Bi-stable optical element actuator device

DOEpatents

Holdener, Fred R.; Boyd, Robert D.

2002-01-01

The present invention is a bistable optical element actuator device utilizing a powered means to move an actuation arm, to which an optical element is attached, between two stable positions. A non-powered means holds the actuation arm in either of the two stable positions. The optical element may be a electromagnetic (EM) radiation or particle source, an instrument, or EM radiation or particle transmissive reflective or absorptive elements. A bearing is used to transfer motion and smoothly transition the actuation arm between the two stable positions.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

SU-F-J-152: Accuracy of Charge Particle Transport in Magnetic Fields Using EGSnrc

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

Mainegra-Hing, E; Bouchard, H; Tessier, F

Purpose: Determine accuracy of the current implementation of electron transport under magnetic fields in EGSnrc by means of single scattering (SS) and Fano convergence tests, and establish quantitatively the electron step size restriction required to achieve a desired level of accuracy for ionization chamber dosimetry. Methods: Condensed history (CH) dose calculations are compared to SS results for a PTW30013 ionization chamber irradiated in air by a 60Co photon beam. CH dose results for this chamber irradiated in a water phantom by a source of mono-energetic electrons are compared to the prediction of Fano’s theorem for step size restrictions EM ESTEPEmore » from 0.01 to 0.1 and strengths of 0.5 T, 1.0 T, and 1.5 T. Results: CH calculations in air for 60Co photons using an EM ESTEPE of 0.25 overestimate SS values by 6% for a 1.5 T field and by 1.5% for a 0.5 T field. Agreement improves with decreasing EM ESTEPE reducing this difference at 0.02 to 0.13% and 0.04% for 1.5 T and 0.5 T respectively. CH results converge with decreasing EM ESTEPE reaching an agreement of 0.2% at a value of EM ESTEPE of 0.01 for 100 keV electrons. SS results at 100 keV for 1.5 T show the same EM ESTEPE dependency as the CH results. Conclusion: Accurate transport of charged particles in magnetic fields is only possible if the step size is significantly restricted. An EM ESTEPE value of 0.02 is required to reproduce SS results at the 0.1% level for a calculation in air. The EM ESTEPE dependency of the SS results suggests SS is bypassed when simulating the transport of charged particles in magnetic fields. Fano test results for in water calculation suggest that only a 0.2% accuracy can be achieved with the current implementation.« less

CUBE: Information-optimized parallel cosmological N-body simulation code

NASA Astrophysics Data System (ADS)

Yu, Hao-Ran; Pen, Ue-Li; Wang, Xin

2018-05-01

CUBE, written in Coarray Fortran, is a particle-mesh based parallel cosmological N-body simulation code. The memory usage of CUBE can approach as low as 6 bytes per particle. Particle pairwise (PP) force, cosmological neutrinos, spherical overdensity (SO) halofinder are included.

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

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

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

2009-10-01

We present a numerical code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is written in Fortran 95 and is designed to be versatile, flexible, and extensible, with modular options that can be selected either at the time the code is compiled or at run time through a text input file. We include a number of general purpose modules describing a variety of physical processes commonly required in the astrophysical community and we expect that the effort required to integrate additional or alternate modules into the code will be small. Inmore » its simplest form the code can evolve the dynamical trajectories of a set of particles in two or three dimensions using a module which implements either a Leapfrog or Runge-Kutta-Fehlberg integrator, selected by the user at compile time. The user may choose to allow the integrator to evolve the system using individual time steps for each particle or with a single, global time step for all. Particles may interact gravitationally as N-body particles, and all or any subset may also interact hydrodynamically, using the smoothed particle hydrodynamic (SPH) method by selecting the SPH module. A third particle species can be included with a module to model massive point particles which may accrete nearby SPH or N-body particles. Such particles may be used to model, e.g., stars in a molecular cloud. Free boundary conditions are implemented by default, and a module may be selected to include periodic boundary conditions. We use a binary 'Press' tree to organize particles for rapid access in gravity and SPH calculations. Modules implementing an interface with special purpose 'GRAPE' hardware may also be selected to accelerate the gravity calculations. If available, forces obtained from the GRAPE coprocessors may be transparently substituted for those obtained from the tree, or both tree and GRAPE may be used as a combination GRAPE/tree code. The code may be run without modification on single processors or in parallel using OpenMP compiler directives on large-scale, shared memory parallel machines. We present simulations of several test problems, including a merger simulation of two elliptical galaxies with 800,000 particles. In comparison to the Gadget-2 code of Springel, the gravitational force calculation, which is the most costly part of any simulation including self-gravity, is {approx}4.6-4.9 times faster with VINE when tested on different snapshots of the elliptical galaxy merger simulation when run on an Itanium 2 processor in an SGI Altix. A full simulation of the same setup with eight processors is a factor of 2.91 faster with VINE. The code is available to the public under the terms of the Gnu General Public License.« less

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

NASA Astrophysics Data System (ADS)

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

2009-10-01

We present a numerical code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is written in Fortran 95 and is designed to be versatile, flexible, and extensible, with modular options that can be selected either at the time the code is compiled or at run time through a text input file. We include a number of general purpose modules describing a variety of physical processes commonly required in the astrophysical community and we expect that the effort required to integrate additional or alternate modules into the code will be small. In its simplest form the code can evolve the dynamical trajectories of a set of particles in two or three dimensions using a module which implements either a Leapfrog or Runge-Kutta-Fehlberg integrator, selected by the user at compile time. The user may choose to allow the integrator to evolve the system using individual time steps for each particle or with a single, global time step for all. Particles may interact gravitationally as N-body particles, and all or any subset may also interact hydrodynamically, using the smoothed particle hydrodynamic (SPH) method by selecting the SPH module. A third particle species can be included with a module to model massive point particles which may accrete nearby SPH or N-body particles. Such particles may be used to model, e.g., stars in a molecular cloud. Free boundary conditions are implemented by default, and a module may be selected to include periodic boundary conditions. We use a binary "Press" tree to organize particles for rapid access in gravity and SPH calculations. Modules implementing an interface with special purpose "GRAPE" hardware may also be selected to accelerate the gravity calculations. If available, forces obtained from the GRAPE coprocessors may be transparently substituted for those obtained from the tree, or both tree and GRAPE may be used as a combination GRAPE/tree code. The code may be run without modification on single processors or in parallel using OpenMP compiler directives on large-scale, shared memory parallel machines. We present simulations of several test problems, including a merger simulation of two elliptical galaxies with 800,000 particles. In comparison to the Gadget-2 code of Springel, the gravitational force calculation, which is the most costly part of any simulation including self-gravity, is ~4.6-4.9 times faster with VINE when tested on different snapshots of the elliptical galaxy merger simulation when run on an Itanium 2 processor in an SGI Altix. A full simulation of the same setup with eight processors is a factor of 2.91 faster with VINE. The code is available to the public under the terms of the Gnu General Public License.

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

PubMed

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

2012-01-01

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

BIM-Sim: Interactive Simulation of Broadband Imaging Using Mie Theory

NASA Astrophysics Data System (ADS)

Berisha, Sebastian; van Dijk, Thomas; Bhargava, Rohit; Carney, P. Scott; Mayerich, David

2017-02-01

Understanding the structure of a scattered electromagnetic (EM) field is critical to improving the imaging process. Mechanisms such as diffraction, scattering, and interference affect an image, limiting the resolution and potentially introducing artifacts. Simulation and visualization of scattered fields thus plays an important role in imaging science. However, the calculation of scattered fields is extremely time-consuming on desktop systems and computationally challenging on task-parallel systems such as supercomputers and cluster systems. In addition, EM fields are high-dimensional, making them difficult to visualize. In this paper, we present a framework for interactively computing and visualizing EM fields scattered by micro and nano-particles. Our software uses graphics hardware for evaluating the field both inside and outside of these particles. We then use Monte-Carlo sampling to reconstruct and visualize the three-dimensional structure of the field, spectral profiles at individual points, the structure of the field at the surface of the particle, and the resulting image produced by an optical system.

Protein secondary structure determination by constrained single-particle cryo-electron tomography.

