant with the laser frequency. In the snowplow frame, trace density protons reflect off the electrostatic potential and get snowplowed, while the heavier background ions are relatively unperturbed. Quasimonoenergetic bunches of velocity equal to twice the snowplow velocity can be obtained and tuned by controlling the snowplow velocity using laser-plasma parameters. An analytical model for the proton energy as a function of laser intensity, rise time, and plasma density gradient is developed and compared to 1D and 2D PIC OSIRIS [Fonseca , Lect. Note Comput. Sci.9783-540410.1007/3-540-47789-6_36 2331, 342 (2002)] simulations. We model the acceleration of protons to GeV energies with tens-of-femtoseconds laser pulses of a few petawatts. The scaling of proton energy with laser power compares favorably to other mechanisms for ultrashort pulses [Schreiber , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.97.045005 97, 045005 (2006); Esirkepov , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.92.175003 92, 175003 (2004); Silva , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.92.015002 92, 015002 (2004); Fiuza , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.109.215001 109, 215001 (2012)].

Electron cyclotron thruster new modeling results preparation for initial experiments

NASA Technical Reports Server (NTRS)

Hooper, E. Bickford

1993-01-01

The following topics are discussed: a whistler-based electron cyclotron resonance heating (ECRH) thruster; cross-field coupling in the helicon approximation; wave propagation; wave structure; plasma density; wave absorption; the electron distribution function; isothermal and adiabatic plasma flow; ECRH thruster modeling; a PIC code model; electron temperature; electron energy; and initial experimental tests. The discussion is presented in vugraph form.

Simulation of Aluminum Micro-mirrors for Space Applications at Cryogenic Temperatures

NASA Technical Reports Server (NTRS)

Kuhn, J. L.; Dutta, S. B.; Greenhouse, M. A.; Mott, D. B.

2000-01-01

Closed form and finite element models are developed to predict the device response of aluminum electrostatic torsion micro-mirrors fabricated on silicon substrate for space applications at operating temperatures of 30K. Initially, closed form expressions for electrostatic pressure arid mechanical restoring torque are used to predict the pull-in and release voltages at room temperature. Subsequently, a detailed mechanical finite element model is developed to predict stresses and vertical beam deflection induced by the electrostatic and thermal loads. An incremental and iterative solution method is used in conjunction with the nonlinear finite element model and closed form electrostatic equations to solve. the coupled electro-thermo-mechanical problem. The simulation results are compared with experimental measurements at room temperature of fabricated micro-mirror devices.

Simplified molecular input line entry system-based: QSAR modelling for MAP kinase-interacting protein kinase (MNK1).

PubMed

Begum, S; Achary, P Ganga Raju

2015-01-01

Quantitative structure-activity relationship (QSAR) models were built for the prediction of inhibition (pIC50, i.e. negative logarithm of the 50% effective concentration) of MAP kinase-interacting protein kinase (MNK1) by 43 potent inhibitors. The pIC50 values were modelled with five random splits, with the representations of the molecular structures by simplified molecular input line entry system (SMILES). QSAR model building was performed by the Monte Carlo optimisation using three methods: classic scheme; balance of correlations; and balance correlation with ideal slopes. The robustness of these models were checked by parameters as rm(2), r(*)m(2), [Formula: see text] and randomisation technique. The best QSAR model based on single optimal descriptors was applied to study in vitro structure-activity relationships of 6-(4-(2-(piperidin-1-yl) ethoxy) phenyl)-3-(pyridin-4-yl) pyrazolo [1,5-a] pyrimidine derivatives as a screening tool for the development of novel potent MNK1 inhibitors. The effects of alkyl group, -OH, -NO2, F, Cl, Br, I, etc. on the IC50 values towards the inhibition of MNK1 were also reported.

Pancreatic cancer-specific cell death induced in vivo by cytoplasmic-delivered polyinosine-polycytidylic acid

PubMed Central

Bhoopathi, Praveen; Quinn, Bridget A.; Gui, Qin; Shen, Xue-Ning; Grossman, Steven R.; Das, Swadesh K.; Sarkar, Devanand; Fisher, Paul B.; Emdad, Luni

2014-01-01

Polyinosine-polycytidylic acid (pIC) is a synthetic dsRNA that acts as an immune agonist of TLR3 and RLR to activate dendritic and NK cells that can kill tumor cells. pIC can also trigger apoptosis in pancreatic ductal adenocarcinoma cells but its mechanism of action is obscure. In this study, we investigated the potential therapeutic activity of a formulation of pIC with polyethylenimine ([pIC]PEI) in PDAC and investigated its mechanism of action. [pIC]PEI stimulated apoptosis in PDAC cells without affecting normal pancreatic epithelial cells. Mechanistically, [pIC]PEI repressed XIAP and survivin expression and activated an immune response by inducing MDA-5, RIG-I and NOXA. Phosphorylation of AKT was inhibited by [pIC]PEI in PDAC and this event was critical for stimulating apoptosis through XIAP and survivin degradation. In vivo administration of [pIC]PEI inhibited tumor growth via AKT-mediated XIAP degradation in both subcutaneous and quasi-orthotopic-models of PDAC. Taken together, these results offer a preclinical proof-of-concept for the evaluation of [pIC]PEI as an immunochemotherapy to treat pancreatic cancer. PMID:25205107

Dynamical mass measurement of the young spectroscopic binary V343 Normae AaAb resolved with the Gemini Planet Imager

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

Nielsen, Eric L.; De Rosa, Robert J.; Wang, Jason

Here, we present new spatially resolved astrometry and photometry from the Gemini Planet Imager of the inner binary of the young multiple star system V343 Normae, which is a member of the β Pictoris (β Pic) moving group. V343 Normae comprises a K0 and mid-M star in a ~4.5 year orbit (AaAb) and a wide 10'' M5 companion (B). By combining these data with archival astrometry and radial velocities we fit the orbit and measure individual masses for both components ofmore » $${M}_{\\mathrm{Aa}}=1.10\\pm 0.10\\,{M}_{\\odot }$$ and $${M}_{\\mathrm{Ab}}=0.290\\pm 0.018\\,{M}_{\\odot }$$. Comparing to theoretical isochrones, we find good agreement for the measured masses and JHK band magnitudes of the two components consistent with the age of the β Pic moving group. We derive a model-dependent age for the β Pic moving group of 26 ± 3 Myr by combining our results for V343 Normae with literature measurements for GJ 3305, which is another group member with resolved binary components and dynamical masses.« less

Fully microscopic analysis of laser-driven finite plasmas using the example of clusters

NASA Astrophysics Data System (ADS)

Peltz, Christian; Varin, Charles; Brabec, Thomas; Fennel, Thomas

2012-06-01

We discuss a microscopic particle-in-cell (MicPIC) approach that allows bridging of the microscopic and macroscopic realms of laser-driven plasma physics. The simultaneous resolution of collisions and electromagnetic field propagation in MicPIC enables the investigation of processes that have been inaccessible to rigorous numerical scrutiny so far. This is illustrated by the two main findings of our analysis of pre-ionized, resonantly laser-driven clusters, which can be realized experimentally in pump-probe experiments. In the linear response regime, MicPIC data are used to extract the individual microscopic contributions to the dielectric cluster response function, such as surface and bulk collision frequencies. We demonstrate that the competition between surface collisions and radiation damping is responsible for the maximum in the size-dependent lifetime of the Mie surface plasmon. The capacity to determine the microscopic underpinning of optical material parameters opens new avenues for modeling nano-plasmonics and nano-photonics systems. In the non-perturbative regime, we analyze the formation and evolution of recollision-induced plasma waves in laser-driven clusters. The resulting dynamics of the electron density and local field hot spots opens a new research direction for the field of attosecond science.

Dynamical mass measurement of the young spectroscopic binary V343 Normae AaAb resolved with the Gemini Planet Imager

DOE PAGES

Nielsen, Eric L.; De Rosa, Robert J.; Wang, Jason; ...

2016-11-22

Here, we present new spatially resolved astrometry and photometry from the Gemini Planet Imager of the inner binary of the young multiple star system V343 Normae, which is a member of the β Pictoris (β Pic) moving group. V343 Normae comprises a K0 and mid-M star in a ~4.5 year orbit (AaAb) and a wide 10'' M5 companion (B). By combining these data with archival astrometry and radial velocities we fit the orbit and measure individual masses for both components ofmore » $${M}_{\\mathrm{Aa}}=1.10\\pm 0.10\\,{M}_{\\odot }$$ and $${M}_{\\mathrm{Ab}}=0.290\\pm 0.018\\,{M}_{\\odot }$$. Comparing to theoretical isochrones, we find good agreement for the measured masses and JHK band magnitudes of the two components consistent with the age of the β Pic moving group. We derive a model-dependent age for the β Pic moving group of 26 ± 3 Myr by combining our results for V343 Normae with literature measurements for GJ 3305, which is another group member with resolved binary components and dynamical masses.« less

The Poisson-Helmholtz-Boltzmann model.

PubMed

Bohinc, K; Shrestha, A; May, S

2011-10-01

We present a mean-field model of a one-component electrolyte solution where the mobile ions interact not only via Coulomb interactions but also through a repulsive non-electrostatic Yukawa potential. Our choice of the Yukawa potential represents a simple model for solvent-mediated interactions between ions. We employ a local formulation of the mean-field free energy through the use of two auxiliary potentials, an electrostatic and a non-electrostatic potential. Functional minimization of the mean-field free energy leads to two coupled local differential equations, the Poisson-Boltzmann equation and the Helmholtz-Boltzmann equation. Their boundary conditions account for the sources of both the electrostatic and non-electrostatic interactions on the surface of all macroions that reside in the solution. We analyze a specific example, two like-charged planar surfaces with their mobile counterions forming the electrolyte solution. For this system we calculate the pressure between the two surfaces, and we analyze its dependence on the strength of the Yukawa potential and on the non-electrostatic interactions of the mobile ions with the planar macroion surfaces. In addition, we demonstrate that our mean-field model is consistent with the contact theorem, and we outline its generalization to arbitrary interaction potentials through the use of a Laplace transformation. © EDP Sciences / Società Italiana di Fisica / Springer-Verlag 2011

Kinetic Modeling of the Lunar Dust-Plasma Environment

NASA Astrophysics Data System (ADS)

Kallio, Esa; Alho, Markku; Alvarez, Francisco; Barabash, Stas; Dyadechkin, Sergey; Fernandes, Vera; Futaana, Yoshifumi; Harri, Ari-Matti; Haunia, Touko; Heilimo, Jyri; Holmström, Mats; Jarvinen, Riku; Lue, Charles; Makela, Jakke; Porjo, Niko; Schmidt, Walter; Shahab, Fatemi; Siili, Tero; Wurz, Peter

2014-05-01

Modeling of the lunar dust and plasma environment is a challenging task because a self-consistent model should include ions, electrons and dust particles and numerous other factors. However, most of the parameters are not well established or constrained by measurements in the lunar environment. More precisely, a comprehensive model should contain electrons originating from 1) the solar wind, 2) the lunar material (photoelectrons, secondary electrons) and 3) the lunar dust. Ions originate from the solar wind, the lunar material, the lunar exosphere and the dust. To model the role of the dust in the lunar plasma environment is a highly complex task since the properties of the dust particles in the exosphere are poorly known (e.g. mass, size, shape, conductivity) or not known (e.g. charge and photoelectron emission) and probably are time dependent. Models should also include the effects of interactions between the surface and solar wind and energetic particles, and micrometeorites. Largely different temporal and spatial scales are also a challenge for the numerical models. In addition, the modeling of a region on the Moon - for example on the South Pole - at a given time requires also knowledge of the solar illumination conditions at that time, mineralogical and electric properties of the local lunar surface, lunar magnetic anomalies, solar UV flux and the properties of the solar wind. Harmful effects of lunar dust to technical devices and to human health as well as modeling of the properties of the lunar plasma and dust environment have been topics of two ESA funded projects L-DEPP and DPEM. In the presentation we will summarize some basic results and characteristics of plasma and fields near and around the Moon as studied and discovered in these projects. Especially, we analyse three different space and time scales by kinetic models: [1] the "microscale" region near surface with an electrostatic PIC (ions and electrons are particles) model, [2] the "mesoscale" region including lunar magnetic anomalies and [3] the global scale Moon-solar wind interaction with hybrid (ions as particles in massless electron fluid) models.

