Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface

PubMed Central

Nägel, Arne; Reiter, Sebastian; Vogel, Andreas; McLauchlan, John; Herrmann, Eva; Wittum, Gabriel

2018-01-01

Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles. PMID:29316722

Local conformational dynamics in alpha-helices measured by fast triplet transfer.

PubMed

Fierz, Beat; Reiner, Andreas; Kiefhaber, Thomas

2009-01-27

Coupling fast triplet-triplet energy transfer (TTET) between xanthone and naphthylalanine to the helix-coil equilibrium in alanine-based peptides allowed the observation of local equilibrium fluctuations in alpha-helices on the nanoseconds to microseconds time scale. The experiments revealed faster helix unfolding in the terminal regions compared with the central parts of the helix with time constants varying from 250 ns to 1.4 micros at 5 degrees C. Local helix formation occurs with a time constant of approximately 400 ns, independent of the position in the helix. Comparing the experimental data with simulations using a kinetic Ising model showed that the experimentally observed dynamics can be explained by a 1-dimensional boundary diffusion with position-independent elementary time constants of approximately 50 ns for the addition and of approximately 65 ns for the removal of an alpha-helical segment. The elementary time constant for helix growth agrees well with previously measured time constants for formation of short loops in unfolded polypeptide chains, suggesting that helix elongation is mainly limited by a conformational search.

Galactic r-process enrichment by neutron star mergers in cosmological simulations of a Milky Way-mass galaxy

NASA Astrophysics Data System (ADS)

van de Voort, Freeke; Quataert, Eliot; Hopkins, Philip F.; Kereš, Dušan; Faucher-Giguère, Claude-André

2015-02-01

We quantify the stellar abundances of neutron-rich r-process nuclei in cosmological zoom-in simulations of a Milky Way-mass galaxy from the Feedback In Realistic Environments project. The galaxy is enriched with r-process elements by binary neutron star (NS) mergers and with iron and other metals by supernovae. These calculations include key hydrodynamic mixing processes not present in standard semi-analytic chemical evolution models, such as galactic winds and hydrodynamic flows associated with structure formation. We explore a range of models for the rate and delay time of NS mergers, intended to roughly bracket the wide range of models consistent with current observational constraints. We show that NS mergers can produce [r-process/Fe] abundance ratios and scatter that appear reasonably consistent with observational constraints. At low metallicity, [Fe/H] ≲ -2, we predict there is a wide range of stellar r-process abundance ratios, with both supersolar and subsolar abundances. Low-metallicity stars or stars that are outliers in their r-process abundance ratios are, on average, formed at high redshift and located at large galactocentric radius. Because NS mergers are rare, our results are not fully converged with respect to resolution, particularly at low metallicity. However, the uncertain rate and delay time distribution of NS mergers introduce an uncertainty in the r-process abundances comparable to that due to finite numerical resolution. Overall, our results are consistent with NS mergers being the source of most of the r-process nuclei in the Universe.

Scaling NS-3 DCE Experiments on Multi-Core Servers

DTIC Science & Technology

2016-06-15

that work well together. 3.2 Simulation Server Details We ran the simulations on a Dell® PowerEdge M520 blade server[8] running Ubuntu Linux 14.04...To minimize the amount of time needed to complete all of the simulations, we planned to run multiple simulations at the same time on a blade server...MacBook was running the simulation inside a virtual machine (Ubuntu 14.04), while the blade server was running the same operating system directly on

Spin-torque driven magnetization switching in ferromagnetic nanopillar with pinned layer biasing configuration

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

Bhoomeeswaran, H.; Sabareesan, P., E-mail: sendtosabari@gmail.com; Bharathi, B. Divya

2016-05-06

Magnetization switching driven by spin transfer torque in a ferromagnetic nanopillar by biasing the angular polarizer with different orientation has been studied. The free layer dynamics includes the spin torque from the oscillating free layer with magneto crystalline anisotropy and shape anisotropy, which is governed by the Landau-Lifshitsz-Gilbert-Slonczweski (LLGS) equation and solving it numerically by using embedded Runge Kutta fourth order method. Results of numerical simulation shows that there is a drastic reduction of switching time in the free layer by the orientation of angular polarizer of the nano pillar device. We fixed the angular polarizer as 0°, 30°, 60°,more » 90° and the corresponding switching time is 6.53 ns, 4.36 ns, 2.25 ns and 1.21 ns respectively for an applied current density of 5 × 10{sup 11} Am{sup −2}.« less

Dynamics and Solubility of He and CO 2 in Brine

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

Ho, Tuan Anh; Tenney, Craig M.

2016-09-01

Molecular dynamics simulation was implemented using LAMMPS simulation package (1) to study the diffusivity of He 3 and CO 2 in NaCl aqueous solution. To simulate at infinite dilute gas concentration, we placed one He 3 or CO 2 molecule in an initial simulation box of 24x24x33Å 3 containing 512 water molecules and a certain number of NaCl molecules depending on the concentration. Initial configuration was set up by placing water, NaCl, and gas molecules into different regions in the simulation box. Calculating diffusion coefficient for one He or CO 2 molecule consistently yields poor results. To overcome this, formore » each simulation at specific conditions (i.e., temperature, pressure, and NaCl concentration), we conducted 50 simulations initiated from 50 different configurations. These configurations are obtained by performing the simulation starting from the initial configuration mentioned above in the NVE ensemble (i.e., constant number of particles, volume, and energy). for 100,000 time steps and collecting one configuration every 2,000 times step. The output temperature of this simulation is about 500K. The collected configurations were then equilibrated for 2ns in the NPT ensemble (i.e., constant number of particles, pressure, and temperature) followed by 9ns simulations in the NVT ensemble (i.e., constant number of particles, volume, and temperature). The time step is 1fs for all simulations.« less

The Effect of Photon Statistics and Pulse Shaping on the Performance of the Wiener Filter Crystal Identification Algorithm Applied to LabPET Phoswich Detectors

NASA Astrophysics Data System (ADS)

Yousefzadeh, Hoorvash Camilia; Lecomte, Roger; Fontaine, Réjean

2012-06-01

A fast Wiener filter-based crystal identification (WFCI) algorithm was recently developed to discriminate crystals with close scintillation decay times in phoswich detectors. Despite the promising performance of WFCI, the influence of various physical factors and electrical noise sources of the data acquisition chain (DAQ) on the crystal identification process was not fully investigated. This paper examines the effect of different noise sources, such as photon statistics, avalanche photodiode (APD) excess multiplication noise, and front-end electronic noise, as well as the influence of different shaping filters on the performance of the WFCI algorithm. To this end, a PET-like signal simulator based on a model of the LabPET DAQ, a small animal APD-based digital PET scanner, was developed. Simulated signals were generated under various noise conditions with CR-RC shapers of order 1, 3, and 5 having different time constants (τ). Applying the WFCI algorithm to these simulated signals showed that the non-stationary Poisson photon statistics is the main contributor to the identification error of WFCI algorithm. A shaping filter of order 1 with τ = 50 ns yielded the best WFCI performance (error 1%), while a longer shaping time of τ = 100 ns slightly degraded the WFCI performance (error 3%). Filters of higher orders with fast shaping time constants (10-33 ns) also produced good WFCI results (error 1.4% to 1.6%). This study shows the advantage of the pulse simulator in evaluating various DAQ conditions and confirms the influence of the detection chain on the WFCI performance.

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation.

PubMed

Kamberaj, Hiqmet

2018-05-01

In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method. In addition, we applied SPMD simulation to calculate the time correlation functions of the transitions in a two dimensional surface to demonstrate the enhancement of transition path sampling. Our results showed that folded structure can be obtained in a shorter simulation time using the new method when compared with non-augmented dynamical system. Typically, in less than 0.5 ns using replica exchange runs assuming that native folded structure is known and within simulation time scale of 40 ns in the case of blind structure prediction. Furthermore, the root mean square deviations from the reference structures were less than 2Å. To demonstrate the performance of new method, we also implemented three simulation protocols using CHARMM software. Comparisons are also performed with standard targeted molecular dynamics simulation method. Copyright © 2018 Elsevier Inc. All rights reserved.

Model-free estimation of the effective correlation time for C–H bond reorientation in amphiphilic bilayers: {sup 1}H–{sup 13}C solid-state NMR and MD simulations

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

Ferreira, Tiago Mendes, E-mail: tiago.ferreira@fkem1.lu.se; Physical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund; Ollila, O. H. Samuli

2015-01-28

Molecular dynamics (MD) simulations give atomically detailed information on structure and dynamics in amphiphilic bilayer systems on timescales up to about 1 μs. The reorientational dynamics of the C–H bonds is conventionally verified by measurements of {sup 13}C or {sup 2}H nuclear magnetic resonance (NMR) longitudinal relaxation rates R{sub 1}, which are more sensitive to motional processes with correlation times close to the inverse Larmor frequency, typically around 1-10 ns on standard NMR instrumentation, and are thus less sensitive to the 10-1000 ns timescale motion that can be observed in the MD simulations. We propose an experimental procedure for atomicallymore » resolved model-free estimation of the C–H bond effective reorientational correlation time τ{sub e}, which includes contributions from the entire range of all-atom MD timescales and that can be calculated directly from the MD trajectories. The approach is based on measurements of {sup 13}C R{sub 1} and R{sub 1ρ} relaxation rates, as well as {sup 1}H−{sup 13}C dipolar couplings, and is applicable to anisotropic liquid crystalline lipid or surfactant systems using a conventional solid-state NMR spectrometer and samples with natural isotopic composition. The procedure is demonstrated on a fully hydrated lamellar phase of 1-palmitoyl-2-oleoyl-phosphatidylcholine, yielding values of τ{sub e} from 0.1 ns for the methyl groups in the choline moiety and at the end of the acyl chains to 3 ns for the g{sub 1} methylene group of the glycerol backbone. MD simulations performed with a widely used united-atom force-field reproduce the τ{sub e}-profile of the major part of the acyl chains but underestimate the dynamics of the glycerol backbone and adjacent molecular segments. The measurement of experimental τ{sub e}-profiles can be used to study subtle effects on C–H bond reorientational motions in anisotropic liquid crystals, as well as to validate the C–H bond reorientation dynamics predicted in MD simulations of amphiphilic bilayers such as lipid membranes.« less

Structure and Dynamics of Confined C-O-H Fluids Relevant to the Subsurface: Application of Magnetic Resonance, Neutron Scattering and Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Gautam, Siddharth S.; Ok, Salim; Cole, David R.

2017-06-01

Geo-fluids consisting of C-O-H volatiles are the main mode of transport of mass and energy throughout the lithosphere and are commonly found confined in pores, grain boundaries and fractures. The confinement of these fluids by porous media at the length scales of a few nanometers gives rise to numerous physical and chemical properties that deviate from the bulk behavior. Studying the structural and dynamical properties of these confined fluids at the length and time scales of nanometers and picoseconds respectively forms an important component of understanding their behavior. To study confined fluids, non-destructive penetrative probes are needed. Nuclear magnetic resonance (NMR) by virtue of its ability to monitor longitudinal and transverse magnetization relaxations of spins, and chemical shifts brought about by the chemical environment of a nucleus, and measuring diffusion coefficient provides a good opportunity to study dynamics and chemical structure at the molecular length and time scales. Another technique that gives insights into the dynamics and structure at these length and time scales is neutron scattering (NS). This is because the wavelength and energies of cold and thermal neutrons used in scattering experiments are in the same range as the spatial features and energies involved in the dynamical processes occurring at the molecular level. Molecular Dynamics (MD) simulations on the other hand help with the interpretation of the NMR and NS data. Simulations can also supplement the experiments by calculating quantities not easily accessible to experiments. Thus using NMR, NS and MD simulations in conjunction, a complete description of the molecular structure and dynamics of confined geo-fluids can be obtained. In the current review, our aim is to show how a synergistic use of these three techniques has helped shed light on the complex behavior of water, CO2, and low molecular weight hydrocarbons. After summarizing the theoretical backgrounds of the techniques, we will discuss some recent examples of the use of NMR, NS, and MD simulations to the study of confined fluids.

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

Côté, Benoit; Belczynski, Krzysztof; Fryer, Chris L.

The role of compact binary mergers as the main production site of r-process elements is investigated by combining stellar abundances of Eu observed in the Milky Way, galactic chemical evolution (GCE) simulations, and binary population synthesis models, and gravitational wave measurements from Advanced LIGO. We compiled and reviewed seven recent GCE studies to extract the frequency of neutron star–neutron star (NS–NS) mergers that is needed in order to reproduce the observed [Eu/Fe] versus [Fe/H] relationship. We used our simple chemical evolution code to explore the impact of different analytical delay-time distribution functions for NS–NS mergers. We then combined our metallicity-dependent population synthesis models with our chemical evolution code to bring their predictions, for both NS–NS mergers and black hole–neutron star mergers, into a GCE context. Finally, we convolved our results with the cosmic star formation history to provide a direct comparison with current and upcoming Advanced LIGO measurements. When assuming that NS–NS mergers are the exclusive r-process sites, and that the ejected r-process mass per merger event is 0.01 Mmore » $${}_{\\odot }$$, the number of NS–NS mergers needed in GCE studies is about 10 times larger than what is predicted by standard population synthesis models. Here, these two distinct fields can only be consistent with each other when assuming optimistic rates, massive NS–NS merger ejecta, and low Fe yields for massive stars. For now, population synthesis models and GCE simulations are in agreement with the current upper limit (O1) established by Advanced LIGO during their first run of observations. Upcoming measurements will provide an important constraint on the actual local NS–NS merger rate, will provide valuable insights on the plausibility of the GCE requirement, and will help to define whether or not compact binary mergers can be the dominant source of r-process elements in the universe.« less

Advanced LIGO constraints on neutron star mergers and r-process sites

DOE PAGES

Côté, Benoit; Belczynski, Krzysztof; Fryer, Chris L.; ...

2017-02-20

The role of compact binary mergers as the main production site of r-process elements is investigated by combining stellar abundances of Eu observed in the Milky Way, galactic chemical evolution (GCE) simulations, and binary population synthesis models, and gravitational wave measurements from Advanced LIGO. We compiled and reviewed seven recent GCE studies to extract the frequency of neutron star–neutron star (NS–NS) mergers that is needed in order to reproduce the observed [Eu/Fe] versus [Fe/H] relationship. We used our simple chemical evolution code to explore the impact of different analytical delay-time distribution functions for NS–NS mergers. We then combined our metallicity-dependent population synthesis models with our chemical evolution code to bring their predictions, for both NS–NS mergers and black hole–neutron star mergers, into a GCE context. Finally, we convolved our results with the cosmic star formation history to provide a direct comparison with current and upcoming Advanced LIGO measurements. When assuming that NS–NS mergers are the exclusive r-process sites, and that the ejected r-process mass per merger event is 0.01 Mmore » $${}_{\\odot }$$, the number of NS–NS mergers needed in GCE studies is about 10 times larger than what is predicted by standard population synthesis models. Here, these two distinct fields can only be consistent with each other when assuming optimistic rates, massive NS–NS merger ejecta, and low Fe yields for massive stars. For now, population synthesis models and GCE simulations are in agreement with the current upper limit (O1) established by Advanced LIGO during their first run of observations. Upcoming measurements will provide an important constraint on the actual local NS–NS merger rate, will provide valuable insights on the plausibility of the GCE requirement, and will help to define whether or not compact binary mergers can be the dominant source of r-process elements in the universe.« less

A 800 kV compact peaking capacitor for nanosecond generator.

PubMed

Jia, Wei; Chen, Zhiqiang; Tang, Junping; Chen, Weiqing; Guo, Fan; Sun, Fengrong; Li, Junna; Qiu, Aici

2014-09-01

An extremely compact high voltage peaking capacitor is developed. The capacitor has a pancake structure with a diameter of 315 mm, a thickness of 59 mm, and a mass of 6.1 kg. The novel structural design endows the capacitor with a better mechanical stability and reliability under hundreds of kilovolts pulse voltage and an inner gas pressure of more than 1.5 MPa. The theoretical value of the capacitor self-inductance is near to 17 nH. Proved by series of electrical experiments, the capacitor can endure a high-voltage pulse with a rise time of about 20 ns, a half-width duration of around 25 ns, and an amplitude of up to 800 kV in a single shot model. When the capacitor was used in an electromagnetic pulse simulator as a peaking capacitor, the rise time of the voltage pulse can be reduced from 20 ns to less than 3 ns. The practical value of the capacitor's inductance deduced from the experimental date is no more than 25 nH.

Translational, rotational and internal dynamics of amyloid β-peptides (Aβ40 and Aβ42) from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bora, Ram Prasad; Prabhakar, Rajeev

2009-10-01

In this study, diffusion constants [translational (DT) and rotational (DR)], correlation times [rotational (τrot) and internal (τint)], and the intramolecular order parameters (S2) of the Alzheimer amyloid-β peptides Aβ40 and Aβ42 have been calculated from 150 ns molecular dynamics simulations in aqueous solution. The computed parameters have been compared with the experimentally measured values. The calculated DT of 1.61×10-6 cm2/s and 1.43×10-6 cm2/s for Aβ40 and Aβ42, respectively, at 300 K was found to follow the correct trend defined by the Debye-Stokes-Einstein relation that its value should decrease with the increase in the molecular weight. The estimated DR for Aβ40 and Aβ42 at 300 K are 0.085 and 0.071 ns-1, respectively. The rotational (Crot(t)) and internal (Cint(t)) correlation functions of Aβ40 and Aβ42 were observed to decay at nano- and picosecond time scales, respectively. The significantly different time decays of these functions validate the factorization of the total correlation function (Ctot(t)) of Aβ peptides into Crot(t) and Cint(t). At both short and long time scales, the Clore-Szabo model that was used as Cint(t) provided the best behavior of Ctot(t) for both Aβ40 and Aβ42. In addition, an effective rotational correlation time of Aβ40 is also computed at 18 °C and the computed value (2.30 ns) is in close agreement with the experimental value of 2.45 ns. The computed S2 parameters for the central hydrophobic core, the loop region, and C-terminal domains of Aβ40 and Aβ42 are in accord with the previous studies.

Numerical Simulations of a Multiscale Model of Stratified Langmuir Circulation

NASA Astrophysics Data System (ADS)

Malecha, Ziemowit; Chini, Gregory; Julien, Keith

2012-11-01

Langmuir circulation (LC), a prominent form of wind and surface-wave driven shear turbulence in the ocean surface boundary layer (BL), is commonly modeled using the Craik-Leibovich (CL) equations, a phase-averaged variant of the Navier-Stokes (NS) equations. Although surface-wave filtering renders the CL equations more amenable to simulation than are the instantaneous NS equations, simulations in wide domains, hundreds of times the BL depth, currently earn the ``grand challenge'' designation. To facilitate simulations of LC in such spatially-extended domains, we have derived multiscale CL equations by exploiting the scale separation between submesoscale and BL flows in the upper ocean. The numerical algorithm for simulating this multiscale model resembles super-parameterization schemes used in meteorology, but retains a firm mathematical basis. We have validated our algorithm and here use it to perform multiscale simulations of the interaction between LC and upper ocean density stratification. ZMM, GPC, KJ gratefully acknowledge funding from NSF CMG Award 0934827.

Modeling, docking and dynamics simulations of a non-specific lipid transfer protein from Peganum harmala L.

PubMed

Shi, Zheng; Wang, Zi-jie; Xu, Huai-long; Tian, Yang; Li, Xin; Bao, Jin-ku; Sun, Su-rong; Yue, Bi-song

2013-12-01

Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure. Moreover, we adopted MEGA to analyze ns-LTPs and other species phylogenetically, which brought out an initial sequence alignment of ns-LTPs. In addition, we used molecular docking and molecular dynamics simulations to further investigate the affinities and stabilities of ns-LTP with several ligands complexes. Taken together, our results about ns-LTPs and their ligand-binding activities can provide a better understanding of the lipid-protein interactions, indicating some future applications of ns-LTP-mediated transport. Copyright © 2013 Elsevier Ltd. All rights reserved.

Collective Langevin dynamics of conformational motions in proteins

NASA Astrophysics Data System (ADS)

Lange, Oliver F.; Grubmüller, Helmut

2006-06-01

Functionally relevant slow conformational motions of proteins are, at present, in most cases inaccessible to molecular dynamics (MD) simulations. The main reason is that the major part of the computational effort is spend for the accurate description of a huge number of high frequency motions of the protein and the surrounding solvent. The accumulated influence of these fluctuations is crucial for a correct treatment of the conformational dynamics; however, their details can be considered irrelevant for most purposes. To accurately describe long time protein dynamics we here propose a reduced dimension approach, collective Langevin dynamics (CLD), which evolves the dynamics of the system within a small subspace of relevant collective degrees of freedom. The dynamics within the low-dimensional conformational subspace is evolved via a generalized Langevin equation which accounts for memory effects via memory kernels also extracted from short explicit MD simulations. To determine the memory kernel with differing levels of regularization, we propose and evaluate two methods. As a first test, CLD is applied to describe the conformational motion of the peptide neurotensin. A drastic dimension reduction is achieved by considering one single curved conformational coordinate. CLD yielded accurate thermodynamical and dynamical behaviors. In particular, the rate of transitions between two conformational states agreed well with a rate obtained from a 150ns reference molecular dynamics simulation, despite the fact that the time scale of the transition (˜50ns) was much longer than the 1ns molecular dynamics simulation from which the memory kernel was extracted.

Rise Time of the Simulated VERITAS 12 m Davies-Cotton Reflector

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

White, Richard J.

The Very Energetic Radiation Imaging Telescope Array System (VERITAS) will utilise Imaging Atmospheric Cherenkov Telescopes (IACTs) based on a Davies-Cotton design with f-number f/1.0 to detect cosmic gamma-rays. Unlike a parabolic reflector, light from the Davies-Cotton does not arrive isochronously at the camera. Here the effect of the telescope geometry on signal rise-time is examined. An almost square-pulse arrival time profile with a rise time of 1.7 ns is found analytically and confirmed through simulation.

Time-resolved observation of protein allosteric communication

PubMed Central

Buchenberg, Sebastian; Sittel, Florian; Stock, Gerhard

2017-01-01

Allostery represents a fundamental mechanism of biological regulation that is mediated via long-range communication between distant protein sites. Although little is known about the underlying dynamical process, recent time-resolved infrared spectroscopy experiments on a photoswitchable PDZ domain (PDZ2S) have indicated that the allosteric transition occurs on multiple timescales. Here, using extensive nonequilibrium molecular dynamics simulations, a time-dependent picture of the allosteric communication in PDZ2S is developed. The simulations reveal that allostery amounts to the propagation of structural and dynamical changes that are genuinely nonlinear and can occur in a nonlocal fashion. A dynamic network model is constructed that illustrates the hierarchy and exceeding structural heterogeneity of the process. In compelling agreement with experiment, three physically distinct phases of the time evolution are identified, describing elastic response (≲0.1 ns), inelastic reorganization (∼100 ns), and structural relaxation (≳1μs). Issues such as the similarity to downhill folding as well as the interpretation of allosteric pathways are discussed. PMID:28760989

A Simulation Program with Latency Exploitation for the Transient Analysis of Digital Circuits.

DTIC Science & Technology

1983-08-01

PW PER) Examples: VIN 3 0 PULSE(-5 5 iNS iNS iNS 50NS lOONS) parameters default values units Vi (initial value) volts or amps V2 (pulsed value) volts...TAUl TD2 TAU2)mU Examples: VIN 3 0 EXP(-5 0 2NS 30NS 60NS 40NS) parameters default values units V1 (initial value) volts or amps V2 (pulsed value

General relativistic magnetohydrodynamic simulations of binary neutron star mergers forming a long-lived neutron star

NASA Astrophysics Data System (ADS)

Ciolfi, Riccardo; Kastaun, Wolfgang; Giacomazzo, Bruno; Endrizzi, Andrea; Siegel, Daniel M.; Perna, Rosalba

2017-03-01

Merging binary neutron stars (BNSs) represent the ultimate targets for multimessenger astronomy, being among the most promising sources of gravitational waves (GWs), and, at the same time, likely accompanied by a variety of electromagnetic counterparts across the entire spectrum, possibly including short gamma-ray bursts (SGRBs) and kilonova/macronova transients. Numerical relativity simulations play a central role in the study of these events. In particular, given the importance of magnetic fields, various aspects of this investigation require general relativistic magnetohydrodynamics (GRMHD). So far, most GRMHD simulations focused the attention on BNS mergers leading to the formation of a hypermassive neutron star (NS), which, in turn, collapses within few tens of ms into a black hole surrounded by an accretion disk. However, recent observations suggest that a significant fraction of these systems could form a long-lived NS remnant, which will either collapse on much longer time scales or remain indefinitely stable. Despite the profound implications for the evolution and the emission properties of the system, a detailed investigation of this alternative evolution channel is still missing. Here, we follow this direction and present a first detailed GRMHD study of BNS mergers forming a long-lived NS. We consider magnetized binaries with different mass ratios and equations of state and analyze the structure of the NS remnants, the rotation profiles, the accretion disks, the evolution and amplification of magnetic fields, and the ejection of matter. Moreover, we discuss the connection with the central engine of SGRBs and provide order-of-magnitude estimates for the kilonova/macronova signal. Finally, we study the GW emission, with particular attention to the post-merger phase.

Mouse Acetylcholinesterase Unliganded and in Complex with Huperzine A: A Comparison of Molecular Dynamics Simulations

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

Tara, Sylvia; Straatsma, TP; Mccammon, Andy

1999-06-01

A 1 ns molecular dynamics simulation of unliganded mouse acetylcholinesterase (AChE) is compared to a previous simulation of mouse AChE complexed with Huperzine A (HupA). Several common features are observed. In both simulations, the active site gorge fluctuates in size during the 1 ns trajectory, and is completely pinched off several times. Many of the residues in the gorge that formed hydrogen bonds with HupA in the simulation of the complex, now form hydrogen bonds with other protein residues and water molecules in the gorge. The opening of a "backdoor" entrance to the active site that was found in themore » simulation of the complex is also observed in the unliganded simulation. Differences between the two simulations include overall lower structural RMS deviations for residues in the gorge in the unliganded simulation, a smaller diameter of the gorge in the absence of HupA, and the disappearance of a side channel that was frequently present in the liganded simulation. The differences between the two simulations can be attributed, in part, to the interaction of AChE with HupA.« less

Wildfire simulation using LES with synthetic-velocity SGS models

NASA Astrophysics Data System (ADS)

McDonough, J. M.; Tang, Tingting

2016-11-01

Wildland fires are becoming more prevalent and intense worldwide as climate change leads to warmer, drier conditions; and large-eddy simulation (LES) is receiving increasing attention for fire spread predictions as computing power continues to improve (see, e.g.,). We report results from wildfire simulations over general terrain employing implicit LES for solution of the incompressible Navier-Stokes (N.-S.) and thermal energy equations with Boussinesq approximation, altered with Darcy, Forchheimer and Brinkman extensions, to represent forested regions as porous media with varying (in both space and time) porosity and permeability. We focus on subgrid-scale (SGS) behaviors computed with a synthetic-velocity model, a discrete dynamical system, based on the poor man's N.-S. equations and investigate the ability of this model to produce fire whirls (tornadoes of fire) at the (unresolved) SGS level. Professor, Mechanical Engineering and Mathematics.

Numerical simulations of microwave heating of liquids: enhancements using Krylov subspace methods

NASA Astrophysics Data System (ADS)

Lollchund, M. R.; Dookhitram, K.; Sunhaloo, M. S.; Boojhawon, R.

2013-04-01

In this paper, we compare the performances of three iterative solvers for large sparse linear systems arising in the numerical computations of incompressible Navier-Stokes (NS) equations. These equations are employed mainly in the simulation of microwave heating of liquids. The emphasis of this work is on the application of Krylov projection techniques such as Generalized Minimal Residual (GMRES) to solve the Pressure Poisson Equations that result from discretisation of the NS equations. The performance of the GMRES method is compared with the traditional Gauss-Seidel (GS) and point successive over relaxation (PSOR) techniques through their application to simulate the dynamics of water housed inside a vertical cylindrical vessel which is subjected to microwave radiation. It is found that as the mesh size increases, GMRES gives the fastest convergence rate in terms of computational times and number of iterations.

On the induced gravitational collapse scenario of gamma-ray bursts associated with supernovae

DOE PAGES

Becerra, L.; Bianco, C. L.; Fryer, C. L.; ...

2016-12-10

Following the induced gravitational collapse (IGC) paradigm of gamma-ray bursts (GRBs) associated with type Ib/c supernovae, we present numerical simulations of the explosion of a carbon–oxygen (CO) core in a binary system with a neutron-star (NS) companion. The supernova ejecta trigger a hypercritical accretion process onto the NS thanks to a copious neutrino emission and the trapping of photons within the accretion flow. We show that temperatures of 1–10 MeV develop near the NS surface, hence electron–positron annihilation into neutrinos becomes the main cooling channel leading to accretion rates of 10–9–more » $${10}^{-1}\\,{M}_{\\odot }$$ s–1 and neutrino luminosities of 10 43–10 52 erg s –1 (the shorter the orbital period the higher the accretion rate). We estimate the maximum orbital period, $${P}_{\\max },$$ as a function of the NS initial mass, up to which the NS companion can reach by hypercritical accretion the critical mass for gravitational collapse leading to black hole formation. We then estimate the effects of the accreting and orbiting NS companion onto a novel geometry of the supernova ejecta density profile. We present the results of a $$1.4\\times {10}^{7}$$ particle simulation which show that the NS induces accentuated asymmetries in the ejecta density around the orbital plane. We elaborate on the observables associated with the above features of the IGC process. We apply this framework to specific GRBs: we find that X-ray flashes (XRFs) and binary-driven hypernovae are produced in binaries with $$P\\gt {P}_{\\max }$$ and $$P\\lt {P}_{\\max },$$ respectively. As a result, we analyze in detail the case of XRF 060218.« less

Experimental and computational study of complex shockwave dynamics in laser ablation plumes in argon atmosphere

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

Harilal, S. S.; Miloshevsky, G. V.; Diwakar, P. K.

2012-08-15

We investigated spatio-temporal evolution of ns laser ablation plumes at atmospheric pressure, a favored condition for laser-induced breakdown spectroscopy and laser-ablation inductively coupled plasma mass-spectrometry. The 1064 nm, 6 ns pulses from a Nd:YAG laser were focused on to an Al target and the generated plasma was allowed to expand in 1 atm Ar. The hydrodynamic expansion features were studied using focused shadowgraphy and gated 2 ns self-emission visible imaging. Shadowgram images showed material ejection and generation of shock fronts. A secondary shock is observed behind the primary shock during the time window of 100-500 ns with instabilities near themore » laser cone angle. By comparing the self-emission images obtained using fast photography, it is concluded that the secondary shocks observed in the shadowgraphy were generated by fast moving target material. The plume front estimates using fast photography exhibited reasonable agreement with data obtained from shadowgraphy at early times {<=}400 ns. However, at later times, fast photography images showed plume confinement while the shadowgraphic images showed propagation of the plume front even at greater times. The structure and dynamics of the plume obtained from optical diagnostic tools were compared to numerical simulations. We have shown that the main features of plume expansion in ambient Ar observed in the experiments can be reproduced using a continuum hydrodynamics model which provided valuable insight into the expansion dynamics and shock structure of the plasma plume.« less

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

PubMed

Paschek, Dietmar; Nymeyer, Hugh; García, Angel E

2007-03-01

We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

NASA Astrophysics Data System (ADS)

Asafi, M. S.; Yildirim, A.; Tekpinar, M.

2016-04-01

Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

Implementation of quantum key distribution network simulation module in the network simulator NS-3

NASA Astrophysics Data System (ADS)

Mehic, Miralem; Maurhart, Oliver; Rass, Stefan; Voznak, Miroslav

2017-10-01

As the research in quantum key distribution (QKD) technology grows larger and becomes more complex, the need for highly accurate and scalable simulation technologies becomes important to assess the practical feasibility and foresee difficulties in the practical implementation of theoretical achievements. Due to the specificity of the QKD link which requires optical and Internet connection between the network nodes, to deploy a complete testbed containing multiple network hosts and links to validate and verify a certain network algorithm or protocol would be very costly. Network simulators in these circumstances save vast amounts of money and time in accomplishing such a task. The simulation environment offers the creation of complex network topologies, a high degree of control and repeatable experiments, which in turn allows researchers to conduct experiments and confirm their results. In this paper, we described the design of the QKD network simulation module which was developed in the network simulator of version 3 (NS-3). The module supports simulation of the QKD network in an overlay mode or in a single TCP/IP mode. Therefore, it can be used to simulate other network technologies regardless of QKD.

Radiometric calibration of the reflective bands of NS001-Thematic Mapper Simulator (TMS) and modular multispectral radiometers (MMR)

NASA Technical Reports Server (NTRS)

Markham, Brian L.; Wood, Frank M., Jr.; Ahmad, Suraiya P.

1988-01-01

The NS001 Thematic Mapper Simulator scanner (TMS) and several modular multispectral radiometers (MMRs) are among the primary instruments used in the First ISLSCP (International Satellite Land Surface Climatology Project) Field Experiment (FIFE). The NS001 has a continuously variable gain setting. Calibration of the NS001 data is influenced by drift in the dark current level of up to six counts during a mirror scan at typical gain settings. The MMR instruments are being used in their 1 deg FOV configuration on the helicopter and 15 deg FOV on the ground.

Enhancing the NS-2 Network Simulator for Near Real-Time Control Feedback and Distributed Simulation

DTIC Science & Technology

2009-03-21

Communication Mediator, see mediator Constant Bit Rate, see cbr Emulation, 8 Georgia Tech Network Simulator, see GT- NetS Globlal Mobile Information ...PAGE Form ApprovedOMB No. 0704–0188 The public reporting burden for this collection of information is estimated to average 1 hour per response...for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704–0188

Combined 3D-QSAR, molecular docking, molecular dynamics simulation, and binding free energy calculation studies on the 5-hydroxy-2H-pyridazin-3-one derivatives as HCV NS5B polymerase inhibitors.

PubMed

Yu, Haijing; Fang, Yu; Lu, Xia; Liu, Yongjuan; Zhang, Huabei

2014-01-01

The NS5B RNA-dependent RNA polymerase (RdRP) is a promising therapeutic target for developing novel anti-hepatitis C virus (HCV) drugs. In this work, a combined molecular modeling study was performed on a series of 193 5-hydroxy-2H-pyridazin-3-one derivatives as inhibitors of HCV NS5B Polymerase. The best 3D-QSAR models, including CoMFA and CoMSIA, are based on receptor (or docking). Furthermore, a 40-ns molecular dynamics (MD) simulation and binding free energy calculations using docked structures of NS5B with ten compounds, which have diverse structures and pIC50 values, were employed to determine the detailed binding process and to compare the binding modes of the inhibitors with different activities. On one side, the stability and rationality of molecular docking and 3D-QSAR results were validated by MD simulation. The binding free energies calculated by the MM-PBSA method gave a good correlation with the experimental biological activity. On the other side, by analyzing some differences between the molecular docking and the MD simulation results, we can find that the MD simulation could also remedy the defects of molecular docking. The analyses of the combined molecular modeling results have identified that Tyr448, Ser556, and Asp318 are the key amino acid residues in the NS5B binding pocket. The results from this study can provide some insights into the development of novel potent NS5B inhibitors. © 2013 John Wiley & Sons A/S.

