CIFOG: Cosmological Ionization Fields frOm Galaxies

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-03-01

CIFOG is a versatile MPI-parallelised semi-numerical tool to perform simulations of the Epoch of Reionization. From a set of evolving cosmological gas density and ionizing emissivity fields, it computes the time and spatially dependent ionization of neutral hydrogen (HI), neutral (HeI) and singly ionized helium (HeII) in the intergalactic medium (IGM). The code accounts for HII, HeII, HeIII recombinations, and provides different descriptions for the photoionization rate that are used to calculate the residual HI fraction in ionized regions. This tool has been designed to be coupled to semi-analytic galaxy formation models or hydrodynamical simulations. The modular fashion of the code allows the user to easily introduce new descriptions for recombinations and the photoionization rate.

Prediction of CMEs and Type II Bursts from Sun to Earth

NASA Astrophysics Data System (ADS)

Cairns, I. H.; Schmidt, J. M.; Gopalswamy, N.; van der Holst, B.

2017-12-01

Most major space weather events are due to fast CMEs and their shocks interacting with Earth's magnetosphere. SImilarly, type II solar radio bursts are well-known signatures of CMEs and their shocks moving through the corona and solar wind. The properties of the space weather events and the type II radio bursts depend sensitively on the CME velocity, shape, and evolution as functions of position and time, as well as on the magnetic field vector in the coronal and solar wind plasma, downstream of the CME shock, and inside the CME. We report simulations of CMEs and type II bursts from the Sun to Earth with the Space Weather Modelling Framework (2015 and 2016 versions), set up carefully using relevant data, and a kinetic radio emission theory. Excellent agreement between observations, simulations, and theory are found for the coronal (metric) type II burst of 7 September 2014 and associated CME, including the lack of radio emission in the solar wind beyond about 10 solar radii. Similarly, simulation of a CME and type II burst from the Sun to 1 AU over the period 29 November - 1 December 2013 yield excellent agreement for the radio burst from 10 MHz to 30 kHz for STEREO A and B and Wind, arrival of the CME at STEREO A within 1 hour reported time, deceleration of the CME in agreement with the Gopalswamy et al. [2011] observational analyses, and Bz rotations at STEREO A from upstream of the CME shock to within the CME. These results provide strong support for the type II theory and also that the Space WeatherModeling Framework can accurately predict the properties and evolution of CMEs and the interplanetary magnetic field and plasma from the Sun to 1 AU when sufficiently carefully initialized.

Laboratory and Field Evaluation of Rapid Setting Cementitious Materials for Large Crater Repair

DTIC Science & Technology

2010-05-01

frame used within which to complete the repair was the current NATO standard of 4 hr. A total of 6 simulated craters were prepared, with each repair...Combat Command 129 Andrews Street Langley Air Force Base, VA 23665 ERDC TR-10-4 ii Abstract: Current practice for expedient runway repair...penalty. Numerous commercial products are available. A full-scale field test was conducted using rapid setting materials to repair simulated bomb craters

Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

PubMed

Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

2016-03-05

The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Magnetic Bianchi type II string cosmological model in loop quantum cosmology

NASA Astrophysics Data System (ADS)

Rikhvitsky, Victor; Saha, Bijan; Visinescu, Mihai

2014-07-01

The loop quantum cosmology of the Bianchi type II string cosmological model in the presence of a homogeneous magnetic field is studied. We present the effective equations which provide modifications to the classical equations of motion due to quantum effects. The numerical simulations confirm that the big bang singularity is resolved by quantum gravity effects.

Ground testing and simulation. II - Aerodynamic testing and simulation: Saving lives, time, and money

NASA Technical Reports Server (NTRS)

Dayman, B., Jr.; Fiore, A. W.

1974-01-01

The present work discusses in general terms the various kinds of ground facilities, in particular, wind tunnels, which support aerodynamic testing. Since not all flight parameters can be simulated simultaneously, an important problem consists in matching parameters. It is pointed out that there is a lack of wind tunnels for a complete Reynolds-number simulation. Using a computer to simulate flow fields can result in considerable reduction of wind-tunnel hours required to develop a given flight vehicle.

A comparison of three approaches for simulating fine-scale surface winds in support of wildland fire management. Part II. An exploratory study of the effect of simulated winds on fire growth simulations

Treesearch

Jason M. Forthofer; Bret W. Butler; Charles W. McHugh; Mark A. Finney; Larry S. Bradshaw; Richard D. Stratton; Kyle S. Shannon; Natalie S. Wagenbrenner

2014-01-01

The effect of fine-resolution wind simulations on fire growth simulations is explored. The wind models are (1) a wind field consisting of constant speed and direction applied everywhere over the area of interest; (2) a tool based on the solution of the conservation of mass only (termed mass-conserving model) and (3) a tool based on a solution of conservation of mass...

Spatial Cognition and Map Interpretation

DTIC Science & Technology

1987-09-01

Terrain association Spatial cognition Map reading Videogames aa mldm II naeaaaaiy and Hontlty by block numbor) Spatial memory span Orientation...ability. Finally, field and classroom performance was compared to wayfinding in a simulated ( videogame ) environment in which position coordinates were...a simulated ( videogame ) environment. Findings: MITAC instruction significantly improved the experimental group’s ability to perform terrain

Numerics and subgrid-scale modeling in large eddy simulations of stratocumulus clouds.

PubMed

Pressel, Kyle G; Mishra, Siddhartha; Schneider, Tapio; Kaul, Colleen M; Tan, Zhihong

2017-06-01

Stratocumulus clouds are the most common type of boundary layer cloud; their radiative effects strongly modulate climate. Large eddy simulations (LES) of stratocumulus clouds often struggle to maintain fidelity to observations because of the sharp gradients occurring at the entrainment interfacial layer at the cloud top. The challenge posed to LES by stratocumulus clouds is evident in the wide range of solutions found in the LES intercomparison based on the DYCOMS-II field campaign, where simulated liquid water paths for identical initial and boundary conditions varied by a factor of nearly 12. Here we revisit the DYCOMS-II RF01 case and show that the wide range of previous LES results can be realized in a single LES code by varying only the numerical treatment of the equations of motion and the nature of subgrid-scale (SGS) closures. The simulations that maintain the greatest fidelity to DYCOMS-II observations are identified. The results show that using weighted essentially non-oscillatory (WENO) numerics for all resolved advective terms and no explicit SGS closure consistently produces the highest-fidelity simulations. This suggests that the numerical dissipation inherent in WENO schemes functions as a high-quality, implicit SGS closure for this stratocumulus case. Conversely, using oscillatory centered difference numerical schemes for momentum advection, WENO numerics for scalars, and explicitly modeled SGS fluxes consistently produces the lowest-fidelity simulations. We attribute this to the production of anomalously large SGS fluxes near the cloud tops through the interaction of numerical error in the momentum field with the scalar SGS model.

Numerics and subgrid‐scale modeling in large eddy simulations of stratocumulus clouds

PubMed Central

Mishra, Siddhartha; Schneider, Tapio; Kaul, Colleen M.; Tan, Zhihong

2017-01-01

Abstract Stratocumulus clouds are the most common type of boundary layer cloud; their radiative effects strongly modulate climate. Large eddy simulations (LES) of stratocumulus clouds often struggle to maintain fidelity to observations because of the sharp gradients occurring at the entrainment interfacial layer at the cloud top. The challenge posed to LES by stratocumulus clouds is evident in the wide range of solutions found in the LES intercomparison based on the DYCOMS‐II field campaign, where simulated liquid water paths for identical initial and boundary conditions varied by a factor of nearly 12. Here we revisit the DYCOMS‐II RF01 case and show that the wide range of previous LES results can be realized in a single LES code by varying only the numerical treatment of the equations of motion and the nature of subgrid‐scale (SGS) closures. The simulations that maintain the greatest fidelity to DYCOMS‐II observations are identified. The results show that using weighted essentially non‐oscillatory (WENO) numerics for all resolved advective terms and no explicit SGS closure consistently produces the highest‐fidelity simulations. This suggests that the numerical dissipation inherent in WENO schemes functions as a high‐quality, implicit SGS closure for this stratocumulus case. Conversely, using oscillatory centered difference numerical schemes for momentum advection, WENO numerics for scalars, and explicitly modeled SGS fluxes consistently produces the lowest‐fidelity simulations. We attribute this to the production of anomalously large SGS fluxes near the cloud tops through the interaction of numerical error in the momentum field with the scalar SGS model. PMID:28943997

Optical design and simulation of a new coherence beamline at NSLS-II

NASA Astrophysics Data System (ADS)

Williams, Garth J.; Chubar, Oleg; Berman, Lonny; Chu, Yong S.; Robinson, Ian K.

2017-08-01

We will discuss the optical design for a proposed beamline at NSLS-II, a late-third generation storage ring source, designed to exploit the spatial coherence of the X-rays to extract high-resolution spatial information from ordered and disordered materials through Coherent Diffractive Imaging, executed in the Bragg- and forward-scattering geometries. This technique offers a powerful tool to image sub-10 nm spatial features and, within ordered materials, sub-Angstrom mapping of deformation fields. Driven by the opportunity to apply CDI to a wide range of samples, with sizes ranging from sub-micron to tens-of-microns, two optical designs have been proposed and simulated under a wide variety of optical configurations using the software package Synchrotron Radiation Workshop. The designs, their goals, and the results of the simulation, including NSLS-II ring and undulator source parameters, of the beamline performance as a function of its variable optical components is described.

A Guide to Computer Simulations of Three Adaptive Instructional Models for the Advanced Instructional System Phases II and III. Final Report.

ERIC Educational Resources Information Center

Hansen, Duncan N.; And Others

Computer simulations of three individualized adaptive instructional models (AIM) were undertaken to determine if these models function as prescribed in Air Force technical training programs. In addition, the project sought to develop a user's guide for effective understanding of adaptive models during field implementation. Successful simulations…

Advancing Virtual Patient Simulations through Design Research and Inter"PLAY": Part II--Integration and Field Test

ERIC Educational Resources Information Center

Hirumi, Atsusi; Johnson, Teresa; Reyes, Ramsamooj Javier; Lok, Benjamin; Johnsen, Kyle; Rivera-Gutierrez, Diego J.; Bogert, Kenneth; Kubovec, Stacey; Eakins, Michael; Kleinsmith, Andrea; Bellew, Michael; Cendan, Juan

2016-01-01

In Part I of this two-part series, we examined the design and development of NERVE: A virtual patient simulation created to give medical students standardized experiences in interviewing, examining, and diagnosing virtual patients with cranial nerve disorders. We illustrated key design features and discussed how design-based research studies…

Stellar Populations and Radial Migrations in Virgo Disk Galaxies

NASA Astrophysics Data System (ADS)

Roediger, Joel C.; Courteau, Stéphane; Sánchez-Blázquez, Patricia; McDonald, Michael

2012-10-01

We present new stellar age profiles, derived from well-resolved optical and near-infrared images of 64 Virgo cluster disk galaxies, whose analysis poses a challenge for current disk galaxy formation models. Our ability to break the age-metallicity degeneracy and the significant size of our sample represent key improvements over complementary studies of field disk galaxies. Our results can be summarized as follows: first, and contrary to observations of disk galaxies in the field, these cluster galaxies are distributed almost equally amongst the three main types of disk galaxy luminosity profiles (I/II/III), indicating that the formation and/or survival of Type II breaks is suppressed within the cluster environment. Second, we find examples of statistically significant inversions ("U-shapes") in the age profiles of all three disk galaxy types, reminiscent of predictions from high-resolution simulations of classically truncated Type II disks in the field. These features characterize the age profiles for only about a third (<=36%) of each disk galaxy type in our sample. An even smaller fraction of cluster disks (~11% of the total sample) exhibit age profiles that decrease outward (i.e., negative age gradients). Instead, flat and/or positive age gradients prevail (>=50%) within our Type I, II, and III subsamples. These observations thus suggest that while stellar migrations and inside-out growth can play a significant role in the evolution of all disk galaxy types, other factors contributing to the evolution of galaxies can overwhelm the predicted signatures of these processes. We interpret our observations through a scenario whereby Virgo cluster disk galaxies formed initially like their brethren in the field but which, upon falling into the cluster, were transformed into their present state through external processes linked to the environment (e.g., ram-pressure stripping and harassment). Current disk galaxy formation models, which have largely focused on field galaxies, fail to reproduce these results, thus calling for adequate hydrodynamical simulations of dense galaxy environments if we are to understand cluster disks. The current paper highlights numerous constraints for such simulations. In the Appendix, we confirm the claim by Erwin et al. that Type II breaks are absent in Virgo cluster S0s and discuss the detection of Type III breaks in such galaxies.

Large-scale dynamo growth rates from numerical simulations and implications for mean-field theories

NASA Astrophysics Data System (ADS)

Park, Kiwan; Blackman, Eric G.; Subramanian, Kandaswamy

2013-05-01

Understanding large-scale magnetic field growth in turbulent plasmas in the magnetohydrodynamic limit is a goal of magnetic dynamo theory. In particular, assessing how well large-scale helical field growth and saturation in simulations match those predicted by existing theories is important for progress. Using numerical simulations of isotropically forced turbulence without large-scale shear with its implications, we focus on several additional aspects of this comparison: (1) Leading mean-field dynamo theories which break the field into large and small scales predict that large-scale helical field growth rates are determined by the difference between kinetic helicity and current helicity with no dependence on the nonhelical energy in small-scale magnetic fields. Our simulations show that the growth rate of the large-scale field from fully helical forcing is indeed unaffected by the presence or absence of small-scale magnetic fields amplified in a precursor nonhelical dynamo. However, because the precursor nonhelical dynamo in our simulations produced fields that were strongly subequipartition with respect to the kinetic energy, we cannot yet rule out the potential influence of stronger nonhelical small-scale fields. (2) We have identified two features in our simulations which cannot be explained by the most minimalist versions of two-scale mean-field theory: (i) fully helical small-scale forcing produces significant nonhelical large-scale magnetic energy and (ii) the saturation of the large-scale field growth is time delayed with respect to what minimalist theory predicts. We comment on desirable generalizations to the theory in this context and future desired work.

Large-scale dynamo growth rates from numerical simulations and implications for mean-field theories.

PubMed

Park, Kiwan; Blackman, Eric G; Subramanian, Kandaswamy

2013-05-01

Understanding large-scale magnetic field growth in turbulent plasmas in the magnetohydrodynamic limit is a goal of magnetic dynamo theory. In particular, assessing how well large-scale helical field growth and saturation in simulations match those predicted by existing theories is important for progress. Using numerical simulations of isotropically forced turbulence without large-scale shear with its implications, we focus on several additional aspects of this comparison: (1) Leading mean-field dynamo theories which break the field into large and small scales predict that large-scale helical field growth rates are determined by the difference between kinetic helicity and current helicity with no dependence on the nonhelical energy in small-scale magnetic fields. Our simulations show that the growth rate of the large-scale field from fully helical forcing is indeed unaffected by the presence or absence of small-scale magnetic fields amplified in a precursor nonhelical dynamo. However, because the precursor nonhelical dynamo in our simulations produced fields that were strongly subequipartition with respect to the kinetic energy, we cannot yet rule out the potential influence of stronger nonhelical small-scale fields. (2) We have identified two features in our simulations which cannot be explained by the most minimalist versions of two-scale mean-field theory: (i) fully helical small-scale forcing produces significant nonhelical large-scale magnetic energy and (ii) the saturation of the large-scale field growth is time delayed with respect to what minimalist theory predicts. We comment on desirable generalizations to the theory in this context and future desired work.

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

Jafarzadeh, S.; Rutten, R. J.; Szydlarski, M.

A dense forest of slender bright fibrils near a small solar active region is seen in high-quality narrowband Ca ii H images from the SuFI instrument onboard the Sunrise balloon-borne solar observatory. The orientation of these slender Ca ii H fibrils (SCF) overlaps with the magnetic field configuration in the low solar chromosphere derived by magnetostatic extrapolation of the photospheric field observed with Sunrise/IMaX and SDO/HMI. In addition, many observed SCFs are qualitatively aligned with small-scale loops computed from a novel inversion approach based on best-fit numerical MHD simulation. Such loops are organized in canopy-like arches over quiet areas thatmore » differ in height depending on the field strength near their roots.« less

An MHD simulation model of time-dependent global solar corona with temporally varying solar-surface magnetic field maps

NASA Astrophysics Data System (ADS)

Hayashi, K.

2013-11-01

We present a model of a time-dependent three-dimensional magnetohydrodynamics simulation of the sub-Alfvenic solar corona and super-Alfvenic solar wind with temporally varying solar-surface boundary magnetic field data. To (i) accommodate observational data with a somewhat arbitrarily evolving solar photospheric magnetic field as the boundary value and (ii) keep the divergence-free condition, we developed a boundary model, here named Confined Differential Potential Field model, that calculates the horizontal components of the magnetic field, from changes in the vertical component, as a potential field confined in a thin shell. The projected normal characteristic method robustly simulates the solar corona and solar wind, in response to the temporal variation of the boundary Br. We conduct test MHD simulations for two periods, from Carrington Rotation number 2009 to 2010 and from Carrington Rotation 2074 to 2075 at solar maximum and minimum of Cycle 23, respectively. We obtained several coronal features that a fixed boundary condition cannot yield, such as twisted magnetic field lines at the lower corona and the transition from an open-field coronal hole to a closed-field streamer. We also obtained slight improvements of the interplanetary magnetic field, including the latitudinal component, at Earth.

Debye screening of dislocations.

PubMed

Groma, I; Györgyi, G; Kocsis, B

2006-04-28

Debye-like screening by edge dislocations of some externally given stress is studied by means of a variational approach to coarse grained field theory. Explicitly given are the force field and the induced geometrically necessary dislocation (GND) distribution, in the special case of a single glide axis in 2D, for (i) a single edge dislocation and (ii) a dislocation wall. Numerical simulation demonstrates that the correlation in relaxed dislocation configurations is in good agreement with the induced GND in case (i). Furthermore, the result (ii) well predicts the experimentally observed decay length for the GND developing close to grain boundaries.

Atomic bonding effects in annular dark field scanning transmission electron microscopy. II. Experiments

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

Odlyzko, Michael L.; Held, Jacob T.; Mkhoyan, K. Andre, E-mail: mkhoyan@umn.edu

2016-07-15

Quantitatively calibrated annular dark field scanning transmission electron microscopy (ADF-STEM) imaging experiments were compared to frozen phonon multislice simulations adapted to include chemical bonding effects. Having carefully matched simulation parameters to experimental conditions, a depth-dependent bonding effect was observed for high-angle ADF-STEM imaging of aluminum nitride. This result is explained by computational predictions, systematically examined in the preceding portion of this study, showing the propagation of the converged STEM beam to be highly sensitive to net interatomic charge transfer. Thus, although uncertainties in experimental conditions and simulation accuracy remain, the computationally predicted experimental bonding effect withstands the experimental testing reportedmore » here.« less

Application of Satellite SAR Imagery in Mapping the Active Layer of Arctic Permafrost

NASA Technical Reports Server (NTRS)

Zhang, Ting-Jun; Li, Shu-Sun

2003-01-01

The objective of this project is to map the spatial variation of the active layer over the arctic permafrost in terms of two parameters: (i) timing and duration of thaw period and (ii) differential frost heave and thaw settlement of the active layer. To achieve this goal, remote sensing, numerical modeling, and related field measurements are required. Tasks for the University of Colorado team are to: (i) determine the timing of snow disappearance in spring through changes in surface albedo (ii) simulate the freezing and thawing processes of the active layer and (iii) simulate the impact of snow cover on permafrost presence.

Origin of threshold voltage fluctuation caused by ion implantation to source and drain extensions of silicon-on-insulator triple-gate fin-type field-effect transistors using three-dimensional process and device simulations

NASA Astrophysics Data System (ADS)

Tsutsumi, Toshiyuki

2018-06-01

The threshold voltage (V th) fluctuation induced by ion implantation (I/I) in the source and drain extensions (SDEs) of a silicon-on-insulator (SOI) triple-gate (Tri-Gate) fin-type field-effect transistor (FinFET) was analyzed by both three-dimensional (3D) process and device simulations collaboratively. The origin of the V th fluctuation induced by the SDE I/I is basically a variation of a bottleneck barrier height (BBH) due to implanted arsenic (As+) ions. In particular, a very low and broad V th distribution in the saturation region is due to percolative conduction in addition to the BBH variation. Moreover, it is surprisingly found that the V th fluctuation is mostly characterized by the BBH of only a top surface center line of a Si fin of the device. Our collaborative approach by 3D process and device simulations is dispensable for the accurate investigation of variability-tolerant devices. The obtained results are beneficial for the research and development of such future devices.

MHD simulation of the shock wave event on October 24, 2003

NASA Astrophysics Data System (ADS)

Ogino, T.; Kajiwara, Y.; Nakao, M.; Park, K. S.; Fukazawa, K.; Yi, Y.

2007-11-01

A three-dimensional global MHD simulation of the interaction between the solar wind and the Earth's magnetosphere has been executed to study the shock wave event on space weather problem on October 24, 2003, when an abnormal operation happened in a satellite for Environment Observation Technology, ADEOS-II (Midori-II). Characteristic features of the event are the long duration of southward IMF, arrival of a strong shock wave, then large variation of IMF By from negative to positive for about 15 min duration. In the simulation, the shock wave compresses the magnetosphere for southward IMF and a hot plasma was injected around the geosynchronous orbit from plasma sheet. During the interval when IMF By changes from negative to positive, the magnitude of IMF extremely decreases to bring attenuation of magnetic reconnection. The open-closed boundary shrinks in the polar cap and the transient expansion of the magnetic field lines occurs to imply enhancement of particle precipitation. The reconnection site moves from dawn to dusk in the dayside magnetopause and a narrow cockscomb closed field region is formed in the high latitude tail.

A model study of assisted adiabatic transfer of population in the presence of collisional dephasing

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

Masuda, Shumpei, E-mail: shumpei.masuda@aalto.fi; Rice, Stuart A., E-mail: s-rice@uchicago.edu

2015-06-28

Previous studies have demonstrated that when experimental conditions generate non-adiabatic dynamics that prevents highly efficient population transfer between states of an isolated system by stimulated Raman adiabatic passage (STIRAP), the addition of an auxiliary counter-diabatic field (CDF) can restore most or all of that efficiency. This paper examines whether that strategy is also successful in a non-isolated system in which the energies of the states fluctuate, e.g., when a solute is subject to collisions with solvent. We study population transfer in two model systems: (i) the three-state system used by Demirplak and Rice [J. Chem. Phys. 116, 8028 (2002)] andmore » (ii) a four-state system, derived from the simulation studies of Demirplak and Rice [J. Chem. Phys. 125, 194517 (2006)], that mimics HCl in liquid Ar. Simulation studies of the vibrational manifold of HCl in dense fluid Ar show that the collision induced vibrational energy level fluctuations have asymmetric distributions. Representations of these asymmetric energy level fluctuation distributions are used in both models (i) and (ii). We identify three sources of degradation of the efficiency of STIRAP generated selective population transfer in model (ii): too small pulse areas of the laser fields, unwanted interference arising from use of strong fields, and the vibrational detuning. For both models (i) and (ii), our examination of the efficiency of STIRAP + CDF population transfer under the influence of the asymmetric distribution of the vibrational energy fluctuations shows that there is a range of field strengths and pulse durations under which STIRAP + CDF control of population transfer has greater efficiency than does STIRAP generated population transfer.« less

Early development of Xenopus embryos is affected by simulated gravity

NASA Technical Reports Server (NTRS)

Yokota, Hiroki; Neff, Anton W.; Malacinski, George M.

1994-01-01

Early amphibian (Xenopus laevis) development under clinostat-simulated weightlessness and centrifuge-simulated hypergravity was studied. The results revealed significant effects on (i) 'morphological patterning' such as the cleavage furrow pattern in the vegetal hemisphere at the eight-cell stage and the shape of the dorsal lip in early gastrulae and (ii) 'the timing of embryonic events' such as the third cleavage furrow completion and the dorsal lip appearance. Substantial variations in sensitivity to simulated force fields were observed, which should be considered in interpreting spaceflight data.

Simulation of PEP-II Accelerator Backgrounds Using TURTLE

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

Barlow, R.J.; Fieguth, T.; /SLAC

2006-02-15

We present studies of accelerator-induced backgrounds in the BaBar detector at the SLAC B-Factory, carried out using LPTURTLE, a modified version of the DECAY TURTLE simulation package. Lost-particle backgrounds in PEP-II are dominated by a combination of beam-gas bremstrahlung, beam-gas Coulomb scattering, radiative-Bhabha events and beam-beam blow-up. The radiation damage and detector occupancy caused by the associated electromagnetic shower debris can limit the usable luminosity. In order to understand and mitigate such backgrounds, we have performed a full program of beam-gas and luminosity-background simulations, that include the effects of the detector solenoidal field, detailed modeling of limiting apertures in bothmore » collider rings, and optimization of the betatron collimation scheme in the presence of large transverse tails.« less

Studies and optimization of Pohang Light Source-II superconducting radio frequency system at stable top-up operation with beam current of 400 mA

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

Joo, Youngdo, E-mail: Ydjoo77@postech.ac.kr; Yu, Inha; Park, Insoo

After three years of upgrading work, the Pohang Light Source-II (PLS-II) is now successfully operating. The final quantitative goal of PLS-II is a top-up user-service operation with beam current of 400 mA to be completed by the end of 2014. During the beam store test up to 400 mA in the storage ring (SR), it was observed that the vacuum pressure around the radio frequency (RF) window of the superconducting cavity rapidly increases over the interlock level limiting the availability of the maximum beam current storing. Although available beam current is enhanced by setting a higher RF accelerating voltage, it is bettermore » to keep the RF accelerating voltage as low as possible in the long time top-up operation. We investigated the cause of the window vacuum pressure increment by studying the changes in the electric field distribution at the superconducting cavity and waveguide according to the beam current. In our simulation, an equivalent physical modeling was developed using a finite-difference time-domain code. The simulation revealed that the electric field amplitude at the RF window is exponentially increased as the beam current increases, thus this high electric field amplitude causes a RF breakdown at the RF window, which comes with the rapid increase of window vacuum pressure. The RF accelerating voltage of PLS-II RF system was set to 4.95 MV, which was estimated using the maximum available beam current that works as a function of RF voltage, and the top-up operation test with the beam current of 400 mA was successfully carried out.« less

Rapid Transient Pressure Field Computations in the Nearfield of Circular Transducers using Frequency Domain Time-Space Decomposition

PubMed Central

Alles, E. J.; Zhu, Y.; van Dongen, K. W. A.; McGough, R. J.

2013-01-01

The fast nearfield method, when combined with time-space decomposition, is a rapid and accurate approach for calculating transient nearfield pressures generated by ultrasound transducers. However, the standard time-space decomposition approach is only applicable to certain analytical representations of the temporal transducer surface velocity that, when applied to the fast nearfield method, are expressed as a finite sum of products of separate temporal and spatial terms. To extend time-space decomposition such that accelerated transient field simulations are enabled in the nearfield for an arbitrary transducer surface velocity, a new transient simulation method, frequency domain time-space decomposition (FDTSD), is derived. With this method, the temporal transducer surface velocity is transformed into the frequency domain, and then each complex-valued term is processed separately. Further improvements are achieved by spectral clipping, which reduces the number of terms and the computation time. Trade-offs between speed and accuracy are established for FDTSD calculations, and pressure fields obtained with the FDTSD method for a circular transducer are compared to those obtained with Field II and the impulse response method. The FDTSD approach, when combined with the fast nearfield method and spectral clipping, consistently achieves smaller errors in less time and requires less memory than Field II or the impulse response method. PMID:23160476

Simulations of Emerging Magnetic Flux. II. The Formation of Unstable Coronal Flux Ropes and the Initiation of Coronal Mass Ejections

NASA Technical Reports Server (NTRS)

Leake, James E.; Linton, Mark G.; Antiochos, Spiro K.

2014-01-01

We present results from three-dimensional magnetohydrodynamic simulations of the emergence of a twisted convection zone flux tube into a pre-existing coronal dipole field. As in previous simulations, following the partial emergence of the sub-surface flux into the corona, a combination of vortical motions and internal magnetic reconnection forms a coronal flux rope. Then, in the simulations presented here, external reconnection between the emerging field and the pre-existing dipole coronal field allows further expansion of the coronal flux rope into the corona. After sufficient expansion, internal reconnection occurs beneath the coronal flux rope axis, and the flux rope erupts up to the top boundary of the simulation domain (approximately 36 Mm above the surface).We find that the presence of a pre-existing field, orientated in a direction to facilitate reconnection with the emerging field, is vital to the fast rise of the coronal flux rope. The simulations shown in this paper are able to self-consistently create many of the surface and coronal signatures used by coronal mass ejection (CME) models. These signatures include surface shearing and rotational motions, quadrupolar geometry above the surface, central sheared arcades reconnecting with oppositely orientated overlying dipole fields, the formation of coronal flux ropes underlying potential coronal field, and internal reconnection which resembles the classical flare reconnection scenario. This suggests that proposed mechanisms for the initiation of a CME, such as "magnetic breakout," are operating during the emergence of new active regions.

Synthetic observations of wave propagation in a sunspot umbra

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

Felipe, T.; Socas-Navarro, H.; Khomenko, E.

2014-11-01

Spectropolarimetric temporal series from Fe I λ6301.5 Å and Ca II infrared triplet lines are obtained by applying the Stokes synthesis code NICOLE to a numerical simulation of wave propagation in a sunspot umbra from MANCHA code. The analysis of the phase difference between Doppler velocity and intensity core oscillations of the Fe I λ6301.5 Å line reveals that variations in the intensity are produced by opacity fluctuations rather than intrinsic temperature oscillations, except for frequencies between 5 and 6.5 mHz. On the other hand, the photospheric magnetic field retrieved from the weak field approximation provides the intrinsic magnetic fieldmore » oscillations associated to wave propagation. Our results suggest that this is due to the low magnetic field gradient of our sunspot model. The Stokes parameters of the chromospheric Ca II infrared triplet lines show striking variations as shock waves travel through the formation height of the lines, including emission self-reversals in the line core and highly abnormal Stokes V profiles. Magnetic field oscillations inferred from the Ca II infrared lines using the weak field approximation appear to be related with the magnetic field strength variation between the photosphere and the chromosphere.« less

Experimental Study of Fluid Structure Interaction Effects on Metal Plates Under Fully Developed Laminar Flow

DTIC Science & Technology

2011-12-01

UU NSN 7540–01–280–5500 Standard Form 298 (Rev. 8–98) Prescribed by ANSI Std. Z39.18 ii THIS PAGE INTENTIONALLY LEFT BLANK iii Approved for...modeled using the finite element analysis simulation code, ANSYS 13.0. The main objective of these simulations was to determine the location at which...transient response of the test plate under FSI conditions, computational studies were carried out in ANSYS 13.0 Multi-field (MFX) simulation

Modeling direct interband tunneling. II. Lower-dimensional structures

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

Pan, Andrew, E-mail: pandrew@ucla.edu; Chui, Chi On; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095

We investigate the applicability of the two-band Hamiltonian and the widely used Kane analytical formula to interband tunneling along unconfined directions in nanostructures. Through comparisons with k·p and tight-binding calculations and quantum transport simulations, we find that the primary correction is the change in effective band gap. For both constant fields and realistic tunnel field-effect transistors, dimensionally consistent band gap scaling of the Kane formula allows analytical and numerical device simulations to approximate non-equilibrium Green's function current characteristics without arbitrary fitting. This allows efficient first-order calibration of semiclassical models for interband tunneling in nanodevices.

Acoustic detection of roller bearing defects. Phase II, Field test.

DOT National Transportation Integrated Search

2000-08-01

The Transportation Technology Center, Inc. (TTCI), a subsidiary of the Association of American Railroads (AAR) Research and Test Department, conducted a series of simulated revenue service tests with a train of eight cars containing wheel sets with s...

Transit signal priority project, phase II : field and simulation evaluation results.

DOT National Transportation Integrated Search

2006-01-01

Transit Signal Priority (TSP) is recognized as an emerging technology that is capable of enhancing traditional transit services. Basic green-extension TSP was implemented on U.S. Route 1 in the Northern Virginia Area (or Washington, DC metropolitan a...

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Assessment of simulation fidelity using measurements of piloting technique in flight. II

NASA Technical Reports Server (NTRS)

Ferguson, S. W.; Clement, W. F.; Hoh, R. H.; Cleveland, W. B.

1985-01-01

Two components of the Vertical Motion Simulator (presently being used to assess the fidelity of UH-60A simulation) are evaluated: (1) the dash/quickstop Nap-of-the-earth (NOE) piloting task, and (2) the bop-up task. Data from these two flight test experiments are presented which provide information on the effect of reduced visual field of view, variation in scene content and texture, and the affect of pure time delay in the closed-loop pilot response. In comparison with task performance results obtained in flight tests, the results from the simulation indicate that the pilot's NOE task performance in the simulator is significantly degraded.

Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides

NASA Astrophysics Data System (ADS)

Todorova, Nevena; Bentvelzen, Alan; English, Niall J.; Yarovsky, Irene

2016-02-01

Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (<0.004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.

Mechanisms of electron acceptor utilization: Implications for simulating anaerobic biodegradation

USGS Publications Warehouse

Schreiber, M.E.; Carey, G.R.; Feinstein, D.T.; Bahr, J.M.

2004-01-01

Simulation of biodegradation reactions within a reactive transport framework requires information on mechanisms of terminal electron acceptor processes (TEAPs). In initial modeling efforts, TEAPs were approximated as occurring sequentially, with the highest energy-yielding electron acceptors (e.g. oxygen) consumed before those that yield less energy (e.g., sulfate). Within this framework in a steady state plume, sequential electron acceptor utilization would theoretically produce methane at an organic-rich source and Fe(II) further downgradient, resulting in a limited zone of Fe(II) and methane overlap. However, contaminant plumes often display much more extensive zones of overlapping Fe(II) and methane. The extensive overlap could be caused by several abiotic and biotic processes including vertical mixing of byproducts in long-screened monitoring wells, adsorption of Fe(II) onto aquifer solids, or microscale heterogeneity in Fe(III) concentrations. Alternatively, the overlap could be due to simultaneous utilization of terminal electron acceptors. Because biodegradation rates are controlled by TEAPs, evaluating the mechanisms of electron acceptor utilization is critical for improving prediction of contaminant mass losses due to biodegradation. Using BioRedox-MT3DMS, a three-dimensional, multi-species reactive transport code, we simulated the current configurations of a BTEX plume and TEAP zones at a petroleum- contaminated field site in Wisconsin. Simulation results suggest that BTEX mass loss due to biodegradation is greatest under oxygen-reducing conditions, with smaller but similar contributions to mass loss from biodegradation under Fe(III)-reducing, sulfate-reducing, and methanogenic conditions. Results of sensitivity calculations document that BTEX losses due to biodegradation are most sensitive to the age of the plume, while the shape of the BTEX plume is most sensitive to effective porosity and rate constants for biodegradation under Fe(III)-reducing and methanogenic conditions. Using this transport model, we had limited success in simulating overlap of redox products using reasonable ranges of parameters within a strictly sequential electron acceptor utilization framework. Simulation results indicate that overlap of redox products cannot be accurately simulated using the constructed model, suggesting either that Fe(III) reduction and methanogenesis are occurring simultaneously in the source area, or that heterogeneities in Fe(III) concentration and/or mineral type cause the observed overlap. Additional field, experimental, and modeling studies will be needed to address these questions. ?? 2004 Elsevier B.V. All rights reserved.

Generation of coherent terahertz radiation in ultrafast laser-gas interactionsa)

NASA Astrophysics Data System (ADS)

Kim, Ki-Yong

2009-05-01

The generation of intense terahertz radiation in ultrafast laser-gas interactions is studied on a basis of transient electron current model. When an ultrashort pulse laser's fundamental and its second harmonic fields are mixed to ionize a gas, a nonvanishing, directional photoelectron current can be produced, which simultaneously emits terahertz radiation in the far field. Here, the generation mechanism is examined with an analytic derivation and numerical simulations, in which tunneling ionization and subsequent electron motion in the combined laser field play a key role. In the simulations, three types of laser-gas interactions are considered: (i) mixing the fundamental and its second harmonic fields, (ii) mixing nonharmonic, two-color fields, and (iii) focusing single-color, few-cycle pulses. In these interactions, terahertz generation and other nonlinear effects driven by the transient current are investigated. In particular, anticorrelation between terahertz and second (or third) harmonic generation is observed and analyzed.

Modeling possible spreadings of a buoyant surface plume with lagrangian and eulerian approaches at different resolutions using flow syntheses from 1992-2007 - a Gulf of Mexico study

NASA Astrophysics Data System (ADS)

Tulloch, R.; Hill, C. N.; Jahn, O.

2010-12-01

We present results from an ensemble of BP oil spill simulations. The oil spill slick is modeled as a buoyant surface plume that is transported by ocean currents modulated, in some experiments, by surface winds. Ocean currents are taken from ECCO2 project (see http://ecco2.org ) observationally constrained state estimates spanning 1992-2007. In this work we (i) explore the role of increased resolution of ocean eddies, (ii) compare inferences from particle based, lagrangian, approaches with eulerian, field based, approaches and (ii) examine the impact of differential response of oil particles and water to normal and extreme, hurricane derived, wind stress. We focus on three main questions. Is the simulated response to an oil spill markedly different for different years, depending on ocean circulation and wind forcing? Does the simulated response depend heavily on resolution and are lagrangian and eulerian estimates comparable? We start from two regional configurations of the MIT General Circulation Model (MITgcm - see http://mitgcm.org ) at 16km and 4km resolutions respectively, both covering the Gulf of Mexico and western North Atlantic regions. The simulations are driven at open boundaries with momentum and hydrographic fields from ECCO2 observationally constrained global circulation estimates. The time dependent surface flow fields from these simulations are used to transport a dye that can optionally decay over time (approximating biological breakdown) and to transport lagrangian particles. Using these experiments we examine the robustness of conclusions regarding the fate of a buoyant slick, injected at a single point. In conclusion we discuss how future drilling operations could use similar approaches to better anticipate outcomes of accidents both in this region and elsewhere.

Theoretical Studies of High Field, High Energy Transport in Gallium Arsenide, Silicon and Heterostructures,

DTIC Science & Technology

1983-01-01

Springfield Ave. Urbana. IL 61801 11. CONTROLLING OFFICE NAME AND ADDRESS 12. REPORT DATE January 1983 13. NUMBER OF PAGES 163 14. MONITORING AGENCY NAME...AOORESS(II different from Controlling Office) IS. SECURITY CLASS. (of this report) IUnclassified ISa. DECLASSIFICATION OOWNGRADING 16. OIST IUTIO...understood and quantitatively calculated by the same approach: A Monte Carlo simulation inclu g a pseudopotential band structure. The Monte Carlo simulation

MLS Multipath Studies. Phase 3. Volume II. Development and Valiadation of Model for MLS Techniques.

DTIC Science & Technology

1980-02-07

2-40 2-32 Coherent interference phenomena encountered during TRSB field tests at JFK airport . 2-41 2-33 JFK airport environment near MLS elevation...24 4-8 Comparison of DMLS simulation and flight test on -380 radial at 2000 feet at JFK airport . 4-26 4-9 Comparison of DMLS simulation and flight...test on +380 radial at 2000 feet at JFK airport . 4-28 xv ( 4-10 Comparison of simulation with DMLS JFK centerline approach data. 4-29 4-11 DMLS "clean

Dark-field imaging in coronary atherosclerosis.

PubMed

Hetterich, Holger; Webber, Nicole; Willner, Marian; Herzen, Julia; Birnbacher, Lorenz; Auweter, Sigrid; Schüller, Ulrich; Bamberg, Fabian; Notohamiprodjo, Susan; Bartsch, Harald; Wolf, Johannes; Marschner, Mathias; Pfeiffer, Franz; Reiser, Maximilian; Saam, Tobias

2017-09-01

Dark-field imaging based on small angle X-ray scattering has been shown to be highly sensitive for microcalcifications, e.g. in breast tissue. We hypothesized (i) that high signal areas in dark-field imaging of atherosclerotic plaque are associated with microcalcifications and (ii) that dark-field imaging is more sensitive for microcalcifications than attenuation-based imaging. Fifteen coronary artery specimens were examined at an experimental set-up consisting of X-ray tube (40kV), grating-interferometer and detector. Tomographic dark-field-, attenuation-, and phase-contrast data were simultaneously acquired. Histopathology served as standard of reference. To explore the potential of dark field imaging in a full-body CT system, simulations were carried out with spherical calcifications of different sizes to simulate small and intermediate microcalcifications. Microcalcifications were present in 10/10 (100%) cross-sections with high dark-field signal and without evidence of calcifications in attenuation- or phase contrast. In positive controls with high signal areas in all three modalities, 10/10 (100%) cross-sections showed macrocalcifications. In negative controls without high signal areas, no calcifications were detected. Simulations showed that the microcalcifications generate substantially higher dark-field than attenuation signal. Dark-field imaging is highly sensitive for microcalcifications in coronary atherosclerotic plaque and might provide complementary information in the assessment of plaque instability. Copyright © 2017 Elsevier B.V. All rights reserved.

Multifrequency Pulsed EPR Studies of Biologically Relevant Manganese(II) Complexes

PubMed Central

Stich, T. A.; Lahiri, S.; Yeagle, G.; Dicus, M.; Brynda, M.; Gunn, A.; Aznar, C.; DeRose, V. J.; Britt, R. D.

2011-01-01

Electron paramagnetic resonance studies at multiple frequencies (MF EPR) can provide detailed electronic structure descriptions of unpaired electrons in organic radicals, inorganic complexes, and metalloenzymes. Analysis of these properties aids in the assignment of the chemical environment surrounding the paramagnet and provides mechanistic insight into the chemical reactions in which these systems take part. Herein, we present results from pulsed EPR studies performed at three different frequencies (9, 31, and 130 GHz) on [Mn(II)(H2O)6]2+, Mn(II) adducts with the nucleotides ATP and GMP, and the Mn(II)-bound form of the hammerhead ribozyme (MnHH). Through line shape analysis and interpretation of the zero-field splitting values derived from successful simulations of the corresponding continuous-wave and field-swept echo-detected spectra, these data are used to exemplify the ability of the MF EPR approach in distinguishing the nature of the first ligand sphere. A survey of recent results from pulsed EPR, as well as pulsed electron-nuclear double resonance and electron spin echo envelope modulation spectroscopic studies applied to Mn(II)-dependent systems, is also presented. PMID:22190766

A plasma source driven predator-prey like mechanism as a potential cause of spiraling intermittencies in linear plasma devices

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

Reiser, D.; Ohno, N.; Tanaka, H.

2014-03-15

Three-dimensional global drift fluid simulations are carried out to analyze coherent plasma structures appearing in the NAGDIS-II linear device (nagoya divertor plasma Simulator-II). The numerical simulations reproduce several features of the intermittent spiraling structures observed, for instance, statistical properties, rotation frequency, and the frequency of plasma expulsion. The detailed inspection of the three-dimensional plasma dynamics allows to identify the key mechanism behind the formation of these intermittent events. The resistive coupling between electron pressure and parallel electric field in the plasma source region gives rise to a quasilinear predator-prey like dynamics where the axisymmetric mode represents the prey and themore » spiraling structure with low azimuthal mode number represents the predator. This interpretation is confirmed by a reduced one-dimensional quasilinear model derived on the basis of the findings in the full three-dimensional simulations. The dominant dynamics reveals certain similarities to the classical Lotka-Volterra cycle.« less

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

Bahrdt, J.; Frentrup, W.; Gaupp, A.

BESSY plans to build a SASE-FEL facility for the energy range from 20 eV to 1000 eV. The energy range will be covered by three APPLE II type undulators with a magnetic length of about 60 m each. This paper summarizes the basic parameters of the FEL-undulators. The magnetic design will be presented. A modified APPLE II design will be discussed which provides higher fields at the expense of reduced horizontal access. GENESIS simulations give an estimate on the tolerances for the beam wander and for gap errors.

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment.

PubMed

Henriques, João; Cragnell, Carolina; Skepö, Marie

2015-07-14

An increasing number of studies using molecular dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and size comparison with recent experimental small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational class analysis. Our results show that, indeed, standard force fields sample conformations that are too compact, being systematically unable to reproduce experimental evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [ Best et al. J. Chem. Theory Comput. 2014, 10, 5113 - 5124.], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with experiment.

Modelling space-based integral-field spectrographs and their application to Type Ia supernova cosmology

NASA Astrophysics Data System (ADS)

Shukla, Hemant; Bonissent, Alain

2017-04-01

We present the parameterized simulation of an integral-field unit (IFU) slicer spectrograph and its applications in spectroscopic studies, namely, for probing dark energy with type Ia supernovae. The simulation suite is called the fast-slicer IFU simulator (FISim). The data flow of FISim realistically models the optics of the IFU along with the propagation effects, including cosmological, zodiacal, instrumentation and detector effects. FISim simulates the spectrum extraction by computing the error matrix on the extracted spectrum. The applications for Type Ia supernova spectroscopy are used to establish the efficacy of the simulator in exploring the wider parametric space, in order to optimize the science and mission requirements. The input spectral models utilize the observables such as the optical depth and velocity of the Si II absorption feature in the supernova spectrum as the measured parameters for various studies. Using FISim, we introduce a mechanism for preserving the complete state of a system, called the partial p/partial f matrix, which allows for compression, reconstruction and spectrum extraction, we introduce a novel and efficient method for spectrum extraction, called super-optimal spectrum extraction, and we conduct various studies such as the optimal point spread function, optimal resolution, parameter estimation, etc. We demonstrate that for space-based telescopes, the optimal resolution lies in the region near R ˜ 117 for read noise of 1 e- and 7 e- using a 400 km s-1 error threshold on the Si II velocity.

The Helioseismic and Magnetic Imager (HMI) Vector Magnetic Field Pipeline: Magnetohydrodynamics Simulation Module for the Global Solar Corona.

PubMed

Hayashi, K; Hoeksema, J T; Liu, Y; Bobra, M G; Sun, X D; Norton, A A

Time-dependent three-dimensional magnetohydrodynamics (MHD) simulation modules are implemented at the Joint Science Operation Center (JSOC) of the Solar Dynamics Observatory (SDO). The modules regularly produce three-dimensional data of the time-relaxed minimum-energy state of the solar corona using global solar-surface magnetic-field maps created from Helioseismic and Magnetic Imager (HMI) full-disk magnetogram data. With the assumption of a polytropic gas with specific-heat ratio of 1.05, three types of simulation products are currently generated: i) simulation data with medium spatial resolution using the definitive calibrated synoptic map of the magnetic field with a cadence of one Carrington rotation, ii) data with low spatial resolution using the definitive version of the synchronic frame format of the magnetic field, with a cadence of one day, and iii) low-resolution data using near-real-time (NRT) synchronic format of the magnetic field on a daily basis. The MHD data available in the JSOC database are three-dimensional, covering heliocentric distances from 1.025 to 4.975 solar radii, and contain all eight MHD variables: the plasma density, temperature, and three components of motion velocity, and three components of the magnetic field. This article describes details of the MHD simulations as well as the production of the input magnetic-field maps, and details of the products available at the JSOC database interface. To assess the merits and limits of the model, we show the simulated data in early 2011 and compare with the actual coronal features observed by the Atmospheric Imaging Assembly (AIA) and the near-Earth in-situ data.

Near-Field Acoustic Power Level Analysis of F31/A31 Open Rotor Model at Simulated Cruise Conditions, Technical Report II

NASA Technical Reports Server (NTRS)

Sree, Dave

2015-01-01

Near-field acoustic power level analysis of F31A31 open rotor model has been performed to determine its noise characteristics at simulated cruise flight conditions. The non-proprietary parts of the test data obtained from experiments in the 8x6 supersonic wind tunnel were provided by NASA-Glenn Research Center. The tone and broadband components of total noise have been separated from raw test data by using a new data analysis tool. Results in terms of sound pressure levels, acoustic power levels, and their variations with rotor speed, freestream Mach number, and input shaft power, with different blade-pitch setting angles at simulated cruise flight conditions, are presented and discussed. Empirical equations relating models acoustic power level and input shaft power have been developed. The near-field acoustic efficiency of the model at simulated cruise conditions is also determined. It is hoped that the results presented in this work will serve as a database for comparison and improvement of other open rotor blade designs and also for validating open rotor noise prediction codes.

Inverted initial conditions: Exploring the growth of cosmic structure and voids

DOE PAGES

Pontzen, Andrew; Roth, Nina; Peiris, Hiranya V.; ...

2016-05-18

We introduce and explore “paired” cosmological simulations. A pair consists of an A and B simulation with initial conditions related by the inversion δ A(x,t initial) = –δ B(x,t initial) (underdensities substituted for overdensities and vice versa). We argue that the technique is valuable for improving our understanding of cosmic structure formation. The A and B fields are by definition equally likely draws from ΛCDM initial conditions, and in the linear regime evolve identically up to the overall sign. As nonlinear evolution takes hold, a region that collapses to form a halo in simulation A will tend to expand tomore » create a void in simulation B. Applications include (i) contrasting the growth of A-halos and B-voids to test excursion-set theories of structure formation, (ii) cross-correlating the density field of the A and B universes as a novel test for perturbation theory, and (iii) canceling error terms by averaging power spectra between the two boxes. Furthermore, generalizations of the method to more elaborate field transformations are suggested.« less

Laminar and Turbulent Dynamos in Chiral Magnetohydrodynamics. II. Simulations

NASA Astrophysics Data System (ADS)

Schober, Jennifer; Rogachevskii, Igor; Brandenburg, Axel; Boyarsky, Alexey; Fröhlich, Jürg; Ruchayskiy, Oleg; Kleeorin, Nathan

2018-05-01

Using direct numerical simulations (DNS), we study laminar and turbulent dynamos in chiral magnetohydrodynamics with an extended set of equations that accounts for an additional contribution to the electric current due to the chiral magnetic effect (CME). This quantum phenomenon originates from an asymmetry between left- and right-handed relativistic fermions in the presence of a magnetic field and gives rise to a chiral dynamo. We show that the magnetic field evolution proceeds in three stages: (1) a small-scale chiral dynamo instability, (2) production of chiral magnetically driven turbulence and excitation of a large-scale dynamo instability due to a new chiral effect (α μ effect), and (3) saturation of magnetic helicity and magnetic field growth controlled by a conservation law for the total chirality. The α μ effect becomes dominant at large fluid and magnetic Reynolds numbers and is not related to kinetic helicity. The growth rate of the large-scale magnetic field and its characteristic scale measured in the numerical simulations agree well with theoretical predictions based on mean-field theory. The previously discussed two-stage chiral magnetic scenario did not include stage (2), during which the characteristic scale of magnetic field variations can increase by many orders of magnitude. Based on the findings from numerical simulations, the relevance of the CME and the chiral effects revealed in the relativistic plasma of the early universe and of proto-neutron stars are discussed.

TORO II simulations of induction heating in ferromagnetic materials

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

Adkins, D.R.; Gartling, D.K.; Kelley, J.B.

TORO II is a finite element computer program that is used in the simulation of electric and magnetic fields. This code, which was developed at Sandia National Laboratories, has been coupled with a finite element thermal code, COYOTE II, to predict temperature profiles in inductively heated parts. The development of an effective technique to account for the nonlinear behavior of the magnetic permeability in ferromagnetic parts is one of the more difficult aspects of solving induction heating problems. In the TORO II code, nonlinear, spatially varying magnetic permeability is approximated by an effective permeability on an element-by-element basis that effectivelymore » provides the same energy deposition that is produced when the true permeability is used. This approximation has been found to give an accurate estimate of the volumetric heating distribution in the part, and predicted temperature distributions have been experimentally verified using a medium carbon steel and a 10kW industrial induction heating unit. Work on the model was funded through a Cooperative Research and Development Agreement (CRADA) between the Department of Energy and General Motors` Delphi Saginaw Steering Systems.« less

A model for multiseasonal spread of verticillium wilt of lettuce.