The Stiffness Variation of a Micro-Ring Driven by a Traveling Piecewise-Electrode

PubMed Central

Li, Yingjie; Yu, Tao; Hu, Yuh-Chung

2014-01-01

In the practice of electrostatically actuated micro devices; the electrostatic force is implemented by sequentially actuated piecewise-electrodes which result in a traveling distributed electrostatic force. However; such force was modeled as a traveling concentrated electrostatic force in literatures. This article; for the first time; presents an analytical study on the stiffness variation of microstructures driven by a traveling piecewise electrode. The analytical model is based on the theory of shallow shell and uniform electrical field. The traveling electrode not only applies electrostatic force on the circular-ring but also alters its dynamical characteristics via the negative electrostatic stiffness. It is known that; when a structure is subjected to a traveling constant force; its natural mode will be resonated as the traveling speed approaches certain critical speeds; and each natural mode refers to exactly one critical speed. However; for the case of a traveling electrostatic force; the number of critical speeds is more than that of the natural modes. This is due to the fact that the traveling electrostatic force makes the resonant frequencies of the forward and backward traveling waves of the circular-ring different. Furthermore; the resonance and stability can be independently controlled by the length of the traveling electrode; though the driving voltage and traveling speed of the electrostatic force alter the dynamics and stabilities of microstructures. This paper extends the fundamental insights into the electromechanical behavior of microstructures driven by electrostatic forces as well as the future development of MEMS/NEMS devices with electrostatic actuation and sensing. PMID:25230308

The stiffness variation of a micro-ring driven by a traveling piecewise-electrode.

PubMed

Li, Yingjie; Yu, Tao; Hu, Yuh-Chung

2014-09-16

In the practice of electrostatically actuated micro devices; the electrostatic force is implemented by sequentially actuated piecewise-electrodes which result in a traveling distributed electrostatic force. However; such force was modeled as a traveling concentrated electrostatic force in literatures. This article; for the first time; presents an analytical study on the stiffness variation of microstructures driven by a traveling piecewise electrode. The analytical model is based on the theory of shallow shell and uniform electrical field. The traveling electrode not only applies electrostatic force on the circular-ring but also alters its dynamical characteristics via the negative electrostatic stiffness. It is known that; when a structure is subjected to a traveling constant force; its natural mode will be resonated as the traveling speed approaches certain critical speeds; and each natural mode refers to exactly one critical speed. However; for the case of a traveling electrostatic force; the number of critical speeds is more than that of the natural modes. This is due to the fact that the traveling electrostatic force makes the resonant frequencies of the forward and backward traveling waves of the circular-ring different. Furthermore; the resonance and stability can be independently controlled by the length of the traveling electrode; though the driving voltage and traveling speed of the electrostatic force alter the dynamics and stabilities of microstructures. This paper extends the fundamental insights into the electromechanical behavior of microstructures driven by electrostatic forces as well as the future development of MEMS/NEMS devices with electrostatic actuation and sensing.

Metadata, PICS and Quality.

ERIC Educational Resources Information Center

Armstrong, C. J.

1997-01-01

Discusses PICS (Platform for Internet Content Selection), the Centre for Information Quality Management (CIQM), and metadata. Highlights include filtering networked information; the quality of information; and standardizing search engines. (LRW)

Electron ionization of SiCl4

NASA Astrophysics Data System (ADS)

King, Simon J.; Price, Stephen D.

2011-02-01

Relative partial ionization cross sections (PICS) for the formation of fragment ions following electron ionization of SiCl4, in the electron energy range 30-200 eV, have been determined using time-of-flight mass spectrometry coupled with an ion coincidence technique. By this method, the contributions to the yield of each fragment ion from dissociative single, double, and triple ionization, are distinguished. These yields are quantified in the form of relative precursor-specific PICS, which are reported here for the first time for SiCl4. For the formation of singly charged ionic fragments, the low-energy maxima appearing in the PICS curves are due to contributions from single ionization involving predominantly indirect ionization processes, while contributions to the yields of these ions at higher electron energies are often dominated by dissociative double ionization. Our data, in the reduced form of relative PICS, are shown to be in good agreement with a previous determination of the PICS of SiCl4. Only for the formation of doubly charged fragment ions are the current relative PICS values lower than those measured in a previous study, although both datasets agree within combined error limits. The relative PICS data presented here include the first quantitative measurements of the formation of Cl2+ fragment ions and of the formation of ion pairs via dissociative double ionization. The peaks appearing in the 2D ion coincidence data are analyzed to provide further information concerning the mechanism and energetics of the charge-separating dissociations of SiCl42+. The lowest energy dicationic precursor state, leading to SiCl3+ + Cl+ formation, lies 27.4 ± 0.3 eV above the ground state of SiCl4 and is in close agreement with a calculated value of the adiabatic double ionization energy (27.3 eV).

Electron ionization of SiCl4.

PubMed

King, Simon J; Price, Stephen D

2011-02-21

Relative partial ionization cross sections (PICS) for the formation of fragment ions following electron ionization of SiCl(4), in the electron energy range 30-200 eV, have been determined using time-of-flight mass spectrometry coupled with an ion coincidence technique. By this method, the contributions to the yield of each fragment ion from dissociative single, double, and triple ionization, are distinguished. These yields are quantified in the form of relative precursor-specific PICS, which are reported here for the first time for SiCl(4). For the formation of singly charged ionic fragments, the low-energy maxima appearing in the PICS curves are due to contributions from single ionization involving predominantly indirect ionization processes, while contributions to the yields of these ions at higher electron energies are often dominated by dissociative double ionization. Our data, in the reduced form of relative PICS, are shown to be in good agreement with a previous determination of the PICS of SiCl(4). Only for the formation of doubly charged fragment ions are the current relative PICS values lower than those measured in a previous study, although both datasets agree within combined error limits. The relative PICS data presented here include the first quantitative measurements of the formation of Cl(2) (+) fragment ions and of the formation of ion pairs via dissociative double ionization. The peaks appearing in the 2D ion coincidence data are analyzed to provide further information concerning the mechanism and energetics of the charge-separating dissociations of SiCl(4) (2+). The lowest energy dicationic precursor state, leading to SiCl(3) (+) + Cl(+) formation, lies 27.4 ± 0.3 eV above the ground state of SiCl(4) and is in close agreement with a calculated value of the adiabatic double ionization energy (27.3 eV).

Elevations in the Fasting Serum Proinsulin-to-C-Peptide Ratio Precede the Onset of Type 1 Diabetes.

PubMed

Sims, Emily K; Chaudhry, Zunaira; Watkins, Renecia; Syed, Farooq; Blum, Janice; Ouyang, Fangqian; Perkins, Susan M; Mirmira, Raghavendra G; Sosenko, Jay; DiMeglio, Linda A; Evans-Molina, Carmella

2016-09-01

We tested whether an elevation in the serum proinsulin-to-C-peptide ratio (PI:C), a biomarker of β-cell endoplasmic reticulum (ER) dysfunction, was associated with progression to type 1 diabetes. Fasting total PI and C levels were measured in banked serum samples obtained from TrialNet Pathway to Prevention (PTP) participants, a cohort of autoantibody-positive relatives without diabetes of individuals with type 1 diabetes. Samples were obtained ∼12 months before diabetes onset from PTP progressors in whom diabetes developed (n = 60), and were compared with age-, sex-, and BMI-matched nonprogressors who remained normoglycemic (n = 58). PI:C ratios were calculated as molar ratios and were multiplied by 100% to obtain PI levels as a percentage of C levels. Although absolute PI levels did not differ between groups, PI:C ratios were significantly increased in antibody-positive subjects in whom there was progression to diabetes compared with nonprogressors (median 1.81% vs. 1.17%, P = 0.03). The difference between groups was most pronounced in subjects who were ≤10 years old, where the median progressor PI:C ratio was nearly triple that of nonprogressors; 90.0% of subjects in this age group within the upper PI:C quartile progressed to the development of diabetes. Logistic regression analysis, adjusted for age and BMI, demonstrated increased odds of progression for higher natural log PI:C ratio values (odds ratio 1.44, 95% CI 1.02, 2.05). These data suggest that β-cell ER dysfunction precedes type 1 diabetes onset, especially in younger children. Elevations in the serum PI:C ratio may have utility in predicting the onset of type 1 diabetes in the presymptomatic phase. © 2016 by the American Diabetes Association.

Elevations in the Fasting Serum Proinsulin–to–C-Peptide Ratio Precede the Onset of Type 1 Diabetes

PubMed Central

Sims, Emily K.; Chaudhry, Zunaira; Watkins, Renecia; Syed, Farooq; Blum, Janice; Ouyang, Fangqian; Perkins, Susan M.; Mirmira, Raghavendra G.; Sosenko, Jay; DiMeglio, Linda A.

2016-01-01

OBJECTIVE We tested whether an elevation in the serum proinsulin–to–C-peptide ratio (PI:C), a biomarker of β-cell endoplasmic reticulum (ER) dysfunction, was associated with progression to type 1 diabetes. RESEARCH DESIGN AND METHODS Fasting total PI and C levels were measured in banked serum samples obtained from TrialNet Pathway to Prevention (PTP) participants, a cohort of autoantibody-positive relatives without diabetes of individuals with type 1 diabetes. Samples were obtained ∼12 months before diabetes onset from PTP progressors in whom diabetes developed (n = 60), and were compared with age-, sex-, and BMI-matched nonprogressors who remained normoglycemic (n = 58). PI:C ratios were calculated as molar ratios and were multiplied by 100% to obtain PI levels as a percentage of C levels. RESULTS Although absolute PI levels did not differ between groups, PI:C ratios were significantly increased in antibody-positive subjects in whom there was progression to diabetes compared with nonprogressors (median 1.81% vs. 1.17%, P = 0.03). The difference between groups was most pronounced in subjects who were ≤10 years old, where the median progressor PI:C ratio was nearly triple that of nonprogressors; 90.0% of subjects in this age group within the upper PI:C quartile progressed to the development of diabetes. Logistic regression analysis, adjusted for age and BMI, demonstrated increased odds of progression for higher natural log PI:C ratio values (odds ratio 1.44, 95% CI 1.02, 2.05). CONCLUSIONS These data suggest that β-cell ER dysfunction precedes type 1 diabetes onset, especially in younger children. Elevations in the serum PI:C ratio may have utility in predicting the onset of type 1 diabetes in the presymptomatic phase. PMID:27385327

Freeing data through The Polar Information Commons

NASA Astrophysics Data System (ADS)

de Bruin, Taco; Chen, Robert; Parsons, Mark; Carlson, David

2010-05-01

The polar regions are changing rapidly with dramatic global effect. Wise management of resources, improved decision support, and effective international cooperation on resource and geopolitical issues require deeper understanding and better prediction of these changes. Unfortunately, polar data and information remain scattered, scarce, and sporadic. Inspired by the Antarctic Treaty of 1959 that established the Antarctic as a global commons to be used only for peaceful purposes and scientific research, we assert that data and information about the polar regions are themselves "public goods" that should be shared ethically and with minimal constraint. We therefore envision the Polar Information Commons (PIC) as an open, virtual repository for vital scientific data and information that would provide a shared, community-based cyber-infrastructure fostering innovation, improving scientific efficiency, and encouraging participation in polar research, education, planning, and management. The PIC will build on the legacy of the International Polar Year (IPY), providing a long-term framework for access to and preservation of both existing and future data and information about the polar regions. Rapid change demands rapid data access. The PIC system will enable scientists to quickly expose their data to the world and share them through open protocols on the Internet. A PIC digital label will alert users and data centers to new polar data and ensure that usage rights are clear. The PIC will utilize the Science Commons Protocol for Implementing Open Access Data, which promotes open data access through the public domain coupled with community norms of practice to ensure use of data in a fair and equitable manner. A set of PIC norms is currently being developed in consultation with key polar data organizations and other stakeholders. We welcome inputs from the broad science community as we further develop and refine the PIC approach and move ahead with implementation.

Freeing data through The Polar Information Commons

NASA Astrophysics Data System (ADS)

de Bruin, T.; Chen, R. S.; Parsons, M. A.; Carlson, D. J.

2009-12-01

The polar regions are changing rapidly with dramatic global effect. Wise management of resources, improved decision support, and effective international cooperation on resource and geopolitical issues require deeper understanding and better prediction of these changes. Unfortunately, polar data and information remain scattered, scarce, and sporadic. Inspired by the Antarctic Treaty of 1959 that established the Antarctic as a global commons to be used only for peaceful purposes and scientific research, we assert that data and information about the polar regions are themselves “public goods” that should be shared ethically and with minimal constraint. We therefore envision the Polar Information Commons (PIC) as an open, virtual repository for vital scientific data and information that would provide a shared, community-based cyber-infrastructure fostering innovation, improving scientific efficiency, and encouraging participation in polar research, education, planning, and management. The PIC will build on the legacy of the International Polar Year (IPY), providing a long-term framework for access to and preservation of both existing and future data and information about the polar regions. Rapid change demands rapid data access. The PIC system will enable scientists to quickly expose their data to the world and share them through open protocols on the Internet. A PIC digital label will alert users and data centers to new polar data and ensure that usage rights are clear. The PIC will utilize the Science Commons Protocol for Implementing Open Access Data, which promotes open data access through the public domain coupled with community norms of practice to ensure use of data in a fair and equitable manner. A set of PIC norms is currently being developed in consultation with key polar data organizations and other stakeholders. We welcome inputs from the broad science community as we further develop and refine the PIC approach and move ahead with implementation.

Planktic foraminifer and coccolith contribution to carbonate export fluxes over the central Kerguelen Plateau

NASA Astrophysics Data System (ADS)

Rembauville, M.; Meilland, J.; Ziveri, P.; Schiebel, R.; Blain, S.; Salter, I.