PubMed

Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

2012-12-05

Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series. Copyright © 2012 Elsevier Ltd. All rights reserved.

Reducing time delays in the management of ischemic stroke patients in Northern Italy.

PubMed

Vidale, Simone; Arnaboldi, Marco; Bezzi, Giacomo; Bono, Giorgio; Grampa, Giampiero; Guidotti, Mario; Perrone, Patrizia; Salmaggi, Andrea; Zarcone, Davide; Zoli, Alberto; Agostoni, Elio

2016-07-15

Thrombolysis represents the best therapy for ischemic stroke but the main limitation of its administration is time. The avoidable delay is a concept reflecting the effectiveness of management pathway. For this reason, we projected a study concerning the detection of main delays with following introduction of corrective factors. In this paper we describe the results after these corrections. Consecutive patients admitted for ischemic stroke during a 3-months period to 35 hospitals of a macro-area of Northern Italy were enrolled. Each time of management was registered, identifying three main intervals: pre-hospital, in-hospital and total times. Previous corrective interventions were: 1.increasing of population awareness to use the Emergency Medical Service (EMS); 2.pre-notification of Emergency Department; 3.use of high urgency codes; 4.use of standardised operational algorithm. Statistical analysis was conducted using time-to-event analysis and Cox proportional hazard regression. 1084 patients were enrolled. EMS was alerted for 56.3% of subjects, mainly in females and severe strokes (p<0.001). Thrombolytic treatment was performed in 4.7% of patients. Median pre-hospital and in-hospital times were 113 and 105min, while total time was 240. High urgency codes at transport contributed to reduce pre-hospital and in-hospital time (p<0.05). EMS use and high urgency codes promoted thrombolysis. Treatment within 4.5hours from symptom onset was performed in 14% of patients more than the first phase of study. The implementation of an organizational system based on EMS and concomitant high urgency codes use was effective to reduce avoidable delay and to increase thrombolysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Cryo-EM in drug discovery: achievements, limitations and prospects.

PubMed

Renaud, Jean-Paul; Chari, Ashwin; Ciferri, Claudio; Liu, Wen-Ti; Rémigy, Hervé-William; Stark, Holger; Wiesmann, Christian

2018-06-08

Cryo-electron microscopy (cryo-EM) of non-crystalline single particles is a biophysical technique that can be used to determine the structure of biological macromolecules and assemblies. Historically, its potential for application in drug discovery has been heavily limited by two issues: the minimum size of the structures it can be used to study and the resolution of the images. However, recent technological advances - including the development of direct electron detectors and more effective computational image analysis techniques - are revolutionizing the utility of cryo-EM, leading to a burst of high-resolution structures of large macromolecular assemblies. These advances have raised hopes that single-particle cryo-EM might soon become an important tool for drug discovery, particularly if they could enable structural determination for 'intractable' targets that are still not accessible to X-ray crystallographic analysis. This article describes the recent advances in the field and critically assesses their relevance for drug discovery as well as discussing at what stages of the drug discovery pipeline cryo-EM can be useful today and what to expect in the near future.

3D Multispecies Nonlinear Perturbative Particle Simulation of Intense Nonneutral Particle Beams (Research supported by the Department of Energy and the Short Pulse Spallation Source Project and LANSCE Division of LANL.)

NASA Astrophysics Data System (ADS)

Qin, Hong; Davidson, Ronald C.; Lee, W. Wei-Li

1999-11-01

The Beam Equilibrium Stability and Transport (BEST) code, a 3D multispecies nonlinear perturbative particle simulation code, has been developed to study collective effects in intense charged particle beams described self-consistently by the Vlasov-Maxwell equations. A Darwin model is adopted for transverse electromagnetic effects. As a 3D multispecies perturbative particle simulation code, it provides several unique capabilities. Since the simulation particles are used to simulate only the perturbed distribution function and self-fields, the simulation noise is reduced significantly. The perturbative approach also enables the code to investigate different physics effects separately, as well as simultaneously. The code can be easily switched between linear and nonlinear operation, and used to study both linear stability properties and nonlinear beam dynamics. These features, combined with 3D and multispecies capabilities, provides an effective tool to investigate the electron-ion two-stream instability, periodically focused solutions in alternating focusing fields, and many other important problems in nonlinear beam dynamics and accelerator physics. Applications to the two-stream instability are presented.

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

StarSmasher: Smoothed Particle Hydrodynamics code for smashing stars and planets

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Shielding NSLS-II light source: Importance of geometry for calculating radiation levels from beam losses

DOE PAGES

Kramer, S. L.; Ghosh, V. J.; Breitfeller, M.; ...

2016-08-10

We present that third generation high brightness light sources are designed to have low emittance and high current beams, which contribute to higher beam loss rates that will be compensated by Top-Off injection. Shielding for these higher loss rates will be critical to protect the projected higher occupancy factors for the users. Top-Off injection requires a full energy injector, which will demand greater consideration of the potential abnormal beam miss-steering and localized losses that could occur. The high energy electron injection beam produces significantly higher neutron component dose to the experimental floor than a lower energy beam injection and rampedmore » operations. Minimizing this dose will require adequate knowledge of where the miss-steered beam can occur and sufficient EM shielding close to the loss point, in order to attenuate the energy of the particles in the EM shower below the neutron production threshold (<10 MeV), which will spread the incident energy on the bulk shield walls and thereby the dose penetrating the shield walls. Designing supplemental shielding near the loss point using the analytic shielding model is shown to be inadequate because of its lack of geometry specification for the EM shower process. To predict the dose rates outside the tunnel requires detailed description of the geometry and materials that the beam losses will encounter inside the tunnel. Modern radiation shielding Monte-Carlo codes, like FLUKA, can handle this geometric description of the radiation transport process in sufficient detail, allowing accurate predictions of the dose rates expected and the ability to show weaknesses in the design before a high radiation incident occurs. The effort required to adequately define the accelerator geometry for these codes has been greatly reduced with the implementation of the graphical interface of FLAIR to FLUKA. In conclusion, this made the effective shielding process for NSLS-II quite accurate and reliable. The principles used to provide supplemental shielding to the NSLS-II accelerators and the lessons learned from this process are presented.« less

Transport calculations and accelerator experiments needed for radiation risk assessment in space.

PubMed

Sihver, Lembit

2008-01-01

The major uncertainties on space radiation risk estimates in humans are associated to the poor knowledge of the biological effects of low and high LET radiation, with a smaller contribution coming from the characterization of space radiation field and its primary interactions with the shielding and the human body. However, to decrease the uncertainties on the biological effects and increase the accuracy of the risk coefficients for charged particles radiation, the initial charged-particle spectra from the Galactic Cosmic Rays (GCRs) and the Solar Particle Events (SPEs), and the radiation transport through the shielding material of the space vehicle and the human body, must be better estimated Since it is practically impossible to measure all primary and secondary particles from all possible position-projectile-target-energy combinations needed for a correct risk assessment in space, accurate particle and heavy ion transport codes must be used. These codes are also needed when estimating the risk for radiation induced failures in advanced microelectronics, such as single-event effects, etc., and the efficiency of different shielding materials. It is therefore important that the models and transport codes will be carefully benchmarked and validated to make sure they fulfill preset accuracy criteria, e.g. to be able to predict particle fluence, dose and energy distributions within a certain accuracy. When validating the accuracy of the transport codes, both space and ground based accelerator experiments are needed The efficiency of passive shielding and protection of electronic devices should also be tested in accelerator experiments and compared to simulations using different transport codes. In this paper different multipurpose particle and heavy ion transport codes will be presented, different concepts of shielding and protection discussed, as well as future accelerator experiments needed for testing and validating codes and shielding materials.

Cosmic muon induced EM showers in NO$$\

DOE PAGES

Yadav, Nitin; Duyang, Hongyue; Shanahan, Peter; ...