PubMed

Wu, B M; Subbarao, K V

2014-09-01

Verticillium wilt, caused by Verticillium dahliae, is a destructive disease in lettuce, and the pathogen is seedborne. Even though maximum seed infestation rates of <5% have been detected in commercial lettuce seed lots, it is necessary to establish acceptable contamination thresholds to prevent introduction and establishment of the pathogen in lettuce production fields. However, introduction of inoculum into lettuce fields for experimental purposes to determine its long term effects is undesirable. Therefore, we constructed a simulation model to study the spread of Verticillium wilt following pathogen introduction from seed. The model consists of four components: the first for simulating infection of host plants, the second for simulating reproduction of microsclerotia on diseased plants, the third for simulating the survival of microsclerotia, and the fourth for simulating the dispersal of microsclerotia. The simulation results demonstrated that the inoculum density-disease incidence curve parameters and the dispersal gradients affect disease spread in the field. Although a steep dispersal gradient facilitated the establishment of the disease in a new field with a low inoculum density, a long-tail gradient allowed microsclerotia to be dispersed over greater distances, promoting the disease spread in fields with high inoculum density. The simulation results also revealed the importance of avoiding successive lettuce crops in the same field, reducing survival rate of microsclerotia between crops, and the need for breeding resistance against V. dahliae in lettuce cultivars to lower the number of microsclerotia formed on each diseased plant. The simulation results, however, suggested that, even with a low seed infestation rate, the pathogen would eventually become established if susceptible lettuce cultivars were grown consecutively in the same field for many years. A threshold for seed infestation can be established only when two of the three drivers of the disease-(i) low microsclerotia production per diseased plant, (ii) long-tail dispersal gradient, and (iii) low microsclerotia survival between lettuce crops-are present.

IMPRINTS OF EXPANSION ON THE LOCAL ANISOTROPY OF SOLAR WIND TURBULENCE

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

Verdini, Andrea; Grappin, Roland

2015-08-01

We study the anisotropy of II-order structure functions (SFs) defined in a frame attached to the local mean field in three-dimensional (3D) direct numerical simulations of magnetohydrodynamic turbulence, with the solar wind expansion both included and not included. We simulate spacecraft flybys through the numerical domain by taking increments along the radial (wind) direction that form an angle of 45° with the ambient magnetic field. We find that only when expansion is taken into account do the synthetic observations match the 3D anisotropy observed in the solar wind, including the change of anisotropy with scale. Our simulations also show thatmore » the anisotropy changes dramatically when considering increments oblique to the radial directions. Both results can be understood by noting that expansion reduces the radial component of the magnetic field at all scales, thus confining fluctuations in the plane perpendicular to the radial. Expansion is thus shown to affect not only the (global) spectral anisotropy, but also the local anisotropy of second-order SF by influencing the distribution of the local mean field, which enters this higher-order statistics.« less

Interrelation of soft and hard X-ray emissions during solar flares. II - Simulation model

NASA Technical Reports Server (NTRS)

Winglee, R. M.; Dulk, G. A.; Bornmann, P. L.; Brown, J. C.

1991-01-01

Two-dimensional electrostatic particle simulations are presented which incorporate the effect of quasi-static electric fields on particle dynamics as well as effects associated with wave-particle interactions induced by the accelerated particles. The properties of the soft and hard X-ray and microwave emissions from such systems are examined. In particular, it is shown that acceleration by quasi-static electric fields and heating via wave-particle interactions produces electron distributions with a broken-power law, similar to those inferred from hard X-ray spectra. Also, heating of the ambient plasma gives rise to a region of hot plasma propagating down to the chromosphere at about the ion sound speed.

High-fidelity Simulation of Jet Noise from Rectangular Nozzles . [Large Eddy Simulation (LES) Model for Noise Reduction in Advanced Jet Engines and Automobiles

NASA Technical Reports Server (NTRS)

Sinha, Neeraj

2014-01-01

This Phase II project validated a state-of-the-art LES model, coupled with a Ffowcs Williams-Hawkings (FW-H) far-field acoustic solver, to support the development of advanced engine concepts. These concepts include innovative flow control strategies to attenuate jet noise emissions. The end-to-end LES/ FW-H noise prediction model was demonstrated and validated by applying it to rectangular nozzle designs with a high aspect ratio. The model also was validated against acoustic and flow-field data from a realistic jet-pylon experiment, thereby significantly advancing the state of the art for LES.

Remote sensing reflectance simulation of coastal optical complex water in the East China Sea

NASA Astrophysics Data System (ADS)

He, Shuo; Lou, Xiulin; Zhang, Huaguo; Zheng, Gang

2018-02-01

In this work, remote sensing reflectance (Rrs) spectra of the Zhejiang coastal water in the East China Sea (ECS) were simulated by using the Hydrolight software with field data as input parameters. The seawater along the Zhejiang coast is typical Case II water with complex optical properties. A field observation was conducted in the Zhejiang coastal region in late May of 2016, and the concentration of ocean color constituents (pigment, SPM and CDOM), IOPs (absorption and backscattering coefficients) and Rrs were measured at 24 stations of 3 sections covering the turbid to clear inshore coastal waters. Referring to these ocean color field data, an ocean color model suitable for the Zhejiang coastal water was setup and applied in the Hydrolight. A set of 11 remote sensing reflectance spectra above water surface were modeled and calculated. Then, the simulated spectra were compared with the filed measurements. Finally, the spectral shape and characteristics of the remote sensing reflectance spectra were analyzed and discussed.

Signatures of quiet Sun reconnection events in Ca II, Hα and Fe I

NASA Astrophysics Data System (ADS)

Shetye, J.; Shelyag, S.; Reid, A. L.; Scullion, E.; Doyle, J. G.; Arber, T. D.

2018-06-01

We use observations of quiet Sun (QS) regions in the Hα 6563 Å, Ca II 8542 Å and Fe I 6302 Å lines. We observe brightenings in the wings of the Hα and Ca II combined with observations of the interacting magnetic concentrations observed in the Stokes signals of Fe I. These brightenings are similar to Ellerman bombs (EBs), i.e. impulsive bursts in the wings of the Balmer lines which leave the line cores unaffected. Such enhancements suggest that these events have similar formation mechanisms to the classical EBs found in active regions, with the reduced intensity enhancements found in the QS regions due to a weaker feeding magnetic flux. The observations also show that the quiet Sun Ellerman bombs (QSEBs) are formed at a higher height in the upper photosphere than the photospheric continuum level. Using simulations, we investigate the formation mechanism associated with the events and suggest that these events are driven by the interaction of magnetic field-lines in the upper photospheric regions. The results of the simulation are in agreement with observations when comparing the light-curves, and in most cases we found that the peak in the Ca II 8542 Å wing occurred before the peak in Hα wing. Moreover, in some cases, the line profiles observed in Ca II are asymmetrical with a raised core profile. The source of heating in these events is shown by the MURaM simulations and is suggested to occur 430 km above the photosphere.

Effects of magnetic fields on photoionized pillars and globules

NASA Astrophysics Data System (ADS)

Mackey, Jonathan; Lim, Andrew J.

2011-04-01

The effects of initially uniform magnetic fields on the formation and evolution of dense pillars and cometary globules at the boundaries of H II regions are investigated using 3D radiation-magnetohydrodynamics simulations. It is shown, in agreement with previous work, that a strong initial magnetic field is required to significantly alter the non-magnetized dynamics because the energy input from photoionization is so large that it remains the dominant driver of the dynamics in most situations. Additionally, it is found that for weak and medium field strengths an initially perpendicular field is swept into alignment with the pillar during its dynamical evolution, matching magnetic field observations of the 'Pillars of Creation' in M16 and also some cometary globules. A strong perpendicular magnetic field remains in its initial configuration and also confines the photoevaporation flow into a bar-shaped dense ionized ribbon which partially shields the ionization front and would be readily observable in recombination lines. A simple analytic model is presented to explain the properties of this bright linear structure. These results show that magnetic field strengths in star-forming regions can in principle be significantly constrained by the morphology of structures which form at the borders of H II regions.

Full-orbit and backward Monte Carlo simulation of runaway electrons

NASA Astrophysics Data System (ADS)

Del-Castillo-Negrete, Diego

2017-10-01

High-energy relativistic runaway electrons (RE) can be produced during magnetic disruptions due to electric fields generated during the thermal and current quench of the plasma. Understanding this problem is key for the safe operation of ITER because, if not avoided or mitigated, RE can severely damage the plasma facing components. In this presentation we report on RE simulation efforts centered in two complementary approaches: (i) Full orbit (6-D phase space) relativistic numerical simulations in general (integrable or chaotic) 3-D magnetic and electric fields, including radiation damping and collisions, using the recently developed particle-based Kinetic Orbit Runaway electron Code (KORC) and (ii) Backward Monte-Carlo (MC) simulations based on a recently developed efficient backward stochastic differential equations (BSDE) solver. Following a description of the corresponding numerical methods, we present applications to: (i) RE synchrotron radiation (SR) emission using KORC and (ii) Computation of time-dependent runaway probability distributions, RE production rates, and expected slowing-down and runaway times using BSDE. We study the dependence of these statistical observables on the electric and magnetic field, and the ion effective charge. SR is a key energy dissipation mechanism in the high-energy regime, and it is also extensively used as an experimental diagnostic of RE. Using KORC we study full orbit effects on SR and discuss a recently developed SR synthetic diagnostic that incorporates the full angular dependence of SR, and the location and basic optics of the camera. It is shown that oversimplifying the angular dependence of SR and/or ignoring orbit effects can significantly modify the shape and overestimate the amplitude of the spectra. Applications to DIII-D RE experiments are discussed.

Numerical simulation of fiber and wire array Z-pinches with Trac-II

NASA Astrophysics Data System (ADS)

Reisman, David Barton

Trac-II is a two dimensional axisymmetric resistive MHD code. It simulates all three spatial components (r, z, φ) of the magnetic field and fluid velocity vectors, and the plasma is treated as a single fluid with two temperatures (Te,Ti). In addition, it can optionally include a self-consistent external circuit. Recent modifications to the code include the addition of the 3-T radiation model, a 4-phase (solid- liquid-vapor-plasma) equation of state model (QEOS), a 4- phase electrical/thermal conductivity model, and an implicit solution of poloidal (Bz,Br) magnetic field diffusion. These changes permit a detailed study of fiber and wire array Z-pinches. Specifically, Trac-II is used to study the wire array Z-pinch at the PBFA-Z pulse power generator at Sandia National Laboratory. First, in 1-D we examine the behavior of a single wire in the Z-pinch. Then, using these results as initial radial conditions in 2-D, we investigate the dynamics of wire array configurations in the r-z and r-θ plane. In the r- z plane we examine the growth of the m = 0 or ``sausage'' instability in single wires within the array. In the r-θ plane we examine the merging behavior between neighboring wires. Special emphasis is placed on trying to explain how instability growth affects the performance of the Z-pinch. Lastly, we introduce Trac-III, a 3-D MHD code, and illustrate the m = 1 or ``kink'' instability. We also discuss how Trac-III can be modified to simulate the wire array Z-pinch.

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

PubMed Central

Xiang, Jin Yu; Ponder, Jay W.

2014-01-01

An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies. PMID:25045338

The effect of bed forms on the dynamics of the fluid mud transport: preliminary insights from field observations and numerical simulations

NASA Astrophysics Data System (ADS)

Ozdemir, C. E.; Traykovski, P.

2014-12-01

Understanding the dynamics and the transport mechanisms of fluidmud is crucial to illuminate the details regarding the attenuation in the surface wave energy over muddy seabed and wave-supported gravity-driven mud flows that take place in nearshore environments. Although there is significant progress through theoretical, experimental, and numerical studies, little attention has been drawn to the intricate alteration in the fluidmud transport over bedforms that inherently exist in the actual field conditions. Specifically, interfacial waves at the fluidmud interface were observed in coastal Louisiana as a part of MURI field experiments in 2010. It is also observed that wave attenuation was dominated by viscous processes during laminar flow and attenuation decreased duing the transition to turbulence. Considering the slow growth of shear instability at the interface, bed forms have a critical role to initiate the growth of interfacial waves and the subsequent transition to turbulence. In this study, we investigate the role of bed forms on the dynamics of moderately thin fluidmud layer via large eddy simulations. Three mud viscosity values, based on the field observations, are tested for a 20 centimeters of mud layer over ripples: (i)ν = 1 x 10-3, (ii) ν = 1 x 10-4 , and (iii) ν = 1 x 10-5 . In Case (i), wave energy dissipation is nearly the same as the one over a flat bed. Case (ii) shows that there is a 10 to 20 percent increase in the wave energy dissipation especially at the fluidmud interface. Finally, in Case (iii), we observe the high-energy transitional flow characteristics. In this presentation, we shall also share the detailed analyses of these simulations.

Human Habitation in a Lunar Electric Rover During a 14-Day Field Trial

NASA Technical Reports Server (NTRS)

Litaker, Harry, Jr.; Thompson, Shelby; Howard, Robert, Jr.

2010-01-01

Various military and commercial entities, as well as the National Aeronautics and Space Administration (NASA), have conducted space cabin confinement studies. However, after an extensive literature search, only one study was found using a simulated lunar rover (LUNEX II), under laboratory conditions, with a crew of two for an eighteen day lunar mission. Forty-three years later, NASA human factors engineers conducted a similar study using the Lunar Electric Rover (LER) in a dynamic real-world lunar simulation at the Black Point Lava Flow in Arizona. The objective of the study was to obtain human-in-the-loop performance data on the vehicle s interior volume with respect to human-system interfaces, crew accommodations, and habitation over a 14-day mission. Though part of a larger study including 212 overall operational elements, this paper will discuss only the performance of fifty different daily habitational elements within the confines of the vehicle carried out by two male subjects. Objective timing data and subjective questionnaire data were collected. Results indicate, much like the LUNEX II study, the LER field study suggest that a crew of two was able to maintain a satisfactory performance of tasks throughout the 14-day field trail within a relative small vehicle volume.

Type-III and IV interacting Weyl points

NASA Astrophysics Data System (ADS)

Nissinen, J.; Volovik, G. E.

2017-04-01

3+1-dimensional Weyl fermions in interacting systems are described by effective quasi-relativistic Green's functions parametrized by a 16-element matrix e α μ in an expansion around the Weyl point. The matrix e α μ can be naturally identified as an effective tetrad field for the fermions. The correspondence between the tetrad field and an effective quasi-relativistic metric gμν governing the Weyl fermions allows for the possibility to simulate different classes of metric fields emerging in general relativity in interacting Weyl semimetals. According to this correspondence, there can be four types of Weyl fermions, depending on the signs of the components g 00 and g 00 of the effective metric. In addition to the conventional type-I fermions with a tilted Weyl cone and type-II fermions with an overtilted Weyl cone for g 00 > 0 and, respectively, g 00 > 0 or g 00 < 0, we find additional "type-III" and "type-IV" Weyl fermions with instabilities (complex frequencies) for g 00 < 0 and g 00 > 0 or g 00 < 0, respectively. While the type-I and type-II Weyl points allow us to simulate the black hole event horizon at an interface where g 00 changes sign, the type-III Weyl point leads to effective spacetimes with closed timelike curves.

Detecting vortices in superconductors: Extracting one-dimensional topological singularities from a discretized complex scalar field

DOE PAGES

Phillips, Carolyn L.; Peterka, Tom; Karpeyev, Dmitry; ...

2015-02-20

In type II superconductors, the dynamics of superconducting vortices determine their transport properties. In the Ginzburg-Landau theory, vortices correspond to topological defects in the complex order parameter. Extracting their precise positions and motion from discretized numerical simulation data is an important, but challenging, task. In the past, vortices have mostly been detected by analyzing the magnitude of the complex scalar field representing the order parameter and visualized by corresponding contour plots and isosurfaces. However, these methods, primarily used for small-scale simulations, blur the fine details of the vortices, scale poorly to large-scale simulations, and do not easily enable isolating andmore » tracking individual vortices. In this paper, we present a method for exactly finding the vortex core lines from a complex order parameter field. With this method, vortices can be easily described at a resolution even finer than the mesh itself. The precise determination of the vortex cores allows the interplay of the vortices inside a model superconductor to be visualized in higher resolution than has previously been possible. Finally, by representing the field as the set of vortices, this method also massively reduces the data footprint of the simulations and provides the data structures for further analysis and feature tracking.« less

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

PubMed Central

Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

2016-01-01

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed. PMID:28773773

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants.

PubMed

Ewen, James P; Gattinoni, Chiara; Thakkar, Foram M; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

2016-08-02

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n -hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n -hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n -hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.

Quantitative analysis of dinuclear manganese(II) EPR spectra

NASA Astrophysics Data System (ADS)

Golombek, Adina P.; Hendrich, Michael P.

2003-11-01

A quantitative method for the analysis of EPR spectra from dinuclear Mn(II) complexes is presented. The complex [(Me 3TACN) 2Mn(II) 2(μ-OAc) 3]BPh 4 ( 1) (Me 3TACN= N, N', N''-trimethyl-1,4,7-triazacyclononane; OAc=acetate 1-; BPh 4=tetraphenylborate 1-) was studied with EPR spectroscopy at X- and Q-band frequencies, for both perpendicular and parallel polarizations of the microwave field, and with variable temperature (2-50 K). Complex 1 is an antiferromagnetically coupled dimer which shows signals from all excited spin manifolds, S=1 to 5. The spectra were simulated with diagonalization of the full spin Hamiltonian which includes the Zeeman and zero-field splittings of the individual manganese sites within the dimer, the exchange and dipolar coupling between the two manganese sites of the dimer, and the nuclear hyperfine coupling for each manganese ion. All possible transitions for all spin manifolds were simulated, with the intensities determined from the calculated probability of each transition. In addition, the non-uniform broadening of all resonances was quantitatively predicted using a lineshape model based on D- and r-strain. As the temperature is increased from 2 K, an 11-line hyperfine pattern characteristic of dinuclear Mn(II) is first observed from the S=3 manifold. D- and r-strain are the dominate broadening effects that determine where the hyperfine pattern will be resolved. A single unique parameter set was found to simulate all spectra arising for all temperatures, microwave frequencies, and microwave modes. The simulations are quantitative, allowing for the first time the determination of species concentrations directly from EPR spectra. Thus, this work describes the first method for the quantitative characterization of EPR spectra of dinuclear manganese centers in model complexes and proteins. The exchange coupling parameter J for complex 1 was determined ( J=-1.5±0.3 cm-1; H ex=-2J S1· S2) and found to be in agreement with a previous determination from magnetization. The phenomenon of exchange striction was found to be insignificant for 1.

Three-dimensional particle-in-cell simulations of a plasma jet/cloud streaming across a transverse magnetic field

NASA Astrophysics Data System (ADS)

Voitcu, Gabriel; Echim, Marius

2014-05-01

The dynamics of collisionless plasma jets/clouds in magnetic field configurations typical for the terrestrial magnetotail and frontside magnetosheath is a topic of interest for understanding the physics of the magnetosphere and its interaction with the solar wind. The presence of high-speed jets in the frontside magnetosheath has been recently proved experimentally by Cluster and THEMIS spacecrafts. There is increasing evidence that the bursty bulk flows in the magnetotail have jet-like features. In the present paper we use fully electromagnetic 3D explicit particle-in-cell (PIC) simulations to investigate the interaction of a localized three-dimensional plasma element/jet/cloud with a transverse magnetic field. We consider a plasma jet/cloud that moves in vacuum and perpendicular to an ambient magnetic field. Ampère and Faraday's laws are used to compute the self-consistent electric and magnetic fields on a three-dimensional spatial grid having a step-size of the order of the Debye length and using a time-step that resolves the plasma frequency. The initial magnetic field inside the simulation domain is uniform and the plasma bulk velocity at the beginning of the simulation is normal to the magnetic field direction. The total time scale of the simulation is of the order of few ion Larmor periods. Space and time variations of the plasma parameters and of the electromagnetic field are analyzed and discussed. We emphasize non-MHD effects like the energy-dispersion signatures at the edges of the plasma element, similar to results previously reported by Voitcu and Echim (2012) using test-kinetic simulations. Acknowledgments: Research supported by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 313038/STORM, and a grant of the Romanian Ministry of National Education, CNCS - UEFISCDI, project number PN-II-ID-PCE-2012-4-0418.

Full particle simulations of quasi-perpendicular shocks

NASA Astrophysics Data System (ADS)

Lembège, B.

This tutorial-style review is dedicated to the different strategies and constraints used for analysing the dynamics of a collisionless shocks with full particle simulations. Main results obtained with such simulations can be found in published materials (recent references are provided in this text); these will be only quoted herein in order to illustrate a few aspects of these simulations. Thanks to the large improvement of super computers, full particle simulations reveal to be quite helpful for analyzing in details the dynamics of collisionless shocks. The main characteristics of such codes can be shortly reminded as follows: one resolves the full set of Poisson and Maxwell's equations without any approximation. Two approaches are commonly used for resolving this equation's set, more precisely the space derivatives: (i) the finite difference approach and (ii) the use of FFT's (Fast Fourier Transform). Two advantages of approach (ii) are that FFT's are highly optimized in supercomputers libraries, and these allow to separate all fields components into two groups: the longitudinal electrostatic component El (solution of Poisson equation) and the transverse electromagnetic components Et and Bt solutions of the Maxwell's equations (so called "fields pusher"). Such a separation is quite helpful in the post processing stage necessary for the data analysis, as will be explained in the presentation. both ions and electrons populations are treated as individual finite-size particles and suffer the effects of all fields via the Lorentz force, so called "particle pusher", which is applied to each particle. Because of the large number of particles commonly used, the particle pusher represents the most expensive part of the calculations on which most efforts of optimisation needs to be performed (in terms of "vectorisation" or of "parallelism"). Relativistic effects may be included in this force via the use of particle momemtum. Each particle has three velocity components (vx, vy, vz), but may have 1, 2 or 3 space coordinates (x, y, z) according to the dimension of the code of concern.

Second-Order Fermi Acceleration and Emission in Blazar Jets

NASA Astrophysics Data System (ADS)

Asano, Katsuaki; Takahara, Fumio; Toma, Kenji; Kusunose, Masaaki; Kakuwa, Jun

The second-order Fermi acceleration (Fermi-II) driven by turbulence may be responsible for the electron acceleration in blazar jets. We test this model with time-dependent simulations, adopt it for 1ES 1101-232, and Mrk 421. The Fermi-II model with radial evolution of the electron injection rate and/or diffusion coefficient can reproduce the spectra from the radio to the gamma-ray regime. For Mrk 421, an external radio photon field with a luminosity of 4.9 begin{math} {times} 10 (38) erg s (-1) is required to agree with the observed GeV flux. The temporal variability of the diffusion coefficient or injection rate causes flare emission. The observed synchronicity of X-ray and TeV flares implies a decrease of the magnetic field in the flaring source region.

NON-LTE INVERSIONS OF THE Mg ii h and k AND UV TRIPLET LINES

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

De la Cruz Rodríguez, Jaime; Leenaarts, Jorrit; Ramos, Andrés Asensio

The Mg ii h and k lines are powerful diagnostics for studying the solar chromosphere. They have become particularly popular with the launch of the Interface Region Imaging Spectrograph ( IRIS ) satellite, and a number of studies that include these lines have lead to great progress in understanding chromospheric heating, in many cases thanks to the support from 3D MHD simulations. In this study, we utilize another approach to analyze observations: non-LTE inversions of the Mg ii h and k and UV triplet lines including the effects of partial redistribution. Our inversion code attempts to construct a model atmospheremore » that is compatible with the observed spectra. We have assessed the capabilities and limitations of the inversions using the FALC atmosphere and a snapshot from a 3D radiation-MHD simulation. We find that Mg ii h and k allow reconstructing a model atmosphere from the middle photosphere to the transition region. We have also explored the capabilities of a multi-line/multi-atom setup, including the Mg ii h and k, the Ca ii 854.2 nm, and the Fe i 630.25 lines to recover the full stratification of physical parameters, including the magnetic field vector, from the photosphere to the chromosphere. Finally, we present the first inversions of observed IRIS spectra from quiet-Sun, plage, and sunspot, with very promising results.« less

A model of nitrous oxide evolution from soil driven by rainfall events. I - Model structure and sensitivity. II - Model applications

NASA Technical Reports Server (NTRS)

Changsheng, LI; Frolking, Steve; Frolking, Tod A.

1992-01-01

Simulations of N2O and CO2 emissions from soils were conducted with a rain-event driven, process-oriented model (DNDC) of nitrogen and carbon cycling processes in soils. The magnitude and trends of simulated N2O (or N2O + N2) and CO2 emissions were consistent with the results obtained in field experiments. The successful simulation of these emissions from the range of soil types examined demonstrates that the DNDC will be a useful tool for the study of linkages among climate, soil-atmosphere interactions, land use, and trace gas fluxes.

Practical Functional Approach to Quality Assessment in Subtitling: "Pocahontas II--Case Study"

ERIC Educational Resources Information Center

Hussain, Alaa Eddin; Khuddro, Ahmad

2016-01-01

The present research work deals with subtitling errors encountered by simulators and proof-readers. The resultant work is of significant contribution to problem decision makings in the field of quality assessment of audiovisual translation (AVT). The outcome of this paper is the result of accumulated working experience in this domain. The relevant…

The Effect of Simulated Altitude on the Visual Fields of Glaucoma Patients and the Elderly

DTIC Science & Technology

1991-01-01

certification policy does not appear to put pilots or passengers with glaucoma at risk for disease progression. Under short-term exposure to mild hypoxia, we...9. Kobrick JL, Crohn E, Shukitt B, Houston CS, Sutton JR, Cymerman A. Operation Everest II: lack of an effect of extreme altitude on visual contrast

Turbulent magnetic fluctuations in laboratory reconnection

NASA Astrophysics Data System (ADS)

Von Stechow, Adrian; Grulke, Olaf; Klinger, Thomas

2016-07-01

The role of fluctuations and turbulence is an important question in astrophysics. While direct observations in space are rare and difficult dedicated laboratory experiments provide a versatile environment for the investigation of magnetic reconnection due to their good diagnostic access and wide range of accessible plasma parameters. As such, they also provide an ideal chance for the validation of space plasma reconnection theories and numerical simulation results. In particular, we studied magnetic fluctuations within reconnecting current sheets for various reconnection parameters such as the reconnection rate, guide field, as well as plasma density and temperature. These fluctuations have been previously interpreted as signatures of current sheet plasma instabilities in space and laboratory systems. Especially in low collisionality plasmas these may provide a source of anomalous resistivity and thereby contribute a significant fraction of the reconnection rate. We present fluctuation measurements from two complementary reconnection experiments and compare them to numerical simulation results. VINETA.II (Greifswald, Germany) is a cylindrical, high guide field reconnection experiment with an open field line geometry. The reconnecting current sheet has a three-dimensional structure that is predominantly set by the magnetic pitch angle which results from the superposition of the guide field and the in-plane reconnecting field. Within this current sheet, high frequency magnetic fluctuations are observed that correlate well with the local current density and show a power law spectrum with a spectral break at the lower hybrid frequency. Their correlation lengths are found to be extremely short, but propagation is nonetheless observed with high phase velocities that match the Whistler dispersion. To date, the experiment has been run with an external driving field at frequencies higher than the ion cyclotron frequency f_{ci}, which implies that the EMHD framework applies. Recent machine upgrades allow the inclusion of ion dynamics by reducing the drive frequency below f_{ci}. Two numerical codes (EMHD and hybrid, respectively) have been developed at the Max Planck Institute for solar physics and are used to investigate instability mechanisms and scaling laws for the observed results. MRX (PPPL. Princeton) is a zero to medium guide field, toroidal reconnection experiment. Despite the differing plasma parameters, the qualitative magnetic fluctuation behavior (amplitude profiles, spectra and propagation properties) is comparable to VINETA.II. Results from a new measurement campaign at several different guide fields provides partial overlap with VINETA.II guide field ratios and thereby extends the accessible parameter space of our studies.

EMERGENCE OF GRANULAR-SIZED MAGNETIC BUBBLES THROUGH THE SOLAR ATMOSPHERE. II. NON-LTE CHROMOSPHERIC DIAGNOSTICS AND INVERSIONS

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

Rodríguez, Jaime de la Cruz; Hansteen, Viggo; Ortiz, Ada

Magnetic flux emergence into the outer layers of the Sun is a fundamental mechanism for releasing energy into the chromosphere and the corona. In this paper, we study the emergence of granular-sized flux concentrations and the structuring of the corresponding physical parameters and atmospheric diagnostics in the upper photosphere and in the chromosphere. We make use of a realistic 3D MHD simulation of the outer layers of the Sun to study the formation of the Ca ii 8542 line. We also derive semi-empirical 3D models from non-LTE inversions of our observations. These models contain information on the line-of-sight stratifications ofmore » temperature, velocity, and the magnetic field. Our analysis explains the peculiar Ca ii 8542 Å profiles observed in the flux emerging region. Additionally, we derive detailed temperature and velocity maps describing the ascent of a magnetic bubble from the photosphere to the chromosphere. The inversions suggest that, in active regions, granular-sized bubbles emerge up to the lower chromosphere where the existing large-scale field hinders their ascent. We report hints of heating when the field reaches the chromosphere.« less

Modelling the impact of climatic conditions and plant species on the nitrogen release from mulch of legumes at the soil surface

NASA Astrophysics Data System (ADS)

Gaudinat, Germain; Lorin, Mathieu; Valantin-morison, Muriel; Garnier, Patricia

2015-04-01

Cover crops provide multiple services to the agro ecosystem. Among them, the use of legumes as cover crop is one of the solutions for limiting the use of herbicides, mineral fertilizers, and insecticides. However, the dynamic of mineralization is difficult to understand because of the difficulty of measuring nitrogen release from mulch in field. Indeed, residues are degraded at the soil surface as mulch, while the nitrogen uptake by the main crop occurred simultaneously in the soil. This work aims to study the dynamics of nitrogen mineralization from legume residues through i) the use of a model able to describe the physical and biological dynamic of mulch and ii) a data set from a field experiment of intercropping systems "oilseed rape-legumes" from different species (grass pea, lentil, Berseem clover, field pea, vetch). The objective of the simulations is to identify the variations of expected quantities of nitrogen from different legumes. The soil-plant model of mulch decomposition PASTIS-Mulch was used to determine the nitrogen supply from mulch available for rapeseed. These simulation results were compared to the data collected in the experimental field of Grignon (France). We performed analyzes of biochemical and physical characteristics of legume residues and monitored the evolution of mulches (moisture, density, cover surface, biomass) in fields. PASTIS simulations of soil temperature, soil moisture, mulch humidity and mulch decomposition were close to the experimental results. The PASTIS model was suitable to simulate the dynamic of legume mulches in the case of "rape - legume" associations. The model simulated nitrogen restitution of aerial and root parts. We found a more rapid nitrogen release by grass pea than other species. Vetch released less nitrogen than the other species. The scenarios for climate conditions were : i) a freezing in December that causes the destruction of plants, or a destruction by herbicide in March, ii) a strong or a weak rainy spring. Climatic conditions had a strong impact on the simulated release of nitrogen. Nitrogen supply was higher when degradation begun early with a rainy spring. Conversely, the degradation was lower when the degradation started late with a dry spring. Root release was less sensitive to climate and most of the nitrogen in the roots returned to the soil in a few weeks. The impact of "species" on the decomposition was explained not only by their chemical properties but also by their physical properties. The climatic conditions had different effects according to the species.

Parallel methodology to capture cyclic variability in motored engines

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

Ameen, Muhsin M.; Yang, Xiaofeng; Kuo, Tang-Wei

2016-07-28

Numerical prediction of of cycle-to-cycle variability (CCV) in SI engines is extremely challenging for two key reasons: (i) high-fidelity methods such as large eddy simulation (LES) are require to accurately capture the in-cylinder turbulent flowfield, and (ii) CCV is experienced over long timescales and hence the simulations need to be performed for hundreds of consecutive cycles. In this study, a new methodology is proposed to dissociate this long time-scale problem into several shorter time-scale problems, which can considerably reduce the computational time without sacrificing the fidelity of the simulations. The strategy is to perform multiple single-cycle simulations in parallel bymore » effectively perturbing the simulation parameters such as the initial and boundary conditions. It is shown that by perturbing the initial velocity field effectively based on the intensity of the in-cylinder turbulence, the mean and variance of the in-cylinder flowfield is captured reasonably well. Adding perturbations in the initial pressure field and the boundary pressure improves the predictions. It is shown that this new approach is able to give accurate predictions of the flowfield statistics in less than one-tenth of time required for the conventional approach of simulating consecutive engine cycles.« less

Inversion of oceanic constituents in case I and II waters with genetic programming algorithms.

PubMed

Chami, Malik; Robilliard, Denis

2002-10-20

A stochastic inverse technique based on agenetic programming (GP) algorithm was developed toinvert oceanic constituents from simulated data for case I and case II water applications. The simulations were carried out with the Ordre Successifs Ocean Atmosphere (OSOA) radiative transfer model. They include the effects of oceanic substances such as algal-related chlorophyll, nonchlorophyllous suspended matter, and dissolved organic matter. The synthetic data set also takes into account the directional effects of particles through a variation of their phase function that makes the simulated data realistic. It is shown that GP can be successfully applied to the inverse problem with acceptable stability in the presence of realistic noise in the data. GP is compared with neural network methodology for case I waters; GP exhibits similar retrieval accuracy, which is greater than for traditional techniques such as band ratio algorithms. The application of GP to real satellite data [a Sea-viewing Wide Field-of-view Sensor (SeaWiFS)] was also carried out for case I waters as a validation. Good agreement was obtained when GP results were compared with the SeaWiFS empirical algorithm. For case II waters the accuracy of GP is less than 33%, which remains satisfactory, at the present time, for remote-sensing purposes.

Parallel Higher-order Finite Element Method for Accurate Field Computations in Wakefield and PIC Simulations

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

Candel, A.; Kabel, A.; Lee, L.

Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell)more » approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.« less

Partial Validation of Multibody Program to Optimize Simulated Trajectories II (POST II) Parachute Simulation With Interacting Forces

NASA Technical Reports Server (NTRS)

Raiszadeh, Ben; Queen, Eric M.

2002-01-01

A capability to simulate trajectories Of Multiple interacting rigid bodies has been developed. This capability uses the Program to Optimize Simulated Trajectories II (POST II). Previously, POST II had the ability to simulate multiple bodies without interacting forces. The current implementation is used for the Simulation of parachute trajectories, in which the parachute and suspended bodies can be treated as rigid bodies. An arbitrary set of connecting lines can be included in the model and are treated as massless spring-dampers. This paper discusses details of the connection line modeling and results of several test cases used to validate the capability.

The Evaporation and Survival of Cluster Galaxies’ Coronae. II. The Effectiveness of Anisotropic Thermal Conduction and Survival of Stripped Galactic Tails

NASA Astrophysics Data System (ADS)

Vijayaraghavan, Rukmani; Sarazin, Craig

2017-10-01

We simulate anisotropic thermal conduction between the intracluster medium (ICM) and the hot coronal interstellar medium (ISM) gas in cluster galaxies. In Paper I, we simulated the evaporation of the hot ISM due to isotropic (possibly saturated) conduction between the ISM and ICM. We found that hot coronae evaporate on ˜ {10}2 {Myr} timescales, significantly shorter than the ˜ {10}3 {Myr} gas loss times due to ram pressure stripping. No tails of stripped gas are formed. This is in tension with the observed ubiquity and implied longevity of compact X-ray coronae and stripped ISM tails, and requires the suppression of evaporation, possibly due to magnetic fields and anisotropic conduction. We perform a series of wind tunnel simulations similar to that in Paper I, now including ISM and ICM magnetic fields. We simulate the effect of anisotropic conduction for a range of extreme magnetic field configurations: parallel and perpendicular to the ICM wind, and continuous and completely disjointed between the ISM and ICM. We find that when conduction is anisotropic, gas loss due to evaporation is severely reduced; the overall gas loss rates with and without anisotropic conduction do not differ by more than 10%-20%. Magnetic fields also prevent stripped tails from evaporating in the ICM by shielding, and providing few pathways for heat transport between the ICM and ISM. The morphology of stripped tails and magnetic fields in the tails and wakes of galaxies are sensitive to the initial magnetic field configuration.

A plasma model for reversed field pinch circuit design

NASA Astrophysics Data System (ADS)

Johnston, J. W.

1981-03-01

A plasma model has been developed for use in the design of circuits for reversed field pinch experiments. The magnetic field is assumed to evolve through a given series of relaxed states with the plasma resistivity specified as a function of time. At any instant the magnetic field configuration is determined by the field energy and the toroidal flux. If the Bessel function model is chosen as the relaxed state then the magnetic helicity can be used as an alternative to the magnetic energy without altering the results. Simulations of discharges on ZETA and ETA BETA II are presented. By suitable choices of the relaxed field configuration and plasma resistivity it is possible to obtain close agreement with the experimental waveforms. Application to the proposed RFX device is discussed.

Clustering, randomness and regularity in cloud fields. I - Theoretical considerations. II - Cumulus cloud fields

NASA Technical Reports Server (NTRS)

Weger, R. C.; Lee, J.; Zhu, Tianri; Welch, R. M.

1992-01-01

The current controversy existing in reference to the regularity vs. clustering in cloud fields is examined by means of analysis and simulation studies based upon nearest-neighbor cumulative distribution statistics. It is shown that the Poisson representation of random point processes is superior to pseudorandom-number-generated models and that pseudorandom-number-generated models bias the observed nearest-neighbor statistics towards regularity. Interpretation of this nearest-neighbor statistics is discussed for many cases of superpositions of clustering, randomness, and regularity. A detailed analysis is carried out of cumulus cloud field spatial distributions based upon Landsat, AVHRR, and Skylab data, showing that, when both large and small clouds are included in the cloud field distributions, the cloud field always has a strong clustering signal.

Quantifying substructures in Hubble Frontier Field clusters: comparison with ΛCDM simulations

DOE PAGES

Mohammed, Irshad; Saha, Prasenjit; Williams, Liliya L. R.; ...

2016-04-13

The Hubble Frontier Fields (HFF) are six clusters of galaxies, all showing indications of recent mergers, which have recently been observed for lensed images. As such they are the natural laboratories to study the merging history of galaxy clusters. In this work, we explore the 2D power spectrum of the mass distributionmore » $$P_{\\rm M}(k)$$ as a measure of substructure. We compare $$P_{\\rm M}(k)$$ of these clusters (obtained using strong gravitational lensing) to that of $$\\Lambda$$CDM simulated clusters of similar mass. In order to compute lensing $$P_{\\rm M}(k)$$, we produced free-form lensing mass reconstructions of HFF clusters, without any light traces mass (LTM) assumption. Moreover, the inferred power at small scales tends to be larger if (i)~the cluster is at lower redshift, and/or (ii)~there are deeper observations and hence more lensed images. In contrast, lens reconstructions assuming LTM show higher power at small scales even with fewer lensed images; it appears the small scale power in the LTM reconstructions is dominated by light information, rather than the lensing data. The average lensing derived $$P_{\\rm M}(k)$$ shows lower power at small scales as compared to that of simulated clusters at redshift zero, both dark-matter only and hydrodynamical. The possible reasons are: (i)~the available strong lensing data are limited in their effective spatial resolution on the mass distribution, (ii)~HFF clusters have yet to build the small scale power they would have at $$z\\sim 0$$, or (iii)~simulations are somehow overestimating the small scale power.« less

Effect of the metal environment on the ferromagnetic interaction in the Co-NC-W pairs of octacyanotungstate(V)-Cobalt(II) three-dimensional networks.

PubMed

Clima, Sergiu; Hendrickx, Marc F A; Chibotaru, Liviu F; Soncini, Alessandro; Mironov, Vladimir; Ceulemans, Arnout

2007-04-02

State of the art CASSCF and CASPT2 calculations have been performed to elucidate the nature of ferromagnetism of CoII-NC-WV pairs in the three-dimensional compound [[WV(CN)2]2[(micro-CN)4CoII(H2O)2]3.4H2O]n, which has been recently synthesized and investigated by a number of experimental techniques (Herrera, J. M.; Bleuzen, A.; Dromzée, Y.; Julve, M.; Lloret, F.; Verdaguer, M. Inorg. Chem. 2003, 42, 7052-7059). In this network, the Co ions are in the high-spin (S = 3/2) state, while the single unpaired electron on the W centers occupies the lowest orbital of the dz2 type of the 5d shell. In agreement with the suggestion made by Herrera et al., we find that the ferromagnetism is due to a certain occupation scheme of the orbitals from the parent octahedral t2g shell on CoII sites, in which the orbital accommodating the unpaired electron is orthogonal to the dz2 orbitals of the surrounding W ions. We investigate the stabilization of such an orbital configuration on the Co sites and find that it cannot be achieved in the ground state of isolated mononuclear fragments [CoII(NC)4(OH2)2]2- for any conformations of the coordinated water molecules and Co-N-C bond angles. On the other hand, it is stabilized by the interaction of the complex with neighboring W ions, which are simulated here by effective potentials. The calculated exchange coupling constants for the CoII-NC-WV binuclear fragments are in reasonable agreement with the measured Curie-Weiss constant for this compound. As additional evidence for the inferred electronic configuration on the Co sites, the ligand-field transitions, the temperature-dependent magnetic susceptibility, and the field-dependent low-temperature magnetization, simulated ab initio for the mononuclear Co fragments, are in agreement with the available data for another compound [WIV[(micro-CN)4-CoII(H2O)2]2.4H2O]n containing diamagnetic W and high-spin Co ions in an isostructural environment.

Retrieving Storm Electric Fields from Aircrfaft Field Mill Data: Part II: Applications

NASA Technical Reports Server (NTRS)

Koshak, William; Mach, D. M.; Christian H. J.; Stewart, M. F.; Bateman M. G.

2006-01-01

The Lagrange multiplier theory developed in Part I of this study is applied to complete a relative calibration of a Citation aircraft that is instrumented with six field mill sensors. When side constraints related to average fields are used, the Lagrange multiplier method performs well in computer simulations. For mill measurement errors of 1 V m(sup -1) and a 5 V m(sup -1) error in the mean fair-weather field function, the 3D storm electric field is retrieved to within an error of about 12%. A side constraint that involves estimating the detailed structure of the fair-weather field was also tested using computer simulations. For mill measurement errors of 1 V m(sup -l), the method retrieves the 3D storm field to within an error of about 8% if the fair-weather field estimate is typically within 1 V m(sup -1) of the true fair-weather field. Using this type of side constraint and data from fair-weather field maneuvers taken on 29 June 2001, the Citation aircraft was calibrated. Absolute calibration was completed using the pitch down method developed in Part I, and conventional analyses. The resulting calibration matrices were then used to retrieve storm electric fields during a Citation flight on 2 June 2001. The storm field results are encouraging and agree favorably in many respects with results derived from earlier (iterative) techniques of calibration.

The High-Excitation Planetary Nebula NCG 246: Optical and Near-Ultraviolet Observations and Two-dimensional Numerical Models

NASA Technical Reports Server (NTRS)

Szentgyorgyi, Andrew; Raymond, John; Franco, Jose; Villaver, Eva; Lopez-Martin, Luis

2003-01-01

We have imaged the planetary nebula (PN) NGC 246 in the near-ultraviolet wavelengths [Ne v] 342.6 nm, the Bowen fluorescence line of 0 111 at 344.4 nm, and a nearby line-free region centered on 338.6 nm, as well as H(alpha), [O III] 500.7 nm, and [S II] 673.0 and 671.5 nm. Imaging in the 344.4 nm line is necessary to deconvolve contamination of the [Ne v] images by O III 342.9 nm. The emission from the shell and inner parts of the nebula is detected in [Ne v]. The radial profiles of the [Ne v] brightness decrease with radius from the exciting star, indicating that the bulk of the emission from this ion is due to the hard UV stellar radiation field, with a (probably) marginal contribution from collisional ionization in a shock between the PN shell and the interstellar medium (ISM). In contrast, the radial profiles of the emission in H(alpha), [0 III] 500.7 nm, and [S II] are flatter and peak at the location of the shell. The emission of [S II] probably traces the interaction of the PN with the ambient ISM. We also present two-dimensional numerical simulations for this PN-ISM interaction. The simulations consider the stellar motion with respect to the ambient ISM, with a velocity of 85 km/s , and include the time evolution of the wind parameters and UV radiation field from the progenitor star.

NOM degradation during river infiltration: effects of the climate variables temperature and discharge.

PubMed

Diem, Samuel; Rudolf von Rohr, Matthias; Hering, Janet G; Kohler, Hans-Peter E; Schirmer, Mario; von Gunten, Urs

2013-11-01

Most peri-alpine shallow aquifers fed by rivers are oxic and the drinking water derived by riverbank filtration is generally of excellent quality. However, observations during past heat waves suggest that water quality may be affected by climate change due to effects on redox processes such as aerobic respiration, denitrification, reductive dissolution of manganese(III/IV)- and iron(III)(hydr)oxides that occur during river infiltration. To assess the dependence of these redox processes on the climate-related variables temperature and discharge, we performed periodic and targeted (summer and winter) field sampling campaigns at the Thur River, Switzerland, and laboratory column experiments simulating the field conditions. Typical summer and winter field conditions could be successfully simulated by the column experiments. Dissolved organic matter (DOM) was found not to be a major electron donor for aerobic respiration in summer and the DOM consumption did not reveal a significant correlation with temperature and discharge. It is hypothesized that under summer conditions, organic matter associated with the aquifer material (particulate organic matter, POM) is responsible for most of the consumption of dissolved oxygen (DO), which was the most important electron acceptor in both the field and the column system. For typical summer conditions at temperatures >20 °C, complete depletion of DO was observed in the column system and in a piezometer located only a few metres from the river. Both in the field system and the column experiments, nitrate acted as a redox buffer preventing the release of manganese(II) and iron(II). For periodic field observations over five years, DO consumption showed a pronounced temperature dependence (correlation coefficient r = 0.74) and therefore a seasonal pattern, which seemed to be mostly explained by the temperature dependence of the calculated POM consumption (r = 0.7). The river discharge was found to be highly and positively correlated with DO consumption (r = 0.85), suggesting an enhanced POM input during flood events. This high correlation could only be observed for the low-temperature range (T < 15 °C). For temperatures >15 °C, DO consumption was already high (almost complete) and the impact of discharge could not be resolved. Based on our results, we estimate the risk for similar river-infiltration systems to release manganese(II) and iron(II) to be low during future average summer conditions. However, long-lasting heat waves might lead to a consumption of the nitrate buffer, inducing a mobilization of manganese and iron. Copyright © 2013 Elsevier Ltd. All rights reserved.

Three-dimensional, time-dependent simulation of free-electron lasers with planar, helical, and elliptical undulators

NASA Astrophysics Data System (ADS)

Freund, H. P.; van der Slot, P. J. M.; Grimminck, D. L. A. G.; Setija, I. D.; Falgari, P.

2017-02-01

Free-electron lasers (FELs) have been built ranging in wavelength from long-wavelength oscillators using partial wave guiding through ultraviolet through hard x-ray that are either seeded or start from noise. In addition, FELs that produce different polarizations of the output radiation ranging from linear through elliptic to circular polarization are currently under study. In this paper, we develop a three-dimensional, time-dependent formulation that is capable of modeling this large variety of FEL configurations including different polarizations. We employ a modal expansion for the optical field, i.e., a Gaussian expansion with variable polarization for free-space propagation. This formulation uses the full Newton-Lorentz force equations to track the particles through the optical and magnetostatic fields. As a result, arbitrary three-dimensional representations for different undulator configurations are implemented, including planar, helical, and elliptical undulators. In particular, we present an analytic model of an APPLE-II undulator to treat arbitrary elliptical polarizations, which is used to treat general elliptical polarizations. To model oscillator configurations, and allow propagation of the optical field outside the undulator and interact with optical elements, we link the FEL simulation with the optical propagation code OPC. We present simulations using the APPLE-II undulator model to produce elliptically polarized output radiation, and present a detailed comparison with recent experiments using a tapered undulator configuration at the Linac Coherent Light Source. Validation of the nonlinear formation is also shown by comparison with experimental results obtained in the Sorgente Pulsata Auto-amplificata di Radiazione Coerente SASE FEL experiment at ENEA Frascati, a seeded tapered amplifier experiment at Brookhaven National Laboratory, and the 10 kW upgrade oscillator experiment at the Thomas Jefferson National Accelerator Facility.

Folding Free Energy Landscape of the Decapeptide Chignolin

NASA Astrophysics Data System (ADS)

Dou, Xianghua; Wang, Jihua

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

Two-dimensional Radiative Magnetohydrodynamic Simulations of Partial Ionization in the Chromosphere. II. Dynamics and Energetics of the Low Solar Atmosphere

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

Martínez-Sykora, Juan; Pontieu, Bart De; Hansteen, Viggo H.

2017-09-20

We investigate the effects of interactions between ions and neutrals on the chromosphere and overlying corona using 2.5D radiative MHD simulations with the Bifrost code. We have extended the code capabilities implementing ion–neutral interaction effects using the generalized Ohm’s law, i.e., we include the Hall term and the ambipolar diffusion (Pedersen dissipation) in the induction equation. Our models span from the upper convection zone to the corona, with the photosphere, chromosphere, and transition region partially ionized. Our simulations reveal that the interactions between ionized particles and neutral particles have important consequences for the magnetothermodynamics of these modeled layers: (1) ambipolarmore » diffusion increases the temperature in the chromosphere; (2) sporadically the horizontal magnetic field in the photosphere is diffused into the chromosphere, due to the large ambipolar diffusion; (3) ambipolar diffusion concentrates electrical currents, leading to more violent jets and reconnection processes, resulting in (3a) the formation of longer and faster spicules, (3b) heating of plasma during the spicule evolution, and (3c) decoupling of the plasma and magnetic field in spicules. Our results indicate that ambipolar diffusion is a critical ingredient for understanding the magnetothermodynamic properties in the chromosphere and transition region. The numerical simulations have been made publicly available, similar to previous Bifrost simulations. This will allow the community to study realistic numerical simulations with a wider range of magnetic field configurations and physics modules than previously possible.« less

Two-dimensional Radiative Magnetohydrodynamic Simulations of Partial Ionization in the Chromosphere. II. Dynamics and Energetics of the Low Solar Atmosphere

NASA Astrophysics Data System (ADS)

Martínez-Sykora, Juan; De Pontieu, Bart; Carlsson, Mats; Hansteen, Viggo H.; Nóbrega-Siverio, Daniel; Gudiksen, Boris V.

2017-09-01

We investigate the effects of interactions between ions and neutrals on the chromosphere and overlying corona using 2.5D radiative MHD simulations with the Bifrost code. We have extended the code capabilities implementing ion-neutral interaction effects using the generalized Ohm’s law, I.e., we include the Hall term and the ambipolar diffusion (Pedersen dissipation) in the induction equation. Our models span from the upper convection zone to the corona, with the photosphere, chromosphere, and transition region partially ionized. Our simulations reveal that the interactions between ionized particles and neutral particles have important consequences for the magnetothermodynamics of these modeled layers: (1) ambipolar diffusion increases the temperature in the chromosphere; (2) sporadically the horizontal magnetic field in the photosphere is diffused into the chromosphere, due to the large ambipolar diffusion; (3) ambipolar diffusion concentrates electrical currents, leading to more violent jets and reconnection processes, resulting in (3a) the formation of longer and faster spicules, (3b) heating of plasma during the spicule evolution, and (3c) decoupling of the plasma and magnetic field in spicules. Our results indicate that ambipolar diffusion is a critical ingredient for understanding the magnetothermodynamic properties in the chromosphere and transition region. The numerical simulations have been made publicly available, similar to previous Bifrost simulations. This will allow the community to study realistic numerical simulations with a wider range of magnetic field configurations and physics modules than previously possible.

Dynamic evolution of Rayleigh-Taylor bubbles from sinusoidal, W-shaped, and random perturbations

NASA Astrophysics Data System (ADS)

Zhou, Zhi-Rui; Zhang, You-Sheng; Tian, Bao-Lin

2018-03-01

Implicit large eddy simulations of two-dimensional Rayleigh-Taylor instability at different density ratios (i.e., Atwood number A =0.05 , 0.5, and 0.9) are conducted to investigate the late-time dynamics of bubbles. To produce a flow field full of bounded, semibounded, and chaotic bubbles, three problems with distinct perturbations are simulated: (I) periodic sinusoidal perturbation, (II) isolated W-shaped perturbation, and (III) random short-wave perturbations. The evolution of height h , velocity v , and diameter D of the (dominant) bubble with time t are formulated and analyzed. In problem I, during the quasisteady stage, the simulations confirm Goncharov's prediction of the terminal speed v∞=Fr√{A g λ /(1 +A ) } , where Fr=1 /√{3 π } . Moreover, the diameter D at this stage is found to be proportional to the initial perturbation wavelength λ as D ≈λ . This differed from Daly's simulation result of D =λ (1 +A )/2 . In problem II, a W-shaped perturbation is designed to produce a bubble environment similar to that of chaotic bubbles in problem III. We obtain a similar terminal speed relationship as above, but Fr is replaced by Frw≈0.63 . In problem III, the simulations show that h grows quadratically with the bubble acceleration constant α ≡h /(A g t2)≈0.05 , and D expands self-similarly with a steady aspect ratio β ≡D /h ≈(1 +A )/2 , which differs from existing theories. Therefore, following the mechanism of self-similar growth, we derive a relationship of β =4 α (1 +A ) /Frw2 to relate the evolution of chaotic bubbles in problem III to that of semibounded bubbles in problem II. The validity of this relationship highlights the fact that the dynamics of chaotic bubbles in problem III are similar to the semibounded isolated bubbles in problem II, but not to that of bounded periodic bubbles in problem I.