2016-05-01

We report the contribution of planktic foraminifers and coccoliths to the particulate inorganic carbon (PIC) export fluxes collected over an annual cycle (October 2011/September 2012) on the central Kerguelen Plateau in the Antarctic Zone (AAZ) south of the Polar Front (PF). The seasonality of PIC flux was decoupled from surface chlorophyll a concentration and particulate organic carbon (POC) fluxes and was characterized by a late summer (February) maximum. This peak was concomitant with the highest satellite-derived sea surface PIC and corresponded to a Emiliania huxleyi coccoliths export event that accounted for 85% of the annual PIC export. The foraminifer contribution to the annual PIC flux was much lower (15%) and dominated by Turborotalita quinqueloba and Neogloboquadrina pachyderma. Foraminifer export fluxes were closely related to the surface chlorophyll a concentration, suggesting food availability as an important factor regulating the foraminifer's biomass. We compared size-normalized test weight (SNW) of the foraminifers with previously published SNW from the Crozet Islands using the same methodology and found no significant difference in SNW between sites for a given species. However, the SNW was significantly species-specific with a threefold increase from T. quinqueloba to Globigerina bulloides. The annual PIC:POC molar ratio of 0.07 was close to the mean ratio for the global ocean and lead to a low carbonate counter pump effect (~5%) compared to a previous study north of the PF (6-32%). We suggest that lowers counter pump effect south of the PF despite similar productivity levels is due to a dominance of coccoliths in the PIC fluxes and a difference in the foraminifers species assemblage with a predominance of polar species with lower SNW.

A MATHEMATICAL MODEL OF ELECTROSTATIC PRECIPITATION. (REVISION 1): VOLUME I. MODELING AND PROGRAMMING

EPA Science Inventory

The report briefly describes the fundamental mechanisms and limiting factors involved in the electrostatic precipitation process. It discusses theories and procedures used in the computer model to describe the physical mechanisms, and generally describes the major operations perf...

Coherent optical monolithic phased-array antenna steering system

DOEpatents

Hietala, Vincent M.; Kravitz, Stanley H.; Vawter, Gregory A.

1994-01-01

An optical-based RF beam steering system for phased-array antennas comprising a photonic integrated circuit (PIC). The system is based on optical heterodyning employed to produce microwave phase shifting by a monolithic PIC constructed entirely of passive components. Microwave power and control signal distribution to the antenna is accomplished by optical fiber, permitting physical separation of the PIC and its control functions from the antenna. The system reduces size, weight, complexity, and cost of phased-array antenna systems.

Appropriateness of the food-pics image database for experimental eating and appetite research with adolescents.

PubMed

Jensen, Chad D; Duraccio, Kara M; Barnett, Kimberly A; Stevens, Kimberly S

2016-12-01

Research examining effects of visual food cues on appetite-related brain processes and eating behavior has proliferated. Recently investigators have developed food image databases for use across experimental studies examining appetite and eating behavior. The food-pics image database represents a standardized, freely available image library originally validated in a large sample primarily comprised of adults. The suitability of the images for use with adolescents has not been investigated. The aim of the present study was to evaluate the appropriateness of the food-pics image library for appetite and eating research with adolescents. Three hundred and seven adolescents (ages 12-17) provided ratings of recognizability, palatability, and desire to eat, for images from the food-pics database. Moreover, participants rated the caloric content (high vs. low) and healthiness (healthy vs. unhealthy) of each image. Adolescents rated approximately 75% of the food images as recognizable. Approximately 65% of recognizable images were correctly categorized as high vs. low calorie and 63% were correctly classified as healthy vs. unhealthy in 80% or more of image ratings. These results suggest that a smaller subset of the food-pics image database is appropriate for use with adolescents. With some modifications to included images, the food-pics image database appears to be appropriate for use in experimental appetite and eating-related research conducted with adolescents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Absorption, excretion and retention of 51Cr from labelled Cr-(III)-picolinate in rats.

PubMed

Kottwitz, Karin; Laschinsky, Niels; Fischer, Roland; Nielsen, Peter

2009-04-01

The bioavailability of chromium from Cr-picolinate (CrPic(3)) and Cr-chloride (CrCl(3)) was studied in rats using (51)Cr-labelled compounds and whole-body-counting. The intestinal absorption of Cr was twice as high from CrPic(3) (1.16% vs 0.55%) than from CrCl(3), however most of the absorbed (51)Cr from CrPic(3) was excreted into the urine within 24 h. After i.v. or i.p. injection, the whole-body retention curves fitted well to a multiexponential function, demonstrating that plasma chromium is in equilibrium with three pools. For CrPic(3), a large pool exists with a very rapid exchange (T (1/2) = <0.5 days), suggesting that CrPic(3) is absorbed as intact molecule, from which the main part is directly excreted by the kidney before degradation of the chromium complex in the liver can occur. CrCl(3) is less well absorbed but the rapid exchange pool is much smaller, resulting in even higher Cr concentrations in tissue such as muscle and fat. However, 1-3 days after application, the relative distribution of (51)Cr from both compounds was similar in all tissues studied, indicating that both compounds contribute to the same storage pool. In summary, the bioavailability of CrPic(3) in rats is not superior compared to CrCl(3).

Aerobic training reduces oxidative stress in skeletal muscle of rats exposed to air pollution and supplemented with chromium picolinate.

PubMed

Marmett, Bruna; Nunes, Ramiro Barcos; de Souza, Kellen Sábio; Lago, Pedro Dal; Rhoden, Cláudia Ramos

2018-12-01

The purpose of this study was to investigate the effects of chromium picolinate (CrPic) supplementation associated with aerobic exercise using measures of oxidative stress in rats exposed to air pollution. Sixty-one male Wistar rats were divided into eight groups: residual oil fly ash (ROFA) exposure and sedentary (ROFA-SED); ROFA exposure, sedentary and supplemented (ROFA-SED-CrPic); ROFA exposure and trained (ROFA-AT); ROFA exposure, supplemented and trained (ROFA-AT-CrPic); sedentary (Sal-SED); sedentary and supplemented (Sal-SED-CrPic); trained (Sal-AT); and supplemented and trained (Sal-AT-CrPic). Rats exposed to ROFA (air pollution) received 50 µg of ROFA daily via intranasal instillation. Supplemented rats received CrPic (1 mg/kg/day) daily by oral gavage. Exercise training was performed on a rat treadmill (5×/week). Oxidative parameters were evaluated at the end of protocols. Trained groups demonstrated lower gain of body mass (P < .001) and increased exercise tolerance (P < .0001). In the gastrocnemius, trained groups demonstrated increased SOD activity (P < .0001) and decrease levels of TBARS (P = .0014), although CAT activity did not differ among groups (P = .4487). Air pollution exposure did not lead to alterations in oxidative markers in lungs and heart, and exercise training was responsible for decreasing oxidative stress of the gastrocnemius.

The impact of electrostatic correlations on Dielectrophoresis of Non-conducting Particles

NASA Astrophysics Data System (ADS)

Alidoosti, Elaheh; Zhao, Hui

2017-11-01

The dipole moment of a charged, dielectric, spherical particle under the influence of a uniform alternating electric field is computed theoretically and numerically by solving the modified continuum Poisson-Nernst-Planck (PNP) equations accounting for ion-ion electrostatic correlations that is important at concentrated electrolytes (Phys. Rev. Lett. 106, 2011). The dependence on the frequency, zeta potential, electrostatic correlation lengths, and double layer thickness is thoroughly investigated. In the limit of thin double layers, we carry out asymptotic analysis to develop simple models which are in good agreement with the modified PNP model. Our results suggest that the electrostatic correlations have a complicated impact on the dipole moment. As the electrostatic correlations length increases, the dipole moment decreases, initially, reach a minimum, and then increases since the surface conduction first decreases and then increases due to the ion-ion correlations. The modified PNP model can improve the theoretical predictions particularly at low frequencies where the simple model can't qualitatively predict the dipole moment. This work was supported, in part, by NIH R15GM116039.

Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations.

PubMed

Cai, Xiao-hui; Zhang, Qing; Ding, Da-fu

2004-12-01

To model the three-dimensional structure and investigate the interaction mechanism of the proprotein convertase furin/kexin and their inhibitors (eglin c mutants). The three-dimensional complex structures of furin/kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition constants to find the correlation between them. High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostatic energies of interaction showed a linear correlation to the experimental inhibition constants. The modeled structures give good explanations of the specificity of eglin c mutants to furin/kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge-charge interactions in the binding of furin/kexin and their inhibitors.

Polarizable multipolar electrostatics for cholesterol

NASA Astrophysics Data System (ADS)

Fletcher, Timothy L.; Popelier, Paul L. A.

2016-08-01

FFLUX is a novel force field under development for biomolecular modelling, and is based on topological atoms and the machine learning method kriging. Successful kriging models have been obtained for realistic electrostatics of amino acids, small peptides, and some carbohydrates but here, for the first time, we construct kriging models for a sizeable ligand of great importance, which is cholesterol. Cholesterol's mean total (internal) electrostatic energy prediction error amounts to 3.9 kJ mol-1, which pleasingly falls below the threshold of 1 kcal mol-1 often cited for accurate biomolecular modelling. We present a detailed analysis of the error distributions.

Triple bag hermetic technology for controlling a bruchid (Spermophagus sp.) (Coleoptera, Chrysomelidae) in stored Hibiscus sabdariffa grain.

PubMed

Amadou, L; Baoua, I B; Baributsa, D; Williams, S B; Murdock, L L

2016-10-01

We assessed the performance of hermetic triple layer Purdue Improved Crop Storage (PICS) bags for protecting Hibiscus sabdariffa grain against storage insects. The major storage pest in the grain was a bruchid, Spermophagus sp.. When we stored infested H. sabdariffa grain for six months in the woven polypropylene bags typically used by farmers, the Spermophagus population increased 33-fold over that initially present. The mean number of emergence holes per 100 seeds increased from 3.3 holes to 35.4 holes during this time period, while grain held for the same length of time in PICS bags experienced no increase in the numbers of holes. Grain weight loss in the woven control bags was 8.6% while no weight loss was observed in the PICS bags. Seed germination rates of grain held in woven bags for six months dropped significantly while germination of grain held in PICS bags did not change from the initial value. PICS bags can be used to safely store Hibiscus grain after harvest to protect against a major insect pest.

PIC simulations of conical magnetically insulated transmission line with LTD generator: Transition from self-limited to load-limited flow

NASA Astrophysics Data System (ADS)

Liu, Laqun; Wang, Huihui; Guo, Fan; Zou, Wenkang; Liu, Dagang

2017-04-01

Based on the 3-dimensional Particle-In-Cell (PIC) code CHIPIC3D, with a new circuit boundary algorithm we developed, a conical magnetically insulated transmission line (MITL) with a 1.0-MV linear transformer driver (LTD) is explored numerically. The values of switch jitter time of LTD are critical parameters for the system, which are difficult to be measured experimentally. In this paper, these values are obtained by comparing the PIC results with experimental data of large diode-gap MITL. By decreasing the diode gap, we find that all PIC results agree well with experimental data only if MITL works on self-limited flow no matter how large the diode gap is. However, when the diode gap decreases to a threshold, the self-limited flow would transfer to a load-limited flow. In this situation, PIC results no longer agree with experimental data anymore due to the anode plasma expansion in the diode load. This disagreement is used to estimate the plasma expansion speed.

The Beta Pictoris Phenomenon in A-Shell Stars: Detection of Accreting Gas

NASA Technical Reports Server (NTRS)

Grady, C. A.; Perez, Mario R.; Talavera, A.; McCollum, B.; Rawley, L. A.; England, M. N.; Schlegel, M.

1996-01-01

We present the results of an expanded survey of A-shell stars using IUE high-dispersion spectra and find accreting, circumstellar gas in the line of sight to nine stars, in addition to the previously identified beta Pic, HR 10, and 131 Tau, which can be followed to between +70 and 100 km/s relative to the star. Two of the program stars, HD 88195 and HD 148283, show variable high-velocity gas. Given the small number of IUE spectra for our program stars, detection of high-velocity, accreting gas in 2/3 of the A-shell stars sampled indicates that accretion is an intrinsic part of the A-shell phenomenon and that beta Pic is not unique among main-sequence A stars in exhibiting such activity. Our program stars, as a group, have smaller column densities of high-velocity gas and smaller near-IR excesses compared with beta Pic. These features are consistent with greater central clearing of a remnant debris disk, compared with beta Pic, and suggest that the majority of field A-shell stars are older than beta Pic.

Exposure of coastal built assets in the South Pacific to climate risks

NASA Astrophysics Data System (ADS)

Kumar, Lalit; Taylor, Subhashni

2015-11-01

Pacific island countries (PICs) are situated in a highly dynamic ocean-atmosphere interface, are dispersed over a large ocean area, and have highly populated urban centres located on the coastal margin. The built infrastructure associated with urban centres is also located within close proximity to the coastlines, exposing such infrastructure to a variety of natural and climate change-related hazards. In this research we undertake a comprehensive analysis of the exposure of built infrastructure assets to climate risk for 12 PICs. We show that 57% of the assessed built infrastructure for the 12 PICs is located within 500 m of their coastlines, amounting to a total replacement value of US$21.9 billion. Eight of the 12 PICs have 50% or more of their built infrastructure located within 500 m of their coastlines. In particular, Kiribati, Marshall Islands and Tuvalu have over 95% of their built infrastructure located within 500 m of their coastlines. Coastal adaptation costs will require substantial financial resources, which may not be available in developing countries such as the PICs, leaving them to face very high impacts but lacking the adaptive capacity.