Evolution of elastic x-ray scattering in laser-shocked warm dense lithium.

PubMed

Kugland, N L; Gregori, G; Bandyopadhyay, S; Brenner, C M; Brown, C R D; Constantin, C; Glenzer, S H; Khattak, F Y; Kritcher, A L; Niemann, C; Otten, A; Pasley, J; Pelka, A; Roth, M; Spindloe, C; Riley, D

2009-12-01

We have studied the dynamics of warm dense Li with near-elastic x-ray scattering. Li foils were heated and compressed using shock waves driven by 4-ns-long laser pulses. Separate 1-ns-long laser pulses were used to generate a bright source of 2.96 keV Cl Ly- alpha photons for x-ray scattering, and the spectrum of scattered photons was recorded at a scattering angle of 120 degrees using a highly oriented pyrolytic graphite crystal operated in the von Hamos geometry. A variable delay between the heater and backlighter laser beams measured the scattering time evolution. Comparison with radiation-hydrodynamics simulations shows that the plasma is highly coupled during the first several nanoseconds, then relaxes to a moderate coupling state at later times. Near-elastic scattering amplitudes have been successfully simulated using the screened one-component plasma model. Our main finding is that the near-elastic scattering amplitudes are quite sensitive to the mean ionization state Z[over ] and by extension to the choice of ionization model in the radiation-hydrodynamics simulations used to predict plasma properties within the shocked Li.

Application of the Precipitation-Runoff Modeling System (PRMS) in the Apalachicola-Chattahoochee-Flint River Basin in the southeastern United States

USGS Publications Warehouse

LaFontaine, Jacob H.; Hay, Lauren E.; Viger, Roland J.; Markstrom, Steve L.; Regan, R. Steve; Elliott, Caroline M.; Jones, John W.

2013-01-01

A hydrologic model of the Apalachicola–Chattahoochee–Flint River Basin (ACFB) has been developed as part of a U.S. Geological Survey (USGS) National Climate Change and Wildlife Science Center effort to provide integrated science that helps resource managers understand the effect of climate change on a range of ecosystem responses. The hydrologic model was developed as part of the Southeast Regional Assessment Project using the Precipitation Runoff Modeling System (PRMS), a deterministic, distributed-parameter, process-based system that simulates the effects of precipitation, temperature, and land use on basin hydrology. The ACFB PRMS model simulates streamflow throughout the approximately 50,700 square-kilometer basin on a daily time step for the period 1950–99 using gridded climate forcings of air temperature and precipitation, and parameters derived from spatial data layers of altitude, land cover, soils, surficial geology, depression storage (small water bodies), and data from 56 USGS streamgages. Measured streamflow data from 35 of the 56 USGS streamgages were used to calibrate and evaluate simulated basin streamflow; the remaining gage locations were used for model delineation only. The model matched measured daily streamflow at 31 of the 35 calibration gages with Nash-Sutcliffe Model Efficiency Index (NS) greater than 0.6. Streamflow data for some calibration gages were augmented for regulation and water use effects to represent more natural flow volumes. Time-static parameters describing land cover limited the ability of the simulation to match historical runoff in the more developed subbasins. Overall, the PRMS simulation of the ACFB provides a good representation of basin hydrology on annual and monthly time steps. Calibration subbasins were analyzed by separating the 35 subbasins into five classes based on physiography, land use, and stream type (tributary or mainstem). The lowest NS values were rarely below 0.6, whereas the median NS for all five classes was within 0.74 to 0.96 for annual mean streamflow, 0.89 to 0.98 for mean monthly streamflow, and 0.82 to 0.98 for monthly mean streamflow. The median bias for all five classes was within –4.3 to 0.8 percent for annual mean streamflow, –6.3 to 0.5 percent for mean monthly streamflow, and –9.3 to 1.3 percent for monthly mean streamflow. The NS results combined with the percent bias results indicated a good to very good streamflow volume simulation for all subbasins. This simulation of the ACFB provides a foundation for future modeling and interpretive studies. Streamflow and other components of the hydrologic cycle simulated by PRMS can be used to inform other types of simulations; water-temperature, hydrodynamic, and ecosystem-dynamics simulations are three examples. In addition, possible future hydrologic conditions could be studied using this model in combination with land cover projections and downscaled general circulation model results.

Radiometric properties of the NS001 Thematic Mapper Simulator aircraft multispectral scanner

NASA Technical Reports Server (NTRS)

Markham, Brian L.; Ahmad, Suraiya P.

1990-01-01

Laboratory tests of the NS001 TM are described emphasizing absolute calibration to determine the radiometry of the simulator's reflective channels. In-flight calibration of the data is accomplished with the NS001 internal integrating-sphere source because instabilities in the source can limit the absolute calibration. The data from 1987-89 indicate uncertainties of up to 25 percent with an apparent average uncertainty of about 15 percent. Also identified are dark current drift and sensitivity changes along the scan line, random noise, and nonlinearity which contribute errors of 1-2 percent. Uncertainties similar to hysteresis are also noted especially in the 2.08-2.35-micron range which can reduce sensitivity and cause errors. The NS001 TM Simulator demonstrates a polarization sensitivity that can generate errors of up to about 10 percent depending on the wavelength.

Equilibration of experimentally determined protein structures for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Walton, Emily B.; Vanvliet, Krystyn J.

2006-12-01

Preceding molecular dynamics simulations of biomolecular interactions, the molecule of interest is often equilibrated with respect to an initial configuration. This so-called equilibration stage is required because the input structure is typically not within the equilibrium phase space of the simulation conditions, particularly in systems as complex as proteins, which can lead to artifactual trajectories of protein dynamics. The time at which nonequilibrium effects from the initial configuration are minimized—what we will call the equilibration time—marks the beginning of equilibrium phase-space exploration. Note that the identification of this time does not imply exploration of the entire equilibrium phase space. We have found that current equilibration methodologies contain ambiguities that lead to uncertainty in determining the end of the equilibration stage of the trajectory. This results in equilibration times that are either too long, resulting in wasted computational resources, or too short, resulting in the simulation of molecular trajectories that do not accurately represent the physical system. We outline and demonstrate a protocol for identifying the equilibration time that is based on the physical model of Normal Mode Analysis. We attain the computational efficiency required of large-protein simulations via a stretched exponential approximation that enables an analytically tractable and physically meaningful form of the root-mean-square deviation of atoms comprising the protein. We find that the fitting parameters (which correspond to physical properties of the protein) fluctuate initially but then stabilize for increased simulation time, independently of the simulation duration or sampling frequency. We define the end of the equilibration stage—and thus the equilibration time—as the point in the simulation when these parameters attain constant values. Compared to existing methods, our approach provides the objective identification of the time at which the simulated biomolecule has entered an energetic basin. For the representative protein considered, bovine pancreatic trypsin inhibitor, existing methods indicate a range of 0.2-10ns of simulation until a local minimum is attained. Our approach identifies a substantially narrower range of 4.5-5.5ns , which will lead to a much more objective choice of equilibration time.

Influence of configuration effects on multiple burst simulation testing

NASA Technical Reports Server (NTRS)

Emanuely, J. L.; Cantaloube, M.

1991-01-01

During the initial phase of a lightning strike attachment on an aircraft, fast current pulses (rise time approximately 100 ns, I(sub max) approximately few kA) were measured, which can create equipment upsets or disturbances. This threat, made of repetitive pulses and usually called 'multiple bursts', can be reproduced at the equipment interfaces assuming that the transfer function of the structure was determined. The normalized waveform H (10 kA - 100 ns rise time) is the reference for one of these pulses. The importance of the coaxial return path termination for the injection of the wave H is emphasized. According to the constitutive materials of the test bed, and the adaptation of the line, the natural oscillations of the structure and the internal coupling mechanisms can be modified. As a conclusion, various test configurations in relation with the nature of the test bed and the characteristics of the generator are detailed, for a more accurate ground simulation of the attachment phase.

Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation.

PubMed

Ni, Duan; Song, Kun; Zhang, Jian; Lu, Shaoyong

2017-10-26

Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras-NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras.

Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation

PubMed Central

Song, Kun; Zhang, Jian; Lu, Shaoyong

2017-01-01

Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras–NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras. PMID:29072601

Novel Flexible Transparent Conductive Films with Enhanced Chemical and Electromechanical Sustainability: TiO2 Nanosheet-Ag Nanowire Hybrid.

PubMed

Sohn, Hiesang; Kim, Seyun; Shin, Weonho; Lee, Jong Min; Lee, Hyangsook; Yun, Dong-Jin; Moon, Kyoung-Seok; Han, In Taek; Kwak, Chan; Hwang, Seong-Ju

2018-01-24

Flexible transparent conductive films (TCFs) of TiO 2 nanosheet (TiO 2 NS) and silver nanowire (Ag NW) network hybrid were prepared through a simple and scalable solution-based process. The as-formed TiO 2 NS-Ag NW hybrid TCF shows a high optical transmittance (TT: 97% (90.2% including plastic substrate)) and low sheet resistance (R s : 40 Ω/sq). In addition, the TiO 2 NS-Ag NW hybrid TCF exhibits a long-time chemical/aging and electromechanical stability. As for the chemical/aging stability, the hybrid TCF of Ag NW and TiO 2 NS reveals a retained initial conductivity (ΔR s /R s < 1%) under ambient oxidant gas over a month, superior to that of bare Ag NW (ΔR s /R s > 4000%) or RuO 2 NS-Ag NW hybrid (ΔR s /R s > 200%). As corroborated by the density functional theory simulation, the superb chemical stability of TiO 2 NS-Ag NW hybrid is attributable to the unique role of TiO 2 NS as a barrier, which prevents Ag NW's chemical corrosion via the attenuated adsorption of sulfidation molecules (H 2 S) on TiO 2 NS. With respect to the electromechanical stability, in contrast to Ag NWs (ΔR/R 0 ∼ 152.9%), our hybrid TCF shows a limited increment of fractional resistivity (ΔR/R 0 ∼ 14.4%) after 200 000 cycles of the 1R bending test (strain: 6.7%) owing to mechanically welded Ag NW networks by TiO 2 NS. Overall, our unique hybrid of TiO 2 NS and Ag NW exhibits excellent electrical/optical properties and reliable chemical/electromechanical stabilities.

A robust fractional-order PID controller design based on active queue management for TCP network

NASA Astrophysics Data System (ADS)

Hamidian, Hamideh; Beheshti, Mohammad T. H.

2018-01-01

In this paper, a robust fractional-order controller is designed to control the congestion in transmission control protocol (TCP) networks with time-varying parameters. Fractional controllers can increase the stability and robustness. Regardless of advantages of fractional controllers, they are still not common in congestion control in TCP networks. The network parameters are time-varying, so the robust stability is important in congestion controller design. Therefore, we focused on the robust controller design. The fractional PID controller is developed based on active queue management (AQM). D-partition technique is used. The most important property of designed controller is the robustness to the time-varying parameters of the TCP network. The vertex quasi-polynomials of the closed-loop characteristic equation are obtained, and the stability boundaries are calculated for each vertex quasi-polynomial. The intersection of all stability regions is insensitive to network parameter variations, and results in robust stability of TCP/AQM system. NS-2 simulations show that the proposed algorithm provides a stable queue length. Moreover, simulations show smaller oscillations of the queue length and less packet drop probability for FPID compared to PI and PID controllers. We can conclude from NS-2 simulations that the average packet loss probability variations are negligible when the network parameters change.

Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: a model from molecular simulations.

PubMed

Lai, Yen-Ting; Cheng, Chao-Sheng; Liu, Yu-Nan; Liu, Yaw-Jen; Lyu, Ping-Chiang

2008-09-01

Plant nonspecific lipid transfer proteins (nsLTPs) are small, basic proteins constituted mainly of alpha-helices and stabilized by four conserved disulfide bridges. They are characterized by the presence of a tunnel-like hydrophobic cavity, capable of transferring various lipid molecules between lipid bilayers in vitro. In this study, molecular dynamics (MD) simulations were performed at room temperature to investigate the effects of lipid binding on the dynamic properties of rice nsLTP1. Rice nsLTP1, either in the free form or complexed with one or two lipids was subjected to MD simulations. The C-terminal loop was very flexible both before and after lipid binding, as revealed by calculating the root-mean-square fluctuation. After lipid binding, the flexibility of some residues that were not in direct contact with lipid molecules increased significantly, indicating an increase of entropy in the region distal from the binding site. Essential dynamics analysis revealed clear differences in motion between unliganded and liganded rice nsLTP1s. In the free form of rice nsLTP1, loop1 exhibited the largest directional motion. This specific essential motion mode diminished after binding one or two lipid molecules. To verify the origin of the essential motion observed in the free form of rice nsLTP1, we performed multiple sequence alignments to probe the intrinsic motion encoded in the primary sequence. We found that the amino acid sequence of loop1 is highly conserved among plant nsLTP1s, thus revealing its functional importance during evolution. Furthermore, the sequence of loop1 is composed mainly of amino acids with short side chains. In this study, we show that MD simulations, together with essential dynamics analysis, can be used to determine structural and dynamic differences of rice nsLTP1 upon lipid binding. 2008 Wiley-Liss, Inc.

Movement of Potassium Ions inside KcsA in the High Concentration Regime using a Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Kim, Myojeong; Jo, Byeong Chul; Yoon, Hyun Jung; Wu, Sangwook; Thangappan, Jayaraman; Eun, Changsun

2018-05-01

The selectivity and conduction specificity of the KcsA channel toward potassium ions is crucial to the activity of this protein and this channel is intricately associated with several osmotic regulation and neuronal signaling processes. Despite multi-ion characteristics, the selective conduction behavior of KcsA is controlled by the size and distance specific electrostatic interaction between the selected residues and the potassium ions. The mechanism describing the movement of potassium ions in the channel and the conformational changes to KcsA that facilitate ion movement were investigated by a molecular dynamics (MD) simulation. In this study, we analyze the movement of potassium ions and water molecules at various time intervals during a 90 ns molecular dynamics simulation in the high potassium ion concentration regime and in the absence of the voltage. Examination of specific (3.6, 17.3, 43.38 and 43.44 ns) simulation periods revealed that key residues in the selectivity filter of KcsA influence the movement of potassium ions in the channel.

Virtual Screening and Molecular Dynamics Simulations from a Bank of Molecules of the Amazon Region Against Functional NS3-4A Protease-Helicase Enzyme of Hepatitis C Virus.

PubMed

Pinheiro, Alan Sena; Duarte, Jaqueline Bianca Carvalho; Alves, Cláudio Nahum; de Molfetta, Fábio Alberto

2015-07-01

Hepatitis C virus (HCV) infection is a disease that affects approximately 3% of the global population and requires new therapeutic agents without the inconvenience associated with current anti-HCV treatment. This paper reports on a study of a virtual screening and a molecular dynamics simulation of compounds derived from natural products from the Amazon region that are potentially effective against the NS3-4A enzyme of HCV, which plays an important role in the replication process of this virus. According to the results of the molecular docking calculations and subsequent consensual analysis, the best scored compounds showed interactions between hydrogen and residues of the catalytic triad as well as interactions with residues that guide ligands to the active site of the enzyme. They also showed stability in the molecular dynamics simulation, as the structures preserved important interactions at the active site of the enzyme. The root mean square deviation (RMSD) values were stabilized at the end of the simulation time. Such compounds are considered promising as novel therapies against HCV.

Temporal variations of electron density and temperature in Kr/Ne/H2 photoionized plasma induced by nanosecond pulses from extreme ultraviolet source

NASA Astrophysics Data System (ADS)

Saber, I.; Bartnik, A.; Wachulak, P.; Skrzeczanowski, W.; Jarocki, R.; Fiedorowicz, H.

2017-06-01

Spectral investigations of low-temperature photoionized plasmas created in a Kr/Ne/H2 gas mixture were performed. The low-temperature plasmas were generated by gas mixture irradiation using extreme ultraviolet pulses from a laser-plasma source. Emission spectra in the ultraviolet/visible range from the photoionized plasmas contained lines that mainly corresponded to neutral atoms and singly charged ions. Temporal variations in the plasma electron temperature and electron density were studied using different characteristic emission lines at various delay times. Results, based on Kr II lines, showed that the electron temperature decreased from 1.7 to 0.9 eV. The electron densities were estimated using different spectral lines at each delay time. In general, except for the Hβ line, in which the electron density decreased from 3.78 × 1016 cm-3 at 200 ns to 5.77 × 1015 cm-3 at 2000 ns, most of the electron density values measured from the different lines were of the order of 1015 cm-3 and decreased slightly while maintaining the same order when the delay time increased. The time dependences of the measured and simulated intensities of a spectral line of interest were also investigated. The validity of the partial or full local thermodynamic equilibrium (LTE) conditions in plasma was explained based on time-resolved electron density measurements. The partial LTE condition was satisfied for delay times in the 200 ns to 1500 ns range. The results are summarized, and the dominant basic atomic processes in the gas mixture photoionized plasma are discussed.

Charge transfer efficiency improvement of 4T pixel for high speed CMOS image sensor

NASA Astrophysics Data System (ADS)

Jin, Xiangliang; Liu, Weihui; Yang, Hongjiao; Tang, Lizhen; Yang, Jia

2015-03-01

The charge transfer efficiency improvement method is proposed by optimizing the electrical potential distribution along the transfer path from the PPD to the FD. In this work, we present a non-uniform doped transfer transistor channel, with the adjustments to the overlap length between the CPIA layer and the transfer gate, and the overlap length between the SEN layer and transfer gate. Theory analysis and TCAD simulation results show that the density of the residual charge reduces from 1e11 /cm3 to 1e9 /cm3, and the transfer time reduces from 500 ns to 143 ns, and the charge transfer efficiency is about 77 e-/ns. This optimizing design effectively improves the charge transfer efficiency of 4T pixel and the performance of 4T high speed CMOS image sensor.

Normal saline as a natural intravascular contrast agent for dynamic perfusion-weighted MRI of the brain: Proof of concept at 1.5T.

PubMed

Jara, Hernán; Mian, Asim; Sakai, Osamu; Anderson, Stephan W; Horn, Mitchel J; Norbash, Alexander M; Soto, Jorge A

2016-12-01

Gadolinium-based contrast agents have associated risks. Normal saline (NS) is a nontoxic sodium chloride water solution that can significantly increase the magnetic resonance imaging (MRI) relaxation times of blood via transient hemodilution (THD). The purpose of this pilot study was to test in vivo in the head the potential of normal saline as a safer, exogenous perfusion contrast agent. This Health Insurance Portability and Accountability Act (HIPAA)-compliant prospective study was approved by the local Institutional Review Board (IRB): 12 patients were scanned with T 1 -weighted inversion recovery turbo spin echo pulse sequence at 1.5T. The dynamic inversion recovery pulse sequence was run before, during, and after the NS injection for up to 5 minutes: 100 ml of NS was power-injected via antecubital veins at 3-4 ml/s. Images were processed to map maximum enhancement area-under-the-curve, time-to-peak, and mean-transit-time. These maps were used to identify the areas showing significant NS injection-related signal and to generate enhancement time curves. Hardware and pulse sequence stability were studied via phantom experimentation. Main features of the time curves were tested against theoretical modeling of THD signal effects using inversion recovery pulse sequences. Pearson correlation coefficient (R) mapping was used to differentiate genuine THD effects from motion confounders and noise. The scans of 8 out of 12 patients showed NS injection-related effects that correlate in magnitude with tissue type (gray matter ∼15% and white matter ∼3%). Motion artifacts prevented ascertaining NS signal effects in the remaining four patients. Positive and negative time curves were observed in vivo and this dual THD signal polarity was also observed in the theoretical simulations. R-histograms that were approximately constant in the range 0.1 < |R| < 0.8 and leading to correlation fractions of F corr (|R| > 0.5) = 0.45 and 0.59 were found to represent scans with genuine THD signal effects. A measurable perfusion effect in brain tissue was demonstrated in vivo using NS as an injectable intravascular contrast agent. J. Magn. Reson. Imaging 2016;44:1580-1591. © 2016 International Society for Magnetic Resonance in Medicine.

NUCLEOSYNTHESIS CONSTRAINTS ON THE NEUTRON STAR-BLACK HOLE MERGER RATE

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

Bauswein, A.; Ardevol Pulpillo, R.; Janka, H.-T.

2014-11-01

We derive constraints on the time-averaged event rate of neutron star-black hole (NS-BH) mergers by using estimates of the population-integrated production of heavy rapid neutron-capture (r-process) elements with nuclear mass numbers A > 140 by such events in comparison to the Galactic repository of these chemical species. Our estimates are based on relativistic hydrodynamical simulations convolved with theoretical predictions of the binary population. This allows us to determine a strict upper limit of the average NS-BH merger rate of ∼6× 10{sup –5} per year. We quantify the uncertainties of this estimate to be within factors of a few mostly becausemore » of the unknown BH spin distribution of such systems, the uncertain equation of state of NS matter, and possible errors in the Galactic content of r-process material. Our approach implies a correlation between the merger rates of NS-BH binaries and of double NS systems. Predictions of the detection rate of gravitational-wave signals from such compact object binaries by Advanced LIGO and Advanced Virgo on the optimistic side are incompatible with the constraints set by our analysis.« less

Accretion from a clumpy massive-star wind in supergiant X-ray binaries

NASA Astrophysics Data System (ADS)

El Mellah, I.; Sundqvist, J. O.; Keppens, R.

2018-04-01

Supergiant X-ray binaries (SgXB) host a compact object, often a neutron star (NS), orbiting an evolved O/B star. Mass transfer proceeds through the intense line-driven wind of the stellar donor, a fraction of which is captured by the gravitational field of the NS. The subsequent accretion process on to the NS is responsible for the abundant X-ray emission from SgXB. They also display peak-to-peak variability of the X-ray flux by a factor of a few 10-100, along with changes in the hardness ratios possibly due to varying absorption along the line of sight. We use recent radiation-hydrodynamic simulations of inhomogeneities (a.k.a. clumps) in the non-stationary wind of massive hot stars to evaluate their impact on the time-variable accretion process. For this, we run 3D hydrodynamic simulations of the wind in the vicinity of the accretor to investigate the formation of the bow shock and follow the inhomogeneous flow over several spatial orders of magnitude, down to the NS magnetosphere. In particular, we show that the impact of the wind clumps on the time variability of the intrinsic mass accretion rate is severely tempered by the crossing of the shock, compared to the purely ballistic Bondi-Hoyle-Lyttleton estimation. We also account for the variable absorption due to clumps passing by the line of sight and estimate the final effective variability of the column density and mass accretion rate for different orbital separations. Finally, we compare our results to the most recent analysis of the X-ray flux and the hardness ratio in Vela X-1.

Early Recognition of Chronic Traumatic Encephalopathy through FDDNP PET Imaging

DTIC Science & Technology

2016-10-01

several cognitive measures: Table 3: Uptake and Verbal Processi Psychomo Reaction cognitive tests Memory ng Speed tor Speed Time amygdala, ns ns ns Ns... hippocampus ns ns ns Ns parahippocampal gyrus ns -.437* -.313 .374 brainstem ns ns ns Ns temporal ns ns ns Ns We have also conducted analyses of

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

PubMed

Toofanny, Rudesh D; Simms, Andrew M; Beck, David A C; Daggett, Valerie

2011-08-10

Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008.

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

PubMed Central

2011-01-01

Background Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Results Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. Conclusions The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008. PMID:21831299

Design of the biosonar simulator for dolphin's clicks waveform reproduction

NASA Astrophysics Data System (ADS)

Ishii, Ken; Akamatsu, Tomonari; Hatakeyama, Yoshimi

1992-03-01

The emitted clicks of Dall's porpoises consist of a pulse train of burst signals with an ultrasonic carrier frequency. The authors have designed a biosonar simulator to reproduce the waveforms associated with a dolphin's clicks underwater. The total reproduction system consists of a click signal acquisition block, a waveform analysis block, a memory unit, a click simulator, and a underwater, ultrasonic wave transmitter. In operation, data stored in an EPROM (Erasable Programmable Read Only Memory) are read out sequentially by a fast clock and converted to analog output signals. Then an ultrasonic power amplifier reproduces these signals through a transmitter. The click signal replaying block is referred to as the BSS (Biosonar Simulator). This is what simulates the clicks. The details of the BSS are described in this report. A unit waveform is defined. The waveform is divided into a burst period and a waiting period. Clicks are a sequence based on a unit waveform, and digital data are sequentially read out from an EPROM of waveform data. The basic parameters of the BSS are as follows: (1) reading clock, 100 ns to 25.4 microseconds; (2) number of reading clock, 34 to 1024 times; (3) counter clock in a waiting period, 100 ns to 25.4 microseconds; (4) number of counter clock, zero to 16,777,215 times; (5) number of burst/waiting repetition cycle, one to 128 times; and (6) transmission level adjustment by a programmable attenuator, zero to 86.5 dB. These basic functions enable the BSS to replay clicks of Dall's porpoise precisely.

Remote detection of canopy water stress in coniferous forests using the NS001 Thematic Mapper Simulator and the thermal infrared multispectral scanner

NASA Technical Reports Server (NTRS)

Pierce, Lars L.; Running, Steven W.; Riggs, George A.

1990-01-01

Water stress was induced in two coniferous forest stands in West Germany by severing tree sapwood. Leaf water potential, Psi(L), measurements indicated that maximum, naturally occurring levels of water stress developed in the stressed plots while control plots exhibited natural diurnal trends. Images of each site were obtained with the Thematic Mapper Simulator (NS001) and the Thermal Infrared Multispectral Scanner (TIMS) 12 to 15 days after stress induction. NS001 bands 2 to 6, NS001 indices combining bands 4 and 6, and NS001 and TIMS thermal bands showed significant radiance differences between stressed and control plots when large differences in Psi(L) and relative water content (RWC) existed during the morning overflights at Munich. However, the NS001 and TIMS sensors could not detect the slightly smaller differences in Psi(L) and RWC during the Munich afternoon and Frankfurt overflights. The results suggest that routine detection of canopy water stress under operational conditions is difficult utilizing current sensor technology.

Anharmonicity and self-similarity of the free energy landscape of protein G.

PubMed

Pontiggia, F; Colombo, G; Micheletti, C; Orland, H

2007-01-26

The near-native free-energy landscape of protein G is investigated through 0.4-micros-long atomistic molecular dynamics simulations in an explicit solvent. A theoretical and computational framework is used to assess the time dependence of salient thermodynamical features. While the quasiharmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free-energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.

Spin Complicates Eccentric BH-NS Mergers

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2015-08-01

When a neutron star (NS) has a glancing encounter with a black hole (BH), its spin has a significant effect on the outcome, according to new simulations run by William East of Stanford University and his collaborators. Spotting an Eccentric Merger. In a traditional BH-NS merger, the two objects orbit each other quasi-circularly as they spiral in. But there's another kind of merger that's possible in high-density environments like galactic nuclei or globular clusters: a dynamical capture merger, in which a NS and BH pass each other just close enough that the gravity of the black hole "catches" the NS, leading the two objects to merge with very eccentric orbits. During an eccentric merger, the NS can be torn apart -- at which point some fraction of the tidally-disrupted material will escape the system, while some fraction instead accretes back onto the BH. Knowing these fractions is important for being able to model the expected electromagnetic signatures for the merger: the unbound material can power transients like kilonovae, whereas the accreting material may be the cause of short gamma-ray bursts. The amount of material available for events like these would change their observable strengths. Testing the Effects of Spin. To see whether NS spin has an impact on the behavior of the merger, East and collaborators use a general-relativistic hydrodynamic code to simulate the glancing encounter of a BH and a NS with dimensionless spin between a=0 (non-spinning) and a=0.756 (rotation period of 1 ms). They also vary the separation of the first encounter. The group finds that changing the NS's spin can change a number of outcomes of the merger. To start with, it can affect whether the NS is captured by the BH, or if the encounter is glancing and then both objects carry on their merry way. And if the NS is trapped by the BH and torn apart, then the higher the NS's spin, the more matter outside of the BH ends up unbound, instead of getting trapped into an accretion disk around the BH. As a result of these simulations, the authors argue that the spin of NSs in dynamical capture mergers is crucially important for correctly modeling the observational signatures that might come out of them. Citation: William E. East et al. 2015 ApJ, 807, L3.

Time resolution of the plastic scintillator strips with matrix photomultiplier readout for J-PET tomograph.

PubMed

Moskal, P; Rundel, O; Alfs, D; Bednarski, T; Białas, P; Czerwiński, E; Gajos, A; Giergiel, K; Gorgol, M; Jasińska, B; Kamińska, D; Kapłon, Ł; Korcyl, G; Kowalski, P; Kozik, T; Krzemień, W; Kubicz, E; Niedźwiecki, Sz; Pałka, M; Raczyński, L; Rudy, Z; Sharma, N G; Słomski, A; Silarski, M; Strzelecki, A; Wieczorek, A; Wiślicki, W; Witkowski, P; Zieliński, M; Zoń, N

2016-03-07

Recent tests of a single module of the Jagiellonian Positron Emission Tomography system (J-PET) consisting of 30 cm long plastic scintillator strips have proven its applicability for the detection of annihilation quanta (0.511 MeV) with a coincidence resolving time (CRT) of 0.266 ns. The achieved resolution is almost by a factor of two better with respect to the current TOF-PET detectors and it can still be improved since, as it is shown in this article, the intrinsic limit of time resolution for the determination of time of the interaction of 0.511 MeV gamma quanta in plastic scintillators is much lower. As the major point of the article, a method allowing to record timestamps of several photons, at two ends of the scintillator strip, by means of matrix of silicon photomultipliers (SiPM) is introduced. As a result of simulations, conducted with the number of SiPM varying from 4 to 42, it is shown that the improvement of timing resolution saturates with the growing number of photomultipliers, and that the [Formula: see text] configuration at two ends allowing to read twenty timestamps, constitutes an optimal solution. The conducted simulations accounted for the emission time distribution, photon transport and absorption inside the scintillator, as well as quantum efficiency and transit time spread of photosensors, and were checked based on the experimental results. Application of the [Formula: see text] matrix of SiPM allows for achieving the coincidence resolving time in positron emission tomography of [Formula: see text]0.170 ns for 15 cm axial field-of-view (AFOV) and [Formula: see text]0.365 ns for 100 cm AFOV. The results open perspectives for construction of a cost-effective TOF-PET scanner with significantly better TOF resolution and larger AFOV with respect to the current TOF-PET modalities.

Time resolution of the plastic scintillator strips with matrix photomultiplier readout for J-PET tomograph

NASA Astrophysics Data System (ADS)

Moskal, P.; Rundel, O.; Alfs, D.; Bednarski, T.; Białas, P.; Czerwiński, E.; Gajos, A.; Giergiel, K.; Gorgol, M.; Jasińska, B.; Kamińska, D.; Kapłon, Ł.; Korcyl, G.; Kowalski, P.; Kozik, T.; Krzemień, W.; Kubicz, E.; Niedźwiecki, Sz; Pałka, M.; Raczyński, L.; Rudy, Z.; Sharma, N. G.; Słomski, A.; Silarski, M.; Strzelecki, A.; Wieczorek, A.; Wiślicki, W.; Witkowski, P.; Zieliński, M.; Zoń, N.

2016-03-01

Recent tests of a single module of the Jagiellonian Positron Emission Tomography system (J-PET) consisting of 30 cm long plastic scintillator strips have proven its applicability for the detection of annihilation quanta (0.511 MeV) with a coincidence resolving time (CRT) of 0.266 ns. The achieved resolution is almost by a factor of two better with respect to the current TOF-PET detectors and it can still be improved since, as it is shown in this article, the intrinsic limit of time resolution for the determination of time of the interaction of 0.511 MeV gamma quanta in plastic scintillators is much lower. As the major point of the article, a method allowing to record timestamps of several photons, at two ends of the scintillator strip, by means of matrix of silicon photomultipliers (SiPM) is introduced. As a result of simulations, conducted with the number of SiPM varying from 4 to 42, it is shown that the improvement of timing resolution saturates with the growing number of photomultipliers, and that the 2× 5 configuration at two ends allowing to read twenty timestamps, constitutes an optimal solution. The conducted simulations accounted for the emission time distribution, photon transport and absorption inside the scintillator, as well as quantum efficiency and transit time spread of photosensors, and were checked based on the experimental results. Application of the 2× 5 matrix of SiPM allows for achieving the coincidence resolving time in positron emission tomography of ≈ 0.170 ns for 15 cm axial field-of-view (AFOV) and ≈ 0.365 ns for 100 cm AFOV. The results open perspectives for construction of a cost-effective TOF-PET scanner with significantly better TOF resolution and larger AFOV with respect to the current TOF-PET modalities.

Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling.

PubMed

Martins-Costa, Marilia T C; Ruiz-López, Manuel F

2017-04-15

We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Rate-Dependent Behavior of the Amorphous Phase of Spider Dragline Silk

PubMed Central

Patil, Sandeep P.; Markert, Bernd; Gräter, Frauke

2014-01-01

The time-dependent stress-strain behavior of spider dragline silk was already observed decades ago, and has been attributed to the disordered sequences in silk proteins, which compose the soft amorphous matrix. However, the actual molecular origin and magnitude of internal friction within the amorphous matrix has remained inaccessible, because experimentally decomposing the mechanical response of the amorphous matrix from the embedded crystalline units is challenging. Here, we used atomistic molecular dynamics simulations to obtain friction forces for the relative sliding of peptide chains of Araneus diadematus spider silk within bundles of these chains as a representative unit of the amorphous matrix in silk fibers. We computed the friction coefficient and coefficient of viscosity of the amorphous phase to be in the order of 10−6 Ns/m and 104 Ns/m2, respectively, by extrapolating our simulation data to the viscous limit. Finally, we used a finite element method for the amorphous phase, solely based on parameters derived from molecular dynamics simulations including the newly determined coefficient of viscosity. With this model the time scales of stress relaxation, creep, and hysteresis were assessed, and found to be in line with the macroscopic time-dependent response of silk fibers. Our results suggest the amorphous phase to be the primary source of viscosity in silk and open up the avenue for finite element method studies of silk fiber mechanics including viscous effects. PMID:24896131

Simulated fissioning of uranium and testing of the fission-track dating method

USGS Publications Warehouse

McGee, V.E.; Johnson, N.M.; Naeser, C.W.