2016-11-15

Here, the NuMI Off-Axis v e Appearance (NOvA) experiment is a ne appearance neutrino oscillation experiment at Fermilab. It identifies the ne signal from the electromagnetic (EM) showers induced by the electrons in the final state of neutrino interactions. Cosmic muon induced EM showers, dominated by bremsstrahlung, are abundant in NOvA far detector. We use the Cosmic Muon- Removal technique to get pure EM shower sample from bremsstrahlung muons in data. We also use Cosmic muon decay in flight EM showers which are highly pure EM showers.The large Cosmic-EM sample can be used, as data driven method, to characterize themore » EM shower signature and provides valuable checks of the simulation, reconstruction, particle identification algorithm, and calibration across the NOvA detector.« less

Cosmic muon induced EM showers in NO$$\

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

Yadav, Nitin; Duyang, Hongyue; Shanahan, Peter

Here, the NuMI Off-Axis v e Appearance (NOvA) experiment is a ne appearance neutrino oscillation experiment at Fermilab. It identifies the ne signal from the electromagnetic (EM) showers induced by the electrons in the final state of neutrino interactions. Cosmic muon induced EM showers, dominated by bremsstrahlung, are abundant in NOvA far detector. We use the Cosmic Muon- Removal technique to get pure EM shower sample from bremsstrahlung muons in data. We also use Cosmic muon decay in flight EM showers which are highly pure EM showers.The large Cosmic-EM sample can be used, as data driven method, to characterize themore » EM shower signature and provides valuable checks of the simulation, reconstruction, particle identification algorithm, and calibration across the NOvA detector.« less

Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs

DOE PAGES

Shatsky, Maxim; Arbelaez, Pablo; Han, Bong-Gyoon; ...

2014-07-01

Tilted electron microscope images are routinely collected for an ab initio structure reconstruction as a part of the Random Conical Tilt (RCT) or Orthogonal Tilt Reconstruction (OTR) methods, as well as for various applications using the "free-hand" procedure. These procedures all require identification of particle pairs in two corresponding images as well as accurate estimation of the tilt-axis used to rotate the electron microscope (EM) grid. Here we present a computational approach, PCT (particle correspondence from tilted pairs), based on tilt-invariant context and projection matching that addresses both problems. The method benefits from treating the two problems as a singlemore » optimization task. It automatically finds corresponding particle pairs and accurately computes tilt-axis direction even in the cases when EM grid is not perfectly planar.« less

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

PubMed Central

Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

2017-01-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

Injury risks of EMS responders: evidence from the National Fire Fighter Near-Miss Reporting System

PubMed Central

Taylor, Jennifer A; Davis, Andrea L; Barnes, Brittany; Lacovara, Alicia V; Patel, Reema

2015-01-01

Objectives We analysed near-miss and injury events reported to the National Fire Fighter Near-Miss Reporting System (NFFNMRS) to investigate the workplace hazards and safety concerns of Emergency Medical Services (EMS) responders in the USA. Methods We reviewed 769 ‘non-fire emergency event’ reports from the NFFNMRS using a mixed methods approach. We identified 185 emergency medical calls and analysed their narrative text fields. We assigned Mechanism of Near-Miss/Injury and Nature of Injury codes and then tabulated frequencies (quantitative). We coded major themes regarding work hazards and safety concerns reported by the EMS responders (qualitative). Results Of the 185 emergency medical calls, the most commonly identified Mechanisms of Near-Miss/Injury to EMS responders was Assaults, followed by Struck-by Motor Vehicle, and Motor Vehicle Collision. The most commonly identified weapon used in an assault was a firearm. We identified 5 major domains of workplace hazards and safety concerns: Assaults by Patients, Risks from Motor Vehicles, Personal Protective Equipment, Relationships between Emergency Responders, and Policies, Procedures and Practices. Conclusions Narrative text from the NFFNMRS is a rich source of data that can be analysed quantitatively and qualitatively to provide insight into near-misses and injuries sustained by EMS responders. Near-miss reporting systems are critical components for occupational hazard surveillance. PMID:26068510

Disaster Relief and Emergency Medical Services Project (DREAMS TM): Digital EMS

DTIC Science & Technology

2000-10-01

exchanges between the hospital and the EMS vehicle. By creating the virtual presence of a physician at or near the emergency scene, more lives will be saved ...address, cross street, zip code etc. The map can be saved to the clipboard or to an EMF graphics file for use by other applications in the system. 29...section can be found in Appendix B. The EMS personnel on board the ambulance can benefit greatly from technology integration. Several time- saving

Two position optical element actuator device

DOEpatents

Holdener, Fred R.; Boyd, Robert D.

2002-01-01

The present invention is a two position optical element actuator device utilizing a powered means to hold an actuation arm, to which an optical element is attached, in a first position. A non-powered means drives the actuation arm to a second position, when the powered means ceases to receive power. The optical element may be a electromagnetic (EM) radiation or particle source, an instrument, or EM radiation or particle transmissive, reflective or absorptive elements. A bearing is used to transfer motion and smoothly transition the actuation arm from the first to second position.

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

DTIC Science & Technology

2009-01-01

proton PARMA PHITS -based Analytical Radiation Model in the Atmosphere PCAIRE Predictive Code for Aircrew Radiation Exposure PHITS Particle and...radiation transport code utilized is called PARMA ( PHITS based Analytical Radiation Model in the Atmosphere) [36]. The particle fluxes calculated from the...same dose equivalent coefficient regulations from the ICRP-60 regulations. As a result, the transport codes utilized by EXPACS ( PHITS ) and CARI-6

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

DTIC Science & Technology

2009-07-05

proton PARMA PHITS -based Analytical Radiation Model in the Atmosphere PCAIRE Predictive Code for Aircrew Radiation Exposure PHITS Particle and Heavy...transport code utilized is called PARMA ( PHITS based Analytical Radiation Model in the Atmosphere) [36]. The particle fluxes calculated from the input...dose equivalent coefficient regulations from the ICRP-60 regulations. As a result, the transport codes utilized by EXPACS ( PHITS ) and CARI-6 (PARMA

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Smoothed Particle Hydrodynamic Simulator

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

2016-10-05

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

How good can cryo-EM become?

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

Glaeser, Robert M.

The suddenness with which single-particle cryo-electron microscopy (cryo-EM) has emerged as a method for determining high-resolution structures of biological macromolecules invites the questions, how much better can this technology get, and how fast is that likely to happen? While we can rightly celebrate the maturation of cryo-EM as a high-resolution structure-determination tool, I believe there still are many developments to look forward to.

Robust w-Estimators for Cryo-EM Class Means

PubMed Central

Huang, Chenxi; Tagare, Hemant D.

2016-01-01

A critical step in cryogenic electron microscopy (cryo-EM) image analysis is to calculate the average of all images aligned to a projection direction. This average, called the “class mean”, improves the signal-to-noise ratio in single particle reconstruction (SPR). The averaging step is often compromised because of outlier images of ice, contaminants, and particle fragments. Outlier detection and rejection in the majority of current cryo-EM methods is done using cross-correlation with a manually determined threshold. Empirical assessment shows that the performance of these methods is very sensitive to the threshold. This paper proposes an alternative: a “w-estimator” of the average image, which is robust to outliers and which does not use a threshold. Various properties of the estimator, such as consistency and influence function are investigated. An extension of the estimator to images with different contrast transfer functions (CTFs) is also provided. Experiments with simulated and real cryo-EM images show that the proposed estimator performs quite well in the presence of outliers. PMID:26841397

Robust w-Estimators for Cryo-EM Class Means.

PubMed

Huang, Chenxi; Tagare, Hemant D

2016-02-01

A critical step in cryogenic electron microscopy (cryo-EM) image analysis is to calculate the average of all images aligned to a projection direction. This average, called the class mean, improves the signal-to-noise ratio in single-particle reconstruction. The averaging step is often compromised because of the outlier images of ice, contaminants, and particle fragments. Outlier detection and rejection in the majority of current cryo-EM methods are done using cross-correlation with a manually determined threshold. Empirical assessment shows that the performance of these methods is very sensitive to the threshold. This paper proposes an alternative: a w-estimator of the average image, which is robust to outliers and which does not use a threshold. Various properties of the estimator, such as consistency and influence function are investigated. An extension of the estimator to images with different contrast transfer functions is also provided. Experiments with simulated and real cryo-EM images show that the proposed estimator performs quite well in the presence of outliers.

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

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

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

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

What variables affect public perceptions for EMS meeting general community needs?