Physical and chemical basics of modification of poly(vinyl chloride) by means of polyisocyanate

NASA Astrophysics Data System (ADS)

Islamov, Anvar; Fakhrutdinova, Venera; Abdrakhmanova, Lyailya

2016-01-01

This research presents data relating to polyvinyl chloride (PVC) modification by means of reactive oligomer and measures technological, physical and mechanical properties of the modified composites. Polyisocyanate (PIC) has been chosen as the modifying reactive oligomer. It has been shown that insertion of the oligomer has a double effect on PVC. Primarily, PIC produces a plasticizing effect on PVC and in particular leads to an increase in thermal stability and melt flow index at the stage of processing. In addition, the molded PVC composites possess higher strength properties and lower deformability when exposed to temperature because of chemical transformations of PIC in polymer matrix and, as the result, the formation of cross-linked systems takes place. In this case, semi-interpenetrating structures are formed based on cross-linked products of PIC chemical transformations homogeneously distributed in the PVC matrix. It has been determined by means of IR-spectroscopy that the basic products of PIC curing are compounds with urea and biuret groups which leads to modifying effect on PVC especially: increase in strength, thermal and mechanical properties, and chemical resistance.

Overlap of copper and iron uptake systems in mitochondria in Saccharomyces cerevisiae

PubMed Central

Wang, Jing; Gammon, Micah G.; Maynard, Margaret K.; White, Olivia L.; Cobine, Jai A.; Mahone, Wilkerson K.

2016-01-01

In Saccharomyces cerevisiae, the mitochondrial carrier family protein Pic2 imports copper into the matrix. Deletion of PIC2 causes defects in mitochondrial copper uptake and copper-dependent growth phenotypes owing to decreased cytochrome c oxidase activity. However, copper import is not completely eliminated in this mutant, so alternative transport systems must exist. Deletion of MRS3, a component of the iron import machinery, also causes a copper-dependent growth defect on non-fermentable carbon. Deletion of both PIC2 and MRS3 led to a more severe respiratory growth defect than either individual mutant. In addition, MRS3 expressed from a high copy number vector was able to suppress the oxygen consumption and copper uptake defects of a strain lacking PIC2. When expressed in Lactococcus lactis, Mrs3 mediated copper and iron import. Finally, a PIC2 and MRS3 double mutant prevented the copper-dependent activation of a heterologously expressed copper sensor in the mitochondrial intermembrane space. Taken together, these data support a role for the iron transporter Mrs3 in copper import into the mitochondrial matrix. PMID:26763345

Structures of transcription pre-initiation complex with TFIIH and Mediator.

PubMed

Schilbach, S; Hantsche, M; Tegunov, D; Dienemann, C; Wigge, C; Urlaub, H; Cramer, P

2017-11-09

For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.

Conformation-Directed Formation of Self-Healing Diblock Copolypeptide Hydrogels via Polyion Complexation.

PubMed

Sun, Yintao; Wollenberg, Alexander L; O'Shea, Timothy Mark; Cui, Yanxiang; Zhou, Z Hong; Sofroniew, Michael V; Deming, Timothy J

2017-10-25

Synthetic diblock copolypeptides were designed to incorporate oppositely charged ionic segments that form β-sheet-structured hydrogel assemblies via polyion complexation when mixed in aqueous media. The observed chain conformation directed assembly was found to be required for efficient hydrogel formation and provided distinct and useful properties to these hydrogels, including self-healing after deformation, microporous architecture, and stability against dilution in aqueous media. While many promising self-assembled materials have been prepared using disordered or liquid coacervate polyion complex (PIC) assemblies, the use of ordered chain conformations in PIC assemblies to direct formation of new supramolecular morphologies is unprecedented. The promising attributes and unique features of the β-sheet-structured PIC hydrogels described here highlight the potential of harnessing conformational order derived from PIC assembly to create new supramolecular materials.

Ewald Summation Approach to Potential Models of Aqueous Electrolytes Involving Gaussian Charges and Induced Dipoles: Formal and Simulation Results

DOE PAGES

Chialvo, Ariel A.; Vlcek, Lukas

2014-11-01

We present a detailed derivation of the complete set of expressions required for the implementation of an Ewald summation approach to handle the long-range electrostatic interactions of polar and ionic model systems involving Gaussian charges and induced dipole moments with a particular application to the isobaricisothermal molecular dynamics simulation of our Gaussian Charge Polarizable (GCP) water model and its extension to aqueous electrolytes solutions. The set comprises the individual components of the potential energy, electrostatic potential, electrostatic field and gradient, the electrostatic force and the corresponding virial. Moreover, we show how the derived expressions converge to known point-based electrostatic counterpartsmore » when the parameters, defining the Gaussian charge and induced-dipole distributions, are extrapolated to their limiting point values. Finally, we illustrate the Ewald implementation against the current reaction field approach by isothermal-isobaric molecular dynamics of ambient GCP water for which we compared the outcomes of the thermodynamic, microstructural, and polarization behavior.« less

Plasma Flowfields Around Low Earth Orbit Objects: Aerodynamics to Underpin Orbit Predictions

NASA Astrophysics Data System (ADS)

Capon, Christopher; Boyce, Russell; Brown, Melrose

2016-07-01

Interactions between orbiting bodies and the charged space environment are complex. The large variation in passive body parameters e.g. size, geometry and materials, makes the plasma-body interaction in Low Earth Orbit (LEO) a region rich in fundamental physical phenomena. The aerodynamic interaction of LEO orbiting bodies with the neutral environment constitutes the largest non-conservative force on the body. However in general, study of the LEO plasma-body interaction has not been concerned with external flow physics, but rather with the effects on surface charging. The impact of ionospheric flow physics on the forces on space debris (and active objects) is not well understood. The work presented here investigates the contribution that plasma-body interactions have on the flow structure and hence on the total atmospheric force vector experienced by a polar orbiting LEO body. This work applies a hybrid Particle-in-Cell (PIC) - Direct Simulation Monte Carlo (DSMC) code, pdFoam, to self-consistently model the electrostatic flowfield about a cylinder with a uniform, fixed surface potential. Flow conditions are representative of the mean conditions experienced by the Earth Observing Satellite (EOS) based on the International Reference Ionosphere model (IRI-86). The electron distribution function is represented by a non-linear Boltzmann electron fluid and ion gas-surface interactions are assumed to be that of a neutralising, conducting, thermally accommodating solid wall with diffuse reflections. The variation in flowfield and aerodynamic properties with surface potential at a fixed flow condition is investigated, and insight into the relative contributions of charged and neutral species to the flow physics experienced by a LEO orbiting body is provided. This in turn is intended to help improve the fidelity of physics-based orbit predictions for space debris and other near-Earth space objects.

ESPVI 4.0 ELECTROSTATIS PRECIPITATOR V-1 AND PERFORMANCE MODEL: USER'S MANUAL

EPA Science Inventory

The manual is the companion document for the microcomputer program ESPVI 4.0, Electrostatic Precipitation VI and Performance Model. The program was developed to provide a user- friendly interface to an advanced model of electrostatic precipitation (ESP) performance. The program i...

Stability, Nonlinearity and Reliability of Electrostatically Actuated MEMS Devices

PubMed Central

Zhang, Wen-Ming; Meng, Guang; Chen, Di

2007-01-01

Electrostatic micro-electro-mechanical system (MEMS) is a special branch with a wide range of applications in sensing and actuating devices in MEMS. This paper provides a survey and analysis of the electrostatic force of importance in MEMS, its physical model, scaling effect, stability, nonlinearity and reliability in detail. It is necessary to understand the effects of electrostatic forces in MEMS and then many phenomena of practical importance, such as pull-in instability and the effects of effective stiffness, dielectric charging, stress gradient, temperature on the pull-in voltage, nonlinear dynamic effects and reliability due to electrostatic forces occurred in MEMS can be explained scientifically, and consequently the great potential of MEMS technology could be explored effectively and utilized optimally. A simplified parallel-plate capacitor model is proposed to investigate the resonance response, inherent nonlinearity, stiffness softened effect and coupled nonlinear effect of the typical electrostatically actuated MEMS devices. Many failure modes and mechanisms and various methods and techniques, including materials selection, reasonable design and extending the controllable travel range used to analyze and reduce the failures are discussed in the electrostatically actuated MEMS devices. Numerical simulations and discussions indicate that the effects of instability, nonlinear characteristics and reliability subjected to electrostatic forces cannot be ignored and are in need of further investigation.

Reexamination of the Coronal Index of Solar Activity

DTIC Science & Technology

2005-08-25

data with measurements made at Pic du Midi and Arosa . The resultant 1939-1992 CI had the interesting property that its value at the peak of the 11-year...1939 observation of the coronal emission line at 5303 A during when Waldmeier initiated green line measurements at Arosa the total solar eclipse of 7...limitations since the values obtained at differ- and Pic du Midi and Pic du Midi and Arosa to extend ent observatories depend on: (1) the accuracy of the the

A one-dimensional with three-dimensional velocity space hybrid-PIC model of the discharge plasma in a Hall thruster

NASA Astrophysics Data System (ADS)

Shashkov, Andrey; Lovtsov, Alexander; Tomilin, Dmitry

2017-04-01

According to present knowledge, countless numerical simulations of the discharge plasma in Hall thrusters were conducted. However, on the one hand, adequate two-dimensional (2D) models require a lot of time to carry out numerical research of the breathing mode oscillations or the discharge structure. On the other hand, existing one-dimensional (1D) models are usually too simplistic and do not take into consideration such important phenomena as neutral-wall collisions, magnetic field induced by Hall current and double, secondary, and stepwise ionizations together. In this paper a one-dimensional with three-dimensional velocity space (1D3V) hybrid-PIC model is presented. The model is able to incorporate all the phenomena mentioned above. A new method of neutral-wall collisions simulation in described space was developed and validated. Simulation results obtained for KM-88 and KM-60 thrusters are in a good agreement with experimental data. The Bohm collision coefficient was the same for both thrusters. Neutral-wall collisions, doubly charged ions, and induced magnetic field were proved to stabilize the breathing mode oscillations in a Hall thruster under some circumstances.

Modeling of neutral entrainment in an FRC thruster

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

Brackbill, Jeremiah; Gimelshein, Natalia; Gimelshein, Sergey

2012-11-27

Neutral entrainment in a field reversed configuration thruster is modeled numerically with an implicit PIC code extended to include thermal and chemical interactions between plasma and neutral particles. The contribution of charge exchange and electron impact ionization reactions is analyzed, and the sensitivity of the entrainment efficiency to the plasmoid translation velocity and neutral density is evaluated.

Imaging latex–carbon nanotube composites by subsurface electrostatic force microscopy

DOE PAGES

Patel, Sajan; Petty, Clayton W.; Krafcik, Karen Lee; ...

2016-09-08

Electrostatic modes of atomic force microscopy have shown to be non-destructive and relatively simple methods for imaging conductors embedded in insulating polymers. Here we use electrostatic force microscopy to image the dispersion of carbon nanotubes in a latex-based conductive composite, which brings forth features not observed in previously studied systems employing linear polymer films. A fixed-potential model of the probe-nanotube electrostatics is presented which in principle gives access to the conductive nanoparticle's depth and radius, and the polymer film dielectric constant. Comparing this model to the data results in nanotube depths that appear to be slightly above the film–air interface.more » Furthermore, this result suggests that water-mediated charge build-up at the film–air interface may be the source of electrostatic phase contrast in ambient conditions.« less

MATHEMATICAL MODEL OF ELECTROSTATIC PRECIPITATION FOR THE TEXAS INSTRUMENTS PROGRAMMABLE 59 CALCULATOR

EPA Science Inventory

The report describes a version of EPA's electrostatic precipitator (ESP) model suitable for use on a Texas Instruments Programmable 59 (TI-59) hand-held calculator. This version of the model allows the calculation of ESP collection efficiency, including corrections for non-ideal ...

DEVELOPMENT OF A MODEL THAT CONTAINS BOTH MULTIPOLE MOMENTS AND GAUSSIANS FOR THE CALCULATION OF MOLECULAR ELECTROSTATIC POTENTIALS

EPA Science Inventory

The electrostatic interaction is a critical component of intermolecular interactions in biological processes. Rapid methods for the computation and characterization of the molecular electrostatic potential (MEP) that segment the molecular charge distribution and replace this cont...