1985-01-01

A computer program (FTD-SIM) faithfully simulates the fissioning of 238U with time and 235U with neutron dose. The simulation is based on first principles of physics where the fissioning of 238U with the flux of time is described by Ns = ??f 238Ut and the fissioning of 235U with the fluence of neutrons is described by Ni = ??235U??. The Poisson law is used to set the stochastic variation of fissioning within the uranium population. The life history of a given crystal can thus be traced under an infinite variety of age and irradiation conditions. A single dating attempt or up to 500 dating attempts on a given crystal population can be simulated by specifying the age of the crystal population, the size and variation in the areas to be counted, the amount and distribution of uranium, the neutron dose to be used and its variation, and the desired ratio of 238U to 235U. A variety of probability distributions can be applied to uranium and counting-area. The Price and Walker age equation is used to estimate age. The output of FTD-SIM includes the tabulated results of each individual dating attempt (sample) on demand and/or the summary statistics and histograms for multiple dating attempts (samples) including the sampling age. An analysis of the results from FTD-SIM shows that: (1) The external detector method is intrinsically more precise than the population method. (2) For the external detector method a correlation between spontaneous track count, Ns, and induced track count, Ni, results when the population of grains has a stochastic uranium content and/or when the counting areas between grains are stochastic. For the population method no correlation can exist. (3) In the external detector method the sampling distribution of age is independent of the number of grains counted. In the population method the sampling distribution of age is highly dependent on the number of grains counted. (4) Grains with zero-track counts, either in Ns or Ni, are in integral part of fissioning theory and under certain circumstances must be included in any estimate of age. (5) In estimating standard error of age the standard error of Ns and Ni and ?? must be accurately estimated and propagated through the age equation. Several statistical models are presently available to do so. ?? 1985.

Post-fall-back evolution of multipolar magnetic fields and radio pulsar activation

NASA Astrophysics Data System (ADS)

Igoshev, A. P.; Elfritz, J. G.; Popov, S. B.

2016-11-01

It has long been unclear if the small-scale magnetic structures on the neutron star (NS) surface could survive the fall-back episode. The study of the Hall cascade by Cumming, Arras & Zweibel hinted that energy in small-scales structures should dissipate on short time-scales. Our new 2D magneto-thermal simulations suggest the opposite. For the first ˜10 kyr after the fall-back episode with accreted mass 10-3 M⊙, the observed NS magnetic field appears dipolar, which is insensitive to the initial magnetic topology. In framework of the Ruderman & Sutherland, vacuum gap model during this interval, non-thermal radiation is strongly suppressed. After this time, the initial (I.e. multipolar) structure begins to re-emerge through the NS crust. We distinguish three evolutionary epochs for the re-emergence process: the growth of internal toroidal field, the advection of buried poloidal field, and slow Ohmic diffusion. The efficiency of the first two stages can be enhanced when small-scale magnetic structure is present. The efficient re-emergence of high-order harmonics might significantly affect the curvature of the magnetospheric field lines in the emission zone. So, only after few 104 yr would be the NS starts shining as a pulsar again, which is in correspondence with radio silence of central compact objects. In addition, these results can explain the absence of good candidates for thermally emitting NSs with freshly re-emerged field among radio pulsars (), as NSs have time to cool down, and supernova remnants can already dissipate.

MODELS OF KILONOVA/MACRONOVA EMISSION FROM BLACK HOLE–NEUTRON STAR MERGERS

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

Kawaguchi, Kyohei; Shibata, Masaru; Kyutoku, Koutarou

2016-07-01

Black hole–neutron star (BH–NS) mergers are among the most promising gravitational-wave sources for ground-based detectors, and gravitational waves from BH–NS mergers are expected to be detected in the next few years. The simultaneous detection of electromagnetic counterparts with gravitational waves would provide rich information about merger events. Among the possible electromagnetic counterparts from BH–NS mergers is the so-called kilonova/macronova, emission powered by the decay of radioactive r-process nuclei, which is one of the best targets for follow-up observations. We derive fitting formulas for the mass and the velocity of ejecta from a generic BH–NS merger based on recently performed numerical-relativitymore » simulations. We combine these fitting formulas with a new semi-analytic model for a BH–NS kilonova/macronova lightcurve, which reproduces the results of radiation-transfer simulations. Specifically, the semi-analytic model reproduces the results of each band magnitude obtained by the previous radiation-transfer simulations within ∼1 mag. By using this semi-analytic model we found that, at 400 Mpc, the kilonova/macronova is as bright as 22–24 mag for cases with a small chirp mass and a high black hole spin, and >28 mag for a large chirp mass and a low black hole spin. We also apply our model to GRB 130603B as an illustration, and show that a BH–NS merger with a rapidly spinning black hole and a large neutron star radius is favored.« less

Molecular dynamics study of unfolding of lysozyme in water and its mixtures with dimethyl sulfoxide.

PubMed

Sedov, Igor A; Magsumov, Timur I

2017-09-01

All-atom explicit solvent molecular dynamics was used to study the process of unfolding of hen egg white lysozyme in water and mixtures of water with dimethyl sulfoxide at different compositions. We have determined the kinetic parameters of unfolding at a constant temperature 450K. For each run, the time of disruption of the tertiary structure of lysozyme t u was defined as the moment when a certain structural criterion computed from the trajectory reaches its critical value. A good agreement is observed between the results obtained using several different criteria. The secondary structure according to DSSP calculations is found to be partially unfolded to the moment of disruption of tertiary structure, but some of its elements keep for a long time after that. The values of t u averaged over ten 30ns-long trajectories for each solvent composition are shown to decrease very rapidly with addition of dimethyl sulfoxide, and rather small amounts of dimethyl sulfoxide are found to change the pathway of unfolding. In pure water, despite the loss of tertiary contacts and disruption of secondary structure elements, the protein preserves its compact globular state at least over 130ns of simulation, while even at 5mol percents of dimethyl sulfoxide it loses its compactness within 30ns. The proposed methodology is a generally applicable tool to quantify the rate of protein unfolding in simulation studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Influence of Voltage Rise Time for Oxidation Treatment of NO in Simulated Exhausted Gas by Polarity-Reversed Pulse Discharge

NASA Astrophysics Data System (ADS)

Shinmoto, Kazuya; Kadowaki, Kazunori; Nishimoto, Sakae; Kitani, Isamu

This paper describes experimental study on NO removal from a simulated exhausted-gas using repetitive surface discharge on a glass barrier subjected to polarity-reversed voltage pulses. The very fast polarity-reversal with a rise time of 20ns is caused by direct grounding of a charged coaxial cable of 10m in length. Influence of voltage rise time on energy efficiency for NO removal is studied. Results of NO removal using a barrier-type plasma reactor with screw-plane electrode system indicates that the energy efficiency for the very fast polarity reversal caused by direct grounding becomes higher than that for the slower polarity reversal caused by grounding through an inductor at the cable end. The energy efficiency for the direct grounding is about 80g/kWh for 50% NO removal ratio and is about 60g/kWh for 100% NO removal ratio. Very intense discharge light is observed at the initial time of 10ns for the fast polarity reversal, whereas the intensity in the initial discharge light for the slower polarity reversal is relatively small. To confirm the effectiveness of the polarity-reversed pulse application, comparison of the energy efficiency between the polarity-reversed voltage pulse and ac 60Hz voltage will be presented.

The mechanism by which P250L mutation impairs flavivirus-NS1 dimerization: an investigation based on molecular dynamics simulations.

PubMed

Oliveira, Edson R A; de Alencastro, Ricardo B; Horta, Bruno A C

2016-09-01

The flavivirus non-structural protein 1 (NS1) is a conserved glycoprotein with as yet undefined biological function. This protein dimerizes when inside infected cells or associated to cell membranes but also forms lipid-associated hexamers when secreted to the extracellular space. A single amino acid substitution (P250L) is capable of preventing the dimerization of NS1 resulting in lower virulence and slower virus replication. In this work, based on molecular dynamics simulations of the dengue-2 virus NS1 [Formula: see text]-ladder monomer as a core model, we found that this mutation can induce several conformational changes that importantly affect critical monomer-monomer interactions. Based on additional simulations, we suggest a mechanism by which a highly orchestrated sequence of events propagate the local perturbations around the mutation site towards the dimer interface. The elucidation of such a mechanism could potentially support new strategies for rational production of live-attenuated vaccines and highlights a step forward in the development of novel anti-flavivirus measures.

SU-G-IeP4-12: Performance of In-111 Coincident Gamma-Ray Counting: A Monte Carlo Simulation

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

Pahlka, R; Kappadath, S; Mawlawi, O

2016-06-15

Purpose: The decay of In-111 results in a non-isotropic gamma-ray cascade, which is normally imaged using a gamma camera. Creating images with a gamma camera using coincident gamma-rays from In-111 has not been previously studied. Our objective was to explore the feasibility of imaging this cascade as coincidence events and to determine the optimal timing resolution and source activity using Monte Carlo simulations. Methods: GEANT4 was used to simulate the decay of the In-111 nucleus and to model the gamma camera. Each photon emission was assigned a timestamp, and the time delay and angular separation for the second gamma-ray inmore » the cascade was consistent with the known intermediate state half-life of 85ns. The gamma-rays are transported through a model of a Siemens dual head Symbia “S” gamma camera with a 5/8-inch thick crystal and medium energy collimators. A true coincident event was defined as a single 171keV gamma-ray followed by a single 245keV gamma-ray within a specified time window (or vice versa). Several source activities (ranging from 10uCi to 5mCi) with and without incorporation of background counts were then simulated. Each simulation was analyzed using varying time windows to assess random events. The noise equivalent count rate (NECR) was computed based on the number of true and random counts for each combination of activity and time window. No scatter events were assumed since sources were simulated in air. Results: As expected, increasing the timing window increased the total number of observed coincidences albeit at the expense of true coincidences. A timing window range of 200–500ns maximizes the NECR at clinically-used source activities. The background rate did not significantly alter the maximum NECR. Conclusion: This work suggests coincident measurements of In-111 gamma-ray decay can be performed with commercial gamma cameras at clinically-relevant activities. Work is ongoing to assess useful clinical applications.« less

Scramjet Combustor Simulations Using Reduced Chemical Kinetics for Practical Fuels

DTIC Science & Technology

2003-12-01

the aerospace industry in reducing prototype and testing costs and the time needed to bring products to market . Accurate simulation of chemical...JP-8 kinetics and soot models into the UNICORN CFD code (Montgomery et al., 2003a) NSF Phase I and II SBIRs for development of a computer-assisted...divided by diameter QSS quasi-steady state REI Reaction Engineering International UNICORN UNsteady Ignition and COmbustion with ReactioNs VULCAN Viscous Upwind aLgorithm for Complex flow ANalysis

A framework for visualization of battlefield network behavior

NASA Astrophysics Data System (ADS)

Perzov, Yury; Yurcik, William

2006-05-01

An extensible network simulation application was developed to study wireless battlefield communications. The application monitors node mobility and depicts broadcast and unicast traffic as expanding rings and directed links. The network simulation was specially designed to support fault injection to show the impact of air strikes on disabling nodes. The application takes standard ns-2 trace files as an input and provides for performance data output in different graphical forms (histograms and x/y plots). Network visualization via animation of simulation output can be saved in AVI format that may serve as a basis for a real-time battlefield awareness system.

The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment

PubMed Central

Condic-Jurkic, Karmen; Subramanian, Nandhitha; Mark, Alan E.

2018-01-01

Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations, many researchers have turned to molecular dynamics simulation studies in order to investigate different aspects of P-gp function. However, such studies are challenging and caution is required when interpreting the results. P-gp is highly flexible and the time scale on which it can be simulated is limited. There is also uncertainty regarding the accuracy of the various crystal structures available, let alone the structure of the protein in a physiologically relevant environment. In this study, three alternative structural models of mouse P-gp (3G5U, 4KSB, 4M1M), all resolved to 3.8 Å, were used to initiate sets of simulations of P-gp in a membrane environment in order to determine: a) the sensitivity of the results to differences in the starting configuration; and b) the extent to which converged results could be expected on the times scales commonly simulated for this system. The simulations suggest that the arrangement of the nucleotide binding domains (NBDs) observed in the crystal structures is not stable in a membrane environment. In all simulations, the NBDs rapidly associated (within 10 ns) and changes within the transmembrane helices were observed. The secondary structure within the transmembrane domain was best preserved in the 4M1M model under the simulation conditions used. However, the extent to which replicate simulations diverged on a 100 to 200 ns timescale meant that it was not possible to draw definitive conclusions as to which structure overall was most stable, or to obtain converged and reliable results for any of the properties examined. The work brings into question the reliability of conclusions made in regard to the nature of specific interactions inferred from previous simulation studies on this system involving similar sampling times. It also highlights the need to demonstrate the statistical significance of any results obtained in simulations of large flexible proteins, especially where the initial structure is uncertain. PMID:29370310

The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment.

PubMed

Condic-Jurkic, Karmen; Subramanian, Nandhitha; Mark, Alan E; O'Mara, Megan L

2018-01-01

Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations, many researchers have turned to molecular dynamics simulation studies in order to investigate different aspects of P-gp function. However, such studies are challenging and caution is required when interpreting the results. P-gp is highly flexible and the time scale on which it can be simulated is limited. There is also uncertainty regarding the accuracy of the various crystal structures available, let alone the structure of the protein in a physiologically relevant environment. In this study, three alternative structural models of mouse P-gp (3G5U, 4KSB, 4M1M), all resolved to 3.8 Å, were used to initiate sets of simulations of P-gp in a membrane environment in order to determine: a) the sensitivity of the results to differences in the starting configuration; and b) the extent to which converged results could be expected on the times scales commonly simulated for this system. The simulations suggest that the arrangement of the nucleotide binding domains (NBDs) observed in the crystal structures is not stable in a membrane environment. In all simulations, the NBDs rapidly associated (within 10 ns) and changes within the transmembrane helices were observed. The secondary structure within the transmembrane domain was best preserved in the 4M1M model under the simulation conditions used. However, the extent to which replicate simulations diverged on a 100 to 200 ns timescale meant that it was not possible to draw definitive conclusions as to which structure overall was most stable, or to obtain converged and reliable results for any of the properties examined. The work brings into question the reliability of conclusions made in regard to the nature of specific interactions inferred from previous simulation studies on this system involving similar sampling times. It also highlights the need to demonstrate the statistical significance of any results obtained in simulations of large flexible proteins, especially where the initial structure is uncertain.

FNCS: A Framework for Power System and Communication Networks Co-Simulation

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

Ciraci, Selim; Daily, Jeffrey A.; Fuller, Jason C.

2014-04-13

This paper describes the Fenix framework that uses a federated approach for integrating power grid and communication network simulators. Compared existing approaches, Fenix al- lows co-simulation of both transmission and distribution level power grid simulators with the communication network sim- ulator. To reduce the performance overhead of time synchro- nization, Fenix utilizes optimistic synchronization strategies that make speculative decisions about when the simulators are going to exchange messages. GridLAB-D (a distribution simulator), PowerFlow (a transmission simulator), and ns-3 (a telecommunication simulator) are integrated with the frame- work and are used to illustrate the enhanced performance pro- vided by speculative multi-threadingmore » on a smart grid applica- tion. Our speculative multi-threading approach achieved on average 20% improvement over the existing synchronization methods« less

Will molecular dynamics simulations of proteins ever reach equilibrium?

PubMed

Genheden, Samuel; Ryde, Ulf

2012-06-28

We show that conformational entropies calculated for five proteins and protein-ligand complexes with dihedral-distribution histogramming, the von Mises approach, or quasi-harmonic analysis do not converge to any useful precision even if molecular dynamics (MD) simulations of 380-500 ns length are employed (the uncertainty is 12-89 kJ mol(-1)). To explain this, we suggest a simple protein model involving dihedrals with effective barriers forming a uniform distribution and show that for such a model, the entropy increases logarithmically with time until all significantly populated dihedral states have been sampled, in agreement with the simulations (during the simulations, 52-70% of the available dihedral phase space has been visited). This is also confirmed by the analysis of the trajectories of a 1 ms simulation of bovine pancreatic trypsin inhibitor (31 kJ mol(-1) difference in the entropy between the first and second part of the simulation). Strictly speaking, this means that it is practically impossible to equilibrate MD simulations of proteins. We discuss the implications of such a lack of strict equilibration of protein MD simulations and show that ligand-binding free energies estimated with the MM/GBSA method (molecular mechanics with generalised Born and surface-area solvation) vary by 3-15 kJ mol(-1) during a 500 ns simulation (the higher estimate is caused by rare conformational changes), although they involve a questionable but well-converged normal-mode entropy estimate, whereas free energies estimated by free-energy perturbation vary by less than 0.6 kJ mol(-1) for the same simulation.

Rate-dependent behavior of the amorphous phase of spider dragline silk.

PubMed

Patil, Sandeep P; Markert, Bernd; Gräter, Frauke

2014-06-03

The time-dependent stress-strain behavior of spider dragline silk was already observed decades ago, and has been attributed to the disordered sequences in silk proteins, which compose the soft amorphous matrix. However, the actual molecular origin and magnitude of internal friction within the amorphous matrix has remained inaccessible, because experimentally decomposing the mechanical response of the amorphous matrix from the embedded crystalline units is challenging. Here, we used atomistic molecular dynamics simulations to obtain friction forces for the relative sliding of peptide chains of Araneus diadematus spider silk within bundles of these chains as a representative unit of the amorphous matrix in silk fibers. We computed the friction coefficient and coefficient of viscosity of the amorphous phase to be in the order of 10(-6) Ns/m and 10(4) Ns/m(2), respectively, by extrapolating our simulation data to the viscous limit. Finally, we used a finite element method for the amorphous phase, solely based on parameters derived from molecular dynamics simulations including the newly determined coefficient of viscosity. With this model the time scales of stress relaxation, creep, and hysteresis were assessed, and found to be in line with the macroscopic time-dependent response of silk fibers. Our results suggest the amorphous phase to be the primary source of viscosity in silk and open up the avenue for finite element method studies of silk fiber mechanics including viscous effects. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A novel high performance ESD power clamp circuit with a small area

NASA Astrophysics Data System (ADS)

Zhaonian, Yang; Hongxia, Liu; Li, Li; Qingqing, Zhuo

2012-09-01

A MOSFET-based electrostatic discharge (ESD) power clamp circuit with only a 10 ns RC time constant for a 0.18-μm process is proposed. A diode-connected NMOSFET is used to maintain a long delay time and save area. The special structure overcomes other shortcomings in this clamp circuit. Under fast power-up events, the gate voltage of the clamp MOSFET does not rise as quickly as under ESD events, the special structure can keep the clamp MOSFET thoroughly off. Under a falsely triggered event, the special structure can turn off the clamp MOSFET in a short time. The clamp circuit can also reject the power supply noise effectively. Simulation results show that the clamp circuit avoids fast false triggering events such as a 30 ns/1.8 V power-up, maintains a 1.2 μs delay time and a 2.14 μs turn-off time, and reduces to about 70% of the RC time constant. It is believed that the proposed clamp circuit can be widely used in high-speed integrated circuits.

Use of regional climate model output for hydrologic simulations

USGS Publications Warehouse

Hay, L.E.; Clark, M.P.; Wilby, R.L.; Gutowski, W.J.; Leavesley, G.H.; Pan, Z.; Arritt, R.W.; Takle, E.S.

2002-01-01

Daily precipitation and maximum and minimum temperature time series from a regional climate model (RegCM2) configured using the continental United States as a domain and run on a 52-km (approximately) spatial resolution were used as input to a distributed hydrologic model for one rainfall-dominated basin (Alapaha River at Statenville, Georgia) and three snowmelt-dominated basins (Animas River at Durango. Colorado; east fork of the Carson River near Gardnerville, Nevada: and Cle Elum River near Roslyn, Washington). For comparison purposes, spatially averaged daily datasets of precipitation and maximum and minimum temperature were developed from measured data for each basin. These datasets included precipitation and temperature data for all stations (hereafter, All-Sta) located within the area of the RegCM2 output used for each basin, but excluded station data used to calibrate the hydrologic model. Both the RegCM2 output and All-Sta data capture the gross aspects of the seasonal cycles of precipitation and temperature. However, in all four basins, the RegCM2- and All-Sta-based simulations of runoff show little skill on a daily basis [Nash-Sutcliffe (NS) values range from 0.05 to 0.37 for RegCM2 and -0.08 to 0.65 for All-Sta]. When the precipitation and temperature biases are corrected in the RegCM2 output and All-Sta data (Bias-RegCM2 and Bias-All, respectively) the accuracy of the daily runoff simulations improve dramatically for the snowmelt-dominated basins (NS values range from 0.41 to 0.66 for RegCM2 and 0.60 to 0.76 for All-Sta). In the rainfall-dominated basin, runoff simulations based on the Bias-RegCM2 output show no skill (NS value of 0.09) whereas Bias-All simulated runoff improves (NS value improved from - 0.08 to 0.72). These results indicate that measured data at the coarse resolution of the RegCM2 output can be made appropriate for basin-scale modeling through bias correction (essentially a magnitude correction). However, RegCM2 output, even when bias corrected, does not contain the day-to-day variability present in the All-Sta dataset that is necessary for basin-scale modeling. Future work is warranted to identify the causes for systematic biases in RegCM2 simulations, develop methods to remove the biases, and improve RegCM2 simulations of daily variability in local climate.

Digital Analysis and Sorting of Fluorescence Lifetime by Flow Cytometry

PubMed Central

Houston, Jessica P.; Naivar, Mark A.; Freyer, James P.

2010-01-01

Frequency-domain flow cytometry techniques are combined with modifications to the digital signal processing capabilities of the Open Reconfigurable Cytometric Acquisition System (ORCAS) to analyze fluorescence decay lifetimes and control sorting. Real-time fluorescence lifetime analysis is accomplished by rapidly digitizing correlated, radiofrequency modulated detector signals, implementing Fourier analysis programming with ORCAS’ digital signal processor (DSP) and converting the processed data into standard cytometric list mode data. To systematically test the capabilities of the ORCAS 50 MS/sec analog-to-digital converter (ADC) and our DSP programming, an error analysis was performed using simulated light scatter and fluorescence waveforms (0.5–25 ns simulated lifetime), pulse widths ranging from 2 to 15 µs, and modulation frequencies from 2.5 to 16.667 MHz. The standard deviations of digitally acquired lifetime values ranged from 0.112 to >2 ns, corresponding to errors in actual phase shifts from 0.0142° to 1.6°. The lowest coefficients of variation (<1%) were found for 10-MHz modulated waveforms having pulse widths of 6 µs and simulated lifetimes of 4 ns. Direct comparison of the digital analysis system to a previous analog phase-sensitive flow cytometer demonstrated similar precision and accuracy on measurements of a range of fluorescent microspheres, unstained cells and cells stained with three common fluorophores. Sorting based on fluorescence lifetime was accomplished by adding analog outputs to ORCAS and interfacing with a commercial cell sorter with a radiofrequency modulated solid-state laser. Two populations of fluorescent microspheres with overlapping fluorescence intensities but different lifetimes (2 and 7 ns) were separated to ~98% purity. Overall, the digital signal acquisition and processing methods we introduce present a simple yet robust approach to phase-sensitive measurements in flow cytometry. The ability to simply and inexpensively implement this system on a commercial flow sorter will both allow better dissemination of this technology and better exploit the traditionally underutilized parameter of fluorescence lifetime. PMID:20662090

Nanostructuring of sapphire using time-modulated nanosecond laser pulses

NASA Astrophysics Data System (ADS)

Lorenz, P.; Zagoranskiy, I.; Ehrhardt, M.; Bayer, L.; Zimmer, K.

2017-02-01

The nanostructuring of dielectric surfaces using laser radiation is still a challenge. The IPSM-LIFE (laser-induced front side etching using in-situ pre-structured metal layer) method allows the easy, large area and fast laser nanostructuring of dielectrics. At IPSM-LIFE a metal covered dielectric is irradiated where the structuring is assisted by a self-organized molten metal layer deformation process. The IPSM-LIFE can be divided into two steps: STEP 1: The irradiation of thin metal layers on dielectric surfaces results in a melting and nanostructuring process of the metal layer and partially of the dielectric surface. STEP 2: A subsequent high laser fluence treatment of the metal nanostructures result in a structuring of the dielectric surface. At this study a sapphire substrate Al2O3(1-102) was covered with a 10 nm thin molybdenum layer and irradiated by an infrared laser with an adjustable time-dependent pulse form with a time resolution of 1 ns (wavelength λ = 1064 nm, pulse duration Δtp = 1 - 600 ns, Gaussian beam profile). The laser treatment allows the fabrication of different surface structures into the sapphire surface due to a pattern transfer process. The resultant structures were investigated by scanning electron microscopy (SEM). The process was simulated and the simulation results were compared with experimental results.

Single-event transient imaging with an ultra-high-speed temporally compressive multi-aperture CMOS image sensor.

PubMed

Mochizuki, Futa; Kagawa, Keiichiro; Okihara, Shin-ichiro; Seo, Min-Woong; Zhang, Bo; Takasawa, Taishi; Yasutomi, Keita; Kawahito, Shoji

2016-02-22

In the work described in this paper, an image reproduction scheme with an ultra-high-speed temporally compressive multi-aperture CMOS image sensor was demonstrated. The sensor captures an object by compressing a sequence of images with focal-plane temporally random-coded shutters, followed by reconstruction of time-resolved images. Because signals are modulated pixel-by-pixel during capturing, the maximum frame rate is defined only by the charge transfer speed and can thus be higher than those of conventional ultra-high-speed cameras. The frame rate and optical efficiency of the multi-aperture scheme are discussed. To demonstrate the proposed imaging method, a 5×3 multi-aperture image sensor was fabricated. The average rising and falling times of the shutters were 1.53 ns and 1.69 ns, respectively. The maximum skew among the shutters was 3 ns. The sensor observed plasma emission by compressing it to 15 frames, and a series of 32 images at 200 Mfps was reconstructed. In the experiment, by correcting disparities and considering temporal pixel responses, artifacts in the reconstructed images were reduced. An improvement in PSNR from 25.8 dB to 30.8 dB was confirmed in simulations.

Hydrophobic Collapse of Ubiquitin Generates Rapid Protein-Water Motions.

PubMed

Wirtz, Hanna; Schäfer, Sarah; Hoberg, Claudius; Reid, Korey M; Leitner, David M; Havenith, Martina

2018-06-04

We report time-resolved measurements of the coupled protein-water modes of solvated ubiquitin during protein folding. Kinetic terahertz absorption (KITA) spectroscopy serves as a label-free technique for monitoring large scale conformational changes and folding of proteins subsequent to a sudden T-jump. We report here KITA measurements at an unprecedented time resolution of 500 ns, a resolution 2 orders of magnitude better than those of any previous KITA measurements, which reveal the coupled ubiquitin-solvent dynamics even in the initial phase of hydrophobic collapse. Complementary equilibrium experiments and molecular simulations of ubiquitin solutions are performed to clarify non-equilibrium contributions and reveal the molecular picture upon a change in structure, respectively. On the basis of our results, we propose that in the case of ubiquitin a rapid (<500 ns) initial phase of the hydrophobic collapse from the elongated protein to a molten globule structure precedes secondary structure formation. We find that these very first steps, including large-amplitude changes within the unfolded manifold, are accompanied by a rapid (<500 ns) pronounced change of the coupled protein-solvent response. The KITA response upon secondary structure formation exhibits an opposite sign, which indicates a distinct effect on the solvent-exposed surface.

Drug-polymer interactions at water-crystal interfaces and implications for crystallization inhibition: molecular dynamics simulations of amphiphilic block copolymer interactions with tolazamide crystals.

PubMed

Gao, Yi; Olsen, Kenneth W

2015-07-01

A diblock copolymer, poly(ethylene glycol)-block-poly(lactic acid) (PEG-b-PLA), modulates the crystal growth of tolazamide (TLZ), resulting in a crystal morphology change from needles to plates in aqueous media. To understand this crystal surface drug-polymer interaction, we conducted molecular dynamics simulations on crystal surfaces of TLZ in water containing PEG-b-PLA. A 130-ns simulation of the polymer in a large water box was run before initiating 50 ns simulations with each of the crystal surfaces. The simulations demonstrated differentiated drug-polymer interactions that are consistent with experimental studies. Interaction of PEG-b-PLA with the (001) face occurred more rapidly (≤10 ns) and strongly (total interaction energy of -121.1 kJ/mol/monomer) than that with the (010) face (∼35 ns, -85.4 kJ/mol/monomer). There was little interaction with the (100) face. Hydrophobic and van der Waals (VDW) interactions were the dominant forces, accounting for more than 90% of total interaction energies. It suggests that polymers capable of forming strong hydrophobic and VDW interactions might be more effective in inhibiting crystallization of poorly water-soluble and hydrophobic drugs in aqueous media (such as gastrointestinal fluid) than those with hydrogen-bonding capacities. Such in-depth analysis and understanding facilitate the rational selection of polymers in designing supersaturation-based enabling formulations. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Accretion Disk Outflows from Compact Object Mergers

NASA Astrophysics Data System (ADS)

Metzger, Brian

Nuclear reactions play a key role in the accretion disks and outflows associated with the merger of binary compact objects and the central engines of gamma-ray bursts and supernovae. The proposed research program will investigate the impact of nucleosynthesis on these events and their observable signatures by means of analytic calculations and numerical simulations. One focus of this research is rapid accretion following the tidal disruption of a white dwarf (WD) by a neutron star (NS) or black hole (BH) binary companion. Tidal disruption shreds the WD into a massive torus composed of C, O, and/or He, which undergoes nuclear reactions and burns to increasingly heavier elements as it flows to smaller radii towards the central compact object. The nuclear energy so released is comparable to that released gravitationally, suggesting that burning could drastically alter the structure and stability of the accretion flow. Axisymmetric hydrodynamic simulations of the evolution of the torus including nuclear burning will be performed to explore issues such as the mass budget of the flow (accretion vs. outflows) and its thermal stability (steady burning and accretion vs. runaway explosion). The mass, velocity, and composition of outflows from the disk will be used in separate radiative transfer calculations to predict the lightcurves and spectra of the 56Ni-decay powered optical transients from WD-NS/WD-BH mergers. The possible connection of such events to recently discovered classes of sub-luminous Type I supernovae will be assessed. The coalescence of NS-NS/NS-BH binaries also results in the formation of a massive torus surrounding a central compact object. Three-dimensional magnetohydrodynamic simulations of the long-term evolution of such accretion disks will be performed, which for the first time follow the effects of weak interactions and the nuclear energy released by Helium recombination. The nucleosynthetic yield of disk outflows will be calculated using a detailed nuclear reaction network along characteristic Lagrangian trajectories. Results of these calculations will be used to (1) reassess NS-NS/NS-BH mergers as an astrophysical source of heavy r-process nuclei; and (2) calculate the light curves of the optical transients (`kilonovae') powered by the radioactive decay. Separate work will assess the effects that neutrino irradiation from a long-lived neutron star remnant has on the electron fraction of the disk outflows. The strong contrast between the opacities of proton- and neutron-rich matter imply that the presence and lifetime of such a remnant could be imprinted on the kilonova emission. Our investigation sheds light on the central engines of GRBs and other high-energy transients and hence is relevant to NASA's Swift, MAXI, and Fermi missions. Our results will also impact the interpretation of future observations of supernovae and their galactic environments with the Hubble Space Telescope (HST). Our results will also impact follow-up observations of kilonovae, maximizing the impact of HST to constrain the key open questions such as the progenitors of gamma-ray bursts and the origin of r-process nuclei.

Heating, Hydrodynamics, and Radiation From a Laser Heated Non-LTE High-Z Target

NASA Astrophysics Data System (ADS)

Gray, William; Foord, M. E.; Schneider, M. B.; Barrios, M. A.; Brown, G. V.; Heeter, R. F.; Jarrott, L. C.; Liedahl, D. A.; Marley, E. V.; Mauche, C. W.; Widmann, K.

2016-10-01

We present 2D R-z simulations that model the hydrodynamics and x-ray output of a laser heated, tamped foil, using the rad-hydro code LASNEX. The foil consists of a thin (2400 A) cylindrical disk of iron/vanadium/gold that is embedded in a thicker Be tamper. The simulations utilize a non-LTE detailed configuration (DCA) model, which generates the emission spectra. Simulated pinhole images are compared with data, finding qualitative agreement with the time-history of the face-on emission profiles, and exhibiting an interesting reduction in emission size over a few ns time period. Furthermore, we find that the simulations recover similar burn through times in both the target and Be tamper as measured by a time-dependent filtered x-ray detector (DANTE). Additional results and characterization of the experimental plasma will be presented. This work performed under the auspices of U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Gradient ascent pulse engineering approach to CNOT gates in donor electron spin quantum computing

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

Tsai, D.-B.; Goan, H.-S.

2008-11-07

In this paper, we demonstrate how gradient ascent pulse engineering (GRAPE) optimal control methods can be implemented on donor electron spin qubits in semiconductors with an architecture complementary to the original Kane's proposal. We focus on the high fidelity controlled-NOT (CNOT) gate and we explicitly find the digitized control sequences for a controlled-NOT gate by optimizing its fidelity using the effective, reduced donor electron spin Hamiltonian with external controls over the hyperfine A and exchange J interactions. We then simulate the CNOT-gate sequence with the full spin Hamiltonian and find that it has an error of 10{sup -6} that ismore » below the error threshold of 10{sup -4} required for fault-tolerant quantum computation. Also the CNOT gate operation time of 100 ns is 3 times faster than 297 ns of the proposed global control scheme.« less

Lattice-level observation of the elastic-to-plastic relaxation process with subnanosecond resolution in shock-compressed Ta using time-resolved in situ Laue diffraction

DOE PAGES

Wehrenberg, C. E.; Comley, A. J.; Barton, N. R.; ...

2015-09-29

We report direct lattice level measurements of plastic relaxation kinetics through time-resolved, in-situ Laue diffraction of shock-compressed single-crystal [001] Ta at pressures of 27-210 GPa. For a 50 GPa shock, a range of shear strains is observed extending up to the uniaxial limit for early data points (<0.6 ns) and the average shear strain relaxes to a near steady state over ~1 ns. For 80 and 125 GPa shocks, the measured shear strains are fully relaxed already at 200 ps, consistent with rapid relaxation associated with the predicted threshold for homogeneous nucleation of dislocations occurring at shock pressure ~65 GPa.more » The relaxation rate and shear stresses are used to estimate the dislocation density and these quantities are compared to the Livermore Multiscale Strength model as well as various molecular dynamics simulations.« less

Lattice Boltzmann and Navier-Stokes Cartesian CFD Approaches for Airframe Noise Predictions

NASA Technical Reports Server (NTRS)

Barad, Michael F.; Kocheemoolayil, Joseph G.; Kiris, Cetin C.

2017-01-01

Lattice Boltzmann (LB) and compressible Navier-Stokes (NS) equations based computational fluid dynamics (CFD) approaches are compared for simulating airframe noise. Both LB and NS CFD approaches are implemented within the Launch Ascent and Vehicle Aerodynamics (LAVA) framework. Both schemes utilize the same underlying Cartesian structured mesh paradigm with provision for local adaptive grid refinement and sub-cycling in time. We choose a prototypical massively separated, wake-dominated flow ideally suited for Cartesian-grid based approaches in this study - The partially-dressed, cavity-closed nose landing gear (PDCC-NLG) noise problem from AIAA's Benchmark problems for Airframe Noise Computations (BANC) series of workshops. The relative accuracy and computational efficiency of the two approaches are systematically compared. Detailed comments are made on the potential held by LB to significantly reduce time-to-solution for a desired level of accuracy within the context of modeling airframes noise from first principles.