PubMed

Blau, Gary; Hochner, Arthur; Portwood, James

2012-01-01

In the fall, 2010, a phone survey of 928 respondents examined two research questions: does the general public perceive Emergency Medical Services (EMS) as meeting their community needs? And what factors or correlates help to explain EMS meeting community needs? To maximize geographical representation across the contiguous United States, a clustered stratified sampling strategy was used based upon zip codes across the 48 states. Results showed strong support by the sample for perceiving that EMS was meeting their general community needs. 17 percent of the variance in EMS meeting community needs was collectively explained by the demographic and perceptual variables in the regression model. Of the correlates tested, the strongest relationship was found between greater admiration for EMS professionals and higher perception of EMS meeting community needs. Study limitations included sampling households with only landline (no cell) phones, using a simulated emergency situation, and not collecting gender data.

CEM2k and LAQGSM Codes as Event-Generators for Space Radiation Shield and Cosmic Rays Propagation Applications

NASA Technical Reports Server (NTRS)

Mashnik, S. G.; Gudima, K. K.; Sierk, A. J.; Moskalenko, I. V.

2002-01-01

Space radiation shield applications and studies of cosmic ray propagation in the Galaxy require reliable cross sections to calculate spectra of secondary particles and yields of the isotopes produced in nuclear reactions induced both by particles and nuclei at energies from threshold to hundreds of GeV per nucleon. Since the data often exist in a very limited energy range or sometimes not at all, the only way to obtain an estimate of the production cross sections is to use theoretical models and codes. Recently, we have developed improved versions of the Cascade-Exciton Model (CEM) of nuclear reactions: the codes CEM97 and CEM2k for description of particle-nucleus reactions at energies up to about 5 GeV. In addition, we have developed a LANL version of the Quark-Gluon String Model (LAQGSM) to describe reactions induced both by particles and nuclei at energies up to hundreds of GeVhucleon. We have tested and benchmarked the CEM and LAQGSM codes against a large variety of experimental data and have compared their results with predictions by other currently available models and codes. Our benchmarks show that CEM and LAQGSM codes have predictive powers no worse than other currently used codes and describe many reactions better than other codes; therefore both our codes can be used as reliable event-generators for space radiation shield and cosmic ray propagation applications. The CEM2k code is being incorporated into the transport code MCNPX (and several other transport codes), and we plan to incorporate LAQGSM into MCNPX in the near future. Here, we present the current status of the CEM2k and LAQGSM codes, and show results and applications to studies of cosmic ray propagation in the Galaxy.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

PubMed Central

Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

2017-01-01

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

Fourier-Bessel Particle-In-Cell (FBPIC) v0.1.0

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

Lehe, Remi; Kirchen, Manuel; Jalas, Soeren

The Fourier-Bessel Particle-In-Cell code is a scientific simulation software for relativistic plasma physics. It is a Particle-In-Cell code whose distinctive feature is to use a spectral decomposition in cylindrical geometry. This decomposition allows to combine the advantages of spectral 3D Cartesian PIC codes (high accuracy and stability) and those of finite-difference cylindrical PIC codes with azimuthal decomposition (orders-of-magnitude speedup when compared to 3D simulations). The code is built on Python and can run both on CPU and GPU (the GPU runs being typically 1 or 2 orders of magnitude faster than the corresponding CPU runs.) The code has the exactmore » same output format as the open-source PIC codes Warp and PIConGPU (openPMD format: openpmd.org) and has a very similar input format as Warp (Python script with many similarities). There is therefore tight interoperability between Warp and FBPIC, and this interoperability will increase even more in the future.« less

DYNECHARM++: a toolkit to simulate coherent interactions of high-energy charged particles in complex structures

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo

2013-08-01

A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.

ZENO: N-body and SPH Simulation Codes

NASA Astrophysics Data System (ADS)

Barnes, Joshua E.

2011-02-01

The ZENO software package integrates N-body and SPH simulation codes with a large array of programs to generate initial conditions and analyze numerical simulations. Written in C, the ZENO system is portable between Mac, Linux, and Unix platforms. It is in active use at the Institute for Astronomy (IfA), at NRAO, and possibly elsewhere. Zeno programs can perform a wide range of simulation and analysis tasks. While many of these programs were first created for specific projects, they embody algorithms of general applicability and embrace a modular design strategy, so existing code is easily applied to new tasks. Major elements of the system include: Structured data file utilities facilitate basic operations on binary data, including import/export of ZENO data to other systems.Snapshot generation routines create particle distributions with various properties. Systems with user-specified density profiles can be realized in collisionless or gaseous form; multiple spherical and disk components may be set up in mutual equilibrium.Snapshot manipulation routines permit the user to sift, sort, and combine particle arrays, translate and rotate particle configurations, and assign new values to data fields associated with each particle.Simulation codes include both pure N-body and combined N-body/SPH programs: Pure N-body codes are available in both uniprocessor and parallel versions.SPH codes offer a wide range of options for gas physics, including isothermal, adiabatic, and radiating models. Snapshot analysis programs calculate temporal averages, evaluate particle statistics, measure shapes and density profiles, compute kinematic properties, and identify and track objects in particle distributions.Visualization programs generate interactive displays and produce still images and videos of particle distributions; the user may specify arbitrary color schemes and viewing transformations.

Electron microscopic investigation and elemental analysis of titanium dioxide in sun lotion.

PubMed

Sysoltseva, M; Winterhalter, R; Wochnik, A S; Scheu, C; Fromme, H

2017-06-01

The objective of this research was to determine the size, shape and aggregation of titanium dioxide (TiO 2 ) particles which are used in sun lotion as UV-blocker. Overall, six sunscreens from various suppliers and two reference substances were analysed by electron microscopy (EM) techniques in combination with energy dispersive X-ray spectroscopy (EDS). Because of a high fat content in sun lotion, it was impossible to visualize the TiO 2 particles without previous EM sample preparation. Different defatting methods for TiO 2 from sun screens were tested. A novel sample preparation method was developed which allowed the characterization of TiO 2 particles with the help of EM and EDS. Aggregates of titanium dioxide with the size of primary particles varying between 15 and 40 nm were observed only in five products. In the sun lotion with the highest SPF, only few small aggregates were found. In the sun screen with the lowest SPF, the largest aggregates of TiO 2 particles were detected with sizes up to 1.6 μm. In one of the sun lotions, neither TiO 2 nor ZnO was found in spite of the labelling. Instead, approx. 500 nm large diamond-shaped particles were observed. These particles are composed of an organic material as only carbon was detected by EDS. A novel defatting method for sample preparation of titanium dioxide nanoparticles used in sun cosmetics was developed. This method was applied to six different sun lotions with SPF between 30 and 50+. TiO 2 particles were found in only five sunscreens. The sizes of the primary particles were below 100 nm and, according to the EU Cosmetic Regulation, have to be listed on the package with the term 'nano'. © 2016 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

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

DTIC Science & Technology

2014-06-01

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

A Descriptive Analysis of US Prehospital Care Response to Law Enforcement Tactical Incidents.

PubMed

Aberle, Sara J; Lohse, Christine M; Sztajnkrycer, Matthew D

2015-01-01

Law enforcement tactical incidents involve high-risk operations that exceed the capabilities of regular, uniformed police. Despite the existence of tactical teams for 50 years, little is known about the frequency or nature of emergency medical services (EMS) response to tactical events in the United States. The purpose of this study was to perform a descriptive analysis of tactical events reported to a national EMS database. Descriptive analysis of the 2012 National Emergency Medical Services Information System (NEMSIS) Public Release research data set, containing EMS emergency response data from 41 states. A total of 17,479,328 EMS events were reported, of which 3,953 events were coded as "Activation-Tactical or SWAT Specialty Service/Response Team." The most common level of prehospital care present on scene was basic life support (55.2%). The majority (72.3%) of tactical incident activations involved a single patient; mass casualty incidents occurred in 0.5% of events. The most common EMS response locations were homes (48.4%), streets or highways (37.0%), and public buildings (6.3%). The mean age of treated patients was 44.1 years ± 22.0 years; 3.5% of tactical incident activation patients were aged 8 years or less. Injuries were coded as firearm assault in 14.8% and as chemical exposure in 8.9% of events. Cardiac arrest occurred in 5.1% of patients, with the majority (92.2%) occurring prior to EMS arrival. The primary symptoms reported by EMS personnel were pain (37.4%), change in responsiveness (13.1%), and bleeding (8.1%). Advanced airway procedures occurred in 30 patients. No patients were documented as receiving tourniquets or needle thoracostomy. Approximately 11 EMS responses in support of law enforcement tactical operations occur daily in the United States. The majority occur in homes and involve a single patient. Advanced airway procedures are required in a minority of patients. Cardiac arrest is rare and occurs prior to EMS response in the majority of cases. Better understanding of the nature and location of EMS responses to tactical incidents is required to develop consistent EMS policies in support of law enforcement tactical operations. 2015.