Material Science Smart Coatings

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

Rubinstein, A. I.; Sabirianov, R. F.; Namavar, Fereydoon

2014-07-01

The contribution of electrostatic interactions to the free energy of binding between model protein and a ceramic implant surface in the aqueous solvent, considered in the framework of the nonlocal electrostatic model, is calculated as a function of the implant low-frequency dielectric constant. We show that the existence of a dynamically ordered (low-dielectric) interfacial solvent layer at the protein-solvent and ceramic-solvent interface markedly increases charging energy of the protein and ceramic implant, and consequently makes the electrostatic contribution to the protein-ceramic binding energy more favorable (attractive). Our analysis shows that the corresponding electrostatic energy between protein and oxide ceramics dependsmore » nonmonotonically on the dielectric constant of ceramic, ε C. Obtained results indicate that protein can attract electrostatically to the surface if ceramic material has a moderate ε C below or about 35 (in particularly ZrO 2 or Ta 2O 5). This is in contrast to classical (local) consideration of the solvent, which demonstrates an unfavorable electrostatic interaction of protein with typical metal oxide ceramic materials (ε C>10). Thus, a solid implant coated by combining oxide ceramic with a reduced dielectric constant can be beneficial to strengthen the electrostatic binding of the protein-implant complex.« less

Investigation of Electrostatic Accelerometer in HUST for Space Science Missions

NASA Astrophysics Data System (ADS)

Bai, Yanzheng; Hu, Ming; Li, Gui; Liu, Li; Qu, Shaobo; Wu, Shuchao; Zhou, Zebing

2014-05-01

High-precision electrostatic accelerometers are significant payload in CHAMP, GRACE and GOCE gravity missions to measure the non-gravitational forces. In our group, space electrostatic accelerometer and inertial sensor based on the capacitive sensors and electrostatic control technique has been investigated for space science research in China such as testing of equivalence principle (TEPO), searching non-Newtonian force in micrometer range, satellite Earth's field recovery and so on. In our group, a capacitive position sensor with a resolution of 10-7pF/Hz1/2 and the μV/Hz1/2 level electrostatic actuator are developed. The fiber torsion pendulum facility is adopt to measure the parameters of the electrostatic controlled inertial sensor such as the resolution, and the electrostatic stiffness, the cross couple between different DOFs. Meanwhile, high voltage suspension and free fall methods are applied to verify the function of electrostatic accelerometer. Last, the engineering model of electrostatic accelerometer has been developed and tested successfully in space and preliminary results are present.

76 FR 2084 - Pacific Fishery Management Council; Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-12

... Pacific Fishery Management Council's (Council) Ad Hoc Groundfish Process Improvement Committee (PIC) will... the PIC work session is to develop an optimum detailed process and schedule for the 2013-14 groundfish...

Flip-chip integration of tilted VCSELs onto a silicon photonic integrated circuit.

PubMed

Lu, Huihui; Lee, Jun Su; Zhao, Yan; Scarcella, Carmelo; Cardile, Paolo; Daly, Aidan; Ortsiefer, Markus; Carroll, Lee; O'Brien, Peter

2016-07-25

In this article we describe a cost-effective approach for hybrid laser integration, in which vertical cavity surface emitting lasers (VCSELs) are passively-aligned and flip-chip bonded to a Si photonic integrated circuit (PIC), with a tilt-angle optimized for optical-insertion into standard grating-couplers. A tilt-angle of 10° is achieved by controlling the reflow of the solder ball deposition used for the electrical-contacting and mechanical-bonding of the VCSEL to the PIC. After flip-chip integration, the VCSEL-to-PIC insertion loss is -11.8 dB, indicating an excess coupling penalty of -5.9 dB, compared to Fibre-to-PIC coupling. Finite difference time domain simulations indicate that the penalty arises from the relatively poor match between the VCSEL mode and the grating-coupler.

Computational modeling of electrostatic charge and fields produced by hypervelocity impact

DOE PAGES

Crawford, David A.

2015-05-19

Following prior experimental evidence of electrostatic charge separation, electric and magnetic fields produced by hypervelocity impact, we have developed a model of electrostatic charge separation based on plasma sheath theory and implemented it into the CTH shock physics code. Preliminary assessment of the model shows good qualitative and quantitative agreement between the model and prior experiments at least in the hypervelocity regime for the porous carbonate material tested. The model agrees with the scaling analysis of experimental data performed in the prior work, suggesting that electric charge separation and the resulting electric and magnetic fields can be a substantial effectmore » at larger scales, higher impact velocities, or both.« less

Monte Carlo simulation of ion-neutral charge exchange collisions and grid erosion in an ion thruster

NASA Technical Reports Server (NTRS)

Peng, Xiaohang; Ruyten, Wilhelmus M.; Keefer, Dennis

1991-01-01

A combined particle-in-cell (PIC)/Monte Carlo simulation model has been developed in which the PIC method is used to simulate the charge exchange collisions. It is noted that a number of features were reproduced correctly by this code, but that its assumption of two-dimensional axisymmetry for a single set of grid apertures precluded the reproduction of the most characteristic feature of actual test data; namely, the concentrated grid erosion at the geometric center of the hexagonal aperture array. The first results of a three-dimensional code, which takes into account the hexagonal symmetry of the grid, are presented. It is shown that, with this code, the experimentally observed erosion patterns are reproduced correctly, demonstrating explicitly the concentration of sputtering between apertures.

Comparisons of angularly and spectrally resolved Bremsstrahlung measurements to two-dimensional multi-stage simulations of short-pulse laser-plasma interactions

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

Chen, C. D.; Kemp, A. J.; Pérez, F.

2013-05-15

A 2-D multi-stage simulation model incorporating realistic laser conditions and a fully resolved electron distribution handoff has been developed and compared to angularly and spectrally resolved Bremsstrahlung measurements from high-Z planar targets. For near-normal incidence and 0.5-1 × 10{sup 20} W/cm{sup 2} intensity, particle-in-cell (PIC) simulations predict the existence of a high energy electron component consistently directed away from the laser axis, in contrast with previous expectations for oblique irradiation. Measurements of the angular distribution are consistent with a high energy component when directed along the PIC predicted direction, as opposed to between the target normal and laser axis asmore » previously measured.« less

Study on the shrinkage behavior and conductivity of silver microwires during electrostatic field assisted sintering

NASA Astrophysics Data System (ADS)

Shangguan, Lei; Ma, Liuhong; Li, Mengke; Peng, Wei; Zhong, Yinghui; Su, Yufeng; Duan, Zhiyong

2018-05-01

An electrostatic field was applied to sintering Ag microwires to achieve a more compact structure and better conductivity. The shrinkage behavior of Ag microwires shows anisotropy, since bigger particle sizes, less micropores and smoother surfaces were observed in the direction of the electrostatic field in comparsion with the direction perpendicular to the electrostatic field, and the shrinkage rate of Ag microwires in the direction of electrostatic field improves about 2.4% with the electrostatic field intensity of 800 V cm‑1. The electrostatic field assisted sintering model of Ag microwires is proposed according to thermal diffuse dynamics analysis and experimental research. Moreover, the grain size of Ag microwres sintered with electrostatic field increases with the electrostatic field intensity and reaches 113 nm when the electrostatic field intensity is 800 V cm‑1, and the resistivity decreases to 2.07  ×  10‑8 Ω m as well. This method may overcome the restriction of metal wires which fabricated by the pseudoplastic metal nanoparticle fluid and be used as interconnects in nanoimprint lithography.

Chromium picolinate and chromium histidinate protects against renal dysfunction by modulation of NF-κB pathway in high-fat diet fed and Streptozotocin-induced diabetic rats.

PubMed

Selcuk, Mustafa Yavuz; Aygen, Bilge; Dogukan, Ayhan; Tuzcu, Zeynep; Akdemir, Fatih; Komorowski, James R; Atalay, Mustafa; Sahin, Kazim

2012-04-08

Diabetic nephropathy is one of major complications of diabetes mellitus. Although chromium is an essential element for carbohydrate and lipid metabolism, its effects on diabetic nephropathy are not well understood. The present study was conducted to investigate the effects of chromium picolinate (CrPic) and chromium histidinate (CrHis) on nuclear factor-kappa B (NF-κB) and nuclear factor-E2-related factor-2 (Nrf2) pathway in the rat kidney. Male Wistar rats were divided into six groups. Group I received a standard diet (8% fat) and served as a control; Group II was fed with a standard diet and received CrPic; Group III was fed with a standard diet and received CrHis; Group IV received a high fat diet (HFD, 40% fat) for 2 weeks and then were injected with streptozotocin (STZ) (HFD/STZ); Group V was treated as group IV (HFD/STZ) but supplemented with CrPic for 12 weeks. Group VI was treated as group IV (HFD/STZ) but supplemented with CrHis. The increased NF-κβ p65 in the HFD/STZ group was inhibited by CrPic and CrHis supplementation (P < 0.05). In STZ-treated rats, a significant decrease in levels of nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IκBα) was found in kidney tissues when compared to control rats (P < 0.05). A significant increase in the levels of IκBα was observed in CrPic- and CrHis-treated rats when compared with STZ-treated rats. Renal Nrf2 levels were significantly decreased in diabetic rats compared with the control rats. There was a higher tendency for increase of kidney Nrf2 level and decrease in kidney NFκBp65 levels and 4- hydroxyl nonenal (4-HNE) protein adducts (P < 0.05) in diabetic rats. Our result show that in kidney tissue CrHis/CrPic increases Nrf2 level, parallelly decreases NF-κB and partially restores IκBα levels in HFD/STZ group, suggesting that CrPic and CrHis may play a role in antioxidant defense system via the Nrf2 pathway by reducing inflammation through NF-κβ p65 inhibition. Moreover, a greater reduction in NF-κB expression and greater increases in expressions of IκBα and Nrf2 in diabetic rats supplemented with CrHis than rats supplemented with CrPic suggest that CrHis has more favorable effects than CrPic.

Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex

PubMed Central

Tramantano, Michael; Sun, Lu; Au, Christy; Labuz, Daniel; Liu, Zhimin; Chou, Mindy; Shen, Chen; Luk, Ed

2016-01-01

The assembly of the preinitiation complex (PIC) occurs upstream of the +1 nucleosome which, in yeast, obstructs the transcription start site and is frequently assembled with the histone variant H2A.Z. To understand the contribution of the transcription machinery in the disassembly of the +1 H2A.Z nucleosome, conditional mutants were used to block PIC assembly. A quantitative ChIP-seq approach, which allows detection of global occupancy change, was employed to measure H2A.Z occupancy. Blocking PIC assembly resulted in promoter-specific H2A.Z accumulation, indicating that the PIC is required to evict H2A.Z. By contrast, H2A.Z eviction was unaffected upon depletion of INO80, a remodeler previously reported to displace nucleosomal H2A.Z. Robust PIC-dependent H2A.Z eviction was observed at active and infrequently transcribed genes, indicating that constitutive H2A.Z turnover is a general phenomenon. Finally, sites with strong H2A.Z turnover precisely mark transcript starts, providing a new metric for identifying cryptic and alternative sites of initiation. DOI: http://dx.doi.org/10.7554/eLife.14243.001 PMID:27438412

Dietary Supplementation with Chromium Picolinate Influences Serum Glucose and Immune Response of Brown-Egg Laying Hens.

PubMed

Zhang, Shumin; Sun, Xiaoming; Liao, Xiudong; Lu, Lin; Zhang, Liyang; Ma, Qiugang; Luo, Xugang

2018-01-29

To investigate the effect of chromium picolinate (CrPic) on egg production performance, egg quality, blood indices, and immune function of laying hens, 270 23-week-old Beijing Red brown-egg laying hens were randomly assigned to one of three treatments with six replicates of 15 birds per replicate for each treatment in a completely randomized design. Laying hens were fed a Cr-unsupplemented corn-soybean meal basal diet (control, containing 0.45 mg Cr/kg by analysis) or the basal diet supplemented with 0.4 or 0.6 mg Cr/kg from CrPic for 10 weeks. Laying hens fed diets supplemented with CrPic had a lower (P < 0.05) serum glucose (GLU) concentration and higher (P < 0.03) serum antibody titer against Newcastle disease than those fed the control diet at 33 weeks of age. However, supplemental CrPic had no effect (P > 0.05) on egg production and egg quality of brown-egg laying hens from 24 to 33 weeks of age. The results from this study indicated that supplemental CrPic decreased serum GLU and enhanced the immune function of brown-egg laying hens.

Tissue accumulation and urinary excretion of Cr in chromium picolinate (CrPic)-supplemented lambs.

PubMed

Dallago, Bruno Stéfano Lima; Lima, Bárbara Alcântara Ferreira; Braz, Shélida Vasconcelos; Mustafa, Vanessa da Silva; McManus, Concepta; Paim, Tiago do Prado; Campeche, Aline; Gomes, Edgard Franco; Louvandini, Helder

2016-05-01

Chromium (Cr) concentrations in liver, kidney, spleen, heart, lymph node, skeletal muscle, bone, testis and urine of lambs were measured to trace the biodistribution and bioaccumulation of Cr after oral supplementation with chromium picolinate (CrPic). Twenty-four Santa Inês lambs were treated with four different concentrations of CrPic: placebo, 0.250, 0.375 and 0.500 mg of CrPic/animal/day for 84 days. The basal diet consisted of Panicum maximum cv Massai hay and concentrate. Cr concentrations were measured by ICP-MS measuring (52)Cr as collected mass. There was a positive linear relationship between dose administered and the accumulation of Cr in the heart, lungs and testis. Urinary excretion of Cr occurred in a time and dose-dependent manner, so the longer or more dietary Cr provided, the greater excretion of the element. As some non-carcass components (such as lungs or heart) are added to bone and visceral meal to feed animals, there is a risk of bioaccumulation and biomagnification due to Cr offered as CrPic in the diet. Copyright © 2016 Elsevier GmbH. All rights reserved.