I. Jet Formation and Evolution Due to 3D Magnetic Reconnection

NASA Astrophysics Data System (ADS)

González-Avilés, J. J.; Guzmán, F. S.; Fedun, V.; Verth, G.; Shelyag, S.; Regnier, S.

2018-04-01

Using simulated data-driven, 3D resistive MHD simulations of the solar atmosphere, we show that 3D magnetic reconnection may be responsible for the formation of jets with the characteristics of Type II spicules. We numerically model the photosphere-corona region using the C7 equilibrium atmosphere model. The initial magnetic configuration is a 3D potential magnetic field, extrapolated up to the solar corona region from a dynamic realistic simulation of the solar photospheric magnetoconvection model that mimics the quiet-Sun. In this case, we consider a uniform and constant value of the magnetic resistivity of 12.56 Ω m. We have found that the formation of the jet depends on the Lorentz force, which helps to accelerate the plasma upward. Analyzing various properties of the jet dynamics, we found that the jet structure shows a Doppler shift close to regions with high vorticity. The morphology, the upward velocity covering a range up to 130 km s‑1, and the timescale formation of the structure between 60 and 90 s, are similar to those expected for Type II spicules.

Characterising large-scale structure with the REFLEX II cluster survey

NASA Astrophysics Data System (ADS)

Chon, Gayoung

2016-10-01

We study the large-scale structure with superclusters from the REFLEX X-ray cluster survey together with cosmological N-body simulations. It is important to construct superclusters with criteria such that they are homogeneous in their properties. We lay out our theoretical concept considering future evolution of superclusters in their definition, and show that the X-ray luminosity and halo mass functions of clusters in superclusters are found to be top-heavy, different from those of clusters in the field. We also show a promising aspect of using superclusters to study the local cluster bias and mass scaling relation with simulations.

Energy storage and dissipation in the magnetotail during substorms. I - Particle simulations. II - MHD simulations

NASA Technical Reports Server (NTRS)

Winglee, R. M.; Steinolfson, R. S.

1993-01-01

2D electromagnetic particle simulations are used to investigate the dynamics of the tail during development of substorms under the influence of the pressure in the magnetospheric boundary layer and the dawn-to-dusk electric field. It is shown that pressure pulses result in thinning of the tail current sheet as the magnetic field becomes pinched near the region where the pressure pulse is applied. The pinching leads to the tailward flow of the current sheet plasma and the eventual formation and injection of a plasmoid. Surges in the dawn-to-dusk electric field cause plasma on the flanks to convect into the center of the current sheet, thereby thinning the current sheet. The pressure in the magnetospheric boundary laser is coupled to the dawn-to-dusk electric field through the conductivity of the tail. Changes in the predicted evolution of the magnetosphere during substorms due to changes in the resistivity are investigated under the assumption that MHD theory provides a suitable representation of the global or large-scale evolution of the magnetotail to changes in the solar wind and to reconnection at the dayside magnetopause. It is shown that the overall evolution of the magnetosphere is about the same for three different resistivity distributions with plasmoid formation and ejection in each case.

Time-dependent Models for Blazar Emission with the Second-order Fermi Acceleration

NASA Astrophysics Data System (ADS)

Asano, Katsuaki; Takahara, Fumio; Kusunose, Masaaki; Toma, Kenji; Kakuwa, Jun

2014-01-01

The second-order Fermi acceleration (Fermi-II) driven by turbulence may be responsible for the electron acceleration in blazar jets. We test this model with time-dependent simulations. The hard electron spectrum predicted by the Fermi-II process agrees with the hard photon spectrum of 1ES 1101-232. For other blazars that show softer spectra, the Fermi-II model requires radial evolution of the electron injection rate and/or diffusion coefficient in the outflow. Such evolutions can yield a curved electron spectrum, which can reproduce the synchrotron spectrum of Mrk 421 from the radio to the X-ray regime. The photon spectrum in the GeV energy range of Mrk 421 is hard to fit with a synchrotron self-Compton model. However, if we introduce an external radio photon field with a luminosity of 4.9 × 1038 erg s-1, GeV photons are successfully produced via inverse Compton scattering. The temporal variability of the diffusion coefficient or injection rate causes flare emission. The observed synchronicity of X-ray and TeV flares implies a decrease of the magnetic field in the flaring source region.

Strong-pinning regimes by spherical inclusions in anisotropic type-II superconductors

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

Willa, R.; Koshelev, A. E.; Sadovskyy, I. A.

2017-11-27

The current-carrying capacity of type-II superconductors is decisively determined by how well material defect structures can immobilize vortex lines. In order to gain deeper insights into intrinsic pinning mechanisms, we have explored the case of vortex trapping by randomly distributed spherical inclusions using large-scale simulations of the time-dependent Ginzburg-Landau equations. We find that for a small density of particles having diameters of two coherence lengths, the vortex lattice preserves its structure and the critical current jc decays with the magnetic field following a power-law B-a with a ~ 0:66, which is consistent with predictions of strong pinning theory. For highermore » density of particles and/or larger inclusions, the lattice becomes progressively more disordered and the exponent smoothly decreases down to a ~ 0:3. At high magnetic fields, all inclusions capture a vortex and the critical current decays faster than B-1 as would be expected by theory. In the case of larger inclusions with diameter of four coherence length, the magnetic-field dependence of the critical current is strongly affected by the ability of inclusions to capture multiple vortex lines. We found that at small densities, the fraction of inclusions trapping two vortex lines rapidly grows within narrow field range leading to a shallow peak in jc(B)-dependence within this range. With increasing inclusion density, this peak transforms into a plateau, which then smooths out. Using the insights gained from simulations, we determine the limits of applicability of strong pinning theory and provide different routes to describe vortex pinning beyond those bounds.« less

Strong-pinning regimes by spherical inclusions in anisotropic type-II superconductors

NASA Astrophysics Data System (ADS)

Willa, R.; Koshelev, A. E.; Sadovskyy, I. A.; Glatz, A.

2018-01-01

The current-carrying capacity of type-II superconductors is decisively determined by how well material defect structures can immobilize vortex lines. In order to gain deeper insights into the fundamental pinning mechanisms, we have explored the case of vortex trapping by randomly distributed spherical inclusions using large-scale simulations of the time-dependent Ginzburg-Landau equations. We find that for a small density of particles having diameters of two coherence lengths, the vortex lattice preserves its structure and the critical current j c decays with the magnetic field following a power-law {B}-α with α ≈ 0.66, which is consistent with predictions of strong-pinning theory. For a higher density of particles and/or larger inclusions, the lattice becomes progressively more disordered and the exponent smoothly decreases down to α ≈ 0.3. At high magnetic fields, all inclusions capture a vortex and the critical current decays faster than {B}-1 as would be expected by theory. In the case of larger inclusions with a diameter of four coherence lengths, the magnetic-field dependence of the critical current is strongly affected by the ability of inclusions to capture multiple vortex lines. We found that at small densities, the fraction of inclusions trapping two vortex lines rapidly grows within narrow field range leading to a peak in j c(B)-dependence within this range. With increasing inclusion density, this peak transforms into a plateau, which then smooths out. Using the insights gained from simulations, we determine the limits of applicability of strong-pinning theory and provide different routes to describe vortex pinning beyond those bounds.

The influence of magnetic field on the cold neutral medium mass fraction and its alignment with density structures

NASA Astrophysics Data System (ADS)

Villagran, M. A.; Gazol, A.

2018-06-01

To contribute to the understanding of the magnetic field's influence on the segregation of cold neutral medium (CNM) in the solar neighbourhood we analyse magnetohydrodynamic simulations that include the main physical characteristics of the local neutral atomic interstellar medium. The simulations have a continuous solenoidal Fourier forcing in a periodic box of 100 pc per side and an initial uniform magnetic field (B_0) with intensities ranging between ˜0.4 and ˜8 μG. Our main results are as follows. (i) The CNM mass fraction diminishes with the increase in magnetic field intensity. (ii) There is a preferred alignment between CNM structures and B in all our B0 range but the preference weakens as B0 increases. It is worth noticing that this preference is also present in two-dimensional projections making an extreme angle (0 or π / 2) with respect to B_0 and it is only lost for the strongest magnetic field when the angle of projection is perpendicular to B_0. (iii) The aforementioned results are prevalent despite the inclusion of self-gravity in our continuously forced simulations with a mean density similar to the average value of the solar neighbourhood. (iv) Given a fixed B0 and slightly higher mean densities, up to double, the effects of self-gravity are still not qualitatively significant.

Prospects of detection of the first sources with SKA using matched filters

NASA Astrophysics Data System (ADS)

Ghara, Raghunath; Choudhury, T. Roy; Datta, Kanan K.; Mellema, Garrelt; Choudhuri, Samir; Majumdar, Suman; Giri, Sambit K.

2018-05-01

The matched filtering technique is an efficient method to detect H ii bubbles and absorption regions in radio interferometric observations of the redshifted 21-cm signal from the epoch of reionization and the Cosmic Dawn. Here, we present an implementation of this technique to the upcoming observations such as the SKA1-low for a blind search of absorption regions at the Cosmic Dawn. The pipeline explores four dimensional parameter space on the simulated mock visibilities using a MCMC algorithm. The framework is able to efficiently determine the positions and sizes of the absorption/H ii regions in the field of view.

Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.

PubMed

Verbaro, Daniel; Ghosh, Indrajit; Nau, Werner M; Schweitzer-Stenner, Reinhard

2010-12-30

Structural preferences in the unfolded state of peptides determined by molecular dynamics still contradict experimental data. A remedy in this regard has been suggested by MD simulations with an optimized Amber force field ff03* ( Best, R. Hummer, G. J. Phys. Chem. B 2009 , 113 , 9004 - 9015 ). The simulations yielded a statistical coil distribution for alanine which is at variance with recent experimental results. To check the validity of this distribution, we investigated the peptide H-A(5)W-OH, which with the exception of the additional terminal tryptophan is analogous to the peptide used to optimize the force fields ff03*. Electronic circular dichroism, vibrational circular dichroism, and infrared spectroscopy as well as J-coupling constants obtained from NMR experiments were used to derive the peptide's conformational ensemble. Additionally, Förster resonance energy transfer between the terminal chromophores of the fluorescently labeled peptide analogue H-Dbo-A(5)W-OH was used to determine its average length, from which the end-to-end distance of the unlabeled peptide was estimated. Qualitatively, the experimental (3)J(H(N),C(α)), VCD, and ECD indicated a preference of alanine for polyproline II-like conformations. The experimental (3)J(H(N),C(α)) for A(5)W closely resembles the constants obtained for A(5). In order to quantitatively relate the conformational distribution of A(5) obtained with the optimized AMBER ff03* force field to experimental data, the former was used to derive a distribution function which expressed the conformational ensemble as a mixture of polyproline II, β-strand, helical, and turn conformations. This model was found to satisfactorily reproduce all experimental J-coupling constants. We employed the model to calculate the amide I' profiles of the IR and vibrational circular dichroism spectrum of A(5)W, as well as the distance between the two terminal peptide carbonyls. This led to an underestimated negative VCD couplet and an overestimated distance between terminal carbonyl groups. In order to more accurately account for the experimental data, we changed the distribution parameters based on results recently obtained for the alanine-based tripeptides. The final model, which satisfactorily reproduced amide I' profiles, J-coupling constant, and the end-to-end distance of A(5)W, reinforces alanine's high structural preference for polyproline II. Our results suggest that distributions obtained from MD simulations suggesting a statistical coil-like distribution for alanine are still based on insufficiently accurate force fields.

Quantum Dot Gate Three-State and Nonvolatile Memory Field-Effect Transistors Using a ZnS/ZnMgS/ZnS Heteroepitaxial Stack as a Tunnel Insulator on Silicon-on-Insulator Substrates

NASA Astrophysics Data System (ADS)

Suarez, Ernesto; Chan, Pik-Yiu; Lingalugari, Murali; Ayers, John E.; Heller, Evan; Jain, Faquir

2013-11-01

This paper describes the use of II-VI lattice-matched gate insulators in quantum dot gate three-state and flash nonvolatile memory structures. Using silicon-on-insulator wafers we have fabricated GeO x -cladded Ge quantum dot (QD) floating gate nonvolatile memory field-effect transistor devices using ZnS-Zn0.95Mg0.05S-ZnS tunneling layers. The II-VI heteroepitaxial stack is nearly lattice-matched and is grown using metalorganic chemical vapor deposition on a silicon channel. This stack reduces the interface state density, improving threshold voltage variation, particularly in sub-22-nm devices. Simulations using self-consistent solutions of the Poisson and Schrödinger equations show the transfer of charge to the QD layers in three-state as well as nonvolatile memory cells.

Zero-field splitting in the isoelectronic aqueous Gd(III) and Eu(II) complexes from a first principles analysis

NASA Astrophysics Data System (ADS)

Khan, S.; Peters, V.; Kowalewski, J.; Odelius, M.

2018-03-01

The zero-field splitting (ZFS) of the ground state octet in aqueous Eu(II) and Gd(III) solutions was investigated through multi- configurational quantum chemical calculations and ab initio molecular dynamics (AIMD) simulations. Investigation of the ZFS of the lanthanide ions is essential to understand the electron spin dynamics and nuclear spin relaxation around paramagnetic ions and consequently the mechanisms underlying applications like magnetic resonance imaging. We found by comparing clusters at identical geometries but different metallic centres that there is not a simple relationship for their ZFS, in spite of the complexes being isoelectronic - each containing 7 unpaired f electrons. Through sampling it was established that inclusion of the first hydration shell has a dominant (over 90 %) influence on the ZFS. Extended sampling of aqueous Gd(III) showed that the 2 nd order spin Hamiltonian formalism is valid and that the rhombic ZFS component is decisive.

Dual-element transducer with phase-inversion for wide depth of field in high-frequency ultrasound imaging.

PubMed

Jeong, Jong Seob

2014-08-05

In high frequency ultrasound imaging (HFUI), the quality of focusing is deeply related to the length of the depth of field (DOF). In this paper, a phase-inversion technique implemented by a dual-element transducer is proposed to enlarge the DOF. The performance of the proposed method was numerically demonstrated by using the ultrasound simulation program called Field-II. A simulated dual-element transducer was composed of a disc- and an annular-type elements, and its aperture was concavely shaped to have a confocal point at 6 mm. The area of each element was identical in order to provide same intensity at the focal point. The outer diameters of the inner and the outer elements were 2.1 mm and 3 mm, respectively. The center frequency of each element was 40 MHz and the f-number (focal depth/aperture size) was two. When two input signals with 0° and 180° phases were applied to inner and outer elements simultaneously, a multi-focal zone was generated in the axial direction. The total -6 dB DOF, i.e., sum of two -6 dB DOFs in the near and far field lobes, was 40% longer than that of the conventional single element transducer. The signal to noise ratio (SNR) was increased by about two times, especially in the far field. The point and cyst phantom simulation were conducted and their results were identical to that of the beam pattern simulation. Thus, the proposed scheme may be a potential method to improve the DOF and SNR in HFUI.

Influence of the Convection Electric Field Models on Predicted Plasmapause Positions During Magnetic Storms

NASA Technical Reports Server (NTRS)

Pierrard, V.; Khazanov, G.; Cabrera, J.; Lemaire, J.

2007-01-01

In the present work, we determine how three well documented models of the magnetospheric electric field, and two different mechanisms proposed for the formation of the plasmapause influence the radial distance, the shape and the evolution of the plasmapause during the geomagnetic storms of 28 October 2001 and of 17 April 2002. The convection electric field models considered are: Mcllwain's E51) electric field model, Volland-Stern's model and Weimer's statistical model compiled from low-Earth orbit satellite data. The mechanisms for the formation of the plasmapause to be tested are: (i) the MHD theory where the plasmapause should correspond to the last-closed- equipotential (LCE) or last-closed-streamline (LCS), if the E-field distribution is stationary or time-dependent respectively; (ii) the interchange mechanism where the plasmapause corresponds to streamlines tangent to a Zero-Parallel-Force surface where the field-aligned plasma distribution becomes convectively unstable during enhancements of the E-field intensity in the nightside local time sector. The results of the different time dependent simulations are compared with concomitant EUV observations when available. The plasmatails or plumes observed after both selected geomagnetic storms are predicted in all simulations and for all E-field models. However, their shapes are quite different depending on the E-field models and the mechanisms that are used. Despite the partial success of the simulations to reproduce plumes during magnetic storms and substorms, there remains a long way to go before the detailed structures observed in the EUV observations during periods of geomagnetic activity can be accounted for very precisely by the existing E-field models. Furthermore, it cannot be excluded that the mechanisms currently identified to explain the formation of "Carpenter's knee" during substorm events, will', have to be revised or complemented in the cases of geomagnetic storms.

Direct comparison of neutral velocity distribution measurements and simulations in the vicinity of an absorbing boundary oblique to a magnetic field

NASA Astrophysics Data System (ADS)

Henriquez, Miguel F.; Thompson, Derek S.; Keniley, Shane; Curreli, Davide; Steinberger, Thomas E.; Caron, David D.; Jemiolo, Andrew J.; McLaughlin, Jacob W.; Dufor, Mikal T.; Neal, Luke A.; Scime, Earl E.; Siddiqui, M. Umair

2017-10-01

Plasma-boundary interactions are strongly affected by the sheath and presheath structures that form near the boundary surface. Recent measurements have observed ion transport across magnetic field lines in regions where the surface is oblique to the background magnetic field (ψ =74°) . In these boundary regions, charge exchange collisions may provide a mechanism through which neutral particles interact with the long distance presheath electric field. We report efforts to directly compare Boltzmann and particle-in-cell simulations with 3D neutral velocity distribution functions (NVDFs) using laser induced fluorescence (LIF) in a magnetized plasma boundary region. We present a novel LIF method for measuring Ar-II metastable velocity distributions, in which we observe the 738.6014 nm fluorescence (2p3 to 1s4 in Paschen's notation), that results from absorption of the 706.9167 nm (1s5 metastable to 2p3) pump laser, providing neutral temperatures and flows. We additionally describe electrostatic probe measurements in the same region.

Electric field induced microstructures in thin films on physicochemically heterogeneous and patterned substrates.

PubMed

Srivastava, Samanvaya; Reddy, P Dinesh Sankar; Wang, Cindy; Bandyopadhyay, Dipankar; Sharma, Ashutosh

2010-05-07

We study by nonlinear simulations the electric field induced pattern formation in a thin viscous film resting on a topographically or chemically patterned substrate. The thin film microstructures can be aligned to the substrate patterns within a window of parameters where the spinodal length scale of the field induced instability is close to the substrate periodicity. We investigate systematically the change in the film morphology and order when (i) the substrate pattern periodicity is varied at a constant film thickness and (ii) the film thickness is varied at a constant substrate periodicity. Simulations show two distinct pathway of evolution when the substrate-topography changes from protrusions to cavities. The isolated substrate defects generate locally ordered ripplelike structures distinct from the structures on a periodically patterned substrate. In the latter case, film morphology is governed by a competition between the pattern periodicity and the length scale of instability. Relating the thin film morphologies to the underlying substrate pattern has implications for field induced patterning and robustness of inter-interface pattern transfer, e.g., coding-decoding of information printed on a substrate.

A new RF window designed for high-power operation in an S-band LINAC RF system

NASA Astrophysics Data System (ADS)

Joo, Youngdo; Kim, Seung-Hwan; Hwang, Woonha; Ryu, Jiwan; Roh, Sungjoo

2016-09-01

A new RF window is designed for high-power operation at the Pohang Light Source-II (PLSII) S-band linear accelerator (LINAC) RF system. In order to reduce the strength of the electric field component perpendicular to the ceramic disk, which is commonly known as the main cause of most discharge breakdowns in ceramic disk, we replace the pill-box type cavity in the conventional RF window with an overmoded cavity. The overmoded cavity is coupled with input and output waveguides through dual side-wall coupling irises to reduce the electric field strength at the iris and the number of possible mode competitions. The finite-difference time-domain (FDTD) simulation, CST MWS, was used in the design process. The simulated maximum electric field component perpendicular to the ceramic for the new RF window is reduced by an order of magnitude compared with taht for the conventional RF window, which holds promise for stable high-power operation.

Software for Engineering Simulations of a Spacecraft

NASA Technical Reports Server (NTRS)

Shireman, Kirk; McSwain, Gene; McCormick, Bernell; Fardelos, Panayiotis

2005-01-01

Spacecraft Engineering Simulation II (SES II) is a C-language computer program for simulating diverse aspects of operation of a spacecraft characterized by either three or six degrees of freedom. A functional model in SES can include a trajectory flight plan; a submodel of a flight computer running navigational and flight-control software; and submodels of the environment, the dynamics of the spacecraft, and sensor inputs and outputs. SES II features a modular, object-oriented programming style. SES II supports event-based simulations, which, in turn, create an easily adaptable simulation environment in which many different types of trajectories can be simulated by use of the same software. The simulation output consists largely of flight data. SES II can be used to perform optimization and Monte Carlo dispersion simulations. It can also be used to perform simulations for multiple spacecraft. In addition to its generic simulation capabilities, SES offers special capabilities for space-shuttle simulations: for this purpose, it incorporates submodels of the space-shuttle dynamics and a C-language version of the guidance, navigation, and control components of the space-shuttle flight software.

Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2003-02-01

We present a continuum approach for efficient and accurate calculation of reaction field forces and energies in classical molecular-dynamics (MD) simulations of proteins in water. The derivation proceeds in two steps. First, we reformulate the electrostatics of an arbitrarily shaped molecular system, which contains partially charged atoms and is embedded in a dielectric continuum representing the water. A so-called fuzzy partition is used to exactly decompose the system into partial atomic volumes. The reaction field is expressed by means of dipole densities localized at the atoms. Since these densities cannot be calculated analytically for general systems, we introduce and carefully analyze a set of approximations in a second step. These approximations allow us to represent the dipole densities by simple dipoles localized at the atoms. We derive a system of linear equations for these dipoles, which can be solved numerically by iteration. After determining the two free parameters of our approximate method we check its quality by comparisons (i) with an analytical solution, which is available for a perfectly spherical system, (ii) with forces obtained from a MD simulation of a soluble protein in water, and (iii) with reaction field energies of small molecules calculated by a finite difference method.

Charged particle transport in magnetic fields in EGSnrc.

PubMed

Malkov, V N; Rogers, D W O

2016-07-01

To accurately and efficiently implement charged particle transport in a magnetic field in EGSnrc and validate the code for the use in phantom and ion chamber simulations. The effect of the magnetic field on the particle motion and position is determined using one- and three-point numerical integrations of the Lorentz force on the charged particle and is added to the condensed history calculation performed by the EGSnrc PRESTA-II algorithm. The code is tested with a Fano test adapted for the presence of magnetic fields. The code is compatible with all EGSnrc based applications, including egs++. Ion chamber calculations are compared to experimental measurements and the effect of the code on the efficiency and timing is determined. Agreement with the Fano test's theoretical value is obtained at the 0.1% level for large step-sizes and in magnetic fields as strong as 5 T. The NE2571 dose calculations achieve agreement with the experiment within 0.5% up to 1 T beyond which deviations up to 1.2% are observed. Uniform air gaps of 0.5 and 1 mm and a misalignment of the incoming photon beam with the magnetic field are found to produce variations in the normalized dose on the order of 1%. These findings necessitate a clear definition of all experimental conditions to allow for accurate Monte Carlo simulations. It is found that ion chamber simulation times are increased by only 38%, and a 10 × 10 × 6 cm(3) water phantom with (3 mm)(3) voxels experiences a 48% increase in simulation time as compared to the default EGSnrc with no magnetic field. The incorporation of the effect of the magnetic fields in EGSnrc provides the capability to calculate high accuracy ion chamber and phantom doses for the use in MRI-radiation systems. Further, the effect of apparently insignificant experimental details is found to be accentuated by the presence of the magnetic field.

Molecular Dynamics Simulations of Protein-Ligand Complexes in Near Physiological Conditions

NASA Astrophysics Data System (ADS)

Wambo, Thierry Oscar

Proteins are important molecules for their key functions. However, under certain circumstances, the function of these proteins needs to be regulated to keep us healthy. Ligands are small molecules often used to modulate the function of proteins. The binding affinity is a quantitative measure of how strong the ligand will modulate the function of the protein: a strong binding affinity will highly impact the performance of the protein. It becomes clear that it is critical to have appropriate techniques to accurately compute the binding affinity. The most difficult task in computer simulations is how to efficiently sample the space spanned by the ligand during the binding process. In this work, we have developed some schemes to compute the binding affinity of a ligand to a protein, and of a metal ion to a protein. Application of these techniques to some complexes yield results in agreement with experimental values. These methods are a brute force approach and make no assumption other than that the complexes are governed by the force field used. Specifically, we computed the free energy of binding between (1) human carbonic anhydrase II and the drug acetazolamide (hcaII-AZM), (2) human carbonic anhydrase II and the zinc ion (hcaII-Zinc), and (3) beta-lactoglobulin and five fatty acids complexes (BLG-FAs). We found the following free energies of binding in unit of kcal/mol: -12.96 +/-2.44 (-15.74) for hcaII-Zinc complex, -5.76+/-0.76 (-5.57) for BLG-OCA , -4.44+/-1.08 (-5.22) for BLG-DKA,-6.89+/-1.25 (-7.24) for BLG-DAO, -8.57+/-0.82 (-8.14) for BLG-MYR, -8.99+/-0.87 (-8.72) for BLG-PLM, and -11.87+/-1.8 (-10.8) for hcaII-AZM. The values inside the parentheses are experimental results. The simulations and quantitative analysis of each system provide interesting insights into the interactions between each entity and helps us to better understand the dynamics of these systems.

Theoretical investigation of GaAsBi/GaAsN tunneling field-effect transistors with type-II staggered tunneling junction

NASA Astrophysics Data System (ADS)

Wang, Yibo; Liu, Yan; Han, Genquan; Wang, Hongjuan; Zhang, Chunfu; Zhang, Jincheng; Hao, Yue

2017-06-01

We investigate GaAsBi/GaAsN system for the design of type-II staggered hetero tunneling field-effect transistor (hetero-TFET). Strain-symmetrized GaAsBi/GaAsN with effective lattice match to GaAs exhibits a type-II band lineup, and the effective bandgap EG,eff at interface is significantly reduced with the incorporation of Bi and N elements. The band-to-band tunneling (BTBT) rate and drive current of GaAsBi/GaAsN hetero-TFETs are boosted due to the utilizing of the type-II staggered tunneling junction with the reduced EG,eff. Numerical simulation shows that the drive current and subthreshold swing (SS) characteristics of GaAsBi/GaAsN hetero-TFETs are remarkably improved by increasing Bi and N compositions. The dilute content GaAs0.85Bi0.15/GaAs0.92N0.08 staggered hetero-nTFET achieves 7.8 and 550 times higher ION compared to InAs and In0.53Ga0.47As homo-TFETs, respectively, at the supply voltage of 0.3 V. GaAsBi/GaAsN heterostructure is a potential candidate for high performance TFET.

Structure, magnetic properties, polarized neutron diffraction, and theoretical study of a copper(II) cubane.

PubMed

Aronica, Christophe; Chumakov, Yurii; Jeanneau, Erwann; Luneau, Dominique; Neugebauer, Petr; Barra, Anne-Laure; Gillon, Béatrice; Goujon, Antoine; Cousson, Alain; Tercero, Javier; Ruiz, Eliseo

2008-01-01

The paper reports the synthesis, X-ray and neutron diffraction crystal structures, magnetic properties, high field-high frequency EPR (HF-EPR), spin density and theoretical description of the tetranuclear CuII complex [Cu4L4] with cubane-like structure (LH2=1,1,1-trifluoro-7-hydroxy-4-methyl-5-aza-hept-3-en-2-one). The simulation of the magnetic behavior gives a predominant ferromagnetic interaction J1 (+30.5 cm(-1)) and a weak antiferromagnetic interaction J2 (-5.5 cm(-1)), which correspond to short and long Cu-Cu distances, respectively, as evidence from the crystal structure [see formulate in text]. It is in agreement with DFT calculations and with the saturation magnetization value of an S=2 ground spin state. HF-EPR measurements at low temperatures (5 to 30 K) provide evidence for a negative axial zero-field splitting parameter D (-0.25+/-0.01 cm(-1)) plus a small rhombic term E (0.025+/-0.001 cm(-1), E/D = 0.1). The experimental spin distribution from polarized neutron diffraction is mainly located in the basal plane of the CuII ion with a distortion of yz-type for one CuII ion. Delocalization on the ligand (L) is observed but to a smaller extent than expected from DFT calculations.

Spectrum simulation in DTSA-II.

PubMed

Ritchie, Nicholas W M

2009-10-01

Spectrum simulation is a useful practical and pedagogical tool. Particularly with complex samples or trace constituents, a simulation can help to understand the limits of the technique and the instrument parameters for the optimal measurement. DTSA-II, software for electron probe microanalysis, provides both easy to use and flexible tools for simulating common and less common sample geometries and materials. Analytical models based on (rhoz) curves provide quick simulations of simple samples. Monte Carlo models based on electron and X-ray transport provide more sophisticated models of arbitrarily complex samples. DTSA-II provides a broad range of simulation tools in a framework with many different interchangeable physical models. In addition, DTSA-II provides tools for visualizing, comparing, manipulating, and quantifying simulated and measured spectra.

Achieving Vibration Stability of the NSLS-II Hard X-ray Nanoprobe Beamline

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

Simos, N.; Chu, Y. N.; Broadbent, A.

2010-08-30

The Hard X-ray Nanoprobe (HXN) Beamline of National Synchrotron Light Source II (NSLS-lI) requires high levels of stability in order to achieve the desired instrument resolution. To ensure that the design of the endstation helps meet the stringent criteria and that natural and cultural vibration is mitigated both passively and actively, a comprehensive study complimentary to the design process has been undertaken. Vibration sources that have the potential to disrupt sensitive experiments such as wind, traffic and NSLS II operating systems have been studied using state of the art simulations and an array of field data. Further, final stage vibrationmore » isolation principles have been explored in order to be utilized in supporting endstation instruments. This paper presents results of the various study aspects and their influence on the HXN design optimization.« less

Design, development, and application of LANDIS-II, a spatial landscape simulation model with flexible temporal and spatial resolution

Treesearch

Robert M. Scheller; James B. Domingo; Brian R. Sturtevant; Jeremy S. Williams; Arnold Rudy; Eric J. Gustafson; David J. Mladenoff

2007-01-01

We introduce LANDIS-II, a landscape model designed to simulate forest succession and disturbances. LANDIS-II builds upon and preserves the functionality of previous LANDIS forest landscape simulation models. LANDIS-II is distinguished by the inclusion of variable time steps for different ecological processes; our use of a rigorous development and testing process used...

Development of fine-resolution analyses and expanded large-scale forcing properties. Part II: Scale-awareness and application to single-column model experiments

DOE PAGES

Feng, Sha; Vogelmann, Andrew M.; Li, Zhijin; ...

2015-01-20

Fine-resolution three-dimensional fields have been produced using the Community Gridpoint Statistical Interpolation (GSI) data assimilation system for the U.S. Department of Energy’s Atmospheric Radiation Measurement Program (ARM) Southern Great Plains region. The GSI system is implemented in a multi-scale data assimilation framework using the Weather Research and Forecasting model at a cloud-resolving resolution of 2 km. From the fine-resolution three-dimensional fields, large-scale forcing is derived explicitly at grid-scale resolution; a subgrid-scale dynamic component is derived separately, representing subgrid-scale horizontal dynamic processes. Analyses show that the subgrid-scale dynamic component is often a major component over the large-scale forcing for grid scalesmore » larger than 200 km. The single-column model (SCM) of the Community Atmospheric Model version 5 (CAM5) is used to examine the impact of the grid-scale and subgrid-scale dynamic components on simulated precipitation and cloud fields associated with a mesoscale convective system. It is found that grid-scale size impacts simulated precipitation, resulting in an overestimation for grid scales of about 200 km but an underestimation for smaller grids. The subgrid-scale dynamic component has an appreciable impact on the simulations, suggesting that grid-scale and subgrid-scale dynamic components should be considered in the interpretation of SCM simulations.« less

Vortices at the magnetic equator generated by hybrid Alfvén resonant waves

NASA Astrophysics Data System (ADS)

Hiraki, Yasutaka

2015-01-01

We performed three-dimensional magnetohydrodynamic simulations of shear Alfvén waves in a full field line system with magnetosphere-ionosphere coupling and plasma non-uniformities. Feedback instability of the Alfvén resonant modes showed various nonlinear features under the field line cavities: (i) a secondary flow shear instability occurs at the magnetic equator, (ii) trapping of the ionospheric Alfvén resonant modes facilitates deformation of field-aligned current structures, and (iii) hybrid Alfvén resonant modes grow to cause vortices and magnetic oscillations around the magnetic equator. Essential features in the initial brightening of auroral arc at substorm onsets could be explained by the dynamics of Alfvén resonant modes, which are the nature of the field line system responding to a background rapid change.

Characterization of naturally occurring radioactive materials in Libyan oil pipe scale using a germanium detector and Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Habib, A. S.; Shutt, A. L.; Regan, P. H.; Matthews, M. C.; Alsulaiti, H.; Bradley, D. A.

2014-02-01

Radioactive scale formation in various oil production facilities is acknowledged to pose a potential significant health and environmental issue. The presence of such an issue in Libyan oil fields was recognized as early as 1998. The naturally occurring radioactive materials (NORM) involved in this matter are radium isotopes (226Ra and 228Ra) and their decay products, precipitating into scales formed on the surfaces of production equipment. A field trip to a number of onshore Libyan oil fields has indicated the existence of elevated levels of specific activity in a number of locations in some of the more mature oil fields. In this study, oil scale samples collected from different parts of Libya have been characterized using gamma spectroscopy through use of a well shielded HPGe spectrometer. To avoid potential alpha-bearing dust inhalation and in accord with safe working practices at this University, the samples, contained in plastic bags and existing in different geometries, are not permitted to be opened. MCNP, a Monte Carlo simulation code, is being used to simulate the spectrometer and the scale samples in order to obtain the system absolute efficiency and then to calculate sample specific activities. The samples are assumed to have uniform densities and homogeneously distributed activity. Present results are compared to two extreme situations that were assumed in a previous study: (i) with the entire activity concentrated at a point on the sample surface proximal to the detector, simulating the sample lowest activity, and; (ii) with the entire activity concentrated at a point on the sample surface distal to the detector, simulating the sample highest activity.

Global Simulation of Bioenergy Crop Productivity: Analytical Framework and Case Study for Switchgrass

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

Kang, Shujiang; Kline, Keith L; Nair, S. Surendran

A global energy crop productivity model that provides geospatially explicit quantitative details on biomass potential and factors affecting sustainability would be useful, but does not exist now. This study describes a modeling platform capable of meeting many challenges associated with global-scale agro-ecosystem modeling. We designed an analytical framework for bioenergy crops consisting of six major components: (i) standardized natural resources datasets, (ii) global field-trial data and crop management practices, (iii) simulation units and management scenarios, (iv) model calibration and validation, (v) high-performance computing (HPC) simulation, and (vi) simulation output processing and analysis. The HPC-Environmental Policy Integrated Climate (HPC-EPIC) model simulatedmore » a perennial bioenergy crop, switchgrass (Panicum virgatum L.), estimating feedstock production potentials and effects across the globe. This modeling platform can assess soil C sequestration, net greenhouse gas (GHG) emissions, nonpoint source pollution (e.g., nutrient and pesticide loss), and energy exchange with the atmosphere. It can be expanded to include additional bioenergy crops (e.g., miscanthus, energy cane, and agave) and food crops under different management scenarios. The platform and switchgrass field-trial dataset are available to support global analysis of biomass feedstock production potential and corresponding metrics of sustainability.« less

Micromagnetic simulation of energy consumption and excited eigenmodes in elliptical nanomagnetic switches

NASA Astrophysics Data System (ADS)

Carlotti, G.; Madami, M.; Gubbiotti, G.; Tacchi, S.

2014-02-01

Sub-200 nm patterned magnetic dots are key elements for the design of magnetic switches, memory cells or elementary units of nanomagnetic logic circuits. In this paper, we analyse by micromagnetic simulations the magnetization reversal, the dissipated energy and the excited spin eigenmodes in bistable magnetic switches, consisting of elliptical nanodots with 100×60 nm lateral dimensions. Two different strategies for reversal are considered and the relative results compared: (i) the irreversible switching obtained by the application of an external field along the easy axis, in the direction opposite to the initial magnetization; (ii) the precessional switching accomplished by the application of a short magnetic field pulse, oriented perpendicular to the initial magnetization direction. The obtained results are discussed in terms of deviation from the macrospin behavior, energy dissipation and characteristics of the spectrum of spin eigenmodes excited during the magnetization reversal process.

Loop propensity of the sequence YKGQP from staphylococcal nuclease: implications for the folding of nuclease.

PubMed

Patel, Sunita; Sasidhar, Yellamraju U

2007-10-01

Recently we performed molecular dynamics (MD) simulations on the folding of the hairpin peptide DTVKLMYKGQPMTFR from staphylococcal nuclease in explicit water. We found that the peptide folds into a hairpin conformation with native and nonnative hydrogen-bonding patterns. In all the folding events observed in the folding of the hairpin peptide, loop formation involving the region YKGQP was an important event. In order to trace the origins of the loop propensity of the sequence YKGQP, we performed MD simulations on the sequence starting from extended, polyproline II and native type I' turn conformations for a total simulation length of 300 ns, using the GROMOS96 force field under constant volume and temperature (NVT) conditions. The free-energy landscape of the peptide YKGQP shows minima corresponding to loop conformation with Tyr and Pro side-chain association, turn and extended conformational forms, with modest free-energy barriers separating the minima. To elucidate the role of Gly in facilitating loop formation, we also performed MD simulations of the mutated peptide YKAQP (Gly --> Ala mutation) under similar conditions starting from polyproline II conformation for 100 ns. Two minima corresponding to bend/turn and extended conformations were observed in the free-energy landscape for the peptide YKAQP. The free-energy barrier between the minima in the free-energy landscape of the peptide YKAQP was also modest. Loop conformation is largely sampled by the YKGQP peptide, while extended conformation is largely sampled by the YKAQP peptide. We also explain why the YKGQP sequence samples type II turn conformation in these simulations, whereas the sequence as part of the hairpin peptide DTVKLMYKGQPMTFR samples type I' turn conformation both in the X-ray crystal structure and in our earlier simulations on the folding of the hairpin peptide. We discuss the implications of our results to the folding of the staphylococcal nuclease. Copyright (c) 2007 European Peptide Society and John Wiley & Sons, Ltd.

Simulation of a Congress at the Chair of Biology II in Bioengineering

NASA Astrophysics Data System (ADS)

Naranjo, A. V.; Reznichenco, V.; López, N.; Hernández, R.; Bajinay, S.

2007-11-01

This work has been developed in the Chair of Biology II, the curricular contents of which correspond to Human Anatomy. This subject is taught in the second semester of the second year of studies in Bioengineering. Our main objective is that the students attending the course may integrate the syllabus contents of Anatomy with those of other subjects in the career. Ever since 1998 we have organized a congress named Congreso Intracátedra de Biología II (Intra Chair Congress on Biology II). This is the last assignment in the semester and is compulsory for regular students of the subject. It consists in simulating a scientific congress with international characteristics. The guidelines for the congress are made known to the students at the beginning of the semester. In groups of up to three members, the students must undertake a work that relates aspects of Anatomy with Bioengineering. Students are expected to investigate on diagnostic and/or therapeutic technology in order to write a paper that must be accepted in advance of the event. The presentation of the work must be made through PowerPoint. The originality of the research work done and the wide range of topics selected are surprising. Problems are tackled from the standpoints both of the various medical fields and of bioengineering despite the fact that they are just students of the second year in Bioengineering.

Rigid Polyurethane Foam (RPF) Technology for Countermines (Sea) Program Phase II

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

WOODFIN,RONALD L.; FAUCETT,DAVID L.; HANCE,BRADLEY G.

This Phase II report documents the results of one subtask initiated under the joint Department of Energy (DOE)/Department of Defense (DoD) Memorandum of Understanding (MOU) for Countermine Warfare. The development of Rigid Polyurethane Foams for neutralization of mines and barriers in amphibious assault was the objective of the tasking. This phase of the program concentrated on formation of RPF in water, explosive mine simulations, and development of foam and fabric pontoons. Field experimentation was done primarily at the Energetic Materials Research and Testing Center (EMRTC) of the New Mexico Institute of Mining and Technology, Socorro, NM between February 1996 andmore » September 1998.« less

Subgrain Rotation Recrystallization During Shearing: Insights From Full-Field Numerical Simulations of Halite Polycrystals

NASA Astrophysics Data System (ADS)

Gomez-Rivas, E.; Griera, A.; Llorens, M.-G.; Bons, P. D.; Lebensohn, R. A.; Piazolo, S.

2017-11-01

We present, for the first time, results of full-field numerical simulations of subgrain rotation recrystallization of halite polycrystals during simple shear deformation. The series of simulations show how microstructures are controlled by the competition between (i) grain size reduction by creep by dislocation glide and (ii) intracrystalline recovery encompassing subgrain coarsening by coalescence through rotation and alignment of the lattices of neighboring subgrains. A strong grain size reduction develops in models without intracrystalline recovery, as a result of the formation of high-angle grain boundaries when local misorientations exceed 15°. The activation of subgrain coarsening associated with recovery decreases the stored strain energy and results in grains with low intracrystalline heterogeneities. However, this type of recrystallization does not significantly modify crystal preferred orientations. Lattice orientation and grain boundary maps reveal that this full-field modeling approach is able to successfully reproduce the evolution of dry halite microstructures from laboratory deformation experiments, thus opening new opportunities in this field of research. We demonstrate how the mean subgrain boundary misorientations can be used to estimate the strain accommodated by dislocation glide using a universal scaling exponent of about 2/3, as predicted by theoretical models. In addition, this strain gauge can be potentially applied to estimate the intensity of intracrystalline recovery, associated with temperature, using quantitative crystallographic analyses in areas with strain gradients.

Insights into unbound-bound states of GPR142 receptor in a membrane-aqueous system using molecular dynamics simulations.

PubMed

Kaushik, Aman Chandra; Sahi, Shakti

2018-05-01

G protein coupled receptors (GPCRs) are source machinery in signal transduction pathways and being one of the major therapeutic targets play a significant in drug discovery. GPR142, an orphan GPCR, has been implicated in the regulation of insulin, thereby having a crucial role in Type II diabetes management. Deciphering of the structures of orphan, GPCRs (O-GPCRs) offer better prospects for advancements in research in ion translocation and transduction of extracellular signals. As the crystallographic structure of GPR142 is not available in PDB, therefore, threading and ab initio-based approaches were used for 3D modeling of GPR142. Molecular dynamic simulations (900 ns) were performed on the 3D model of GPR142 and complexes of GPR142 with top five hits, obtained through virtual screening, embedded in lipid bilayer with aqueous system using OPLS force field. Compound 1, 3, and 4 may act as scaffolds for designing potential lead agonists for GPR142. The finding of GPR142 MD simulation study provides more comprehensive representation of the functional properties. The concern for Type II diabetes is increasing worldwide and successful treatment of this disease demands novel drugs with better efficacy.

Efficient Simulation of Secondary Fluorescence Via NIST DTSA-II Monte Carlo.

PubMed

Ritchie, Nicholas W M

2017-06-01

Secondary fluorescence, the final term in the familiar matrix correction triumvirate Z·A·F, is the most challenging for Monte Carlo models to simulate. In fact, only two implementations of Monte Carlo models commonly used to simulate electron probe X-ray spectra can calculate secondary fluorescence-PENEPMA and NIST DTSA-II a (DTSA-II is discussed herein). These two models share many physical models but there are some important differences in the way each implements X-ray emission including secondary fluorescence. PENEPMA is based on PENELOPE, a general purpose software package for simulation of both relativistic and subrelativistic electron/positron interactions with matter. On the other hand, NIST DTSA-II was designed exclusively for simulation of X-ray spectra generated by subrelativistic electrons. NIST DTSA-II uses variance reduction techniques unsuited to general purpose code. These optimizations help NIST DTSA-II to be orders of magnitude more computationally efficient while retaining detector position sensitivity. Simulations execute in minutes rather than hours and can model differences that result from detector position. Both PENEPMA and NIST DTSA-II are capable of handling complex sample geometries and we will demonstrate that both are of similar accuracy when modeling experimental secondary fluorescence data from the literature.

A model for the infrared emission from an OB star cluster environment

NASA Technical Reports Server (NTRS)

Leisawitz, D.

1991-01-01

A model for the infrared emission from the neighborhood of an OB star cluster is described. The distribution of gas and dust around the stars, properties of the dust, and the cluster and interstellar radiation fields are variable. The model can be applied to regions around clusters embedded to various degrees in their parental molecular clouds (i.e., compact H II regions, blister-type H II regions, and the tenuous H II regions ionized by naked O stars). The model is used to simulate IRAS observations of a typical blister H II region. Infrared surface brightness and spectral energy distributions are predicted and the impact of limited spatial resolution is illustrated. The model results are shown to be consistent with observations of the exemplary outer Galaxy OB cluster NGC 7380. It is planned to use the model as a diagnostic tool to probe the physical conditions and dust properties in star-formation regions and, ultimately, in an interpretation of the spectral energy distributions of spiral galaxies.

New Distributed Multipole Methods for Accurate Electrostatics for Large-Scale Biomolecular Simultations

NASA Astrophysics Data System (ADS)

Sagui, Celeste

2006-03-01

An accurate and numerically efficient treatment of electrostatics is essential for biomolecular simulations, as this stabilizes much of the delicate 3-d structure associated with biomolecules. Currently, force fields such as AMBER and CHARMM assign ``partial charges'' to every atom in a simulation in order to model the interatomic electrostatic forces, so that the calculation of the electrostatics rapidly becomes the computational bottleneck in large-scale simulations. There are two main issues associated with the current treatment of classical electrostatics: (i) how does one eliminate the artifacts associated with the point-charges (e.g., the underdetermined nature of the current RESP fitting procedure for large, flexible molecules) used in the force fields in a physically meaningful way? (ii) how does one efficiently simulate the very costly long-range electrostatic interactions? Recently, we have dealt with both of these challenges as follows. In order to improve the description of the molecular electrostatic potentials (MEPs), a new distributed multipole analysis based on localized functions -- Wannier, Boys, and Edminston-Ruedenberg -- was introduced, which allows for a first principles calculation of the partial charges and multipoles. Through a suitable generalization of the particle mesh Ewald (PME) and multigrid method, one can treat electrostatic multipoles all the way to hexadecapoles all without prohibitive extra costs. The importance of these methods for large-scale simulations will be discussed, and examplified by simulations from polarizable DNA models.

Jovian Plasmas Torus Interaction with Europa. Plasma Wake Structure and Effect of Inductive Magnetic Field: 3D Hybrid Kinetic Simulation

NASA Technical Reports Server (NTRS)

Lipatov, A. S.; Cooper, J F.; Paterson, W. R.; Sittler, E. C., Jr.; Hartle, R. E.; Simpson, David G.

2013-01-01

The hybrid kinetic model supports comprehensive simulation of the interaction between different spatial and energetic elements of the Europa moon-magnetosphere system with respect to a variable upstream magnetic field and flux or density distributions of plasma and energetic ions, electrons, and neutral atoms. This capability is critical for improving the interpretation of the existing Europa flyby measurements from the Galileo Orbiter mission, and for planning flyby and orbital measurements (including the surface and atmospheric compositions) for future missions. The simulations are based on recent models of the atmosphere of Europa (Cassidy et al., 2007; Shematovich et al., 2005). In contrast to previous approaches with MHD simulations, the hybrid model allows us to fully take into account the finite gyroradius effect and electron pressure, and to correctly estimate the ion velocity distribution and the fluxes along the magnetic field (assuming an initial Maxwellian velocity distribution for upstream background ions). Photoionization, electron-impact ionization, charge exchange and collisions between the ions and neutrals are also included in our model. We consider the models with Oþ þ and Sþ þ background plasma, and various betas for background ions and electrons, and pickup electrons. The majority of O2 atmosphere is thermal with an extended non-thermal population (Cassidy et al., 2007). In this paper, we discuss two tasks: (1) the plasma wake structure dependence on the parameters of the upstream plasma and Europa's atmosphere (model I, cases (a) and (b) with a homogeneous Jovian magnetosphere field, an inductive magnetic dipole and high oceanic shell conductivity); and (2) estimation of the possible effect of an induced magnetic field arising from oceanic shell conductivity. This effect was estimated based on the difference between the observed and modeled magnetic fields (model II, case (c) with an inhomogeneous Jovian magnetosphere field, an inductive magnetic dipole and low oceanic shell conductivity).

Time-dependent models for blazar emission with the second-order Fermi acceleration

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

Asano, Katsuaki; Takahara, Fumio; Toma, Kenji

The second-order Fermi acceleration (Fermi-II) driven by turbulence may be responsible for the electron acceleration in blazar jets. We test this model with time-dependent simulations. The hard electron spectrum predicted by the Fermi-II process agrees with the hard photon spectrum of 1ES 1101–232. For other blazars that show softer spectra, the Fermi-II model requires radial evolution of the electron injection rate and/or diffusion coefficient in the outflow. Such evolutions can yield a curved electron spectrum, which can reproduce the synchrotron spectrum of Mrk 421 from the radio to the X-ray regime. The photon spectrum in the GeV energy range ofmore » Mrk 421 is hard to fit with a synchrotron self-Compton model. However, if we introduce an external radio photon field with a luminosity of 4.9 × 10{sup 38} erg s{sup –1}, GeV photons are successfully produced via inverse Compton scattering. The temporal variability of the diffusion coefficient or injection rate causes flare emission. The observed synchronicity of X-ray and TeV flares implies a decrease of the magnetic field in the flaring source region.« less

Simulation of mixed convection in a horizontal channel heated from below by the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Sahraoui, Nassim M.; Houat, Samir; Saidi, Nawal

2017-05-01

We perform a contribution with a simulation study of the mixed convection in horizontal channel heated from below. The lattice Boltzmann method (LBM) is used with the Boussinesq approximation to solve the coupled phenomenon that governs the systems thermo-hydrodynamics. The double populations thermal lattice Boltzmann model (TLBM) is used with the D2Q5 for the thermal field and D2Q9 model for the dynamic field. A comparison of the results of the averaged Nusselt number obtained by the TLBM with other references is presented for an area stretching. The streamlines, the vortices, the isotherms, the velocity profiles and other parameters of the study, are presented at a certain time tT which is chosen arbitrarily. The results presented here are in good agreement with those reported in the scientific literature which gives us high expectations about the reliability of the TLBM to simulate this kind of physical phenomena. Contribution to the topical issue "Materials for Energy harvesting, conversion and storage II (ICOME 2016)", edited by Jean-Michel Nunzi, Rachid Bennacer and Mohammed El Ganaoui

Computer simulation of the linear and nonlinear optical susceptibilities of p-nitroaniline in cyclohexane, 1,4-dioxane, and tetrahydrofuran in quadrupolar approximation. II. Local field effects and optical susceptibilitities.

PubMed

Reis, H; Papadopoulos, M G; Grzybowski, A

2006-09-21

This is the second part of a study to elucidate the local field effects on the nonlinear optical properties of p-nitroaniline (pNA) in three solvents of different multipolar character, that is, cyclohexane (CH), 1,4-dioxane (DI), and tetrahydrofuran (THF), employing a discrete description of the solutions. By the use of liquid structure information from molecular dynamics simulations and molecular properties computed by high-level ab initio methods, the local field and local field gradients on p-nitroaniline and the solvent molecules are computed in quadrupolar approximation. To validate the simulations and the induction model, static and dynamic (non)linear properties of the pure solvents are also computed. With the exception of the static dielectric constant of pure THF, a good agreement between computed and experimental refractive indices, dielectric constants, and third harmonic generation signals is obtained for the solvents. For the solutions, it is found that multipole moments up to two orders higher than quadrupole have a negligible influence on the local fields on pNA, if a simple distribution model is employed for the electric properties of pNA. Quadrupole effects are found to be nonnegligible in all three solvents but are especially pronounced in the 1,4-dioxane solvent, in which the local fields are similar to those in THF, although the dielectric constant of DI is 2.2 and that of the simulated THF is 5.4. The electric-field-induced second harmonic generation (EFISH) signal and the hyper-Rayleigh scattering signal of pNA in the solutions computed with the local field are in good to fair agreement with available experimental results. This confirms the effect of the "dioxane anomaly" also on nonlinear optical properties. Predictions based on an ellipsoidal Onsager model as applied by experimentalists are in very good agreement with the discrete model predictions. This is in contrast to a recent discrete reaction field calculation of pNA in 1,4-dioxane, which found that the predicted first hyperpolarizability of pNA deviated strongly from the predictions obtained using Onsager-Lorentz local field factors.