Sandia Simple Particle Tracking (Sandia SPT) v. 1.0

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

Anthony, Stephen M.

2015-06-15

Sandia SPT is designed as software to accompany a book chapter being published a methods chapter which provides an introduction on how to label and track individual proteins. The Sandia Simple Particle Tracking code uses techniques common to the image processing community, where its value is that it facilitates implementing the methods described in the book chapter by providing the necessary open-source code. The code performs single particle spot detection (or segmentation and localization) followed by tracking (or connecting the detected particles into trajectories). The book chapter, which along with the headers in each file, constitutes the documentation for themore » code is: Anthony, S.M.; Carroll-Portillo, A.; Timlon, J.A., Dynamics and Interactions of Individual Proteins in the Membrane of Living Cells. In Anup K. Singh (Ed.) Single Cell Protein Analysis Methods in Molecular Biology. Springer« less

The Particle Accelerator Simulation Code PyORBIT

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

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

2015-01-01

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

Neptune: An astrophysical smooth particle hydrodynamics code for massively parallel computer architectures

NASA Astrophysics Data System (ADS)

Sandalski, Stou

Smooth particle hydrodynamics is an efficient method for modeling the dynamics of fluids. It is commonly used to simulate astrophysical processes such as binary mergers. We present a newly developed GPU accelerated smooth particle hydrodynamics code for astrophysical simulations. The code is named neptune after the Roman god of water. It is written in OpenMP parallelized C++ and OpenCL and includes octree based hydrodynamic and gravitational acceleration. The design relies on object-oriented methodologies in order to provide a flexible and modular framework that can be easily extended and modified by the user. Several pre-built scenarios for simulating collisions of polytropes and black-hole accretion are provided. The code is released under the MIT Open Source license and publicly available at http://code.google.com/p/neptune-sph/.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

What do emergency medicine learners want from their teachers? A multicenter focus group analysis.

PubMed

Thurgur, Lisa; Bandiera, Glen; Lee, Shirley; Tiberius, Richard

2005-09-01

To the best of the authors' knowledge, there are no reports describing what learners believe are good emergency medicine (EM) teaching practices. EM faculty developers are compromised by this lack of knowledge about what EM learners appreciate in their teachers. To determine what Canadian EM learners consider to be good prerequisites and strategies for effective teaching in the emergency department (ED). Clinical clerks and residents from the Canadian College of Family Physicians, Emergency Medicine certification [CCFP(EM)] fellowship program, the Royal College of Physicians and Surgeons of Canada, Emergency Medicine certification [FRCP(EM)] fellowship program, and off-service programs from all five Ontario medical schools participated in monitored focus-group sessions. Conversations were recorded, transcribed by a third party, and coded by two independent assessors using standard grounded theory methods. The text was categorized based on the final code into basic themes and specific qualifiers, which were then sorted by frequency of mention in the focus groups. Results are presented in descriptive fashion. Twenty-eight learners participated. They identified 14 major principles for good EM teaching, and a further 30 specific qualifiers. The top five principles were: "has a positive teacher attitude," "takes time to teach," "uses teachable moments well," "tailors teaching to the learner," and "gives appropriate feedback." Agreement on classification of ideas was 86%. Learners are sensitive to the constraints of the ED teaching environment, and have consistent views about good ED teaching practices. Among 14 general principles identified, "takes time to teach," "gives feedback," "tailors teaching to the learner," "uses teachable moments," and "has a good teacher attitude" were the most commonly reported.

Low frequency electromagnetic fluctuations in Kappa magnetized plasmas

NASA Astrophysics Data System (ADS)

Kim, Sunjung; Lazar, M.; Schlickeiser, R.; López, R. A.; Yoon, P. H.

2018-07-01

The present paper provides a theoretical approach for the evaluation of the low frequency spontaneously emitted electromagnetic (EM) fluctuations in Kappa magnetized plasmas, which include the kinetic Alfvén, fast magnetosonic/whistler, kinetic slow mode, ion Bernstein cyclotron modes, and higher-order modes. The model predictions are consistent with particle-in-cell simulations. Effects of suprathermal particles on low frequency fluctuations are studied by varying the power index, either for ions (κ i) or for electrons (κ e). Computations for an arbitrary wave vector orientation and wave polarization provide the intensity of spontaneous emissions to be enhanced in the presence of suprathermal populations. These results strongly suggest that spontaneous fluctuations may significantly contribute to the EM fluctuations observed in space plasmas, where suprathermal Kappa distributed particles are ubiquitous.

Virus Assembly and Maturation

NASA Astrophysics Data System (ADS)

Johnson, John E.

2004-03-01

We use two techniques to look at three-dimensional virus structure: electron cryomicroscopy (cryoEM) and X-ray crystallography. Figure 1 is a gallery of virus particles whose structures Timothy Baker, one of my former colleagues at Purdue University, used cryoEM to determine. It illustrates the variety of sizes of icosahedral virus particles. The largest virus particle on this slide is the Herpes simplex virus, around 1200Å in diameter; the smallest we examined was around 250Å in diameter. Viruses bear their genomic information either as positive-sense DNA and RNA, double-strand DNA, double-strand RNA, or negative-strand RNA. Viruses utilize the various structure and function "tactics" seen throughout cell biology to replicate at high levels. Many of the biological principles that we consider general were in fact discovered in the context of viruses ...

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

Fu, Guoyong; Budny, Robert; Gorelenkov, Nikolai

We report here the work done for the FY14 OFES Theory Performance Target as given below: "Understanding alpha particle confinement in ITER, the world's first burning plasma experiment, is a key priority for the fusion program. In FY 2014, determine linear instability trends and thresholds of energetic particle-driven shear Alfven eigenmodes in ITER for a range of parameters and profiles using a set of complementary simulation models (gyrokinetic, hybrid, and gyrofluid). Carry out initial nonlinear simulations to assess the effects of the unstable modes on energetic particle transport". In the past year (FY14), a systematic study of the alpha-driven Alfvenmore » modes in ITER has been carried out jointly by researchers from six institutions involving seven codes including the transport simulation code TRANSP (R. Budny and F. Poli, PPPL), three gyrokinetic codes: GEM (Y. Chen, Univ. of Colorado), GTC (J. McClenaghan, Z. Lin, UCI), and GYRO (E. Bass, R. Waltz, UCSD/GA), the hybrid code M3D-K (G.Y. Fu, PPPL), the gyro-fluid code TAEFL (D. Spong, ORNL), and the linear kinetic stability code NOVA-K (N. Gorelenkov, PPPL). A range of ITER parameters and profiles are specified by TRANSP simulation of a hybrid scenario case and a steady-state scenario case. Based on the specified ITER equilibria linear stability calculations are done to determine the stability boundary of alpha-driven high-n TAEs using the five initial value codes (GEM, GTC, GYRO, M3D-K, and TAEFL) and the kinetic stability code (NOVA-K). Both the effects of alpha particles and beam ions have been considered. Finally, the effects of the unstable modes on energetic particle transport have been explored using GEM and M3D-K.« less

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).

Particle In Cell Codes on Highly Parallel Architectures

NASA Astrophysics Data System (ADS)

Tableman, Adam

2014-10-01

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

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

DTIC Science & Technology

1984-08-01

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

Missed surgical intensive care unit billing: potential financial impact of 24/7 faculty presence.