Evaluation of the Main Ceos Pseudo Calibration Sites Using Modis Brdf/albedo Products

NASA Astrophysics Data System (ADS)

Kharbouche, Said; Muller, Jan-Peter

2016-06-01

This work describes our findings about an evaluation of the stability and the consistency of twenty primary PICSs (Pseudo-Invariant Calibration Sites). We present an analysis of 13 years of 8-daily MODIS products of BRDF parameters and white-sky-albedos (WSA) over the shortwave band. This time series of WSA and BRDFs shows the variation of the "stability" varies significantly from site to site. Using a 10x10 km window size over all the sites, the change in of WSA stability is around 4% but the isotropicity, which is an important element in inter-satellite calibration, can vary from 75% to 98%. Moreover, some PICS, especially, Libya-4 which is one of the PICS which is most employed, has significant and relatively fast changes in wintertime. PICS observations of BRDF/albedo shows that the Libya-4 PICS has the best performance but it is not too far from some sites such as Libya-1 and Mali. This study also reveals that Niger-3 PICS has the longest continuous period of high stability per year, and Sudan has the most isotropic surface. These observations have important implications for the use of these sites.

Web Service Model for Plasma Simulations with Automatic Post Processing and Generation of Visual Diagnostics*

NASA Astrophysics Data System (ADS)

Exby, J.; Busby, R.; Dimitrov, D. A.; Bruhwiler, D.; Cary, J. R.

2003-10-01

We present our design and initial implementation of a web service model for running particle-in-cell (PIC) codes remotely from a web browser interface. PIC codes have grown significantly in complexity and now often require parallel execution on multiprocessor computers, which in turn requires sophisticated post-processing and data analysis. A significant amount of time and effort is required for a physicist to develop all the necessary skills, at the expense of actually doing research. Moreover, parameter studies with a computationally intensive code justify the systematic management of results with an efficient way to communicate them among a group of remotely located collaborators. Our initial implementation uses the OOPIC Pro code [1], Linux, Apache, MySQL, Python, and PHP. The Interactive Data Language is used for visualization. [1] D.L. Bruhwiler et al., Phys. Rev. ST-AB 4, 101302 (2001). * This work is supported by DOE grant # DE-FG02-03ER83857 and by Tech-X Corp. ** Also University of Colorado.

Decadal covariability of Atlantic SSTs and western Amazon dry-season hydroclimate in observations and CMIP5 simulations

NASA Astrophysics Data System (ADS)

Fernandes, Katia; Giannini, Alessandra; Verchot, Louis; Baethgen, Walter; Pinedo-Vasquez, Miguel

2015-08-01

The unusual severity and return time of the 2005 and 2010 dry-season droughts in western Amazon is attributed partly to decadal climate fluctuations and a modest drying trend. Decadal variability of western Amazon hydroclimate is highly correlated to the Atlantic sea surface temperature (SST) north-south gradient (NSG). Shifts of dry and wet events frequencies are also related to the NSG phase, with a 66% chance of 3+ years of dry events per decade when NSG > 0 and 19% when NSG < 0. The western Amazon and NSG decadal covariability is well reproduced in general circulation models (GCMs) historical (HIST) and preindustrial control (PIC) experiments of the Coupled Model Intercomparison Project Phase 5 (CMIP5). The HIST and PIC also reproduce the shifts in dry and wet events probabilities, indicating potential for decadal predictability based on GCMs. Persistence of the current NSG positive phase favors above normal frequency of western Amazon dry events in coming decades.

On the electrostatic and steric similarity of lactam compounds and the natural substrate for bacterial cell-wall biosynthesis

NASA Astrophysics Data System (ADS)

Frau, J.; Price, S. L.

1996-04-01

Electrostatic and structural properties of a set of β-lactam, γ-lactam and nonlactam compounds have been analyzed and compared with those of a model of the natural substrate d-alanyl- d-alanine for the carboxy- and transpeptidase enzymes. This first comparison of the electrostatic properties has been based on a distributed multipole analysis of high-quality ab initio wave functions of the substrate and potential antibiotics. The electrostatic similarity of the substrate and active compounds is apparent, and contrasts with the electrostatic properties of the noninhibitors. This has been quantified to give a reasonable correlation with the MIC (Minimum Concentration for Inhibition) and with kinetic data (k2/K) in accordance with the model for interaction of the lactam compounds with dd-peptidase. These correlations provide a better prediction of antibacterial activity than purely structural criteria.

A view on thermodynamics of concentrated electrolytes: Modification necessity for electrostatic contribution of osmotic coefficient

NASA Astrophysics Data System (ADS)

Sahu, Jyoti; Juvekar, Vinay A.

2018-05-01

Prediction of the osmotic coefficient of concentrated electrolytes is needed in a wide variety of industrial applications. There is a need to correctly segregate the electrostatic contribution to osmotic coefficient from nonelectrostatic contribution. This is achieved in a rational way in this work. Using the Robinson-Stokes-Glueckauf hydrated ion model to predict non-electrostatic contribution to the osmotic coefficient, it is shown that hydration number should be independent of concentration so that the observed linear dependence of osmotic coefficient on electrolyte concentration in high concentration range could be predicted. The hydration number of several electrolytes (LiCl, NaCl, KCl, MgCl2, and MgSO4) has been estimated by this method. The hydration number predicted by this model shows correct dependence on temperature. It is also shown that the electrostatic contribution to osmotic coefficient is underpredicted by the Debye-Hückel theory at concentration beyond 0.1 m. The Debye-Hückel theory is modified by introducing a concentration dependent hydrated ionic size. Using the present analysis, it is possible to correctly estimate the electrostatic contribution to the osmotic coefficient, beyond the range of validation of the D-H theory. This would allow development of a more fundamental model for electrostatic interaction at high electrolyte concentrations.

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

PubMed

Robinson, Philip J; Trnka, Michael J; Bushnell, David A; Davis, Ralph E; Mattei, Pierre-Jean; Burlingame, Alma L; Kornberg, Roger D

2016-09-08

A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

New Distributed Multipole Methods for Accurate Electrostatics for Large-Scale Biomolecular Simultations

NASA Astrophysics Data System (ADS)

Sagui, Celeste

2006-03-01

An accurate and numerically efficient treatment of electrostatics is essential for biomolecular simulations, as this stabilizes much of the delicate 3-d structure associated with biomolecules. Currently, force fields such as AMBER and CHARMM assign ``partial charges'' to every atom in a simulation in order to model the interatomic electrostatic forces, so that the calculation of the electrostatics rapidly becomes the computational bottleneck in large-scale simulations. There are two main issues associated with the current treatment of classical electrostatics: (i) how does one eliminate the artifacts associated with the point-charges (e.g., the underdetermined nature of the current RESP fitting procedure for large, flexible molecules) used in the force fields in a physically meaningful way? (ii) how does one efficiently simulate the very costly long-range electrostatic interactions? Recently, we have dealt with both of these challenges as follows. In order to improve the description of the molecular electrostatic potentials (MEPs), a new distributed multipole analysis based on localized functions -- Wannier, Boys, and Edminston-Ruedenberg -- was introduced, which allows for a first principles calculation of the partial charges and multipoles. Through a suitable generalization of the particle mesh Ewald (PME) and multigrid method, one can treat electrostatic multipoles all the way to hexadecapoles all without prohibitive extra costs. The importance of these methods for large-scale simulations will be discussed, and examplified by simulations from polarizable DNA models.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

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

Jurrus, Elizabeth; Engel, Dave; Star, Keith

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suitemore » of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.« less

Improvements to the APBS biomolecular solvation software suite.

PubMed

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

CE: critical care recovery center: an innovative collaborative care model for ICU survivors.

PubMed

Khan, Babar A; Lasiter, Sue; Boustani, Malaz A

2015-03-01

Five million Americans require admission to ICUs annually owing to life-threatening illnesses. Recent medical advances have resulted in higher survival rates for critically ill patients, who often have significant cognitive, physical, and psychological sequelae, known as postintensive care syndrome (PICS). This growing population threatens to overwhelm the current U.S. health care system, which lacks established clinical models for managing their care. Novel innovative models are urgently needed. To this end, the pulmonary/critical care and geriatrics divisions at the Indiana University School of Medicine joined forces to develop and implement a collaborative care model, the Critical Care Recovery Center (CCRC). Its mission is to maximize the cognitive, physical, and psychological recovery of ICU survivors. Developed around the principles of implementation and complexity science, the CCRC opened in 2011 as a clinical center with a secondary research focus. Care is provided through a pre-CCRC patient and caregiver needs assessment, an initial diagnostic workup visit, and a follow-up visit that includes a family conference. With its sole focus on the prevention and treatment of PICS, the CCRC represents an innovative prototype aimed at modifying post-critical illness morbidities and improving the ICU survivor's quality of life.

Electron Acceleration in the Magnetotail during Substorms in Semi-Global PIC Simulations

NASA Astrophysics Data System (ADS)

Richard, R. L.; Schriver, D.; Ashour-Abdalla, M.; El-Alaoui, M.; Lapenta, G.; Walker, R. J.

2015-12-01

To understand the acceleration of electrons during a substorm reconnection event we have applied a semi-global particle in cell (PIC) simulation box embedded within a global magnetohydrodynamic (MHD) simulation of Earth's magnetosphere for an event on February 15, 2008. The MHD results were used to populate the PIC simulation and to set the boundary conditions. In the magnetotail we found that a series of dipolarizations formed due to unsteady reconnection. We also found that the most energetic electrons were in the separatrices far from the x-point. We attributed the acceleration to a streaming instability in the separatrices. To further understand electron acceleration we have applied the large scale kinetic (LSK) technique in which tens- to hundreds- of thousands of electrons are followed within the electric and magnetic fields from the PIC simulations., Electrons are already included in the PIC simulation, but the LSK simulations will allow selected individual particles to be followed and analyzed. Initially we performed electron LSK calculations in a two dimensional version of the PIC simulation in which electrons were allowed to move in the ignorable cross tail direction. These LSK calculations showed that electrons gained energy primarily for two reasons: (1) acceleration by the average dawn to dusk electric field and (2) acceleration by intense but localized electric field structures. The overall electron transport was more dawnward than duskward due to the average electric field. At the same time electrons typically moved away from the reconnection region in both the earthward and tailward directions. Superimposed on this large-scale transport was motion in both the dusk and dawn directions across the tail because of the electric field structures, which were particularly intense in the separatrices. LSK calculations are now being carried out by using the full three-dimensional magnetic and electric fields from the PIC simulation and these results will be compared with the two-dimensional results for the same substorm event.

Inappropriate care in European ICUs: confronting views from nurses and junior and senior physicians.

PubMed

Piers, Ruth D; Azoulay, Elie; Ricou, Bara; DeKeyser Ganz, Freda; Max, Adeline; Michalsen, Andrej; Azevedo Maia, Paulo; Owczuk, Radoslaw; Rubulotta, Francesca; Meert, Anne-Pascale; Reyners, Anna K; Decruyenaere, Johan; Benoit, Dominique D

2014-08-01

ICU care providers often feel that the care given to a patient may be inconsistent with their professional knowledge or beliefs. This study aimed to assess differences in, and reasons for, perceived inappropriate care (PIC) across ICU care providers with varying levels of decision-making power. We present subsequent analysis from the Appropricus Study, a cross-sectional study conducted on May 11, 2010, which included 1,218 nurses and 180 junior and 227 senior physicians in 82 European adult ICUs. The study was designed to evaluate PIC. The current study focuses on differences across health-care providers regarding the reasons for PIC in real patient situations. By multivariate analysis, nurses were found to have higher PIC rates compared with senior and junior physicians. However, nurses and senior physicians were more distressed by perceived disproportionate care than were junior physicians (33%, 25%, and 9%, respectively; P = .026). A perceived mismatch between level of care and prognosis (mostly excessive care) was the most common cause of PIC. The main reasons for PIC were prognostic uncertainty among physicians, poor team and family communication, the fact that no one was taking the initiative to challenge the inappropriateness of care, and financial incentives to provide excessive care among nurses. Senior physicians, compared with nurses and junior physicians, more frequently reported pressure from the referring physician as a reason. Family-related factors were reported by similar proportions of participants in the three groups. ICU care providers agree that excessive care is a true issue in the ICU. However, they differ in the reasons for the PIC, reflecting the roles each caregiver has in the ICU. Nurses charge physicians with a lack of initiative and poor communication, whereas physicians more often ascribe prognostic uncertainty. Teaching ICU physicians to deal with prognostic uncertainty in more adequate ways and to promote ethical discussions in their teams may be pivotal to improving moral distress and the quality of patient care.