Fungal colonization in soils with different management histories: modeling growth in three-dimensional pore volumes.

PubMed

Kravchenko, Alexandra; Falconer, Ruth E; Grinev, Dmitri; Otten, Wilfred

2011-06-01

Despite the importance of fungi in soil functioning they have received comparatively little attention, and our understanding of fungal interactions and communities is lacking. This study aims to combine a physiologically based model of fungal growth with digitized images of internal pore volume of samples of undisturbed soil from contrasting management practices to determine the effect of physical structure on fungal growth dynamics. We quantified pore geometries of the undisturbed-soil samples from two contrasting agricultural practices, conventionally plowed (chisel plow) (CT) and no till (NT), and from native-species vegetation land use on land that was taken out of production in 1989 (NS). Then we modeled invasion of a fungal species within the soil samples and evaluated the role of soil structure on the progress of fungal colonization of the soil pore space. The size of the studied pores was > or =110 microm. The dynamics of fungal invasion was quantified through parameters of a mathematical model fitted to the fungal invasion curves. Results indicated that NT had substantially lower porosity and connectivity than CT and NS soils. For example, the largest connected pore volume occupied 79% and 88% of pore space in CT and NS treatments, respectively, while it only occupied 45% in NT. Likewise, the proportion of pore space available to fungal colonization was much greater in NS and CT than in NT treatment, and the dynamics of the fungal invasion differed among the treatments. The relative rate of fungal invasion at the onset of simulation was higher in NT samples, while the invasion followed a more sigmoidal pattern with relatively slow invasion rates at the initial time steps in NS and CT samples. Simulations allowed us to elucidate the contribution of physical structure to the rates and magnitudes of fungal invasion processes. It appeared that fragmented pore space disadvantaged fungal invasion in soils under long-term no-till, while large connected pores in soils under native vegetation or in tilled agriculture promoted the invasion.

Structure of Alzheimer's 10-35 β peptide from replica-exchange molecular dynamics simulations in explicit water

NASA Astrophysics Data System (ADS)

Baumketner, Andriy; Shea, Joan-Emma

2006-03-01

We report a replica-exchange molecular dynamics study of the 10-35 fragment of Alzheimer's disease amyloid β peptide, Aβ10-35, in aqueous solution. This fragment was previously seen [J. Str. Biol. 130 (2000) 130] to possess all the most important amyloidogenic properties characteristic of full-length Aβ peptides. Our simulations attempted to fold Aβ10-35 from first principles. The peptide was modeled using all-atom OPLS/AA force field in conjunction with the TIP3P explicit solvent model. A total of 72 replicas were considered and simulated over 40 ns of total time, including 5 ns of initial equilibration. We find that Aβ10-35 does not possess any unique folded state, a 3D structure of predominant population, under normal temperature and pressure. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is seen to be dominated by random coil and bend structures with insignificant presence of α-helical or β-sheet structure. We find that, overall, the 3D structure of Aβ10-35 is shaped by salt bridges formed between oppositely charged residues.Of all possible salt bridges, K28-D23 was seen to have the highest formation probability, totaling more than 60% of the time.

Virtual screening of commercial cyclic peptides as NS2B-NS3 protease inhibitor of dengue virus serotype 2 through molecular docking simulation

NASA Astrophysics Data System (ADS)

Nasution, M. A. F.; Aini, R. N.; Tambunan, U. S. F.

2017-04-01

A disease caused by dengue virus infection has become one of the major health problems in the world, particularly in Asia, Africa, and South America. This disease has become endemic in more than 100 countries, and approximately 100 million cases occur each year with 2.5 billion people or 40% of the world population at risk of having this virus infection. Therefore, we need an antiviral drug that can inhibit the activity of the enzymes that involved in the virus replication in the body. Lately, the peptide-based drug design has been developed and proved to have interesting pharmacological properties. This study uses commercially cyclic peptides that have already marketed. The purpose of this study is to screen the commercial cyclic peptides that can be used as an inhibitor of the NS2B-NS3 protease of dengue virus serotype 2 (DENV-2) through molecular docking simulations. Inhibition of NS3 protease enzyme can lead to enzymatic inhibition activity so the formed polyprotein from the translation of RNA cannot be cut into pieces and remain in the long strand form. Consequently, proteins that are vital for the sustainability of dengue virus replication cannot be formed. This research resulted in [alpha]-ANF (1-28), rat, Brain Natriuretic Peptide, porcine, Atrial Natriuretic Factor (3-28) (human) and Atrial Natriuretic Peptide (126-150) (rat) as the best drug candidate for inhibiting the NS2B-NS3 protease of DENV-2.

Fundamental limits of scintillation detector timing precision

NASA Astrophysics Data System (ADS)

Derenzo, Stephen E.; Choong, Woon-Seng; Moses, William W.

2014-07-01

In this paper we review the primary factors that affect the timing precision of a scintillation detector. Monte Carlo calculations were performed to explore the dependence of the timing precision on the number of photoelectrons, the scintillator decay and rise times, the depth of interaction uncertainty, the time dispersion of the optical photons (modeled as an exponential decay), the photodetector rise time and transit time jitter, the leading-edge trigger level, and electronic noise. The Monte Carlo code was used to estimate the practical limits on the timing precision for an energy deposition of 511 keV in 3 mm × 3 mm × 30 mm Lu2SiO5:Ce and LaBr3:Ce crystals. The calculated timing precisions are consistent with the best experimental literature values. We then calculated the timing precision for 820 cases that sampled scintillator rise times from 0 to 1.0 ns, photon dispersion times from 0 to 0.2 ns, photodetector time jitters from 0 to 0.5 ns fwhm, and A from 10 to 10 000 photoelectrons per ns decay time. Since the timing precision R was found to depend on A-1/2 more than any other factor, we tabulated the parameter B, where R = BA-1/2. An empirical analytical formula was found that fit the tabulated values of B with an rms deviation of 2.2% of the value of B. The theoretical lower bound of the timing precision was calculated for the example of 0.5 ns rise time, 0.1 ns photon dispersion, and 0.2 ns fwhm photodetector time jitter. The lower bound was at most 15% lower than leading-edge timing discrimination for A from 10 to 10 000 photoelectrons ns-1. A timing precision of 8 ps fwhm should be possible for an energy deposition of 511 keV using currently available photodetectors if a theoretically possible scintillator were developed that could produce 10 000 photoelectrons ns-1.

Fundamental Limits of Scintillation Detector Timing Precision

PubMed Central

Derenzo, Stephen E.; Choong, Woon-Seng; Moses, William W.

2014-01-01

In this paper we review the primary factors that affect the timing precision of a scintillation detector. Monte Carlo calculations were performed to explore the dependence of the timing precision on the number of photoelectrons, the scintillator decay and rise times, the depth of interaction uncertainty, the time dispersion of the optical photons (modeled as an exponential decay), the photodetector rise time and transit time jitter, the leading-edge trigger level, and electronic noise. The Monte Carlo code was used to estimate the practical limits on the timing precision for an energy deposition of 511 keV in 3 mm × 3 mm × 30 mm Lu2SiO5:Ce and LaBr3:Ce crystals. The calculated timing precisions are consistent with the best experimental literature values. We then calculated the timing precision for 820 cases that sampled scintillator rise times from 0 to 1.0 ns, photon dispersion times from 0 to 0.2 ns, photodetector time jitters from 0 to 0.5 ns fwhm, and A from 10 to 10,000 photoelectrons per ns decay time. Since the timing precision R was found to depend on A−1/2 more than any other factor, we tabulated the parameter B, where R = BA−1/2. An empirical analytical formula was found that fit the tabulated values of B with an rms deviation of 2.2% of the value of B. The theoretical lower bound of the timing precision was calculated for the example of 0.5 ns rise time, 0.1 ns photon dispersion, and 0.2 ns fwhm photodetector time jitter. The lower bound was at most 15% lower than leading-edge timing discrimination for A from 10 to 10,000 photoelectrons/ns. A timing precision of 8 ps fwhm should be possible for an energy deposition of 511 keV using currently available photodetectors if a theoretically possible scintillator were developed that could produce 10,000 photoelectrons/ns. PMID:24874216

Effect of 10.5 M Aqueous Urea on Helicobacter pylori Urease: A Molecular Dynamics Study.

PubMed

Minkara, Mona S; Weaver, Michael N; Merz, Kenneth M

2015-07-07

The effects of a 10.5 M solution of aqueous urea on Helicobacter pylori urease were investigated over the course of a 500 ns molecular dynamics (MD) simulation. The enzyme was solvated by 25321 water molecules, and additionally, 4788 urea molecules were added to the solution. Although concentrated urea solutions are known laboratory denaturants, the protein secondary structure is retained throughout the simulation largely because of the short simulation time (urea denaturation occurs on the millisecond time scale). The relatively constant solvent accessible surface area over the last 400 ns of the simulation further confirms the overall lack of denaturation. The wide-open flap state observed previously in Klebsiella areogenes urease [Roberts, B. P., et al. (2012) J. Am. Chem. Soc. 134, 9934] and H. pylori [Minkara, M. S., et al. (2014) J. Chem. Theory Comput. 10, 1852-1862] was also identified in this aqueous urea simulation. Over the course of the trajectory, we were able to observe urea molecules entering the active site in proportions related to the extent of opening of the active site-covering flap. Furthermore, urea molecules were observed to approach the pentacoordinate Ni(2+) ion in position to bind in a manner consistent with the proposed initial coordination step of the hydrolysis mechanism. We also observed a specific and unique pattern in the regions of the protein with a high root-mean-square fluctuation (rmsf). The high-rmsf regions in the β-chain form a horseshoelike arrangement surrounding the active site-covering flap on the surface of the protein. We hypothesize that the function of these regions is to both attract and shuttle urea toward the loop of the active site-covering flap before entry into the cavity. Indeed, urea is observed to interact with these regions for extended periods of simulation time before active site ingress.

Computational Study on the Inhibitor Binding Mode and Allosteric Regulation Mechanism in Hepatitis C Virus NS3/4A Protein

PubMed Central

Xue, Weiwei; Yang, Ying; Wang, Xiaoting; Liu, Huanxiang; Yao, Xiaojun

2014-01-01

HCV NS3/4A protein is an attractive therapeutic target responsible for harboring serine protease and RNA helicase activities during the viral replication. Small molecules binding at the interface between the protease and helicase domains can stabilize the closed conformation of the protein and thus block the catalytic function of HCV NS3/4A protein via an allosteric regulation mechanism. But the detailed mechanism remains elusive. Here, we aimed to provide some insight into the inhibitor binding mode and allosteric regulation mechanism of HCV NS3/4A protein by using computational methods. Four simulation systems were investigated. They include: apo state of HCV NS3/4A protein, HCV NS3/4A protein in complex with an allosteric inhibitor and the truncated form of the above two systems. The molecular dynamics simulation results indicate HCV NS3/4A protein in complex with the allosteric inhibitor 4VA adopts a closed conformation (inactive state), while the truncated apo protein adopts an open conformation (active state). Further residue interaction network analysis suggests the communication of the domain-domain interface play an important role in the transition from closed to open conformation of HCV NS3/4A protein. However, the inhibitor stabilizes the closed conformation through interaction with several key residues from both the protease and helicase domains, including His57, Asp79, Asp81, Asp168, Met485, Cys525 and Asp527, which blocks the information communication between the functional domains interface. Finally, a dynamic model about the allosteric regulation and conformational changes of HCV NS3/4A protein was proposed and could provide fundamental insights into the allosteric mechanism of HCV NS3/4A protein function regulation and design of new potent inhibitors. PMID:24586263

Measurement of Low-Energy Nuclear-Recoil Quenching Factors in CsI[Na] and Statistical Analysis of the First Observation of Coherent, Elastic Neutrino-Nucleus Scattering

NASA Astrophysics Data System (ADS)

Rich, Grayson Currie

The COHERENT Collaboration has produced the first-ever observation, with a significance of 6.7sigma, of a process consistent with coherent, elastic neutrino-nucleus scattering (CEnuNS) as first predicted and described by D.Z. Freedman in 1974. Physics of the CEnuNS process are presented along with its relationship to future measurements in the arenas of nuclear physics, fundamental particle physics, and astroparticle physics, where the newly-observed interaction presents a viable tool for investigations into numerous outstanding questions about the nature of the universe. To enable the CEnuNS observation with a 14.6-kg CsI[Na] detector, new measurements of the response of CsI[Na] to low-energy nuclear recoils, which is the only mechanism by which CEnuNS is detectable, were carried out at Triangle Universities Nuclear Laboratory; these measurements are detailed and an effective nuclear-recoil quenching factor of 8.78 +/- 1.66% is established for CsI[Na] in the recoil-energy range of 5-30 keV, based on new and literature data. Following separate analyses of the CEnuNS-search data by groups at the University of Chicago and the Moscow Engineering and Physics Institute, information from simulations, calculations, and ancillary measurements were used to inform statistical analyses of the collected data. Based on input from the Chicago analysis, the number of CEnuNS events expected from the Standard Model is 173 +/- 48; interpretation as a simple counting experiment finds 136 +/- 31 CEnuNS counts in the data, while a two-dimensional, profile likelihood fit yields 134 +/- 22 CEnuNS counts. Details of the simulations, calculations, and supporting measurements are discussed, in addition to the statistical procedures. Finally, potential improvements to the CsI[Na]-based CEnuNS measurement are presented along with future possibilities for COHERENT Collaboration, including new CEnuNS detectors and measurement of the neutrino-induced neutron spallation process.

Simulation study of the structure and phase behavior of ceramide bilayers and the role of lipid head group chemistry

PubMed Central

Guo, Shan; Moore, Timothy C.; Iacovella, Christopher R.; Strickland, L. Anderson; McCabe, Clare

2014-01-01

Ceramides are known to be a key component of the stratum corneum, the outermost protective layer of the skin that controls barrier function. In this work, molecular dynamics simulations are used to examine the behavior of ceramide bilayers, focusing on non-hydroxy sphingosine (NS) and non-hydroxy phytosphingosine (NP) ceramides. Here, we propose a modified version of the CHARMM force field for ceramide simulation, which is directly compared to the more commonly used GROMOS-based force field of Berger (Biophys. J. 1997, 72); while both force fields are shown to closely match experiment from a structural standpoint at the physiological temperature of skin, the modified CHARMM force field is better able to capture the thermotropic phase transitions observed in experiment. The role of ceramide chemistry and its impact on structural ordering is examined by comparing ceramide NS to NP, using the validated CHARMM-based force field. These simulations demonstrate that changing from ceramide NS to NP results in changes to the orientation of the OH groups in the lipid headgroups. The arrangement of OH groups perpendicular to the bilayer normal for ceramide NP, verse parallel for NS, results in the formation of a distinct hydrogen bonding network, that is ultimately responsible for shifting the gel-to-liquid phase transition to higher temperature, in direct agreement with experiment. PMID:24501589

Multiple Sensing Application on Wireless Sensor Network Simulation using NS3

NASA Astrophysics Data System (ADS)

Kurniawan, I. F.; Bisma, R.

2018-01-01

Hardware enhancement provides opportunity to install various sensor device on single monitoring node which then enables users to acquire multiple data simultaneously. Constructing multiple sensing application in NS3 is a challenging task since numbers of aspects such as wireless communication, packet transmission pattern, and energy model must be taken into account. Despite of numerous types of monitoring data available, this study only considers two types such as periodic, and event-based data. Periodical data will generate monitoring data follows configured interval, while event-based transmit data when certain determined condition is met. Therefore, this study attempts to cover mentioned aspects in NS3. Several simulations are performed with different number of nodes on arbitrary communication scheme.

Molecular dynamics analysis of transitions between rotational isomers in polymethylene

NASA Astrophysics Data System (ADS)

Zúñiga, Ignacio; Bahar, Ivet; Dodge, Robert; Mattice, Wayne L.

1991-10-01

Molecular dynamics trajectories have been computed and analyzed for linear chains, with sizes ranging from C10H22 to C100H202, and for cyclic C100H200. All hydrogen atoms are included discretely. All bond lengths, bond angles, and torsion angles are variable. Hazard plots show a tendency, at very short times, for correlations between rotational isomeric transitions at bond i and i±2, in much the same manner as in the Brownian dynamics simulations reported by Helfand and co-workers. This correlation of next nearest neighbor bonds in isolated polyethylene chains is much weaker than the correlation found for next nearest neighbor CH-CH2 bonds in poly(1,4-trans-butadiene) confined to the channel formed by crystalline perhydrotriphenylene [Dodge and Mattice, Macromolecules 24, 2709 (1991)]. Less than half of the rotational isomeric transitions observed in the entire trajectory for C50H102 can be described as strongly coupled next nearest neighbor transitions. If correlated motions are identified with successive transitions, which occur within a time interval of Δt≤1 ps, only 18% of the transitions occur through cooperative motion of bonds i and i±2. An analysis of the entire data set of 2482 rotational isomeric state transitions, observed in a 3.7 ns trajectory for C50H102 at 400 K, was performed using a formalism that treats the transitions at different bonds as being independent. On time scales of 0.1 ns or longer, the analysis based on independent bonds accounts reasonably well for the results from the molecular dynamics simulations. At shorter times the molecular dynamics simulation reveals a higher mobility than implied by the analysis assuming independent bonds, presumably due to the influence of correlations that are important at shorter times.

Non-solenoidal Plasma Startup in the Pegasus Toroidal Experiment

NASA Astrophysics Data System (ADS)

Sontag, Aaron

2008-11-01

Non-solenoidal (NS) startup will simplify the design of future tokamaks by eliminating need for a central solenoid and is required for an ST based CTF. In Pegasus, washer-stack current sources (plasma guns) are used to initiate NS discharges via point-source DC helicity injection. Current injected parallel to the helical vacuum field can relax into a tokamak-like configuration with toroidally-averaged closed flux and tokamak-like confinement. This requires no modification of the vacuum vessel and is scalable to fusion grade systems with proper geometry. Guns in the divertor region create discharges with Ip up to 50 kA, 3 times the vacuum windup. Nonlinear 3D simulation with NIMROD shows excitation of a line-tied kink, producing poloidal flux amplification. Evidence of flux amplification includes: reversal of edge poloidal magnetic flux; Ip increase over vacuum geometric windup; plasma position subject to radial force balance; and persistence of Ip after gun shut-off. Equilibria show high edge current (li = 0.2) and elevated q (qmin> 6), allowing access to high IN (IN> 12). Guns at the outboard midplane produce Ip up to 7 times the vacuum windup with large n=1 activity when edge q passes through rational surfaces. Line averaged density up to 2x10^19 m-3 after relaxation shows an increase in particle confinement over non-relaxed cases. Maximum Ip is determined by helicity and radial force balance, tokamak stability, and Taylor relaxation. Coupling midplane gun discharges to other CD is straightforward due to Ip decay times >3 ms. Poloidal field induction has been used to create NS discharges up to 80 kA and gun plasmas with Ip of 60 kA have been ramped to over 100 kA by including OH drive. Present research is aimed at understanding the physics of this technique in order to form NS targets in excess of 200 kA and design NS startup systems for larger devices.

Use of Regional Climate Model Output for Hydrologic Simulations

NASA Astrophysics Data System (ADS)

Hay, L. E.; Clark, M. P.; Wilby, R. L.; Gutowski, W. J.; Leavesley, G. H.; Pan, Z.; Arritt, R. W.; Takle, E. S.

2001-12-01

Daily precipitation and maximum and minimum temperature time series from a Regional Climate Model (RegCM2) were used as input to a distributed hydrologic model for a rainfall-dominated basin (Alapaha River at Statenville, Georgia) and three snowmelt-dominated basins (Animas River at Durango, Colorado; East Fork of the Carson River near Gardnerville, Nevada; and Cle Elum River near Roslyn, Washington). For comparison purposes, spatially averaged daily data sets of precipitation and maximum and minimum temperature were developed from measured data. These datasets included precipitation and temperature data for all stations that are located within the area of the RegCM2 model output used for each basin, but excluded station data used to calibrate the hydrologic model. Both the RegCM2 output and station data capture the gross aspects of the seasonal cycles of precipitation and temperature. However, in all four basins, the RegCM2- and station-based simulations of runoff show little skill on a daily basis (Nash-Sutcliffe (NS) values ranging from 0.05-0.37 for RegCM2 and -0.08-0.65 for station). When the precipitation and temperature biases are corrected in the RegCM2 output and station data sets (Bias-RegCM2 and Bias-station, respectively) the accuracy of the daily runoff simulations improve dramatically for the snowmelt-dominated basins. In the rainfall-dominated basin, runoff simulations based on the Bias-RegCM2 output show no skill (NS value of 0.09) whereas Bias-All simulated runoff improves (NS value improved from -0.08 to 0.72). These results indicate that the resolution of the RegCM2 output is appropriate for basin-scale modeling, but RegCM2 model output does not contain the day-to-day variability needed for basin-scale modeling in rainfall-dominated basins. Future work is warranted to identify the causes for systematic biases in RegCM2 simulations, develop methods to remove the biases, and improve RegCM2 simulations of daily variability in local climate.

Simulating Hadronic-to-Quark-Matter with Burn-UD: Recent work and astrophysical applications

NASA Astrophysics Data System (ADS)

Welbanks, Luis; Ouyed, Amir; Koning, Nico; Ouyed, Rachid

2017-06-01

We present the new developments in Burn-UD, our in-house hydrodynamic combustion code used to model the phase transition of hadronic-to-quark matter. Our two new modules add neutrino transport and the time evolution of a (u, d, s) quark star (QS). Preliminary simulations show that the inclusion of neutrino transport points towards new hydrodynamic instabilities that increase the burning speed. A higher burning speed could elicit the deflagration to detonation of a neutron star (NS) into a QS. We propose that a Quark-Nova (QN: the explosive transition of a NS to a QS) could help us explain the most energetic astronomical events to this day: superluminous supernovae (SLSNe). Our models consider a QN occurring in a massive binary, experiencing two common envelope stages and a QN occurring after the supernova explosion of a Wolf-Rayet (WO) star. Both models have been successful in explaining the double humped light curves of over half a dozen SLSNe. We also introduce SiRop our r-process simulation code and propose that a QN site has the hot temperatures and neutron densities required to make it an ideal site for the r-process.

Mechanism of Acetylcholinesterase Inhibition by Fasciculin: A 5-ns Molecular Dynamics Simulation

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

Tai, Kaihsu; Shen, T Y.; Henchman, Richard H.

Our previous molecular dynamics simulation (10 ns) of mouse acetylcholinesterase (EC 3.1.1.7) revealed complex fluctuation of the enzyme active site gorge. Now we report a 5-ns simulation of acetylcholinesterase complexed with fasciculin 2. Fasciculin 2 binds to the gorge entrance of acetylcholinesterase with excellent complementarity and many polar and hydrophobic interactions. In this simulation of the protein-protein complex, where fasciculin 2 appears to sterically block access of ligands to the gorge, again we observe a two-peaked probability distribution of the gorge width. When fasciculin is present, the gorge width distribution is altered such that the gorge is more likely tomore » be narrow. Moreover, there are large increases in the opening of alternative passages, namely, the side door (near Thr 75) and the back door (near Tyr 449). Finally, the catalytic triad arrangement in the acetylcholinesterase active site is disrupted with fasciculin bound. These data support that, in addition to the steric obstruction seen in the crystal structure, fasciculin may inhibit acetylcholinesterase by combined allosteric and dynamical means. Additional data from these simulations can be found at http://mccammon.ucsd.edu/.« less

HYPERCRITICAL ACCRETION, INDUCED GRAVITATIONAL COLLAPSE, AND BINARY-DRIVEN HYPERNOVAE

DOE PAGES

Fryer, Chris L.; Rueda, Jorge A.; Ruffini, Remo

2014-09-16

We successfully, applied the induced gravitational collapse (IGC) paradigm to the explanation of GRB-SNe. The progenitor is a tight binary system composed of a CO core and a NS companion. Furthermore, the explosion of the SN leads to hypercritical accretion onto the NS companion, which reaches the critical mass, gravitationally collapsing to a BH with consequent emission of the GRB. The first estimates of this process were based on a simplified model of the binary parameters and the Bondi-Hoyle-Lyttleton accretion rate. We present the first full numerical simulations of the IGC process. We simulate the core-collapse, the SN explosion, andmore » the hydrodynamic evolution of the accreting material falling into the Bondi-Hoyle surface of the NS. For appropriate binary parameters, the IGC occurs in short timescale 102–103 s due to the combined action of photon trapping and neutrino cooling near the NS surface. We also address the observational features of this process.« less

Experiments of a 100 kV-level pulse generator based on metal-oxide varistor

NASA Astrophysics Data System (ADS)

Cui, Yan-cheng; Wu, Qi-lin; Yang, Han-wu; Gao, Jing-ming; Li, Song; Shi, Cheng-yu

2018-03-01

This paper introduces the development and experiments of a 100 kV-level pulse generator based on a metal-oxide varistor (MOV). MOV has a high energy handling capacity and nonlinear voltage-current (V-I) characteristics, which makes it useful for high voltage pulse shaping. Circuit simulations based on the measured voltage-current characteristics of MOV verified the shaping concept and showed that a circuit containing a two-section pulse forming network (PFN) will result in better defined square pulse than a simple L-C discharging circuit. A reduced-scale experiment was carried out and the result agreed well with simulation prediction. Then a 100 kV-level pulse generator with multiple MOVs in a stack and a two-section pulse forming network (PFN) was experimented. A pulse with a voltage amplitude of 90 kV, rise time of about 50 ns, pulse width of 500 ns, and flat top of about 400 ns was obtained with a water dummy load of 50 Ω. The results reveal that the combination of PFN and MOV is a practical way to generate high voltage pulses with better flat top waveforms, and the load voltage is stable even if the load's impedance varies. Such pulse generator can be applied in many fields such as surface treatment, corona plasma generation, industrial dedusting, and medical disinfection.

Neutron Star Kicks by the Gravitational Tug-boat Mechanism in Asymmetric Supernova Explosions: Progenitor and Explosion Dependence

NASA Astrophysics Data System (ADS)

Janka, Hans-Thomas

2017-03-01

Asymmetric mass ejection in the early phase of supernova (SN) explosions can impart a kick velocity to the new-born neutron star (NS). For neutrino-driven explosions the NS acceleration has been shown to be mainly caused by the gravitational attraction of the anisotropically expelled inner ejecta, while hydrodynamic forces contribute on a subdominant level, and asymmetric neutrino emission plays only a secondary role. Two- and three-dimensional hydrodynamic simulations have demonstrated that this gravitational tug-boat mechanism can explain the observed space velocities of young NSs up to more than 1000 km s-1. Here, we discuss how the NS kick depends on the energy, ejecta mass, and asymmetry of the SN explosion, and what role the compactness of the pre-collapse stellar core plays for the momentum transfer to the NS. We also provide simple analytic expressions for the NS velocity in terms of these quantities. Referring to results of hydrodynamic simulations in the literature, we argue why, within the discussed scenario of NS acceleration, electron-capture SNe, low-mass Fe-core SNe, and ultra-stripped SNe can be expected to have considerably lower intrinsic NS kicks than core-collapse SNe of massive stellar cores. Our basic arguments also remain valid if progenitor stars possess large-scale asymmetries in their convective silicon and oxygen burning layers. Possible scenarios for spin-kick alignment are sketched. Much of our discussion stays on a conceptual and qualitative level, and more work is necessary on the numerical modeling side to determine the dependences of involved parameters, whose prescriptions will be needed for recipes that can be used to better describe NS kicks in binary evolution and population synthesis studies.

Neutron Star Kicks by the Gravitational Tug-boat Mechanism in Asymmetric Supernova Explosions: Progenitor and Explosion Dependence

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

Janka, Hans-Thomas

Asymmetric mass ejection in the early phase of supernova (SN) explosions can impart a kick velocity to the new-born neutron star (NS). For neutrino-driven explosions the NS acceleration has been shown to be mainly caused by the gravitational attraction of the anisotropically expelled inner ejecta, while hydrodynamic forces contribute on a subdominant level, and asymmetric neutrino emission plays only a secondary role. Two- and three-dimensional hydrodynamic simulations have demonstrated that this gravitational tug-boat mechanism can explain the observed space velocities of young NSs up to more than 1000 km s{sup −1}. Here, we discuss how the NS kick depends onmore » the energy, ejecta mass, and asymmetry of the SN explosion, and what role the compactness of the pre-collapse stellar core plays for the momentum transfer to the NS. We also provide simple analytic expressions for the NS velocity in terms of these quantities. Referring to results of hydrodynamic simulations in the literature, we argue why, within the discussed scenario of NS acceleration, electron-capture SNe, low-mass Fe-core SNe, and ultra-stripped SNe can be expected to have considerably lower intrinsic NS kicks than core-collapse SNe of massive stellar cores. Our basic arguments also remain valid if progenitor stars possess large-scale asymmetries in their convective silicon and oxygen burning layers. Possible scenarios for spin-kick alignment are sketched. Much of our discussion stays on a conceptual and qualitative level, and more work is necessary on the numerical modeling side to determine the dependences of involved parameters, whose prescriptions will be needed for recipes that can be used to better describe NS kicks in binary evolution and population synthesis studies.« less

Mapping Ad Hoc Communications Network of a Large Number Fixed-Wing UAV Swarm

DTIC Science & Technology

2017-03-01

partitioned sub-swarms. The work covered in this thesis is to build a model of the NPS swarm’s communication network in ns-3 simulation software and use...partitioned sub- swarms. The work covered in this thesis is to build a model of the NPS swarm’s communication network in ns-3 simulation software and...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS MAPPING AD HOC COMMUNICATIONS NETWORK OF A LARGE NUMBER FIXED-WING UAV SWARM by Alexis

Particle-in-cell simulations for virtual cathode oscillator including foil ablation effects

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

Singh, Gursharn; Chaturvedi, S.

2011-06-15

We have performed two- and three-dimensional, relativistic, electromagnetic, particle-in-cell simulations of an axially extracted virtual cathode oscillator (vircator). The simulations include, for the first time, self-consistent dynamics of the anode foil under the influence of the intense electron beam. This yields the variation of microwave output power as a function of time, including the role of anode ablation and anode-cathode gap closure. These simulations have been done using locally developed particle-in-cell (PIC) codes. The codes have been validated using two vircator designs available from the literature. The simulations reported in the present paper take account of foil ablation due tomore » the intense electron flux, the resulting plasma expansion and shorting of the anode-cathode gap. The variation in anode transparency due to plasma formation is automatically taken into account. We find that damage is generally higher near the axis. Also, at all radial positions, there is little damage in the early stages, followed by a period of rapid erosion, followed in turn by low damage rates. A physical explanation has been given for these trends. As a result of gap closure due to plasma formation from the foil, the output microwave power initially increases, reaches a near-flat-top and then decreases steadily, reaching a minimum around 230 ns. This is consistent with a typical plasma expansion velocity of {approx}2 cm/{mu}s reported in the literature. We also find a significant variation in the dominant output frequency, from 6.3 to 7.6 GHz. This variation is small as long as the plasma density is small, up to {approx}40 ns. As the AK gap starts filling with plasma, there is a steady increase in this frequency.« less

Research on a solid state-streak camera based on an electro-optic crystal

NASA Astrophysics Data System (ADS)

Wang, Chen; Liu, Baiyu; Bai, Yonglin; Bai, Xiaohong; Tian, Jinshou; Yang, Wenzheng; Xian, Ouyang

2006-06-01

With excellent temporal resolution ranging from nanosecond to sub-picoseconds, a streak camera is widely utilized in measuring ultrafast light phenomena, such as detecting synchrotron radiation, examining inertial confinement fusion target, and making measurements of laser-induced discharge. In combination with appropriate optics or spectroscope, the streak camera delivers intensity vs. position (or wavelength) information on the ultrafast process. The current streak camera is based on a sweep electric pulse and an image converting tube with a wavelength-sensitive photocathode ranging from the x-ray to near infrared region. This kind of streak camera is comparatively costly and complex. This paper describes the design and performance of a new-style streak camera based on an electro-optic crystal with large electro-optic coefficient. Crystal streak camera accomplishes the goal of time resolution by direct photon beam deflection using the electro-optic effect which can replace the current streak camera from the visible to near infrared region. After computer-aided simulation, we design a crystal streak camera which has the potential of time resolution between 1ns and 10ns.Some further improvements in sweep electric circuits, a crystal with a larger electro-optic coefficient, for example LN (γ 33=33.6×10 -12m/v) and the optimal optic system may lead to better time resolution less than 1ns.

Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions.

PubMed

Buchenberg, Sebastian; Schaudinnus, Norbert; Stock, Gerhard

2015-03-10

Biomolecules exhibit structural dynamics on a number of time scales, including picosecond (ps) motions of a few atoms, nanosecond (ns) local conformational transitions, and microsecond (μs) global conformational rearrangements. Despite this substantial separation of time scales, fast and slow degrees of freedom appear to be coupled in a nonlinear manner; for example, there is theoretical and experimental evidence that fast structural fluctuations are required for slow functional motion to happen. To elucidate a microscopic mechanism of this multiscale behavior, Aib peptide is adopted as a simple model system. Combining extensive molecular dynamics simulations with principal component analysis techniques, a hierarchy of (at least) three tiers of the molecule's free energy landscape is discovered. They correspond to chiral left- to right-handed transitions of the entire peptide that happen on a μs time scale, conformational transitions of individual residues that take about 1 ns, and the opening and closing of structure-stabilizing hydrogen bonds that occur within tens of ps and are triggered by sub-ps structural fluctuations. Providing a simple mechanism of hierarchical dynamics, fast hydrogen bond dynamics is found to be a prerequisite for the ns local conformational transitions, which in turn are a prerequisite for the slow global conformational rearrangement of the peptide. As a consequence of the hierarchical coupling, the various processes exhibit a similar temperature behavior which may be interpreted as a dynamic transition.

Radiometric calibration of an airborne multispectral scanner. [of Thematic Mapper Simulator

NASA Technical Reports Server (NTRS)

Markham, Brian L.; Ahmad, Suraiya P.; Jackson, Ray D.; Moran, M. S.; Biggar, Stuart F.; Gellman, David I.; Slater, Philip N.

1991-01-01

The absolute radiometric calibration of the NS001 Thematic Mapper Simulator reflective channels was examined based on laboratory tests and in-flight comparisons to ground measurements. The NS001 data are calibrated in-flight by reference to the NS001 internal integrating sphere source. This source's power supply or monitoring circuitry exhibited greater instability in-flight during 1988-1989 than in the laboratory. Extrapolating laboratory behavior to in-flight data resulted in 7-20 percent radiance errors relative to ground measurements and atmospheric modeling. Assuming constancy in the source's output between laboraotry and in-flight resulted in generally smaller errors. Upgrades to the source's power supply and monitoring circuitry in 1990 improved its in-flight stability, though in-flight ground reflectance based calibration tests have not yet been performed.