PubMed

Hendershot, Kimberly M; Bollins, John P; Armen, Scott B; Thomas, Yalaunda M; Steinberg, Steven M; Cook, Charles H

2009-07-01

To efficiently capture evaluation and management (E&M) and procedural billing in our surgical intensive care unit (SICU), we have developed an electronic billing system that links to the electronic medical record (EMR). In this system, only notes electronically signed and coded by an attending generate billing charges. We hypothesized that capture of missed billing during nighttime and weekends might be sufficient to subsidize 24/7 in-house attending coverage. A retrospective chart EMR review was performed of the EMRs for all SICU patients during a 2-month period. Note type, date, time, attending signature, and coding were analyzed. Notes without attending signature, diagnosis, or current procedural terminology (CPT) code were considered incomplete and identified as "missed billing." Four hundred and forty-three patients had 465 admissions generating 2,896 notes. Overall, 76% of notes were signed and coded by an attending and billed. Incomplete (not billed) notes represented an overall missed billing opportunity of $159,138 for the 2-month time period (approximately $954,000 annually). Unbilled E&M encounters during weekdays totaled $54,758, whereas unbilled E&M and procedures from weeknights and weekends totaled $88,408 ($44,566 and $43,842, respectively). Missed billing after-hours thus represents approximately $530K annually, extrapolating to approximately $220K in collections from our payer mix. Surprisingly, missed E&M and procedural billing during weekdays totaled $70,730 (approximately $425K billing, approximately $170K collections annually), and typically represented patients seen, but transferred from the SICU before attending documentation was completed. Capture of nighttime and weekend ICU collections alone may be insufficient to add faculty or incentivize in-house coverage, but could certainly complement other in-house derived revenues to such ends. In addition, missed daytime billing in busy modern ICUs can be substantial, and use of an EMR to identify missed billing opportunities can help create solutions to recover these revenues.

General Relativistic Smoothed Particle Hydrodynamics code developments: A progress report

NASA Astrophysics Data System (ADS)

Faber, Joshua; Silberman, Zachary; Rizzo, Monica

2017-01-01

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

Estimation for general birth-death processes.

PubMed

Crawford, Forrest W; Minin, Vladimir N; Suchard, Marc A

2014-04-01

Birth-death processes (BDPs) are continuous-time Markov chains that track the number of "particles" in a system over time. While widely used in population biology, genetics and ecology, statistical inference of the instantaneous particle birth and death rates remains largely limited to restrictive linear BDPs in which per-particle birth and death rates are constant. Researchers often observe the number of particles at discrete times, necessitating data augmentation procedures such as expectation-maximization (EM) to find maximum likelihood estimates. For BDPs on finite state-spaces, there are powerful matrix methods for computing the conditional expectations needed for the E-step of the EM algorithm. For BDPs on infinite state-spaces, closed-form solutions for the E-step are available for some linear models, but most previous work has resorted to time-consuming simulation. Remarkably, we show that the E-step conditional expectations can be expressed as convolutions of computable transition probabilities for any general BDP with arbitrary rates. This important observation, along with a convenient continued fraction representation of the Laplace transforms of the transition probabilities, allows for novel and efficient computation of the conditional expectations for all BDPs, eliminating the need for truncation of the state-space or costly simulation. We use this insight to derive EM algorithms that yield maximum likelihood estimation for general BDPs characterized by various rate models, including generalized linear models. We show that our Laplace convolution technique outperforms competing methods when they are available and demonstrate a technique to accelerate EM algorithm convergence. We validate our approach using synthetic data and then apply our methods to cancer cell growth and estimation of mutation parameters in microsatellite evolution.

Hamiltonian structure of classical N-body systems of finite-size particles subject to EM interactions

NASA Astrophysics Data System (ADS)

Cremaschini, C.; Tessarotto, M.

2012-01-01

An open issue in classical relativistic mechanics is the consistent treatment of the dynamics of classical N-body systems of mutually interacting particles. This refers, in particular, to charged particles subject to EM interactions, including both binary interactions and self-interactions ( EM-interacting N- body systems). The correct solution to the question represents an overriding prerequisite for the consistency between classical and quantum mechanics. In this paper it is shown that such a description can be consistently obtained in the context of classical electrodynamics, for the case of a N-body system of classical finite-size charged particles. A variational formulation of the problem is presented, based on the N -body hybrid synchronous Hamilton variational principle. Covariant Lagrangian and Hamiltonian equations of motion for the dynamics of the interacting N-body system are derived, which are proved to be delay-type ODEs. Then, a representation in both standard Lagrangian and Hamiltonian forms is proved to hold, the latter expressed by means of classical Poisson Brackets. The theory developed retains both the covariance with respect to the Lorentz group and the exact Hamiltonian structure of the problem, which is shown to be intrinsically non-local. Different applications of the theory are investigated. The first one concerns the development of a suitable Hamiltonian approximation of the exact equations that retains finite delay-time effects characteristic of the binary interactions and self-EM-interactions. Second, basic consequences concerning the validity of Dirac generator formalism are pointed out, with particular reference to the instant-form representation of Poincaré generators. Finally, a discussion is presented both on the validity and possible extension of the Dirac generator formalism as well as the failure of the so-called Currie "no-interaction" theorem for the non-local Hamiltonian system considered here.

Geographic Discordance Between Patient Residence and Incident Location in Emergency Medical Services Responses.

PubMed

Hsia, Renee Y; Dai, Mengtao; Wei, Ran; Sabbagh, Sarah; Mann, N Clay

2017-01-01

The location of a patient's residence is often used for emergency medical services (EMS) system planning. Our objective is to evaluate the association between patient residence and emergency incident zip codes for 911 calls. We used data from the 2013 National Emergency Medical Services Information System (NEMSIS) Public-Release Research Dataset. We studied all 911 calls with a valid complaint by dispatch, identifying zip codes for both the residence and incident locations (n=12,376,784). The primary outcomes were geographic and distance discordances between patient residence and incident zip codes. We used a multivariate logistic regression model to determine geographic discordance between residence and incident zip codes by dispatch complaint, age, and sex. We also measured distances between locations with geospatial processing. The overall proportion of geographic discordance for all 911 calls was 27.7% (95% confidence interval [CI] 27.7% to 27.8%) and the median distance discordance was 11.5 miles (95% CI 11.5 to 11.5 miles). Lower geographic discordance rates were found among patients aged 65 to 79 years (20.2%; 95% CI 20.1% to 20.2%) and 80 years and older (14.5%; 95% CI 14.5% to 14.6%). Motor vehicle crashes (63.5%; 95% CI 63.5% to 63.6%), industrial accidents (59.3%; 95% CI 58.0% to 60.6%), and mass casualty incidents (50.6%; 95% CI 49.6% to 51.5%) were more likely to occur outside a patient's residence zip code. Median network distance between home and incident zip centroid codes ranged from 8.6 to 23.5 miles. In NEMSIS, there was geographic discordance between patient residence zip code and call location zip code in slightly more than one quarter of EMS responses records. The geographic discordance rates between residence and incident zip codes were associated with dispatch complaints and age. Although a patient's residence might be a valid proxy for incident location for elderly patients, this relationship holds less true for other age groups and among different complaints. Our findings have important implications for EMS system planning, resource allocation, and injury surveillance. Copyright © 2016 American College of Emergency Physicians. Published by Elsevier Inc. All rights reserved.

A method for determining electrophoretic and electroosmotic mobilities using AC and DC electric field particle displacements.

PubMed

Oddy, M H; Santiago, J G

2004-01-01

We have developed a method for measuring the electrophoretic mobility of submicrometer, fluorescently labeled particles and the electroosmotic mobility of a microchannel. We derive explicit expressions for the unknown electrophoretic and the electroosmotic mobilities as a function of particle displacements resulting from alternating current (AC) and direct current (DC) applied electric fields. Images of particle displacements are captured using an epifluorescent microscope and a CCD camera. A custom image-processing code was developed to determine image streak lengths associated with AC measurements, and a custom particle tracking velocimetry (PTV) code was devised to determine DC particle displacements. Statistical analysis was applied to relate mobility estimates to measured particle displacement distributions.

SPAMCART: a code for smoothed particle Monte Carlo radiative transfer

NASA Astrophysics Data System (ADS)

Lomax, O.; Whitworth, A. P.