Chromium picolinate positively influences the glucose transporter system via affecting cholesterol homeostasis in adipocytes cultured under hyperglycemic diabetic conditions

PubMed Central

Pattar, Guruprasad R.; Tackett, Lixuan; Liu, Ping; Elmendorf, Jeffrey S.

2008-01-01

Since trivalent chromium (Cr3+) enhances glucose metabolism, interest in the use of Cr3+as a therapy for type 2 diabetes has grown in the mainstream medical community. Moreover, accumulating evidence suggests that Cr3+ may also benefit cardiovascular disease (CVD) and atypical depression. We have found that cholesterol, a lipid implicated in both CVD and neurodegenerative disorders, also influences cellular glucose uptake. A recent study in our laboratory shows that exposure of 3T3-L1 adipocytes to chromium picolinate (CrPic, 10 nM) induces a loss of plasma membrane cholesterol. Concomitantly, accumulation of intracellularly sequestered glucose transporter GLUT4 at the plasma membrane was dependent on the CrPic-induced cholesterol loss. Since CrPic supplementation has the greatest benefit on glucose metabolism in hyperglycemic insulin-resistant individuals, we asked here if the CrPic effect on cells was glucose-dependent. We found that GLUT4 redistribution in cells treated with CrPic occurs only in cells cultured under high glucose (25 mM) conditions that resemble the diabetic-state, and not in cells cultured under non-diabetic (5.5 mM glucose) conditions. Examination of the effect of CrPic on proteins involved in cholesterol homeostasis revealed that the activity of sterol regulatory element-binding protein (SREBP), a membrane-bound transcription factor ultimately responsible for controlling cellular cholesterol balance, was upregulated by CrPic. In addition, ABCA1, a major player in mediating cholesterol efflux was decreased, consistent with SREBP transcriptional repression of the ABCA1 gene. Although the exact mechanism of Cr3+-induced cholesterol loss remains to be determined, these cellular responses highlight a novel and significant effect of chromium on cholesterol homeostasis. Furthermore, these findings provide an important clue to our understanding of how chromium supplementation might benefit hypercholesterolemia-associated disorders. PMID:16870493

Chromium picolinate positively influences the glucose transporter system via affecting cholesterol homeostasis in adipocytes cultured under hyperglycemic diabetic conditions.

PubMed

Pattar, Guruprasad R; Tackett, Lixuan; Liu, Ping; Elmendorf, Jeffrey S

2006-11-07

Since trivalent chromium (Cr(3+)) enhances glucose metabolism, interest in the use of Cr(3+)as a therapy for type 2 diabetes has grown in the mainstream medical community. Moreover, accumulating evidence suggests that Cr(3+) may also benefit cardiovascular disease (CVD) and atypical depression. We have found that cholesterol, a lipid implicated in both CVD and neurodegenerative disorders, also influences cellular glucose uptake. A recent study in our laboratory shows that exposure of 3T3-L1 adipocytes to chromium picolinate (CrPic, 10 nM) induces a loss of plasma membrane cholesterol. Concomitantly, accumulation of intracellularly sequestered glucose transporter GLUT4 at the plasma membrane was dependent on the CrPic-induced cholesterol loss. Since CrPic supplementation has the greatest benefit on glucose metabolism in hyperglycemic insulin-resistant individuals, we asked here if the CrPic effect on cells was glucose-dependent. We found that GLUT4 redistribution in cells treated with CrPic occurs only in cells cultured under high glucose (25 mM) conditions that resemble the diabetic-state, and not in cells cultured under non-diabetic (5.5 mM glucose) conditions. Examination of the effect of CrPic on proteins involved in cholesterol homeostasis revealed that the activity of sterol regulatory element-binding protein (SREBP), a membrane-bound transcription factor ultimately responsible for controlling cellular cholesterol balance, was upregulated by CrPic. In addition, ABCA1, a major player in mediating cholesterol efflux was decreased, consistent with SREBP transcriptional repression of the ABCA1 gene. Although the exact mechanism of Cr(3+)-induced cholesterol loss remains to be determined, these cellular responses highlight a novel and significant effect of chromium on cholesterol homeostasis. Furthermore, these findings provide an important clue to our understanding of how chromium supplementation might benefit hypercholesterolemia-associated disorders.

MO-DE-207B-03: Improved Cancer Classification Using Patient-Specific Biological Pathway Information Via Gene Expression Data

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

Young, M; Craft, D

Purpose: To develop an efficient, pathway-based classification system using network biology statistics to assist in patient-specific response predictions to radiation and drug therapies across multiple cancer types. Methods: We developed PICS (Pathway Informed Classification System), a novel two-step cancer classification algorithm. In PICS, a matrix m of mRNA expression values for a patient cohort is collapsed into a matrix p of biological pathways. The entries of p, which we term pathway scores, are obtained from either principal component analysis (PCA), normal tissue centroid (NTC), or gene expression deviation (GED). The pathway score matrix is clustered using both k-means and hierarchicalmore » clustering, and a clustering is judged by how well it groups patients into distinct survival classes. The most effective pathway scoring/clustering combination, per clustering p-value, thus generates various ‘signatures’ for conventional and functional cancer classification. Results: PICS successfully regularized large dimension gene data, separated normal and cancerous tissues, and clustered a large patient cohort spanning six cancer types. Furthermore, PICS clustered patient cohorts into distinct, statistically-significant survival groups. For a suboptimally-debulked ovarian cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00127) showed significant improvement over that of a prior gene expression-classified study (p = .0179). For a pancreatic cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00141) showed significant improvement over that of a prior gene expression-classified study (p = .04). Pathway-based classification confirmed biomarkers for the pyrimidine, WNT-signaling, glycerophosphoglycerol, beta-alanine, and panthothenic acid pathways for ovarian cancer. Despite its robust nature, PICS requires significantly less run time than current pathway scoring methods. Conclusion: This work validates the PICS method to improve cancer classification using biological pathways. Patients are classified with greater specificity and physiological relevance as compared to current gene-specific approaches. Focus now moves to utilizing PICS for pan-cancer patient-specific treatment response prediction.« less

Helping Lower Secondary Students Develop Conceptual Understanding of Electrostatic Forces

ERIC Educational Resources Information Center

Moynihan, Richard; van Kampen, Paul; Finlayson, Odilla; McLoughlin, Eilish

2016-01-01

This article describes the development of a lesson sequence that supports secondary-level students to construct an explanatory model for electrostatic attraction using a guided enquiry method. The students examine electrostatic interactions at a macro level and explain the phenomena at the atomic level. Pre-tests, post-tests, homework assignments…

Modelling short pulse, high intensity laser plasma interactions

NASA Astrophysics Data System (ADS)

Evans, R. G.

2006-06-01

Modelling the interaction of ultra-intense laser pulses with solid targets is made difficult through the large range of length and time scales involved in the transport of relativistic electrons. An implicit hybrid PIC-fluid model using the commercial code LSP (LSP is marketed by MRC (Albuquerque), New Mexico, USA) reveals a variety of complex phenomena which seem to be borne out in experiments and some existing theories.

Prediction of p38 map kinase inhibitory activity of 3, 4-dihydropyrido [3, 2-d] pyrimidone derivatives using an expert system based on principal component analysis and least square support vector machine

PubMed Central

Shahlaei, M.; Saghaie, L.

2014-01-01

A quantitative structure–activity relationship (QSAR) study is suggested for the prediction of biological activity (pIC50) of 3, 4-dihydropyrido [3,2-d] pyrimidone derivatives as p38 inhibitors. Modeling of the biological activities of compounds of interest as a function of molecular structures was established by means of principal component analysis (PCA) and least square support vector machine (LS-SVM) methods. The results showed that the pIC50 values calculated by LS-SVM are in good agreement with the experimental data, and the performance of the LS-SVM regression model is superior to the PCA-based model. The developed LS-SVM model was applied for the prediction of the biological activities of pyrimidone derivatives, which were not in the modeling procedure. The resulted model showed high prediction ability with root mean square error of prediction of 0.460 for LS-SVM. The study provided a novel and effective approach for predicting biological activities of 3, 4-dihydropyrido [3,2-d] pyrimidone derivatives as p38 inhibitors and disclosed that LS-SVM can be used as a powerful chemometrics tool for QSAR studies. PMID:26339262

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

PubMed

Beard, D A; Schlick, T

2001-01-01

Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-Hückel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-Hückel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels. Copyright 2000 John Wiley & Sons, Inc.

A teaching proposal on electrostatics based on the history of science through the reading of historical texts and argumentative discussions

NASA Astrophysics Data System (ADS)

Castells, Marina; Konstantinidou, Aikaterini; Cerveró, Josep M.

2016-05-01

Researches on electrostatics' conceptions found that students have ideas and conceptions that disagree with the scientific models and that might explain students' learning difficulties. To favour the change of student's ideas and conceptions, a teaching sequence that relies on a historical study of electrostatics is proposed. It begins with an exploration of electrostatics phenomena that students would do with everyday materials. About these phenomena they must draw their own explanations that will be shared and discussed in the class. The teacher will collect and summarize the ideas and explanations which are nearer the history of science. A brief history of electrostatics is introduced then, and some texts from scientists are used in an activity role-play-debate type in which the "supporters of a single fluid" and "supporters of two fluids" have to present arguments for their model and/or against the other model to explain the phenomena observed in the exploration phase. In the following, students will read texts related to science applications, the main aim of this activity is to relate electrostatics phenomena with current electricity. The first text explains how Franklin understood the nature of the lightning and the lightning rod and the second is a chapter of a roman about one historical episode situated in the Barcelona of the XVIII Century. Students will use the historical models of one and of two fluids to explain these two phenomena, and will compare them with the scientific explanation of the "accepted" science of nowadays introduced by the teacher. With this type of teaching proposal, conceptual aspect of electrostatics will be learnt, but also the students will learn about the nature and history of science and culture, as well as about the practice of argumentation.

Eukaryotic translation initiation factor 3 plays distinct roles at the mRNA entry and exit channels of the ribosomal preinitiation complex

PubMed Central

Aitken, Colin Echeverría; Beznosková, Petra; Vlčkova, Vladislava; Chiu, Wen-Ling; Zhou, Fujun; Valášek, Leoš Shivaya; Hinnebusch, Alan G; Lorsch, Jon R

2016-01-01

Eukaryotic translation initiation factor 3 (eIF3) is a central player in recruitment of the pre-initiation complex (PIC) to mRNA. We probed the effects on mRNA recruitment of a library of S. cerevisiae eIF3 functional variants spanning its 5 essential subunits using an in vitro-reconstituted system. Mutations throughout eIF3 disrupt its interaction with the PIC and diminish its ability to accelerate recruitment to a native yeast mRNA. Alterations to the eIF3a CTD and eIF3b/i/g significantly slow mRNA recruitment, and mutations within eIF3b/i/g destabilize eIF2•GTP•Met-tRNAi binding to the PIC. Using model mRNAs lacking contacts with the 40S entry or exit channels, we uncovered a critical role for eIF3 requiring the eIF3a NTD, in stabilizing mRNA interactions at the exit channel, and an ancillary role at the entry channel requiring residues of the eIF3a CTD. These functions are redundant: defects at each channel can be rescued by filling the other channel with mRNA. DOI: http://dx.doi.org/10.7554/eLife.20934.001 PMID:27782884

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.

Polymer impregnated bridge slabs : interim report.

DOT National Transportation Integrated Search

1979-01-01

The procedure used for producing precast slabs of polymer impregnated concrete (PIC) and described in this report was generally satisfactory from an operational standpoint. A strength loss of 14%, attributable to the drying step, was observed in PIC ...

Expression of recombinant myostatin propeptide pPIC9K-Msp plasmid in Pichia pastoris.

PubMed

Du, W; Xia, J; Zhang, Y; Liu, M J; Li, H B; Yan, X M; Zhang, J S; Li, N; Zhou, Z Y; Xie, W Z

2015-12-28

Myostatin propeptide can inhibit the biological activity of myostatin protein and promote muscle growth. To express myostatin propeptide in vitro with a higher biological activity, we performed codon optimization on the sheep myostatin propeptide gene sequence, and mutated aspartic acid-76 to alanine based on the codon usage bias of Pichia pastoris and the enhanced biological activity of myostatin propeptide mutant. Modified myostatin propeptide gene was cloned into the pPIC9K plasmid to form the recombinant plasmid pPIC9K-Msp. Recombinant plasmid pPIC9K-Msp was transformed into Pichia pastoris GS115 by electrotransformation. Transformed cells were screened, and methanol was used to induce expression. SDS-PAGE and western blotting were used to verify the successful expression of myostatin propeptide with biological activity in Pichia pastoris, providing the basis for characterization of this protein.