Simulating ungulate herbivory across forest landscapes: A browsing extension for LANDIS-II

USGS Publications Warehouse

DeJager, Nathan R.; Drohan, Patrick J.; Miranda, Brian M.; Sturtevant, Brian R.; Stout, Susan L.; Royo, Alejandro; Gustafson, Eric J.; Romanski, Mark C.

2017-01-01

Browsing ungulates alter forest productivity and vegetation succession through selective foraging on species that often dominate early succession. However, the long-term and large-scale effects of browsing on forest succession are not possible to project without the use of simulation models. To explore the effects of ungulates on succession in a spatially explicit manner, we developed a Browse Extension that simulates the effects of browsing ungulates on the growth and survival of plant species cohorts within the LANDIS-II spatially dynamic forest landscape simulation model framework. We demonstrate the capabilities of the new extension and explore the spatial effects of ungulates on forest composition and dynamics using two case studies. The first case study examined the long-term effects of persistently high white-tailed deer browsing rates in the northern hardwood forests of the Allegheny National Forest, USA. In the second case study, we incorporated a dynamic ungulate population model to simulate interactions between the moose population and boreal forest landscape of Isle Royale National Park, USA. In both model applications, browsing reduced total aboveground live biomass and caused shifts in forest composition. Simulations that included effects of browsing resulted in successional patterns that were more similar to those observed in the study regions compared to simulations that did not incorporate browsing effects. Further, model estimates of moose population density and available forage biomass were similar to previously published field estimates at Isle Royale and in other moose-boreal forest systems. Our simulations suggest that neglecting effects of browsing when modeling forest succession in ecosystems known to be influenced by ungulates may result in flawed predictions of aboveground biomass and tree species composition.

Simulating pre-galactic metal enrichment for JWST deep-field observations

NASA Astrophysics Data System (ADS)

Jaacks, Jason

2017-08-01

We propose to create a new suite of mesoscale cosmological volume simulations with custom built sub-grid physics in which we independently track the contribution from Population III and Population II star formation to the total metals in the interstellar medium (ISM) of the first galaxies, and in the diffuse IGM at an epoch prior to reionization. These simulations will fill a gap in our simulation knowledge about chemical enrichment in the pre-reionization universe, which is a crucial need given the impending observational push into this epoch with near-future ground and space-based telescopes. This project is the natural extension of our successful Cycle 24 theory proposal (HST-AR-14569.001-A; PI Jaacks) in which we developed a new Pop III star formation sub-grid model which is currently being utilized to study the baseline metal enrichment of pre-reionization systems.

A "simulation chain" to define a Multidisciplinary Decision Support System for landslide risk management in pyroclastic soils

NASA Astrophysics Data System (ADS)

Damiano, E.; Mercogliano, P.; Netti, N.; Olivares, L.

2012-04-01

This paper proposes a Multidisciplinary Decision Support System (MDSS) as an approach to manage rainfall-induced shallow landslides of the flow type (flowslides) in pyroclastic deposits. We stress the need to combine information from the fields of meteorology, geology, hydrology, geotechnics and economics to support the agencies engaged in land monitoring and management. The MDSS consists of a "simulation chain" to link rainfall to effects in terms of infiltration, slope stability and vulnerability. This "simulation chain" was developed at the Euro-Mediterranean Centre for Climate Change (CMCC) (meteorological aspects), at the Geotechnical Laboratory of the Second University of Naples (hydrological and geotechnical aspects) and at the Department of Economics of the University of Naples "Federico II" (economic aspects). The results obtained from the application of this simulation chain in the Cervinara area during eleven years of research allowed in-depth analysis of the mechanisms underlying a flowslide in pyroclastic soil.

Plasma Radiation and Acceleration Effectiveness of CME-driven Shocks

NASA Astrophysics Data System (ADS)

Gopalswamy, N.; Schmidt, J. M.

2008-05-01

CME-driven shocks are effective radio radiation generators and accelerators for Solar Energetic Particles (SEPs). We present simulated 3 D time-dependent radio maps of second order plasma radiation generated by CME- driven shocks. The CME with its shock is simulated with the 3 D BATS-R-US CME model developed at the University of Michigan. The radiation is simulated using a kinetic plasma model that includes shock drift acceleration of electrons and stochastic growth theory of Langmuir waves. We find that in a realistic 3 D environment of magnetic field and solar wind outflow of the Sun the CME-driven shock shows a detailed spatial structure of the density, which is responsible for the fine structure of type II radio bursts. We also show realistic 3 D reconstructions of the magnetic cloud field of the CME, which is accelerated outward by magnetic buoyancy forces in the diverging magnetic field of the Sun. The CME-driven shock is reconstructed by tomography using the maximum jump in the gradient of the entropy. In the vicinity of the shock we determine the Alfven speed of the plasma. This speed profile controls how steep the shock can grow and how stable the shock remains while propagating away from the Sun. Only a steep shock can provide for an effective particle acceleration.

Plasma radiation and acceleration effectiveness of CME-driven shocks

NASA Astrophysics Data System (ADS)

Schmidt, Joachim

CME-driven shocks are effective radio radiation generators and accelerators for Solar Energetic Particles (SEPs). We present simulated 3 D time-dependent radio maps of second order plasma radiation generated by CME-driven shocks. The CME with its shock is simulated with the 3 D BATS-R-US CME model developed at the University of Michigan. The radiation is simulated using a kinetic plasma model that includes shock drift acceleration of electrons and stochastic growth theory of Langmuir waves. We find that in a realistic 3 D environment of magnetic field and solar wind outflow of the Sun the CME-driven shock shows a detailed spatial structure of the density, which is responsible for the fine structure of type II radio bursts. We also show realistic 3 D reconstructions of the magnetic cloud field of the CME, which is accelerated outward by magnetic buoyancy forces in the diverging magnetic field of the Sun. The CME-driven shock is reconstructed by tomography using the maximum jump in the gradient of the entropy. In the vicinity of the shock we determine the Alfven speed of the plasma. This speed profile controls how steep the shock can grow and how stable the shock remains while propagating away from the Sun. Only a steep shock can provide for an effective particle acceleration.

Modelling interstellar structures around Vela X-1

NASA Astrophysics Data System (ADS)

Gvaramadze, V. V.; Alexashov, D. B.; Katushkina, O. A.; Kniazev, A. Y.

2018-03-01

We report the discovery of filamentary structures stretched behind the bow-shock-producing high-mass X-ray binary Vela X-1 using the SuperCOSMOS H-alpha Survey and present the results of optical spectroscopy of the bow shock carried out with the Southern African Large Telescope. The geometry of the detected structures suggests that Vela X-1 has encountered a wedge-like layer of enhanced density on its way and that the shocked material of the layer partially outlines a wake downstream of Vela X-1. To substantiate this suggestion, we carried out 3D magnetohydrodynamic simulations of interaction between Vela X-1 and the layer for three limiting cases. Namely, we run simulations in which (i) the stellar wind and the interstellar medium (ISM) were treated as pure hydrodynamic flows, (ii) a homogeneous magnetic field was added to the ISM, while the stellar wind was assumed to be unmagnetized, and (iii) the stellar wind was assumed to possess a helical magnetic field, while there was no magnetic field in the ISM. We found that although the first two simulations can provide a rough agreement with the observations, only the third one allowed us to reproduce not only the wake behind Vela X-1, but also the general geometry of the bow shock ahead of it.

TD-CI simulation of the electronic optical response of molecules in intense fields II: comparison of DFT functionals and EOM-CCSD.

PubMed

Sonk, Jason A; Schlegel, H Bernhard

2011-10-27

Time-dependent configuration interaction (TD-CI) simulations can be used to simulate molecules in intense laser fields. TD-CI calculations use the excitation energies and transition dipoles calculated in the absence of a field. The EOM-CCSD method provides a good estimate of the field-free excited states but is rather expensive. Linear-response time-dependent density functional theory (TD-DFT) is an inexpensive alternative for computing the field-free excitation energies and transition dipoles needed for TD-CI simulations. Linear-response TD-DFT calculations were carried out with standard functionals (B3LYP, BH&HLYP, HSE2PBE (HSE03), BLYP, PBE, PW91, and TPSS) and long-range corrected functionals (LC-ωPBE, ωB97XD, CAM-B3LYP, LC-BLYP, LC-PBE, LC-PW91, and LC-TPSS). These calculations used the 6-31G(d,p) basis set augmented with three sets of diffuse sp functions on each heavy atom. Butadiene was employed as a test case, and 500 excited states were calculated with each functional. Standard functionals yield average excitation energies that are significantly lower than the EOM-CC, while long-range corrected functionals tend to produce average excitation energies slightly higher. Long-range corrected functionals also yield transition dipoles that are somewhat larger than EOM-CC on average. The TD-CI simulations were carried out with a three-cycle Gaussian pulse (ω = 0.06 au, 760 nm) with intensities up to 1.26 × 10(14) W cm(-2) directed along the vector connecting the end carbons. The nonlinear response as indicated by the residual populations of the excited states after the pulse is far too large with standard functionals, primarily because the excitation energies are too low. The LC-ωPBE, LC-PBE, LC-PW91, and LC-TPSS long-range corrected functionals produce responses comparable to EOM-CC.

Curvature-undulation coupling as a basis for curvature sensing and generation in bilayer membranes.

PubMed

Bradley, Ryan P; Radhakrishnan, Ravi

2016-08-30

We present coarse-grained molecular dynamics simulations of the epsin N-terminal homology domain interacting with a lipid bilayer and demonstrate a rigorous theoretical formalism and analysis method for computing the induced curvature field in varying concentrations of the protein in the dilute limit. Our theory is based on the description of the height-height undulation spectrum in the presence of a curvature field. We formulated an objective function to compare the acquired undulation spectrum from the simulations to that of the theory. We recover the curvature field parameters by minimizing the objective function even in the limit where the protein-induced membrane curvature is of the same order as the amplitude due to thermal undulations. The coupling between curvature and undulations leads to significant predictions: (i) Under dilute conditions, the proteins can sense a site of spontaneous curvature at distances much larger than their size; (ii) as the density of proteins increases the coupling focuses and stabilizes the curvature field to the site of the proteins; and (iii) the mapping of the protein localization and the induction of a stable curvature is a cooperative process that can be described through a Hill function.

Curvature–undulation coupling as a basis for curvature sensing and generation in bilayer membranes

PubMed Central

Bradley, Ryan P.; Radhakrishnan, Ravi

2016-01-01

We present coarse-grained molecular dynamics simulations of the epsin N-terminal homology domain interacting with a lipid bilayer and demonstrate a rigorous theoretical formalism and analysis method for computing the induced curvature field in varying concentrations of the protein in the dilute limit. Our theory is based on the description of the height–height undulation spectrum in the presence of a curvature field. We formulated an objective function to compare the acquired undulation spectrum from the simulations to that of the theory. We recover the curvature field parameters by minimizing the objective function even in the limit where the protein-induced membrane curvature is of the same order as the amplitude due to thermal undulations. The coupling between curvature and undulations leads to significant predictions: (i) Under dilute conditions, the proteins can sense a site of spontaneous curvature at distances much larger than their size; (ii) as the density of proteins increases the coupling focuses and stabilizes the curvature field to the site of the proteins; and (iii) the mapping of the protein localization and the induction of a stable curvature is a cooperative process that can be described through a Hill function. PMID:27531962

Tracing Magnetic Fields With The Polarization Of Submillimeter Lines

NASA Astrophysics Data System (ADS)

Zhang, Heshou; Yan, Huirong

2017-10-01

Magnetic fields play important roles in many astrophysical processes. However, there is no universal diagnostic for the magnetic fields in the interstellar medium (ISM) and each magnetic tracer has its limitation. Any new detection method is thus valuable. Theoretical studies have shown that submillimeter fine-structure lines are polarized due to atomic alignment by Ultraviolet (UV) photon-excitation, which opens up a new avenue to probe interstellar magnetic fields. The method is applicable to all radiative-excitation dominant region, e.g., H II Regions, PDRs. The polarization of the submillimeter fine-structure lines induced by atomic alignment could be substantial and the applicability of using the spectro-polarimetry of atomic lines to trace magnetic fields has been supported by synthetic observations of simulated ISM in our recent paper. Our results demonstrate that the polarization of submillimeter atomic lines is a powerful magnetic tracer and add great value to the observational studies of the submilimeter astronomy.

Collisionless Coupling between Explosive Debris Plasma and Magnetized Ambient Plasma

NASA Astrophysics Data System (ADS)

Bondarenko, Anton

2016-10-01

The explosive expansion of a dense debris plasma cloud into relatively tenuous, magnetized, ambient plasma characterizes a wide variety of astrophysical and space phenomena, including supernova remnants, interplanetary coronal mass ejections, and ionospheric explosions. In these rarified environments, collective electromagnetic processes rather than Coulomb collisions typically mediate the transfer of momentum and energy from the debris plasma to the ambient plasma. In an effort to better understand the detailed physics of collisionless coupling mechanisms in a reproducible laboratory setting, the present research jointly utilizes the Large Plasma Device (LAPD) and the Phoenix laser facility at UCLA to study the super-Alfvénic, quasi-perpendicular expansion of laser-produced carbon (C) and hydrogen (H) debris plasma through preformed, magnetized helium (He) ambient plasma via a variety of diagnostics, including emission spectroscopy, wavelength-filtered imaging, and magnetic field induction probes. Large Doppler shifts detected in a He II ion spectral line directly indicate initial ambient ion acceleration transverse to both the debris plasma flow and the background magnetic field, indicative of a fundamental process known as Larmor coupling. Characterization of the laser-produced debris plasma via a radiation-hydrodynamics code permits an explicit calculation of the laminar electric field in the framework of a ``hybrid'' model (kinetic ions, charge-neutralizing massless fluid electrons), thus allowing for a simulation of the initial response of a distribution of He II test ions. A synthetic Doppler-shifted spectrum constructed from the simulated velocity distribution of the accelerated test ions excellently reproduces the spectroscopic measurements, confirming the role of Larmor coupling in the debris-ambient interaction.

Solar polarimetry through the K I lines at 770 nm

NASA Astrophysics Data System (ADS)

Quintero Noda, C.; Uitenbroek, H.; Katsukawa, Y.; Shimizu, T.; Oba, T.; Carlsson, M.; Orozco Suárez, D.; Ruiz Cobo, B.; Kubo, M.; Anan, T.; Ichimoto, K.; Suematsu, Y.

2017-09-01

We characterize the K I D1 & D2 lines in order to determine whether they could complement the 850 nm window, containing the Ca II infrared triplet lines and several Zeeman sensitive photospheric lines, that was studied previously. We investigate the effect of partial redistribution on the intensity profiles, their sensitivity to changes in different atmospheric parameters, and the spatial distribution of Zeeman polarization signals employing a realistic magnetohydrodynamic simulation. The results show that these lines form in the upper photosphere at around 500 km, and that they are sensitive to the line-of-sight velocity and magnetic field strength at heights where neither the photospheric lines nor the Ca II infrared lines are. However, at the same time, we found that their sensitivity to the temperature essentially comes from the photosphere. Then, we conclude that the K I lines provide a complement to the lines in the 850 nm window for the determination of atmospheric parameters in the upper photosphere, especially for the line-of-sight velocity and the magnetic field.

On intracluster Faraday rotation. II - Statistical analysis

NASA Technical Reports Server (NTRS)

Lawler, J. M.; Dennison, B.

1982-01-01

The comparison of a reliable sample of radio source Faraday rotation measurements seen through rich clusters of galaxies, with sources seen through the outer parts of clusters and therefore having little intracluster Faraday rotation, indicates that the distribution of rotation in the former population is broadened, but only at the 80% level of statistical confidence. Employing a physical model for the intracluster medium in which the square root of magnetic field strength/turbulent cell per gas core radius number ratio equals approximately 0.07 microgauss, a Monte Carlo simulation is able to reproduce the observed broadening. An upper-limit analysis figure of less than 0.20 microgauss for the field strength/turbulent cell ratio, combined with lower limits on field strength imposed by limitations on the Compton-scattered flux, shows that intracluster magnetic fields must be tangled on scales greater than about 20 kpc.

Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

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

Li, Yulan; Hu, Shenyang Y.; Sun, Xin

2011-06-15

Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubblemore » evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux, and sink strength of interstitial loop for interstitials. In part II, we present a generic phase field model and discuss the thermodynamic and kinetic properties in phase-field models including the reaction kinetics of radiation defects and local free energy of irradiated materials. In particular, a two-sublattice thermodynamic model is suggested to describe the local free energy of alloys with irradiated defects. Fe-Cr alloy is taken as an example to explain the required thermodynamic and kinetic properties for quantitative phase-field modeling. Finally the great challenges in phase-field modeling will be discussed.« less

Planck intermediate results. XX. Comparison of polarized thermal emission from Galactic dust with simulations of MHD turbulence

NASA Astrophysics Data System (ADS)

Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Alina, D.; Alves, M. I. R.; Aniano, G.; Armitage-Caplan, C.; Arnaud, M.; Arzoumanian, D.; Ashdown, M.; Atrio-Barandela, F.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Battaner, E.; Benabed, K.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Boulanger, F.; Bracco, A.; Burigana, C.; Cardoso, J.-F.; Catalano, A.; Chamballu, A.; Chiang, H. C.; Christensen, P. R.; Colombi, S.; Colombo, L. P. L.; Combet, C.; Couchot, F.; Coulais, A.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Dickinson, C.; Diego, J. M.; Donzelli, S.; Doré, O.; Douspis, M.; Dupac, X.; Efstathiou, G.; Enßlin, T. A.; Eriksen, H. K.; Falgarone, E.; Fanciullo, L.; Ferrière, K.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Galeotta, S.; Ganga, K.; Ghosh, T.; Giard, M.; Giraud-Héraud, Y.; González-Nuevo, J.; Górski, K. M.; Gregorio, A.; Gruppuso, A.; Guillet, V.; Hansen, F. K.; Harrison, D. L.; Helou, G.; Hernández-Monteagudo, C.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Huffenberger, K. M.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Kneissl, R.; Knoche, J.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lamarre, J.-M.; Lasenby, A.; Lawrence, C. R.; Leonardi, R.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maino, D.; Mandolesi, N.; Maris, M.; Marshall, D. J.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; Mazzotta, P.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Noviello, F.; Novikov, D.; Novikov, I.; Oxborrow, C. A.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Pelkonen, V.-M.; Perdereau, O.; Perotto, L.; Perrotta, F.; Piacentini, F.; Piat, M.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Popa, L.; Pratt, G. W.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Reinecke, M.; Remazeilles, M.; Renault, C.; Ricciardi, S.; Riller, T.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Roudier, G.; Rusholme, B.; Sandri, M.; Scott, D.; Soler, J. D.; Spencer, L. D.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Umana, G.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Zonca, A.

2015-04-01

Polarized emission observed by Planck HFI at 353 GHz towards a sample of nearby fields is presented, focusing on the statistics of polarization fractions p and angles ψ. The polarization fractions and column densities in these nearby fields are representative of the range of values obtained over the whole sky. We find that: (i) the largest polarization fractions are reached in the most diffuse fields; (ii) the maximum polarization fraction pmax decreases with column density NH in the more opaque fields with NH> 1021 cm-2; and (iii) the polarization fraction along a given line of sight is correlated with the local spatial coherence of the polarization angle. These observations are compared to polarized emission maps computed in simulations of anisotropic magnetohydrodynamical turbulence in which we assume a uniform intrinsic polarization fraction of the dust grains. We find that an estimate of this parameter may be recovered from the maximum polarization fraction pmax in diffuse regions where the magnetic field is ordered on large scales and perpendicular to the line of sight. This emphasizes the impact of anisotropies of the magnetic field on the emerging polarization signal. The decrease of the maximum polarization fraction with column density in nearby molecular clouds is well reproduced in the simulations, indicating that it is essentially due to the turbulent structure of the magnetic field: an accumulation of variously polarized structures along the line of sight leads to such an anti-correlation. In the simulations, polarization fractions are also found to anti-correlate with the angle dispersion function 𝒮. However, the dispersion of the polarization angle for a given polarization fraction is found to be larger in the simulations than in the observations, suggesting a shortcoming in the physical content of these numerical models. In summary, we find that the turbulent structure of the magnetic field is able to reproduce the main statistical properties of the dust polarization as observed in a variety of nearby clouds, dense cores excluded, and that the large-scale field orientation with respect to the line of sight plays a major role in the quantitative analysis of these statistical properties. Appendices are available in electronic form at http://www.aanda.org

Chromospheric polarimetry through multiline observations of the 850-nm spectral region - II. A magnetic flux tube scenario

NASA Astrophysics Data System (ADS)

Quintero Noda, C.; Kato, Y.; Katsukawa, Y.; Oba, T.; de la Cruz Rodríguez, J.; Carlsson, M.; Shimizu, T.; Orozco Suárez, D.; Ruiz Cobo, B.; Kubo, M.; Anan, T.; Ichimoto, K.; Suematsu, Y.

2017-11-01

In this publication, we continue the work started in Quintero Noda et al., examining this time a numerical simulation of a magnetic flux tube concentration. Our goal is to study if the physical phenomena that take place in it, in particular, the magnetic pumping, leaves a specific imprint on the examined spectral lines. We find that the profiles from the interior of the flux tube are periodically doppler shifted following an oscillation pattern that is also reflected in the amplitude of the circular polarization signals. In addition, we analyse the properties of the Stokes profiles at the edges of the flux tube discovering the presence of linear polarization signals for the Ca II lines, although they are weak with an amplitude around 0.5 per cent of the continuum intensity. Finally, we compute the response functions to perturbations in the longitudinal field, and we estimate the field strength using the weak-field approximation. Our results indicate that the height of formation of the spectral lines changes during the magnetic pumping process, which makes the interpretation of the inferred magnetic field strength and its evolution more difficult. These results complement those from previous works, demonstrating the capabilities and limitations of the 850-nm spectrum for chromospheric Zeeman polarimetry in a very dynamic and complex atmosphere.

Monitoring, field experiments, and geochemical modeling of Fe(II) oxidation kinetics in a stream dominated by net-alkaline coal-mine drainage, Pennsylvania, USA

USGS Publications Warehouse

Cravotta, Charles A.

2015-01-01

Watershed-scale monitoring, field aeration experiments, and geochemical equilibrium and kinetic modeling were conducted to evaluate interdependent changes in pH, dissolved CO2, O2, and Fe(II) concentrations that typically take place downstream of net-alkaline, circumneutral coal-mine drainage (CMD) outfalls and during aerobic treatment of such CMD. The kinetic modeling approach, using PHREEQC, accurately simulates observed variations in pH, Fe(II) oxidation, alkalinity consumption, and associated dissolved gas concentrations during transport downstream of the CMD outfalls (natural attenuation) and during 6-h batch aeration tests on the CMD using bubble diffusers (enhanced attenuation). The batch aeration experiments demonstrated that aeration promoted CO2 outgassing, thereby increasing pH and the rate of Fe(II) oxidation. The rate of Fe(II) oxidation was accurately estimated by the abiotic homogeneous oxidation rate law −d[Fe(II)]/dt = k1·[O2]·[H+]−2·[Fe(II)] that indicates an increase in pH by 1 unit at pH 5–8 and at constant dissolved O2 (DO) concentration results in a 100-fold increase in the rate of Fe(II) oxidation. Adjusting for sample temperature, a narrow range of values for the apparent homogeneous Fe(II) oxidation rate constant (k1′) of 0.5–1.7 times the reference value of k1 = 3 × 10−12 mol/L/min (for pH 5–8 and 20 °C), reported by Stumm and Morgan (1996), was indicated by the calibrated models for the 5-km stream reach below the CMD outfalls and the aerated CMD. The rates of CO2 outgassing and O2ingassing in the model were estimated with first-order asymptotic functions, whereby the driving force is the gradient of the dissolved gas concentration relative to equilibrium with the ambient atmosphere. Although the progressive increase in DO concentration to saturation could be accurately modeled as a kinetic function for the conditions evaluated, the simulation of DO as an instantaneous equilibrium process did not affect the model results for Fe(II) or pH. In contrast, the model results for pH and Fe(II) were sensitive to the CO2 mass transfer rate constant (kL,CO2a). The value of kL,CO2a estimated for the stream (0.010 min−1) was within the range for the batch aeration experiments (0–0.033 min−1). These results indicate that the abiotic homogeneous Fe(II) oxidation rate law, with adjustments for variations in temperature and CO2 outgassing rate, may be applied to predict changes in aqueous iron and pH for net-alkaline, ferruginous waters within a stream (natural conditions) or a CMD treatment system (engineered conditions).

Field Demonstration and Validation of TREECS (trademark) and CTS for the Risk Assessment of Contaminants on Department of Defense (DoD) Ranges

DTIC Science & Technology

2017-04-01

unlimited. N/A The objective of this project was to demonstrate and validate the integrated Training Range Environmental Evaluation and Characterization...Defense (DoD) training and testing ranges. Training Range Environmental Evaluation and Characterization System (TREECS™), Environmental Fate Simulator...Defense (DoD) Ranges” ERDC/EL TR-17-5 ii Abstract The Training Range Environmental Evaluation and Characterization Sys- tem (TREECS™) was developed to

Improved importance sampling technique for efficient simulation of digital communication systems

NASA Technical Reports Server (NTRS)

Lu, Dingqing; Yao, Kung

1988-01-01

A new, improved importance sampling (IIS) approach to simulation is considered. Some basic concepts of IS are introduced, and detailed evolutions of simulation estimation variances for Monte Carlo (MC) and IS simulations are given. The general results obtained from these evolutions are applied to the specific previously known conventional importance sampling (CIS) technique and the new IIS technique. The derivation for a linear system with no signal random memory is considered in some detail. For the CIS technique, the optimum input scaling parameter is found, while for the IIS technique, the optimum translation parameter is found. The results are generalized to a linear system with memory and signals. Specific numerical and simulation results are given which show the advantages of CIS over MC and IIS over CIS for simulations of digital communications systems.

Direct numerical simulation of stochastically forced laminar plane couette flow: peculiarities of hydrodynamic fluctuations.

PubMed

Khujadze, G; Oberlack, M; Chagelishvili, G

2006-07-21

The background of three-dimensional hydrodynamic (vortical) fluctuations in a stochastically forced, laminar, incompressible, plane Couette flow is simulated numerically. The fluctuating field is anisotropic and has well pronounced peculiarities: (i) the hydrodynamic fluctuations exhibit nonexponential, transient growth; (ii) fluctuations with the streamwise characteristic length scale about 2 times larger than the channel width are predominant in the fluctuating spectrum instead of streamwise constant ones; (iii) nonzero cross correlations of velocity (even streamwise-spanwise) components appear; (iv) stochastic forcing destroys the spanwise reflection symmetry (inherent to the linear and full Navier-Stokes equations in a case of the Couette flow) and causes an asymmetry of the dynamical processes.

Tidally driven pore water exchange within offshore intertidal sandbanks: Part II numerical simulations

NASA Astrophysics Data System (ADS)

Gibbes, B.; Robinson, C.; Li, L.; Lockington, D.; Li, H.

2008-12-01

Field measurements presented by [Gibbes, B., Robinson, C., Li, L., Lockington, D.A., Carey, H., 2008. Tidally driven pore water exchange within offshore intertidal sandbanks: Part I Field measurements. Estuarine, Coastal and Shelf Science 79, pp. 121-132.] revealed a tidally driven pore water flow system within an offshore intertidal sandbank in Moreton Bay, Australia. The field data suggested that this flow system might be capable of delivering nutrients, and in particular bio-available iron, across the sediment-water interface. Bio-available iron has been implicated as a key nutrient in the growth of the toxic marine cyanobacteria Lyngbya majuscula and therefore this pore water exchange process is of interest at sites where L. majuscula blooms have been observed. In this study two-dimensional numerical simulations were used in conjunction with hydraulic data from field measurements to further investigate the tidally induced pore water flow patterns. Simulation results generally showed good agreement with the field data and revealed a more complex residual pore water flow system in the sandbank than shown by the field data. The flow system, strongly influenced by the geometry of the sandbank, was characterized by two circulation cells which resulted in pore water discharge at the bank edge and also to a permanently ponded area within the sandbank interior. Simulated discharge volumes in these two zones were in the order of 0.813 m 3 and 0.143 m 3 per meter width (along shore) of sandbank per tidal cycle at the bank edge and sandbank interior respectively. Transit times of pore water circulating through these cells were found to range from ≈ 17 days to > 60 years with an average time of 780 days. The results suggest that the tidally driven flow systems might provide a mechanism for transport of bio-available iron across the sediment-water interface. This flow could constitute a previously unrecognized source of bio-available iron for L. majuscula blooms in the Bay.

MIZEX. A Program for Mesoscale Air-Ice-Ocean Interaction Experiments in Arctic Marginal Ice Zones. III. Modeling the Marginal Ice Zone,

DTIC Science & Technology

1984-04-01

Ii TS C]r.I2 TAB 0] Unzanro’ unoed 0 justi fica ~r: 0 April 1984 vs - ASValabilitY Codes lvyall and/or U.S. Army Cold Regions Research and Engineering...coupled model. Fig. 1. Annual average simulated velocity fields. 3 192 Aloka 190 / 902 190+ WOO S’,. o Ice OnlY Mod" D"’, 55*w F~tth Yea’ Ice Ocean Model...A more precise delinga- inflow boundary conditions. 12 4- a. [ o ll ii traspert 00 0 0- 0e a I " i i , - - I I 1161 63 15 67 69 Ti 73 75 77 1980 *= 4h

Statistical inferences with jointly type-II censored samples from two Pareto distributions

NASA Astrophysics Data System (ADS)

Abu-Zinadah, Hanaa H.

2017-08-01

In the several fields of industries the product comes from more than one production line, which is required to work the comparative life tests. This problem requires sampling of the different production lines, then the joint censoring scheme is appeared. In this article we consider the life time Pareto distribution with jointly type-II censoring scheme. The maximum likelihood estimators (MLE) and the corresponding approximate confidence intervals as well as the bootstrap confidence intervals of the model parameters are obtained. Also Bayesian point and credible intervals of the model parameters are presented. The life time data set is analyzed for illustrative purposes. Monte Carlo results from simulation studies are presented to assess the performance of our proposed method.

Effects of starvation on intermolt development in Calanus finmarchicus copepodites: a comparison between theoretical models and field studies1

NASA Astrophysics Data System (ADS)

Crain, Jennifer A.; Miller, Charles B.

Campbell et al . (Deep Sea Research II, 48 (2001) 531) have shown that there was a localized starvation event affecting Calanus finmarchicus on the southern flank of Georges Bank in April 1997. Growth and molting rates of this dominant copepod were reduced. We have used the morphology of tooth development in field-collected samples to show that this starvation affected animals living continuously in the field, as well as those in Campbell et al .'s experimental tanks. Assuming a point of reserve saturation (PRS) response of Calanus to food limitation, and correspondence between PRS and advance from the postmolt jaw facies, the proportion of individuals with postmolt jaws should increase in all copepodite stages under starvation. Individuals that have developed past PRS should molt to the next stage, acquiring postmolt facies. Thus, the fraction of postmolt jaws should increase, while the fraction of jaws in later phases should decrease. This was observed for a drifter-marked station over five days. Numerical simulations of jaw phase distributions expected under full nutrition, and both total and patchy starvation were generated from individual-based models of development. Proportions of copepodites in postmolt phase do not increase with full nutrition. A simulation of a total starvation event showed a marked increase in postmolts during food limitation, but the increase was more extreme than the field data. A modification of the starvation simulation, representing patchy feeding conditions, matched the level of increase of postmolt individuals in all stages that was observed in the field samples.

On the Radial Abundance Gradients of Europium and Oxygen of Stars Inside the Disk of a Simulated Milky Way

NASA Astrophysics Data System (ADS)

Ruiz-Rocha, Krystal; Montes, Gabriela; Ramirez-Ruiz, Enrico

2017-01-01

Studies of galaxy evolution and formation through simulations and observations have yielded valuable insight into the life of stars. Abundance gradients, in particular, provide useful information about the element assembly history in the Milky Way. To study these gradients we use data from a simulation titled Eris which has been constructed with the goal of reproducing the properties of the Milky Way, to find the gradients of stars located in the disk that have been enriched by Supernovae and Neutron Star Mergers. We compare these gradients to the observations acquired from looking at Cepheids and field stars in the disk of our Milky Way. We also aim to understand whether radial metallicity gradients can be used to differentiate between Neutron Star Merger versus Type II Supernovae enrichment.

RAiSE II: resolved spectral evolution in radio AGN

NASA Astrophysics Data System (ADS)

Turner, Ross J.; Rogers, Jonathan G.; Shabala, Stanislav S.; Krause, Martin G. H.

2018-01-01

The active galactic nuclei (AGN) lobe radio luminosities modelled in hydrodynamical simulations and most analytical models do not address the redistribution of the electron energies due to adiabatic expansion, synchrotron radiation and inverse-Compton scattering of cosmic microwave background photons. We present a synchrotron emissivity model for resolved sources that includes a full treatment of the loss mechanisms spatially across the lobe, and apply it to a dynamical radio source model with known pressure and volume expansion rates. The bulk flow and dispersion of discrete electron packets is represented by tracer fields in hydrodynamical simulations; we show that the mixing of different aged electrons strongly affects the spectrum at each point of the radio map in high-powered Fanaroff & Riley type II (FR-II) sources. The inclusion of this mixing leads to a factor of a few discrepancy between the spectral age measured using impulsive injection models (e.g. JP model) and the dynamical age. The observable properties of radio sources are predicted to be strongly frequency dependent: FR-II lobes are expected to appear more elongated at higher frequencies, while jetted FR-I sources appear less extended. The emerging FR0 class of radio sources, comprising gigahertz peaked and compact steep spectrum sources, can potentially be explained by a population of low-powered FR-Is. The extended emission from such sources is shown to be undetectable for objects within a few orders of magnitude of the survey detection limit and to not contribute to the curvature of the radio spectral energy distribution.

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

PubMed

Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; Luo, Ray; Lee, Taisung; Caldwell, James; Wang, Junmei; Kollman, Peter

2003-12-01

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999-2012, 2003

High-frequency intrinsic dynamics of the electrocaloric effect from direct atomistic simulations

NASA Astrophysics Data System (ADS)

Lisenkov, S.; Ponomareva, I.

2018-05-01

We propose a computational methodology capable of harvesting isothermal heat and entropy change in molecular dynamics simulations. The methodology is applied to study high-frequency dynamics of the electrocaloric effect (ECE) in ferroelectric PbTiO3. ECE is associated with a reversible change in temperature under adiabatic application of electric field or with a reversible change in entropy under isothermal application of the electric field. Accurate assessment of electrocaloric performance requires the knowledge of three quantities: isothermal heat, isothermal entropy change, and adiabatic temperature change. Our methodology allows computations of all these quantities directly, that is, without restoring to the reversible thermodynamical models. Consequently, it captures both reversible and irreversible effects, which is critical for ECE simulations. The approach is well suited to address the dynamics of the ECE, which so far remains underexplored. We report the following basic features of the intrinsic dynamics of ECE: (i) the ECE is independent of the electric field frequency, rate of application, or field profile; (ii) the effect persists up to the frequencies associated with the onset of dielectric losses and deteriorates from there due to the creation of irreversible entropy; and (iii) in the vicinity of the phase transition and in the paraelectric phase the onset of irreversible dynamics occurs at lower frequency as compared to the ferroelectric phase. The latter is attributed to lower intrinsic soft-mode frequencies and and larger losses in the paraelectric phase.

Instructional authoring by direct manipulation of simulations: Exploratory applications of RAPIDS. RAPIDS 2 authoring manual

NASA Technical Reports Server (NTRS)

1990-01-01

RAPIDS II is a simulation-based intelligent tutoring system environment. It is a system for producing computer-based training courses that are built on the foundation of graphical simulations. RAPIDS II simulations can be animated and they can have continuously updating elements.

Application of the GERTS II simulator in the industrial environment.

NASA Technical Reports Server (NTRS)

Whitehouse, G. E.; Klein, K. I.

1971-01-01

GERT was originally developed to aid in the analysis of stochastic networks. GERT can be used to graphically model and analyze complex systems. Recently a simulator model, GERTS II, has been developed to solve GERT Networks. The simulator language used in the development of this model was GASP II A. This paper discusses the possible application of GERTS II to model and analyze (1) assembly line operations, (2) project management networks, (3) conveyor systems and (4) inventory systems. Finally, an actual application dealing with a job shop loading problem is presented.

EEAP boiler and chiller study II at Fort Sam Houston, San Antonio, Texas. Volume II

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

NONE

The following assumptions and estimates were used in the modeling of the existing buildings which are served by the boilers and chillers included in this study. (1) The Trace 600 weather data for San Antonio, Texas was used in all of the computer simulations. (2) The Trace 600 computer simulations were performed for the months of January through December to determine annual HVAC equipment energy consumptions. (3) A special holiday schedule was created to incorporate the additional holidays that military personnel living in the area 1300 barracks buildings receive. This schedule includes the seven standard holidays plus the period frommore » December 17 through 31. The standard seven day holiday schedule was used for all other areas. (4) All building dimensions and construction data were determined from as-built drawings when available, or from field measurements taken during the site visit. (5) Design room temperatures for comfort conditions (thermostat setpoints) were obtained from CEMP-E (9 December 1991) Chapter 13, Section 3. These temperatures were 78 deg F, 50% relative humidity for cooling and 70 deg F for heating. No cooling or heating temperature setback control was included in the simulations. The design room conditions for the hospital were determined as follows: Surgery / Critical Care 68 deg F, 55%; Ancillary 72 deg F, 50%; Nursing / Patient Care 76 deg F, 50%; and Computer Room 72 deg F, 50%. (6) The shading coefficient for all windows with interior shading devices was estimated at 0.67 per ASHRAE data. (7) The number of people in each building or room was estimated from interviews with post personnel or field notes taken during the site visit. The sensible and latent heat gain rates used for the people in each room were taken from ASHRAE data.« less

The dynamical oscillation and propulsion of magnetic fields in the convective zone of a star. II - Thermal shadows. III - Accumulation of heat and the onset of the Rayleigh-Taylor instability

NASA Technical Reports Server (NTRS)

Parker, E. N.

1987-01-01

The dynamics of thermal shadows which develop in the convective zone of a star around an insulating obstacle such as a horizontal band in intense magnetic field are studied. The depth of the shadow on the cool side of the obstacle is found to depend largely on the width of the obstacle multiplied by the temperature gradient. Thermal shadows pressing fields up to 10,000 G downward against the bottom of the convective zone are produced by the broad bands of the azimuthal field in the sun's convective zone. In the third part, the time-dependent accumulation of heat beneath a thermal barrier simulating such a band in the lower convective zone of the sun is considered. The resulting Rayleigh-Taylor instability is shown to cause tongues of heated gas to penetrate upward through the field, providing the emerging magnetic fields that give rise to the activity of the sun.

Comparison of DSMC and CFD Solutions of Fire II Including Radiative Heating

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Johnston, Christopher O.; Lewis, Mark J.

2011-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. These flows may also contain significant radiative heating. To prepare for these missions, NASA is developing the capability to simulate rarefied, ionized flows and to then calculate the resulting radiative heating to the vehicle's surface. In this study, the DSMC codes DAC and DS2V are used to obtain charge-neutral ionization solutions. NASA s direct simulation Monte Carlo code DAC is currently being updated to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced Quantum-Kinetic chemistry model, and to include electronic energy levels as an additional internal energy mode. The Fire II flight test is used in this study to assess these new capabilities. The 1634 second data point was chosen for comparisons to be made in order to include comparisons to computational fluid dynamics solutions. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid. It is shown that there can be quite a bit of variability in the vibrational temperature inferred from DSMC solutions and that, from how radiative heating is computed, the electronic temperature is much better suited for radiative calculations. To include the radiative portion of heating, the flow-field solutions are post-processed by the non-equilibrium radiation code HARA. Acceptable agreement between CFD and DSMC flow field solutions is demonstrated and the progress of the updates to DAC, along with an appropriate radiative heating solution, are discussed. In addition, future plans to generate more high fidelity radiative heat transfer solutions are discussed.

Electronic Equipment Reliability Data,

DTIC Science & Technology

1986-04-02

MTBF RELATIONSHIPS 2- 60 (INDEPENDENT OF PREDICTED MTBF) vii LIST OF FIGURES Page FIGURE 1: CONTROLS/DISPLAYS FIELD MTBF VERSUS PREDICTED MTBF 2-9 FIGURE...LJ LO C-.. c’J - - IL D LLLJ c c 1,P, 4-) CD ui on LU V)4-> LD 2 2- 60 field maintenance data (MTBMAFIELD) and observed field failure data (MTBFFIELD...w N w DLM I_, II II uh II |II II II II L II II it 00I II I-. m . LI I I I I I I I I I I I I- - - - - I I I I I I I Of m- I C II ~ 1 1 10 0 0 0 01 1 1

Counting defects in an instantaneous quench.

PubMed

Ibaceta, D; Calzetta, E

1999-09-01

We consider the formation of defects in a nonequilibrium second-order phase transition induced by an instantaneous quench to zero temperature in a type II superconductor. We perform a full nonlinear simulation where we follow the evolution in time of the local order parameter field. We determine how far into the phase transition theoretical estimates of the defect density based on the Gaussian approximation yield a reliable prediction for the actual density. We also characterize quantitatively some aspects of the out of equilibrium phase transition.

Confirmation of the modified Bean model from simulations of superconducting vortices

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

Richardson, R.A.; Pla, O.; Nori, F.

From a very simple description of vortices and pinning centers, we obtain nonlinear density profiles of vortices in type-II dirty superconductors that result from changing an external magnetic field. The results confirm a modified Bean model description of these systems, following the Kim empirical form that relates the current inside the material to the local magnetic field. We also obtain realistic magnetization hysteresis loops and examine the discrete evolution of the density profiles in our systems. This evolution is not continuous, but takes place by the occurrence of avalanches of vortices promoted by the addition or extraction of vortices frommore » the edges of the system.« less

The evaluation and validation of copper (II) force field parameters of the Auxiliary Activity family 9 enzymes

NASA Astrophysics Data System (ADS)

Moses, Vuyani; Tastan Bishop, Özlem; Lobb, Kevin A.

2017-06-01

The Auxiliary Activity family 9 (AA9) proteins are Cu2+ coordinating enzymes which are crucial for the early stages of cellulose degradation. In this study, the force field parameters for copper-containing bonds in the Type 1 AA9 protein active site were established and used in a molecular dynamics simulation on a solvated, neutralized system containing an AA9 protein, Cu2+ and a β-cellulose surface. The copper to cellulose interaction was evident during the dynamics, which could also be accelerated by the use of high Cusbnd O van der Waals parameters. The interaction of AA9, Cu2+ and cellulose is described in detail.

Simulation of phase equilibria

NASA Astrophysics Data System (ADS)

Martin, Marcus Gary

The focus of this thesis is on the use of configurational bias Monte Carlo in the Gibbs ensemble. Unlike Metropolis Monte Carlo, which is reviewed in chapter I, configurational bias Monte Carlo uses an underlying Markov chain transition matrix which is asymmetric in such a way that it is more likely to attempt to move to a molecular conformation which has a lower energy than to one with a higher energy. Chapter II explains how this enables efficient simulation of molecules with complex architectures (long chains and branched molecules) for coexisting fluid phases (liquid, vapor, or supercritical), and also presents several of our recent extensions to this method. In chapter III we discuss the development of the Transferable Potentials for Phase Equilibria United Atom (TraPPE-UA) force field which accurately describes the fluid phase coexistence for linear and branched alkanes. Finally, in the fourth chapter the methods and the force field are applied to systems ranging from supercritical extraction to gas chromatography to illustrate the power and versatility of our approach.

Measurement of the transient shielding effectiveness of shielding cabinets

NASA Astrophysics Data System (ADS)

Herlemann, H.; Koch, M.

2008-05-01

Recently, new definitions of shielding effectiveness (SE) for high-frequency and transient electromagnetic fields were introduced by Klinkenbusch (2005). Analytical results were shown for closed as well as for non closed cylindrical shields. In the present work, the shielding performance of different shielding cabinets is investigated by means of numerical simulations and measurements inside a fully anechoic chamber and a GTEM-cell. For the GTEM-cell-measurements, a downscaled model of the shielding cabinet is used. For the simulations, the numerical tools CONCEPT II and COMSOL MULTIPHYSICS were available. The numerical results agree well with the measurements. They can be used to interpret the behaviour of the shielding effectiveness of enclosures as function of frequency. From the measurement of the electric and magnetic fields with and without the enclosure in place, the electric and magnetic shielding effectiveness as well as the transient shielding effectiveness of the enclosure are calculated. The transient SE of four different shielding cabinets is determined and discussed.

Numerical simulation of the compressible Orszag-Tang vortex. II. Supersonic flow. Interim report

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

Picone, J.M.; Dahlburg, R.B.

The numerical investigation of the Orszag-Tang vortex system in compressible magnetofluids will consider initial conditions with embedded supersonic regions. The simulations have initial average Mach numbers M = 1.0 and 1.5 and beta = 10/3 with Lundquist numbers S = 50, 100, or 200. The behavior of the system differs significantly from that found previously for the incompressible and subsonic analogs. Shocks form at the downstream boundaries of the embedded supersonic regions outside the central magnetic X-point and produce strong local current sheets which dissipate appreciable magnetic energy. Reconnection at the central X-point, which dominates the incompressible and subsonic systems,more » peaks later and has a smaller impact as M increases from 0.6 to 1.5. Similarly, correlation between the momentum and magnetic field begins significant growth later than in subsonic and incompressible flows. The shocks bound large compression regions, which dominate the wavenumber spectra of autocorrelations in mass density, velocity, and magnetic field.« less

Probing HeII Reionization at z>3.5 with Resolved HeII Lyman Alpha Forest Spectra

NASA Astrophysics Data System (ADS)

Worseck, Gabor

2017-08-01

The advent of GALEX and COS have revolutionized our view of HeII reionization, the final major phase transition of the intergalactic medium. COS spectra of the HeII Lyman alpha forest have confirmed with high confidence the high HeII transmission that signifies the completion of HeII reionization at z 2.7. However, the handful of z>3.5 quasars observed to date show a set of HeII transmission 'spikes' and larger regions with non-zero transmission that suggest HeII reionization was well underway by z=4. This is in striking conflict with predictions from state-of-the-art radiative transfer simulations of a HeII reionization driven by bright quasars. Explaining these measurements may require either faint quasars or more exotic sources of hard photons at z>4, with concomitant implications for HI reionization. However, many of the observed spikes are unresolved in G140L spectra and are significantly impacted by Poisson noise. Current data cannot reliably probe the ionization state of helium at z>3.5.We request 41 orbits to obtain science-grade G130M spectra of the two UV-brightest HeII-transmitting QSOs at z>3.5 to confirm and resolve their HeII transmission spikes as an unequivocal test of early HeII reionization. These spectra are complemented by recently obtained data from 8m telescopes: (1) Echelle spectra of the coeval HI Lya forest to map the underlying density field that modulates the HeII absorption, and (2) Our dedicated survey for foreground QSOs that may source the HeII transmission. Our recent HST programs revealed the only two viable targets to resolve the z>3.5 HeII Lyman alpha forest, and to conclusively solve this riddle.

Simulations of the Mg II K and Ca II 8542 Lines From an Alfvén Wave-Heated Flare Chromosphere

NASA Technical Reports Server (NTRS)

Kerr, Graham S.; Fletcher, Lyndsay; Russell, Alexander J. B.; Allred, Joel C.

2016-01-01

We use radiation hydrodynamic simulations to examine two models of solar flare chromospheric heating: Alfven wave dissipation and electron beam collisional losses. Both mechanisms are capable of strong chromospheric heating, and we show that the distinctive atmospheric evolution in the mid-to-upper chromosphere results in Mg II k-line emission that should be observably different between wave-heated and beam-heated simulations. We also present Ca II 8542 A profiles that are formed slightly deeper in the chromosphere. The Mg II k-line profiles from our wave-heated simulation are quite different from those from a beam-heated model and are more consistent with Interface Region Imaging Spectrograph observations. The predicted differences between the Ca II 8542 A in the two models are small. We conclude that careful observational and theoretical study of lines formed in the mid-to-upper chromosphere holds genuine promise for distinguishing between competing models for chromospheric heating inflares.

Comparing cosmological hydrodynamic simulations with observations of high- redshift galaxy formation

NASA Astrophysics Data System (ADS)

Finlator, Kristian Markwart

We use cosmological hydrodynamic simulations to study the impact of outflows and radiative feedback on high-redshift galaxies. For outflows, we consider simulations that assume (i) no winds, (ii) a "constant-wind" model in which the mass-loading factor and outflow speed are constant, and (iii) "momentum-driven" winds in which both parameters vary smoothly with mass. In order to treat radiative feedback, we develop a moment-based radiative transfer technique that operates in both post-processing and coupled radiative hydrodynamic modes. We first ask how outflows impact the broadband spectral energy distributions (SEDs) of six observed reionization-epoch galaxies. Simulations reproduce five regardless of the outflow prescription, while the sixth suggests an unusually bursty star formation history. We conclude that (i) simulations broadly account for available constraints on reionization-epoch galaxies, (ii) individual SEDs do not constrain outflows, and (iii) SED comparisons efficiently isolate objects that challenge simulations. We next study how outflows impact the galaxy mass metallicity relation (MZR). Momentum-driven outflows uniquely reproduce observations at z = 2. In this scenario, galaxies obey two equilibria: (i) The rate at which a galaxy processes gas into stars and outflows tracks its inflow rate; and (ii) The gas enrichment rate owing to star formation balances the dilution rate owing to inflows. Combining these conditions indicates that the MZR is dominated by the (instantaneous) variation of outflows with mass, with more-massive galaxies driving less gas into outflows per unit stellar mass formed. Turning to radiative feedback, we use post-processing simulations to study the topology of reionization. Reionization begins in overdensities and then "leaks" directly into voids, with filaments reionizing last owing to their high density and low emissivity. This result conflicts with previous findings that voids ionize last. We argue that it owes to the uniqely-biased emissivity field produced by our star formation prescriptions, which have previously been shown to reproduce numerous post-reionization constraints. Finally, preliminary results from coupled radiative hydrodynamic simulations indicate that reionization suppresses the star formation rate density by at most 10-20% by z = 5. This is much less than previous estimates, which we attribute to our unique reionization topology although confirmation will have to await more detailed modeling.

Pressure-anisotropy-induced nonlinearities in the kinetic magnetorotational instability

NASA Astrophysics Data System (ADS)

Squire, J.; Quataert, E.; Kunz, M. W.

2017-12-01

In collisionless and weakly collisional plasmas, such as hot accretion flows onto compact objects, the magnetorotational instability (MRI) can differ significantly from the standard (collisional) MRI. In particular, pressure anisotropy with respect to the local magnetic-field direction can both change the linear MRI dispersion relation and cause nonlinear modifications to the mode structure and growth rate, even when the field and flow perturbations are very small. This work studies these pressure-anisotropy-induced nonlinearities in the weakly nonlinear, high-ion-beta regime, before the MRI saturates into strong turbulence. Our goal is to better understand how the saturation of the MRI in a low-collisionality plasma might differ from that in the collisional regime. We focus on two key effects: (i) the direct impact of self-induced pressure-anisotropy nonlinearities on the evolution of an MRI mode, and (ii) the influence of pressure anisotropy on the `parasitic instabilities' that are suspected to cause the mode to break up into turbulence. Our main conclusions are: (i) The mirror instability regulates the pressure anisotropy in such a way that the linear MRI in a collisionless plasma is an approximate nonlinear solution once the mode amplitude becomes larger than the background field (just as in magnetohyrodynamics). This implies that differences between the collisionless and collisional MRI become unimportant at large amplitudes. (ii) The break up of large-amplitude MRI modes into turbulence via parasitic instabilities is similar in collisionless and collisional plasmas. Together, these conclusions suggest that the route to magnetorotational turbulence in a collisionless plasma may well be similar to that in a collisional plasma, as suggested by recent kinetic simulations. As a supplement to these findings, we offer guidance for the design of future kinetic simulations of magnetorotational turbulence.