2016-10-01

We present a code for generating synthetic spectral energy distributions and intensity maps from smoothed particle hydrodynamics simulation snapshots. The code is based on the Lucy Monte Carlo radiative transfer method, I.e. it follows discrete luminosity packets as they propagate through a density field, and then uses their trajectories to compute the radiative equilibrium temperature of the ambient dust. The sources can be extended and/or embedded, and discrete and/or diffuse. The density is not mapped on to a grid, and therefore the calculation is performed at exactly the same resolution as the hydrodynamics. We present two example calculations using this method. First, we demonstrate that the code strictly adheres to Kirchhoff's law of radiation. Secondly, we present synthetic intensity maps and spectra of an embedded protostellar multiple system. The algorithm uses data structures that are already constructed for other purposes in modern particle codes. It is therefore relatively simple to implement.

Modeling anomalous radial transport in kinetic transport codes

NASA Astrophysics Data System (ADS)

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

2009-11-01

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

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

NASA Astrophysics Data System (ADS)

Gassmöller, Rene; Bangerth, Wolfgang

2016-04-01

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

Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports

PubMed Central

Meyerson, Joel R.; Rao, Prashant; Kumar, Janesh; Chittori, Sagar; Banerjee, Soojay; Pierson, Jason; Mayer, Mark L.; Subramaniam, Sriram

2014-01-01

Poor partitioning of macromolecules into the holes of holey carbon support grids frequently limits structural determination by single particle cryo-electron microscopy (cryo-EM). Here, we present a method to deposit, on gold-coated carbon grids, a self-assembled monolayer whose surface properties can be controlled by chemical modification. We demonstrate the utility of this approach to drive partitioning of ionotropic glutamate receptors into the holes, thereby enabling 3D structural analysis using cryo-EM methods. PMID:25403871

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Relating quantum discord with the quantum dense coding capacity

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

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

2015-01-15

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

Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in Cryo-EM

PubMed Central

Fran, Joachim; Ourmazd, Abbas

2016-01-01

Cryo-electron microscopy, when combined with single-particle reconstruction, is a powerful method for studying macromolecular structure. Recent developments in detector technology have pushed the resolution into a range comparable to that of X-ray crystallography. However, cryo-EM is able to separate and thus recover the structure of each of several discrete structures present in the sample. For the more general case involving continuous structural changes, a novel technique employing manifold embedding has been recently demonstrated. Potentially, the entire work-cycle of a molecular machine may be observed as it passes through a continuum of states, and its free-energy landscape may be mapped out. This technique will be outlined and discussed in the context of its application to a large single-particle dataset of yeast ribosomes. PMID:26884261

A comprehensive study of MPI parallelism in three-dimensional discrete element method (DEM) simulation of complex-shaped granular particles

NASA Astrophysics Data System (ADS)

Yan, Beichuan; Regueiro, Richard A.

2018-02-01

A three-dimensional (3D) DEM code for simulating complex-shaped granular particles is parallelized using message-passing interface (MPI). The concepts of link-block, ghost/border layer, and migration layer are put forward for design of the parallel algorithm, and theoretical scalability function of 3-D DEM scalability and memory usage is derived. Many performance-critical implementation details are managed optimally to achieve high performance and scalability, such as: minimizing communication overhead, maintaining dynamic load balance, handling particle migrations across block borders, transmitting C++ dynamic objects of particles between MPI processes efficiently, eliminating redundant contact information between adjacent MPI processes. The code executes on multiple US Department of Defense (DoD) supercomputers and tests up to 2048 compute nodes for simulating 10 million three-axis ellipsoidal particles. Performance analyses of the code including speedup, efficiency, scalability, and granularity across five orders of magnitude of simulation scale (number of particles) are provided, and they demonstrate high speedup and excellent scalability. It is also discovered that communication time is a decreasing function of the number of compute nodes in strong scaling measurements. The code's capability of simulating a large number of complex-shaped particles on modern supercomputers will be of value in both laboratory studies on micromechanical properties of granular materials and many realistic engineering applications involving granular materials.

Appearance of the bona fide spiral tubule of ORF virus is dependent on an intact 10-kilodalton viral protein.

PubMed

Spehner, D; De Carlo, S; Drillien, R; Weiland, F; Mildner, K; Hanau, D; Rziha, H-J

2004-08-01

Parapoxviruses can be morphologically distinguished from other poxviruses in conventional negative staining electron microscopy (EM) by their ovoid appearance and the spiral tubule surrounding the virion's surface. However, this technique may introduce artifacts. We have examined Orf virus (ORFV; the prototype species of the Parapoxvirus genus) by cryoelectron microscopy (cryo-EM) and cryo-negative staining EM. From these studies we suggest that the shape and unique spiral tubule are authentic features of the parapoxviruses. We also constructed an ORFV mutant deleted of a gene encoding a 10-kDa protein, which is an orthologue of the vaccinia virus (VACV) 14-kDa fusion protein, and investigated its ultrastructure. This mutant virus multiplied slowly in permissive cells and produced infectious but morphologically aberrant particles. Mutant virions lacked the spiral tubule but displayed short disorganized tubules similar to those observed on the surface of VACV. In addition, thin extensions or loop-like structures were appended to the ORFV mutant particles. We suggest that these appended structures arise from a failure of the mutant virus particles to properly seal and that the sealing activity is dependent on the 10-kDa protein.

Colour-barcoded magnetic microparticles for multiplexed bioassays.

PubMed

Lee, Howon; Kim, Junhoi; Kim, Hyoki; Kim, Jiyun; Kwon, Sunghoon

2010-09-01

Encoded particles have a demonstrated value for multiplexed high-throughput bioassays such as drug discovery and clinical diagnostics. In diverse samples, the ability to use a large number of distinct identification codes on assay particles is important to increase throughput. Proper handling schemes are also needed to readout these codes on free-floating probe microparticles. Here we create vivid, free-floating structural coloured particles with multi-axis rotational control using a colour-tunable magnetic material and a new printing method. Our colour-barcoded magnetic microparticles offer a coding capacity easily into the billions with distinct magnetic handling capabilities including active positioning for code readouts and active stirring for improved reaction kinetics in microscale environments. A DNA hybridization assay is done using the colour-barcoded magnetic microparticles to demonstrate multiplexing capabilities.

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

A fast method for finding bound systems in numerical simulations: Results from the formation of asteroid binaries

NASA Astrophysics Data System (ADS)

Leinhardt, Zoë M.; Richardson, Derek C.

2005-08-01

We present a new code ( companion) that identifies bound systems of particles in O(NlogN) time. Simple binaries consisting of pairs of mutually bound particles and complex hierarchies consisting of collections of mutually bound particles are identifiable with this code. In comparison, brute force binary search methods scale as O(N) while full hierarchy searches can be as expensive as O(N), making analysis highly inefficient for multiple data sets with N≳10. A simple test case is provided to illustrate the method. Timing tests demonstrating O(NlogN) scaling with the new code on real data are presented. We apply our method to data from asteroid satellite simulations [Durda et al., 2004. Icarus 167, 382-396; Erratum: Icarus 170, 242; reprinted article: Icarus 170, 243-257] and note interesting multi-particle configurations. The code is available at http://www.astro.umd.edu/zoe/companion/ and is distributed under the terms and conditions of the GNU Public License.

The FLUKA Code: An Overview

NASA Technical Reports Server (NTRS)

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

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

NASA Astrophysics Data System (ADS)

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

2007-09-01

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

Simulation of Hypervelocity Impact on Aluminum-Nextel-Kevlar Orbital Debris Shields

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.

2000-01-01

An improved hybrid particle-finite element method has been developed for hypervelocity impact simulation. The method combines the general contact-impact capabilities of particle codes with the true Lagrangian kinematics of large strain finite element formulations. Unlike some alternative schemes which couple Lagrangian finite element models with smooth particle hydrodynamics, the present formulation makes no use of slidelines or penalty forces. The method has been implemented in a parallel, three dimensional computer code. Simulations of three dimensional orbital debris impact problems using this parallel hybrid particle-finite element code, show good agreement with experiment and good speedup in parallel computation. The simulations included single and multi-plate shields as well as aluminum and composite shielding materials. at an impact velocity of eleven kilometers per second.