Particle-In-Cell simulations of high pressure plasmas using graphics processing units

NASA Astrophysics Data System (ADS)

Gebhardt, Markus; Atteln, Frank; Brinkmann, Ralf Peter; Mussenbrock, Thomas; Mertmann, Philipp; Awakowicz, Peter

2009-10-01

Particle-In-Cell (PIC) simulations are widely used to understand the fundamental phenomena in low-temperature plasmas. Particularly plasmas at very low gas pressures are studied using PIC methods. The inherent drawback of these methods is that they are very time consuming -- certain stability conditions has to be satisfied. This holds even more for the PIC simulation of high pressure plasmas due to the very high collision rates. The simulations take up to very much time to run on standard computers and require the help of computer clusters or super computers. Recent advances in the field of graphics processing units (GPUs) provides every personal computer with a highly parallel multi processor architecture for very little money. This architecture is freely programmable and can be used to implement a wide class of problems. In this paper we present the concepts of a fully parallel PIC simulation of high pressure plasmas using the benefits of GPU programming.

Epicyclic helical channels for parametric resonance ionization cooling

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

Johson, Rolland Paul; Derbenev, Yaroslav

Proposed next-generation muon colliders will require major technical advances to achieve rapid muon beam cooling requirements. Parametric-resonance Ionization Cooling (PIC) is proposed as the final 6D cooling stage of a high-luminosity muon collider. In PIC, a half-integer parametric resonance causes strong focusing of a muon beam at appropriately placed energy absorbers while ionization cooling limits the beam’s angular spread. Combining muon ionization cooling with parametric resonant dynamics in this way should then allow much smaller final transverse muon beam sizes than conventional ionization cooling alone. One of the PIC challenges is compensation of beam aberrations over a sufficiently wide parametermore » range while maintaining the dynamical stability with correlated behavior of the horizontal and vertical betatron motion and dispersion. We explore use of a coupling resonance to reduce the dimensionality of the problem and to shift the dynamics away from non-linear resonances. PIC simulations are presented.« less

Field Modeling, Symplectic Tracking, and Spin Decoherence for EDM and Muon $$g\\textrm{-}2$$ Lattices

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

Valetov, Eremey Vladimirovich

2017-01-01

While the first particle accelerators were electrostatic machines, and several electrostatic storage rings were subsequently commissioned and operated, electrostatic storage rings pose a number of challenges. Unlike motion in the magnetic field, where particle energy remains constant, particle energy generally changes in electrostatic elements. Conservation of energy in an electrostatic element is, in practice, only approximate, and it requires careful and accurate design, manufacturing, installation, and operational use. Electrostatic deflectors require relatively high electrostatic fields, tend to introduce nonlinear aberrations of all orders, and are more challenging to manufacture than homogeneous magnetic dipoles. Accordingly, magnetic storage rings are overwhelmingly prevalent.more » The search for electric dipole moments (EDMs) of fundamental particles is of key importance in the study of C and CP violations and their sources. C and CP violations are part of the Sakharov conditions that explain the matter–antimatter asymmetry in the universe. Determining the source of CP violations would provide valuable empirical insight for beyond-Standard-Model physics. EDMs of fundamental particles have not to this date been experimentally observed. The search for fundamental particle EDMs has narrowed the target search region; however, an EDM signal is yet to be discovered. In 2008, Brookhaven National Laboratory (BNL) had proposed the frozen spin (FS) concept for the search of a deuteron EDM. The FS concept envisions launching deuterons through a storage ring with combined electrostatic and magnetic fields. The electrostatic and magnetic fields are in a proportion that would, without an EDM, freeze the deuteron’s spin along its momentum as the deuteron moves around the lattice. The radial electrostatic field would result in a torque on the spin vector, proportional to a deuteron EDM, rotating the spin vector out of the midplane.« less

Electrostatic Discharge Initiation Experiments using PVDF Pressure Transducers

DTIC Science & Technology

1991-12-01

ignition sensitivity. The results are discussed within the context of a preliminary model of electrostatic initiation. iii/iv NAVSWC TR 91-666 CONTENTS...Chapter Page 1 INTRODUCTION .......................................... 1-1 TWO PHASE IGNITION MODEL ....................... 1-1 SENSITIZING FACTORS...is necessary to establish effective techniques to reduce the hazards associated with ESD ignition. TWO-PHASE IGNITION MODEL A model has been proposed

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach.

PubMed

Rubinstein, Alexander I; Sabirianov, Renat F; Namavar, Fereydoon

2016-10-14

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ∼80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, Alexander I.; Sabirianov, Renat F.; Namavar, Fereydoon

2016-10-01

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ˜80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Enhanced expression by the brain matrix of P-glycoprotein in brain capillary endothelial cells.

PubMed

Tatsuta, T; Naito, M; Mikami, K; Tsuruo, T

1994-10-01

P-glycoprotein (PGP), an active efflux pump of antitumor agents in multidrug-resistant tumor cells, exists in brain capillary endothelium and could be functionally involved in the blood-brain barrier. To study the regulatory mechanism of PGP expression in brain capillary endothelium, various mouse tissue matrices were tested for their abilities to enhance the expression of PGP in mouse brain capillary endothelial cells (MBEC), which express relatively small amounts of PGP. Of the four tissue matrices we examined, PGP expression in MBEC cultured on the brain matrix increased 2.0-fold. The PGP-inducing activity was similarly detected in bovine brain matrix, and the activity was enriched in the fraction of pl 9.0 by isoelectric focusing. The fraction, named PIC-fraction (PGP-inducing component), increased the PGP expression in MBEC 3.5-fold. By Northern blot analysis, a 3.3-fold enhancement of mdr gene expression was observed in MBEC cultured on the PIC-fraction. The PGP-inducing activity of the PIC-fraction was reduced by the treatment with trypsin but not with collagenase, suggesting that a proteinaceous factor distinct from type I collagen might be responsible for the PGP-inducing activity of PIC-fraction. Although the PIC-fraction increased the PGP expression in other mouse brain capillary endothelial cells, the PIC-fraction did not increase PGP expression in mouse aortic endothelial cells and KB carcinoma cell lines expressing various amounts of PGP. These observations suggest that PGP expression in brain capillary endothelium is specifically regulated by a tissue-specific factor in the brain matrix.

Effect of substituent groups (R= sbnd CH3, sbnd Br and sbnd CF3) on the structure, stability and redox property of [Cr(R-pic)2(H2O)2]NO3·H2O complexes

NASA Astrophysics Data System (ADS)

Chai, Jie; Liu, Yanfei; Liu, Bin; Yang, Binsheng

2017-12-01

Complexes [Cr(3-CH3-pic)2(H2O)2]NO3·H2O (1), [Cr(5-Br-pic)2(H2O)2]NO3·H2O (2) and [Cr(5-CF3-pic)2(H2O)2]NO3·H2O (3) were synthesized (pic = pyridine-2-carboxylic acid) and characterized by X-ray crystal diffraction. Crystal structure indicates that two bidentate ligands occupy equatorial position and two H2O occupy axial positions in trans-configuration. (i) Decomposition of complexes 1, 2 and 3 in different medium (phosphate buffered saline (PBS), apo-ovotransferrin (apootf) and EDTA) indicates that decomposition rate constants of these complexes follow the sequence of 1 < 2 < 3. (ii) The redox potential of Cr(III)/Cr(II) by cyclic voltammetry follows the sequence of 1 (-1.20 V) > 3 (-1.29 V) > 2 (-1.31 V). (iii) In addition, ·OH-generation of the new synthesized complexes was determined by Fenton-like reaction in comparison with Cr(pic)3, and it may be related to the reduction potential of the complexes. (iv) Moreover, Hammett substituent constants σp (inductive) and σm (resonance) (R = 3-CH3, 5-Br, 5-CF3) were introduced to evaluate the impact of substituent groups on the bond length and decomposition kinetics. The substituent group on the ligand has great effect on the properties of the complexes.

Hand washing compliance among retail food establishment workers in Minnesota.

PubMed

Allwood, Paul B; Jenkins, Timothy; Paulus, Colleen; Johnson, Lars; Hedberg, Craig W

2004-12-01

Inadequate hand washing by food workers is an important contributing factor to foodborne disease outbreaks in retail food establishments (RFEs). We conducted a survey of RFEs to investigate the effect of hand washing training, availability of hand washing facilities, and the ability of the person in charge (PIC) to describe hand washing according to the Minnesota Food Code (food code) on workers' ability to demonstrate food code-compliant hand washing. Only 52% of the PICs could describe the hand washing procedure outlined in the food code, and only 48% of workers could demonstrate code-compliant hand washing. The most common problems observed were failure to wash for 20 s and failure to use a fingernail brush. There was a strong positive association between the PIC being a certified food manager and being able to describe the food code hand washing procedure (odds ratio [OR], 5.5; 95% confidence interval [CI], 2.2 to 13.7), and there was an even stronger association between the PIC being able to describe hand washing and workers being able to demonstrate code-compliant hand washing (OR, 15; 95% CI, 6 to 37). Significant associations were detected among correct hand washing demonstration, physical infrastructure for hand washing, and the hand washing training methods used by the establishment. However, the principal determinant of successful hand washing demonstration was the PIC's ability to describe proper hand washing procedure. These results suggest that improving hand washing practices among food workers will require interventions that address PIC knowledge of hand washing requirement and procedure and the development and implementation of effective hand washing training methods.

Preparation and Single-Crystal X-Ray Structures of Four Related Mixed-Ligand 4-Methylpyridine Indium Halide Complexes

NASA Technical Reports Server (NTRS)

Hepp, Aloysius F.; Clark, Eric B.; Schupp, John D.; Williams, Jennifer N.; Duraj, Stan A.; Fanwick, Philip E.

2013-01-01

We describe the structures of four related indium complexes obtained during synthesis of solid-state materials precursors. Indium adducts of halides and 4-methylpyridine, InX3(pic)3 (X = Cl, Br; pic = 4-methylpyridine) consist of octahedral molecules with meridional (mer) geometry. Crystals of mer-InCl3(pic)3 (1) are triclinic, space group P1(bar) (No. 2), with a = 9.3240(3), b = 13.9580(6), c = 16.7268 (7) A, alpha = 84.323(2), beta = 80.938(2), gamma = 78.274(3)Z = 4, R = 0.035 for 8820 unique reflections. Crystals of mer-InBr3(pic)3 (2) are monoclinic, space group P21/n (No. 14), with a = 15.010(2), b = 19.938(2), c = 16.593(3), beta = 116.44(1)Z = 8, R = 0.053 for 4174 unique reflections. The synthesis and structures of related compounds with phenylsulfide (chloride) (3) and a dimeric complex with bridging hydroxide (bromide) (4) coordination is also described. Crystals of trans-In(SC6H5)Cl2(pic)3 (3) are monoclinic, space group P21/n (No. 14), with a = 9.5265(2), b = 17.8729(6), c = 13.8296(4), beta = 99.7640(15)Z = 4, R = 0.048 for 5511 unique reflections. Crystals of [In(mu-OH)Br2(pic)22 (4) are tetragonal, space group = I41cd (No. 110) with a = 19.8560(4), b = 19.8560(4), c = 25.9528(6), Z = 8, R = 0.039 for 5982 unique reflections.

Electrostatic Model Applied to ISS Charged Water Droplet Experiment

NASA Technical Reports Server (NTRS)

Stevenson, Daan; Schaub, Hanspeter; Pettit, Donald R.

2015-01-01

The electrostatic force can be used to create novel relative motion between charged bodies if it can be isolated from the stronger gravitational and dissipative forces. Recently, Coulomb orbital motion was demonstrated on the International Space Station by releasing charged water droplets in the vicinity of a charged knitting needle. In this investigation, the Multi-Sphere Method, an electrostatic model developed to study active spacecraft position control by Coulomb charging, is used to simulate the complex orbital motion of the droplets. When atmospheric drag is introduced, the simulated motion closely mimics that seen in the video footage of the experiment. The electrostatic force's inverse dependency on separation distance near the center of the needle lends itself to analytic predictions of the radial motion.

Electrostatic lower hybrid waves excited by electromagnetic whistler mode waves scattering from planar magnetic-field-aligned plasma density irregularities

NASA Technical Reports Server (NTRS)

Bell, T. F.; Ngo, H. D.

1990-01-01

This paper presents a theoretical model for electrostatic lower hybrid waves excited by electromagnetic whistler mode waves propagating in regions of the magnetosphere and the topside ionosphere, where small-scale magnetic-field-aligned plasma density irregularities are thought to exist. In this model, the electrostatic waves are excited by linear mode coupling as the incident electromagnetic whistler mode waves scatter from the magnetic-field-aligned plasma density irregularities. Results indicate that high-amplitude short-wavelength (5 to 100 m) quasi-electrostatic whistler mode waves can be excited when electromagnetic whistler mode waves scatter from small-scale planar magnetic-field-aligned plasma density irregularities in the topside ionosphere and magnetosphere.

Electrostatic Precipitator (ESP) TRAINING MANUAL

EPA Science Inventory

The manual assists engineers in using a computer program, the ESPVI 4.0W, that models all elements of an electrostatic precipitator (ESP). The program is a product of the Electric Power Research Institute and runs in the Windows environment. Once an ESP is accurately modeled, the...

Biomolecular electrostatics and solvation: a computational perspective

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

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. Thismore » review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we summarize the common characteristics of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide reasonable backgrounds to understand the solvation models.« less