MAGNETOHYDRODYNAMIC SIMULATION OF THE X2.2 SOLAR FLARE ON 2011 FEBRUARY 15. II. DYNAMICS CONNECTING THE SOLAR FLARE AND THE CORONAL MASS EJECTION

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

Inoue, S.; Magara, T.; Choe, G. S.

2015-04-20

We clarify a relationship between the dynamics of a solar flare and a growing coronal mass ejection (CME) by investigating the dynamics of magnetic fields during the X2.2-class flare taking place in the solar active region 11158 on 2011 February 15, based on simulation results obtained from Inoue et al. We found that the strongly twisted lines formed through tether-cutting reconnection in the twisted lines of a nonlinear force-free field can break the force balance within the magnetic field, resulting in their launch from the solar surface. We further discover that a large-scale flux tube is formed during the eruptionmore » as a result of the tether-cutting reconnection between the eruptive strongly twisted lines and these ambient weakly twisted lines. The newly formed large flux tube exceeds the critical height of the torus instability. Tether-cutting reconnection thus plays an important role in the triggering of a CME. Furthermore, we found that the tangential fields at the solar surface illustrate different phases in the formation of the flux tube and its ascending phase over the threshold of the torus instability. We will discuss these dynamics in detail.« less

On the plasma flow inside magnetic tornadoes on the Sun

NASA Astrophysics Data System (ADS)

Wedemeyer, Sven; Steiner, Oskar

2014-12-01

High-resolution observations with the Swedish 1-m Solar Telescope (SST) and the Solar Dynamics Observatory (SDO) reveal rotating magnetic field structures that extend from the solar surface into the chromosphere and the corona. These so-called magnetic tornadoes are primarily detected as rings or spirals of rotating plasma in the Ca II 854.2 nm line core (also known as chromospheric swirls). Detailed numerical simulations show that the observed chromospheric plasma motion is caused by the rotation of magnetic field structures, which again are driven by photospheric vortex flows at their footpoints. Under the right conditions, two vortex flow systems are stacked on top of each other. We refer to the lower vortex, which extends from the low photosphere into the convection zone, as intergranular vortex flow (IVF). Once a magnetic field structure is co-located with an IVF, the rotation is mediated into the upper atmospheric layers and an atmospheric vortex flow (AVF, or magnetic tornado) is generated. In contrast to the recent work by Shelyag et al. (2013, ApJ, 776, L4), we demonstrate that particle trajectories in a simulated magnetic tornado indeed follow spirals and argue that the properties of the trajectories decisively depend on the location in the atmosphere and the strength of the magnetic field.

Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases

PubMed Central

Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.

2014-01-01

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374

The dynamics of copper intercalated molybdenum ditelluride

NASA Astrophysics Data System (ADS)

Onofrio, Nicolas; Guzman, David; Strachan, Alejandro

2016-11-01

Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties, and interaction with metals are needed in order to accelerate their incorporation into commercial products. Interatomic potentials enable large-scale atomistic simulations connecting first principle methods and devices. We present a ReaxFF reactive force field to describe molybdenum ditelluride and its interactions with copper. We optimized the force field parameters to describe the energetics, atomic charges, and mechanical properties of (i) layered MoTe2, Mo, and Cu in various phases, (ii) the intercalation of Cu atoms and small clusters within the van der Waals gap of MoTe2, and (iii) bond dissociation curves. The training set consists of an extensive set of first principles calculations computed using density functional theory (DFT). We validate the force field via the prediction of the adhesion of a single layer MoTe2 on a Cu(111) surface and find good agreement with DFT results not used in the training set. We characterized the mobility of the Cu ions intercalated into MoTe2 under the presence of an external electric field via finite temperature molecular dynamics simulations. The results show a significant increase in drift velocity for electric fields of approximately 0.4 V/Å and that mobility increases with Cu ion concentration.

Modelling the impulse diffraction field of shear waves in transverse isotropic viscoelastic medium

NASA Astrophysics Data System (ADS)

Chatelin, Simon; Gennisson, Jean-Luc; Bernal, Miguel; Tanter, Mickael; Pernot, Mathieu

2015-05-01

The generation of shear waves from an ultrasound focused beam has been developed as a major concept for remote palpation using shear wave elastography (SWE). For muscular diagnostic applications, characteristics of the shear wave profile will strongly depend on characteristics of the transducer as well as the orientation of muscular fibers and the tissue viscoelastic properties. The numerical simulation of shear waves generated from a specific probe in an anisotropic viscoelastic medium is a key issue for further developments of SWE in fibrous soft tissues. In this study we propose a complete numerical tool allowing 3D simulation of a shear wave front in anisotropic viscoelastic media. From the description of an ultrasonic transducer, the shear wave source is simulated by using Field’s II software and shear wave propagation described by using the Green’s formalism. Finally, the comparison between simulations and experiments are successively performed for both shear wave velocity and dispersion profile in a transverse isotropic hydrogel phantom, in vivo forearm muscle and in vivo biceps brachii.

An AeroCom Assessment of Black Carbon in Arctic Snow and Sea Ice

NASA Technical Reports Server (NTRS)

Jiao, C.; Flanner, M. G.; Balkanski, Y.; Bauer, S. E.; Bellouin, N.; Bernsten, T. K.; Bian, H.; Carslaw, K. S.; Chin, M.; DeLuca, N.;

Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

NASA Astrophysics Data System (ADS)

Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

2005-09-01

Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

Formation of Accelerated Backstreaming Particles within the Quasi-perpendicular Ion Terrestrial Foreshock: 2D Full-Particle and Test-particles simulations

NASA Astrophysics Data System (ADS)

Savoini, P.; Lembege, B.

2016-12-01

Backstreaming ion populations are observed upstream of the Terrestrial bow shock and form the ion foreshock. Two distinct populations have been firmly identified by spacecrafts within the quasi-perpendicular shock region (i.e. for 45° ≤ ΘBn ≤ 90°, where ΘBn is the angle between the shock normal and the upstream magnetostatic field): so called (i) field-aligned ion beams (« FAB ») characterized by a gyrotropic distribution, and (ii) gyro-phase bunched ions («GPB »), characterized by a NON gyrotropic distribution.The origin of these backstreaming ions is still an important unresolved question which can be partially analyzed with the help of 2D PIC simulation of a curved shock, where full curvature effects, time of flight effects and both electrons and ions dynamics are fully included by a self consistent approach. Our previous analysis (Savoini et Lembege, 2015) has evidenced that these two populations can be generated directly by the macroscopic fields at the shock front itself. Present results based on ion trajectories analysis confirm: (i) the importance of the interaction time ΔTinter spent by ions within the shock front. "GPB" population is characterized by a very short interaction time (ΔTinter = 1 to 2 tci) in comparison to the "FAB" population (ΔTinter = 2 tci to 10 tci), where tci is the upstream ion gyroperiod. (ii) the key role of the injection angle (i.e. defined between the normal of the shock front and the gyration velocity at the time incoming ions hit the shock front) which strongly differs between FAB and GPB ions. (iii) that "FAB" ions drift along the shock front and « scan » a large ΘBn range (up to 20°) which explains the loss of their initial gyro-phase, before being re-injected into the upstream region. Moreover, our test-particule simulations evidence the importance of the shock wave profile for both the « FAB » and « GPB » populations. Such results show that the reflection process is not continuous in time and in space, but strongly depends of the local shock front profile met by incoming ions at their hitting time. The same simulations also emphasize the slight decrease of backstreaming ions density when the electric field space charge effect present within the shock front is artificially canceled. A comparison between self-consistent and test-particles results will be presented in more details.

Development of Partially-Coherent Wavefront Propagation Simulation Methods for 3rd and 4th Generation Synchrotron Radiation Sources.

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

Chubar O.; Berman, L; Chu, Y.S.

2012-04-04

Partially-coherent wavefront propagation calculations have proven to be feasible and very beneficial in the design of beamlines for 3rd and 4th generation Synchrotron Radiation (SR) sources. These types of calculations use the framework of classical electrodynamics for the description, on the same accuracy level, of the emission by relativistic electrons moving in magnetic fields of accelerators, and the propagation of the emitted radiation wavefronts through beamline optical elements. This enables accurate prediction of performance characteristics for beamlines exploiting high SR brightness and/or high spectral flux. Detailed analysis of radiation degree of coherence, offered by the partially-coherent wavefront propagation method, ismore » of paramount importance for modern storage-ring based SR sources, which, thanks to extremely small sub-nanometer-level electron beam emittances, produce substantial portions of coherent flux in X-ray spectral range. We describe the general approach to partially-coherent SR wavefront propagation simulations and present examples of such simulations performed using 'Synchrotron Radiation Workshop' (SRW) code for the parameters of hard X-ray undulator based beamlines at the National Synchrotron Light Source II (NSLS-II), Brookhaven National Laboratory. These examples illustrate general characteristics of partially-coherent undulator radiation beams in low-emittance SR sources, and demonstrate advantages of applying high-accuracy physical-optics simulations to the optimization and performance prediction of X-ray optical beamlines in these new sources.« less

Effects of single and combined low frequency electromagnetic fields and simulated microgravity on gene expression of human mesenchymal stem cells during chondrogenesis

PubMed Central

Hammerschmid, Florian; Blum, Helmut; Krebs, Stefan; Redeker, Julia I.; Holzapfel, Boris M.; Jansson, Volkmar; Müller, Peter E.

2016-01-01

Introduction Low frequency electromagnetic fields (LF-EMF) and simulated microgravity (SMG) have been observed to affect chondrogenesis. A controlled bioreactor system was developed to apply LF-EMF and SMG singly or combined during chondrogenic differentiation of human mesenchymal stem cells (hMSCs) in 3D culture. Material and methods An external motor gear SMG bioreactor was combined with magnetic Helmholtz coils for EMF (5 mT; 15 Hz). Pellets of hMSCs (±TGF-β3) were cultured (P5) under SMG, LF-EMF, LF-EMF/SMG and control (1 g) conditions for 3 weeks. Sections were stained with safranin-O and collagen type II. Gene expression was evaluated by microarray and real-time polymerase chain reaction analysis. Results Simulated microgravity application significantly changed gene expression; specifically, COLXA1 but also COL2A1, which represents the chondrogenic potential, were reduced (p < 0.05). Low frequency electromagnetic fields application showed no gene expression changes on a microarray basis. LF-EMF/SMG application obtained significant different expression values from cultures obtained under SMG conditions with a re-increase of COL2A1, therefore rescuing the chondrogenic potential, which had been lowered by SMG. Conclusions Simulated microgravity lowered hypertrophy but also the chondrogenic potential of hMSCs. Combined LF-EMF/SMG provided a rescue effect of the chondrogenic potential of hMSCs although no LF-EMF effect was observed under optimal conditions. The study provides new insights into how LF-EMF and SMG affect chondrogenesis of hMSCs and how they generate interdependent effects. PMID:29765449

Modelling of the Saturnian Kilometric Radiation (SKR)

NASA Astrophysics Data System (ADS)

Cecconi, B.; Lamy, L.; Prangé, R.; Zarka, P.; Hess, S.; Clarke, J. T.; Nichols, J.

2008-12-01

The Saturnian Kilometric Radiation (SKR), discovered by the Voyager spacecraft in the 1980's, is observed quasi-continuously by Cassini since 2003. Study of 3 years of SKR observations by RPWS (Radio and Plasma Wave Science) revealed three recurrent features of SKR dynamic spectra : (i) discrete arcs, presumably caused by the anisotropy of the radio emission pattern combined to the observer's motion, (ii) an equatorial shadow zone around the planet (observed near perikrones) and (iii) signal extinctions at high northern latitudes. We model these features using the code PRES (Planetary Radio Emission Simulator) that assumes radio emissions to be generated via the Cyclotron Maser Instability for simulating observed dynamic spectra. We show that observed arc-like structures imply radio sources in partial (~90%) corotation, located on magnetic field lines of invariant latitude 70° to 75°, and emitting at oblique angle from the local magnetic field with a cone angle that varies with frequency. Then, based on the previously demonstrated conjugacy between UV and SKR sources, we successfully model the equatorial shadow zone as well as northern latitude SKR extinctions assuming time variable radio sources distributed along field lines with footprints along the daily UV oval measured from HST images.

Rotor Wake Vortex Definition: Initial Evaluation of 3-C PIV Results of the Hart-II Study

NASA Technical Reports Server (NTRS)

Burley, Casey L.; Brooks, Thomas F.; vanderWall, Berend; Richard, Hughes; Raffel, Markus; Beaumier, Philippe; Delrieux, Yves; Lim, Joon W.; Yu, Yung H.; Tung, Chee

2002-01-01

An initial evaluation is made of extensive three-component (3C) particle image velocimetry (PIV) measurements within the wake across a rotor disk plane. The model is a 40 percent scale BO-105 helicopter main rotor in forward flight simulation. This study is part of the HART II test program conducted in the German-Dutch Wind Tunnel (DNW). Included are wake vortex field measurements over the advancing and retreating sides of the rotor operating at a typical descent landing condition important for impulsive blade-vortex interaction (BVI) noise. Also included are advancing side results for rotor angle variations from climb to steep descent. Using detailed PIV vector maps of the vortex fields, methods of extracting key vortex parameters are examined and a new method was developed and evaluated. An objective processing method, involving a center-of-vorticity criterion and a vorticity 'disk' integration, was used to determine vortex core size, strength, core velocity distribution characteristics, and unsteadiness. These parameters are mapped over the rotor disk and offer unique physical insight for these parameters of importance for rotor noise and vibration prediction.

Electronic, magnetic properties and phase diagrams of system with Fe4N compound: An ab initio calculations and Monte Carlo study

NASA Astrophysics Data System (ADS)

Masrour, R.; Jabar, A.; Hlil, E. K.

2018-05-01

Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate the electronic and magnetic properties of the Fe4N compound. Polarized spin and spin-orbit coupling are included in calculations within the framework of the ferromagnetic state between Fe(I) and Fe(II) in Fe4N compound. We have used the obtained data from abinitio calculations as an input in Monte Carlo simulation to calculate the magnetic properties of this compounds such as the ground state phase diagrams, total and partial magnetization of Fe(I) and Fe(II) as well as the transition temperatures are computed. The variation of magnetization with the crystal field are also studied. The magnetic hysteresis cycle of the same Fe4N compound are determined for different values of temperatures and crystal field values. The two-step hysteresis loop are evidenced, which is typical for Fe4N structure. The ferromagnetic and superparamagnetic phase is observed as well.

Modeling microbiological and chemical processes in municipal solid waste bioreactor, Part II: Application of numerical model BIOKEMOD-3P.

PubMed

Gawande, Nitin A; Reinhart, Debra R; Yeh, Gour-Tsyh

2010-02-01

Biodegradation process modeling of municipal solid waste (MSW) bioreactor landfills requires the knowledge of various process reactions and corresponding kinetic parameters. Mechanistic models available to date are able to simulate biodegradation processes with the help of pre-defined species and reactions. Some of these models consider the effect of critical parameters such as moisture content, pH, and temperature. Biomass concentration is a vital parameter for any biomass growth model and often not compared with field and laboratory results. A more complex biodegradation model includes a large number of chemical and microbiological species. Increasing the number of species and user defined process reactions in the simulation requires a robust numerical tool. A generalized microbiological and chemical model, BIOKEMOD-3P, was developed to simulate biodegradation processes in three-phases (Gawande et al. 2009). This paper presents the application of this model to simulate laboratory-scale MSW bioreactors under anaerobic conditions. BIOKEMOD-3P was able to closely simulate the experimental data. The results from this study may help in application of this model to full-scale landfill operation.

Formation of gyrotropic and non gyrotropic field-aligned beams in the Earth's quasi-perpendicular Ion Foreshock: Full-particle 2D simulation results

NASA Astrophysics Data System (ADS)

Savoini, P.; Lembege, B.

2013-12-01

The ion foreshock located upstream of the Earth's bow shock is populated with ions reflected back by the shock front with an high energy gain. In-situ spacecraft measurements have clearly established the existence of two distinct populations in the foreshock upstream of quasi-perpendicular shock region (i.e. for 45° ≤ ΘBn≤ 90°, where ΘBn is the angle between the shock normal and the upstream magnetostatic field): (i) field-aligned (';FAB') ion beams characterized by a gyrotropic distribution, and (ii) gyro-phase bunched (';GPB') ions characterized by a NON gyrotropic distribution, which exhibits a non-vanishing perpendicular bulk velocity. The purpose of the present work is to identify the possible sources of the different backstreaming ions and is based on the use of 2D PIC simulations of a curved shock, where full curvature effects, time of flight effects and both electrons and ions dynamics are fully described by a self consistent approach. Our analysis evidences that the two populations mentionned above may have different origins identified both in terms of interaction time and distance of penetration within the shock front. In particular, ours simulations evidence that "GPB" and ';FAB' populations are characterized by a short (Δinter= 1 to 2 tci) and much larger (Δinter= 1 to 10 tci) interaction time respectively, where τci is the ion upstream gyroperiod. In addition, a deeper statistical analysis of ion trajectories evidences that: (i) both populations can be discriminated in terms of injection angle into the shock front (i.e. defined between the local normal to the shock front and the gyration velocity vector at the time ions reach the front). Such a behavior explains how reflected ions can be splitted in the observed two populations "FAB" and "GPB". (ii) ion trajectories strongly differ between the "FAB" and "GPB" populations at the shock front. In particular, ';FAB' ions suffer multi-bounces whereas ';GPB '; ions make only one bounce. Such differences can explain why the ';FAB' population loses their gyro-phase coherency and become gyrotropic which is not the case for the "GPB". As evidenced by these simulations the origin of both populations can be associated directly to their interaction with the shock front itself and do not require any upstream instability which can be another source for such backstreaming ions.

Earth as a Tool for Astrobiology—A European Perspective

NASA Astrophysics Data System (ADS)

Martins, Zita; Cottin, Hervé; Kotler, Julia Michelle; Carrasco, Nathalie; Cockell, Charles S.; de la Torre Noetzel, Rosa; Demets, René; de Vera, Jean-Pierre; d'Hendecourt, Louis; Ehrenfreund, Pascale; Elsaesser, Andreas; Foing, Bernard; Onofri, Silvano; Quinn, Richard; Rabbow, Elke; Rettberg, Petra; Ricco, Antonio J.; Slenzka, Klaus; Stalport, Fabien; ten Kate, Inge L.; van Loon, Jack J. W. A.; Westall, Frances

2017-07-01

Scientists use the Earth as a tool for astrobiology by analyzing planetary field analogues (i.e. terrestrial samples and field sites that resemble planetary bodies in our Solar System). In addition, they expose the selected planetary field analogues in simulation chambers to conditions that mimic the ones of planets, moons and Low Earth Orbit (LEO) space conditions, as well as the chemistry occurring in interstellar and cometary ices. This paper reviews the ways the Earth is used by astrobiologists: (i) by conducting planetary field analogue studies to investigate extant life from extreme environments, its metabolisms, adaptation strategies and modern biosignatures; (ii) by conducting planetary field analogue studies to investigate extinct life from the oldest rocks on our planet and its biosignatures; (iii) by exposing terrestrial samples to simulated space or planetary environments and producing a sample analogue to investigate changes in minerals, biosignatures and microorganisms. The European Space Agency (ESA) created a topical team in 2011 to investigate recent activities using the Earth as a tool for astrobiology and to formulate recommendations and scientific needs to improve ground-based astrobiological research. Space is an important tool for astrobiology (see Horneck et al. in Astrobiology, 16:201-243, 2016; Cottin et al., 2017), but access to space is limited. Complementing research on Earth provides fast access, more replications and higher sample throughput. The major conclusions of the topical team and suggestions for the future include more scientifically qualified calls for field campaigns with planetary analogy, and a centralized point of contact at ESA or the EU for the organization of a survey of such expeditions. An improvement of the coordinated logistics, infrastructures and funding system supporting the combination of field work with planetary simulation investigations, as well as an optimization of the scientific return and data processing, data storage and data distribution is also needed. Finally, a coordinated EU or ESA education and outreach program would improve the participation of the public in the astrobiological activities.

Element specific determination of the magnetic properties of two macrocyclic tetranuclear 3d-4f complexes with a Cu3Tb core by means of X-ray magnetic circular dichroism (XMCD).

PubMed

Balinski, K; Schneider, L; Wöllermann, J; Buling, A; Joly, L; Piamonteze, C; Feltham, H L C; Brooker, S; Powell, A K; Delley, B; Kuepper, K

2018-06-20

We apply X-ray magnetic circular dichroism to study the internal magnetic structure of two very promising star shaped macrocyclic complexes with a CuII3TbIII core. These complexes are rare examples prepared with a macrocyclic ligand that show indications of SMM (Single Molecule Magnet) behavior, and they differ only in ring size: one has a propylene linked macrocycle, [CuII3TbIII(LPr)(NO3)2(MeOH)(H2O)2](NO3)·3H2O (nickname: Cu3Tb(LPr)), and the other has the butylene linked analogue, [CuII3TbIII(LBu)(NO3)2(MeOH)(H2O)](NO3)·3H2O (nickname: Cu3Tb(LBu)). We analyze the orbital and spin contributions to the Cu and Tb ions quantitatively by applying the spin and orbital sum rules concerning the L2 (M4)/L3 (M5) edges. In combination with appropriate ligand field simulations, we demonstrate that the Tb(iii) ions contribute with high orbital magnetic moments to the magnetic anisotropy, whereas the ligand field determines the easy axis of magnetization. Furthermore, we confirm that the Cu(ii) ions in both molecules are in a divalent valence state, the magnetic moments of the three Cu ions appear to be canted due to 3d-3d intramolecular magnetic interactions. For Cu3Tb(LPr), the corresponding element specific magnetization loops reflect that the Cu(ii) contribution to the overall magnetic picture becomes more important as the temperature is lowered. This implies a low value for the 3d-4f coupling.

Suitability of open-field autorefractors as pupillometers and instrument design effects.

PubMed

Otero, Carles; Aldaba, Mikel; Ferrer, Oriol; Gascón, Andrea; Ondategui-Parra, Juan C; Pujol, Jaume

2017-01-01

To determine the agreement and repeatability of the pupil measurement obtained with VIP-200 (Neuroptics), PowerRef II (Plusoptix), WAM-5500 (Grand Seiko) and study the effects of instrument design on pupillometry. Forty patients were measured twice in low, mid and high mesopic. Repeatability was analyzed with the within-subject standard deviation (Sw) and paired t -tests. Agreement was studied with Bland-Altman plots and repeated measures ANOVA. Instrument design analysis consisted on measuring pupil size with PowerRef II simulating monocular and binocular conditions as well as with proximity cues and without proximity cues. The mean difference (±standard deviation) between test-retest for low, mid and high mesopic conditions were, respectively: -0.09 (±0.16), -0.05 (±0.18) and -0.08 (±0.23) mm for Neuroptics, -0.05 (±0.17), -0.12 (±0.23) and -0.17 (±0.34) mm for WAM-5500, -0.04 (±0.27), -0.13 (±0.37) and -0.11 (±0.28) mm for PowerRef II. Regarding agreement with Neuroptics, the mean difference for low, mid and high mesopic conditions were, respectively: -0.48 (±0.35), -0.83 (±0.52) and -0.38 (±0.56) mm for WAM-5500, -0.28 (±0.56), -0.70 (±0.55) and -0.61 (±0.54) mm for PowerRef II. The mean difference of binocular minus monocular pupil measurements was: -0.83 (±0.87) mm; and with proximity cues minus without proximity cues was: -0.30 (±0.77) mm. All the instruments show similar repeat-ability. In all illumination conditions, agreement of Neuroptics with WAM-5500 and PowerRef II is not good enough, which can be partially induced due to their open field design.

Java-based Graphical User Interface for MAVERIC-II

NASA Technical Reports Server (NTRS)

Seo, Suk Jai

2005-01-01

A computer program entitled "Marshall Aerospace Vehicle Representation in C II, (MAVERIC-II)" is a vehicle flight simulation program written primarily in the C programming language. It is written by James W. McCarter at NASA/Marshall Space Flight Center. The goal of the MAVERIC-II development effort is to provide a simulation tool that facilitates the rapid development of high-fidelity flight simulations for launch, orbital, and reentry vehicles of any user-defined configuration for all phases of flight. MAVERIC-II has been found invaluable in performing flight simulations for various Space Transportation Systems. The flexibility provided by MAVERIC-II has allowed several different launch vehicles, including the Saturn V, a Space Launch Initiative Two-Stage-to-Orbit concept and a Shuttle-derived launch vehicle, to be simulated during ascent and portions of on-orbit flight in an extremely efficient manner. It was found that MAVERIC-II provided the high fidelity vehicle and flight environment models as well as the program modularity to allow efficient integration, modification and testing of advanced guidance and control algorithms. In addition to serving as an analysis tool for techno logy development, many researchers have found MAVERIC-II to be an efficient, powerful analysis tool that evaluates guidance, navigation, and control designs, vehicle robustness, and requirements. MAVERIC-II is currently designed to execute in a UNIX environment. The input to the program is composed of three segments: 1) the vehicle models such as propulsion, aerodynamics, and guidance, navigation, and control 2) the environment models such as atmosphere and gravity, and 3) a simulation framework which is responsible for executing the vehicle and environment models and propagating the vehicle s states forward in time and handling user input/output. MAVERIC users prepare data files for the above models and run the simulation program. They can see the output on screen and/or store in files and examine the output data later. Users can also view the output stored in output files by calling a plotting program such as gnuplot. A typical scenario of the use of MAVERIC consists of three-steps; editing existing input data files, running MAVERIC, and plotting output results.

Field emission electric propulsion thruster modeling and simulation

NASA Astrophysics Data System (ADS)

Vanderwyst, Anton Sivaram

Electric propulsion allows space rockets a much greater range of capabilities with mass efficiencies that are 1.3 to 30 times greater than chemical propulsion. Field emission electric propulsion (FEEP) thrusters provide a specific design that possesses extremely high efficiency and small impulse bits. Depending on mass flow rate, these thrusters can emit both ions and droplets. To date, fundamental experimental work has been limited in FEEP. In particular, detailed individual droplet mechanics have yet to be understood. In this thesis, theoretical and computational investigations are conducted to examine the physical characteristics associated with droplet dynamics relevant to FEEP applications. Both asymptotic analysis and numerical simulations, based on a new approach combining level set and boundary element methods, were used to simulate 2D-planar and 2D-axisymmetric probability density functions of the droplets produced for a given geometry and electrode potential. The combined algorithm allows the simulation of electrostatically-driven liquids up to and after detachment. Second order accuracy in space is achieved using a volume of fluid correction. The simulations indicate that in general, (i) lowering surface tension, viscosity, and potential, or (ii) enlarging electrode rings, and needle tips reduce operational mass efficiency. Among these factors, surface tension and electrostatic potential have the largest impact. A probability density function for the mass to charge ratio (MTCR) of detached droplets is computed, with a peak around 4,000 atoms per electron. High impedance surfaces, strong electric fields, and large liquid surface tension result in a lower MTCR ratio, which governs FEEP droplet evolution via the charge on detached droplets and their corresponding acceleration. Due to the slow mass flow along a FEEP needle, viscosity is of less importance in altering the droplet velocities. The width of the needle, the composition of the propellant, the current and the mass efficiency are interrelated. The numerical simulations indicate that more electric power per Newton of thrust on a narrow needle with a thin, high surface tension fluid layer gives better performance.

Deep-Earth reactor: nuclear fission, helium, and the geomagnetic field.

PubMed

Hollenbach, D F; Herndon, J M

2001-09-25

Geomagnetic field reversals and changes in intensity are understandable from an energy standpoint as natural consequences of intermittent and/or variable nuclear fission chain reactions deep within the Earth. Moreover, deep-Earth production of helium, having (3)He/(4)He ratios within the range observed from deep-mantle sources, is demonstrated to be a consequence of nuclear fission. Numerical simulations of a planetary-scale geo-reactor were made by using the SCALE sequence of codes. The results clearly demonstrate that such a geo-reactor (i) would function as a fast-neutron fuel breeder reactor; (ii) could, under appropriate conditions, operate over the entire period of geologic time; and (iii) would function in such a manner as to yield variable and/or intermittent output power.

Linear simulation of the stationary eddies in a GCM. II - The 'Mountain' model

NASA Technical Reports Server (NTRS)

Nigam, Sumant; Held, Isaac M.; Lyons, Steven W.

1988-01-01

Linear stationary wave theory is used to account for zonal asymmetries of the winter-averaged tropospheric circulation obtained in a GCM. The eddy zonal velocity field in the upper troposphere indicates that the orographic and thermal plus transient contributions are nearly equal in amplitude, while the eddy meridional velocity field (which is dominated by shorter zonal scales) shows the orographic contribution to be dominant. The two contributions are found to be roughly in phase over the east Asian coast, and they contribute roughly equal amounts to the low level Siberian high. Results indicate that the 300 mb extratropical response to tropical forcing reaches 50 gpm over Alaska, and that the responses to sensible heating and lower tropospheric transients are strongly anticorrelated.

New Constraints on the Hard Ionizing Photon Budget and the Lifetime and Obscuration of Quasars During the Epoch of Helium Reionization

NASA Astrophysics Data System (ADS)

Davies, Frederick

2017-08-01

The epoch of helium reionization was a major milestone in the history of the Universe, a direct consequence of supermassive black hole growth and the cumulative output of hard ionizing photons by quasars. Our observations of the He II Ly-alpha forest with HST/COS in 26 quasar sightlines show strong fluctuations at z 3, consistent with our state-of-the-art simulations of the He II reionization epoch. However, our detection of transmission at z > 3.5 is inconsistent with all He II reionization models. Resolving this puzzle requires an extensive parameter study of He II reionization, which we propose to carry out using our fast, efficient simulations. The He II Ly-alpha forest is also sensitive to the effect of quasar radiation illuminating the intergalactic medium, known as the proximity effect. We have performed an ambitious ground-based imaging and spectroscopic survey for z 3 quasars in the foreground of HeII sightlines observed with HST/COS, and statistically detected the transverse proximity effect for the first time. The strength of this effect depends on both the quasar lifetime and the opening angle of quasar emission (or the fraction of obscured quasars), and we propose to use our He II reionization simulations to interpret this new measurement. Finally, the line-of-sight proximity effect due to the background quasar provides an independent constraint on the quasar lifetime. Our preliminary comparison of He II spectra to our radiative transfer simulations suggests a quasar lifetime > 10 Myr. We propose to use our He II reionization simulations to model this diverse set of observations and fully capitalize on the far-UV legacy of HST.

Intrinsic alignments of galaxies in the MassiveBlack-II simulation: Analysis of two-point statistics

DOE PAGES

Tenneti, Ananth; Singh, Sukhdeep; Mandelbaum, Rachel; ...

2015-03-11

The intrinsic alignment of galaxies with the large-scale density field in an important astrophysical contaminant in upcoming weak lensing surveys. We present detailed measurements of the galaxy intrinsic alignments and associated ellipticity-direction (ED) and projected shape (w g₊) correlation functions for galaxies in the cosmological hydrodynamic MassiveBlack-II (MB-II) simulation. We carefully assess the effects on galaxy shapes, misalignment of the stellar component with the dark matter shape and two-point statistics of iterative weighted (by mass and luminosity) definitions of the (reduced and unreduced) inertia tensor. We find that iterative procedures must be adopted for a reliable measurement of the reducedmore » tensor but that luminosity versus mass weighting has only negligible effects. Both ED and w g₊ correlations increase in amplitude with subhalo mass (in the range of 10¹⁰ – 6.0 X 10¹⁴h⁻¹ M ⊙), with a weak redshift dependence (from z = 1 to z = 0.06) at fixed mass. At z ~ 0.3, we predict a w g₊ that is in reasonable agreement with SDSS LRG measurements and that decreases in amplitude by a factor of ~ 5–18 for galaxies in the LSST survey. We also compared the intrinsic alignment of centrals and satellites, with clear detection of satellite radial alignments within the host halos. Finally, we show that w g₊ (using subhalos as tracers of density and w δ (using dark matter density) predictions from the simulations agree with that of non-linear alignment models (NLA) at scales where the 2-halo term dominates in the correlations (and tabulate associated NLA fitting parameters). The 1-halo term induces a scale dependent bias at small scales which is not modeled in the NLA model.« less

Hydrogeologic setting, hydraulic properties, and ground-water flow at the O-Field area of Aberdeen Proving Ground, Maryland

USGS Publications Warehouse

Banks, W.S.; Smith, B.S.; Donnelly, C.A.

1996-01-01

The U.S. Army disposed chemical agents, laboratory materials, and unexploded ordnance at O-Field in the Edgewood area of Aberdeen Proving Ground, Maryland, from before World War II until at least the 1950's. Soil, ground water, surface water,and wetland sediments in the O-Field area were contaminated from the disposal activity. A ground-water-flow model of the O-Field area was constructed by the U.S. Geological Survey (USGS) in 1989 to simulate flow in the central and southern part of the Gunpowder Neck. The USGS began an additional study of the contamination in the O-Field area in cooperation with the U.S. Army in 1990 to (1) further define the hydrogeologic framework of the O-Field area, (2) characterize the hydraulic properties of the aquifers and confining units, and (3) define ground-water flow paths at O-Field based on the current data and simulations of ground-water flow. A water-table aquifer, an upper confining unit, and an upper confined aquifer comprise the shallow ground-water aquifer system of the O-Field area. A lower confining unit, through which ground-water movement is negligible, is considered a lower boundary to the shallow aquifer system. These units are all part of the Pleistocene Talbot Formation. The model developed in the previous study was redesigned using the data collected during this study and emphasized New O-Field. The current steady-state model was calibrated to water levels of June 1993. The rate of ground-water flow calculated by the model was approximately 0.48 feet per day (ft/d) and the rate determined from chlorofluorocarbon dates was approximately 0.39 ft/d.

FAST MAGNETIC FIELD AMPLIFICATION IN THE EARLY UNIVERSE: GROWTH OF COLLISIONLESS PLASMA INSTABILITIES IN TURBULENT MEDIA

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

Falceta-Gonçalves, D.; Kowal, G.

2015-07-20

In this work we report on a numerical study of the cosmic magnetic field amplification due to collisionless plasma instabilities. The collisionless magnetohydrodynamic equations derived account for the pressure anisotropy that leads, in specific conditions, to the firehose and mirror instabilities. We study the time evolution of seed fields in turbulence under the influence of such instabilities. An approximate analytical time evolution of the magnetic field is provided. The numerical simulations and the analytical predictions are compared. We found that (i) amplification of the magnetic field was efficient in firehose-unstable turbulent regimes, but not in the mirror-unstable models; (ii) the growthmore » rate of the magnetic energy density is much faster than the turbulent dynamo; and (iii) the efficient amplification occurs at small scales. The analytical prediction for the correlation between the growth timescales and pressure anisotropy is confirmed by the numerical simulations. These results reinforce the idea that pressure anisotropies—driven naturally in a turbulent collisionless medium, e.g., the intergalactic medium, could efficiently amplify the magnetic field in the early universe (post-recombination era), previous to the collapse of the first large-scale gravitational structures. This mechanism, though fast for the small-scale fields (∼kpc scales), is unable to provide relatively strong magnetic fields at large scales. Other mechanisms that were not accounted for here (e.g., collisional turbulence once instabilities are quenched, velocity shear, or gravitationally induced inflows of gas into galaxies and clusters) could operate afterward to build up large-scale coherent field structures in the long time evolution.« less

Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation.

PubMed

Wang, Yu; Helminen, Emily; Jiang, Jingfeng

2015-09-01

Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time. Representative examples were used to demonstrate capabilities of this virtual simulation platform. In the first set of three ultrasound simulation examples, three heterogeneous volumes of interest were selected from a virtual breast ultrasound phantom to perform sophisticated ultrasound simulations. These resultant B-mode images realistically represented the underlying complex but known media. In the second set of three QUE examples, advanced applications in QUE were simulated. The first QUE example was to show breast tumors with complex shapes and/or compositions. The resultant strain images showed complex patterns that were normally seen in freehand clinical ultrasound data. The second and third QUE examples demonstrated (deformation-dependent) nonlinear strain imaging and time-dependent strain imaging, respectively. The proposed virtual QUE platform was implemented and successfully tested in this study. Through show-case examples, the proposed work has demonstrated its capabilities of creating sophisticated QUE data in a way that cannot be done through the manufacture of physical tissue-mimicking phantoms and other software. This open software architecture will soon be made available in the public domain and can be readily adapted to meet specific needs of different research groups to drive innovations in QUE.

Modeling hexavalent chromium reduction in groundwater in field-scale transport and laboratory batch experiments

USGS Publications Warehouse

Friedly, J.C.; Davis, J.A.; Kent, D.B.

1995-01-01

A plausible and consistent model is developed to obtain a quantitative description of the gradual disappearance of hexavalent chromium (Cr(VI)) from groundwater in a small-scale field tracer test and in batch kinetic experiments using aquifer sediments under similar chemical conditions. The data exhibit three distinct timescales. Fast reduction occurs in well-stirred batch reactors in times much less than 1 hour and is followed by slow reduction over a timescale of the order of 2 days. In the field, reduction occurs on a timescale of the order of 8 days. The model is based on the following hypotheses. The chemical reduction reaction occurs very fast, and the longer timescales are caused by diffusion resistance. Diffusion into the secondary porosity of grains causes the apparent slow reduction rate in batch experiments. In the model of the field experiments, the reducing agent, heavy Fe(II)-bearing minerals, is heterogeneously distributed in thin strata located between larger nonreducing sand lenses that comprise the bulk of the aquifer solids. It is found that reducing strata of the order of centimeters thick are sufficient to contribute enough diffusion resistance to cause the observed longest timescale in the field. A one-dimensional advection/dispersion model is formulated that describes the major experimental trends. Diffusion rates are estimated in terms of an elementary physical picture of flow through a stratified medium containing identically sized spherical grains. Both reduction and sorption reactions are included. Batch simulation results are sensitive to the fraction of reductant located at or near the surface of grains, which controls the amount of rapid reduction, and the secondary porosity, which controls the rate of slow reduction observed in batch experiments. Results of Cr(VI) transport simulations are sensitive to the thickness and relative size of the reducing stratum. Transport simulation results suggest that nearly all of the reductant must be located in the reducing stratum. Within this context and as long as there is adequate reductive capacity present, the transport simulation results are insensitive to the parameters important for the batch simulations. The results illustrate how a combination of field measurements and batch laboratory studies can be used to improve predictive modeling of contaminant transport.

Proceedings of the International Workshop on Computational Electronics Held at Leeds University (United Kingdom) on August 11-13 1993

DTIC Science & Technology

1993-08-01

Drury , Sponsored by UK SERC and MIA-COM (USA). Apart from any fair dealing for the purposes of research or private study, or criticism or review, as...field effect 128 transistors R Drury , R E Miles and C M Snowden, University of Leeds Poster Session II Determination of diffusion coefficients and...V V V y V V V Device simulation by means of a direct solution of the coupled Poisson/Boltzmann Transport enuations Conor J. Donnelly and Colin Lyden

Mathematical modelling of oil spill fate and transport in the marine environment incorporating biodegradation kinetics of oil droplets

NASA Astrophysics Data System (ADS)

Spanoudaki, Katerina

2016-04-01

Oil biodegradation by native bacteria is one of the most important natural processes that can attenuate the environmental impacts of marine oil spills. However, very few numerical models of oil spill fate and transport include biodegradation kinetics of spilled oil. Furthermore, in models where biodegradation is included amongst the oil transformation processes simulated, it is mostly represented as a first order decay process neglecting the effect of several important parameters that can limit biodegradation rate, such as oil composition and oil droplets-water interface. To this end, the open source numerical model MEDSKIL-II, which simulates oil spill fate and transport in the marine environment, has been modified to include biodegradation kinetics of oil droplets dispersed in the water column. MEDSLIK-II predicts the transport and weathering of oil spills following a Lagrangian approach for the solution of the advection-diffusion equation. Transport is governed by the 3D sea currents and wave field provided by ocean circulation models. In addition to advective and diffusive displacements, the model simulates several physical and chemical processes that transform the oil (evaporation, emulsification, dispersion in the water column, adhesion to coast). The fate algorithms employed in MEDSLIK-II consider the oil as a uniform substance whose properties change as the slick weathers, an approach that can lead to reduced accuracy, especially in the estimation of oil evaporation and biodegradation. Therefore MEDSLIK-II has been modified by adopting the "pseudo-component" approach for simulating weathering processes. Spilled oil is modelled as a relatively small number of discrete, non-interacting components (pseudo-components). Chemicals in the oil mixture are grouped by physical-chemical properties and the resulting pseudo-component behaves as if it were a single substance with characteristics typical of the chemical group. The fate (evaporation, dispersion, biodegradation) of each component is tracked separately. Biodegradation of oil droplets is modelled by Monod kinetics. The kinetics of oil particles size reduction due to the microbe-mediated degradation at water-oil particle interface is represented by the shrinking core model. In order to test the performance of the modified MEDSLIK-II model, it has been applied to a test case built-in the original code. The total fate of the oil spill is simulated both without biodegradation kinetics and when biodegradation is taken into account, for reasons of comparison. Several parameters that control biodegradation rate, including initial oil concentration and composition, size distribution of oil droplets and initial microbial concentration have been investigated. This upgraded version of MEDSLIK-II can be useful not only for predicting the transport and fate of spilled oil in the short term but also for evaluating different bioremediation strategies and risk assessment for the mid- and long term. Acknowledgements: The financial support by the EU project DECATASTROPHIZE: Use of SDSS and MCDA to Prepare for Disasters or Plan for Multiple Hazards, GA no. ECHO/SUB/2015/713788/PREP02, is greatly acknowledged.

Electrostatic measures for a piezoelectric thin film with an embedded crack in the substrate: II. Mode II

NASA Astrophysics Data System (ADS)

Ali, Rizwaan; Mahapatra, D. Roy; Gopalakrishnan, S.

2008-04-01

This paper is a successor to the previous paper by Ali et al (2008 Smart Mater. Struct. 17 025037); it presents the analysis for sensing an embedded mode-II crack in a substrate. The displacement field kinematics for the film-substrate system is extended to the problem of applied surface shear stress. This extension requires modifying the model presented in the previous paper to include the differences due to changes in boundary and excitation conditions. The film response in terms of voltage pattern over the film area—peculiar to the presence of a mode-II crack in the substrate—is illustrated here through the results of numerical simulations. Our analysis shows that the proposed electrostatic measures of the voltage and its gradients are useful in identifying the axial and depth-wise location, as well as the crack-face area of a planar mode-II crack. There is a marked difference in the pattern of results presented in this paper with the results in part I of this work for a mode-I crack. This distinction is of utmost importance, for it singularly suffices to identify the mode of crack in a substrate for a given set of boundary conditions.

Design and synthesis of core-shell Fe3O4@PTMT composite magnetic microspheres for adsorption of heavy metals from high salinity wastewater.

PubMed

Huang, Xin; Yang, Jinyue; Wang, Jingkang; Bi, Jingtao; Xie, Chuang; Hao, Hongxun

2018-05-10

In this study, a novel magnetic nanoparticles (MNP) modified by an organodisulfide polymer (PTMT) was designed for adsorption of heavy metals (Hg(II), Pb(II) and Cd(II)) from simulated coal chemical high salinity wastewater. The MNP-PTMT nano-composite was synthesize and characterized by SEM, TEM, FTIR, BET, VSM, TGA and XRD. The results indicate that the wanted MNP-PTMT magnetic nanoparticles were successfully obtained by modification. Adsorption experiments were systematically carried out to evaluate the performance of the obtained nanoparticles and to build up the adsorption models. The results demonstrate that the adsorption kinetic and isotherms thermodynamic followed the pseudo-second-order model and the Freundlich equation, respectively. In the presence of the inorganic salt in high salinity wastewater, the adsorption efficiency of MNP-PTMT for heavy metals was still excellent. The magnetic adsorbent could be recovered from aqueous solution by an external magnetic field in 20s and the subsequent regeneration of Hg(II)/Pb(II) loaded MNP-PTMT can be efficiently achieved by using EDTA-2Na solution as desorbent. The novel MNP-PTMT nanoparticles could be used reproductively for five times without apparent decrease in sorption capacity. Copyright © 2018 Elsevier Ltd. All rights reserved.

A hydrodynamic approach to cosmology - Methodology

NASA Technical Reports Server (NTRS)

Cen, Renyue

1992-01-01

The present study describes an accurate and efficient hydrodynamic code for evolving self-gravitating cosmological systems. The hydrodynamic code is a flux-based mesh code originally designed for engineering hydrodynamical applications. A variety of checks were performed which indicate that the resolution of the code is a few cells, providing accuracy for integral energy quantities in the present simulations of 1-3 percent over the whole runs. Six species (H I, H II, He I, He II, He III) are tracked separately, and relevant ionization and recombination processes, as well as line and continuum heating and cooling, are computed. The background radiation field is simultaneously determined in the range 1 eV to 100 keV, allowing for absorption, emission, and cosmological effects. It is shown how the inevitable numerical inaccuracies can be estimated and to some extent overcome.

Hard Sphere Simulation by Event-Driven Molecular Dynamics: Breakthrough, Numerical Difficulty, and Overcoming the issues

NASA Astrophysics Data System (ADS)

Isobe, Masaharu

Hard sphere/disk systems are among the simplest models and have been used to address numerous fundamental problems in the field of statistical physics. The pioneering numerical works on the solid-fluid phase transition based on Monte Carlo (MC) and molecular dynamics (MD) methods published in 1957 represent historical milestones, which have had a significant influence on the development of computer algorithms and novel tools to obtain physical insights. This chapter addresses the works of Alder's breakthrough regarding hard sphere/disk simulation: (i) event-driven molecular dynamics, (ii) long-time tail, (iii) molasses tail, and (iv) two-dimensional melting/crystallization. From a numerical viewpoint, there are serious issues that must be overcome for further breakthrough. Here, we present a brief review of recent progress in this area.

Solar Pilot Plant, Phase I. Preliminary design report. Volume II, Book 2. Central receiver optical model users manual. CDRL item 2. [HELIAKI code

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

None

1977-05-01

HELIAKI is a FORTRAN computer program which simulates the optical/thermal performance of a central receiver solar thermal power plant for the dynamic conversion of solar-generated heat to electricity. The solar power plant which this program simulates consists of a field of individual sun tracking mirror units, or heliostats, redirecting sunlight into a cavity, called the receiver, mounted atop a tower. The program calculates the power retained by that cavity receiver at any point in time or the energy into the receiver over a year's time using a Monte Carlo ray trace technique to solve the multiple integral equations. An artist'smore » concept of this plant is shown.« less

Warmer and drier conditions and nitrogen fertilizer application altered methanotroph abundance and methane emissions in a vegetable soil.

PubMed

Ran, Yu; Xie, Jianli; Xu, Xiaoya; Li, Yong; Liu, Yapeng; Zhang, Qichun; Li, Zheng; Xu, Jianming; Di, Hongjie

2017-01-01

Methane (CH 4 ) is a potent greenhouse gas, and soil can both be a source and sink for atmospheric CH 4 . It is not clear how future climate change may affect soil CH 4 emissions and related microbial communities. The aim of this study was to determine the interactive effects of a simulated warmer and drier climate scenarios and the application of different nitrogen (N) sources (urea and manure) on CH 4 emissions and related microbial community abundance in a vegetable soil. Greenhouses were used to control simulated climate conditions which gave 2.99 °C warmer and 6.2% lower water content conditions. The field experiment was divided into two phases. At the beginning of phase II, half of the greenhouses were removed to study possible legacy effects of the simulated warmer and drier conditions. The responses in methanogen and methanotroph abundance to a simulated climate change scenario were determined using real-time PCR. The results showed that the simulated warmer and drier conditions in the greenhouses significantly decreased CH 4 emissions largely due to the lower soil moisture content. For the same reason, CH 4 emissions of treatments in phase I were much lower than the same treatments in phase II. The abundance of methanotrophs showed a more significant response than methanogens to the simulated climate change scenario, increasing under simulated drier conditions. Methanogenic community abundance remained low, except where manure was applied which provided a source of organic C that stimulated methanogen growth. Soil moisture content was a major driver for methanotroph abundance and strongly affected CH 4 emissions. The application of N source decreased CH 4 emissions probably because of increased methanotrophic activity. CH 4 emissions were positively correlated to methanogenic abundance and negatively correlated to methanotrophic abundance. These results demonstrate that projected future climate change conditions can have a feedback impact on CH 4 emissions from the soil by altering soil conditions (particularly soil moisture) and related microbial communities.

Verification of high resolution simulation of precipitation and wind in Portugal

NASA Astrophysics Data System (ADS)

Menezes, Isilda; Pereira, Mário; Moreira, Demerval; Carvalheiro, Luís; Bugalho, Lourdes; Corte-Real, João

2017-04-01

Demand of energy and freshwater continues to grow as the global population and demands increase. Precipitation feed the freshwater ecosystems which provides a wealth of goods and services for society and river flow to sustain native species and natural ecosystem functions. The adoption of the wind and hydro-electric power supplies will sustain energy demands/services without restricting the economic growth and accelerated policies scenarios. However, the international meteorological observation network is not sufficiently dense to directly support high resolution climatic research. In this sense, coupled global and regional atmospheric models constitute the most appropriate physical and numerical tool for weather forecasting and downscaling in high resolution grids with the capacity to solve problems resulting from the lack of observed data and measuring errors. Thus, this study aims to calibrate and validate of the WRF regional model from precipitation and wind fields simulation, in high spatial resolution grid cover in Portugal. The simulations were performed in two-way nesting with three grids of increasing resolution (60 km, 20 km and 5 km) and the model performance assessed for the summer and winter months (January and July), using input variables from two different reanalyses and forecasted databases (ERA-Interim and NCEP-FNL) and different forcing schemes. The verification procedure included: (i) the use of several statistics error estimators, correlation based measures and relative errors descriptors; and, (ii) an observed dataset composed by time series of hourly precipitation, wind speed and direction provided by the Portuguese meteorological institute for a comprehensive set of weather stations. Main results suggested the good ability of the WRF to: (i) reproduce the spatial patterns of the mean and total observed fields; (ii) with relatively small values of bias and other errors; and, (iii) and good temporal correlation. These findings are in good agreements with the conclusions of other previous studies with WRF. It is also important to underline the relative independence of the simulations with the datasets used to feed the model and a relatively better performance with one of the tested forced scheme. These findings suggest the skill and robustness of the WRF to produce high resolution simulations of both precipitation and wind. Acknowledgements: This work was supported by: (i) the project Interact - Integrative Research in Environment,Agro-Chain and Technology, NORTE-01-0145-FEDER-000017, research line BEST, cofinanced by FEDER/NORTE 2020; (ii) the FIREXTR project, PTDC/ATP¬GEO/0462/2014; and, (iii) European Investment Funds by FEDER/COMPETE/POCI-Operacional Competitiveness and Internacionalization Programme, under Project POCI-01-0145-FEDER-006958 and National Funds by FCT - Portuguese Foundation for Science and Technology, under the project UID/AGR/04033.

On the use of multiple-point statistics to improve groundwater flow modeling in karst aquifers: A case study from the Hydrogeological Experimental Site of Poitiers, France

NASA Astrophysics Data System (ADS)

Le Coz, Mathieu; Bodin, Jacques; Renard, Philippe

2017-02-01

Limestone aquifers often exhibit complex groundwater flow behaviors resulting from depositional heterogeneities and post-lithification fracturing and karstification. In this study, multiple-point statistics (MPS) was applied to reproduce karst features and to improve groundwater flow modeling. For this purpose, MPS realizations were used in a numerical flow model to simulate the responses to pumping test experiments observed at the Hydrogeological Experimental Site of Poitiers, France. The main flow behaviors evident in the field data were simulated, particularly (i) the early-time inflection of the drawdown signal at certain observation wells and (ii) the convex behavior of the drawdown curves at intermediate times. In addition, it was shown that the spatial structure of the karst features at various scales is critical with regard to the propagation of the depletion wave induced by pumping. Indeed, (i) the spatial shape of the cone of depression is significantly affected by the karst proportion in the vicinity of the pumping well, and (ii) early-time inflection of the drawdown signal occurs only at observation wells crossing locally well-developed karst features.

Comparison with CLPX II airborne data using DMRT model

USGS Publications Warehouse

Xu, X.; Liang, D.; Andreadis, K.M.; Tsang, L.; Josberger, E.G.