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

Pang, Yuan-Ping, E-mail: pang@mayo.edu

Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its nativemore » conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.« less

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Exploring the molecular basis of dsRNA recognition by NS1 protein of influenza A virus using molecular dynamics simulation and free energy calculation.

PubMed

Pan, Dabo; Sun, Huijun; Shen, Yulin; Liu, Huanxiang; Yao, Xiaojun

2011-12-01

The frequent outbreak of influenza pandemic and the limited available anti-influenza drugs highlight the urgent need for the development of new antiviral drugs. The dsRNA-binding surface of nonstructural protein 1 of influenza A virus (NS1A) is a promising target. The detailed understanding of NS1A-dsRNA interaction will be valuable for structure-based anti-influenza drug discovery. To characterize and explore the key interaction features between dsRNA and NS1A, molecular dynamics simulation combined with MM-GBSA calculations were performed. Based on the MM-GBSA calculations, we find that the intermolecular van der Waals interaction and the nonpolar solvation term provide the main driving force for the binding process. Meanwhile, 17 key residues from NS1A were identified to be responsible for the dsRNA binding. Compared with the wild type NS1A, all the studied mutants S42A, T49A, R38A, R35AR46A have obvious reduced binding free energies with dsRNA reflecting in the reduction of the polar and/or nonpolar interactions. In addition, the structural and energy analysis indicate the mutations have a small effect to the backbone structures but the loss of side chain interactions is responsible for the decrease of the binding affinity. The uncovering of NS1A-dsRNA recognition mechanism will provide some useful insights and new chances for the development of anti-influenza drugs. Copyright © 2011 Elsevier B.V. All rights reserved.

In-silico identification and evaluation of plant flavonoids as dengue NS2B/NS3 protease inhibitors using molecular docking and simulation approach.

PubMed

Qamar, Muhammad Tahirul; Ashfaq, Usman Ali; Tusleem, Kishver; Mumtaz, Arooj; Tariq, Quratulain; Goheer, Alina; Ahmed, Bilal

2017-11-01

Dengue infection is prevailing among the people not only from the developing countries but also from the developed countries due to its high morbidity rate around the globe. Hence, due to the unavailability of any suitable vaccine for rigorous dengue virus (DENV), the only mode of its treatment is prevention. The circumstances require an urgent development of efficient and practical treatment to deal with these serotypes. The severe effects and cost of synthetic vaccines simulated researchers to find anti-viral agents from medicinal plants. Flavonoids present in medicinal plants, holds anti-viral activity and can be used as vaccine against viruses. Therefore, present study was planned to find anti-viral potential of 2500 flavonoids inhibitors against the DENVNS2B/NS3 protease through computational screening which can hinder the viral replication within the host cell. By using molecular docking, it was revealed that flavonoids showed strong and stable bonding in the binding pocket of DENV NS2B/NS3 protease and had strong interactions with catalytic triad. Drug capability and anti-dengue potential of the flavonoids was also evaluated by using different bioinformatics tools. Some flavonoids effectively blocked the catalytic triad of DENV NS2B/NS3 protease and also passed through drug ability evaluation. It can be concluded from this study that these flavonoids could act as potential inhibitors to stop the replication of DENV and there is a need to study the action of these molecules in-vitro to confirm their action and other properties.

FORMATION OF STABLE MAGNETARS FROM BINARY NEUTRON STAR MERGERS

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

Giacomazzo, Bruno; Perna, Rosalba

2013-07-10

By performing fully general relativistic magnetohydrodynamic simulations of binary neutron star mergers, we investigate the possibility that the end result of the merger is a stable magnetar. In particular, we show that, for a binary composed of two equal-mass neutron stars (NSs) of gravitational mass M {approx} 1.2 M{sub Sun} and equation of state similar to Shen et al. at high densities, the merger product is a stable NS. Such NS is found to be differentially rotating and ultraspinning with spin parameter J/M{sup 2} {approx} 0.86, where J is its total angular momentum, and it is surrounded by a diskmore » of Almost-Equal-To 0.1 M{sub Sun }. While in our global simulations the magnetic field is amplified by about two orders of magnitude, local simulations have shown that hydrodynamic instabilities and the onset of the magnetorotational instability could further increase the magnetic field strength up to magnetar levels. This leads to the interesting possibility that, for some NS mergers, a stable and magnetized NS surrounded by an accretion disk could be formed. We discuss the impact of these new results for the emission of electromagnetic counterparts of gravitational wave signals and for the central engine of short gamma-ray bursts.« less

Molecular dynamics simulations of domain motions of substrate-free S-adenosyl- L-homocysteine hydrolase in solution.

PubMed

Hu, Chen; Fang, Jianwen; Borchardt, Ronald T; Schowen, Richard L; Kuczera, Krzysztof

2008-04-01

S-Adenosyl-L-homocysteine hydrolase (SAHH) is an enzyme regulating intracellular methylation reactions. The homotetrameric SAHH exists in an open conformation in absence of substrate, while enzyme:inhibitor complexes crystallize in the closed conformation, in which the ligands are engulfed by the protein due to an 18 degrees domain reorientation within each of the four subunits. We present a microscopic description of the structure and dynamics of the substrate-free, NAD(+)-bound SAHH in solution, based on a 15-ns molecular dynamics simulation in explicit solvent. In the trajectory, the four cofactor-binding domains formed a relatively rigid core with structure very similar to the crystal conformation. The four substrate-binding domains, located at the protein exterior, also retained internal structures similar to the crystal, while undergoing large amplitude rigid-body reorientations. The trajectory domain motions exhibited two interesting properties. First, within each subunit the domains fluctuated between open and closed conformations, while at the tetramer level 80% of the domain motions were perpendicular to the direction of the open-to-closed structural transition. Second, the domain reorientations in solution could be represented as a sum of two components, faster, with 20-50 ps correlation time and 3-4 degrees amplitude, and slower, with 8-23 ns correlation time and amplitude of 14-22 degrees . The faster motion is similar to the 1.5 cm(-1) frequency hinge-bending vibrations found in our recent normal mode analysis (Wang et al., Biochemistry 2005;44:7228-7239). The slower motion agrees with fluorescence anisotropy decay measurements, which detected a 10-20 ns domain reorientation of ca. 26 degrees amplitude in the substrate-free enzyme (Wang et al., Biochemistry 2006;45:7778-7786). Our simulations are thus in excellent agreement with experimental data. The simulations allow us to assign the observed nanosecond fluorescence anisotropy signal to fluctuations in domain orientations, and indicate that the microscopic mechanism of the motion involves rotational diffusion within a cone of 10-20 degrees . Overall, our simulation results complement the existing experimental data and provide important new insights into SAHH domain motions in solution, which play a crucial role in the catalytic mechanism of SAHH. (c) 2007 Wiley-Liss, Inc.

Structure-based discovery of clinically approved drugs as Zika virus NS2B-NS3 protease inhibitors that potently inhibit Zika virus infection in vitro and in vivo.

PubMed

Yuan, Shuofeng; Chan, Jasper Fuk-Woo; den-Haan, Helena; Chik, Kenn Ka-Heng; Zhang, Anna Jinxia; Chan, Chris Chung-Sing; Poon, Vincent Kwok-Man; Yip, Cyril Chik-Yan; Mak, Winger Wing-Nga; Zhu, Zheng; Zou, Zijiao; Tee, Kah-Meng; Cai, Jian-Piao; Chan, Kwok-Hung; de la Peña, Jorge; Pérez-Sánchez, Horacio; Cerón-Carrasco, José Pedro; Yuen, Kwok-Yung

2017-09-01

Zika virus (ZIKV) infection may be associated with severe complications in fetuses and adults, but treatment options are limited. We performed an in silico structure-based screening of a large chemical library to identify potential ZIKV NS2B-NS3 protease inhibitors. Clinically approved drugs belonging to different drug classes were selected among the 100 primary hit compounds with the highest predicted binding affinities to ZIKV NS2B-NS3-protease for validation studies. ZIKV NS2B-NS3 protease inhibitory activity was validated in most of the selected drugs and in vitro anti-ZIKV activity was identified in two of them (novobiocin and lopinavir-ritonavir). Molecular docking and molecular dynamics simulations predicted that novobiocin bound to ZIKV NS2B-NS3-protease with high stability. Dexamethasone-immunosuppressed mice with disseminated ZIKV infection and novobiocin treatment had significantly (P < 0.05) higher survival rate (100% vs 0%), lower mean blood and tissue viral loads, and less severe histopathological changes than untreated controls. This structure-based drug discovery platform should facilitate the identification of additional enzyme inhibitors of ZIKV. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular dynamics study of naturally existing cavity couplings in proteins.

PubMed

Barbany, Montserrat; Meyer, Tim; Hospital, Adam; Faustino, Ignacio; D'Abramo, Marco; Morata, Jordi; Orozco, Modesto; de la Cruz, Xavier

2015-01-01

Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.

Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins

PubMed Central

Barbany, Montserrat; Meyer, Tim; Hospital, Adam; Faustino, Ignacio; D'Abramo, Marco; Morata, Jordi; Orozco, Modesto; de la Cruz, Xavier

2015-01-01

Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results. PMID:25816327

Monte Carlo calculations of PET coincidence timing: single and double-ended readout

PubMed Central

Derenzo, Stephen E; Choong, Woon-Seng; Moses, William W

2016-01-01

We present Monte Carlo computational methods for estimating the coincidence resolving time (CRT) of scintillator detector pairs in positron emission tomography (PET) and present results for Lu2SiO5 : Ce (LSO), LaBr3 : Ce, and a hypothetical ultra-fast scintillator with a 1 ns decay time. The calculations were applied to both single-ended and double-ended photodetector readout with constant-fraction triggering. They explicitly include (1) the intrinsic scintillator properties (luminosity, rise time, decay time, and index of refraction), (2) the exponentially distributed depths of interaction, (3) the optical photon transport efficiency, delay, and time dispersion, (4) the photodetector properties (fill factor, quantum efficiency, transit time jitter, and single electron response), and (5) the determination of the constant fraction trigger level that minimizes the CRT. The calculations for single-ended readout include the delayed photons from the opposite reflective surface. The calculations for double-ended readout include (1) the simple average of the two photodetector trigger times, (2) more accurate estimators of the annihilation photon entrance time using the pulse height ratio to estimate the depth of interaction and correct for annihilation photon, optical photon, and trigger delays, and (3) the statistical lower bound for interactions at the center of the crystal. For time-of-flight (TOF) PET we combine stopping power and TOF information in a figure of merit equal to the sensitivity gain relative to whole-body non-TOF PET using LSO. For LSO crystals 3 mm × 3 mm × 30 mm, a decay time of 37 ns, a total photoelectron count of 4000, and a photodetector with 0.2 ns full-width at half-maximum (fwhm) timing jitter, single-ended readout has a CRT of 0.16 ns fwhm and double-ended readout has a CRT of 0.111 ns fwhm. For LaBr3 : Ce crystals 3 mm × 3 mm × 30 mm, a rise time of 0.2 ns, a decay time of 18 ns, and a total of 7600 photoelectrons the CRT numbers are 0.14 ns and 0.072 ns fwhm, respectively. For a hypothetical ultra-fast scintillator 3 mm × 3 mm × 30 mm, a decay time of 1 ns, and a total of 4000 photoelectrons, the CRT numbers are 0.070 and 0.020 ns fwhm, respectively. Over a range of examples, values for double-ended readout are about 10% larger than the statistical lower bound. PMID:26350162

Long pulse Soft X-ray Emission from Laser Generated Irradiated Gold Foils

NASA Astrophysics Data System (ADS)

Davis, Joshua; Frank, Yechiel; Raicher, Erez; Fraenkel, Moshe; Keiter, Paul; Klein, Sallee; Drake, R. P.; Shvarts, Dov

2016-10-01

Long pulse soft x-ray sources (SXS) allow for flexibility in high-energy-density experimental designs by providing a means of driving matter to the high temperatures needed, for example to study radiation waves in different materials. SXSs can be made by using lasers to heat a high-Z thin foil, which then acts as a quasi-blackbody emitter. Previous studies of the x-ray emission characteristics of gold foils have focused on laser pulses of 1ns or less. We performed experiments using a 6.0ns laser pulse with energy of 2kJ on the Omega-60 system to generate and characterize multi-ns laser heated Au foils of thicknesses between 0.5-2.0 μm. We measured the 2D spatial profile of the emission with a soft x-ray camera and the time history of the emission with the Dante photodiode array . Effective temperatures for the emission were then calculated using the Dante measurements. Discussion of experimental results and a comparison with 1-D Rad-Hydro NLTE simulations will be presented.

Note: Tesla based pulse generator for electrical breakdown study of liquid dielectrics

NASA Astrophysics Data System (ADS)

Veda Prakash, G.; Kumar, R.; Patel, J.; Saurabh, K.; Shyam, A.

2013-12-01

In the process of studying charge holding capability and delay time for breakdown in liquids under nanosecond (ns) time scales, a Tesla based pulse generator has been developed. Pulse generator is a combination of Tesla transformer, pulse forming line, a fast closing switch, and test chamber. Use of Tesla transformer over conventional Marx generators makes the pulse generator very compact, cost effective, and requires less maintenance. The system has been designed and developed to deliver maximum output voltage of 300 kV and rise time of the order of tens of nanoseconds. The paper deals with the system design parameters, breakdown test procedure, and various experimental results. To validate the pulse generator performance, experimental results have been compared with PSPICE simulation software and are in good agreement with simulation results.

Computing Rates of Small Molecule Diffusion Through Protein Channels Using Markovian Milestoning

NASA Astrophysics Data System (ADS)

Abrams, Cameron

2014-03-01

Measuring diffusion rates of ligands plays a key role in understanding the kinetic processes inside proteins. For example, although many molecular simulation studies have reported free energy barriers to infer rates for CO diffusion in myoglobin (Mb), they typically do not include direct calculation of diffusion rates because of the long simulation times needed to infer these rates with statistical accuracy. We show in this talk how to apply Markovian milestoning along minimum free-energy pathways to calculate diffusion rates of CO inside Mb. In Markovian milestoning, one partitions a suitable reaction coordinate space into regions and performs restrained molecular dynamics in each region to accumulate kinetic statistics that, when assembled across regions, provides an estimate of the mean first-passage time between states. The mean escape time for CO directly from the so-called distal pocket (DP) through the histidine gate (HG) is estimated at about 24 ns, confirming the importance of this portal for CO. But Mb is known to contain several internal cavities, and cavity-to-cavity diffusion rates are also computed and used to build a complete kinetic network as a Markov state model. Within this framework, the effective mean time of escape to the solvent through HG increases to 30 ns. Our results suggest that carrier protein structure may have evolved under pressure to modulate dissolved gas release rates using a network of ligand-accessible cavities. Support: NIH R01GM100472.

Optimal preconditioning of lattice Boltzmann methods

NASA Astrophysics Data System (ADS)

Izquierdo, Salvador; Fueyo, Norberto

2009-09-01

A preconditioning technique to accelerate the simulation of steady-state problems using the single-relaxation-time (SRT) lattice Boltzmann (LB) method was first proposed by Guo et al. [Z. Guo, T. Zhao, Y. Shi, Preconditioned lattice-Boltzmann method for steady flows, Phys. Rev. E 70 (2004) 066706-1]. The key idea in this preconditioner is to modify the equilibrium distribution function in such a way that, by means of a Chapman-Enskog expansion, a time-derivative preconditioner of the Navier-Stokes (NS) equations is obtained. In the present contribution, the optimal values for the free parameter γ of this preconditioner are searched both numerically and theoretically; the later with the aid of linear-stability analysis and with the condition number of the system of NS equations. The influence of the collision operator, single- versus multiple-relaxation-times (MRT), is also studied. Three steady-state laminar test cases are used for validation, namely: the two-dimensional lid-driven cavity, a two-dimensional microchannel and the three-dimensional backward-facing step. Finally, guidelines are suggested for an a priori definition of optimal preconditioning parameters as a function of the Reynolds and Mach numbers. The new optimally preconditioned MRT method derived is shown to improve, simultaneously, the rate of convergence, the stability and the accuracy of the lattice Boltzmann simulations, when compared to the non-preconditioned methods and to the optimally preconditioned SRT one. Additionally, direct time-derivative preconditioning of the LB equation is also studied.

AFRL Combustion Science Branch Research Activities and Capabilities

DTIC Science & Technology

2003-03-01

a wide variety of partners that include other DoD organizations, NASA, DoE, . engine companies , universities, small businesses, and on-site...Dynamics with Chemistry (CFDC) code (Katta et aI., 1994) known as UNICORN (UNsteady Ignition and COmbustion with ReactioNs). UNICORN is a time- dependent...simulate a variety of dynamic flames (Roquemore and Katta, 1998). From its conception, the development of UNICORN has been strongly coupled with

Classifier for gravitational-wave inspiral signals in nonideal single-detector data

NASA Astrophysics Data System (ADS)

Kapadia, S. J.; Dent, T.; Dal Canton, T.

2017-11-01

We describe a multivariate classifier for candidate events in a templated search for gravitational-wave (GW) inspiral signals from neutron-star-black-hole (NS-BH) binaries, in data from ground-based detectors where sensitivity is limited by non-Gaussian noise transients. The standard signal-to-noise ratio (SNR) and chi-squared test for inspiral searches use only properties of a single matched filter at the time of an event; instead, we propose a classifier using features derived from a bank of inspiral templates around the time of each event, and also from a search using approximate sine-Gaussian templates. The classifier thus extracts additional information from strain data to discriminate inspiral signals from noise transients. We evaluate a random forest classifier on a set of single-detector events obtained from realistic simulated advanced LIGO data, using simulated NS-BH signals added to the data. The new classifier detects a factor of 1.5-2 more signals at low false positive rates as compared to the standard "reweighted SNR" statistic, and does not require the chi-squared test to be computed. Conversely, if only the SNR and chi-squared values of single-detector events are available, random forest classification performs nearly identically to the reweighted SNR.

Novel crystal timing calibration method based on total variation

NASA Astrophysics Data System (ADS)

Yu, Xingjian; Isobe, Takashi; Watanabe, Mitsuo; Liu, Huafeng

2016-11-01

A novel crystal timing calibration method based on total variation (TV), abbreviated as ‘TV merge’, has been developed for a high-resolution positron emission tomography (PET) system. The proposed method was developed for a system with a large number of crystals, it can provide timing calibration at the crystal level. In the proposed method, the timing calibration process was formulated as a linear problem. To robustly optimize the timing resolution, a TV constraint was added to the linear equation. Moreover, to solve the computer memory problem associated with the calculation of the timing calibration factors for systems with a large number of crystals, the merge component was used for obtaining the crystal level timing calibration values. Compared with other conventional methods, the data measured from a standard cylindrical phantom filled with a radioisotope solution was sufficient for performing a high-precision crystal-level timing calibration. In this paper, both simulation and experimental studies were performed to demonstrate the effectiveness and robustness of the TV merge method. We compare the timing resolutions of a 22Na point source, which was located in the field of view (FOV) of the brain PET system, with various calibration techniques. After implementing the TV merge method, the timing resolution improved from 3.34 ns at full width at half maximum (FWHM) to 2.31 ns FWHM.

Is the minimum enough? Affordability of a nutritious diet for minimum wage earners in Nova Scotia (2002-2012).

PubMed

Newell, Felicia D; Williams, Patricia L; Watt, Cynthia G

2014-05-09

This paper aims to assess the affordability of a nutritious diet for households earning minimum wage in Nova Scotia (NS) from 2002 to 2012 using an economic simulation that includes food costing and secondary data. The cost of the National Nutritious Food Basket (NNFB) was assessed with a stratified, random sample of grocery stores in NS during six time periods: 2002, 2004/2005, 2007, 2008, 2010 and 2012. The NNFB's cost was factored into affordability scenarios for three different household types relying on minimum wage earnings: a household of four; a lone mother with three children; and a lone man. Essential monthly living expenses were deducted from monthly net incomes using methods that were standardized from 2002 to 2012 to determine whether adequate funds remained to purchase a basic nutritious diet across the six time periods. A 79% increase to the minimum wage in NS has resulted in a decrease in the potential deficit faced by each household scenario in the period examined. However, the household of four and the lone mother with three children would still face monthly deficits ($44.89 and $496.77, respectively, in 2012) if they were to purchase a nutritiously sufficient diet. As a social determinant of health, risk of food insecurity is a critical public health issue for low wage earners. While it is essential to increase the minimum wage in the short term, adequately addressing income adequacy in NS and elsewhere requires a shift in thinking from a focus on minimum wage towards more comprehensive policies ensuring an adequate livable income for everyone.

High power radiators of ultra-short electromagnetic quasi-unipolar pulses

NASA Astrophysics Data System (ADS)

Fedorov, V. M.; Ostashev, V. E.; Tarakanov, V. P.; Ul'yanov, A. V.

2017-05-01

Results of creation, operation, and diagnostics of the high power radiators for ultra-short length electromagnetic pulses (USEMPs) with a quasi-unipolar profile, which have been developed in our laboratory, are presented. The radiating module contains: the ultra-wideband (UWB) antenna array, the exciting high voltage pulse semiconductor generator (a pulser), the power source and the control unit. The principles of antenna array with a high efficiency aperture about 0.9 were developed using joint four TEM-horns with shielding electrodes in every TEM-horn. Sizes of the antenna apertures were (16-60) cm. The pulsers produced by “FID Technology” company had the following parameters: 50 Ohm connector impedance, unipolar pulses voltages (10-100) kV, the rise-time (0.04-0.15) ns, and the width (0.2-1) ns. The modules radiate the USEMPs of (0.1-10) GHz spectrum, their repetition rate is (1-100) kHz, and the effective potential is E*R = (20-400) kV, producing the peak E-field into the far-zone of R-distance. Parameters of the USEMP waves were measured by a calibrated sensor with the following characteristics: the sensitivity 0.32V/(kV/m), the rise-time 0.03 ns, the duration up to 7 ns. The measurements were in agreement with the simulation results, which were obtained using the 3-D code “KARAT”. The USEMP waves with amplitudes (1-10) kV/m and the pulse repetition rate (0.5-100) kHz were successfully used to examine various electronic devices for an electromagnetic immunity.

Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant

DTIC Science & Technology

2011-03-25

379 1317617 BG1320 (06415) NS pksR – Polyketide synthase BSU17720 (71.0) G:C C:S 1698/2574 1326096 BG1327 (06450) NS ebrB – multidrug resistance...frameshift mutation in the mmgD gene on the C-terminus of the 2-methylcitrate synthase homolog of B. atrophaeus strain Detrick-1. Arrow indicates the...lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole

Food Matrix Effects of Polyphenol Bioaccessibility from Almond Skin during Simulated Human Digestion

PubMed Central

Mandalari, Giuseppina; Vardakou, Maria; Faulks, Richard; Bisignano, Carlo; Martorana, Maria; Smeriglio, Antonella; Trombetta, Domenico

2016-01-01

The goal of the present study was to quantify the rate and extent of polyphenols released in the gastrointestinal tract (GIT) from natural (NS) and blanched (BS) almond skins. A dynamic gastric model of digestion which provides a realistic simulation of the human stomach was used. In order to establish the effect of a food matrix on polyphenols bioaccessibility, NS and BS were either digested in water (WT) or incorporated into home-made biscuits (HB), crisp-bread (CB) and full-fat milk (FM). Phenolic acids were the most bioaccessible class (68.5% release from NS and 64.7% from BS). WT increased the release of flavan-3-ols (p < 0.05) and flavonols (p < 0.05) from NS after gastric plus duodenal digestion, whereas CB and HB were better vehicles for BS. FM lowered the % recovery of polyphenols, the free total phenols and the antioxidant status in the digestion medium, indicating that phenolic compounds could bind protein present in the food matrix. The release of bioactives from almond skins could explain the beneficial effects associated with almond consumption. PMID:27649239

In silico prediction of a disease-associated STIL mutant and its affect on the recruitment of centromere protein J (CENPJ).

PubMed

Kumar, Ambuj; Rajendran, Vidya; Sethumadhavan, Rao; Purohit, Rituraj

2012-01-01

Human STIL (SCL/TAL1 interrupting locus) protein maintains centriole stability and spindle pole localisation. It helps in recruitment of CENPJ (Centromere protein J)/CPAP (centrosomal P4.1-associated protein) and other centrosomal proteins. Mutations in STIL protein are reported in several disorders, especially in deregulation of cell cycle cascades. In this work, we examined the non-synonymous single nucleotide polymorphisms (nsSNPs) reported in STIL protein for their disease association. Different SNP prediction tools were used to predict disease-associated nsSNPs. Our evaluation technique predicted rs147744459 (R242C) as a highly deleterious disease-associated nsSNP and its interaction behaviour with CENPJ protein. Molecular modelling, docking and molecular dynamics simulation were conducted to examine the structural consequences of the predicted disease-associated mutation. By molecular dynamic simulation we observed structural consequences of R242C mutation which affects interaction of STIL and CENPJ functional domains. The result obtained in this study will provide a biophysical insight into future investigations of pathological nsSNPs using a computational platform.

Simulation of runoff and nutrient export from a typical small watershed in China using the Hydrological Simulation Program-Fortran.

PubMed

Li, Zhaofu; Liu, Hongyu; Luo, Chuan; Li, Yan; Li, Hengpeng; Pan, Jianjun; Jiang, Xiaosan; Zhou, Quansuo; Xiong, Zhengqin

2015-05-01

The Hydrological Simulation Program-Fortran (HSPF), which is a hydrological and water-quality computer model that was developed by the United States Environmental Protection Agency, was employed to simulate runoff and nutrient export from a typical small watershed in a hilly eastern monsoon region of China. First, a parameter sensitivity analysis was performed to assess how changes in the model parameters affect runoff and nutrient export. Next, the model was calibrated and validated using measured runoff and nutrient concentration data. The Nash-Sutcliffe efficiency (E NS ) values of the yearly runoff were 0.87 and 0.69 for the calibration and validation periods, respectively. For storms runoff events, the E NS values were 0.93 for the calibration period and 0.47 for the validation period. Antecedent precipitation and soil moisture conditions can affect the simulation accuracy of storm event flow. The E NS values for the total nitrogen (TN) export were 0.58 for the calibration period and 0.51 for the validation period. In addition, the correlation coefficients between the observed and simulated TN concentrations were 0.84 for the calibration period and 0.74 for the validation period. For phosphorus export, the E NS values were 0.89 for the calibration period and 0.88 for the validation period. In addition, the correlation coefficients between the observed and simulated orthophosphate concentrations were 0.96 and 0.94 for the calibration and validation periods, respectively. The nutrient simulation results are generally satisfactory even though the parameter-lumped HSPF model cannot represent the effects of the spatial pattern of land cover on nutrient export. The model parameters obtained in this study could serve as reference values for applying the model to similar regions. In addition, HSPF can properly describe the characteristics of water quantity and quality processes in this area. After adjustment, calibration, and validation of the parameters, the HSPF model is suitable for hydrological and water-quality simulations in watershed planning and management and for designing best management practices.

Investigation of the limitations of the highly pixilated CdZnTe detector for PET applications

PubMed Central

Komarov, Sergey; Yin, Yongzhi; Wu, Heyu; Wen, Jie; Krawczynski, Henric; Meng, Ling-Jian; Tai, Yuan-Chuan

2016-01-01

We are investigating the feasibility of a high resolution positron emission tomography (PET) insert device based on the CdZnTe detector with 350 μm anode pixel pitch to be integrated into a conventional animal PET scanner to improve its image resolution. In this paper, we have used a simplified version of the multi pixel CdZnTe planar detector, 5 mm thick with 9 anode pixels only. This simplified 9 anode pixel structure makes it possible to carry out experiments without a complete application-specific integrated circuits readout system that is still under development. Special attention was paid to the double pixel (or charge sharing) detections. The following characteristics were obtained in experiment: energy resolution full-width-at-half-maximum (FWHM) is 7% for single pixel and 9% for double pixel photoelectric detections of 511 keV gammas; timing resolution (FWHM) from the anode signals is 30 ns for single pixel and 35 ns for double pixel detections (for photoelectric interactions only the corresponding values are 20 and 25 ns); position resolution is 350 μm in x,y-plane and ~0.4 mm in depth-of-interaction. The experimental measurements were accompanied by Monte Carlo (MC) simulations to find a limitation imposed by spatial charge distribution. Results from MC simulations suggest the limitation of the intrinsic spatial resolution of the CdZnTe detector for 511 keV photoelectric interactions is 170 μm. The interpixel interpolation cannot recover the resolution beyond the limit mentioned above for photoelectric interactions. However, it is possible to achieve higher spatial resolution using interpolation for Compton scattered events. Energy and timing resolution of the proposed 350 μm anode pixel pitch detector is no better than 0.6% FWHM at 511 keV, and 2 ns FWHM, respectively. These MC results should be used as a guide to understand the performance limits of the pixelated CdZnTe detector due to the underlying detection processes, with the understanding of the inherent limitations of MC methods. PMID:23079763

Investigation of the limitations of the highly pixilated CdZnTe detector for PET applications.

PubMed

Komarov, Sergey; Yin, Yongzhi; Wu, Heyu; Wen, Jie; Krawczynski, Henric; Meng, Ling-Jian; Tai, Yuan-Chuan

2012-11-21

We are investigating the feasibility of a high resolution positron emission tomography (PET) insert device based on the CdZnTe detector with 350 µm anode pixel pitch to be integrated into a conventional animal PET scanner to improve its image resolution. In this paper, we have used a simplified version of the multi pixel CdZnTe planar detector, 5 mm thick with 9 anode pixels only. This simplified 9 anode pixel structure makes it possible to carry out experiments without a complete application-specific integrated circuits readout system that is still under development. Special attention was paid to the double pixel (or charge sharing) detections. The following characteristics were obtained in experiment: energy resolution full-width-at-half-maximum (FWHM) is 7% for single pixel and 9% for double pixel photoelectric detections of 511 keV gammas; timing resolution (FWHM) from the anode signals is 30 ns for single pixel and 35 ns for double pixel detections (for photoelectric interactions only the corresponding values are 20 and 25 ns); position resolution is 350 µm in x,y-plane and ∼0.4 mm in depth-of-interaction. The experimental measurements were accompanied by Monte Carlo (MC) simulations to find a limitation imposed by spatial charge distribution. Results from MC simulations suggest the limitation of the intrinsic spatial resolution of the CdZnTe detector for 511 keV photoelectric interactions is 170 µm. The interpixel interpolation cannot recover the resolution beyond the limit mentioned above for photoelectric interactions. However, it is possible to achieve higher spatial resolution using interpolation for Compton scattered events. Energy and timing resolution of the proposed 350 µm anode pixel pitch detector is no better than 0.6% FWHM at 511 keV, and 2 ns FWHM, respectively. These MC results should be used as a guide to understand the performance limits of the pixelated CdZnTe detector due to the underlying detection processes, with the understanding of the inherent limitations of MC methods.

On the Induced Gravitational Collapse Scenario of Gamma-ray Bursts Associated with Supernovae

NASA Astrophysics Data System (ADS)

Becerra, L.; Bianco, C. L.; Fryer, C. L.; Rueda, J. A.; Ruffini, R.

2016-12-01

Following the induced gravitational collapse (IGC) paradigm of gamma-ray bursts (GRBs) associated with type Ib/c supernovae, we present numerical simulations of the explosion of a carbon-oxygen (CO) core in a binary system with a neutron-star (NS) companion. The supernova ejecta trigger a hypercritical accretion process onto the NS thanks to a copious neutrino emission and the trapping of photons within the accretion flow. We show that temperatures of 1-10 MeV develop near the NS surface, hence electron-positron annihilation into neutrinos becomes the main cooling channel leading to accretion rates of 10-9-{10}-1 {M}⊙ s-1 and neutrino luminosities of 1043-1052 erg s-1 (the shorter the orbital period the higher the accretion rate). We estimate the maximum orbital period, {P}\\max , as a function of the NS initial mass, up to which the NS companion can reach by hypercritical accretion the critical mass for gravitational collapse leading to black hole formation. We then estimate the effects of the accreting and orbiting NS companion onto a novel geometry of the supernova ejecta density profile. We present the results of a 1.4× {10}7 particle simulation which show that the NS induces accentuated asymmetries in the ejecta density around the orbital plane. We elaborate on the observables associated with the above features of the IGC process. We apply this framework to specific GRBs: we find that X-ray flashes (XRFs) and binary-driven hypernovae are produced in binaries with P\\gt {P}\\max and P\\lt {P}\\max , respectively. We analyze in detail the case of XRF 060218.

Relativistic neutron star merger simulations with non-zero temperature equations of state. I. Variation of binary parameters and equation of state

NASA Astrophysics Data System (ADS)

Oechslin, R.; Janka, H.-T.; Marek, A.

2007-05-01

An extended set of binary neutron star (NS) merger simulations is performed with an approximative treatment of general relativity to systematically investigate the influence of the nuclear equation of state (EoS), the NS masses, and the NS spin states prior to merging. The general relativistic hydrodynamics simulations are based on a conformally flat approximation to the Einstein equations and a Smoothed Particle Hydrodynamics code for the gas treatment. We employ the two non-zero temperature EoSs of Shen et al. (1998a, Nucl. Phys. A, 637, 435; 1998b, Prog. Theor. Phys., 100, 1013) and Lattimer & Swesty (1991, Nucl. Phys. A, 535, 331), which represent a "harder" and a "softer" behavior, respectively, with characteristic differences in the incompressibility at supernuclear densities and in the maximum mass of nonrotating, cold neutron stars. In addition, we use the cold EoS of Akmal et al. (1998, Phys. Rev. C, 58, 1804) with a simple ideal-gas-like extension according to Shibata & Taniguchi (2006, Phys. Rev. D, 73, 064027), in order to compare with their results, and an ideal-gas EoS with parameters fitted to the supernuclear part of the Shen-EoS. We estimate the mass sitting in a dilute "torus" around the future black hole (BH) by requiring the specific angular momentum of the torus matter to be larger than the angular momentum of the ISCO around a Kerr BH with the mass and spin parameter of the compact central remnant. The dynamics and outcome of the models is found to depend strongly on the EoS and on the binary parameters. Larger torus masses are found for asymmetric systems (up to 0.3 M_⊙ for a mass ratio of 0.55), for large initial NSs, and for a NS spin state which corresponds to a larger total angular momentum. We find that the postmerger remnant collapses either immediately or after a short time when employing the soft EoS of Lattimer& Swesty, whereas no sign of post-merging collapse is found within tens of dynamical timescales for all other EoSs used. The typical temperatures in the torus are found to be about 3{-}10 MeV depending on the strength of the shear motion at the collision interface between the NSs and thus depending on the initial NS spins. About 10-3{-}10-2 M_⊙ of NS matter become gravitationally unbound during or right after the merging process. This matter consists of a hot/high-entropy component from the collision interface and (only in case of asymmetric systems) of a cool/low-entropy component from the spiral arm tips. Appendices are only available in electronic form at http://www.aanda.org

Accelerated Time-Domain Modeling of Electromagnetic Pulse Excitation of Finite-Length Dissipative Conductors over a Ground Plane via Function Fitting and Recursive Convolution

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

Campione, Salvatore; Warne, Larry K.; Sainath, Kamalesh

In this report we overview the fundamental concepts for a pair of techniques which together greatly hasten computational predictions of electromagnetic pulse (EMP) excitation of finite-length dissipative conductors over a ground plane. In a time- domain, transmission line (TL) model implementation, predictions are computationally bottlenecked time-wise, either for late-time predictions (about 100ns-10000ns range) or predictions concerning EMP excitation of long TLs (order of kilometers or more ). This is because the method requires a temporal convolution to account for the losses in the ground. Addressing this to facilitate practical simulation of EMP excitation of TLs, we first apply a techniquemore » to extract an (approximate) complex exponential function basis-fit to the ground/Earth's impedance function, followed by incorporating this into a recursion-based convolution acceleration technique. Because the recursion-based method only requires the evaluation of the most recent voltage history data (versus the entire history in a "brute-force" convolution evaluation), we achieve necessary time speed- ups across a variety of TL/Earth geometry/material scenarios. Intentionally Left Blank« less

Novel Insights into the Molecular Interaction of a Panduratin A Derivative with the Non Structural Protein (NS3) of Dengue Serotypes: A Molecular Dynamics Study.