Integrating Geochemical Reactions with a Particle-Tracking Approach to Simulate Nitrogen Transport and Transformation in Aquifers

NASA Astrophysics Data System (ADS)

Cui, Z.; Welty, C.; Maxwell, R. M.

2011-12-01

Lagrangian, particle-tracking models are commonly used to simulate solute advection and dispersion in aquifers. They are computationally efficient and suffer from much less numerical dispersion than grid-based techniques, especially in heterogeneous and advectively-dominated systems. Although particle-tracking models are capable of simulating geochemical reactions, these reactions are often simplified to first-order decay and/or linear, first-order kinetics. Nitrogen transport and transformation in aquifers involves both biodegradation and higher-order geochemical reactions. In order to take advantage of the particle-tracking approach, we have enhanced an existing particle-tracking code SLIM-FAST, to simulate nitrogen transport and transformation in aquifers. The approach we are taking is a hybrid one: the reactive multispecies transport process is operator split into two steps: (1) the physical movement of the particles including the attachment/detachment to solid surfaces, which is modeled by a Lagrangian random-walk algorithm; and (2) multispecies reactions including biodegradation are modeled by coupling multiple Monod equations with other geochemical reactions. The coupled reaction system is solved by an ordinary differential equation solver. In order to solve the coupled system of equations, after step 1, the particles are converted to grid-based concentrations based on the mass and position of the particles, and after step 2 the newly calculated concentration values are mapped back to particles. The enhanced particle-tracking code is capable of simulating subsurface nitrogen transport and transformation in a three-dimensional domain with variably saturated conditions. Potential application of the enhanced code is to simulate subsurface nitrogen loading to the Chesapeake Bay and its tributaries. Implementation details, verification results of the enhanced code with one-dimensional analytical solutions and other existing numerical models will be presented in addition to a discussion of implementation challenges.

Examining End-Of-Chapter Problems Across Editions of an Introductory Calculus-Based Physics Textbook

NASA Astrophysics Data System (ADS)

Xiao, Bin

End-Of-Chapter (EOC) problems have been part of many physics education studies. Typically, only problems "localized" as relevant to a single chapter were used. This work examines how well this type of problem represents all EOC problems and whether EOC problems found in leading textbooks have changed over the past several decades. To investigate whether EOC problems have connections between chapters, I solved all problems of the E&M; chapters of the most recent edition of a popular introductory level calculus-based textbook and coded the equations used to solve each problem. These results were compared to the first edition of the same text. Also, several relevant problem features were coded for those problems and results were compared for sample chapters across all editions. My findings include two parts. The result of equation usage shows that problems in the E&M; chapters do use equations from both other E&M; chapters and non-E&M; chapters. This out-of-chapter usage increased from the first edition to the last edition. Information about the knowledge structure of E&M; chapters was also revealed. The results of the problem feature study show that most EOC problems have common features but there was an increase of diversity in some of the problem features across editions.

Sequential Immunofluorescent Light Microscopy and Electron Microscopy of Recombination Nodules During Meiotic Prophase I.

PubMed

Anderson, Lorinda K

2017-01-01

Immunolocalization using either fluorescence for light microscopy (LM) or gold particles for electron microscopy (EM) has become a common tool to pinpoint proteins involved in recombination during meiotic prophase. Each method has its advantages and disadvantages. For example, LM immunofluorescence is comparatively easier and higher throughput compared to immunogold EM localization. In addition, immunofluorescence has the advantages that a faint signal can often be enhanced by longer exposure times and colocalization using two (or more) probes with different absorbance and emission spectra is straightforward. However, immunofluorescence is not useful if the object of interest does not label with an antibody probe and is below the resolution of the LM. In comparison, immunogold EM localization is higher resolution than immunofluorescent LM localization, and individual nuclear structures, such as recombination nodules, can be identified by EM regardless of whether they are labeled or not. However, immunogold localization has other disadvantages including comparatively low signal-to-noise ratios, more difficult colocalization using gold particles of different sizes, and the inability to evaluate labeling efficiency before examining the sample using EM (a more expensive and time-consuming technique than LM). Here we describe a method that takes advantage of the good points of both immunofluorescent LM and EM to analyze two classes of late recombination nodules (RNs), only one of which labels with antibodies to MLH1 protein, a marker of crossovers. The method can be used readily with other antibodies to analyze early recombination nodules or other prophase I structures.

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

NASA Astrophysics Data System (ADS)

Rose, Laura P.

This thesis discusses the development of a 1D particle-in-cell (PIC) code and the analysis of plasma-wall interactions. The 1D code (Plasma and Wall Simulation -- PAWS) is a kinetic simulation of plasma done by treating both electrons and ions as particles. The goal of this thesis is to study near wall plasma interaction to better understand the mechanism that occurs in this region. The main focus of this investigation is the effects that secondary electrons have on the sheath profile. The 1D code is modeled using the PIC method. Treating both the electrons and ions as macroparticles the field is solved on each node and weighted to each macro particle. A pre-ionized plasma was loaded into the domain and the velocities of particles were sampled from the Maxwellian distribution. An important part of this code is the boundary conditions at the wall. If a particle hits the wall a secondary electron may be produced based on the incident energy. To study the sheath profile the simulations were run for various cases. Varying background neutral gas densities were run with the 2D code and compared to experimental values. Different wall materials were simulated to show their effects of SEE. In addition different SEE yields were run, including one study with very high SEE yields to show the presence of a space charge limited sheath. Wall roughness was also studied with the 1D code using random angles of incidence. In addition to the 1D code, an external 2D code was also used to investigate wall roughness without secondary electrons. The roughness profiles where created upon investigation of wall roughness inside Hall Thrusters based off of studies done on lifetime erosion of the inner and outer walls of these devices. The 2D code, Starfish[33], is a general 2D axisymmetric/Cartesian code for modeling a wide a range of plasma and rarefied gas problems. These results show that higher SEE yield produces a smaller sheath profile and that wall roughness produces a lower SEE yield. Modeling near wall interactions is not a simple or perfected task. Due to the lack of a second dimension and a sputtering model it is not possible with this study to show the positive effects wall roughness could have on Hall thruster performance since roughness occurs from the negative affect of sputtering.

Creation of fully vectorized FORTRAN code for integrating the movement of dust grains in interplanetary environments

NASA Technical Reports Server (NTRS)

Colquitt, Walter

1989-01-01

The main objective is to improve the performance of a specific FORTRAN computer code from the Planetary Sciences Division of NASA/Johnson Space Center when used on a modern vectorizing supercomputer. The code is used to calculate orbits of dust grains that separate from comets and asteroids. This code accounts for influences of the sun and 8 planets (neglecting Pluto), solar wind, and solar light pressure including Poynting-Robertson drag. Calculations allow one to study the motion of these particles as they are influenced by the Earth or one of the other planets. Some of these particles become trapped just beyond the Earth for long periods of time. These integer period resonances vary from 3 orbits of the Earth and 2 orbits of the particles to as high as 14 to 13.

Simulation of halo particles with Simpsons

NASA Astrophysics Data System (ADS)

Machida, Shinji

2003-12-01

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

2011.2 Revision of the Evaluated Nuclear Data Library (ENDL2011.2)

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

Beck, B.; Descalles, M. A.; Mattoon, C.

LLNL's Computational Nuclear Physics Group and Nuclear Theory and Modeling Group have col- laborated to create the 2011.2 revised release of the Evaluated Nuclear Data Library (ENDL2011.2). ENDL2011.2 is designed to support LLNL's current and future nuclear data needs and will be em- ployed in nuclear reactor, nuclear security and stockpile stewardship simulations with ASC codes. This database is currently the most complete nuclear database for Monte Carlo and deterministic transport of neutrons and charged particles. This library was assembled with strong support from the ASC PEM and Attribution programs, leveraged with support from Campaign 4 and the DOE/O cemore » of Science's US Nuclear Data Program. This document lists the revisions made in ENDL2011.2 compared with the data existing in the original ENDL2011.0 release and the ENDL2011.1-rc4 re- lease candidate of April 2015. These changes are made in parallel with some similar revisions for ENDL2009.2.« less