2009-01-01

In this paper, we considered a physical-based model which use numerical solution of Maxwell Equations in three-dimensional simulations and apply into Dense Media Radiative Theory (DMRT). The model is validated in two specific dataset from the second Cold Land Processes Experiment (CLPX II) at Alaska and Colorado. The data were all obtain by the Ku-band (13.95GHz) observations using airborne imaging polarimetric scatterometer (POLSCAT). Snow is a densely packed media. To take into account the collective scattering and incoherent scattering, analytical Quasi-Crystalline Approximation (QCA) and Numerical Maxwell Equation Method of 3-D simulation (NMM3D) are used to calculate the extinction coefficient and phase matrix. DMRT equations were solved by iterative solution up to 2nd order for the case of small optical thickness and full multiple scattering solution by decomposing the diffuse intensities into Fourier series was used when optical thickness exceed unity. It was shown that the model predictions agree with the field experiment not only co-polarization but also cross-polarization. For Alaska region, the input snow structure data was obtain by the in situ ground observations, while for Colorado region, we combined the VIC model to get the snow profile. ??2009 IEEE.

A reactive force field study of Li/C systems for electrical energy storage

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

Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.

Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphitemore » with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. As a result, this is a key step toward modeling of realistic carbon materials for energy applications.« less

A reactive force field study of Li/C systems for electrical energy storage

DOE PAGES

Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.; ...

2015-04-02

Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphitemore » with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. As a result, this is a key step toward modeling of realistic carbon materials for energy applications.« less

Simulation of Sound Waves Using the Lattice Boltzmann Method for Fluid Flow: Benchmark Cases for Outdoor Sound Propagation

PubMed Central

Salomons, Erik M.; Lohman, Walter J. A.; Zhou, Han

2016-01-01

Propagation of sound waves in air can be considered as a special case of fluid dynamics. Consequently, the lattice Boltzmann method (LBM) for fluid flow can be used for simulating sound propagation. In this article application of the LBM to sound propagation is illustrated for various cases: free-field propagation, propagation over porous and non-porous ground, propagation over a noise barrier, and propagation in an atmosphere with wind. LBM results are compared with solutions of the equations of acoustics. It is found that the LBM works well for sound waves, but dissipation of sound waves with the LBM is generally much larger than real dissipation of sound waves in air. To circumvent this problem it is proposed here to use the LBM for assessing the excess sound level, i.e. the difference between the sound level and the free-field sound level. The effect of dissipation on the excess sound level is much smaller than the effect on the sound level, so the LBM can be used to estimate the excess sound level for a non-dissipative atmosphere, which is a useful quantity in atmospheric acoustics. To reduce dissipation in an LBM simulation two approaches are considered: i) reduction of the kinematic viscosity and ii) reduction of the lattice spacing. PMID:26789631

Simulation of Sound Waves Using the Lattice Boltzmann Method for Fluid Flow: Benchmark Cases for Outdoor Sound Propagation.

PubMed

Salomons, Erik M; Lohman, Walter J A; Zhou, Han

2016-01-01

Propagation of sound waves in air can be considered as a special case of fluid dynamics. Consequently, the lattice Boltzmann method (LBM) for fluid flow can be used for simulating sound propagation. In this article application of the LBM to sound propagation is illustrated for various cases: free-field propagation, propagation over porous and non-porous ground, propagation over a noise barrier, and propagation in an atmosphere with wind. LBM results are compared with solutions of the equations of acoustics. It is found that the LBM works well for sound waves, but dissipation of sound waves with the LBM is generally much larger than real dissipation of sound waves in air. To circumvent this problem it is proposed here to use the LBM for assessing the excess sound level, i.e. the difference between the sound level and the free-field sound level. The effect of dissipation on the excess sound level is much smaller than the effect on the sound level, so the LBM can be used to estimate the excess sound level for a non-dissipative atmosphere, which is a useful quantity in atmospheric acoustics. To reduce dissipation in an LBM simulation two approaches are considered: i) reduction of the kinematic viscosity and ii) reduction of the lattice spacing.

Testing core creation in hydrodynamical simulations using the HI kinematics of field dwarfs

NASA Astrophysics Data System (ADS)

Papastergis, E.; Ponomareva, A. A.

2017-05-01

The majority of recent hydrodynamical simulations indicate the creation of central cores in the mass profiles of low-mass halos, a process that is attributed to star formation-related baryonic feedback. Core creation is regarded as one of the most promising solutions to potential issues faced by lambda cold dark matter (ΛCDM) cosmology on small scales. For example, the reduced dynamical mass enclosed by cores can explain the low rotational velocities measured for nearby dwarf galaxies, thus possibly lifting the seeming contradiction with the ΛCDM expectations (the so-called "too big to fail" problem). Here we test core creation as a solution of cosmological issues by using a sample of dwarfs with measurements of their atomic hydrogen (HI) kinematics extending to large radii. Using the NIHAO hydrodynamical simulation as an example, we show that core creation can successfully reproduce the kinematics of dwarfs with small kinematic radii, R ≲ 1.5 kpc. However, the agreement with observations becomes poor once galaxies with kinematic measurements extending beyond the core region, R ≈ 1.5-4 kpc, are considered. This result illustrates the importance of testing the predictions of hydrodynamical simulations that are relevant for cosmology against a broad range of observational samples. We would like to stress that our result is valid only under the following set of assumptions: I) that our sample of dwarfs with HI kinematics is representative of the overall population of field dwarfs; II) that there are no severe measurement biases in the observational parameters of our HI dwarfs (e.g., related to inclination estimates); and III) that the HI velocity fields of dwarfs are regular enough to allow the recovery of the true enclosed dynamical mass.

Simulation of water flow and nitrogen transport for a Bulgarian experimental plot using SWAP and ANIMO models.

PubMed

Marinov, Dimitar; Querner, Erik; Roelsma, Jan

2005-04-01

Unsaturated zone models are useful tools in predicting effects of measures and can be used to optimise agricultural practice aiming to minimise the impact on the environment. However, current soil models have a varying degree of abstraction level referring to simulated processes in time and space. In the framework of an EU funded project the SWAP (Soil-Water-Atmosphere-Plant) and ANIMO (Agricultural-Nutrient-Model) models were tested for an experimental arable plot in Bulgaria. SWAP was used to simulate water flow in the soil while ANIMO describes nitrogen movement and transformations. The objectives of this study are: (i) to show results of the combined application of water and nitrogen dynamics of originally Dutch models SWAP and ANIMO for specific Bulgarian soil and hydrological conditions; (ii) to calibrate and evaluate SWAP and ANIMO models by comparing numerical results with field measurements collected for an arable field in western Bulgaria and (iii) to analyse possible contamination of groundwater due to agricultural practice in the considered region. Further a short description of the experimental plot, as well as information about parameters of the investigated soil profiles, is provided. The obtained SWAP results evidenced that the model gives sufficient adaptation for soil water dynamics. The simulations of ANIMO for nitrogen cycle show greater divergence with observations but are satisfactory precise for the purposes of assessing land use impact on groundwater quality. In general, differences between model results and field measurements do not exceed 10-15%. For the experimental plot predictions indicate nitrate-N concentrations less then 5 mg/l in deeper soil compartments and low downward annual flux containing 0.133 kg N/ha. These results indicate that there is no serious pollution of the shallow groundwater table by nitrogen resulting from land use and agricultural activities.

A Semi-analytical Line Transfer (SALT) Model. II: The Effects of a Bi-conical Geometry

NASA Astrophysics Data System (ADS)

Carr, Cody; Scarlata, Claudia; Panagia, Nino; Henry, Alaina

2018-06-01

We generalize the semi-analytical line transfer model recently introduced by Scarlata & Panagia for modeling galactic outflows, to account for bi-conical geometries of various opening angles and orientations with respect to the line of sight to the observer, as well as generalized velocity fields. We model the absorption and emission component of the line profile resulting from resonant absorption in the bi-conical outflow. We show how the outflow geometry impacts the resulting line profile. We use simulated spectra with different geometries and velocity fields to study how well the outflow parameters can be recovered. We find that geometrical parameters (including the opening angle and the orientation) are always well recovered. The density and velocity field parameters are reliably recovered when both an absorption and an emission component are visible in the spectra. This condition implies that the velocity and density fields for narrow cones oriented perpendicular to the line of sight will remain unconstrained.

Characterization of cumulus cloud fields using trajectories in the center of gravity versus water mass phase space: 1. Cloud tracking and phase space description: CENTER OF GRAVITY VERSUS WATER MASS 1

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

Heiblum, Reuven H.; Altaratz, Orit; Koren, Ilan

We study the evolution of warm convective cloud fields using large eddy simulations of continental and trade cumulus. Individual clouds are tracked a posteriori from formation to dissipation using a 3D cloud tracking algorithm and results are presented in the phase- space of center of gravity altitude versus cloud liquid water mass (CvM space). The CvM space is shown to contain rich information on cloud field characteristics, cloud morphology, and common cloud development pathways, together facilitating a comprehensive understanding of the cloud field. In this part we show how the meteorological (thermodynamic) conditions that determine the cloud properties are projectedmore » on the CvM phase space and how changes in the initial conditions affect the clouds' trajectories in this space. This part sets the stage for a detailed microphysical analysis that will be shown in part II.« less

Rapid reaction of nanomolar Mn(II) with superoxide radical in seawater and simulated freshwater

USGS Publications Warehouse

Hansard, S.P.; Easter, H.D.; Voelker, Bettina M.

2011-01-01

Superoxide radical (O2-) has been proposed to be an important participant in oxidation-reduction reactions of metal ions in natural waters. Here, we studied the reaction of nanomolar Mn(II) with O 2- in seawater and simulated freshwater, using chemiluminescence detection of O2- to quantify the effect of Mn(II) on the decay kinetics of O2-. With 3-24 nM added [Mn(II)] and <0.7 nM [O2-], we observed effective second-order rate constants for the reaction of Mn(II) with O2- of 6 ?? 106 to 1 ?? 107 M -1???s-1 in various seawater samples. In simulated freshwater (pH 8.6), the effective rate constant of Mn(II) reaction with O 2- was somewhat lower, 1.6 ?? 106 M -1???s-1. With higher initial [O2-], in excess of added [Mn(II)], catalytic decay of O 2- by Mn was observed, implying that a Mn(II/III) redox cycle occurred. Our results show that reactions with nanomolar Mn(II) could be an important sink of O2- in natural waters. In addition, reaction of Mn(II) with superoxide could maintain a significant fraction of dissolved Mn in the +III oxidation state. ?? 2011 American Chemical Society.

In-situ temperature field measurements and direct observation of crystal/melt at vertical Bridgman growth of lead chloride under stationary and dynamic arrangement

NASA Astrophysics Data System (ADS)

Král, Robert; Nitsch, Karel

2015-10-01

Influence of growth conditions, i.e. temperature gradient in the furnace and the pulling rate, on the position and the shape of the crystal/melt interface during vertical Bridgman growth was studied. The position and the shape of the crystal/melt interface are a key factor for describing the final quality of growing crystal. Following two methods for characterization of its position and shape were used: (i) direct observation and (ii) direct temperature field measurement during simulated vertical Bridgman growth. As a model compound a lead chloride is used. Three different ampoule positions in two different temperature gradients in the furnace and two experimental arrangements - stationary (0 mm/h pulling rate) and dynamic (3 mm/h pulling rate) were analyzed. Obtained temperature data were projected as 2D planar cut under radial symmetry and denoted as isolevels. Their further conversion by linear approximation into isotherms allowed detail analysis of heat conditions in the system during simulated growth by comparison of isotherms 500 °C (m.p. of lead chloride) at different growth conditions.

New insights into insect's silent flight. Part II: sound source and noise control

NASA Astrophysics Data System (ADS)

Xue, Qian; Geng, Biao; Zheng, Xudong; Liu, Geng; Dong, Haibo

2016-11-01

The flapping flight of aerial animals has excellent aerodynamic performance but meanwhile generates low noise. In this study, the unsteady flow and acoustic characteristics of the flapping wing are numerically investigated for three-dimensional (3D) models of Tibicen linnei cicada at free forward flight conditions. Single cicada wing is modelled as a membrane with prescribed motion reconstructed by Wan et al. (2015). The flow field and acoustic field around the flapping wing are solved with immersed-boundary-method based incompressible flow solver and linearized-perturbed-compressible-equations based acoustic solver. The 3D simulation allows examination of both directivity and frequency composition of the produced sound in a full space. The mechanism of sound generation of flapping wing is analyzed through correlations between acoustic signals and flow features. Along with a flexible wing model, a rigid wing model is also simulated. The results from these two cases will be compared to investigate the effects of wing flexibility on sound generation. This study is supported by NSF CBET-1313217 and AFOSR FA9550-12-1-0071.

Capabilities of a Global 3D MHD Model for Monitoring Extremely Fast CMEs

NASA Astrophysics Data System (ADS)

Wu, C. C.; Plunkett, S. P.; Liou, K.; Socker, D. G.; Wu, S. T.; Wang, Y. M.

2015-12-01

Since the start of the space era, spacecraft have recorded many extremely fast coronal mass ejections (CMEs) which have resulted in severe geomagnetic storms. Accurate and timely forecasting of the space weather effects of these events is important for protecting expensive space assets and astronauts and avoiding communications interruptions. Here, we will introduce a newly developed global, three-dimensional (3D) magnetohydrodynamic (MHD) model (G3DMHD). The model takes the solar magnetic field maps at 2.5 solar radii (Rs) and intepolates the solar wind plasma and field out to 18 Rs using the algorithm of Wang and Sheeley (1990, JGR). The output is used as the inner boundary condition for a 3D MHD model. The G3DMHD model is capable of simulating (i) extremely fast CME events with propagation speeds faster than 2500 km/s; and (ii) multiple CME events in sequence or simultaneously. We will demonstrate the simulation results (and comparison with in-situ observation) for the fastest CME in record on 23 July 2012, the shortest transit time in March 1976, and the well-known historic Carrington 1859 event.

Emission of energetic protons from relativistic intensity laser interaction with a cone-wire target.

PubMed

Paradkar, B S; Yabuuchi, T; Sawada, H; Higginson, D P; Link, A; Wei, M S; Stephens, R B; Krasheninnikov, S I; Beg, F N

2012-11-01

Emission of energetic protons (maximum energy ∼18 MeV) from the interaction of relativistic intensity laser with a cone-wire target is experimentally measured and numerically simulated with hybrid particle-in-cell code, lsp [D. R. Welch et al., Phys. Plasmas 13, 063105 (2006)]. The protons originate from the wire attached to the cone after the OMEGA EP laser (670 J, 10 ps, 5 × 10^{18} W/cm^{2}) deposits its energy inside the cone. These protons are accelerated from the contaminant layer on the wire surface, and are measured in the radial direction, i.e., in a direction transverse to the wire length. Simulations show that the radial electric field, responsible for the proton acceleration, is excited by three factors, viz., (i) transverse momentum of the relativistic fast electrons beam entering into the wire, (ii) scattering of electrons inside the wire, and (iii) refluxing of escaped electrons by "fountain effect" at the end of the wire. The underlying physics of radial electric field and acceleration of protons is discussed.

Operation of a 500 MHz high temperature superconducting NMR: towards an NMR spectrometer operating beyond 1 GHz.

PubMed

Yanagisawa, Y; Nakagome, H; Tennmei, K; Hamada, M; Yoshikawa, M; Otsuka, A; Hosono, M; Kiyoshi, T; Takahashi, M; Yamazaki, T; Maeda, H

2010-04-01

We have begun a project to develop an NMR spectrometer that operates at frequencies beyond 1 GHz (magnetic field strength in excess of 23.5 T) using a high temperature superconductor (HTS) innermost coil. As the first step, we developed a 500 MHz NMR with a Bi-2223 HTS innermost coil, which was operated in external current mode. The temporal magnetic field change of the NMR magnet after the coil charge was dominated by (i) the field fluctuation due to a DC power supply and (ii) relaxation in the screening current in the HTS tape conductor; effect (i) was stabilized by the 2H field-frequency lock system, while effect (ii) decreased with time due to relaxation of the screening current induced in the HTS coil and reached 10(-8)(0.01 ppm)/h on the 20th day after the coil charge, which was as small as the persistent current mode of the NMR magnet. The 1D (1)H NMR spectra obtained by the 500 MHz LTS/HTS magnet were nearly equivalent to those obtained by the LTS NMR magnet. The 2D-NOESY, 3D-HNCO and 3D-HNCACB spectra were achieved for ubiquitin by the 500 MHz LTS/HTS magnet; their quality was closely equivalent to that achieved by a conventional LTS NMR. Based on the results of numerical simulation, the effects of screening current-induced magnetic field changes are predicted to be harmless for the 1.03 GHz NMR magnet system. 2010 Elsevier Inc. All rights reserved.

Equatorial E Region Electric Fields and Sporadic E Layer Responses to the Recovery Phase of the November 2004 Geomagnetic Storm

NASA Astrophysics Data System (ADS)

Moro, J.; Resende, L. C. A.; Denardini, C. M.; Xu, J.; Batista, I. S.; Andrioli, V. F.; Carrasco, A. J.; Batista, P. P.; Schuch, N. J.

2017-12-01

Equatorial E region electric fields (EEFs) inferred from coherent radar data, sporadic-E (Es) layers observed from a digital ionosonde data, and modeling results are used to study the responses of the equatorial E region over São Luís (SLZ, 2.3°S, 44.2°W, -7° dip angle), Brazil, during the super storm of November 2004. The EEF is presented in terms of the zonal (Ey) and vertical (Ez) components in order to analyze the corresponding characteristics of different types of Es seen in ionograms and simulated with the E region ionospheric model. We bring out the variabilities of Ey and Ez components with storm time changes in the equatorial E region. In addition, some aspects of the electric fields and Es behavior in three cases of weak, very weak, and strong Type II occurrences during the recovery phase of the geomagnetic storm are discussed. The connection between the enhanced occurrence and suppressions of the Type II irregularities and the q-type Es (Esq) controlled by electric fields, with the development or disruption of the blanketing sporadic E (Esb) layers produced by wind shear mechanism, is also presented. The mutual presence of Esq along with the Esb occurrences is a clear indicator of the secular drift of the magnetic equator and hence that of the equatorial electrojet (EEJ) over SLZ. The results show evidence about the EEJ and Es layer electrodynamics and coupling during geomagnetic disturbance time electric fields.

CHARACTERIZATION OF CoRoT TARGET FIELDS WITH BERLIN EXOPLANET SEARCH TELESCOPE. II. IDENTIFICATION OF PERIODIC VARIABLE STARS IN THE LRc2 FIELD

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

Kabath, P.; Fruth, T.; Rauer, H.

2009-04-15

We report on photometric observations of the CoRoT LRc2 field with the new robotic Berlin Exoplanet Search Telescope II (BEST II). The telescope system was installed and commissioned at the Observatorio Cerro Armazones, Chile, in 2007. BEST II is a small aperture telescope with a wide field of view dedicated to the characterization of the stellar variability primarily in CoRoT target fields with high stellar densities. The CoRoT stellar field LRc2 was observed with BEST II up to 20 nights in 2007 July and August. From the acquired data containing about 100,000 stars, 426 new periodic variable stars were identifiedmore » and 90% of them are located within the CoRoT exoplanetary CCD segments and may be of further interest for CoRoT additional science programs.« less

Empirical Modeling of the Redshift Evolution of the [{\\rm{N}}\\,{\\rm{II}}]/Hα Ratio for Galaxy Redshift Surveys

NASA Astrophysics Data System (ADS)

Faisst, Andreas L.; Masters, Daniel; Wang, Yun; Merson, Alexander; Capak, Peter; Malhotra, Sangeeta; Rhoads, James E.

2018-03-01

We present an empirical parameterization of the [N II]/Hα flux ratio as a function of stellar mass and redshift valid at 0 < z < 2.7 and 8.5< {log}(M/{M}ȯ )< 11.0. This description can (i) easily be applied to simulations for modeling [N II]λ6584 line emission, (ii) deblend [N II] and Hα in current low-resolution grism and narrow-band observations to derive intrinsic Hα fluxes, and (iii) reliably forecast the number counts of Hα emission-line galaxies for future surveys, such as those planned for Euclid and the Wide Field Infrared Survey Telescope (WFIRST). Our model combines the evolution of the locus on the Baldwin, Phillips & Terlevich (BPT) diagram measured in spectroscopic data out to z ∼ 2.5 with the strong dependence of [N II]/Hα on stellar mass and [O III]/Hβ observed in local galaxy samples. We find large variations in the [N II]/Hα flux ratio at a fixed redshift due to its dependency on stellar mass; hence, the assumption of a constant [N II] flux contamination fraction can lead to a significant under- or overestimate of Hα luminosities. Specifically, measurements of the intrinsic Hα luminosity function derived from current low-resolution grism spectroscopy assuming a constant 29% contamination of [N II] can be overestimated by factors of ∼8 at {log}(L)> 43.0 for galaxies at redshifts z ∼ 1.5. This has implications for the prediction of Hα emitters for Euclid and WFIRST. We also study the impact of blended Hα and [N II] on the accuracy of measured spectroscopic redshifts.

A new way of setting the phases for cosmological multiscale Gaussian initial conditions

NASA Astrophysics Data System (ADS)

Jenkins, Adrian

2013-09-01

We describe how to define an extremely large discrete realization of a Gaussian white noise field that has a hierarchical structure and the property that the value of any part of the field can be computed quickly. Tiny subregions of such a field can be used to set the phase information for Gaussian initial conditions for individual cosmological simulations of structure formation. This approach has several attractive features: (i) the hierarchical structure based on an octree is particularly well suited for generating follow-up resimulation or zoom initial conditions; (ii) the phases are defined for all relevant physical scales in advance so that resimulation initial conditions are, by construction, consistent both with their parent simulation and with each other; (iii) the field can easily be made public by releasing a code to compute it - once public, phase information can be shared or published by specifying a spatial location within the realization. In this paper, we describe the principles behind creating such realizations. We define an example called Panphasia and in a companion paper by Jenkins and Booth (2013) make public a code to compute it. With 50 octree levels Panphasia spans a factor of more than 1015 in linear scale - a range that significantly exceeds the ratio of the current Hubble radius to the putative cold dark matter free-streaming scale. We show how to modify a code used for making cosmological and resimulation initial conditions so that it can take the phase information from Panphasia and, using this code, we demonstrate that it is possible to make good quality resimulation initial conditions. We define a convention for publishing phase information from Panphasia and publish the initial phases for several of the Virgo Consortium's most recent cosmological simulations including the 303 billion particle MXXL simulation. Finally, for reference, we give the locations and properties of several dark matter haloes that can be resimulated within these volumes.

Mössbauer spectroscopic studies on the iron forms of deep-sea sediments

NASA Astrophysics Data System (ADS)

Drodt, M.; Trautwein, A. X.; König, I.; Suess, E.; Koch, C. Bender

Mössbauer spectroscopy was applied to characterize the valence states Fe(II) and Fe(III) in sedimentary minerals from a core of the Peru Basin. The procedure in unraveling this information includes temperature-dependent measurements from 275 K to very low temperature (300 mK) in zero-field and also at 4.2 K in an applied field (up to 6.2 T) and by mathematical procedures (least-squares fits and spectral simulations) in order to resolve individual spectral components. The depth distribution of the amount of Fe(II) is about 11% of the total Fe to a depth of 19 cm with a subsequent steep increase (within 3 cm) to about 37%, after which it remains constant to the lower end of the sediment core (at about 40 cm). The steep increase of the amount of Fe(II) defines a redox boundary which coincides with the position where the tan/green color transition of the sediment occurs. The isomer shifts and quadrupole splittings of Fe(II) and Fe(III) in the sediment are consistent with hexacoordination by oxygen or hydroxide ligands as in oxide and silicate minerals. Goethite and traces of hematite are observed only above the redox boundary, with a linear gradient extending from about 20% of the total Fe close to the sediment surface to about zero at the redox boundary. The superparamagnetic relaxation behavior allows to estimate the order of magnitude for the size of the largest goethite and hematite particles within the particle-site distribution, e.g. 170 Å and 50 Å, respectively. The composition of the sediment spectra recorded at 300 mK in zero-field, apart from the contributions due to goethite and hematite, resembles that of the sheet silicates smectite, illite and chlorite, which have been identified as major constituents of the sediment in the <2 μm fraction by X-ray diffraction. The specific ``ferromagnetic'' type of magnetic ordering in the sediment, as detected at 4.2 K in an applied field, also resembles that observed in sheet silicates and indicates that both Fe(II) and Fe(III) are involved in magnetic ordering. This ``ferromagnetic'' behavior is probably due to the double-exchange mechanism known from other mixed-valence Fe(II)-Fe(III) systems. A significant part of the clay-mineral iron is redox sensitive. It is proposed that the color change of the sediment at the redox boundary from tan to green is related to the increase of Fe(II)-Fe(III) pairs in the layer silicates, because of the intervalence electron transfer bands which are caused by such pairs.

Software Reviews.

ERIC Educational Resources Information Center

Bitter, Gary G., Ed.

1989-01-01

Reviews three software packages: (1) "Physics," tutorial, grades 11-12, Macintosh; (2) "Hands On Math: Volume I," interactive math exploration/simulation of manipulatives use, grades K-7, Apple II; and (3) "A.I.: An Experience with Artificial Intelligence," simulation, grades 5-12, Apple II. (MVL)

Dynamics of Ring Current and Electric Fields in the Inner Magnetosphere During Disturbed Periods: CRCM-BATS-R-US Coupled Model

NASA Technical Reports Server (NTRS)

Buzulukova, N.; Fok, M.-C.; Pulkkinen, A.; Kuznetsova, M.; Moore, T. E.; Glocer, A.; Brandt, P. C.; Toth, G.; Rastaetter, L.

2010-01-01

We present simulation results from a one-way coupled global MHD model (Block-Adaptive-Tree Solar-Wind Roe-Type Upwind Scheme, BATS-R-US) and kinetic ring current models (Comprehensive Ring Current Model, CRCM, and Fok Ring Current, FokRC). The BATS-R-US provides the CRCM/FokRC with magnetic field information and plasma density/temperature at the polar CRCM/FokRC boundary. The CRCM uses an electric potential from the BATS-R-US ionospheric solver at the polar CRCM boundary in order to calculate the electric field pattern consistent with the CRCM pressure distribution. The FokRC electric field potential is taken from BATS-R-US ionospheric solver everywhere in the modeled region, and the effect of Region II currents is neglected. We show that for an idealized case with southward-northward-southward Bz IMF turning, CRCM-BATS-R-US reproduces well known features of inner magnetosphere electrodynamics: strong/weak convection under the southward/northward Bz; electric field shielding/overshielding/penetration effects; an injection during the substorm development; Subauroral Ion Drift or Polarization Jet (SAID/PJ) signature in the dusk sector. Furthermore, we find for the idealized case that SAID/PJ forms during the substorm growth phase, and that substorm injection has its own structure of field-aligned currents which resembles a substorm current wedge. For an actual event (12 August 2000 storm), we calculate ENA emissions and compare with Imager for Magnetopause-to-Aurora Global Exploration/High Energy Neutral Atom data. The CRCM-BATS-R-US reproduces both the global morphology of ring current and the fine structure of ring current injection. The FokRC-BATS-R-US shows the effect of a realistic description of Region II currents in ring current-MHD coupled models.

Demonstration of a viable quantitative theory for interplanetary type II radio bursts

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

Schmidt, J. M., E-mail: jschmidt@physics.usyd.edu.au; Cairns, Iver H.

Between 29 November and 1 December 2013 the two widely separated spacecraft STEREO A and B observed a long lasting, intermittent, type II radio burst for the extended frequency range ≈ 4 MHz to 30 kHz, including an intensification when the shock wave of the associated coronal mass ejection (CME) reached STEREO A. We demonstrate for the first time our ability to quantitatively and accurately simulate the fundamental (F) and harmonic (H) emission of type II bursts from the higher corona (near 11 solar radii) to 1 AU. Our modeling requires the combination of data-driven three-dimensional magnetohydrodynamic simulations for the CME andmore » plasma background, carried out with the BATS-R-US code, with an analytic quantitative kinetic model for both F and H radio emission, including the electron reflection at the shock, growth of Langmuir waves and radio waves, and the radiations propagation to an arbitrary observer. The intensities and frequencies of the observed radio emissions vary hugely by factors ≈ 10{sup 6} and ≈ 10{sup 3}, respectively; the theoretical predictions are impressively accurate, being typically in error by less than a factor of 10 and 20 %, for both STEREO A and B. We also obtain accurate predictions for the timing and characteristics of the shock and local radio onsets at STEREO A, the lack of such onsets at STEREO B, and the z-component of the magnetic field at STEREO A ahead of the shock, and in the sheath. Very strong support is provided by these multiple agreements for the theory, the efficacy of the BATS-R-US code, and the vision of using type IIs and associated data-theory iterations to predict whether a CME will impact Earth’s magnetosphere and drive space weather events.« less

Demonstration of a viable quantitative theory for interplanetary type II radio bursts

NASA Astrophysics Data System (ADS)

Schmidt, J. M.; Cairns, Iver H.

2016-03-01

Between 29 November and 1 December 2013 the two widely separated spacecraft STEREO A and B observed a long lasting, intermittent, type II radio burst for the extended frequency range ≈ 4 MHz to 30 kHz, including an intensification when the shock wave of the associated coronal mass ejection (CME) reached STEREO A. We demonstrate for the first time our ability to quantitatively and accurately simulate the fundamental (F) and harmonic (H) emission of type II bursts from the higher corona (near 11 solar radii) to 1 AU. Our modeling requires the combination of data-driven three-dimensional magnetohydrodynamic simulations for the CME and plasma background, carried out with the BATS-R-US code, with an analytic quantitative kinetic model for both F and H radio emission, including the electron reflection at the shock, growth of Langmuir waves and radio waves, and the radiations propagation to an arbitrary observer. The intensities and frequencies of the observed radio emissions vary hugely by factors ≈ 106 and ≈ 103, respectively; the theoretical predictions are impressively accurate, being typically in error by less than a factor of 10 and 20 %, for both STEREO A and B. We also obtain accurate predictions for the timing and characteristics of the shock and local radio onsets at STEREO A, the lack of such onsets at STEREO B, and the z-component of the magnetic field at STEREO A ahead of the shock, and in the sheath. Very strong support is provided by these multiple agreements for the theory, the efficacy of the BATS-R-US code, and the vision of using type IIs and associated data-theory iterations to predict whether a CME will impact Earth's magnetosphere and drive space weather events.

On the active site of mononuclear B1 metallo β-lactamases: a computational study

NASA Astrophysics Data System (ADS)

Sgrignani, Jacopo; Magistrato, Alessandra; Dal Peraro, Matteo; Vila, Alejandro J.; Carloni, Paolo; Pierattelli, Roberta

2012-04-01

Metallo-β-lactamases (MβLs) are Zn(II)-based bacterial enzymes that hydrolyze β-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from Bacillus Cereus point to either two zinc ions in two metal sites (the so-called `3H' and `DCH' sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from B. Cereus in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum-classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common β-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 MβL from Serratia fonticola (Sfh-I). These are MβLs from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the ɛɛδ and δɛδ protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the MβL reactivity and to the drug design process.

The simulation library of the Belle II software system

NASA Astrophysics Data System (ADS)

Kim, D. Y.; Ritter, M.; Bilka, T.; Bobrov, A.; Casarosa, G.; Chilikin, K.; Ferber, T.; Godang, R.; Jaegle, I.; Kandra, J.; Kodys, P.; Kuhr, T.; Kvasnicka, P.; Nakayama, H.; Piilonen, L.; Pulvermacher, C.; Santelj, L.; Schwenker, B.; Sibidanov, A.; Soloviev, Y.; Starič, M.; Uglov, T.

2017-10-01

SuperKEKB, the next generation B factory, has been constructed in Japan as an upgrade of KEKB. This brand new e+ e- collider is expected to deliver a very large data set for the Belle II experiment, which will be 50 times larger than the previous Belle sample. Both the triggered physics event rate and the background event rate will be increased by at least 10 times than the previous ones, and will create a challenging data taking environment for the Belle II detector. The software system of the Belle II experiment is designed to execute this ambitious plan. A full detector simulation library, which is a part of the Belle II software system, is created based on Geant4 and has been tested thoroughly. Recently the library has been upgraded with Geant4 version 10.1. The library is behaving as expected and it is utilized actively in producing Monte Carlo data sets for various studies. In this paper, we will explain the structure of the simulation library and the various interfaces to other packages including geometry and beam background simulation.

Mitigation of Hydrogen Gas Generation from the Reaction of Uranium Metal with Water in K Basin Sludge and Sludge Waste Forms

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

Sinkov, Sergey I.; Delegard, Calvin H.; Schmidt, Andrew J.

2011-06-08

Prior laboratory testing identified sodium nitrate and nitrite to be the most promising agents to minimize hydrogen generation from uranium metal aqueous corrosion in Hanford Site K Basin sludge. Of the two, nitrate was determined to be better because of higher chemical capacity, lower toxicity, more reliable efficacy, and fewer side reactions than nitrite. The present lab tests were run to determine if nitrate’s beneficial effects to lower H2 generation in simulated and genuine sludge continued for simulated sludge mixed with agents to immobilize water to help meet the Waste Isolation Pilot Plant (WIPP) waste acceptance drainable liquid criterion. Testsmore » were run at ~60°C, 80°C, and 95°C using near spherical high-purity uranium metal beads and simulated sludge to emulate uranium-rich KW containerized sludge currently residing in engineered containers KW-210 and KW-220. Immobilization agents tested were Portland cement (PC), a commercial blend of PC with sepiolite clay (Aquaset II H), granulated sepiolite clay (Aquaset II G), and sepiolite clay powder (Aquaset II). In all cases except tests with Aquaset II G, the simulated sludge was mixed intimately with the immobilization agent before testing commenced. For the granulated Aquaset II G clay was added to the top of the settled sludge/solution mixture according to manufacturer application directions. The gas volumes and compositions, uranium metal corrosion mass losses, and nitrite, ammonia, and hydroxide concentrations in the interstitial solutions were measured. Uranium metal corrosion rates were compared with rates forecast from the known uranium metal anoxic water corrosion rate law. The ratios of the forecast to the observed rates were calculated to find the corrosion rate attenuation factors. Hydrogen quantities also were measured and compared with quantities expected based on non-attenuated H2 generation at the full forecast anoxic corrosion rate to arrive at H2 attenuation factors. The uranium metal corrosion rates in water alone and in simulated sludge were near or slightly below the metal-in-water rate while nitrate-free sludge/Aquaset II decreased rates by about a factor of 3. Addition of 1 M nitrate to simulated sludge decreased the corrosion rate by a factor of ~5 while 1 M nitrate in sludge/Aquaset II mixtures decreased the corrosion rate by ~2.5 compared with the nitrate-free analogues. Mixtures of simulated sludge with Aquaset II treated with 1 M nitrate had uranium corrosion rates about a factor of 8 to 10 lower than the water-only rate law. Nitrate was found to provide substantial hydrogen mitigation for immobilized simulant sludge waste forms containing Aquaset II or Aquaset II G clay. Hydrogen attenuation factors of 1000 or greater were determined at 60°C for sludge-clay mixtures at 1 M nitrate. Hydrogen mitigation for tests with PC and Aquaset II H (which contains PC) were inconclusive because of suspected failure to overcome induction times and fully enter into anoxic corrosion. Lessening of hydrogen attenuation at ~80°C and ~95°C for simulated sludge and Aquaset II was observed with attenuation factors around 100 to 200 at 1 M nitrate. Valuable additional information has been obtained on the ability of nitrate to attenuate hydrogen gas generation from solution, simulant K Basin sludge, and simulant sludge with immobilization agents. Details on characteristics of the associated reactions were also obtained. The present testing confirms prior work which indicates that nitrate is an effective agent to attenuate hydrogen from uranium metal corrosion in water and simulated K Basin sludge to show that it is also effective in potential candidate solidified K Basin waste forms for WIPP disposal. The hydrogen mitigation afforded by nitrate appears to be sufficient to meet the hydrogen generation limits for shipping various sludge waste streams based on uranium metal concentrations and assumed waste form loadings.« less

Photoionization of High-altitude Gas in a Supernova-driven Turbulent Interstellar Medium

NASA Astrophysics Data System (ADS)

Wood, Kenneth; Hill, Alex S.; Joung, M. Ryan; Mac Low, Mordecai-Mark; Benjamin, Robert A.; Haffner, L. Matthew; Reynolds, R. J.; Madsen, G. J.

2010-10-01

We investigate models for the photoionization of the widespread diffuse ionized gas (DIG) in galaxies. In particular, we address the long standing question of the penetration of Lyman continuum photons from sources close to the galactic midplane to large heights in the galactic halo. We find that recent hydrodynamical simulations of a supernova-driven interstellar medium (ISM) have low-density paths and voids that allow for ionizing photons from midplane OB stars to reach and ionize gas many kiloparsecs above the midplane. We find that ionizing fluxes throughout our simulation grids are larger than predicted by one-dimensional slab models, thus allowing for photoionization by O stars of low altitude neutral clouds in the Galaxy that are also detected in Hα. In previous studies of such clouds, the photoionization scenario had been rejected and the Hα had been attributed to enhanced cosmic ray ionization or scattered light from midplane H II regions. We do find that the emission measure distributions in our simulations are wider than those derived from Hα observations in the Milky Way. In addition, the horizontally averaged height dependence of the gas density in the hydrodynamical models is lower than inferred in the Galaxy. These discrepancies are likely due to the absence of magnetic fields in the hydrodynamic simulations and we discuss how magnetohydrodynamic effects may reconcile models and observations. Nevertheless, we anticipate that the inclusion of magnetic fields in the dynamical simulations will not alter our primary finding that midplane OB stars are capable of producing high-altitude DIG in a realistic three-dimensional ISM.

Soil-test N recommendations augmented with PEST-optimized RZWQM simulations

USGS Publications Warehouse

Malone, R.W.; Jaynes, D.B.; Ma, Liwang; Nolan, B.T.; Meek, D.W.; Karlen, D.L.

2010-01-01

Improved understanding of year-to-year late-spring soil nitrate test (LSNT) variability could help make it more attractive to producers. We test the ability of the Root Zone Water Quality Model (RZWQM) to simulate watershed-scale variability due to the LSNT, and we use the optimized model to simulate long-term field N dynamics under related conditions. Autoregressive techniques and the automatic parameter calibration program PEST were used to show that RZWQM simulates significantly lower nitrate concentration in discharge from LSNT treatments compared with areas receiving fall N fertilizer applications within the tile-drained Walnut Creek, Iowa, watershed (>5 mg N L-1 difference for the third year of the treatment, 1999). This result is similar to field-measured data from a paired watershed experiment. A statistical model we developed using RZWQM simulations from 1970 to 2005 shows that early-season precipitation and early-season temperature account for 90% of the interannual variation in LSNT-based fertilizer N rates. Long-term simulations with similar average N application rates for corn (Zea mays L.) (151 kg N ha-1) show annual average N loss in tile flow of 20.4, 22.2, and 27.3 kg N ha -1 for LSNT, single spring, and single fall N applications. These results suggest that (i) RZWQM is a promising tool to accurately estimate the water quality effects of LSNT; (ii) the majority of N loss difference between LSNT and fall applications is because more N remains in the root zone for crop uptake; and (iii) year-to-year LSNT-based N rate differences are mainly due to variation in early-season precipitation and temperature. Copyright ?? 2010 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Ion trap simulation program, ITSIM: A powerful heuristic and predictive tool in ion trap mass spectrometry

NASA Astrophysics Data System (ADS)

Bui, Huy Anh

The multi-particle simulation program, ITSIM version 4.0, takes advantage of the enhanced performance of the Windows 95 and NT operating systems in areas such as memory management, user friendliness, flexibility of graphics and speed, to investigate the motion of ions in the quadrupole ion trap. The objective of this program is to use computer simulations based on mathematical models to improve the performance of the ion trap mass spectrometer. The simulation program can provide assistance in understanding fundamental aspects of ion trap mass spectrometry, precede and help to direct the course of experiments, as well as having didactic value in elucidating and allowing visualization of ion behavior under different experimental conditions. The program uses the improved Euler method to calculate ion trajectories as numerical solutions to the Mathieu differential equation. This Windows version can simultaneously simulate the trajectories of ions with a virtually unlimited number of different mass-to-charge ratios and hence allows realistic mass spectra, ion kinetic energy distributions and other experimentally measurable properties to be simulated. The large number of simulated ions allows examination of (i) the offsetting effects of mutual ion repulsion and collisional cooling in an ion trap and (ii) the effects of higher order fields. Field inhomogeneities arising from exit holes, electrode misalignment, imperfect electrode surfaces or new trap geometries can be simulated with the program. The simulated data are used to obtain mass spectra from mass-selective instability scans as well as by Fourier transformation of image currents induced by coherently moving ion clouds. Complete instruments, from an ion source through the ion trap mass analyzer to a detector, can now be simulated. Applications of the simulation program are presented and discussed. Comparisons are made between the simulations and experimental data. Fourier transformed experiments and a novel six-electrode ion trap mass spectrometer illustrate cases in which simulations precede new experiments. Broadband non-destructive ion detection based on induced image current measurements are described in the case of a quadrupole ion trap having cylindrical geometry.

ELUCID—Exploring the Local Universe with the reConstructed Initial Density Field. II. Reconstruction Diagnostics, Applied to Numerical Halo Catalogs

NASA Astrophysics Data System (ADS)

Tweed, Dylan; Yang, Xiaohu; Wang, Huiyuan; Cui, Weiguang; Zhang, Youcai; Li, Shijie; Jing, Y. P.; Mo, H. J.

2017-05-01

The ELUCID project aims to build a series of realistic cosmological simulations that reproduce the spatial and mass distributions of the galaxies as observed in the Sloan Digital Sky Survey. This requires powerful reconstruction techniques to create constrained initial conditions (ICs). We test the reconstruction method by applying it to several N-body simulations. We use two medium-resolution simulations, which each produced three additional constrained N-body simulations. We compare the resulting friend-of-friend catalogs by using the particle indexes as tracers, and quantify the quality of the reconstruction by varying the main smoothing parameter. The cross-identification method we use proves to be efficient, and the results suggest that the most massive reconstructed halos are effectively traced from the same Lagrangian regions in the ICs. A preliminary time-dependence analysis indicates that high-mass-end halos converge only at a redshift close to the reconstruction redshift. This suggests that, for earlier snapshots, only collections of progenitors may be effectively cross-identified.

Carotid artery phantom designment and simulation using field II

NASA Astrophysics Data System (ADS)

Lin, Yuan; Yang, Xin; Ding, Mingyue

2013-10-01

Carotid atherosclerosis is the major cause of ischemic stroke, a leading cause of mortality and disability. Morphology and structure features of carotid plaques are the keys to identify plaques and monitoring the disease. Manually segmentation on the ultrasonic images to get the best-fitted actual size of the carotid plaques based on physicians personal experience, namely "gold standard", is a important step in the study of plaque size. However, it is difficult to qualitatively measure the segmentation error caused by the operator's subjective factors. In order to reduce the subjective factors, and the uncertainty factors of quantification, the experiments in this paper were carried out. In this study, we firstly designed a carotid artery phantom, and then use three different beam-forming algorithms of medical ultrasound to simulate the phantom. Finally obtained plaques areas were analyzed through manual segmentation on simulation images. We could (1) directly evaluate the different beam-forming algorithms for the ultrasound imaging simulation on the effect of carotid artery; (2) also analyze the sensitivity of detection on different size of plaques; (3) indirectly reflect the accuracy of the manual segmentation base on segmentation results the evaluation.

Large Eddy Simulation of Vertical Axis Wind Turbine wakes; Part II: effects of inflow turbulence

NASA Astrophysics Data System (ADS)

Duponcheel, Matthieu; Chatelain, Philippe; Caprace, Denis-Gabriel; Winckelmans, Gregoire

2017-11-01

The aerodynamics of Vertical Axis Wind Turbines (VAWTs) is inherently unsteady, which leads to vorticity shedding mechanisms due to both the lift distribution along the blade and its time evolution. Large-scale, fine-resolution Large Eddy Simulations of the flow past Vertical Axis Wind Turbines have been performed using a state-of-the-art Vortex Particle-Mesh (VPM) method combined with immersed lifting lines. Inflow turbulence with a prescribed turbulence intensity (TI) is injected at the inlet of the simulation from a precomputed synthetic turbulence field obtained using the Mann algorithm. The wake of a standard, medium-solidity, H-shaped machine is simulated for several TI levels. The complex wake development is captured in details and over long distances: from the blades to the near wake coherent vortices, then through the transitional ones to the fully developed turbulent far wake. Mean flow and turbulence statistics are computed over more than 10 diameters downstream of the machine. The sensitivity of the wake topology and decay to the TI level is assessed.

Aliasing errors in measurements of beam position and ellipticity

NASA Astrophysics Data System (ADS)

Ekdahl, Carl

2005-09-01

Beam position monitors (BPMs) are used in accelerators and ion experiments to measure currents, position, and azimuthal asymmetry. These usually consist of discrete arrays of electromagnetic field detectors, with detectors located at several equally spaced azimuthal positions at the beam tube wall. The discrete nature of these arrays introduces systematic errors into the data, independent of uncertainties resulting from signal noise, lack of recording dynamic range, etc. Computer simulations were used to understand and quantify these aliasing errors. If required, aliasing errors can be significantly reduced by employing more than the usual four detectors in the BPMs. These simulations show that the error in measurements of the centroid position of a large beam is indistinguishable from the error in the position of a filament. The simulations also show that aliasing errors in the measurement of beam ellipticity are very large unless the beam is accurately centered. The simulations were used to quantify the aliasing errors in beam parameter measurements during early experiments on the DARHT-II accelerator, demonstrating that they affected the measurements only slightly, if at all.

Gas propagation following a sudden loss of vacuum in a pipe cooled by He I and He II.

NASA Astrophysics Data System (ADS)

Garceau, N.; Guo, W.; Dodamead, T.

2017-12-01

Many cryogenic systems around the world are concerned with the sudden catastrophic loss of vacuum for cost, preventative damage, safety or other reasons. The experiments in this paper were designed to simulate the sudden vacuum break in the beam-line pipe of a liquid helium cooled superconducting particle accelerator. This paper expands previous research conducted at the National High Magnetic Field Laboratory and evaluates the differences between normal helium (He I) and superfluid helium (He II). For the experiments, a straight pipe and was evacuated and immersed in liquid helium at 4.2 K and below 2.17 K. Vacuum loss was simulated by opening a solenoid valve on a buffer tank filled nitrogen gas. Gas front arrival was observed by a temperature rise of the tube. Preliminary results suggested that the speed of the gas front through the experiment decreased exponentially along the tube for both normal liquid helium and super-fluid helium. The system was modified to a helical pipe system to increase propagation length. Testing and analysis on these two systems revealed there was minor difference between He I and He II despite the difference between the two distinct helium phases heat transfer mechanisms: convection vs thermal counterflow. Furthermore, the results indicated that the temperature of the tube wall above the LHe bath also plays a significant role in the initial front propagation. More systematic measurements are planned in with the helical tube system to further verify the results.

Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-03-01

In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call "Hamiltonian dielectric solvent" (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

Nonlocal elasticity tensors in dislocation and disclination cores

DOE PAGES

Taupin, V.; Gbemou, K.; Fressengeas, C.; ...

2017-01-07

We introduced nonlocal elastic constitutive laws for crystals containing defects such as dislocations and disclinations. Additionally, the pointwise elastic moduli tensors adequately reflect the elastic response of defect-free regions by relating stresses to strains and couple-stresses to curvatures, elastic cross-moduli tensors relating strains to couple-stresses and curvatures to stresses within convolution integrals are derived from a nonlocal analysis of strains and curvatures in the defects cores. Sufficient conditions are derived for positive-definiteness of the resulting free energy, and stability of elastic solutions is ensured. The elastic stress/couple stress fields associated with prescribed dislocation/disclination density distributions and solving the momentum andmore » moment of momentum balance equations in periodic media are determined by using a Fast Fourier Transform spectral method. Here, the convoluted cross-moduli bring the following results: (i) Nonlocal stresses and couple stresses oppose their local counterparts in the defects core regions, playing the role of restoring forces and possibly ensuring spatio-temporal stability of the simulated defects, (ii) The couple stress fields are strongly affected by nonlocality. Such effects favor the stability of the simulated grain boundaries and allow investigating their elastic interactions with extrinsic defects, (iii) Driving forces inducing grain growth or refinement derive from the self-stress and couple stress fields of grain boundaries in nanocrystalline configurations.« less

An AeroCom assessment of black carbon in Arctic snow and sea ice

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

Jiao, C.; Flanner, M. G.; Balkanski, Y.

2014-01-01

Though many global aerosols models prognose surface deposition, only a few models have been used to directly simulate the radiative effect from black carbon (BC) deposition to snow and sea ice. In this paper, we apply aerosol deposition fields from 25 models contributing to two phases of the Aerosol Comparisons between Observations and Models (AeroCom) project to simulate and evaluate within-snow BC concentrations and radiative effect in the Arctic. We accomplish this by driving the offline land and sea ice components of the Community Earth System Model with different deposition fields and meteorological conditions from 2004 to 2009, during whichmore » an extensive field campaign of BC measurements in Arctic snow occurred. We find that models generally underestimate BC concentrations in snow in northern Russia and Norway, while overestimating BC amounts elsewhere in the Arctic. Although simulated BC distributions in snow are poorly correlated with measurements, mean values are reasonable. The multi-model mean (range) bias in BC concentrations, sampled over the same grid cells, snow depths, and months of measurements, are -4.4 (-13.2 to +10.7) ng g -1 for an earlier phase of AeroCom models (phase I), and +4.1 (-13.0 to +21.4) ng g -1 for a more recent phase of AeroCom models (phase II), compared to the observational mean of 19.2 ng g -1. Factors determining model BC concentrations in Arctic snow include Arctic BC emissions, transport of extra-Arctic aerosols, precipitation, deposition efficiency of aerosols within the Arctic, and meltwater removal of particles in snow. Sensitivity studies show that the model–measurement evaluation is only weakly affected by meltwater scavenging efficiency because most measurements were conducted in non-melting snow. The Arctic (60–90° N) atmospheric residence time for BC in phase II models ranges from 3.7 to 23.2 days, implying large inter-model variation in local BC deposition efficiency. Combined with the fact that most Arctic BC deposition originates from extra-Arctic emissions, these results suggest that aerosol removal processes are a leading source of variation in model performance. The multi-model mean (full range) of Arctic radiative effect from BC in snow is 0.15 (0.07–0.25) W m -2 and 0.18 (0.06–0.28) W m -2 in phase I and phase II models, respectively. After correcting for model biases relative to observed BC concentrations in different regions of the Arctic, we obtain a multi-model mean Arctic radiative effect of 0.17 W m -2 for the combined AeroCom ensembles. Finally, there is a high correlation between modeled BC concentrations sampled over the observational sites and the Arctic as a whole, indicating that the field campaign provided a reasonable sample of the Arctic.« less

Validation of Multibody Program to Optimize Simulated Trajectories II Parachute Simulation with Interacting Forces

NASA Technical Reports Server (NTRS)

Raiszadeh, Behzad; Queen, Eric M.; Hotchko, Nathaniel J.

2009-01-01

A capability to simulate trajectories of multiple interacting rigid bodies has been developed, tested and validated. This capability uses the Program to Optimize Simulated Trajectories II (POST 2). The standard version of POST 2 allows trajectory simulation of multiple bodies without force interaction. In the current implementation, the force interaction between the parachute and the suspended bodies has been modeled using flexible lines, allowing accurate trajectory simulation of the individual bodies in flight. The POST 2 multibody capability is intended to be general purpose and applicable to any parachute entry trajectory simulation. This research paper explains the motivation for multibody parachute simulation, discusses implementation methods, and presents validation of this capability.

State diagram of magnetostatic coupling phase-locked spin-torque oscillators

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

Zhang, Mengwei; Wang, Longze; Wei, Dan, E-mail: weidan@mail.tsinghua.edu.cn

2015-05-07

The state diagram of magnetostatic coupling phase-locked spin torque oscillator (STO) with perpendicular reference layer and planar field generation layer (FGL) is studied by the macrospin model and the micromagnetic model. The state diagrams of current densities are calculated under various external fields. The simulation shows that there are two phase-lock current density regions. In the phase-locked STOs in low current region I, the spin configuration of FGL is uniform; in high current region II, the spin configuration of FGL is highly nonuniform. In addition, the results with different STOs separation L{sub s} are compared, and the coupling between twomore » STOs is largely decreased when L{sub s} is increased from 40 nm to 60 nm.« less

Torsion limits from t t macr production at the LHC

NASA Astrophysics Data System (ADS)

de Almeida, F. M. L.; de Andrade, F. R.; do Vale, M. A. B.; Nepomuceno, A. A.