PubMed

Parida, Pratap; Yadav, Raj Narain Singh; Dehury, Budheswar; Ghosh, Debosree; Mahapatra, Namita; Mitra, Analava; Mohanta, Tapan Kumar

2017-01-01

The ligand PKP10 having substitution of Cl- at R2 and R3 positions of ring A of Panduratin A i.e., ((1R,2S,5S)-5-(2,3-dichlorophenyl)-3-methyl-2-(3-methylbut-2-nyl)cyclohex-3- enyl)(2,6-dihydroxy-4-methylphenyl)methanone hydrate) has been observed to block the Nuclear Receptor Binding Protein binding site of Non Structural protein 3 in all dengue serotypes. In continuation with our earlier study, we have reported sixty novel Panduratin A derivatives compounds where substitution was done in positions 2 and 3 position of the benzyl ring A of Panduratin A with various substituents. We selected ((1R,2S,5S)-5-(2,3-dichlorophenyl)-3-methyl-2-(3-methylbut-2-nyl)cyclohex-3- nyl) (2,6-dihydroxy-4-methylphenyl) methanone hydrate) (PKP10) for molecular dynamics (MD) simulations as it constantly produced lowest CDocker interaction energy of among all the sixty five derivatives. The CDocker interaction energy was predicted to be -140.804, -79.807, -78.217 and -84.073 Kcalmol-1 respectively against NS3 protein of dengue serotypes (DENV1-4). To understand the dynamics of the PKP10 with NS3 protein, each complex was subjected to molecular dynamics simulations of 50 ns in aqueous solution. MD (Molecular Dynamics) simulation study revealed that the binding of ligand PKP10 at the active site of NS3 induces a conformational change in all serotypes which was well supported by principal component analysis. To the best of our knowledge, this is first ever study which provided atomistic insights into the interaction of PKP10 with NS3 protein of dengue serotypes. The result from our study along with in vitro studies is expected to open up better avenues to develop inhibitors for dengue virus in the near future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Time Domain Stability Margin Assessment of the NS Space Launch System GN&C Design for Exploration Mission One

NASA Technical Reports Server (NTRS)

Clements, Keith; Wall, John

2017-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

Supernova neutrino detection in LZ

NASA Astrophysics Data System (ADS)

Khaitan, D.

2018-02-01

In the first 10 seconds of a core-collapse supernova, almost all of its progenitor's gravitational potential, O(1053 ergs), is carried away in the form of neutrinos. These neutrinos, with O(10 MeV) kinetic energy, can interact via coherent elastic neutrino-nucleus scattering (CEνNS) depositing O(1 keV) in detectors. In this work we describe the performances of low-background dark matter detectors, such as LUX-ZEPLIN (LZ), optimized for detecting low-energy depositions, in detecting these neutrino interactions. For instance, a 27 Msolar supernova at 10 kpc is expected to produce ~350 neutrino interactions in the 7-tonne liquid xenon active volume of LZ. Based on the LS220 EoS neutrino flux model for a SN, the Noble Element Simulation Technique (NEST), and predicted CEνNS cross-sections for xenon, to study energy deposition and detection of SN neutrinos in LZ. We simulate the response of the LZ data acquisition system (DAQ) and demonstrate its capability and limitations in handling this interaction rate. We present an overview of the LZ detector, focusing on the benefits of liquid xenon for supernova neutrino detection. We discuss energy deposition and detector response simulations and their results. We present an analysis technique to reconstruct the total number of neutrinos and the time of the supernova core bounce.

Multi-objective Calibration of DHSVM Based on Hydrologic Key Elements in Jinhua River Basin, East China

NASA Astrophysics Data System (ADS)

Pan, S.; Liu, L.; Xu, Y. P.

2017-12-01

Abstract: In physically based distributed hydrological model, large number of parameters, representing spatial heterogeneity of watershed and various processes in hydrologic cycle, are involved. For lack of calibration module in Distributed Hydrology Soil Vegetation Model, this study developed a multi-objective calibration module using Epsilon-Dominance Non-Dominated Sorted Genetic Algorithm II (ɛ-NSGAII) and based on parallel computing of Linux cluster for DHSVM (ɛP-DHSVM). In this study, two hydrologic key elements (i.e., runoff and evapotranspiration) are used as objectives in multi-objective calibration of model. MODIS evapotranspiration obtained by SEBAL is adopted to fill the gap of lack of observation for evapotranspiration. The results show that good performance of runoff simulation in single objective calibration cannot ensure good simulation performance of other hydrologic key elements. Self-developed ɛP-DHSVM model can make multi-objective calibration more efficiently and effectively. The running speed can be increased by more than 20-30 times via applying ɛP-DHSVM. In addition, runoff and evapotranspiration can be simulated very well simultaneously by ɛP-DHSVM, with superior values for two efficiency coefficients (0.74 for NS of runoff and 0.79 for NS of evapotranspiration, -10.5% and -8.6% for PBIAS of runoff and evapotranspiration respectively).

The High Time Resolution Universe Pulsar Survey - XIII. PSR J1757-1854, the most accelerated binary pulsar

NASA Astrophysics Data System (ADS)

Cameron, A. D.; Champion, D. J.; Kramer, M.; Bailes, M.; Barr, E. D.; Bassa, C. G.; Bhandari, S.; Bhat, N. D. R.; Burgay, M.; Burke-Spolaor, S.; Eatough, R. P.; Flynn, C. M. L.; Freire, P. C. C.; Jameson, A.; Johnston, S.; Karuppusamy, R.; Keith, M. J.; Levin, L.; Lorimer, D. R.; Lyne, A. G.; McLaughlin, M. A.; Ng, C.; Petroff, E.; Possenti, A.; Ridolfi, A.; Stappers, B. W.; van Straten, W.; Tauris, T. M.; Tiburzi, C.; Wex, N.

2018-03-01

We report the discovery of PSR J1757-1854, a 21.5-ms pulsar in a highly-eccentric, 4.4-h orbit with a neutron star (NS) companion. PSR J1757-1854 exhibits some of the most extreme relativistic parameters of any known pulsar, including the strongest relativistic effects due to gravitational-wave damping, with a merger time of 76 Myr. Following a 1.6-yr timing campaign, we have measured five post-Keplerian parameters, yielding the two component masses (mp = 1.3384(9) M⊙ and mc = 1.3946(9) M⊙) plus three tests of general relativity, which the theory passes. The larger mass of the NS companion provides important clues regarding the binary formation of PSR J1757-1854. With simulations suggesting 3-σ measurements of both the contribution of Lense-Thirring precession to the rate of change of the semimajor axis and the relativistic deformation of the orbit within ˜7-9 yr, PSR J1757-1854 stands out as a unique laboratory for new tests of gravitational theories.

Monte Carlo calculations of PET coincidence timing: single and double-ended readout

NASA Astrophysics Data System (ADS)

Derenzo, Stephen E.; Choong, Woon-Seng; Moses, William W.

2015-09-01

We present Monte Carlo computational methods for estimating the coincidence resolving time (CRT) of scintillator detector pairs in positron emission tomography (PET) and present results for Lu2SiO5 : Ce (LSO), LaBr3 : Ce, and a hypothetical ultra-fast scintillator with a 1 ns decay time. The calculations were applied to both single-ended and double-ended photodetector readout with constant-fraction triggering. They explicitly include (1) the intrinsic scintillator properties (luminosity, rise time, decay time, and index of refraction), (2) the exponentially distributed depths of interaction, (3) the optical photon transport efficiency, delay, and time dispersion, (4) the photodetector properties (fill factor, quantum efficiency, transit time jitter, and single electron response), and (5) the determination of the constant fraction trigger level that minimizes the CRT. The calculations for single-ended readout include the delayed photons from the opposite reflective surface. The calculations for double-ended readout include (1) the simple average of the two photodetector trigger times, (2) more accurate estimators of the annihilation photon entrance time using the pulse height ratio to estimate the depth of interaction and correct for annihilation photon, optical photon, and trigger delays, and (3) the statistical lower bound for interactions at the center of the crystal. For time-of-flight (TOF) PET we combine stopping power and TOF information in a figure of merit equal to the sensitivity gain relative to whole-body non-TOF PET using LSO. For LSO crystals 3 mm  ×  3 mm  ×  30 mm, a decay time of 37 ns, a total photoelectron count of 4000, and a photodetector with 0.2 ns full-width at half-maximum (fwhm) timing jitter, single-ended readout has a CRT of 0.16 ns fwhm and double-ended readout has a CRT of 0.111 ns fwhm. For LaBr3 : Ce crystals 3 mm  ×  3 mm  ×  30 mm, a rise time of 0.2 ns, a decay time of 18 ns, and a total of 7600 photoelectrons the CRT numbers are 0.14 ns and 0.072 ns fwhm, respectively. For a hypothetical ultra-fast scintillator 3 mm  ×  3 mm  ×  30 mm, a decay time of 1 ns, and a total of 4000 photoelectrons, the CRT numbers are 0.070 and 0.020 ns fwhm, respectively. Over a range of examples, values for double-ended readout are about 10% larger than the statistical lower bound.

Monte Carlo calculations of PET coincidence timing: single and double-ended readout.

PubMed

Derenzo, Stephen E; Choong, Woon-Seng; Moses, William W

2015-09-21

We present Monte Carlo computational methods for estimating the coincidence resolving time (CRT) of scintillator detector pairs in positron emission tomography (PET) and present results for Lu2SiO5 : Ce (LSO), LaBr3 : Ce, and a hypothetical ultra-fast scintillator with a 1 ns decay time. The calculations were applied to both single-ended and double-ended photodetector readout with constant-fraction triggering. They explicitly include (1) the intrinsic scintillator properties (luminosity, rise time, decay time, and index of refraction), (2) the exponentially distributed depths of interaction, (3) the optical photon transport efficiency, delay, and time dispersion, (4) the photodetector properties (fill factor, quantum efficiency, transit time jitter, and single electron response), and (5) the determination of the constant fraction trigger level that minimizes the CRT. The calculations for single-ended readout include the delayed photons from the opposite reflective surface. The calculations for double-ended readout include (1) the simple average of the two photodetector trigger times, (2) more accurate estimators of the annihilation photon entrance time using the pulse height ratio to estimate the depth of interaction and correct for annihilation photon, optical photon, and trigger delays, and (3) the statistical lower bound for interactions at the center of the crystal. For time-of-flight (TOF) PET we combine stopping power and TOF information in a figure of merit equal to the sensitivity gain relative to whole-body non-TOF PET using LSO. For LSO crystals 3 mm  ×  3 mm  ×  30 mm, a decay time of 37 ns, a total photoelectron count of 4000, and a photodetector with 0.2 ns full-width at half-maximum (fwhm) timing jitter, single-ended readout has a CRT of 0.16 ns fwhm and double-ended readout has a CRT of 0.111 ns fwhm. For LaBr3 : Ce crystals 3 mm  ×  3 mm  ×  30 mm, a rise time of 0.2 ns, a decay time of 18 ns, and a total of 7600 photoelectrons the CRT numbers are 0.14 ns and 0.072 ns fwhm, respectively. For a hypothetical ultra-fast scintillator 3 mm  ×  3 mm  ×  30 mm, a decay time of 1 ns, and a total of 4000 photoelectrons, the CRT numbers are 0.070 and 0.020 ns fwhm, respectively. Over a range of examples, values for double-ended readout are about 10% larger than the statistical lower bound.

Muon Creation in Supernova Matter Facilitates Neutrino-Driven Explosions.

PubMed

Bollig, R; Janka, H-T; Lohs, A; Martínez-Pinedo, G; Horowitz, C J; Melson, T

2017-12-15

Muons can be created in nascent neutron stars (NSs) due to the high electron chemical potentials and the high temperatures. Because of their relatively lower abundance compared to electrons, their role has so far been ignored in numerical simulations of stellar core collapse and NS formation. However, the appearance of muons softens the NS equation of state, triggers faster NS contraction, and thus leads to higher luminosities and mean energies of the emitted neutrinos. This strengthens the postshock heating by neutrinos and can facilitate explosions by the neutrino-driven mechanism.

Charged residues in the H-NS linker drive DNA binding and gene silencing in single cells.

PubMed

Gao, Yunfeng; Foo, Yong Hwee; Winardhi, Ricksen S; Tang, Qingnan; Yan, Jie; Kenney, Linda J

2017-11-21

Nucleoid-associated proteins (NAPs) facilitate chromosome organization in bacteria, but the precise mechanism remains elusive. H-NS is a NAP that also plays a major role in silencing pathogen genes. We used genetics, single-particle tracking in live cells, superresolution microscopy, atomic force microscopy, and molecular dynamics simulations to examine H-NS/DNA interactions in single cells. We discovered a role for the unstructured linker region connecting the N-terminal oligomerization and C-terminal DNA binding domains. In the present work we demonstrate that linker amino acids promote engagement with DNA. In the absence of linker contacts, H-NS binding is significantly reduced, although no change in chromosome compaction is observed. H-NS is not localized to two distinct foci; rather, it is scattered all around the nucleoid. The linker makes DNA contacts that are required for gene silencing, while chromosome compaction does not appear to be an important H-NS function.

Exploring resistance mechanisms of HCV NS3/4A protease mutations to MK5172: insight from molecular dynamics simulations and free energy calculations.

PubMed

Guan, Yan; Sun, Huiyong; Pan, Peichen; Li, Youyong; Li, Dan; Hou, Tingjun

2015-09-01

Mutations at a number of key positions (Ala156, Asp168 and Arg155) of the HCV NS3/4A protease can induce medium to high resistance to MK5172. The emergence of the resistant mutations seriously compromises the antiviral therapy efficacy to hepatitis C. In this study, molecular dynamics (MD) simulations, free energy calculations and free energy decomposition were used to explore the interaction profiles of MK5172 with the wild-type (WT) and four mutated (R155K, D168A, D168V and A156T) HCV NS3/4A proteases. The binding free energies predicted by Molecular Mechanics/Generalized Born Solvent Area (MM/GBSA) are consistent with the trend of the experimental drug resistance data. The free energy decomposition analysis shows that the resistant mutants may change the protein-MK5172 interaction profiles, resulting in the unbalanced energetic distribution amongst the catalytic triad, the strand 135-139 and the strand 154-160. Moreover, umbrella sampling (US) simulations were employed to elucidate the unbinding processes of MK5172 from the active pockets of the WT HCV NS3/4A protease and the four mutants. The US simulations demonstrate that the dissociation pathways of MK5172 escaping from the binding pockets of the WT and mutants are quite different, and it is quite possible that MK5172 will be harder to get access to the correct binding sites of the mutated proteases, thereafter leading to drug resistance.

Simulation of Voltage SET Operation in Phase-Change Random Access Memories with Heater Addition and Ring-Type Contactor for Low-Power Consumption by Finite Element Modeling

NASA Astrophysics Data System (ADS)

Gong, Yue-Feng; Song, Zhi-Tang; Ling, Yun; Liu, Yan; Li, Yi-Jin

2010-06-01

A three-dimensional finite element model for phase change random access memory is established to simulate electric, thermal and phase state distribution during (SET) operation. The model is applied to simulate the SET behaviors of the heater addition structure (HS) and the ring-type contact in the bottom electrode (RIB) structure. The simulation results indicate that the small bottom electrode contactor (BEC) is beneficial for heat efficiency and reliability in the HS cell, and the bottom electrode contactor with size Fx = 80 nm is a good choice for the RIB cell. Also shown is that the appropriate SET pulse time is 100 ns for the low power consumption and fast operation.

DISCRETE EVENT SIMULATION OF OPTICAL SWITCH MATRIX PERFORMANCE IN COMPUTER NETWORKS

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

Imam, Neena; Poole, Stephen W

2013-01-01

In this paper, we present application of a Discrete Event Simulator (DES) for performance modeling of optical switching devices in computer networks. Network simulators are valuable tools in situations where one cannot investigate the system directly. This situation may arise if the system under study does not exist yet or the cost of studying the system directly is prohibitive. Most available network simulators are based on the paradigm of discrete-event-based simulation. As computer networks become increasingly larger and more complex, sophisticated DES tool chains have become available for both commercial and academic research. Some well-known simulators are NS2, NS3, OPNET,more » and OMNEST. For this research, we have applied OMNEST for the purpose of simulating multi-wavelength performance of optical switch matrices in computer interconnection networks. Our results suggest that the application of DES to computer interconnection networks provides valuable insight in device performance and aids in topology and system optimization.« less

A 45-ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the earth simulator: dynamics of tertiary and quaternary structures.

PubMed

Saito, Minoru; Okazaki, Isao

2007-04-30

Molecular dynamics (MD) simulations of human adult hemoglobin (HbA) were carried out for 45 ns in water with all degrees of freedom including bond stretching and without any artificial constraints. To perform such large-scale simulations, one of the authors (M.S.) accelerated his own software COSMOS90 on the Earth Simulator by vectorization and parallelization. The dynamical features of HbA were investigated by evaluating root-mean-square deviations from the initial X-ray structure (an oxy T-state hemoglobin with PDB code: 1GZX) and root-mean-square fluctuations around the average structure from the simulation trajectories. The four subunits (alpha(1), alpha(2), beta(1), and beta(2)) of HbA maintained structures close to their respective X-ray structures during the simulations even though no constraints were applied to HbA in the simulations. Dimers alpha(1)beta(1) and alpha(2)beta(2) also maintained structures close to their respective X-ray structures while they moved relative to each other like two stacks of dumbbells. The distance between the two dimers (alpha(1)beta(1) and alpha(2)beta(2)) increased by 2 A (7.4%) in the initial 15 ns and stably fluctuated at the distance with the standard deviation 0.2 A. The relative orientation of the two dimers fluctuated between the initial X-ray angle -100 degrees and about -105 degrees with intervals of a few tens of nanoseconds.

Understanding the conformation transition in the activation pathway of β2 adrenergic receptor via a targeted molecular dynamics simulation.

PubMed

Xiao, Xiuchan; Zeng, Xiaojun; Yuan, Yuan; Gao, Nan; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

2015-01-28

G protein coupled receptors (GPCRs) play a crucial role in regulating signal recognition and transduction through their activation. The conformation transition in the activation pathway is of particular importance for their function. However, it has been poorly elucidated due to experimental difficulties in determining the conformations and the time limitation of conventional molecular dynamics (CMD) simulation. Thus, in this work, we employed a targeted molecular dynamic (TMD) simulation to study the activation process from an inactive structure to a fully active one for β2 adrenergic receptor (β2AR). As a reference, 110 ns CMD simulations on wild β2AR and its D130N mutant were also carried out. TMD results show that there is at least an intermediate conformation cluster in the activation process, evidenced by the principal component analysis and the structural and dynamic differences of some important motifs. It is noteworthy that the activation of the ligand binding site lags the G-protein binding site, displaying uncoupled correlation. Comparisons between the CMD and TMD results show that the D130N mutation significantly speeds up ICL2 and key ionic lock to enter into the intermediate state, which to some extent facilitates the activation involved in the NPxxY, DRY region and the separation between TM3 and TM6. However, the contribution from the D130N mutation to the activation of the ligand binding site could not be observed within the scale of 110 ns time. These observations could provide novel insights into previous studies for better understanding of the activation mechanism for β2AR.

Evaluation of asymmetric quadrupoles for a non-scaling fixed field alternating gradient accelerator

NASA Astrophysics Data System (ADS)

Lee, Sang-Hun; Park, Sae-Hoon; Kim, Yu-Seok

2017-12-01

A non-scaling fixed field alternating gradient (NS-FFAG) accelerator was constructed, which employs conventional quadrupoles. The possible demerit is the beam instability caused by the variable focusing strength when the orbit radius of the beam changes. To overcome this instability, it was suggested that the asymmetric quadrupole has different current flows in each coil. The magnetic field of the asymmetric quadrupole was found to be more similar to the magnetic field required for the FFAG accelerator than the constructed NS-FFAG accelerator. In this study, a simulation of the beam dynamics was carried out to evaluate the improvement to the beam stability for the NS-FFAG accelerator using the SIMION program. The beam dynamics simulation was conducted with the `hard edge' model; it ignored the fringe field at the end of the magnet. The magnetic field map of the suggested magnet was created using the SIMION program. The lattices for the simulation combined the suggested magnets. The magnets were evaluated for beam stability in the lattices through the SIMION program.

Sialyldisaccharide conformations: a molecular dynamics perspective

NASA Astrophysics Data System (ADS)

Selvin, Jeyasigamani F. A.; Priyadarzini, Thanu R. K.; Veluraja, Kasinadar

2012-04-01

Sialyldisaccharides are significant terminal components of glycoconjugates and their negative charge and conformation are extensively utilized in molecular recognition processes. The conformation and flexibility of four biologically important sialyldisaccharides [Neu5Acα(2-3)Gal, Neu5Acα(2-6)Gal, Neu5Acα(2-8)Neu5Ac and Neu5Acα(2-9)Neu5Ac] are studied using Molecular Dynamics simulations of 20 ns duration to deduce the conformational preferences of the sialyldisaccharides and the interactions which stabilize the conformations. This study clearly describes the possible conformational models of sialyldisaccharides deduced from 20 ns Molecular Dynamics simulations and our results confirm the role of water in the structural stabilization of sialyldisaccharides. An extensive analysis on the sialyldisaccharide structures available in PDB also confirms the conformational regions found by experiments are detected in MD simulations of 20 ns duration. The three dimensional structural coordinates for all the MD derived sialyldisaccharide conformations are deposited in the 3DSDSCAR database and these conformational models will be useful for glycobiologists and biotechnologists to understand the biological functions of sialic acid containing glycoconjugates.

Multiscale modeling and general theory of non-equilibrium plasma-assisted ignition and combustion

NASA Astrophysics Data System (ADS)

Yang, Suo; Nagaraja, Sharath; Sun, Wenting; Yang, Vigor

2017-11-01

A self-consistent framework for modeling and simulations of plasma-assisted ignition and combustion is established. In this framework, a ‘frozen electric field’ modeling approach is applied to take advantage of the quasi-periodic behaviors of the electrical characteristics to avoid the re-calculation of electric field for each pulse. The correlated dynamic adaptive chemistry (CO-DAC) method is employed to accelerate the calculation of large and stiff chemical mechanisms. The time-step is dynamically updated during the simulation through a three-stage multi-time scale modeling strategy, which utilizes the large separation of time scales in nanosecond pulsed plasma discharges. A general theory of plasma-assisted ignition and combustion is then proposed. Nanosecond pulsed plasma discharges for ignition and combustion can be divided into four stages. Stage I is the discharge pulse, with time scales of O (1-10 ns). In this stage, input energy is coupled into electron impact excitation and dissociation reactions to generate charged/excited species and radicals. Stage II is the afterglow during the gap between two adjacent pulses, with time scales of O (1 0 0 ns). In this stage, quenching of excited species dissociates O2 and fuel molecules, and provides fast gas heating. Stage III is the remaining gap between pulses, with time scales of O (1-100 µs). The radicals generated during Stages I and II significantly enhance exothermic reactions in this stage. The cumulative effects of multiple pulses is seen in Stage IV, with time scales of O (1-1000 ms), which include preheated gas temperatures and a large pool of radicals and fuel fragments to trigger ignition. For flames, plasma could significantly enhance the radical generation and gas heating in the pre-heat zone, thereby enhancing the flame establishment.

Dynamic response and residual stress fields of Ti6Al4V alloy under shock wave induced by laser shock peening

NASA Astrophysics Data System (ADS)

Sun, Rujian; Li, Liuhe; Zhu, Ying; Zhang, Lixin; Guo, Wei; Peng, Peng; Li, Bo; Guo, Chao; Liu, Lei; Che, Zhigang; Li, Weidong; Sun, Jianfei; Qiao, Hongchao

2017-09-01

Laser shock peening (LSP), an innovative surface treatment technique, generates compressive residual stress on the surface of metallic components to improve their fatigue performance, wear resistance and corrosion resistance. To illustrate the dynamic response during LSP and residual stress fields after LSP, this study conducted FEM simulations of LSP in a Ti6Al4V alloy. Results showed that when power density was 7 GW cm-2, a plastic deformation occurred at 10 ns during LSP and increased until the shock pressure decayed below the dynamic yield strength of Ti6Al4V after 60 ns. A maximum tensile region appeared beneath the surface at around 240 ns, forming a compressive-tensile-compressive stress sandwich structure with a thickness of 98, 1020 and 606 μm for each layer. After the model became stabilized, the value of the surface residual compressive stress was 564 MPa at the laser spot center. Higher value of residual stress across the surface and thicker compressive residual stress layers were achieved by increasing laser power density, impact times and spot sizes during LSP. A ‘Residual stress hole’ occurred with a high laser power density of 9 GW cm-2 when laser pulse duration was 10 ns, or with a long laser pulse duration of 20 ns when laser power density was 7 GW cm-2 for Ti6Al4V. This phenomenon occurred because of the permanent reverse plastic deformation generated at laser spot center.

Optimization of a PCRAM Chip for high-speed read and highly reliable reset operations

NASA Astrophysics Data System (ADS)

Li, Xiaoyun; Chen, Houpeng; Li, Xi; Wang, Qian; Fan, Xi; Hu, Jiajun; Lei, Yu; Zhang, Qi; Tian, Zhen; Song, Zhitang

2016-10-01

The widely used traditional Flash memory suffers from its performance limits such as its serious crosstalk problems, and increasing complexity of floating gate scaling. Phase change random access memory (PCRAM) becomes one of the most potential nonvolatile memories among the new memory techniques. In this paper, a 1M-bit PCRAM chip is designed based on the SMIC 40nm CMOS technology. Focusing on the read and write performance, two new circuits with high-speed read operation and highly reliable reset operation are proposed. The high-speed read circuit effectively reduces the reading time from 74ns to 40ns. The double-mode reset circuit improves the chip yield. This 1M-bit PCRAM chip has been simulated on cadence. After layout design is completed, the chip will be taped out for post-test.

Note: A rectangular pulse generator for 50 kV voltage, 0.8 ns rise time, and 10 ns pulse width based on polymer-film switch.

PubMed

Wu, Hanyu; Zhang, Xinjun; Sun, Tieping; Zeng, Zhengzhong; Cong, Peitian; Zhang, Shaoguo

2015-10-01

In this article, we describe a rectangular pulse generator, consisting of a polymer-film switch, a tri-plate transmission line, and parallel post-shaped ceramic resistor load, for 50-kV voltage, 0.8-ns rise time, and 10-ns width. The switch and resistors are arranged in atmospheric air and the transmission line can work in atmospheric air or in transformer oil to change the pulse width from 6.7 ns to 10 ns. The fast switching and low-inductance characteristics of the polymer-film switch ensure the fast rising wavefront of <1 ns. This generator can be applied in the calibration of nanosecond voltage dividers and used for electromagnetic pulse tests as a fast-rising current injection source.

Association between neurosyphilis and diabetes mellitus: resurgence of an old problem.

PubMed

Yang, Tianci; Tong, Manli; Xi, Ya; Guo, Xiaojing; Chen, Yuyan; Zhang, Yafeng; Zhang, Qiao; Liu, Long; Chen, Fuyi; Huang, Songjie; Zhang, Huilin; Zheng, Weihong; Lin, Lirong; Liu, Lili; Jiang, Jie

2014-09-01

Syphilis, a sexually transmitted disease, is commonly referred to as the "great imitator" because of its wide-ranging clinical presentations. Recently, we noticed that patients with neurosyphilis (NS) seemed to be more susceptible to complications of diabetes mellitus (DM). This is an interesting phenomenon, but it also puzzles clinicians because of scant knowledge about this situation. A case-control study was conducted to explore the association between NS and DM. Clinical data and the prevalence of DM among NS patients, patients with syphilis but not NS (syphilis/non-NS), non-syphilis patients, and healthy controls were analyzed. In addition, we explored the time of occurrence of NS and DM. Fasting plasma glucose and HbA1c levels in NS patients were significantly higher than in syphilis/non-NS patients, non-syphilis patients, and healthy controls (P < 0.05). In all, 45 of 149 NS patients (30.2%) were diagnosed with DM. The prevalence of DM in NS patients was significantly higher than in the other three groups (P < 0.05). There was no relationship between the prevalence of DM and the type of NS (e.g. asymptomatic NS, syphilitic meningitis, meningovascular NS, general paresis, and tabes dosalis). In the study population, 57.8% of NS patients were diagnosed with DM at the same time, whereas 80.0% were diagnosed with DM within 5 years of their diagnosis of NS. Based on the results of the present study, DM is not merely an occasional chance occurrence in NS patients. There is an association between NS and DM. © 2014 Ruijin Hospital, Shanghai Jiaotong University School of Medicine and Wiley Publishing Asia Pty Ltd.

3D-QSAR pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation toward identifying lead compounds for NS2B-NS3 protease inhibitors.

PubMed

Luo, Pei H; Zhang, Xuan R; Huang, Lan; Yuan, Lun; Zhou, Xang Z; Gao, X; Li, Ling S

2017-10-01

NS2B-NS3 protease has been identified to serve as lead drug design target due to its significant role in West Nile viral (WNV) and dengue virus (DENV) reproduction and replication. There are currently no approved chemotherapeutic drugs and effective vaccines to inhibit DENV and WNV infections. In this work, 3D-QSAR pharmacophore model has been developed to discover potential inhibitory candidates. Validation through Fischer's model and decoy test indicate that the developed 3D pharmacophore model is highly predictive for DENV inhibitors, which was then employed to screen ZINC chemical library to obtain reasonable hits. Following ADMET filtering, 15 hits were subjected to further filter through molecular docking and CoMFA modeling. Finally, top three hits were identified as lead compounds or potential inhibitory candidates with IC 50 values of ∼0.4637 µM and fitness of ∼57.73. It is implied from CoMFA modeling that substituents at the side site of benzotriazole such as a p-nitro group (e.g. biphenyl head) and a carbonyl (e.g. carboxylate function) at the side site of furan or amino group may improve bioactivity of ZINC85645245, respectively. Molecular dynamics simulations (MDS) were performed to discover new interactions and reinforce the binding modes from docking for the hits also. The QSAR and MDS results obtained from this work should be useful in determining structural requirements for inhibitor development as well as in designing more potential inhibitors for NS2B-NS3 protease.

Angular momentum role in the hypercritical accretion of binary-driven hypernovae

DOE PAGES

Becerra, L.; Cipolletta, F.; Fryer, Chris L.; ...

2015-10-12

Here, the induced gravitational collapse paradigm explains a class of energetic,more » $${E}_{{\\rm{iso}}}\\gtrsim {10}^{52}$$ erg, long-duration gamma-ray bursts (GRBs) associated with Ic supernovae, recently named binary-driven hypernovae. The progenitor is a tight binary system formed of a carbon–oxygen (CO) core and a neutron star (NS) companion. The supernova ejecta of the exploding CO core trigger a hypercritical accretion process onto the NS, which reaches the critical mass in a few seconds, and gravitationally collapses to a black hole, emitting a GRB. In our previous simulations of this process, we adopted a spherically symmetric approximation to compute the features of the hypercritical accretion process. We here present the first estimates of the angular momentum transported by the supernova ejecta, $${L}_{{\\rm{acc}}},$$ and perform numerical simulations of the angular momentum transfer to the NS during the hyperaccretion process in full general relativity. We show that the NS (1) reaches either the mass-shedding limit or the secular axisymmetric instability in a few seconds depending on its initial mass, (2) reaches a maximum dimensionless angular momentum value, $${[{cJ}/({{GM}}^{2})]}_{{\\rm{max}}}\\approx 0.7$$, and (3) can support less angular momentum than the one transported by supernova ejecta, $${L}_{{\\rm{acc}}}\\gt {J}_{{\\rm{NS,max}}},$$ hence there is an angular momentum excess that necessarily leads to jetted emission.« less

Angular momentum role in the hypercritical accretion of binary-driven hypernovae

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

Becerra, L.; Cipolletta, F.; Fryer, Chris L.

Here, the induced gravitational collapse paradigm explains a class of energetic,more » $${E}_{{\\rm{iso}}}\\gtrsim {10}^{52}$$ erg, long-duration gamma-ray bursts (GRBs) associated with Ic supernovae, recently named binary-driven hypernovae. The progenitor is a tight binary system formed of a carbon–oxygen (CO) core and a neutron star (NS) companion. The supernova ejecta of the exploding CO core trigger a hypercritical accretion process onto the NS, which reaches the critical mass in a few seconds, and gravitationally collapses to a black hole, emitting a GRB. In our previous simulations of this process, we adopted a spherically symmetric approximation to compute the features of the hypercritical accretion process. We here present the first estimates of the angular momentum transported by the supernova ejecta, $${L}_{{\\rm{acc}}},$$ and perform numerical simulations of the angular momentum transfer to the NS during the hyperaccretion process in full general relativity. We show that the NS (1) reaches either the mass-shedding limit or the secular axisymmetric instability in a few seconds depending on its initial mass, (2) reaches a maximum dimensionless angular momentum value, $${[{cJ}/({{GM}}^{2})]}_{{\\rm{max}}}\\approx 0.7$$, and (3) can support less angular momentum than the one transported by supernova ejecta, $${L}_{{\\rm{acc}}}\\gt {J}_{{\\rm{NS,max}}},$$ hence there is an angular momentum excess that necessarily leads to jetted emission.« less

Comparison between initial Magnetized Liner Inertial Fusion experiments and integrated simulations

NASA Astrophysics Data System (ADS)

Sefkow, A. B.; Gomez, M. R.; Geissel, M.; Hahn, K. D.; Hansen, S. B.; Harding, E. C.; Peterson, K. J.; Slutz, S. A.; Koning, J. M.; Marinak, M. M.

2014-10-01

The Magnetized Liner Inertial Fusion (MagLIF) approach to ICF has obtained thermonuclear fusion yields using the Z facility. Integrated magnetohydrodynamic simulations provided the design for the first neutron-producing experiments using capabilities that presently exist, and the initial experiments measured stagnation radii rstag < 75 μm, temperatures around 3 keV, and isotropic neutron yields up to YnDD = 2 ×1012 from imploded liners reaching peak velocities around 70 km/s over an implosion time of about 60 ns. We present comparisons between the experimental observables and post-shot degraded integrated simulations. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Collisional-radiative simulations of a supersonic and radiatively cooled aluminum plasma jet

NASA Astrophysics Data System (ADS)

Espinosa, G.; Gil, J. M.; Rodriguez, R.; Rubiano, J. G.; Mendoza, M. A.; Martel, P.; Minguez, E.; Suzuki-Vidal, F.; Lebedev, S. V.; Swadling, G. F.; Burdiak, G.; Pickworth, L. A.; Skidmore, J.

2015-12-01

A computational investigation based on collisional-radiative simulations of a supersonic and radiatively cooled aluminum plasma jet is presented. The jet, both in vacuum and in argon ambient gas, was produced on the MAGPIE (Mega Ampere Generator for Plasma Implosion Experiments) generator and is formed by ablation of an aluminum foil driven by a 1.4 MA, 250 ns current pulse in a radial foil Z-pinch configuration. In this work, population kinetics and radiative properties simulations of the jet in different theoretical approximations were performed. In particular, local thermodynamic equilibrium (LTE), non-LTE steady state (SS) and non-LTE time dependent (TD) models have been considered. This study allows us to make a convenient microscopic characterization of the aluminum plasma jet.

Large scale atomistic simulation of single-layer graphene growth on Ni(111) surface: molecular dynamics simulation based on a new generation of carbon-metal potential

NASA Astrophysics Data System (ADS)

Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng

2015-12-01

To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06016h

Dynamics of a high-current relativistic electron beam

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

Strelkov, P. S., E-mail: strelkov@fpl.gpi.ru; Tarakanov, V. P., E-mail: karat@gmail.ru; Ivanov, I. E., E-mail: iei@fpl.gpi.ru

2015-06-15

The dynamics of a high-current relativistic electron beam is studied experimentally and by numerical simulation. The beam is formed in a magnetically insulated diode with a transverse-blade explosive-emission cathode. It is found experimentally that the radius of a 500-keV beam with a current of 2 kA and duration of 500 ns decreases with time during the beam current pulse. The same effect was observed in numerical simulations. This effect is explained by a change in the shape of the cathode plasma during the current pulse, which, according to calculations, leads to a change in the beam parameters, such as themore » electron pitch angle and the spread over the longitudinal electron momentum. These parameters are hard to measure experimentally; however, the time evolution of the radial profile of the beam current density, which can be measured reliably, coincides with the simulation results. This allows one to expect that the behavior of the other beam parameters also agrees with numerical simulations.« less

Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics

PubMed Central

Stadler, A. M.; Garvey, C. J.; Bocahut, A.; Sacquin-Mora, S.; Digel, I.; Schneider, G. J.; Natali, F.; Artmann, G. M.; Zaccai, G.

2012-01-01

Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus; domestic chicken, Gallus gallus domesticus and human, Homo sapiens) and an ectotherm (salt water crocodile, Crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits. PMID:22696485

Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics.

PubMed

Stadler, A M; Garvey, C J; Bocahut, A; Sacquin-Mora, S; Digel, I; Schneider, G J; Natali, F; Artmann, G M; Zaccai, G

2012-11-07

Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus; domestic chicken, Gallus gallus domesticus and human, Homo sapiens) and an ectotherm (salt water crocodile, Crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.

Irreversible transformation of ferromagnetic ordered stripe domains in single-shot infrared-pump/resonant-x-ray-scattering-probe experiments

NASA Astrophysics Data System (ADS)

Bergeard, Nicolas; Schaffert, Stefan; López-Flores, Víctor; Jaouen, Nicolas; Geilhufe, Jan; Günther, Christian M.; Schneider, Michael; Graves, Catherine; Wang, Tianhan; Wu, Benny; Scherz, Andreas; Baumier, Cédric; Delaunay, Renaud; Fortuna, Franck; Tortarolo, Marina; Tudu, Bharati; Krupin, Oleg; Minitti, Michael P.; Robinson, Joe; Schlotter, William F.; Turner, Joshua J.; Lüning, Jan; Eisebitt, Stefan; Boeglin, Christine

2015-02-01

The evolution of a magnetic domain structure upon excitation by an intense, femtosecond infrared (IR) laser pulse has been investigated using single-shot based time-resolved resonant x-ray scattering at the x-ray free electron laser LCLS. A well-ordered stripe domain pattern as present in a thin CoPd alloy film has been used as a prototype magnetic domain structure for this study. The fluence of the IR laser pump pulse was sufficient to lead to an almost complete quenching of the magnetization within the ultrafast demagnetization process taking place within the first few hundreds of femtoseconds following the IR laser pump pulse excitation. On longer time scales this excitation gave rise to subsequent irreversible transformations of the magnetic domain structure. Under our specific experimental conditions, it took about 2 ns before the magnetization started to recover. After about 5 ns the previously ordered stripe domain structure had evolved into a disordered labyrinth domain structure. Surprisingly, we observe after about 7 ns the occurrence of a partially ordered stripe domain structure reoriented into a novel direction. It is this domain structure in which the sample's magnetization stabilizes as revealed by scattering patterns recorded long after the initial pump-probe cycle. Using micromagnetic simulations we can explain this observation based on changes of the magnetic anisotropy going along with heat dissipation in the film.

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

PubMed

Yoneda, Shigetaka; Sugawara, Yoko; Urabe, Hisako

2005-01-27

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

Spectroscopic characteristics of H α /OI atomic lines generated by nanosecond pulsed corona-like discharge in deionized water

NASA Astrophysics Data System (ADS)

Pongrác, Branislav; Šimek, Milan; Člupek, Martin; Babický, Václav; Lukeš, Petr

2018-03-01

Basic emission fingerprints of nanosecond discharges produced in deionized water by fast rise-time positive high-voltage pulses (duration of 6 ns and amplitude of  +100 kV) in a point-to-plane electrode geometry were investigated by means of time-resolved intensified charge-coupled device (ICCD) spectroscopy. Time-resolved emission spectra were measured via ICCD kinetic series during the discharge ignition and later phases over the 350-850 nm spectral range with fixed, either 3 ns or 30 ns, acquisition time and with 3 ns or 30 ns time resolution, respectively. The luminous phase of the initial discharge expansion and its subsequent collapse was characterized by a broadband vis-NIR continuum emission evolving during the first few nanoseconds which shifted more toward the UV with further increase of time. After ~30 ns from the discharge onset, the continuum gradually disappeared followed by the emission of H α and OI atomic lines. The electron densities calculated from the H α profile fit were estimated to be of the order of 1018-1019 cm-3. It is unknown if the H α and OI atomic lines are generated even in earlier times (before ~30 ns) because such signals were not detectable due to the superposition with the strong continuum. However, subsequent events caused by the reflected HV pulses were observed to have significant effects on the emission spectra profiles of the nanosecond discharge. By varying the time delay of the reflected pulse from 45 to 90 ns after the primary pulse, the intensities of the H α /OI atomic lines in the emission spectra of the secondary discharges were clearly visible and their intensities were greater with shorter time delay between primary and reflected pulses. These results indicate that the discharges generated due to the reflected pulses were very likely generated in the non-relaxed environment.

Healthcare Supported by Data Mule Networks in Remote Communities of the Amazon Region

PubMed Central

Coutinho, Mauro Margalho; Efrat, Alon; Richa, Andrea

2014-01-01

This paper investigates the feasibility of using boats as data mule nodes, carrying medical ultrasound videos from remote and isolated communities in the Amazon region in Brazil, to the main city of that area. The videos will be used by physicians to perform remote analysis and follow-up routine of prenatal examinations of pregnant women. Two open source simulators (the ONE and NS-2) were used to evaluate the results obtained utilizing a CoDPON (continuous displacement plan oriented network). The simulations took into account the connection times between the network nodes (boats) and the number of nodes on each boat route. PMID:27433519

Multiscale simulations on conformational dynamics and membrane interactions of the non-structural 2 (NS2) transmembrane domain.

PubMed

Hung, Huynh Minh; Hang, Tran Dieu; Nguyen, Minh Tho

2016-09-09

Hepatitis C virus (HCV) is one of the most crucial global health issues, in which the HCV non-structural protein 2 (NS2), particularly its three transmembrane segments, plays a crucial role in HCV assembly. In this context, multiscale MD simulations have been applied to investigate the preferred orientation of transmembrane domain of NS2 protein (TNS2) in a POPC bilayer, structural stability and characteristic of intramembrane protein-lipid and protein-protein interaction. Our study indicates that NS2 protein adopts three trans-membrane segments with highly stable α-helix structure in a POPC bilayer and a short helical luminal segment. While the first and second TM segment involved in continuous helical domain, the third TM segment is however cleaved into two sub-segments with different tilt angles via a kink at L87G88. Salt bridges K81-E45, R32-PO4 and R43-PO4 are determined as the key factor to stabilize the structure of TM2 and TM3 which consist of charged residues located in the hydrophobic region of the membrane. Copyright © 2016 Elsevier Inc. All rights reserved.

Phase control and fast start-up of a magnetron using modulation of an addressable faceted cathode

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

Browning, J., E-mail: JimBrowning@BoiseState.edu; Fernandez-Gutierrez, S.; Lin, M. C.

The use of an addressable, faceted cathode has been proposed as a method of modulating current injection in a magnetron to improve performance and control phase. To implement the controllable electron emission, five-sided and ten-sided faceted planar cathodes employing gated field emitters are considered as these emitters could be fabricated on flat substrates. For demonstration, the conformal finite-difference time-domain particle-in-cell simulation, as implemented in VORPAL, has been used to model a ten-cavity, rising sun magnetron using the modulated current sources and benchmarked against a typical continuous current source. For the modulated, ten-sided faceted cathode case, the electrons are injected frommore » three emitter elements on each of the ten facets. Each emitter is turned ON and OFF in sequence at the oscillating frequency with five emitters ON at one time to drive the five electron spokes of the π-mode. The emitter duty cycle is then 1/6th the Radio-Frequency (RF) period. Simulations show a fast start-up time as low as 35 ns for the modulated case compared to 100 ns for the continuous current cases. Analysis of the RF phase using the electron spoke locations and the RF magnetic field components shows that the phase is controlled for the modulated case while it is random, as typical, for the continuous current case. Active phase control during oscillation was demonstrated by shifting the phase of the electron injection 180° after oscillations started. The 180° phase shift time was approximately 25 RF cycles.« less

The Hydrogen Epoch of Reionization Array Dish. II. Characterization of Spectral Structure with Electromagnetic Simulations and Its Science Implications.

NASA Astrophysics Data System (ADS)

Ewall-Wice, Aaron; Bradley, Richard; Deboer, David; Hewitt, Jacqueline; Parsons, Aaron; Aguirre, James; Ali, Zaki S.; Bowman, Judd; Cheng, Carina; Neben, Abraham R.; Patra, Nipanjana; Thyagarajan, Nithyanandan; Venter, Mariet; de Lera Acedo, Eloy; Dillon, Joshua S.; Dickenson, Roger; Doolittle, Phillip; Egan, Dennis; Hedrick, Mike; Klima, Patricia; Kohn, Saul; Schaffner, Patrick; Shelton, John; Saliwanchik, Benjamin; Taylor, H. A.; Taylor, Rusty; Tegmark, Max; Wirt, Butch

2016-11-01

We use time-domain electromagnetic simulations to determine the spectral characteristics of the Hydrogen Epoch of Reionization Arrays (HERA) antenna. These simulations are part of a multi-faceted campaign to determine the effectiveness of the dish’s design for obtaining a detection of redshifted 21 cm emission from the epoch of reionization. Our simulations show the existence of reflections between HERA’s suspended feed and its parabolic dish reflector that fall below -40 dB at 150 ns and, for reasonable impedance matches, have a negligible impact on HERA’s ability to constrain EoR parameters. It follows that despite the reflections they introduce, dishes are effective for increasing the sensitivity of EoR experiments at a relatively low cost. We find that electromagnetic resonances in the HERA feed’s cylindrical skirt, which is intended to reduce cross coupling and beam ellipticity, introduces significant power at large delays (-40 dB at 200 ns), which can lead to some loss of measurable Fourier modes and a modest reduction in sensitivity. Even in the presence of this structure, we find that the spectral response of the antenna is sufficiently smooth for delay filtering to contain foreground emission at line-of-sight wave numbers below k ∥ ≲ 0.2 h Mpc-1, in the region where the current PAPER experiment operates. Incorporating these results into a Fisher Matrix analysis, we find that the spectral structure observed in our simulations has only a small effect on the tight constraints HERA can achieve on parameters associated with the astrophysics of reionization.

Functional domain motions in proteins on the ~1-100 ns timescale: comparison of neutron spin-echo spectroscopy of phosphoglycerate kinase with molecular-dynamics simulation.

PubMed

Smolin, N; Biehl, R; Kneller, G R; Richter, D; Smith, J C

2012-03-07

Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ~1-100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Functional Domain Motions in Proteins on the ∼1–100 ns Timescale: Comparison of Neutron Spin-Echo Spectroscopy of Phosphoglycerate Kinase with Molecular-Dynamics Simulation

PubMed Central

Smolin, N.; Biehl, R.; Kneller, G.R.; Richter, D.; Smith, J.C.

2012-01-01

Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ∼1–100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins. PMID:22404933

Early diagnosis of dengue in travelers: comparison of a novel real-time RT-PCR, NS1 antigen detection and serology.

PubMed

Huhtamo, Eili; Hasu, Essi; Uzcátegui, Nathalie Y; Erra, Elina; Nikkari, Simo; Kantele, Anu; Vapalahti, Olli; Piiparinen, Heli

2010-01-01

The increased traveling to dengue endemic regions and the numerous epidemics have led to a rise in imported dengue. The laboratory diagnosis of acute dengue requires several types of tests and often paired samples are needed for obtaining reliable results. Although several diagnostic methods are available, proper comparative data on their performance are lacking. To compare the performance of novel methods including a novel pan-DENV real-time RT-PCR and a commercially available NS1 capture-EIA in regard to IgM detection for optimizing the early diagnosis of DENV in travelers. A panel of 99 selected early phase serum samples of dengue patients was studied by real-time RT-PCR, NS1 antigen ELISA, IgM-EIA, IgG-IFA and cell culture virus isolation. The novel real-time RT-PCR was shown specific and sensitive for detection of DENV-1-4 RNA and suitable for diagnostic use. The diagnostic rate using combination of RNA and IgM detection was 99% and using NS1 and IgM detection 95.9%. The results of RNA and NS1 antigen detection disagreed in 15.5% of samples that had only RNA or NS1 antigen detected. The diagnostic rates of early samples are higher when either RNA or NS1 antigen detection is combined with IgM detection. Besides the differences in the RNA and NS1 detection assays, the observed discrepancy of results could suggest individual variation or differences in timing of these markers in patient serum. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Microwave Plasma-Activated Chemical Vapor Deposition of Nitrogen-Doped Diamond. II: CH4/N2/H2 Plasmas

PubMed Central

2016-01-01

We report a combined experimental and modeling study of microwave-activated dilute CH4/N2/H2 plasmas, as used for chemical vapor deposition (CVD) of diamond, under very similar conditions to previous studies of CH4/H2, CH4/H2/Ar, and N2/H2 gas mixtures. Using cavity ring-down spectroscopy, absolute column densities of CH(X, v = 0), CN(X, v = 0), and NH(X, v = 0) radicals in the hot plasma have been determined as functions of height, z, source gas mixing ratio, total gas pressure, p, and input power, P. Optical emission spectroscopy has been used to investigate, with respect to the same variables, the relative number densities of electronically excited species, namely, H atoms, CH, C2, CN, and NH radicals and triplet N2 molecules. The measurements have been reproduced and rationalized from first-principles by 2-D (r, z) coupled kinetic and transport modeling, and comparison between experiment and simulation has afforded a detailed understanding of C/N/H plasma-chemical reactivity and variations with process conditions and with location within the reactor. The experimentally validated simulations have been extended to much lower N2 input fractions and higher microwave powers than were probed experimentally, providing predictions for the gas-phase chemistry adjacent to the diamond surface and its variation across a wide range of conditions employed in practical diamond-growing CVD processes. The strongly bound N2 molecule is very resistant to dissociation at the input MW powers and pressures prevailing in typical diamond CVD reactors, but its chemical reactivity is boosted through energy pooling in its lowest-lying (metastable) triplet state and subsequent reactions with H atoms. For a CH4 input mole fraction of 4%, with N2 present at 1–6000 ppm, at pressure p = 150 Torr, and with applied microwave power P = 1.5 kW, the near-substrate gas-phase N atom concentration, [N]ns, scales linearly with the N2 input mole fraction and exceeds the concentrations [NH]ns, [NH2]ns, and [CN]ns of other reactive nitrogen-containing species by up to an order of magnitude. The ratio [N]ns/[CH3]ns scales proportionally with (but is 102–103 times smaller than) the ratio of the N2 to CH4 input mole fractions for the given values of p and P, but [N]ns/[CN]ns decreases (and thus the potential importance of CN in contributing to N-doped diamond growth increases) as p and P increase. Possible insights regarding the well-documented effects of trace N2 additions on the growth rates and morphologies of diamond films formed by CVD using MW-activated CH4/H2 gas mixtures are briefly considered. PMID:27718565

Compact Binary Progenitors of Short Gamma-Ray Bursts

NASA Technical Reports Server (NTRS)

Giacomazzo, Bruno; Perna, Rosalba; Rezzolla, Luciano; Troja, Eleonora; Lazzati, Davide

2013-01-01

In recent years, detailed observations and accurate numerical simulations have provided support to the idea that mergers of compact binaries containing either two neutron stars (NSs) or an NS and a black hole (BH) may constitute the central engine of short gamma-ray bursts (SGRBs). The merger of such compact binaries is expected to lead to the production of a spinning BH surrounded by an accreting torus. Several mechanisms can extract energy from this system and power the SGRBs. Here we connect observations and numerical simulations of compact binary mergers, and use the current sample of SGRBs with measured energies to constrain the mass of their powering tori. By comparing the masses of the tori with the results of fully general-relativistic simulations, we are able to infer the properties of the binary progenitors that yield SGRBs. By assuming a constant efficiency in converting torus mass into jet energy epsilon(sub jet) = 10%, we find that most of the tori have masses smaller than 0.01 Solar M, favoring "high-mass" binary NSs mergers, i.e., binaries with total masses approx >1.5 the maximum mass of an isolated NS. This has important consequences for the gravitational wave signals that may be detected in association with SGRBs, since "high-mass" systems do not form a long-lived hypermassive NS after the merger. While NS-BH systems cannot be excluded to be the engine of at least some of the SGRBs, the BH would need to have an initial spin of approx. 0.9 or higher.

Possible repetitive pulse operation of diode-pumped alkali laser (DPAL)

NASA Astrophysics Data System (ADS)

Endo, Masamori

2017-01-01

A theoretical study has been conducted for investigating the possibility of a diode-pumped alkali laser (DPAL) operating in repetitive pulsed mode. A one-dimensional, time-dependent rate-equation simulation of a Cs DPAL was developed to calculate the dynamic behavior of the active medium when Q-switching or cavity dumping was applied. The simulation modeled our small-scale experimental apparatus. In the continuous-wave (CW) mode, the calculated output power was in good agreement with the experimental value. Q-switching was shown to be ineffective because of the short spontaneous lifetime of the active medium, on the order of 10 ns. On the other hand, cavity dumping was proven to be effective. In typical operational conditions, a 54 times increase in peak power with respect to the CW power was predicted.

Circuit design and simulation of a transmit beamforming ASIC for high-frequency ultrasonic imaging systems.

PubMed

Athanasopoulos, Georgios I; Carey, Stephen J; Hatfield, John V

2011-07-01

This paper describes the design of a programmable transmit beamformer application-specific integrated circuit (ASIC) with 8 channels for ultrasound imaging systems. The system uses a 20-MHz reference clock. A digital delay-locked loop (DLL) was designed with 50 variable delay elements, each of which provides a clock with different phase from a single reference. Two phase detectors compare the phase difference of the reference clock with the feedback clock, adjusting the delay of the delay elements to bring the feedback clock signal in phase with the reference clock signal. Two independent control voltages for the delay elements ensure that the mark space ratio of the pulses remain at 50%. By combining a 10- bit asynchronous counter with the delays from the DLL, each channel can be programmed to give a maximum time delay of 51 μs with 1 ns resolution. It can also give bursts of up to 64 pulses. Finally, for a single pulse, it can adjust the pulse width between 9 ns and 100 ns by controlling the current flowing through a capacitor in a one-shot circuit, for use with 40-MHz and 5-MHz transducers, respectively.

Wire Array Z-pinches on Sphinx Machine: Experimental Results and Relevant Points of Microsecond Implosion Physics

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

Calamy, H.; Hamann, F.; Lassalle, F.

Centre d'Etudes de Gramat (France) has developed an efficient long implosion time (800 ns) Aluminum plasma radiation source (PRS). Based on the LTD technology, the SPHINX facility is developed as a 1-3MJ, 1{mu}s rise time, 4-10 MA current driver. In this paper, it was used in 1MJ, 4MA configuration to drive Aluminum nested wire arrays Z-pinches with K-shell yield up to 20 kJ and a FWHM of the x-ray pulse of about 50 ns. We present latest SPHINX experiments and some of the main physic issues of the microsecond regime. Experimental setup and results are described with the aim ofmore » giving trends that have been obtained. The main features of microsecond implosion of wire arrays can be analyzed thanks to same methods and theories as used for faster Z-pinches. The effect of load polarity was examined. The stability of the implosion , one of the critical point of microsecond wire arrays due to the load dimensions imposed by the time scale, is tackled. A simple scaling from 100 ns Z-pinch results to 800 ns ones gives good results and the use of nested arrays improves dramatically the implosion quality and the Kshell yield of the load. However, additional effects such as the impact of the return current can geometry on the implosion have to be taken into account on our loads. Axial inhomogeneity of the implosion the origin of which is not yet well understood occurs in some shots and impacts the radiation output. The shape of the radiative pulse is discussed and compared with the homogeneity of the implosion. Numerical 2D R-Z and R-{theta} simulations are used to highlight some experimental results and understand the plasma conditions during these microsecond wire arrays implosions.« less

Wire Array Z-pinches on Sphinx Machine: Experimental Results and Relevant Points of Microsecond Implosion Physics

NASA Astrophysics Data System (ADS)

Calamy, H.; Hamann, F.; Lassalle, F.; Bayol, F.; Mangeant, C.; Morell, A.; Huet, D.; Bedoch, J. P.; Chittenden, J. P.; Lebedev, S. V.; Jennings, C. A.; Bland, S. N.

2006-01-01

Centre d'Etudes de Gramat (France) has developed an efficient long implosion time (800 ns) Aluminum plasma radiation source (PRS). Based on the LTD technology, the SPHINX facility is developed as a 1-3MJ, 1μs rise time, 4-10 MA current driver. In this paper, it was used in 1MJ, 4MA configuration to drive Aluminum nested wire arrays Z-pinches with K-shell yield up to 20 kJ and a FWHM of the x-ray pulse of about 50 ns. We present latest SPHINX experiments and some of the main physic issues of the microsecond regime. Experimental setup and results are described with the aim of giving trends that have been obtained. The main features of microsecond implosion of wire arrays can be analyzed thanks to same methods and theories as used for faster Z-pinches. The effect of load polarity was examined. The stability of the implosion , one of the critical point of microsecond wire arrays due to the load dimensions imposed by the time scale, is tackled. A simple scaling from 100 ns Z-pinch results to 800 ns ones gives good results and the use of nested arrays improves dramatically the implosion quality and the Kshell yield of the load. However, additional effects such as the impact of the return current can geometry on the implosion have to be taken into account on our loads. Axial inhomogeneity of the implosion the origin of which is not yet well understood occurs in some shots and impacts the radiation output. The shape of the radiative pulse is discussed and compared with the homogeneity of the implosion. Numerical 2D R-Z and R-θ simulations are used to highlight some experimental results and understand the plasma conditions during these microsecond wire arrays implosions.

Report on the Acceptance Test of the CRI Y-MP 8128, 10 February - 12 March 1990

NASA Technical Reports Server (NTRS)

Carter, Russell; Kutler, Paul (Technical Monitor)

1998-01-01

The NAS Numerical Aerodynamic Simulation Facility's HSP 2 computer system, a CRI Y-MP 832 SN #1002, underwent a major hardware upgrade in February of 1990. The 32 MWord, 6.3 ns mainframe component of the system was replaced with a 128 MWord, 6.0 ns CRI Y-MP 8128 mainframe, SN #1030. A 30 day Acceptance Test of the computer system was performed by the NAS RND HSP group from 08:00 February 10, 1990 to 08:00 March 12, 1990. Overall responsibility for the RND HSP Acceptance Test was assumed by Duane Carbon. The terms of the contract required that the SN #1030 achieve an effectiveness level of greater than or equal to ninety (90) percent for 30 consecutive days within a 60 day time frame. After the first thirty days, the effectiveness level of SN #1030 was 94.4 percent, hence the acceptance test was passed.

Effective Control of Computationally Simulated Wing Rock in Subsonic Flow

NASA Technical Reports Server (NTRS)

Kandil, Osama A.; Menzies, Margaret A.

1997-01-01

The unsteady compressible, full Navier-Stokes (NS) equations and the Euler equations of rigid-body dynamics are sequentially solved to simulate the delta wing rock phenomenon. The NS equations are solved time accurately, using the implicit, upwind, Roe flux-difference splitting, finite-volume scheme. The rigid-body dynamics equations are solved using a four-stage Runge-Kutta scheme. Once the wing reaches the limit-cycle response, an active control model using a mass injection system is applied from the wing surface to suppress the limit-cycle oscillation. The active control model is based on state feedback and the control law is established using pole placement techniques. The control law is based on the feedback of two states: the roll-angle and roll velocity. The primary model of the computational applications consists of a 80 deg swept, sharp edged, delta wing at 30 deg angle of attack in a freestream of Mach number 0.1 and Reynolds number of 0.4 x 10(exp 6). With a limit-cycle roll amplitude of 41.1 deg, the control model is applied, and the results show that within one and one half cycles of oscillation, the wing roll amplitude and velocity are brought to zero.

Preparation and in-vitro/in-vivo evaluation of curcumin nanosuspension with solubility enhancement.

PubMed

Li, Xin; Yuan, Huiling; Zhang, Caiyun; Chen, Weidong; Cheng, Weiye; Chen, Xin; Ye, Xi

2016-08-01

We developed Cur nanosuspension (Cur-NS) with PVPK30 and SDS as stabilizers to improve poor water solubility and short biological half-time of Cur. Physicochemical characterization of Cur-NS was characterized systematically. The in-vitro dissolution, cytotoxicity and in-vivo pharmacokinetic experiments of Cur-NS were also evaluated. Scanning electron microscope indicated that the morphologies of Cur-NS were spherical or ellipsoidal in shape. X-ray diffraction verified that Cur was successfully developed as nanoparticles with an amorphous phase in Cur-NS. Fourier transform infrared spectroscopy suggested there was no degradation about Cur in the Cur-NS. Furthermore, the in-vitro study showed that the cumulative release of the Cur-NS was 82.16 ± 2.62% within 34 h and the cytotoxicity of the Cur-NS against HepG2 cells was much better than raw Cur. Besides, in-vivo pharmacokinetics in rats by intravenous injection displayed that the in-vivo process of Cur-NS pertained to two-compartment model. Meanwhile, the t1/2 and AUC0-t of Cur-NS were enhanced by 11.0-fold and 4.2-fold comparing to Cur solution. The Cur-NS significantly increased the water solubility and half-time of Cur, suggesting its potential as a nanocarrier in the delivery of Cur for future clinical application. © 2016 Royal Pharmaceutical Society.

The effectiveness of and satisfaction with high-fidelity simulation to teach cardiac surgical resuscitation skills to nurses.

PubMed

McRae, Marion E; Chan, Alice; Hulett, Renee; Lee, Ai Jin; Coleman, Bernice

2017-06-01

There are few reports of the effectiveness or satisfaction with simulation to learn cardiac surgical resuscitation skills. To test the effect of simulation on the self-confidence of nurses to perform cardiac surgical resuscitation simulation and nurses' satisfaction with the simulation experience. A convenience sample of sixty nurses rated their self-confidence to perform cardiac surgical resuscitation skills before and after two simulations. Simulation performance was assessed. Subjects completed the Satisfaction with Simulation Experience scale and demographics. Self-confidence scores to perform all cardiac surgical skills as measured by paired t-tests were significantly increased after the simulation (d=-0.50 to 1.78). Self-confidence and cardiac surgical work experience were not correlated with time to performance. Total satisfaction scores were high (mean 80.2, SD 1.06) indicating satisfaction with the simulation. There was no correlation of the satisfaction scores with cardiac surgical work experience (τ=-0.05, ns). Self-confidence scores to perform cardiac surgical resuscitation procedures were higher after the simulation. Nurses were highly satisfied with the simulation experience. Copyright © 2016 Elsevier Ltd. All rights reserved.

Three-dimensional numerical and experimental studies on transient ignition of hybrid rocket motor

NASA Astrophysics Data System (ADS)

Tian, Hui; Yu, Ruipeng; Zhu, Hao; Wu, Junfeng; Cai, Guobiao

2017-11-01

This paper presents transient simulations and experimental studies of the ignition process of the hybrid rocket motors (HRMs) using 90% hydrogen peroxide (HP) as the oxidizer and polymethyl methacrylate (PMMA) and Polyethylene (PE) as fuels. A fluid-solid coupling numerically method is established based on the conserved form of the three-dimensional unsteady Navier-Stokes (N-S) equations, considering gas fluid with chemical reactions and heat transfer between the fluid and solid region. Experiments are subsequently conducted using high-speed camera to record the ignition process. The flame propagation, chamber pressurizing process and average fuel regression rate of the numerical simulation results show good agreement with the experimental ones, which demonstrates the validity of the simulations in this study. The results also indicate that the flame propagation time is mainly affected by fluid dynamics and it increases with an increasing grain port area. The chamber pressurizing process begins when the flame propagation completes in the grain port. Furthermore, the chamber pressurizing time is about 4 times longer than the time of flame propagation.

Functional brain imaging of a complex navigation task following one night of total sleep deprivation

NASA Technical Reports Server (NTRS)

Strangman, Gary; Thompson, John H.; Strauss, Monica M.; Marshburn, Thomas H.; Sutton, Jeffrey P.

2006-01-01

Study Objectives: To assess the cerebral effects associated with sleep deprivation in a simulation of a complex, real-world, high-risk task. Design and Interventions: A two-week, repeated measures, cross-over experimental protocol, with counterbalanced orders of normal sleep (NS) and total sleep deprivation (TSD). Setting: Each subject underwent functional magnetic resonance imaging (fMRI) while performing a dual-joystick, 3D sensorimotor navigation task (simulated orbital docking). Scanning was performed twice per subject, once following a night of normal sleep (NS), and once following a single night of total sleep deprivation (TSD). Five runs (eight 24s docking trials each) were performed during each scanning session. Participants: Six healthy, young, right-handed volunteers (2 women; mean age 20) participated. Measurements and Results: Behavioral performance on multiple measures was comparable in the two sleep conditions. Neuroimaging results within sleep conditions revealed similar locations of peak activity for NS and TSD, including left sensorimotor cortex, left precuneus (BA 7), and right visual areas (BA 18/19). However, cerebral activation following TSD was substantially larger and exhibited higher amplitude modulations from baseline. When directly comparing NS and TSD, most regions exhibited TSD>NS activity, including multiple prefrontal cortical areas (BA 8/9,44/45,47), lateral parieto-occipital areas (BA 19/39, 40), superior temporal cortex (BA 22), and bilateral thalamus and amygdala. Only left parietal cortex (BA 7) demonstrated NS>TSD activity. Conclusions: The large network of cerebral differences between the two conditions, even with comparable behavioral performance, suggests the possibility of detecting TSD-induced stress via functional brain imaging techniques on complex tasks before stress-induced failures.

XaNSoNS: GPU-accelerated simulator of diffraction patterns of nanoparticles

NASA Astrophysics Data System (ADS)

Neverov, V. S.

XaNSoNS is an open source software with GPU support, which simulates X-ray and neutron 1D (or 2D) diffraction patterns and pair-distribution functions (PDF) for amorphous or crystalline nanoparticles (up to ∼107 atoms) of heterogeneous structural content. Among the multiple parameters of the structure the user may specify atomic displacements, site occupancies, molecular displacements and molecular rotations. The software uses general equations nonspecific to crystalline structures to calculate the scattering intensity. It supports four major standards of parallel computing: MPI, OpenMP, Nvidia CUDA and OpenCL, enabling it to run on various architectures, from CPU-based HPCs to consumer-level GPUs.

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

Azarkh, Eugene; Robinson, Erin; Hirunkanokpun, Supanee

Mosquito densonucleosis viruses synthesize two non-structural proteins, NS1 and NS2. While NS1 has been studied relatively well, little is known about NS2. Antiserum was raised against a peptide near the N-terminus of NS2, and used to conduct Western blot analysis and immuno-fluorescence assays. Western blots revealed a prominent band near the expected size (41 kDa). Immuno-fluorescence studies of mosquito cells transfected with AeDNV indicate that NS2 has a wider distribution pattern than does NS1, and the distribution pattern appears to be a function of time post-infection. Nuclear localization of NS2 requires intact C-terminus but does not require additional viral proteins.more » Mutations ranging from complete NS2 knock-out to a single missense amino acid substitution in NS2 can significantly reduce viral replication and production of viable progeny.« less

Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches.

PubMed

Nguyen, Phuong T V; Yu, Haibo; Keller, Paul A

2015-04-01

The nsP2 protease of chikungunya virus (CHIKV) is one of the essential components of viral replication and it plays a crucial role in the cleavage of polyprotein precursors for the viral replication process. Therefore, it is gaining attention as a potential drug design target against CHIKV. Based on the recently determined crystal structure of the nsP2 protease of CHIKV, this study identified potential inhibitors of the virus using structure-based approaches with a combination of molecular docking, virtual screening and molecular dynamics (MD) simulations. The top hit compounds from database searching, using the NCI Diversity Set II, with targeting at five potential binding sites of the nsP2 protease, were identified by blind dockings and focused dockings. These complexes were then subjected to MD simulations to investigate the stability and flexibility of the complexes and to gain a more detailed insight into the interactions between the compounds and the enzyme. The hydrogen bonds and hydrophobic contacts were characterized for the complexes. Through structural alignment, the catalytic residues Cys1013 and His1083 were identified in the N-terminal region of the nsP2 protease. The absolute binding free energies were estimated by the linear interaction energy approach and compared with the binding affinities predicted with docking. The results provide valuable information for the development of inhibitors for CHIKV. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

Model for the interpretation of nuclear magnetic resonance relaxometry of hydrated porous silicate materials

NASA Astrophysics Data System (ADS)

Faux, D. A.; Cachia, S.-H. P.; McDonald, P. J.; Bhatt, J. S.; Howlett, N. C.; Churakov, S. V.