2018-04-01

Torsion models constitute a well-known class of extended quantum gravity models. In this work, one investigates the phenomenological consequences of a torsion field interacting with top quarks at the LHC. A torsion field could appear as a new heavy state characterized by its mass and couplings to fermions. This new state would form a resonance decaying into a top antitop pair. The latest ATLAS t t ¯ production results from LHC 13 TeV data are used to set limits on torsion parameters. The integrated luminosity needed to observe torsion resonance at the next LHC upgrades are also evaluated, considering different values for the torsion mass and its couplings to Standard Model fermions. Finally, prospects for torsion exclusion at the future LHC phases II and III are obtained using fast detector simulations.

Deep-Earth reactor: Nuclear fission, helium, and the geomagnetic field

PubMed Central

Hollenbach, D. F.; Herndon, J. M.

2001-01-01

Geomagnetic field reversals and changes in intensity are understandable from an energy standpoint as natural consequences of intermittent and/or variable nuclear fission chain reactions deep within the Earth. Moreover, deep-Earth production of helium, having 3He/4He ratios within the range observed from deep-mantle sources, is demonstrated to be a consequence of nuclear fission. Numerical simulations of a planetary-scale geo-reactor were made by using the SCALE sequence of codes. The results clearly demonstrate that such a geo-reactor (i) would function as a fast-neutron fuel breeder reactor; (ii) could, under appropriate conditions, operate over the entire period of geologic time; and (iii) would function in such a manner as to yield variable and/or intermittent output power. PMID:11562483

Tuning the DARHT Axis-II linear induction accelerator focusing

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

Ekdahl, Carl A.

2012-04-24

Flash radiography of large hydrodynamic experiments driven by high explosives is a well-known diagnostic technique in use at many laboratories, and the Dual-Axis Radiography for Hydrodynamic Testing (DARHT) facility at Los Alamos produces flash radiographs of large hydrodynamic experiments. Two linear induction accelerators (LIAs) make the bremsstrahlung radiographic source spots for orthogonal views of each test. The 2-kA, 20-MeV Axis-I LIA creates a single 60-ns radiography pulse. The 1.7-kA, 16.5-MeV Axis-II LIA creates up to four radiography pulses by kicking them out of a longer pulse that has a 1.6-{mu}s flattop. The Axis-II injector, LIA, kicker, and downstream transport (DST)more » to the bremsstrahlung converter are described. Adjusting the magnetic focusing and steering elements to optimize the electron-beam transport through an LIA is often called 'tuning.' As in all high-current LIAs, the focusing field is designed to be as close to that of the ideal continuous solenoid as physically possible. In ideal continuous solenoidal transport a smoothly varying beam size can easily be found for which radial forces balance, and the beam is said to be 'matched' to the focusing field. A 'mismatched' beam exhibits unwanted oscillations in size, which are a source of free energy that contributes to emittance growth. This is undesirable, because in the absence of beam-target effects, the radiographic spot size is proportional to the emittance. Tuning the Axis-II LIA is done in two steps. First, the solenoidal focusing elements are set to values designed to provide a matched beam with little or no envelope oscillations, and little or no beam-breakup (BBU) instability growth. Then, steering elements are adjusted to minimize the motion of the centroid of a well-centered beam at the LIA exit. This article only describes the design of the tune for the focusing solenoids. The DARHT Axis-II LIA was required to be re-tuned after installing an accelerator cell to replace a failed solenoid in March of 2012. We took advantage of this opportunity to improve the design of the focusing tune with better models of the remaining partially failed solenoids, better estimates of beam initial conditions, and better values for pulsed-power voltages. As with all previous tunes for Axis-II, this one incorporates measures to mitigate beam-breakup (BBU) instability, image displacement instability (IDI), corkscrew (sweep), and emittance growth. Section II covers the general approach to of design of focusing solenoid tunes for the DARHT Axis-2 LIA. Section III explains the specific requirements and simulations needed to design the tune for the injector, which includes the thermionic electron source, diode, and six induction cells. Section IV explains the requirements and simulations for tuning the main accelerator, which consists of 68 induction cells. Finally, Section V explores sensitivity of the tune to deviations of parameters from nominal, random variations, and uncertainties in values. Four appendices list solenoid settings for this new tune, discuss comparisons of different simulation codes, show halo formation in mismatched beams, and present a brief discussion of the beam envelope equation, which is the heart of the method used to design LIA solenoid tunes.« less

Plasma dynamics on current-carrying magnetic flux tubes. II - Low potential simulation

NASA Technical Reports Server (NTRS)

Swift, Daniel W.

1992-01-01

The evolution of plasma in a current-carrying magnetic flux tube of variable cross section is investigated using a one-dimensional numerical simulation. The flux tube is narrow at the two ends and broad in the middle. The middle part of the flux tube is loaded with a hot, magnetically trapped population, and the two ends have a more dense, gravitationally bound population. A potential difference larger than the gravitational potential but less than the energy of the hot population is applied across the domain. The general result is that the potential change becomes distributed along the anode half of the domain, with negligible potential change on the cathode half. The potential is supported by the mirror force of magnetically trapped particles. The simulations show a steady depletion of plasma on the anode side of the flux tube. The current steadily decreases on a time scale of an ion transit time. The results may provide an explanation for the observed plasma depletions on auroral field lines carrying upward currents.

Probing adsorption sites of carbon dioxide in metal organic framework of [Zn(bdc)(dpds)]n: A molecular simulation study

NASA Astrophysics Data System (ADS)

Lu, Shih-I.; Liao, Jian-Min; Huang, Xiao-Zhuang; Lin, Chia-Hsun; Ke, Szu-Yu; Wang, Chih-Chieh

2017-11-01

We used force-field based grand-canonical Monte Carlo simulation method and density functional theory to study adsorption characteristics of carbon dioxide (CO2) molecules in a metal-organic framework (MOF) compound, [Zn(bdc)(dpds)]n. The studied MOF include a metal ion (Zn(II)), an anion organic linker (dianion of benzene dicarboxylicacid, bdc2-) and a neutral organic linker (4,4‧-dipyridyldisulfide, dpds). Results from calculated adsorption isotherms and enthalpies of adsorption agree with the experimental data. The interactions between the adsorbed CO2 and the organic linkers were examined in simulations. Calculated results show available absorption sites are surrounded by two dpds ligands in which an S-S bond as an N-N‧ spacer connect two pyridines. In contrast, the bdc2- ligand does not give a significant contribution to the substantial adsorption amount even though it contains the carboxylate group that provides available bonding site to CO2.

A discrete twin-boundary approach for simulating the magneto-mechanical response of Ni-Mn-Ga

NASA Astrophysics Data System (ADS)

Faran, Eilon; Shilo, Doron

2016-09-01

The design and optimization of ferromagnetic shape memory alloys (FSMA)-based devices require quantitative understanding of the dynamics of twin boundaries within these materials. Here, we present a discrete twin boundary modeling approach for simulating the behavior of an FSMA Ni-Mn-Ga crystal under combined magneto-mechanical loading conditions. The model is based on experimentally measured kinetic relations that describe the motion of individual twin boundaries over a wide range of velocities. The resulting calculations capture the dynamic response of Ni-Mn-Ga and reveal the relations between fundamental material parameters and actuation performance at different frequencies of the magnetic field. In particular, we show that at high field rates, the magnitude of the lattice barrier that resists twin boundary motion is the important property that determines the level of actuation strain, while the contribution of twinning stress property is minor. Consequently, type II twin boundaries, whose lattice barrier is smaller compared to type I, are expected to show better actuation performance at high rates, irrespective of the differences in the twinning stress property between the two boundary types. In addition, the simulation enables optimization of the actuation strain of a Ni-Mn-Ga crystal by adjusting the magnitude of the bias mechanical stress, thus providing direct guidelines for the design of actuating devices. Finally, we show that the use of a linear kinetic law for simulating the twinning-based response is inadequate and results in incorrect predictions.

Two Topics in Seasonal Streamflow Forecasting: Soil Moisture Initialization Error and Precipitation Downscaling

NASA Technical Reports Server (NTRS)

Koster, Randal; Walker, Greg; Mahanama, Sarith; Reichle, Rolf

2012-01-01

Continental-scale offline simulations with a land surface model are used to address two important issues in the forecasting of large-scale seasonal streamflow: (i) the extent to which errors in soil moisture initialization degrade streamflow forecasts, and (ii) the extent to which the downscaling of seasonal precipitation forecasts, if it could be done accurately, would improve streamflow forecasts. The reduction in streamflow forecast skill (with forecasted streamflow measured against observations) associated with adding noise to a soil moisture field is found to be, to first order, proportional to the average reduction in the accuracy of the soil moisture field itself. This result has implications for streamflow forecast improvement under satellite-based soil moisture measurement programs. In the second and more idealized ("perfect model") analysis, precipitation downscaling is found to have an impact on large-scale streamflow forecasts only if two conditions are met: (i) evaporation variance is significant relative to the precipitation variance, and (ii) the subgrid spatial variance of precipitation is adequately large. In the large-scale continental region studied (the conterminous United States), these two conditions are met in only a somewhat limited area.

New Editions for the Apple II of the Chelsea Science Simulations.

ERIC Educational Resources Information Center

Pipeline, 1983

1983-01-01

Ten computer simulations for the Apple II are described. Subject areas of programs include: population dynamics, plant competition, enzyme kinetics, evolution and natural selection, genetic mapping, ammonia synthesis, reaction kinetics, wave interference/diffraction, satellite orbits, and particle scattering. (JN)

Numerical Analysis of Constrained Dynamical Systems, with Applications to Dynamic Contact of Solids, Nonlinear Elastodynamics and Fluid-Structure Interactions

DTIC Science & Technology

2000-12-01

Numerical Simulations ..... ................. .... 42 1.4.1. Impact of a rod on a rigid wall ..... ................. .... 42 1.4.2. Impact of two...dissipative properties of the proposed scheme . . . . 81 II.4. Representative Numerical Simulations ...... ................. ... 84 11.4.1. Forging of...Representative numerical simulations ...... ............. .. 123 111.3. Model Problem II: a Simplified Model of Thin Beams ... ......... ... 127 III

Long-term transport behavior of psychoactive compounds in sewage-affected groundwater

NASA Astrophysics Data System (ADS)

Nham, Hang Thuy Thi; Greskowiak, Janek; Hamann, Enrico; Meffe, Raffaella; Hass, Ulrike; Massmann, Gudrun

2016-11-01

The present study provides a model-based characterization of the long-term transport behavior of five psychoactive compounds (meprobamate, pyrithyldione, primidone, phenobarbital and phenylethylmalonamide) introduced into groundwater via sewage irrigation in Berlin, Germany. Compounds are still present in the groundwater despite the sewage farm closure in the year 1980. Due to the limited information on (i) compound concentrations in the source water and (ii) substance properties, a total of 180 cross-sectional model realizations for each compound were carried out, covering a large range of possible parameter combinations. Results were compared with the present-day contamination patterns in the aquifer and the most likely scenarios were identified based on a number of model performance criteria. The simulation results show that (i) compounds are highly persistent under the present field conditions, and (ii) sorption is insignificant. Thus, back-diffusion from low permeability zones appears as the main reason for the compound retardation.

Enhanced infrared detectors using resonant structures combined with thin type-II superlattice absorbers

DOE PAGES

Goldflam, Michael D.; Kadlec, Emil Andrew; Olson, Ben V.; ...

2016-12-22

Here we examined the spectral responsivity of a 1.77μm thick type-II superlattice based long-wave infrared detector in combination with metallic nanoantennas. Coupling between the Fabry-Pérot cavity formed by the semiconductor layer and the resonant nanoantennas on its surface enables spectral selectivity, while also increasing peak quantum efficiency to over 50%. Electromagnetic simulations reveal that this high responsivity is a direct result of field-enhancement in the absorber layer, enabling significant absorption in spite of the absorber’s subwavelength thickness. Notably, thinning of the absorbing material could ultimately yield lower photodetector noise through a reduction in dark current while improving photocarrier collection efficiency.more » The temperature- and incident-angle-independent spectral response observed in these devices allows for operation over a wide range of temperatures and optical systems. This detector paradigm demonstrates potential benefits to device performance with applications throughout the infrared.« less

Engine dynamic analysis with general nonlinear finite element codes. II - Bearing element implementation, overall numerical characteristics and benchmarking

NASA Technical Reports Server (NTRS)

Padovan, J.; Adams, M.; Lam, P.; Fertis, D.; Zeid, I.

1982-01-01

Second-year efforts within a three-year study to develop and extend finite element (FE) methodology to efficiently handle the transient/steady state response of rotor-bearing-stator structure associated with gas turbine engines are outlined. The two main areas aim at (1) implanting the squeeze film damper element into a general purpose FE code for testing and evaluation; and (2) determining the numerical characteristics of the FE-generated rotor-bearing-stator simulation scheme. The governing FE field equations are set out and the solution methodology is presented. The choice of ADINA as the general-purpose FE code is explained, and the numerical operational characteristics of the direct integration approach of FE-generated rotor-bearing-stator simulations is determined, including benchmarking, comparison of explicit vs. implicit methodologies of direct integration, and demonstration problems.

Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation

PubMed Central

Wang, Yu; Helminen, Emily; Jiang, Jingfeng

2015-01-01

Purpose: Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. Methods: The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time. Results: Representative examples were used to demonstrate capabilities of this virtual simulation platform. In the first set of three ultrasound simulation examples, three heterogeneous volumes of interest were selected from a virtual breast ultrasound phantom to perform sophisticated ultrasound simulations. These resultant B-mode images realistically represented the underlying complex but known media. In the second set of three QUE examples, advanced applications in QUE were simulated. The first QUE example was to show breast tumors with complex shapes and/or compositions. The resultant strain images showed complex patterns that were normally seen in freehand clinical ultrasound data. The second and third QUE examples demonstrated (deformation-dependent) nonlinear strain imaging and time-dependent strain imaging, respectively. Conclusions: The proposed virtual QUE platform was implemented and successfully tested in this study. Through show-case examples, the proposed work has demonstrated its capabilities of creating sophisticated QUE data in a way that cannot be done through the manufacture of physical tissue-mimicking phantoms and other software. This open software architecture will soon be made available in the public domain and can be readily adapted to meet specific needs of different research groups to drive innovations in QUE. PMID:26328994

Long-term soil organic carbon changes in cereal and ley rotations: model testing

NASA Astrophysics Data System (ADS)

Kynding Borgen, Signe; Dörsch, Peter; Krogstad, Tore; Azzaroli Bleken, Marina

2015-04-01

Reliable modeling of soil organic carbon (SOC) dynamics in agroecosystems is crucial to define mitigation strategies related to crop management on the farm scale as well as the regional scale. International climate agreements and national political decisions rely to a large extent on the National Greenhouse gas Inventory Reports that are submitted annually to the UNFCCC. However, lower tier methods are used to estimate SOC changes on cropland in most country reports. The application of mechanistic models in national greenhouse gas inventory estimation requires proper model testing against measurements in order to verify the estimated emissions. Few long-term field experiments measuring SOC stock changes have been conducted in Norway. We evaluate the performance of the Introductory Carbon Balance Model (ICBM) in simulating SOC changes over 60 years in a field experiment conducted in Ås from 1953-2013. The site is located in south-eastern Norway, on the boarder of the boreal and temperate climate zone, where the majority of the country's grain production occurs. The field trial consisted of four rotations: I) continuous cereal, II) cereal + row crops, III) 2 years of ley + 4 years of cereal, IV) 4 years of ley + 2 years of cereal, and four treatments per rotation: a) low NPK, b) high NPK, c) low NPK + FYM, and d) straw (on rotations I and II) or high NPK + FYM (on rotations III and IV). The annual external modifying factor of the decomposition rate was calculated based on daily minimum and maximum temperature, precipitation, relative humidity, wind speed, and net radiation, and adjusted for soil type and crop management according to default ICBM calibration. We present results of simulated C changes for the long term plots and explore options to improve parameter calibration. Finally, we provide suggestions for how problems regarding model verification can be handled with when applying the model on a national scale for inventory reporting.

A Neutron Radiography System for Field Use

DTIC Science & Technology

1989-06-01

provoked a major renewal of interest in neutron radiography because it promises to bring neutron radiography to the workplace , a convenience provided...II I~F I C II i IiH i ii MTL TR 89-52 I-AD A NEUTRON RADIOGRAPHY SYSTEM N FOR FIELD USE e~m JOHN J. ANTAL and ALFRED S. MAROTTA, and LOUIS J. FARESE...COVERED A NEUTRON RADIOGRAPHY SYSTEM FOR FIELD USE Final Report 6. PERFORMING OR1. REPORT NUMBER 7. AUTHOR(s) S. CONTRACT OR GRANT NUMBER(s) John J

77 FR 59339 - Cross Waivers of Liability Clauses

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-27

... facilities and services; and (ii) All activities related to ground support, test, training, simulation, or... develop further a Payload's product or process for use other than for ISS-related activities in... (ii) All activities related to ground support, test, training, simulation, or guidance and control...

CFD simulation of copper(II) extraction with TFA in non-dispersive hollow fiber membrane contactors.

PubMed

Muhammad, Amir; Younas, Mohammad; Rezakazemi, Mashallah

2018-04-01

This study presents computational fluid dynamics (CFD) simulation of dispersion-free liquid-liquid extraction of copper(II) with trifluoroacetylacetone (TFA) in hollow fiber membrane contactor (HFMC). Mass and momentum balance Navier-Stokes equations were coupled to address the transport of copper(II) solute across membrane contactor. Model equations were simulated using COMSOL Multiphysics™. The simulation was run to study the detailed concentration distribution of copper(II) and to investigate the effects of various parameters like membrane characteristics, partition coefficient, and flow configuration on extraction efficiency. Once-through extraction was found to be increased from 10 to 100% when partition coefficient was raised from 1 to 10. Similarly, the extraction efficiency was almost doubled when porosity to tortuosity ratio of membrane was increased from 0.05 to 0.81. Furthermore, the study revealed that CFD can be used as an effective optimization tool for the development of economical membrane-based dispersion-free extraction processes.

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

PubMed Central

2016-01-01

The nucleation of crystals in liquids is one of nature’s most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560

POMICS: A Simulation Disease Model for Timing Fungicide Applications in Management of Powdery Mildew of Cucurbits.

PubMed

Sapak, Z; Salam, M U; Minchinton, E J; MacManus, G P V; Joyce, D C; Galea, V J

2017-09-01

A weather-based simulation model, called Powdery Mildew of Cucurbits Simulation (POMICS), was constructed to predict fungicide application scheduling to manage powdery mildew of cucurbits. The model was developed on the principle that conditions favorable for Podosphaera xanthii, a causal pathogen of this crop disease, generate a number of infection cycles in a single growing season. The model consists of two components that (i) simulate the disease progression of P. xanthii in secondary infection cycles under natural conditions and (ii) predict the disease severity with application of fungicides at any recurrent disease cycles. The underlying environmental factors associated with P. xanthii infection were quantified from laboratory and field studies, and also gathered from literature. The performance of the POMICS model when validated with two datasets of uncontrolled natural infection was good (the mean difference between simulated and observed disease severity on a scale of 0 to 5 was 0.02 and 0.05). In simulations, POMICS was able to predict high- and low-risk disease alerts. Furthermore, the predicted disease severity was responsive to the number of fungicide applications. Such responsiveness indicates that the model has the potential to be used as a tool to guide the scheduling of judicious fungicide applications.

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.

PubMed

Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos

2016-06-22

The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.

Galaxy Formation through Filamentary Accretion at z = 6.1

NASA Astrophysics Data System (ADS)

Jones, G. C.; Willott, C. J.; Carilli, C. L.; Ferrara, A.; Wang, R.; Wagg, J.

2017-08-01

We present Atacama Large Millimeter/submillimeter Array observations of the dust continuum and [C II] 158 μm line emission from the z = 6.0695 Lyman-Break Galaxy (LBG) WMH5. These observations at 0.″3 spatial resolution show a compact (˜3 kpc) main galaxy in dust and [C II] emission, with a “tail” of emission extending to the east by about 5 kpc (in projection). The [C II] tail is comprised predominantly of two distinct sub-components in velocity, separated from the core by ˜100 and 250 km s-1, with narrow intrinsic widths of about 80 km s-1, which we call “sub-galaxies.” The sub-galaxies themselves are extended east-west by about 3 kpc in individual channel images. The [C II] tail joins smoothly into the main galaxy velocity field. The [C II] line to continuum ratios are comparable for the main and sub-galaxy positions, within a factor two. In addition, these ratios are comparable to z˜ 5.5 LBGs. We conjecture that the WMH5 system represents the early formation of a galaxy through the accretion of smaller satellite galaxies, embedded in a smoother gas distribution, along a possibly filamentary structure. The results are consistent with current cosmological simulations of early galaxy formation and support the idea of very early enrichment with dust and heavy elements of the accreting material.

Visualization of grid-generated turbulence in He II using PTV

NASA Astrophysics Data System (ADS)

Mastracci, B.; Guo, W.

2017-12-01

Due to its low viscosity, cryogenic He II has potential use for simulating large-scale, high Reynolds number turbulent flow in a compact and efficient apparatus. To realize this potential, the behavior of the fluid in the simplest cases, such as turbulence generated by flow past a mesh grid, must be well understood. We have designed, constructed, and commissioned an apparatus to visualize the evolution of turbulence in the wake of a mesh grid towed through He II. Visualization is accomplished using the particle tracking velocimetry (PTV) technique, where μm-sized tracer particles are introduced to the flow, illuminated with a planar laser sheet, and recorded by a scientific imaging camera; the particles move with the fluid, and tracking their motion with a computer algorithm results in a complete map of the turbulent velocity field in the imaging region. In our experiment, this region is inside a carefully designed He II filled cast acrylic channel measuring approximately 16 × 16 × 330 mm. One of three different grids, which have mesh numbers M = 3, 3.75, or 5 mm, can be attached to the pulling system which moves it through the channel with constant velocity up to 600 mm/s. The consequent motion of the solidified deuterium tracer particles is used to investigate the energy statistics, effective kinematic viscosity, and quantized vortex dynamics in turbulent He II.

Electrostatics of proteins in dielectric solvent continua. II. First applications in molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Stork, Martina; Tavan, Paul

2007-04-01

In the preceding paper by Stork and Tavan, [J. Chem. Phys. 126, 165105 (2007)], the authors have reformulated an electrostatic theory which treats proteins surrounded by dielectric solvent continua and approximately solves the associated Poisson equation [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)]. The resulting solution comprises analytical expressions for the electrostatic reaction field (RF) and potential, which are generated within the protein by the polarization of the surrounding continuum. Here the field and potential are represented in terms of Gaussian RF dipole densities localized at the protein atoms. Quite like in a polarizable force field, also the RF dipole at a given protein atom is induced by the partial charges and RF dipoles at the other atoms. Based on the reformulated theory, the authors have suggested expressions for the RF forces, which obey Newton's third law. Previous continuum approaches, which were also built on solutions of the Poisson equation, used to violate the reactio principle required by this law, and thus were inapplicable to molecular dynamics (MD) simulations. In this paper, the authors suggest a set of techniques by which one can surmount the few remaining hurdles still hampering the application of the theory to MD simulations of soluble proteins and peptides. These techniques comprise the treatment of the RF dipoles within an extended Lagrangian approach and the optimization of the atomic RF polarizabilities. Using the well-studied conformational dynamics of alanine dipeptide as the simplest example, the authors demonstrate the remarkable accuracy and efficiency of the resulting RF-MD approach.

A phase-field lattice Boltzmann model for simulating multiphase flows in porous media: Application and comparison to experiments of CO2 sequestration at pore scale

NASA Astrophysics Data System (ADS)

Fakhari, Abbas; Li, Yaofa; Bolster, Diogo; Christensen, Kenneth T.

2018-04-01

We implement a phase-field based lattice-Boltzmann (LB) method for numerical simulation of multiphase flows in heterogeneous porous media at pore scales with wettability effects. The present method can handle large density and viscosity ratios, pertinent to many practical problems. As a practical application, we study multiphase flow in a micromodel representative of CO2 invading a water-saturated porous medium at reservoir conditions, both numerically and experimentally. We focus on two flow cases with (i) a crossover from capillary fingering to viscous fingering at a relatively small capillary number, and (ii) viscous fingering at a relatively moderate capillary number. Qualitative and quantitative comparisons are made between numerical results and experimental data for temporal and spatial CO2 saturation profiles, and good agreement is found. In particular, a correlation analysis shows that any differences between simulations and results are comparable to intra-experimental differences from replicate experiments. A key conclusion of this work is that system behavior is highly sensitive to boundary conditions, particularly inlet and outlet ones. We finish with a discussion on small-scale flow features, such as the emergence of strong recirculation zones as well as flow in which the residual phase is trapped, including a close look at the detailed formation of a water cone. Overall, the proposed model yields useful information, such as the spatiotemporal evolution of the CO2 front and instantaneous velocity fields, which are valuable for understanding the mechanisms of CO2 infiltration at the pore scale.

InterGeo II: International Geographical Achievement Test. Field Trials Report and Test (Secondary Schools, Grade 8).

ERIC Educational Resources Information Center

Niemz, Gunter; Stoltman, Joseph P.

InterGeo II, a project of the Commission on Geographical Education (CGE) of the International Geographical Union (IGU), has developed a broadly based, field-trialed testing instrument for making cross-national comparisons of achievement in geography. Field trials of InterGeo II were held in 23 countries. Data were analyzed for national achievement…

Arsenic removal with iron(II) and iron(III) in waters with high silicate and phosphate concentrations.

PubMed

Roberts, Linda C; Hug, Stephan J; Ruettimann, Thomas; Billah, Morsaline; Khan, Abdul Wahab; Rahman, Mohammad Tariqur

2004-01-01

Arsenic removal by passive treatment, in which naturally present Fe(II) is oxidized by aeration and the forming iron(III) (hydr)oxides precipitate with adsorbed arsenic, is the simplest conceivable water treatment option. However, competing anions and low iron concentrations often require additional iron. Application of Fe(II) instead of the usually applied Fe(III) is shown to be advantageous, as oxidation of Fe(II) by dissolved oxygen causes partial oxidation of As(III) and iron(III) (hydr)oxides formed from Fe(II) have higher sorption capacities. In simulated groundwater (8.2 mM HCO3(-), 2.5 mM Ca2+, 1.6 mM Mg2+, 30 mg/L Si, 3 mg/L P, 500 ppb As(III), or As(V), pH 7.0 +/- 0.1), addition of Fe(II) clearly leads to better As removal than Fe(III). Multiple additions of Fe(II) further improved the removal of As(II). A competitive coprecipitation model that considers As(III) oxidation explains the observed results and allows the estimation of arsenic removal under different conditions. Lowering 500 microg/L As(III) to below 50 microg/L As(tot) in filtered water required > 80 mg/L Fe(III), 50-55 mg/L Fe(II) in one single addition, and 20-25 mg/L in multiple additions. With As(V), 10-12 mg/L Fe(II) and 15-18 mg/L Fe(III) was required. In the absence of Si and P, removal efficiencies for Fe(II) and Fe(III) were similar: 30-40 mg/L was required for As(II), and 2.0-2.5 mg/L was required for As(V). In a field study with 22 tubewells in Bangladesh, passive treatment efficiently removed phosphate, but iron contents were generally too low for efficient arsenic removal.

Investigation on aerodynamic characteristics of baseline-II E-2 blended wing-body aircraft with canard via computational simulation

NASA Astrophysics Data System (ADS)

Nasir, Rizal E. M.; Ali, Zurriati; Kuntjoro, Wahyu; Wisnoe, Wirachman

2012-06-01

Previous wind tunnel test has proven the improved aerodynamic charasteristics of Baseline-II E-2 Blended Wing-Body (BWB) aircraft studied in Universiti Teknologi Mara. The E-2 is a version of Baseline-II BWB with modified outer wing and larger canard, solely-designed to gain favourable longitudinal static stability during flight. This paper highlights some results from current investigation on the said aircraft via computational fluid dynamics simulation as a mean to validate the wind tunnel test results. The simulation is conducted based on standard one-equation turbulence, Spalart-Allmaras model with polyhedral mesh. The ambience of the flight simulation is made based on similar ambience of wind tunnel test. The simulation shows lift, drag and moment results to be near the values found in wind tunnel test but only within angles of attack where the lift change is linear. Beyond the linear region, clear differences between computational simulation and wind tunnel test results are observed. It is recommended that different type of mathematical model be used to simulate flight conditions beyond linear lift region.

Effect of Accessory Power Take-off Variation on a Turbofan Engine Performance

DTIC Science & Technology

2012-09-26

amount of energy from the low pressure spool shaft. A high bypass turbofan engine was modeled using the Numerical Propulsion System Simulation ( NPSS ...4 II.2 Power Extraction Techniques ..........................................................................8 II.3 NPSS ...Methodology and Simulation Setup ...........................................................................25 III.1 Engine NPSS Model

Parallel magnetic field suppresses dissipation in superconducting nanostrips

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

Wang, Yong-Lei; Glatz, Andreas; Kimmel, Gregory J.

The motion of Abrikosov vortices in type-II superconductors results in a finite resistance in the presence of an applied electric current. Elimination or reduction of the resistance via immobilization of vortices is the "holy grail" of superconductivity research. Common wisdom dictates that an increase in the magnetic field escalates the loss of energy since the number of vortices increases. Here we show that this is no longer true if the magnetic field and the current are applied parallel to each other. Our experimental studies on the resistive behavior of a superconducting Mo0.79Ge0.21 nanostrip reveal the emergence of a dissipative statemore » with increasing magnetic field, followed by a pronounced resistance drop, signifying a reentrance to the superconducting state. Large-scale simulations of the 3D time-dependent Ginzburg-Landau model indicate that the intermediate resistive state is due to an unwinding of twisted vortices. When the magnetic field increases, this instability is suppressed due to a better accommodation of the vortex lattice to the pinning configuration. Our findings show that magnetic field and geometrical confinement can suppress the dissipation induced by vortex motion and thus radically improve the performance of superconducting materials.« less

Type-II Superlattice Avalanche Photodiodes

NASA Astrophysics Data System (ADS)

Huang, Jun

Type-II superlattice avalanche photodiodes have shown advantages compared to conventional mercury cadmium telluride photodiodes for infrared wavelength detection. However, surface or interface leakage current has been a major issue for superlattice avalanche photodiodes, especially in infrared wavelength region. First, passivation of the superlattice device with ammonium sulfide and thioacetamide was carried out, and its surface quality was studied by X-ray Photoelectron Spectroscopy. The study showed that both ammonium sulfide and thiacetamide passivation can actively remove the native oxide at the surface. Thiacetamide passivation combine more sulfur bonds with III-V elements than that of ammonium sulfide. Another X-ray photoelectron spectra of thiacetamide-treated atomic layer deposited zinc sulfide capped InAs/GaSb superlattice was performed to investigate the interface sulfur bond conditions. Sb--S and As--S bonds disappear while In-S bond gets enhanced, indicating that Indium Sulfide should be the major components at the interface after ZnS deposition. Second, the simulation of electrical characteristics for zinc sulfide, silicon nitride and silicon dioxide passivated superlattice devices was performed by SILVACO software to fit the experimental results and to discover the surface current mechanism. Different surface current mechanism strengths were found. Third, several novel dual-carrier avalanche photodiode structures were designed and simulated. The structures had alternate carrier multiplication regions, placed next to a wider electron multiplication region, creating dual-carrier multiplication feedback systems. Gain and excess noise factor of these structures were simulated and compared based on the dead space multiplication theory under uniform electric field. From the simulation, the applied bias can be greatly lowered or the thickness can be shrunk to achieve the same gain from the conventional device. The width of the thin region was the most critical parameter determining the device performance.

Accuracy of prostate radiation therapy using a fiducial point-pair registration technique based on the computer-assisted portal imaging quality assurance program PIPSpro.

PubMed

Mermershtain, Wilmosh; Cohen, Yoram; Krutman, Yanai

2003-06-01

The aim of this study was to assess portal imaging for quality assurance of patient positioning in external beam radiotherapy. We present a retrospective study of the variability of patient position in the treatment of 34 prostate cancer patients who were treated with whole pelvic irradiation followed by arc therapy or boost field (Series I) and 25 patients treated by 'small' pelvic 4-field box technique (Series II). Weekly anteroposterior-posteranterior (AP-PA) and left-lateral portal images were compared to simulation films by using a fiducial point-pair registration technique based on the computer-assisted portal imaging quality assurance program PIPSpro, developed specifically for the verification of treatment positioning in radiation therapy. Series I consisted of 34 patients and 194 portal films (97 AP-PA and 97 left-lateral). Overirradiated (OA) and underirradiated (UA) areas were computed in terms of percentage of the reference field size. For the AP-PA portals, the average OA was 2.75% and average UA was 2.74%. For left-lateral portals, an average OA of 2.49% and UA of 2.78% were measured. Series II consisted of 25 patients and 194 portal films (98 AP-PA and 96 left-lateral). The average OA was 0.88% and average UA was 0.86% in AP-PA portals, and 1.03 and 0.82% for left-lateral portals, respectively. The accuracy of patient positioning in irradiation of prostate cancer in our institution is in the range of 2.69% for whole pelvic fields and 1.0% for small fields. We conclude that PIPSpro is an effective and useful tool for quality assurance in radiotherapy.

Geostatistical Sampling Methods for Efficient Uncertainty Analysis in Flow and Transport Problems

NASA Astrophysics Data System (ADS)

Liodakis, Stylianos; Kyriakidis, Phaedon; Gaganis, Petros

2015-04-01

In hydrogeological applications involving flow and transport of in heterogeneous porous media the spatial distribution of hydraulic conductivity is often parameterized in terms of a lognormal random field based on a histogram and variogram model inferred from data and/or synthesized from relevant knowledge. Realizations of simulated conductivity fields are then generated using geostatistical simulation involving simple random (SR) sampling and are subsequently used as inputs to physically-based simulators of flow and transport in a Monte Carlo framework for evaluating the uncertainty in the spatial distribution of solute concentration due to the uncertainty in the spatial distribution of hydraulic con- ductivity [1]. Realistic uncertainty analysis, however, calls for a large number of simulated concentration fields; hence, can become expensive in terms of both time and computer re- sources. A more efficient alternative to SR sampling is Latin hypercube (LH) sampling, a special case of stratified random sampling, which yields a more representative distribution of simulated attribute values with fewer realizations [2]. Here, term representative implies realizations spanning efficiently the range of possible conductivity values corresponding to the lognormal random field. In this work we investigate the efficiency of alternative methods to classical LH sampling within the context of simulation of flow and transport in a heterogeneous porous medium. More precisely, we consider the stratified likelihood (SL) sampling method of [3], in which attribute realizations are generated using the polar simulation method by exploring the geometrical properties of the multivariate Gaussian distribution function. In addition, we propose a more efficient version of the above method, here termed minimum energy (ME) sampling, whereby a set of N representative conductivity realizations at M locations is constructed by: (i) generating a representative set of N points distributed on the surface of a M-dimensional, unit radius hyper-sphere, (ii) relocating the N points on a representative set of N hyper-spheres of different radii, and (iii) transforming the coordinates of those points to lie on N different hyper-ellipsoids spanning the multivariate Gaussian distribution. The above method is applied in a dimensionality reduction context by defining flow-controlling points over which representative sampling of hydraulic conductivity is performed, thus also accounting for the sensitivity of the flow and transport model to the input hydraulic conductivity field. The performance of the various stratified sampling methods, LH, SL, and ME, is compared to that of SR sampling in terms of reproduction of ensemble statistics of hydraulic conductivity and solute concentration for different sample sizes N (numbers of realizations). The results indicate that ME sampling constitutes an equally if not more efficient simulation method than LH and SL sampling, as it can reproduce to a similar extent statistics of the conductivity and concentration fields, yet with smaller sampling variability than SR sampling. References [1] Gutjahr A.L. and Bras R.L. Spatial variability in subsurface flow and transport: A review. Reliability Engineering & System Safety, 42, 293-316, (1993). [2] Helton J.C. and Davis F.J. Latin hypercube sampling and the propagation of uncertainty in analyses of complex systems. Reliability Engineering & System Safety, 81, 23-69, (2003). [3] Switzer P. Multiple simulation of spatial fields. In: Heuvelink G, Lemmens M (eds) Proceedings of the 4th International Symposium on Spatial Accuracy Assessment in Natural Resources and Environmental Sciences, Coronet Books Inc., pp 629?635 (2000).

Clathrate structure-type recognition: Application to hydrate nucleation and crystallisation

NASA Astrophysics Data System (ADS)

Lauricella, Marco; Meloni, Simone; Liang, Shuai; English, Niall J.; Kusalik, Peter G.; Ciccotti, Giovanni

2015-06-01

For clathrate-hydrate polymorphic structure-type (sI versus sII), geometric recognition criteria have been developed and validated. These are applied to the study of the rich interplay and development of both sI and sII motifs in a variety of hydrate-nucleation events for methane and H2S hydrate studied by direct and enhanced-sampling molecular dynamics (MD) simulations. In the case of nucleation of methane hydrate from enhanced-sampling simulation, we notice that already at the transition state, ˜80% of the enclathrated CH4 molecules are contained in a well-structured (sII) clathrate-like crystallite. For direct MD simulation of nucleation of H2S hydrate, some sI/sII polymorphic diversity was encountered, and it was found that a realistic dissipation of the nucleation energy (in view of non-equilibrium relaxation to either microcanonical (NVE) or isothermal-isobaric (NPT) distributions) is important to determine the relative propensity to form sI versus sII motifs.

The effect of a longitudinal density gradient on electron plasma wake field acceleration

NASA Astrophysics Data System (ADS)

Tsiklauri, David

2016-12-01

Three-dimensional, particle-in-cell, fully electromagnetic simulations of electron plasma wake field acceleration in the blow-out regime are presented. Earlier results are extended by (i) studying the effect of a longitudinal density gradient, (ii) avoiding the use of a co-moving simulation box, (iii) inclusion of ion motion, and (iv) studying fully electromagnetic plasma wake fields. It is established that injecting driving and trailing electron bunches into a positive density gradient of 10-fold increasing density over 10 cm long lithium vapour plasma results in spatially more compact and three times larger, compared with the uniform density case, electric fields (-6.4×1010 V m-1), leading to acceleration of the trailing bunch up to 24.4 GeV (starting from an initial 20.4 GeV), with energy transfer efficiencies from the leading to trailing bunch of 75%. In the uniform density case, a -2.5×1010 V m-1 wake is created leading to acceleration of the trailing bunch up to 22.4 GeV, with energy transfer efficiencies of 65%. It is also established that injecting the electron bunches into a negative density gradient of 10-fold decreasing density over 10 cm long plasma results in spatially more spread and two and a half smaller electric fields (-1.0×1010 V m-1), leading to a weaker acceleration of the trailing bunch up to 21.4 GeV, with energy transfer efficiencies of 45%. Taking ion motions into consideration shows that in the plasma wake ion number density can increase over a few times the background value. It is also shown that transverse electromagnetic fields in a plasma wake are of the same order as the longitudinal (electrostatic) ones.

Dynamics of H II regions around exiled O stars

NASA Astrophysics Data System (ADS)

Mackey, Jonathan; Langer, Norbert; Gvaramadze, Vasilii V.

2013-11-01

At least 25 per cent of massive stars are ejected from their parent cluster, becoming runaways or exiles, travelling with often-supersonic space velocities through the interstellar medium (ISM). Their overpressurized H II regions impart kinetic energy and momentum to the ISM, compress and/or evaporate dense clouds, and can constrain properties of both the star and the ISM. Here, we present one-, two- and (the first) three-dimensional simulations of the H II region around a massive star moving supersonically through a uniform, magnetized ISM, with properties appropriate for the nearby O star ζ Oph. The H II region leaves an expanding overdense shell behind the star and, inside this, an underdense wake that should be filled with hot gas from the shocked stellar wind. The gas column density in the shell is strongly influenced by the ISM magnetic field strength and orientation. Hα emission maps show that H II region remains roughly circular, although the star is displaced somewhat from the centre of emission. For our model parameters, the kinetic energy feedback from the H II region is comparable to the mechanical luminosity of the stellar wind, and the momentum feedback rate is >100 times larger than that from the wind and ≈10 times larger than the total momentum input rate available from radiation pressure. Compared to the star's eventual supernova explosion, the kinetic energy feedback from the H II region over the star's main-sequence lifetime is >100 times less, but the momentum feedback is up to 4 times larger. H II region dynamics are found to have only a small effect on the ISM conditions that a bow shock close to the star would encounter.

Atomistic simulations of the optical absorption of type-II CdSe/ZnTe superlattices

PubMed Central

2012-01-01

We perform accurate tight binding simulations to design type-II short-period CdSe/ZnTe superlattices suited for photovoltaic applications. Absorption calculations demonstrate a very good agreement with optical results with threshold strongly depending on the chemical species near interfaces. PMID:23031315

Launch Vehicle Ascent Trajectory Simulation Using the Program to Optimize Simulated Trajectories II (POST2)

NASA Technical Reports Server (NTRS)

Lugo, Rafael A.; Shidner, Jeremy D.; Powell, Richard W.; Marsh, Steven M.; Hoffman, James A.; Litton, Daniel K.; Schmitt, Terri L.

2017-01-01

The Program to Optimize Simulated Trajectories II (POST2) has been continuously developed for over 40 years and has been used in many flight and research projects. Recently, there has been an effort to improve the POST2 architecture by promoting modularity, flexibility, and ability to support multiple simultaneous projects. The purpose of this paper is to provide insight into the development of trajectory simulation in POST2 by describing methods and examples of various improved models for a launch vehicle liftoff and ascent.

MMS Observations of Reconnection at Dayside Magnetopause Crossings During Transitions of the Solar Wind to Sub-Alfvenic Flow

NASA Astrophysics Data System (ADS)

Farrugia, C. J.; Lugaz, N.; Alm, L.; Vasquez, B. J.; Argall, M. R.; Kucharek, H.; Matsui, H.; Torbert, R. B.; Lavraud, B.; Le Contel, O.; Shuster, J. R.; Burch, J. L.; Khotyaintsev, Y. V.; Giles, B. L.; Fuselier, S. A.; Gershman, D. J.; Ergun, R.; Eastwood, J. P.; Cohen, I. J.; Dorelli, J.; Lindqvist, P. A.; Strangeway, R. J.; Russell, C. T.; Marklund, G. T.; Paulson, K.; Petrinec, S.; Phan, T.; Pollock, C.

2017-12-01

We present MMS) observations during two dayside magnetopause crossingsunder hitherto unexamined conditions: (i) when the bow shock is weakening and the solar wind transitioning to sub-Alfvenic flow, and (ii) when it is reforming. Interplanetary conditions consist of a magnetic cloud with (i) a strong B ( 20 nT) pointing south, and (ii) a density profile with episodic decreases to values of 0.3 /cc followed by moderate recovery. During the crossings he magnetosheath magnetic field is stronger than the magnetosphere field by a factor of 2.2. As a result, during the outbound crossing through the ion diffusion region, MMS observed an inversion of relative positions of the X and stagnation (S) lines from that typically the case: the S line was closer to the magnetosheath side. The S-line appears in the form of a slow expansion fan near which most of the energy dissipation is taking place. While in the magnetosphere between the crossings, MMS observed strong field and flow perturbations, which we argue to be due kinetic Alfvén waves.During the reconnection interval, whistler mode waves generated by an electron temperature anisotropy (Tperp>Tpar) were observed. Another aim of the paper isto distinguish bow shock-induced field and flow perturbations from reconnection-related signatures.The high resolution MMS data together with 2D hybrid simulations of bow shock dynamics helped us to distinguish between the two sources. We show examples of bow shock-related effects (such as heating) and reconnection effects such as accelerated flows satisfying the Walen relation.

I. Advances in NMR Signal Processing. II. Spin Dynamics in Quantum Dissipative Systems

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

Lin, Yung-Ya

1998-11-01

Part I. Advances in IVMR Signal Processing. Improvements of sensitivity and resolution are two major objects in the development of NMR/MRI. A signal enhancement method is first presented which recovers signal from noise by a judicious combination of a priordmowledge to define the desired feasible solutions and a set theoretic estimation for restoring signal properties that have been lost due to noise contamination. The effect of noise can be significantly mitigated through the process of iteratively modifying the noisy data set to the smallest degree necessary so that it possesses a collection of prescribed properties and also lies closest tomore » the original data set. A novel detection-estimation scheme is then introduced to analyze noisy and/or strongly damped or truncated FIDs. Based on exponential modeling, the number of signals is detected based on information estimated using the matrix pencil method. theory and the spectral parameters are Part II. Spin Dynamics in body dipole-coupled systems Quantum Dissipative Systems. Spin dynamics in manyconstitutes one of the most fundamental problems in magnetic resonance and condensed-matter physics. Its many-spin nature precludes any rigorous treatment. ‘Therefore, the spin-boson model is adopted to describe in the rotating frame the influence of the dipolar local fields on a tagged spin. Based on the polaronic transform and a perturbation treatment, an analytical solution is derived, suggesting the existence of self-trapped states in the. strong coupling limit, i.e., when transverse local field >> longitudinal local field. Such nonlinear phenomena originate from the joint action of the lattice fluctuations and the reaction field. Under semiclassical approximation, it is found that the main effect of the reaction field is the renormalization of the Hamiltonian of interest. Its direct consequence is the two-step relaxation process: the spin is initially localized in a quasiequilibrium state, which is later detrapped by the lattice fluctuations in an extended time scale. Lowtemperature measurements and classical-spin simulations are carried out to verify the above analysis. To promote the implementation and future study on the topics described in this thesis, program packages of advanced NMR signal processing and many-spin FID simulations are summarized and listed in the Appendix.« less

Estimating the effect of shallow groundwater on diurnal heat transport in a vadose zone

NASA Astrophysics Data System (ADS)

Jiang, Jianmei; Zhao, Lin; Zhai, Zhe

2016-09-01

The influence of shallow groundwater on the diurnal heat transport of the soil profile was analyzed using a soil sensor automatic monitoring system that continuously measures temperature and water content of soil profiles to simulate heat transport based on the Philip and de Vries (PDV) model. Three experiments were conducted to measure soil properties at depths of 5 cm, 10 cm, 20 cm, and 30 cm when groundwater tables reached 10 cm, 30 cm, and 60 cm (Experiments I, II, and III). Results show that both the soil temperature near shallow groundwater and the soil water content were effectively simulated by the PDV model. The root mean square errors of the temperature at depths of 5 cm, 10 cm, and 20 cm were 1.018°C, 0.909°C, and 0.255°C, respectively. The total heat flux generated the convergent and divergent planes in space-time fields with valley values of-161.5W•m-2 at 7:30 and-234.6W•m-2 at 11:10 in Experiments II and III, respectively. The diurnal heat transport of the saturated soil occurred in five stages, while that of saturated-unsaturated and unsaturated soil profiles occurred in four stages because high moisture content led to high thermal conductivity, which hastened the heat transport.

Dynamical Evolution of a Coronal Streamer-Flux Rope System: 2. A Self-Consistent Non-Planar Magnetohydrodynamic Simulation

NASA Technical Reports Server (NTRS)

Wu, S. T.; Guo, W. P.; Dryer, Murray

1996-01-01

The dynamical response of a helmet streamer to a flux rope escape from the sub-photosphere is examined in a physically self-consistent manner within the approximation of axisymmetric three-dimensional magnetohydrodynamics (i.e., so-called '2 1/2 D'). In contrast to the previous planar analyses of Paper 1 (Wu, Guo, and Wang), the present study shows, with the inclusion of out-of-plane components of magnetic and velocity fields, that the magnetic configuration represents a helical flux rope instead of a planar bubble as shown in Paper 1. Because of this more physically-realistic configuration, we are able to examine the dynamical evolution of the helical flux rope's interaction with the helmet streamer. This process leads to the formation of two parts of the solar mass ejection: (i) the expulsion of the helmet dome due to eruption of this flux rope, and (ii) the flux rope's eruption itself. When this two-part feature propagates out to the interplanetary space, it exhibits all the physical characteristics of observed interplanetary magnetic clouds. These numerical simulations also show that the dynamical behavior of the streamer-flux rope system has three distinct states: (i) quasi-equilibrium, (ii) non-equilibrium, and (iii) eruptive state depending on the energy level of the flux rope.

Radio emission of SN1993J: the complete picture. II. Simultaneous fit of expansion and radio light curves

NASA Astrophysics Data System (ADS)

Martí-Vidal, I.; Marcaide, J. M.; Alberdi, A.; Guirado, J. C.; Pérez-Torres, M. A.; Ros, E.

2011-02-01

We report on a simultaneous modelling of the expansion and radio light curves of the supernova SN1993J. We developed a simulation code capable of generating synthetic expansion and radio light curves of supernovae by taking into consideration the evolution of the expanding shock, magnetic fields, and relativistic electrons, as well as the finite sensitivity of the interferometric arrays used in the observations. Our software successfully fits all the available radio data of SN 1993J with a standard emission model for supernovae, which is extended with some physical considerations, such as an evolution in the opacity of the ejecta material, a radial decline in the magnetic fields within the radiating region, and a changing radial density profile for the circumstellar medium starting from day 3100 after the explosion.

Counteracting radio frequency inhomogeneity in the human brain at 7 Tesla using strongly modulating pulses.

PubMed

Boulant, N; Mangin, J-F; Amadon, A

2009-05-01

We report flip angle and spoiled gradient echo measurements at 7 Tesla on human brains in three-dimensional imaging, using strongly modulating pulses to counteract the transmitted radiofrequency inhomogeneity problem. Compared with the standard square pulse results, three points of improvement are demonstrated, namely: (i) the removal of the bright center (typical at high fields when using a quadrature head coil), (ii) the substantial gain of signal in the regions of low B(1) intensity, and (iii) an increased 35% signal uniformity over the whole brain at the flip angle where maximum contrast between white and gray matter occurs. We also find by means of simulations that standard BIR-4 adiabatic pulses need several times more energy to reach a similar performance at the same field strength. (c) 2009 Wiley-Liss, Inc.

Extracting, Tracking, and Visualizing Magnetic Flux Vortices in 3D Complex-Valued Superconductor Simulation Data.

PubMed

Guo, Hanqi; Phillips, Carolyn L; Peterka, Tom; Karpeyev, Dmitry; Glatz, Andreas

2016-01-01

We propose a method for the vortex extraction and tracking of superconducting magnetic flux vortices for both structured and unstructured mesh data. In the Ginzburg-Landau theory, magnetic flux vortices are well-defined features in a complex-valued order parameter field, and their dynamics determine electromagnetic properties in type-II superconductors. Our method represents each vortex line (a 1D curve embedded in 3D space) as a connected graph extracted from the discretized field in both space and time. For a time-varying discrete dataset, our vortex extraction and tracking method is as accurate as the data discretization. We then apply 3D visualization and 2D event diagrams to the extraction and tracking results to help scientists understand vortex dynamics and macroscale superconductor behavior in greater detail than previously possible.

Model to interpret pulsed-field-gradient NMR data including memory and superdispersion effects.

PubMed

Néel, Marie-Christine; Bauer, Daniela; Fleury, Marc

2014-06-01

We propose a versatile model specifically designed for the quantitative interpretation of NMR velocimetry data. We use the concept of mobile or immobile tracer particles applied in dispersion theory in its Lagrangian form, adding two mechanisms: (i) independent random arrests of finite average representing intermittent periods of very low velocity zones in the mean flow direction and (ii) the possibility of unexpectedly long (but rare) displacements simulating the occurrence of very high velocities in the porous medium. Based on mathematical properties related to subordinated Lévy processes, we give analytical expressions of the signals recorded in pulsed-field-gradient NMR experiments. We illustrate how to use the model for quantifying dispersion from NMR data recorded for water flowing through a homogeneous grain pack column in single- and two-phase flow conditions.

Multisite Evaluation of APEX for Water Quality: II. Regional Parameterization.

PubMed

Nelson, Nathan O; Baffaut, Claire; Lory, John A; Anomaa Senaviratne, G M M M; Bhandari, Ammar B; Udawatta, Ranjith P; Sweeney, Daniel W; Helmers, Matt J; Van Liew, Mike W; Mallarino, Antonio P; Wortmann, Charles S

2017-11-01

Phosphorus (P) Index assessment requires independent estimates of long-term average annual P loss from fields, representing multiple climatic scenarios, management practices, and landscape positions. Because currently available measured data are insufficient to evaluate P Index performance, calibrated and validated process-based models have been proposed as tools to generate the required data. The objectives of this research were to develop a regional parameterization for the Agricultural Policy Environmental eXtender (APEX) model to estimate edge-of-field runoff, sediment, and P losses in restricted-layer soils of Missouri and Kansas and to assess the performance of this parameterization using monitoring data from multiple sites in this region. Five site-specific calibrated models (SSCM) from within the region were used to develop a regionally calibrated model (RCM), which was further calibrated and validated with measured data. Performance of the RCM was similar to that of the SSCMs for runoff simulation and had Nash-Sutcliffe efficiency (NSE) > 0.72 and absolute percent bias (|PBIAS|) < 18% for both calibration and validation. The RCM could not simulate sediment loss (NSE < 0, |PBIAS| > 90%) and was particularly ineffective at simulating sediment loss from locations with small sediment loads. The RCM had acceptable performance for simulation of total P loss (NSE > 0.74, |PBIAS| < 30%) but underperformed the SSCMs. Total P-loss estimates should be used with caution due to poor simulation of sediment loss. Although we did not attain our goal of a robust regional parameterization of APEX for estimating sediment and total P losses, runoff estimates with the RCM were acceptable for P Index evaluation. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Ground-water flow and the possible effects of remedial actions at J-Field, Aberdeen Proving Ground, Maryland

USGS Publications Warehouse

Hughes, W.B.

1995-01-01

J-Field, located in the Edgewood Area of Aberdeen Proving Ground, Md, has been used since World War II to test and dispose of explosives, chemical warfare agents, and industrial chemicals resulting in ground-water, surface-water, and soil contami- nation. The U.S. Geological Survey finite-difference model was used to better understand ground-water flow at the site and to simulate the effects of remedial actions. A surficial aquifer and a confined aquifer were simulated with the model. A confining unit separates these units and is represented by leakance between the layers. The area modeled is 3.65 mi2; the model was constructed with a variably spaced 40 X 38 grid. The horizontal and lower boundaries of the model are all no-flow boundaries. Steady-state conditions were used. Ground water at the areas under investigation flows from disposal pit areas toward discharge areas in adjacent estuaries or wetlands. Simulations indicate that capping disposal areas with an impermeable cover effectively slows advective ground water flow by 0.7 to 0.5 times. Barriers to lateral ground-water flow were simulated and effectively prevented the movement of ground water toward discharge areas. Extraction wells were simulated as a way to contain ground-water contamination and to extract ground water for treatment. Two wells pumping 5 gallons per minute each at the toxic-materials disposal area and a single well pumping 2.5 gallons per minute at the riot-control-agent disposal area effectively contained contamination at these sites. A combi- nation of barriers to horizontal flow east and south of the toxic-materials disposal area, and a single extraction well pumping at 5 gallons per minute can extract contaminated ground water and prevent pumpage of marsh water.

Identification of Distinct Conformations of the Angiotensin-II Type 1 Receptor Associated with the Gq/11 Protein Pathway and the β-Arrestin Pathway Using Molecular Dynamics Simulations.

PubMed

Cabana, Jérôme; Holleran, Brian; Leduc, Richard; Escher, Emanuel; Guillemette, Gaétan; Lavigne, Pierre

2015-06-19

Biased signaling represents the ability of G protein-coupled receptors to engage distinct pathways with various efficacies depending on the ligand used or on mutations in the receptor. The angiotensin-II type 1 (AT1) receptor, a prototypical class A G protein-coupled receptor, can activate various effectors upon stimulation with the endogenous ligand angiotensin-II (AngII), including the Gq/11 protein and β-arrestins. It is believed that the activation of those two pathways can be associated with distinct conformations of the AT1 receptor. To verify this hypothesis, microseconds of molecular dynamics simulations were computed to explore the conformational landscape sampled by the WT-AT1 receptor, the N111G-AT1 receptor (constitutively active and biased for the Gq/11 pathway), and the D74N-AT1 receptor (biased for the β-arrestin1 and -2 pathways) in their apo-forms and in complex with AngII. The molecular dynamics simulations of the AngII-WT-AT1, N111G-AT1, and AngII-N111G-AT1 receptors revealed specific structural rearrangements compared with the initial and ground state of the receptor. Simulations of the D74N-AT1 receptor revealed that the mutation stabilizes the receptor in the initial ground state. The presence of AngII further stabilized the ground state of the D74N-AT1 receptor. The biased agonist [Sar(1),Ile(8)]AngII also showed a preference for the ground state of the WT-AT1 receptor compared with AngII. These results suggest that activation of the Gq/11 pathway is associated with a specific conformational transition stabilized by the agonist, whereas the activation of the β-arrestin pathway is linked to the stabilization of the ground state of the receptor. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Identification of Distinct Conformations of the Angiotensin-II Type 1 Receptor Associated with the Gq/11 Protein Pathway and the β-Arrestin Pathway Using Molecular Dynamics Simulations*

PubMed Central

Cabana, Jérôme; Holleran, Brian; Leduc, Richard; Escher, Emanuel; Guillemette, Gaétan; Lavigne, Pierre

2015-01-01

Biased signaling represents the ability of G protein-coupled receptors to engage distinct pathways with various efficacies depending on the ligand used or on mutations in the receptor. The angiotensin-II type 1 (AT1) receptor, a prototypical class A G protein-coupled receptor, can activate various effectors upon stimulation with the endogenous ligand angiotensin-II (AngII), including the Gq/11 protein and β-arrestins. It is believed that the activation of those two pathways can be associated with distinct conformations of the AT1 receptor. To verify this hypothesis, microseconds of molecular dynamics simulations were computed to explore the conformational landscape sampled by the WT-AT1 receptor, the N111G-AT1 receptor (constitutively active and biased for the Gq/11 pathway), and the D74N-AT1 receptor (biased for the β-arrestin1 and -2 pathways) in their apo-forms and in complex with AngII. The molecular dynamics simulations of the AngII-WT-AT1, N111G-AT1, and AngII-N111G-AT1 receptors revealed specific structural rearrangements compared with the initial and ground state of the receptor. Simulations of the D74N-AT1 receptor revealed that the mutation stabilizes the receptor in the initial ground state. The presence of AngII further stabilized the ground state of the D74N-AT1 receptor. The biased agonist [Sar1,Ile8]AngII also showed a preference for the ground state of the WT-AT1 receptor compared with AngII. These results suggest that activation of the Gq/11 pathway is associated with a specific conformational transition stabilized by the agonist, whereas the activation of the β-arrestin pathway is linked to the stabilization of the ground state of the receptor. PMID:25934394

Coronal magnetic fields from multiple type II bursts

NASA Astrophysics Data System (ADS)

Honnappa, Vijayakumar; Raveesha, K. H.; Subramanian, K. R.

Coronal magnetic fields from multiple type II bursts Vijayakumar H Doddamani1*, Raveesha K H2 and Subramanian3 1Bangalore University, Bangalore, Karnataka state, India 2CMR Institute of Technology, Bangalore, Karnataka state, India 3 Retd, Indian Institute of Astrophysics, Bangalore, Karnataka state, India Abstract Magnetic fields play an important role in the astrophysical processes occurring in solar corona. In the solar atmosphere, magnetic field interacts with the plasma, producing abundant eruptive activities. They are considered to be the main factors for coronal heating, particle acceleration and the formation of structures like prominences, flares and Coronal Mass Ejections. The magnetic field in solar atmosphere in the range of 1.1-3 Rsun is especially important as an interface between the photospheric magnetic field and the solar wind. Its structure and time dependent change affects space weather by modifying solar wind conditions, Cho (2000). Type II doublet bursts can be used for the estimation of the strength of the magnetic field at two different heights. Two type II bursts occur sometimes in sequence. By relating the speed of the type II radio burst to Alfven Mach Number, the Alfven speed of the shock wave generating type II radio burst can be calculated. Using the relation between the Alfven speed and the mean frequency of emission, the magnetic field strength can be determined at a particular height. We have used the relative bandwidth and drift rate properties of multiple type II radio bursts to derive magnetic field strengths at two different heights and also the gradient of the magnetic field in the outer corona. The magnetic field strength has been derived for different density factors. It varied from 1.2 to 2.5 gauss at a solar height of 1.4 Rsun. The empirical relation of the variation of the magnetic field with height is found to be of the form B(R) = In the present case the power law index ‘γ’ varied from -3 to -2 for variation of density factor from 1 to 5. Key Words: Magnetic field, photosphere, corona, solar wind, bursts *Email:drvkdmani@gmail.com

2D dark-count-rate modeling of PureB single-photon avalanche diodes in a TCAD environment

NASA Astrophysics Data System (ADS)

Knežević, Tihomir; Nanver, Lis K.; Suligoj, Tomislav

2018-02-01

PureB silicon photodiodes have nm-shallow p+n junctions with which photons/electrons with penetration-depths of a few nanometer can be detected. PureB Single-Photon Avalanche Diodes (SPADs) were fabricated and analysed by 2D numerical modeling as an extension to TCAD software. The very shallow p+ -anode has high perimeter curvature that enhances the electric field. In SPADs, noise is quantified by the dark count rate (DCR) that is a measure for the number of false counts triggered by unwanted processes in the non-illuminated device. Just like for desired events, the probability a dark count increases with increasing electric field and the perimeter conditions are critical. In this work, the DCR was studied by two 2D methods of analysis: the "quasi-2D" (Q-2D) method where vertical 1D cross-sections were assumed for calculating the electron/hole avalanche-probabilities, and the "ionization-integral 2D" (II-2D) method where crosssections were placed where the maximum ionization-integrals were calculated. The Q-2D method gave satisfactory results in structures where the peripheral regions had a small contribution to the DCR, such as in devices with conventional deepjunction guard rings (GRs). Otherwise, the II-2D method proved to be much more precise. The results show that the DCR simulation methods are useful for optimizing the compromise between fill-factor and p-/n-doping profile design in SPAD devices. For the experimentally investigated PureB SPADs, excellent agreement of the measured and simulated DCR was achieved. This shows that although an implicit GR is attractively compact, the very shallow pn-junction gives a risk of having such a low breakdown voltage at the perimeter that the DCR of the device may be negatively impacted.

SMBH Seeds: Model Discrimination with High-energy Emission Based on Scaling Relation Evolution

NASA Astrophysics Data System (ADS)

Ben-Ami, Sagi; Vikhlinin, Alexey; Loeb, Abraham

2018-02-01

We explore the expected X-ray (0.5–2 keV) signatures from supermassive black holes (SMBHs) at high redshifts (z∼ 5{--}12) assuming various models for their seeding mechanism and evolution. Seeding models are approximated through deviations from the {M}{BH}{--}σ relation observed in the local universe, while N-body simulations of the large-scale structure are used to estimate the density of observable SMBHs. We focus on two seeding model families: (i) light seed BHs from remnants of Pop-III stars and (ii) heavy seeds from the direct collapse of gas clouds. We investigate several models for the accretion history, such as sub-Eddington accretion, slim disk models, and torque-limited growth models. We consider observations with two instruments: (i) the Chandra X-ray Observatory and (ii) the proposed Lynx. We find that all of the simulated models are in agreement with the current results from the Chandra Deep Field South, i.e., consistent with zero SMBHs in the field of view. In deep Lynx exposures, the number of observed objects is expected to become statistically significant. We demonstrate the capability to limit the phase space of plausible scenarios of the birth and evolution of SMBHs by performing deep observations at a flux limit of 1× {10}-19 {erg} {{cm}}-2 {{{s}}}-1. Finally, we show that our models are in agreement with current limits on the cosmic X-ray background (CXRB) and the expected contribution from unresolved quasars. We find that an analysis of CXRB contributions down to the Lynx confusion limit yields valuable information that can help identify the correct scenario for the birth and evolution of SMBHs.

Full cycle trigonometric function on Intel Quartus II Verilog

NASA Astrophysics Data System (ADS)

Mustapha, Muhazam; Zulkarnain, Nur Antasha

2018-02-01

This paper discusses about an improvement of a previous research on hardware based trigonometric calculations. Tangent function will also be implemented to get a complete set. The functions have been simulated using Quartus II where the result will be compared to the previous work. The number of bits has also been extended for each trigonometric function. The design is based on RTL due to its resource efficient nature. At earlier stage, a technology independent test bench simulation was conducted on ModelSim due to its convenience in capturing simulation data so that accuracy information can be obtained. On second stage, Intel/Altera Quartus II will be used to simulate on technology dependent platform, particularly on the one belonging to Intel/Altera itself. Real data on no. logic elements used and propagation delay have also been obtained.

Class III Mid-Term Project, "Increasing Heavy Oil Reserves in the Wilmington Oil Field Through Advanced Reservoir Characterization and Thermal Production Technologies"

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

Scott Hara

2007-03-31

The overall objective of this project was to increase heavy oil reserves in slope and basin clastic (SBC) reservoirs through the application of advanced reservoir characterization and thermal production technologies. The project involved improving thermal recovery techniques in the Tar Zone of Fault Blocks II-A and V (Tar II-A and Tar V) of the Wilmington Field in Los Angeles County, near Long Beach, California. A primary objective has been to transfer technology that can be applied in other heavy oil formations of the Wilmington Field and other SBC reservoirs, including those under waterflood. The first budget period addressed several producibilitymore » problems in the Tar II-A and Tar V thermal recovery operations that are common in SBC reservoirs. A few of the advanced technologies developed include a three-dimensional (3-D) deterministic geologic model, a 3-D deterministic thermal reservoir simulation model to aid in reservoir management and subsequent post-steamflood development work, and a detailed study on the geochemical interactions between the steam and the formation rocks and fluids. State of the art operational work included drilling and performing a pilot steam injection and production project via four new horizontal wells (2 producers and 2 injectors), implementing a hot water alternating steam (WAS) drive pilot in the existing steamflood area to improve thermal efficiency, installing a 2400-foot insulated, subsurface harbor channel crossing to supply steam to an island location, testing a novel alkaline steam completion technique to control well sanding problems, and starting on an advanced reservoir management system through computer-aided access to production and geologic data to integrate reservoir characterization, engineering, monitoring, and evaluation. The second budget period phase (BP2) continued to implement state-of-the-art operational work to optimize thermal recovery processes, improve well drilling and completion practices, and evaluate the geomechanical characteristics of the producing formations. The objectives were to further improve reservoir characterization of the heterogeneous turbidite sands, test the proficiency of the three-dimensional geologic and thermal reservoir simulation models, identify the high permeability thief zones to reduce water breakthrough and cycling, and analyze the nonuniform distribution of the remaining oil in place. This work resulted in the redevelopment of the Tar II-A and Tar V post-steamflood projects by drilling several new wells and converting idle wells to improve injection sweep efficiency and more effectively drain the remaining oil reserves. Reservoir management work included reducing water cuts, maintaining or increasing oil production, and evaluating and minimizing further thermal-related formation compaction. The BP2 project utilized all the tools and knowledge gained throughout the DOE project to maximize recovery of the oil in place.« less

Comparing Noah-MP simulations of energy and water fluxes in the soil-vegetation-atmosphere continuum with plot scale measurements

NASA Astrophysics Data System (ADS)

Gayler, Sebastian; Wöhling, Thomas; Högy, Petra; Ingwersen, Joachim; Wizemann, Hans-Dieter; Wulfmeyer, Volker; Streck, Thilo

2013-04-01

During the last years, land-surface models have proven to perform well in several studies that compared simulated fluxes of water and energy from the land surface to the atmosphere against measured fluxes at the plot-scale. In contrast, considerable deficits of land-surface models have been identified to simulate soil water fluxes and vertical soil moisture distribution. For example, Gayler et al. (2013) showed that simplifications in the representation of root water uptake can result in insufficient simulations of the vertical distribution of soil moisture and its dynamics. However, in coupled simulations of the terrestrial water cycle, both sub-systems, the atmosphere and the subsurface hydrogeo-system, must fit together and models are needed, which are able to adequately simulate soil moisture, latent heat flux, and their interrelationship. Consequently, land-surface models must be further improved, e.g. by incorporation of advanced biogeophysics models. To improve the conceptual realism in biophysical and hydrological processes in the community land surface model Noah, this model was recently enhanced to Noah-MP by a multi-options framework to parameterize individual processes (Niu et al., 2011). Thus, in Noah-MP the user can choose from several alternative models for vegetation and hydrology processes that can be applied in different combinations. In this study, we evaluate the performance of different Noah-MP model settings to simulate water and energy fluxes across the land surface at two contrasting field sites in South-West Germany. The evaluation is done in 1D offline-mode, i.e. without coupling to an atmospheric model. The atmospheric forcing is provided by measured time series of the relevant variables. Simulation results are compared with eddy covariance measurements of turbulent fluxes and measured time series of soil moisture at different depths. The aims of the study are i) to carve out the most appropriate combination of process parameterizations in Noah-MP to simultaneously match the different components of the water and energy cycle at the field sites under consideration, and ii) to estimate the uncertainty in model structure. We further investigate the potential to improve simulation results by incorporating concepts of more advanced root water uptake models from agricultural field scale models into the land-surface-scheme. Gayler S, Ingwersen J, Priesack E, Wöhling T, Wulfmeyer V, Streck T (2013): Assessing the relevance of sub surface processes for the simulation of evapotranspiration and soil moisture dynamics with CLM3.5: Comparison with field data and crop model simulations. Environ. Earth Sci., 69(2), under revision. Niu G-Y, Yang Z-L, Mitchell KE, Chen F, Ek MB, Barlage M, Kumar A, Manning K, Niyogi D, Rosero E, Tewari M and Xia Y (2011): The community Noah land surface model with multiparameterization options (Noah-MP): 1. Model description and evaluation with local-scale measurements. Journal of Geophysical Research 116(D12109).

Tilted hexagonal post arrays: DNA electrophoresis in anisotropic media

PubMed Central

Chen, Zhen; Dorfman, Kevin D.

2013-01-01

Using Brownian dynamics simulations, we show that DNA electrophoresis in a hexagonal array of micron-sized posts changes qualitatively when the applied electric field vector is not coincident with the lattice vectors of the array. DNA electrophoresis in such “tilted” post arrays is superior to the standard “un-tilted” approach; while the time required to achieve a resolution of unity in a tilted post array is similar to an un-tilted array at a low electric field strengths, this time (i) decreases exponentially with electric field strength in a tilted array and (ii) increases exponentially with electric field strength in an un-tilted array. Although the DNA dynamics in a post array are complicated, the electrophoretic mobility results indicate that the “free path”, i.e., the average distance of ballistic trajectories of point sized particles launched from random positions in the unit cell until they intersect the next post, is a useful proxy for the detailed DNA trajectories. The analysis of the free path reveals a fundamental connection between anisotropy of the medium and DNA transport therein that goes beyond simply improving the separation device. PMID:23868490

Detailed validation of the bidirectional effect in various Case I and Case II waters.

PubMed

Gleason, Arthur C R; Voss, Kenneth J; Gordon, Howard R; Twardowski, Michael; Sullivan, James; Trees, Charles; Weidemann, Alan; Berthon, Jean-François; Clark, Dennis; Lee, Zhong-Ping

2012-03-26

Simulated bidirectional reflectance distribution functions (BRDF) were compared with measurements made just beneath the water's surface. In Case I water, the set of simulations that varied the particle scattering phase function depending on chlorophyll concentration agreed more closely with the data than other models. In Case II water, however, the simulations using fixed phase functions agreed well with the data and were nearly indistinguishable from each other, on average. The results suggest that BRDF corrections in Case II water are feasible using single, average, particle scattering phase functions, but that the existing approach using variable particle scattering phase functions is still warranted in Case I water.

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.

PubMed

Aliev, Abil E; Courtier-Murias, Denis

2010-09-30

Experimental NMR verification of MD simulations using 12 different force fields (AMBER, CHARMM, GROMOS, and OPLS-AA) and 5 different water models has been undertaken to identify reliable MD protocols for structure and dynamics elucidations of small open chain peptides containing Gly and Pro. A conformationally flexible tetrapeptide Gly-Pro-Gly-Gly was selected for NMR (3)J-coupling, chemical shift, and internuclear distance measurements, followed by their calculations using 2 μs long MD simulations in water. In addition, Ramachandran population maps for Pro-2 and Gly-3 residues of GPGG obtained from MD simulations were used for detailed comparisons with similar maps from the protein data bank (PDB) for large number of Gly and Pro residues in proteins. The MD simulations revealed strong dependence of the populations and geometries of preferred backbone and side chain conformations, as well as the time scales of the peptide torsional transitions on the force field used. On the basis of the analysis of the measured and calculated data, AMBER99SB is identified as the most reliable force field for reproducing NMR measured parameters, which are dependent on the peptide backbone and the Pro side chain geometries and dynamics. Ramachandran maps showing the dependence of conformational populations as a function of backbone ϕ/ψ angles for Pro-2 and Gly-3 residues of GPGG from MD simulations using AMBER99SB, AMBER03, and CHARMM were found to resemble similar maps for Gly and Pro residues from the PDB survey. Three force fields (AMBER99, AMBER99ϕ, and AMBER94) showed the least satisfactory agreement with both the solution NMR and the PDB survey data. The poor performance of these force fields is attributed to their propensity to overstabilize helical peptide backbone conformations at the Pro-2 and Gly-3 residues. On the basis of the similarity of the MD and PDB Ramachandran plots, the following sequence of transitions is suggested for the Gly backbone conformation: α(L) ⇆ β(PR) ⇆ β(S) ⇆ β(P) ⇆ α, where backbone secondary structures α(L) and α are associated with helices and turns, β(P) and β(PR) correspond to the left- and right-handed polyproline II structures and β(S) denotes the fully stretched backbone conformation. Compared to the force field dependence, less significant, but noteworthy, variations in the populations of the peptide backbone conformations were observed. For different solvent models considered, a correlation was noted between the number of torsional transitions in GPGG and the water self-diffusion coefficient on using TIP3P, TIP4P, and TIP5P models. In addition to MD results, we also report DFT derived Karplus relationships for Gly and Pro residues using B972 and B3LYP functionals.

Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

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

Vlcek, Lukas; Uhlik, Filip; Moucka, Filip

We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ionmore » hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.« less

Controlling the emission profile of an H2 discharge lamp to simulate interstellar radiation fields

NASA Astrophysics Data System (ADS)

Ligterink, N. F. W.; Paardekooper, D. M.; Chuang, K.-J.; Both, M. L.; Cruz-Diaz, G. A.; van Helden, J. H.; Linnartz, H.

2015-12-01

Context. Microwave discharge hydrogen-flow lamps have been used for more than half a century to simulate interstellar ultraviolet radiation fields in the laboratory. Recent discrepancies between identical measurements in different laboratories, as well as clear wavelength dependent results obtained in monochromatic (synchrotron) experiments, hint at a more elaborate dependence on the exact discharge settings than assumed so far. Aims: We have investigated systematically two lamp geometries in full dependence of a large number of different running conditions and the spectral emission patterns are characterized for the first time with fully calibrated absolute flux numbers. Methods: A sophisticated plasma lamp calibration set-up has been used to record the vacuum-ultraviolet emission spectra with a spectral resolution of 0.5 nm and bandwidth of 1.6 nm in the 116-220 nm region. Spectra are compared with the output of a calibrated D2-lamp which allows a derivation of absolute radiance values. Results: The general findings of over 200 individual measurements are presented, illustrating how the lamp emission pattern depends on i) microwave power; ii) gas and gas mixing ratios; iii) discharge lamp geometry; iv) cavity positioning; and v) gas pressure.

Validations of Coupled CSD/CFD and Particle Vortex Transport Method for Rotorcraft Applications: Hover, Transition, and High Speed Flights

NASA Technical Reports Server (NTRS)

Anusonti-Inthra, Phuriwat

2010-01-01

This paper presents validations of a novel rotorcraft analysis that coupled Computational Fluid Dynamics (CFD), Computational Structural Dynamics (CSD), and Particle Vortex Transport Method (PVTM) methodologies. The CSD with associated vehicle trim analysis is used to calculate blade deformations and trim parameters. The near body CFD analysis is employed to provide detailed near body flow field information which is used to obtain high-fidelity blade aerodynamic loadings. The far field wake dominated region is simulated using the PVTM analysis which provides accurate prediction of the evolution of the rotor wake released from the near body CFD domains. A loose coupling methodology between the CSD and CFD/PVTM modules are used with appropriate information exchange amongst the CSD/CFD/PVTM modules. The coupled CSD/CFD/PVTM methodology is used to simulate various rotorcraft flight conditions (i.e. hover, transition, and high speed flights), and the results are compared with several sets of experimental data. For the hover condition, the results are compared with hover data for the HART II rotor tested at DLR Institute of Flight Systems, Germany. For the forward flight conditions, the results are validated with the UH-60A flight test data.

The impact of reduced gastric acid secretion on dissolution of salts of weak bases in the fasted upper gastrointestinal lumen: Data in biorelevant media and in human aspirates.

PubMed

Litou, Chara; Vertzoni, Maria; Xu, Wei; Kesisoglou, Filippos; Reppas, Christos

2017-06-01

To propose media for simulating the intragastric environment under reduced gastric acid secretion in the fasted state at three levels of simulation of the gastric environment and evaluate their usefulness in evaluating the intragastric dissolution of salts of weak bases. To evaluate the importance of bicarbonate buffer in biorelevant in vitro dissolution testing when using Level II biorelevant media simulating the environment in the fasted upper small intestine, regardless of gastric acid secretions. Media for simulating the hypochlorhydric and achlorhydric conditions in stomach were proposed using phosphates, maleates and bicarbonates buffers. The impact of bicarbonates in Level II biorelevant media simulating the environment in upper small intestine was evaluated so that pH and bulk buffer capacity were maintained. Dissolution data were collected using two model compounds, pioglitazone hydrochloride and semifumarate cocrystal of Compound B, and the mini-paddle dissolution apparatus in biorelevant media and in human aspirates. Simulated gastric fluids proposed in this study were in line with pH, buffer capacity, pepsin content, total bile salt/lecithin content and osmolality of the fasted stomach under partial and under complete inhibition of gastric acid secretion. Fluids simulating the conditions under partial inhibition of acid secretion were useful in simulating concentrations of both model compounds in gastric aspirates. Bicarbonates in Level III biorelevant gastric media and in Level II biorelevant media simulating the composition in the upper intestinal lumen did not improve simulation of concentrations in human aspirates. Level III biorelevant media for simulating the intragastric environment under hypochlorhydric conditions were proposed and their usefulness in the evaluation of concentrations of two model salts of weak bases in gastric aspirates was shown. Level II biorelevant media for simulating the environment in upper intestinal lumen led to underestimation of concentrations in aspirates, even when bicarbonate buffer was used. Copyright © 2017 Elsevier B.V. All rights reserved.

Progress in the development of an H{sup −} ion source for cyclotrons

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

Etoh, H., E-mail: Hrh-Etoh@shi.co.jp; Aoki, Y.; Mitsubori, H.

2015-04-08

A multi-cusp DC H{sup −} ion source has been developed for cyclotrons in medical use. Beam optics of the H{sup −} ion beam is studied using a 2D beam trajectory code. The simulation results are compared with the experimental results obtained in the Mark I source, which has produced up to 16 mA H{sup −} ion beams. The optimum extraction voltages show good agreement between the calculation and the experimental results. A new ion source, Mark II source, is designed to achieve the next goal of producing an H{sup −} beam of 20 mA. The magnetic field configurations and the plasma electrodemore » design are optimized for Cs-seeded operation. Primary electron trajectory simulation shows that primary electrons are confined well and the magnetic filter prevents the primary electrons from entering into the extraction region.« less

Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations

NASA Astrophysics Data System (ADS)

Nam, Hoang Bao; Kouza, Maksim; Zung, Hoang; Li, Mai Suan

2010-04-01

Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.

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

NASA Astrophysics Data System (ADS)

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

1997-04-01

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

New cellular automaton designed to simulate geometration in gel electrophoresis

NASA Astrophysics Data System (ADS)

Krawczyk, M. J.; Kułakowski, K.; Maksymowicz, A. Z.

2002-08-01

We propose a new kind of cellular automaton to simulate transportation of molecules of DNA through agarose gel. Two processes are taken into account: reptation at strong electric field E, described in the particle model, and geometration, i.e. subsequent hookings and releases of long molecules at and from gel fibres. The automaton rules are deterministic and they are designed to describe both processes within one unified approach. Thermal fluctuations are not taken into account. The number of simultaneous hookings is limited by the molecule length. The features of the automaton are: (i) the size of the cell neighbourhood for the automaton rule varies dynamically, from nearest neighbors to the entire molecule; (ii) the length of the time step is determined at each step according to dynamic rules. Calculations are made up to N=244 reptons in a molecule. Two subsequent stages of the motion are found. Firstly, an initial set of random configurations of molecules is transformed into a more ordered phase, where most molecules are elongated along the applied field direction. After some transient time, the mobility μ reaches a constant value. Then, it varies with N as 1/ N for long molecules. The band dispersion varies with time t approximately as Nt1/2. Our results indicate that the well-known plateau of the mobility μ vs. N does not hold at large electric fields.

Theoretical model of the effect of potassium on the uptake of radiocesium by rice.

PubMed

Fujimura, Shigeto; Ishikawa, Junko; Sakuma, Yuuki; Saito, Takashi; Sato, Mutsuto; Yoshioka, Kunio

2014-12-01

After the accident at the Fukushima Dai-ichi Nuclear Power Plant owned by Tokyo Electric Power Company on 11 March 2011, potassium was applied to fields in the Tohoku and Kanto areas of Japan to reduce radiocesium uptake by crops. Despite the intense studies relating to the effect of potassium application on availability of radiocesium in the soil, physiological changes of radiocesium uptake by crops in response to K(+) concentration around roots remains elusive. In the present study, we developed physiological models describing the effect of K(+) on the uptake of radiocesium by rice. Two Cs(+):K(+) competition models were evaluated using a wide range of data obtained from pot and field experiments: the model assuming a uniformity in the gene expression of K(+) transporter (Model I) and the model assuming the increase in the gene expression of K(+) transporter in response to K(+) concentration below threshold (Model II). The root-mean-square deviation between the measured and estimated values was larger in Model I than in Model II. Residuals were positively correlated with K(+) in Model I but showed no deflection in Model II. These results indicate that Model II explains the effect of K(+) on the uptake of radiocesium better than Model I. Model II may provide the appropriate countermeasures in inhibiting the transfer of radiocesium from soil to crop. The effect of changes in the variables in Model II on the relationship between available K(+) in soil and (137)Cs uptake by plant was simulated. An increase in available (137)Cs(+) in soil enhanced the response of (137)Cs uptake to K(+). The effects of Michaelis-Menten constant for Cs(+) were the inverse of the (137)Cs(+) effect. The effect of Michaelis-Menten constant for K(+) showed the same tendency as that of (137)Cs(+), but the effect was much less than that of (137)Cs(+). An increase in the threshold of K(+) below which the gene expression of K(+) transporter increases enhanced the response of (137)Cs uptake to K(+) in the high-K(+) range. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.

PubMed

Hayakawa, Daichi; Nishiyama, Yoshiharu; Mazeau, Karim; Ueda, Kazuyoshi

2017-09-08

Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A). Copyright © 2017 Elsevier Ltd. All rights reserved.

Advanced Diagnostics for the Study of Linearly Polarized Emission. II. Application to Diffuse Interstellar Radio Synchrotron Emission

NASA Astrophysics Data System (ADS)

Herron, C. A.; Burkhart, Blakesley; Gaensler, B. M.; Lewis, G. F.; McClure-Griffiths, N. M.; Bernardi, G.; Carretti, E.; Haverkorn, M.; Kesteven, M.; Poppi, S.; Staveley-Smith, L.

2018-03-01

Diagnostics of polarized emission provide us with valuable information on the Galactic magnetic field and the state of turbulence in the interstellar medium, which cannot be obtained from synchrotron intensity alone. In Paper I, we derived polarization diagnostics that are rotationally and translationally invariant in the Q–U plane, similar to the polarization gradient. In this paper, we apply these diagnostics to simulations of ideal magnetohydrodynamic turbulence that have a range of sonic and Alfvénic Mach numbers. We generate synthetic images of Stokes Q and U for these simulations for the cases where the turbulence is illuminated from behind by uniform polarized emission and where the polarized emission originates from within the turbulent volume. From these simulated images, we calculate the polarization diagnostics derived in Paper I for different lines of sight relative to the mean magnetic field and for a range of frequencies. For all of our simulations, we find that the polarization gradient is very similar to the generalized polarization gradient and that both trace spatial variations in the magnetoionic medium for the case where emission originates within the turbulent volume, provided that the medium is not supersonic. We propose a method for distinguishing the cases of emission coming from behind or within a turbulent, Faraday rotating medium and a method to partly map the rotation measure of the observed region. We also speculate on statistics of these diagnostics that may allow us to constrain the physical properties of an observed turbulent region.

TET Offensive II Field Force Vietnam After Action Report 31 January - 18 February 1968

DTIC Science & Technology

1968-03-01

and the 5th VC Division. V During this same period of time there were no majur shifts in ARVN forces . However III Corps shifted three...8217-".•: ’ ’SSIFJED U.S. ARMY. VIETNAM. II FIELD FORCE . TET OFFENSIVE II FIELD FORCE VIETNAM AFTER ACTION REPORT, 31 JANUARY-18 FEB- RUARY 1968...H FIELD FORCE VIETNAM AFTER ACTION REPORT 31 January-18 February 1968 RECORD K0- ! FlSjl fi-.-A-,>-•: it tT*\\ : *si h s» -wP Mr-, £< St

Prediction of solubility parameters and miscibility of pharmaceutical compounds by molecular dynamics simulations.

PubMed

Gupta, Jasmine; Nunes, Cletus; Vyas, Shyam; Jonnalagadda, Sriramakamal

2011-03-10

The objectives of this study were (i) to develop a computational model based on molecular dynamics technique to predict the miscibility of indomethacin in carriers (polyethylene oxide, glucose, and sucrose) and (ii) to experimentally verify the in silico predictions by characterizing the drug-carrier mixtures using thermoanalytical techniques. Molecular dynamics (MD) simulations were performed using the COMPASS force field, and the cohesive energy density and the solubility parameters were determined for the model compounds. The magnitude of difference in the solubility parameters of drug and carrier is indicative of their miscibility. The MD simulations predicted indomethacin to be miscible with polyethylene oxide and to be borderline miscible with sucrose and immiscible with glucose. The solubility parameter values obtained using the MD simulations values were in reasonable agreement with those calculated using group contribution methods. Differential scanning calorimetry showed melting point depression of polyethylene oxide with increasing levels of indomethacin accompanied by peak broadening, confirming miscibility. In contrast, thermal analysis of blends of indomethacin with sucrose and glucose verified general immiscibility. The findings demonstrate that molecular modeling is a powerful technique for determining the solubility parameters and predicting miscibility of pharmaceutical compounds. © 2011 American Chemical Society

Development of an Efficient Binaural Simulation for the Analysis of Structural Acoustic Data

NASA Technical Reports Server (NTRS)

Johnson, Marty E.; Lalime, Aimee L.; Grosveld, Ferdinand W.; Rizzi, Stephen A.; Sullivan, Brenda M.

2003-01-01

Applying binaural simulation techniques to structural acoustic data can be very computationally intensive as the number of discrete noise sources can be very large. Typically, Head Related Transfer Functions (HRTFs) are used to individually filter the signals from each of the sources in the acoustic field. Therefore, creating a binaural simulation implies the use of potentially hundreds of real time filters. This paper details two methods of reducing the number of real-time computations required by: (i) using the singular value decomposition (SVD) to reduce the complexity of the HRTFs by breaking them into dominant singular values and vectors and (ii) by using equivalent source reduction (ESR) to reduce the number of sources to be analyzed in real-time by replacing sources on the scale of a structural wavelength with sources on the scale of an acoustic wavelength. The ESR and SVD reduction methods can be combined to provide an estimated computation time reduction of 99.4% for the structural acoustic data tested. In addition, preliminary tests have shown that there is a 97% correlation between the results of the combined reduction methods and the results found with the current binaural simulation techniques

Simulation of nanopowder compaction in terms of granular dynamics

NASA Astrophysics Data System (ADS)

Boltachev, G. Sh.; Volkov, N. B.

2011-07-01

The uniaxial compaction of nanopowders is simulated using the granular dynamics in the 2D geometry. The initial arrangement of particles is represented by (i) a layer of particles executing Brownian motion (isotropic structures) and (ii) particles falling in the gravity field (anisotropic structures). The influence of size effects and the size of a model cell on the properties of the structures are studied. The compaction of the model cell is simulated with regard to Hertz elastic forces between particles, Cattaneo-Mindlin-Deresiewicz shear friction forces, and van der Waals-Hamaker dispersion forces of attraction. Computation is performed for monodisperse powders with particle sizes ranging from 10 to 400 nm and for "cohesionless" powder, in which attractive forces are absent. It is shown that taking into account dispersion forces makes it possible to simulate the size effect in the nanopowder compaction: the compressibility of the nanopowder drops as the particles get finer. The mean coordination number and the axial and lateral pressures in the powder systems are found, and the effect of the density and isotropy of the initial structure on the compressibility is analyzed. The applicability of well-known Rumpf's formula for the size effect is discussed.

Simulation results of corkscrew motion in DARHT-II

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

Chan, K. D.; Ekdahl, C. A.; Chen, Y. J.

2003-01-01

DARHT-II, the second axis of the Dual-Axis Radiographic Hydrodynamics Test Facility, is being commissioned. DARHT-II is a linear induction accelerator producing 2-microsecond electron beam pulses at 20 MeV and 2 kA. These 2-microsecond pulses will be chopped into four short pulses to produce time resolved x-ray images. Radiographic application requires the DARHT-II beam to have excellent beam quality, and it is important to study various beam effects that may cause quality degradation of a DARHT-II beam. One of the beam dynamic effects under study is 'corkscrew' motion. For corkscrew motion, the beam centroid is deflected off axis due to misalignmentsmore » of the solenoid magnets. The deflection depends on the beam energy variation, which is expected to vary by {+-}0.5% during the 'flat-top' part of a beam pulse. Such chromatic aberration will result in broadening of beam spot size. In this paper, we will report simulation results of our study of corkscrew motion in DARHT-II. Sensitivities of beam spot size to various accelerator parameters and the strategy for minimizing corkscrew motion will be described. Measured magnet misalignment is used in the simulation.« less

First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors

PubMed Central

2016-01-01

Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gas equilibrium constants. We apply RxFPMC to investigate a nitrogen/oxygen mixture at T = 3000 K and p = 30 GPa, i.e., conditions that are present in atmospheric lightning strikes and explosions. The RxFPMC simulations show that the solvation environment leads to a significantly enhanced NO concentration that reaches a maximum when oxygen is present in slight excess. In addition, the RxFPMC simulations indicate the formation of NO2 and N2O in mole fractions approaching 1%, whereas N3 and O3 are not observed. The equilibrium distributions obtained from the RxFPMC simulations agree well with those from a thermochemical computer code parametrized to experimental data. PMID:27413785

Numerical simulation support to the ESA/THOR mission

NASA Astrophysics Data System (ADS)

Valentini, F.; Servidio, S.; Perri, S.; Perrone, D.; De Marco, R.; Marcucci, M. F.; Daniele, B.; Bruno, R.; Camporeale, E.

2016-12-01

THOR is a spacecraft concept currently undergoing study phase as acandidate for the next ESA medium size mission M4. THOR has been designedto solve the longstanding physical problems of particle heating andenergization in turbulent plasmas. It will provide high resolutionmeasurements of electromagnetic fields and particle distribution functionswith unprecedented resolution, with the aim of exploring the so-calledkinetic scales. We present the numerical simulation framework which is supporting the THOR mission during the study phase. The THOR teamincludes many scientists developing and running different simulation codes(Eulerian-Vlasov, Particle-In-Cell, Gyrokinetics, Two-fluid, MHD, etc.),addressing the physics of plasma turbulence, shocks, magnetic reconnectionand so on.These numerical codes are being used during the study phase, mainly withthe aim of addressing the following points:(i) to simulate the response of real particle instruments on board THOR, byemploying an electrostatic analyser simulator which mimics the response ofthe CSW, IMS and TEA instruments to the particle velocity distributions ofprotons, alpha particle and electrons, as obtained from kinetic numericalsimulations of plasma turbulence.(ii) to compare multi-spacecraft with single-spacecraft configurations inmeasuring current density, by making use of both numerical models ofsynthetic turbulence and real data from MMS spacecraft.(iii) to investigate the validity of the Taylor hypothesis indifferent configurations of plasma turbulence

Parameterization of the proline analogue Aze (azetidine-2-carboxylic acid) for molecular dynamics simulations and evaluation of its effect on homo-pentapeptide conformations.

PubMed

Bessonov, Kyrylo; Vassall, Kenrick A; Harauz, George

2013-02-01

We have parameterized and evaluated the proline homologue Aze (azetidine-2-carboxylic acid) for the gromos56a3 force-field for use in molecular dynamics simulations using GROMACS. Using bi-phasic cyclohexane/water simulation systems and homo-pentapeptides, we measured the Aze solute interaction potential energies, ability to hydrogen bond with water, and overall compaction, for comparison to Pro, Gly, and Lys. Compared to Pro, Aze has a slightly higher H-bonding potential, and stronger electrostatic but weaker non-electrostatic interactions with water. The 20-ns simulations revealed the preferential positioning of Aze and Pro at the interface of the water and cyclohexane layers, with Aze spending more time in the aqueous layer. We also demonstrated through simulations of the homo-pentapeptides that Aze has a greater propensity than Pro to undergo trans→cis peptide bond isomerization, which results in a severe 180° bend in the polypeptide chain. The results provide evidence for the hypothesis that the misincorporation of Aze within proline-rich regions of proteins could disrupt the formation of poly-proline type II structures and compromise events such as recognition and binding by SH3-domains. Copyright © 2012 Elsevier Inc. All rights reserved.

Hydroxyl Radical Formation from HULIS and Fe(II) Interactions: Fulvic Acid-Fe(II) Complexes in Simulated and Human Lung Fluids

NASA Astrophysics Data System (ADS)

Gonzalez, D.

2017-12-01

Inhalation of fine particulate matter (PM2.5) has long been associated with adverse health outcomes. However, the causative agents and underlying mechanisms for these health effects have yet to be identified. One hypothesis is that PM2.5 deposited in the alveoli produce an excess of highly reactive radicals, leading to oxidative stress. The OH radical may be the most physiologically damaging, capable of oxidizing of lipids, proteins and DNA. Due to the variability and uncertainty in PM2.5 composition, the components that contribute to OH formation are not well understood. Soluble Fe is a component of PM2.5that produces OH under physiological conditions. Humic-like substances are water soluble organics found in biomass burning and tobacco smoke. Humic-like substances are capable of binding to Fe and enhancing OH formation, but this chemistry is not well understood. In this work, we use soil derived fulvic acid as a surrogate for Humic-like substances and investigate its effect on OH formation from Fe(II) under conditions relevant to the lungs. We use a fluorescent OH trapping probe, chemical kinetics and thermodynamic modeling to investigate OH formation from fulvic acid and Fe(II) dissolved in simulated and human lung fluids. In simulated lung fluid, we find that fulvic acid binds to Fe(II) and enhances the rate of key reactions that form OH. When fulvic acid is added to human lung fluids containing Fe(II), an enhancement of OH formation is observed. In human lung fluid, fulvic acid and metal binding proteins compete for Fe binding. These metal binding proteins are typically not found in simulated lung fluids. Results show that fulvic acid strongly binds Fe(II) and catalyzes key reactions that form OH in both simulated and human lung fluids. These results may help explain the role of Humic-like substances and Fe in oxidative stress and adverse health outcomes. Furthermore, we suggest that future studies employ simulated lung fluids containing metal binding proteins to better reflect human lung fluids.

Implementation of unsteady sampling procedures for the parallel direct simulation Monte Carlo method

NASA Astrophysics Data System (ADS)

Cave, H. M.; Tseng, K.-C.; Wu, J.-S.; Jermy, M. C.; Huang, J.-C.; Krumdieck, S. P.

2008-06-01

An unsteady sampling routine for a general parallel direct simulation Monte Carlo method called PDSC is introduced, allowing the simulation of time-dependent flow problems in the near continuum range. A post-processing procedure called DSMC rapid ensemble averaging method (DREAM) is developed to improve the statistical scatter in the results while minimising both memory and simulation time. This method builds an ensemble average of repeated runs over small number of sampling intervals prior to the sampling point of interest by restarting the flow using either a Maxwellian distribution based on macroscopic properties for near equilibrium flows (DREAM-I) or output instantaneous particle data obtained by the original unsteady sampling of PDSC for strongly non-equilibrium flows (DREAM-II). The method is validated by simulating shock tube flow and the development of simple Couette flow. Unsteady PDSC is found to accurately predict the flow field in both cases with significantly reduced run-times over single processor code and DREAM greatly reduces the statistical scatter in the results while maintaining accurate particle velocity distributions. Simulations are then conducted of two applications involving the interaction of shocks over wedges. The results of these simulations are compared to experimental data and simulations from the literature where there these are available. In general, it was found that 10 ensembled runs of DREAM processing could reduce the statistical uncertainty in the raw PDSC data by 2.5-3.3 times, based on the limited number of cases in the present study.

Deep Subaru Hyper Suprime-Cam Observations of Milky Way Satellites Columba I and Triangulum II

NASA Astrophysics Data System (ADS)

Carlin, Jeffrey L.; Sand, David J.; Muñoz, Ricardo R.; Spekkens, Kristine; Willman, Beth; Crnojević, Denija; Forbes, Duncan A.; Hargis, Jonathan; Kirby, Evan; Peter, Annika H. G.; Romanowsky, Aaron J.; Strader, Jay

2017-12-01

We present deep, wide-field Subaru Hyper Suprime-Cam photometry of two recently discovered satellites of the Milky Way (MW): Columba I (Col I) and Triangulum II (Tri II). The color-magnitude diagrams of both objects point to exclusively old and metal-poor stellar populations. We re-derive structural parameters and luminosities of these satellites, and find {M}{{V},{Col}{{I}}}=-4.2+/- 0.2 for Col I and {M}{{V},{Tri}{II}}=-1.2+/- 0.4 for Tri II, with corresponding half-light radii of {r}{{h},{Col}{{I}}}=117+/- 17 pc and {r}{{h},{Tri}{II}}=21+/- 4 pc. The properties of both systems are consistent with observed scaling relations for MW dwarf galaxies. Based on archival data, we derive upper limits on the neutral gas content of these dwarfs, and find that they lack H I, as do the majority of observed satellites within the MW virial radius. Neither satellite shows evidence of tidal stripping in the form of extensions or distortions in matched-filter stellar density maps or surface-density profiles. However, the smaller Tri II system is relatively metal-rich for its luminosity (compared to other MW satellites), possibly because it has been tidally stripped. Through a suite of orbit simulations, we show that Tri II is approaching pericenter of its eccentric orbit, a stage at which tidal debris is unlikely to be seen. In addition, we find that Tri II may be on its first infall into the MW, which helps explain its unique properties among MW dwarfs. Further evidence that Tri II is likely an ultra-faint dwarf comes from its stellar mass function, which is similar to those of other MW dwarfs. Based in part on data collected at the Subaru Telescope, which is operated by the National Astronomical Observatory of Japan.

Grid Sensitivity Study for Slat Noise Simulations

NASA Technical Reports Server (NTRS)

Lockard, David P.; Choudhari, Meelan M.; Buning, Pieter G.

2014-01-01

The slat noise from the 30P/30N high-lift system is being investigated through computational fluid dynamics simulations in conjunction with a Ffowcs Williams-Hawkings acoustics solver. Many previous simulations have been performed for the configuration, and the case was introduced as a new category for the Second AIAA workshop on Benchmark problems for Airframe Noise Configurations (BANC-II). However, the cost of the simulations has restricted the study of grid resolution effects to a baseline grid and coarser meshes. In the present study, two different approaches are being used to investigate the effect of finer resolution of near-field unsteady structures. First, a standard grid refinement by a factor of two is used, and the calculations are performed by using the same CFL3D solver employed in the majority of the previous simulations. Second, the OVERFLOW code is applied to the baseline grid, but with a 5th-order upwind spatial discretization as compared with the second-order discretization used in the CFL3D simulations. In general, the fine grid CFL3D simulation and OVERFLOW calculation are in very good agreement and exhibit the lowest levels of both surface pressure fluctuations and radiated noise. Although the smaller scales resolved by these simulations increase the velocity fluctuation levels, they appear to mitigate the influence of the larger scales on the surface pressure. These new simulations are used to investigate the influence of the grid on unsteady high-lift simulations and to gain a better understanding of the physics responsible for the noise generation and radiation.

Simulation of lung alveolar epithelial wound healing in vitro.

PubMed

Kim, Sean H J; Matthay, Michael A; Mostov, Keith; Hunt, C Anthony

2010-08-06

The mechanisms that enable and regulate alveolar type II (AT II) epithelial cell wound healing in vitro and in vivo remain largely unknown and need further elucidation. We used an in silico AT II cell-mimetic analogue to explore and better understand plausible wound healing mechanisms for two conditions: cyst repair in three-dimensional cultures and monolayer wound healing. Starting with the analogue that validated for key features of AT II cystogenesis in vitro, we devised an additional cell rearrangement action enabling cyst repair. Monolayer repair was enabled by providing 'cells' a control mechanism to switch automatically to a repair mode in the presence of a distress signal. In cyst wound simulations, the revised analogue closed wounds by adhering to essentially the same axioms available for alveolar-like cystogenesis. In silico cell proliferation was not needed. The analogue recovered within a few simulation cycles but required a longer recovery time for larger or multiple wounds. In simulated monolayer wound repair, diffusive factor-mediated 'cell' migration led to repair patterns comparable to those of in vitro cultures exposed to different growth factors. Simulations predicted directional cell locomotion to be critical for successful in vitro wound repair. We anticipate that with further use and refinement, the methods used will develop as a rigorous, extensible means of unravelling mechanisms of lung alveolar repair and regeneration.

A structural model for apolipoprotein C-II amyloid fibrils: experimental characterization and molecular dynamics simulations.

PubMed

Teoh, Chai Lean; Pham, Chi L L; Todorova, Nevena; Hung, Andrew; Lincoln, Craig N; Lees, Emma; Lam, Yuen Han; Binger, Katrina J; Thomson, Neil H; Radford, Sheena E; Smith, Trevor A; Müller, Shirley A; Engel, Andreas; Griffin, Michael D W; Yarovsky, Irene; Gooley, Paul R; Howlett, Geoffrey J

2011-02-04

The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple 'letter-G-like' β-strand-loop-β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops. Copyright © 2010 Elsevier Ltd. All rights reserved.

Forebody and base region real gas flow in severe planetary entry by a factored implicit numerical method. II - Equilibrium reactive gas

NASA Technical Reports Server (NTRS)

Davy, W. C.; Green, M. J.; Lombard, C. K.

1981-01-01

The factored-implicit, gas-dynamic algorithm has been adapted to the numerical simulation of equilibrium reactive flows. Changes required in the perfect gas version of the algorithm are developed, and the method of coupling gas-dynamic and chemistry variables is discussed. A flow-field solution that approximates a Jovian entry case was obtained by this method and compared with the same solution obtained by HYVIS, a computer program much used for the study of planetary entry. Comparison of surface pressure distribution and stagnation line shock-layer profiles indicates that the two solutions agree well.

Analysis of potential errors in real-time streamflow data and methods of data verification by digital computer

USGS Publications Warehouse

Lystrom, David J.

1972-01-01

Various methods of verifying real-time streamflow data are outlined in part II. Relatively large errors (those greater than 20-30 percent) can be detected readily by use of well-designed verification programs for a digital computer, and smaller errors can be detected only by discharge measurements and field observations. The capability to substitute a simulated discharge value for missing or erroneous data is incorporated in some of the verification routines described. The routines represent concepts ranging from basic statistical comparisons to complex watershed modeling and provide a selection from which real-time data users can choose a suitable level of verification.

Nonlinear propagation model for ultrasound hydrophones calibration in the frequency range up to 100 MHz.

PubMed

Radulescu, E G; Wójcik, J; Lewin, P A; Nowicki, A

2003-06-01

To facilitate the implementation and verification of the new ultrasound hydrophone calibration techniques described in the companion paper (somewhere in this issue) a nonlinear propagation model was developed. A brief outline of the theoretical considerations is presented and the model's advantages and disadvantages are discussed. The results of simulations yielding spatial and temporal acoustic pressure amplitude are also presented and compared with those obtained using KZK and Field II models. Excellent agreement between all models is evidenced. The applicability of the model in discrete wideband calibration of hydrophones is documented in the companion paper somewhere in this volume.

Optical Properties of a Semimagnetic Quantum Well in a Proximity of a Superconducting Film

NASA Astrophysics Data System (ADS)

Lebecki, K. M.; Kłopotowski, Ł.; Kossut, J.

2006-11-01

We consider, via numerical calculations, a hybrid structure made of a semimagnetic Cd1-xMnxTe quantum well deposited in a close proximity to superconducting niobium film. We simulate photoluminescence and the Faraday rotation spectra, modified by the presence of vortices in this type II superconductor. The magnitude of the evaluated effects is small - the vortex induced spectral line shape variation is of the order of 1% at 1 K and 0.1% at 3 K and is expected to occur mainly in the field range between 0.03 T and 0.05 T.