2015-03-01

Nuclear magnetic resonance (NMR) relaxation experimentation is an effective technique for probing the dynamics of proton spins in porous media, but interpretation requires the application of appropriate spin-diffusion models. Molecular dynamics (MD) simulations of porous silicate-based systems containing a quasi-two-dimensional water-filled pore are presented. The MD simulations suggest that the residency time of the water on the pore surface is in the range 0.03-12 ns, typically 2-5 orders of magnitude less than values determined from fits to experimental NMR measurements using the established surface-layer (SL) diffusion models of Korb and co-workers [Phys. Rev. E 56, 1934 (1997), 10.1103/PhysRevE.56.1934]. Instead, MD identifies four distinct water layers in a tobermorite-based pore containing surface Ca2 + ions. Three highly structured water layers exist within 1 nm of the surface and the central region of the pore contains a homogeneous region of bulklike water. These regions are referred to as layer 1 and 2 (L1, L2), transition layer (TL), and bulk (B), respectively. Guided by the MD simulations, a two-layer (2L) spin-diffusion NMR relaxation model is proposed comprising two two-dimensional layers of slow- and fast-moving water associated with L2 and layers TL+B, respectively. The 2L model provides an improved fit to NMR relaxation times obtained from cementitious material compared to the SL model, yields diffusion correlation times in the range 18-75 ns and 28-40 ps in good agreement with MD, and resolves the surface residency time discrepancy. The 2L model, coupled with NMR relaxation experimentation, provides a simple yet powerful method of characterizing the dynamical properties of proton-bearing porous silicate-based systems such as porous glasses, cementitious materials, and oil-bearing rocks.

Exploiting molecular dynamics in Nested Sampling simulations of small peptides

NASA Astrophysics Data System (ADS)

Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

2016-04-01

Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

Modelling the line shape of very low energy peaks of positron beam induced secondary electrons measured using a time of flight spectrometer

NASA Astrophysics Data System (ADS)

Fairchild, A. J.; Chirayath, V. A.; Gladen, R. W.; Chrysler, M. D.; Koymen, A. R.; Weiss, A. H.

2017-01-01

In this paper, we present results of numerical modelling of the University of Texas at Arlington’s time of flight positron annihilation induced Auger electron spectrometer (UTA TOF-PAES) using SIMION® 8.1 Ion and Electron Optics Simulator. The time of flight (TOF) spectrometer measures the energy of electrons emitted from the surface of a sample as a result of the interaction of low energy positrons with the sample surface. We have used SIMION® 8.1 to calculate the times of flight spectra of electrons leaving the sample surface with energies and angles dispersed according to distribution functions chosen to model the positron induced electron emission process and have thus obtained an estimate of the true electron energy distribution. The simulated TOF distribution was convolved with a Gaussian timing resolution function and compared to the experimental distribution. The broadening observed in the simulated TOF spectra was found to be consistent with that observed in the experimental secondary electron spectra of Cu generated as a result of positrons incident with energy 1.5 eV to 901 eV, when a timing resolution of 2.3 ns was assumed.

Wire array K-shell sources on the SPHINX generator

NASA Astrophysics Data System (ADS)

D'Almeida, Thierry; Lassalle, Francis; Grunenwald, Julien; Maury, Patrick; Zucchini, Frédéric; Niasse, Nicolas; Chittenden, Jeremy

2014-10-01

The SPHINX machine is a LTD based Z-pinch driver operated by the CEA Gramat (France) and primarily used for studying K-shell radiation effects. We present the results of experiments carried out with single and nested large diameter aluminium wire array loads driven by a current of ~5 MA in ~800 ns. The dynamic of the implosion is studied with filtered X-UV time-integrated pin-hole cameras. The plasma electron temperature and the characteristics of the sources are estimated with time and spatially dependent spectrographs and PCDs. It is shown that Al K-shell yields (>1 keV) up to 27 kJ are obtained for a total radiation of ~ 230 kJ. These results are compared with simulations performed using the latest implementation of the non-LTE DCA code Spk in the 3D Eulerian MHD framework Gorgon developed at Imperial College. Filtered synthetic bolometers and PCD signals, time-dependent spatially integrated spectra and X-UV images are produced and show a good agreement with the experimental data. The capabilities of a prospective SPHINX II machine (20 MA ~ 800 ns) are also assessed for a wider variety of sources (Ti, Cu and W).

Neutron-powered precursors of kilonovae

NASA Astrophysics Data System (ADS)

Metzger, Brian D.; Bauswein, Andreas; Goriely, Stephane; Kasen, Daniel

2015-01-01

The merger of binary neutron stars (NSs) ejects a small quantity of neutron-rich matter, the radioactive decay of which powers a day to week long thermal transient known as a kilonova. Most of the ejecta remains sufficiently dense during its expansion that all neutrons are captured into nuclei during the r-process. However, recent general relativistic merger simulations by Bauswein and collaborators show that a small fraction of the ejected mass (a few per cent, or ˜10-4 M⊙) expands sufficiently rapidly for most neutrons to avoid capture. This matter originates from the shocked-heated interface between the merging NSs. Here, we show that the β-decay of these free neutrons in the outermost ejecta powers a `precursor' to the main kilonova emission, which peaks on a time-scale of ˜ few hours following merger at U-band magnitude ˜22 (for an assumed distance of 200 Mpc). The high luminosity and blue colours of the neutron precursor render it a potentially important counterpart to the gravitational wave source, that may encode valuable information on the properties of the merging binary (e.g. NS-NS versus NS-black hole) and the NS equation of state. Future work is necessary to assess the robustness of the fast-moving ejecta and the survival of free neutrons in the face of neutrino absorptions, although the precursor properties are robust to a moderate amount of leptonization. Our results provide additional motivation for short latency gravitational wave triggers and rapid follow-up searches with sensitive ground-based telescopes.

Numerical simulation of steady and unsteady asymmetric vortical flow

NASA Technical Reports Server (NTRS)

Kandil, Osama A.; Wong, Tin-Chee; Liu, C. H.

1992-01-01

The unsteady, compressible, thin-layer, Navier-Stokes (NS) equations are solved to simulate steady and unsteady, asymmetric, vortical laminar flow around cones at high incidences and supersonic Mach numbers. The equations are solved by using an implicit, upwind, flux-difference splitting (FDS), finite-volume scheme. The locally conical flow assumption is used and the solutions are obtained by forcing the conserved components of the flowfield vector to be equal at two axial stations located at 0.95 and 1.0. Computational examples cover steady and unsteady asymmetric flows around a circular cone and its control using side strakes. The unsteady asymmetric flow solution around the circular cone has also been validated using the upwind, flux-vector splitting (FVS) scheme with the thin-layer NS equations and the upwind FDS with the full NS equations. The results are in excellent agreement with each other. Unsteady asymmetric flows are also presented for elliptic- and diamond-section cones, which model asymmetric vortex shedding around round- and sharp-edged delta winds.

Mechanical Behavior of Nanostructured and Ultrafine Grained Materials under Shock Wave Loadings. Experimental Data and Results of Computer Simulation.

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir

2011-06-01

Features of mechanical behavior of nanostructured (NS) and ultrafine grained (UFG) metal and ceramic materials under quasistatic and shock wave loadings are discussed in this report. Multilevel models developed within the approach of computational mechanics of materials were used for simulation mechanical behavior of UFG and NS metals and ceramics. Comparisons of simulation results with experimental data are presented. Models of mechanical behavior of nanostructured metal alloys takes into account a several structural factors influencing on the mechanical behavior of materials (type of a crystal lattice, density of dislocations, a size of dislocation substructures, concentration and size of phase precipitation, and distribution of grains sizes). Results show the strain rate sensitivity of the yield stress of UFG and polycrystalline alloys is various in a range from 103 up to 106 1/s. But the difference of the Hugoniot elastic limits of a UFG and coarse-grained alloys may be not considerable. The spall strength, the yield stress of UFG and NS alloys are depend not only on grains size, but a number of factors such as a distribution of grains sizes, a concentration and sizes of voids and cracks, a concentration and sizes of phase precipitation. Some titanium alloys with grain sizes from 300 to 500 nm have the quasi-static yield strength and the tensile strength twice higher than that of coarse grained counterparts. But the spall strength of the UFG titanium alloys is only 10 percents above than that of coarse grained alloys. At the same time it was found the spall strength of the bulk UFG aluminium and magnesium alloys with precipitation strengthening is essentially higher in comparison of coarse-grained counterparts. The considerable decreasing of the strain before failure of UFG alloys was predicted at high strain rates. The Hugoniot elastic limits of oxide nanoceramics depend not only on the porosity, but also on sizes and volume distribution of voids.

Energy Deposition into a Collisional Gas from Optical Lattices Formed in an Optical Cavity (PREPRINT)

DTIC Science & Technology

2008-07-02

In order to cover a range of molecular species, argon , nitrogen, and methane were used as test gases. The polarizability to mass ratio of these gases...Japan, 21-25 July 2008. 14. ABSTRACT The Direct Simulation Monte Carlo (DSMC) method was used to investigate the interaction between argon ...reducing the maximum temperature. The optimal intervening time was found to be 0.7, 1.0 and 0.25 ns for argon , nitrogen, and methane at one atmosphere

Exploring Beta-Amyloid Protein Transmembrane Insertion Behavior and Residue-Specific Lipid Interactions in Lipid Bilayers Using Multiscale MD Simulations

NASA Astrophysics Data System (ADS)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2013-03-01

Beta-amyloid (Abeta) interactions with neurons are linked to Alzheimer's. Using a multiscale MD simulation strategy that combines the high efficiency of phase space sampling of coarse-grained MD (CGD) and the high spatial resolution of Atomistic MD (AMD) simulations, we studied the Abeta insertion dynamics in cholesterol-enriched and -depleted lipid bilayers that mimic the neuronal membranes domains. Forward (AMD-CGD) and reverse (CGD-AMD) mappings were used. At the atomistic level, cholesterol promoted insertion of Abeta with high (folded) or low (unfolded) helical contents of the lipid insertion domain (Lys28-Ala42), and the insertions were stabilized by the Lys28 snorkeling and Ala42-anchoring to the polar lipid groups of the bilayer up to 200ns. After the forward mapping, the folded inserted state switched to a new extended inserted state with the Lys28 descended to the middle of the bilayer while the unfolded inserted state migrated to the membrane surface up to 4000ns. The two new states remained stable for 200ns at the atomistic scale after the reverse mapping. Our results suggested that different Abeta membrane-orientation states separated by free energy barriers can be explored by the multiscale MD more effectively than by Atomistic MD simulations alone. NIH RC1-GM090897-02

Coagulase-negative staphylococcal bacteraemia in cancer patients. Time to positive culture can distinguish bacteraemia from contamination.

PubMed

Morioka, Shinichiro; Ichikawa, Mika; Mori, Keita; Kurai, Hanako

2018-03-16

Coagulase-negative staphylococci (CoNS) are the most common contaminants of blood cultures, however, we sometimes have difficulties in determining their clinical significance. It is still controversial that there is a significant difference between the contamination group and the true bacteraemia group in the time to positivity (TTP) of blood cultures. We validated the relationship between a TTP and the presence of CoNS bacteraemia in cancer patients by using an objective, non-judgmental definition for CoNS contamination. We retrospectively reviewed 175 sets of blood cultures drawn from 95 patients that yielded CoNS from October 2011 to March 2013. We considered as contamination if an isolate of CoNS was identified in one out of multiple sets of blood cultures. We investigated the TTP, the threshold values and corresponding likelihood ratios to distinguish CoNS bacteraemia from contamination. The median TTP in CoNS bacteraemia group was significantly shorter than that in contamination group (14 h 45 min and 20 h 31 min, respectively, p = .0157). A TTP of ≤16 h had a specificity of 83% for predicting CoNS bacteraemia, and that of >20 h had a sensitivity of 86% for predicting CoNS contamination. We validated that the median TTP in CoNS bacteraemia group was significantly shorter than that in their contamination group, and that a TTP of ≤16 h was associated with CoNS bacteraemia, while that of >20 h was associated with CoNS contamination, if evaluated with an objective, non-judgmental definition for CoNS contamination.

Ion Move Brownian Dynamics (IMBD)--simulations of ion transport.

PubMed

Kurczynska, Monika; Kotulska, Malgorzata

2014-01-01

Comparison of the computed characteristics and physiological measurement of ion transport through transmembrane proteins could be a useful method to assess the quality of protein structures. Simulations of ion transport should be detailed but also timeefficient. The most accurate method could be Molecular Dynamics (MD), which is very time-consuming, hence is not used for this purpose. The model which includes ion-ion interactions and reduces the simulation time by excluding water, protein and lipid molecules is Brownian Dynamics (BD). In this paper a new computer program for BD simulation of the ion transport is presented. We evaluate two methods for calculating the pore accessibility (round and irregular shape) and two representations of ion sizes (van der Waals diameter and one voxel). Ion Move Brownian Dynamics (IMBD) was tested with two nanopores: alpha-hemolysin and potassium channel KcsA. In both cases during the simulation an ion passed through the pore in less than 32 ns. Although two types of ions were in solution (potassium and chloride), only ions which agreed with the selectivity properties of the channels passed through the pores. IMBD is a new tool for the ion transport modelling, which can be used in the simulations of wide and narrow pores.

Iterative demodulation and decoding of coded non-square QAM

NASA Technical Reports Server (NTRS)

Li, L.; Divsalar, D.; Dolinar, S.

2003-01-01

Simulation results show that, with iterative demodulation and decoding, coded NS-8QAM performs 0.5 dB better than standard 8QAM and 0.7 dB better than 8PSK at BER= 10(sup -5), when the FEC code is the (15, 11) Hamming code concatenated with a rate-1 accumulator code, while coded NS-32QAM performs 0.25 dB better than standard 32QAM.

A Coarse-grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS

PubMed Central

Moore, Timothy C.; Iacovella, Christopher R.; Hartkamp, Remco; Bunge, Annette L.; McCabe, Clare

2017-01-01

Ceramide (CER)-based biological membranes are used both experimentally and in simulations as simplified model systems of the skin barrier. Molecular dynamics studies have generally focused on simulating preassembled structures using atomistically detailed models of CERs, which limit the system sizes and timescales that can practically be probed, rendering them ineffective for studying particular phenomena, including self-assembly into bilayer and lamellar superstructures. Here, we report on the development of a coarse-grained (CG) model for CER NS, the most abundant CER in human stratum corneum. Multistate iterative Boltzmann inversion is used to derive the intermolecular pair potentials, resulting in a force field that is applicable over a range of state points and suitable for studying ceramide self-assembly. The chosen CG mapping, which includes explicit interaction sites for hydroxyl groups, captures the directional nature of hydrogen bonding and allows for accurate predictions of several key structural properties of CER NS bilayers. Simulated wetting experiments allow the hydrophobicity of CG beads to be accurately tuned to match atomistic wetting behavior, which affects the whole system since inaccurate hydrophobic character is found to unphysically alter the lipid packing in hydrated lamellar states. We find that CER NS can self-assemble into multilamellar structures, enabling the study of lipid systems more representative of the multilamellar lipid structures present in the skin barrier. The coarse-grained force field derived herein represents an important step in using molecular dynamics to study the human skin barrier, which gives a resolution not available through experiment alone. PMID:27564869

High performance thyratron driver with low jitter.

PubMed

Verma, Rishi; Lee, P; Springham, S V; Tan, T L; Rawat, R S

2007-08-01

We report the design and development of insulated gate bipolar junction transistor based high performance driver for operating thyratrons in grounded grid mode. With careful design, the driver meets the specification of trigger output pulse rise time less than 30 ns, jitter less than +/-1 ns, and time delay less than 160 ns. It produces a -600 V pulse of 500 ns duration (full width at half maximum) at repetition rate ranging from 1 Hz to 1.14 kHz. The developed module also facilitates heating and biasing units along with protection circuitry in one complete package.

Hierarchical Petascale Simulation Framework for Stress Corrosion Cracking

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

Vashishta, Priya

2014-12-01

Reaction Dynamics in Energetic Materials: Detonation is a prototype of mechanochemistry, in which mechanically and thermally induced chemical reactions far from equilibrium exhibit vastly different behaviors. It is also one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. The CACS group has performed multimillion-atom reactive MD simulations to reveal a novel two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine (RDX) crystal. Rapid production of N2 and H2O within ~10 ps is followed by delayed production of CO molecules within ~ 1 ns. They found that further decomposition towards the final products ismore » inhibited by the formation of large metastable C- and O-rich clusters with fractal geometry. The CACS group has also simulated the oxidation dynamics of close-packed aggregates of aluminum nanoparticles passivated by oxide shells. Their simulation results suggest an unexpectedly active role of the oxide shell as a nanoreactor.« less

THE HYDROGEN EPOCH OF REIONIZATION ARRAY DISH. II. CHARACTERIZATION OF SPECTRAL STRUCTURE WITH ELECTROMAGNETIC SIMULATIONS AND ITS SCIENCE IMPLICATIONS

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

Ewall-Wice, Aaron; Hewitt, Jacqueline; Neben, Abraham R.

We use time-domain electromagnetic simulations to determine the spectral characteristics of the Hydrogen Epoch of Reionization Arrays (HERA) antenna. These simulations are part of a multi-faceted campaign to determine the effectiveness of the dish’s design for obtaining a detection of redshifted 21 cm emission from the epoch of reionization. Our simulations show the existence of reflections between HERA’s suspended feed and its parabolic dish reflector that fall below -40 dB at 150 ns and, for reasonable impedance matches, have a negligible impact on HERA’s ability to constrain EoR parameters. It follows that despite the reflections they introduce, dishes are effectivemore » for increasing the sensitivity of EoR experiments at a relatively low cost. We find that electromagnetic resonances in the HERA feed’s cylindrical skirt, which is intended to reduce cross coupling and beam ellipticity, introduces significant power at large delays (-40 dB at 200 ns), which can lead to some loss of measurable Fourier modes and a modest reduction in sensitivity. Even in the presence of this structure, we find that the spectral response of the antenna is sufficiently smooth for delay filtering to contain foreground emission at line-of-sight wave numbers below k {sub ∥} ≲ 0.2 h Mpc{sup -1}, in the region where the current PAPER experiment operates. Incorporating these results into a Fisher Matrix analysis, we find that the spectral structure observed in our simulations has only a small effect on the tight constraints HERA can achieve on parameters associated with the astrophysics of reionization.« less

An important step forward in continuous spectroscopic imaging of ionising radiations using ASICs

NASA Astrophysics Data System (ADS)

Fessler, P.; Coffin, J.; Eberlé, H.; de Raad Iseli, C.; Hilt, B.; Huss, D.; Krummenacher, F.; Lutz, J. R.; Prévot, G.; Renouprez, A.; Sigward, M. H.; Schwaller, B.; Voltolini, C.

1999-01-01

Characterization results are given for an original ASIC allowing continuous acquisition of ionising radiation images in spectroscopic mode. Ionising radiation imaging in general and spectroscopic imaging in particular must primarily be guided by the attempt to decrease statistical noise, which requires detection systems designed to allow very high counting rates. Any source of dead time must therefore be avoided. Thus, the use of on-line corrections of the inevitable dispersion of characteristics between the large number of electronic channels of the detection system, shall be precluded. Without claiming to achieve ultimate noise levels, the work described is focused on how to prevent good individual acquisition channel noise performance from being totally destroyed by the dispersion between channels without introducing dead times. With this goal, we developed an automatic charge amplifier output voltage offset compensation system which operates regardless of the cause of the offset (detector or electronic). The main performances of the system are the following: the input equivalent noise charge is 190 e rms (input non connected, peaking time 500 ns), the highest gain is 255 mV/fC, the peaking time is adjustable between 200 ns and 2 μs and the power consumption is 10 mW per channel. The agreement between experimental data and theoretical simulation results is excellent.

Therapeutic Effects of Monoclonal Antibody against Dengue Virus NS1 in a STAT1 Knockout Mouse Model of Dengue Infection.

PubMed

Wan, Shu-Wen; Chen, Pei-Wei; Chen, Chin-Yu; Lai, Yen-Chung; Chu, Ya-Ting; Hung, Chia-Yi; Lee, Han; Wu, Hsuan Franziska; Chuang, Yung-Chun; Lin, Jessica; Chang, Chih-Peng; Wang, Shuying; Liu, Ching-Chuan; Ho, Tzong-Shiann; Lin, Chiou-Feng; Lee, Chien-Kuo; Wu-Hsieh, Betty A; Anderson, Robert; Yeh, Trai-Ming; Lin, Yee-Shin

2017-10-15

Dengue virus (DENV) is the causative agent of dengue fever, dengue hemorrhagic fever, and dengue shock syndrome and is endemic to tropical and subtropical regions of the world. Our previous studies showed the existence of epitopes in the C-terminal region of DENV nonstructural protein 1 (NS1) which are cross-reactive with host Ags and trigger anti-DENV NS1 Ab-mediated endothelial cell damage and platelet dysfunction. To circumvent these potentially harmful events, we replaced the C-terminal region of DENV NS1 with the corresponding region from Japanese encephalitis virus NS1 to create chimeric DJ NS1 protein. Passive immunization of DENV-infected mice with polyclonal anti-DJ NS1 Abs reduced viral Ag expression at skin inoculation sites and shortened DENV-induced prolonged bleeding time. We also investigated the therapeutic effects of anti-NS1 mAb. One mAb designated 2E8 does not recognize the C-terminal region of DENV NS1 in which host-cross-reactive epitopes reside. Moreover, mAb 2E8 recognizes NS1 of all four DENV serotypes. We also found that mAb 2E8 caused complement-mediated lysis in DENV-infected cells. In mouse model studies, treatment with mAb 2E8 shortened DENV-induced prolonged bleeding time and reduced viral Ag expression in the skin. Importantly, mAb 2E8 provided therapeutic effects against all four serotypes of DENV. We further found that mAb administration to mice as late as 1 d prior to severe bleeding still reduced prolonged bleeding time and hemorrhage. Therefore, administration with a single dose of mAb 2E8 can protect mice against DENV infection and pathological effects, suggesting that NS1-specific mAb may be a therapeutic option against dengue disease. Copyright © 2017 by The American Association of Immunologists, Inc.

Long-term comparisons between two-way satellite and geodetic time transfer systems.

PubMed

Plumb, John F; Larson, Kristine M

2005-11-01

Global Positioning System (GPS) observations recorded in the United States and Europe were used to evaluate time transfer capabilities of GETT (geodetic time transfer). Timing estimates were compared with two-way satellite time and frequency transfer (TWSTFT) systems. A comparison of calibrated links at the U.S. Naval Observatory, Washington, D.C., and Colorado Springs, CO, yielded agreement of 2.17 ns over 6 months with a standard deviation of 0.73 ns. An uncalibrated link between the National Institute of Standards and Technology (NIST) and Physikalisch-Technische Bundesanstalt, Braunschweig, Germany, has a standard deviation of 0.79 ns over the same time period.

A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue.

PubMed

Chuang, Chih-Hung; Chiou, Shean-Jaw; Cheng, Tian-Lu; Wang, Yeng-Tseng

2018-04-20

Since 2015, widespread Zika virus outbreaks in Central and South America have caused increases in microcephaly cases, and this acute problem requires urgent attention. We employed molecular dynamics and Gaussian accelerated molecular dynamics techniques to investigate the structure of Zika NS5 protein with S-adenosyl-L-homocysteine (SAH) and an RNA analogue, namely 7-methylguanosine 5'-triphosphate (m7GTP). For the binding motif of Zika virus NS5 protein and SAH, we suggest that the four Zika NS5 substructures (residue orders: 101-112, 54-86, 127-136 and 146-161) and the residues (Ser56, Gly81, Arg84, Trp87, Thr104, Gly106, Gly107, His110, Asp146, Ile147, and Gly148) might be responsible for the selectivity of the new Zika virus drugs. For the binding motif of Zika NS5 protein and m7GTP, we suggest that the three Zika NS5 substructures (residue orders: 11-31, 146-161 and 207-218) and the residues (Asn17, Phe24, Lys28, Lys29, Ser150, Arg213, and Ser215) might be responsible for the selectivity of the new Zika virus drugs.

Identification of potential hit compounds for Dengue virus NS2B/NS3 protease inhibitors by combining virtual screening and binding free energy calculations.

PubMed

Wichapong, K; Nueangaudom, A; Pianwanit, S; Sippl, W; Kokpol, S

2013-09-01

Dengue virus (DV) infections are a serious public health problem and there is currently no vaccine or drug treatment. NS2B/NS3 protease, an essential enzyme for viral replication, is one of the promising targets in the search for drugs against DV. In this research work, virtual screening (VS) was carried out on four multi-conformational databases using several criteria. Firstly, molecular dynamics simulations of the NS2B/NS3 protease and four known inhibitors, which reveal an importance of both electrostatic and van der Waals interactions in stabilizing the ligand-enzyme interaction, were used to generate three different pharmacophore models (a structure-based, a static and a dynamic). Subsequently, these three models were employed for pharmacophore search in the VS. Secondly, compounds passing the first criterion were further reduced using the Lipinski's rule of five to keep only compounds with drug-like properties. Thirdly, molecular docking calculations were performed to remove compounds with unsuitable ligand-enzyme interactions. Finally, binding free energy of each compound was calculated. Compounds having better energy than the known inhibitors were selected and thus 20 potential hits were obtained.

IGBT Switching Characteristic Curve Embedded Half-Bridge MMC Modelling and Real Time Simulation Realization

NASA Astrophysics Data System (ADS)

Zhengang, Lu; Hongyang, Yu; Xi, Yang

2017-05-01

The Modular Multilevel Converter (MMC) is one of the most attractive topologies in recent years for medium or high voltage industrial applications, such as high voltage dc transmission (HVDC) and medium voltage varying speed motor drive. The wide adoption of MMCs in industry is mainly due to its flexible expandability, transformer-less configuration, common dc bus, high reliability from redundancy, and so on. But, when the sub module number of MMC is more, the test of MMC controller will cost more time and effort. Hardware in the loop test based on real time simulator will save a lot of time and money caused by the MMC test. And due to the flexible of HIL, it becomes more and more popular in the industry area. The MMC modelling method remains an important issue for the MMC HIL test. Specifically, the VSC model should realistically reflect the nonlinear device switching characteristics, switching and conduction losses, tailing current, and diode reverse recovery behaviour of a realistic converter. In this paper, an IGBT switching characteristic curve embedded half-bridge MMC modelling method is proposed. This method is based on the switching curve referring and sample circuit calculation, and it is sample for implementation. Based on the proposed method, a FPGA real time simulation is carried out with 200ns sample time. The real time simulation results show the proposed method is correct.

N-S/DSMC hybrid simulation of hypersonic flow over blunt body including wakes

NASA Astrophysics Data System (ADS)

Li, Zhonghua; Li, Zhihui; Li, Haiyan; Yang, Yanguang; Jiang, Xinyu

2014-12-01

A hybrid N-S/DSMC method is presented and applied to solve the three-dimensional hypersonic transitional flows by employing the MPC (modular Particle-Continuum) technique based on the N-S and the DSMC method. A sub-relax technique is adopted to deal with information transfer between the N-S and the DSMC. The hypersonic flows over a 70-deg spherically blunted cone under different Kn numbers are simulated using the CFD, DSMC and hybrid N-S/DSMC method. The present computations are found in good agreement with DSMC and experimental results. The present method provides an efficient way to predict the hypersonic aerodynamics in near-continuum transitional flow regime.

Error Analyses of the North Alabama Lightning Mapping Array (LMA)

NASA Technical Reports Server (NTRS)

Koshak, W. J.; Solokiewicz, R. J.; Blakeslee, R. J.; Goodman, S. J.; Christian, H. J.; Hall, J. M.; Bailey, J. C.; Krider, E. P.; Bateman, M. G.; Boccippio, D. J.

2003-01-01

Two approaches are used to characterize how accurately the North Alabama Lightning Mapping Array (LMA) is able to locate lightning VHF sources in space and in time. The first method uses a Monte Carlo computer simulation to estimate source retrieval errors. The simulation applies a VHF source retrieval algorithm that was recently developed at the NASA-MSFC and that is similar, but not identical to, the standard New Mexico Tech retrieval algorithm. The second method uses a purely theoretical technique (i.e., chi-squared Curvature Matrix theory) to estimate retrieval errors. Both methods assume that the LMA system has an overall rms timing error of 50ns, but all other possible errors (e.g., multiple sources per retrieval attempt) are neglected. The detailed spatial distributions of retrieval errors are provided. Given that the two methods are completely independent of one another, it is shown that they provide remarkably similar results, except that the chi-squared theory produces larger altitude error estimates than the (more realistic) Monte Carlo simulation.

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

PubMed

Ollila, O H Samuli; Heikkinen, Harri A; Iwaï, Hideo

2018-06-14

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

Sucrose in Aqueous Solution Revisited: 2. Adaptively Biased Molecular Dynamics Simulations and Computational Analysis of NMR Relaxation

PubMed Central

Xia, Junchao; Case, David A.

2012-01-01

We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4 M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R1) and transverse (R2) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S2) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80–90% of the conformations having φ – ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures. PMID:22058066

Hydrodynamic instabilities in laser pulse-produced melts of metal films

NASA Astrophysics Data System (ADS)

Bostanjoglo, O.; Nink, T.

1996-06-01

The dynamics of melts, as induced by 7 ns laser pulses in Al and Au films, were investigated by in situ time-resolved transmission electron microscopy. Melting, motion of the liquid, and crystallization were observed by tracing the image intensity with a photomultiplier (space/time resolution 100 nm/3 ns) and by streak imaging (streak times 15 ns-4 μs). Films with native oxides/adsorbed atmospheric contaminations and films purified by pulse melting were found to show a completely different behavior of their melts. The melts of purified films either remained almost flat (Al) or revealed a gradual pileup of liquid in cold regions within 500 ns (Au), caused by thermocapillarity with the negative thermal coefficient of the surface tension of pure metals. In contrast, contaminated films showed three distinctly different types of perturbations: (1) a fast expulsion of the melt from the center of the laser spot within 20 ns after the laser pulse; (2) a gradual contraction of liquid at the center within 0.5-1 μs; (3) thickness oscillations with frequencies of 5-10 MHz and time constants of 500 ns. These effects are explained by recoil from evaporating contaminations, by thermocapillary flow with a positive thermal coefficient of the surface tension, caused by surface active impurity atoms, and by thermocapillary waves.

Simulations of transient membrane behavior in cells subjected to a high-intensity ultrashort electric pulse.

PubMed

Hu, Q; Viswanadham, S; Joshi, R P; Schoenbach, K H; Beebe, S J; Blackmore, P F

2005-03-01

A molecular dynamics (MD) scheme is combined with a distributed circuit model for a self-consistent analysis of the transient membrane response for cells subjected to an ultrashort (nanosecond) high-intensity (approximately 0.01-V/nm spatially averaged field) voltage pulse. The dynamical, stochastic, many-body aspects are treated at the molecular level by resorting to a course-grained representation of the membrane lipid molecules. Coupling the Smoluchowski equation to the distributed electrical model for current flow provides the time-dependent transmembrane fields for the MD simulations. A good match between the simulation results and available experimental data is obtained. Predictions include pore formation times of about 5-6 ns. It is also shown that the pore formation process would tend to begin from the anodic side of an electrically stressed membrane. Furthermore, the present simulations demonstrate that ions could facilitate pore formation. This could be of practical importance and have direct relevance to the recent observations of calcium release from the endoplasmic reticulum in cells subjected to such ultrashort, high-intensity pulses.

[System of ns time-resolved spectroscopy diagnosis and radioprotection].

PubMed

Yao, Wei-Bo; Guo, Jian-Ming; Zhang, Yong-min; Tang, Jun-Ping; Cheng, Liang; Xu, Qi-fuo

2014-06-01

Cathode plasma of high current electron beam diode is an important research on high power microwave and strong pulsed radio accelerator. It is a reliable method to study cathode plasma by diagnosing the cathode plasma parameters with non-contact spectroscopy measurement system. The present paper introduced the work principle, system composition and performance of the nanosecond (ns) time-resolved spectroscopy diagnosis system. Furthermore, it introduced the implementing method and the temporal relation of lower jitter synchronous trigger system. Simultaneously, the authors designed electromagnetic and radio shield room to protect the diagnosis system due to the high electromagnetic and high X-ray and γ-ray radiation, which seriously interferes with the system. Time-resolved spectroscopy experiment on brass (H62) cathode shows that, the element and matter composition of cathode plasma is clearly increase with the increase in the diode pulsed voltage and current magnitude. The spectroscopy diagnosis system could be of up to 10 ns time resolve capability. It's least is 2 ns. Synchronous trigger system's jitter is less than 4 ns. The spectroscopy diagnosis system will open a new way to study the cathode emission mechanism in depth.

Perturbation analysis of 6DoF flight dynamics and passive dynamic stability of hovering fruit fly Drosophila melanogaster.

PubMed

Gao, Na; Aono, Hikaru; Liu, Hao

2011-02-07

Insects exhibit exquisite control of their flapping flight, capable of performing precise stability and steering maneuverability. Here we develop an integrated computational model to investigate flight dynamics of insect hovering based on coupling the equations of 6 degree of freedom (6DoF) motion with the Navier-Stokes (NS) equations. Unsteady aerodynamics is resolved by using a biology-inspired dynamic flight simulator that integrates models of realistic wing-body morphology and kinematics, and a NS solver. We further develop a dynamic model to solve the rigid body equations of 6DoF motion by using a 4th-order Runge-Kutta method. In this model, instantaneous forces and moments based on the NS-solutions are represented in terms of Fourier series. With this model, we perform a systematic simulation-based analysis on the passive dynamic stability of a hovering fruit fly, Drosophila melanogaster, with a specific focus on responses of state variables to six one-directional perturbation conditions during latency period. Our results reveal that the flight dynamics of fruit fly hovering does not have a straightforward dynamic stability in a conventional sense that perturbations damp out in a manner of monotonous convergence. However, it is found to exist a transient interval containing an initial converging response observed for all the six perturbation variables and a terminal instability that at least one state variable subsequently tends to diverge after several wing beat cycles. Furthermore, our results illustrate that a fruit fly does have sufficient time to apply some active mediation to sustain a steady hovering before losing body attitudes. Copyright © 2010 Elsevier Ltd. All rights reserved.

Structural and mechanical characterization of hybrid metallic-inorganic nanosprings

NASA Astrophysics Data System (ADS)

Habtoun, Sabrina; Houmadi, Said; Reig, Benjamin; Pouget, Emilie; Dedovets, Dmytro; Delville, Marie-Hélène; Oda, Reiko; Cristiano, Fuccio; Bergaud, Christian

2017-10-01

Silica nanosprings (NS) are fabricated by a sol-gel deposition of silica precursors onto a template made of self-assembled organic chiral nanostructures. They are deposited and assembled on microstructured silicon substrates, and then metallized and clamped in a single lithography-free step using a focused ion beam (FIB). The resulting suspended hybrid metallic/inorganic NS are then characterized with high-resolution transmission electron microscopy (HRTEM) and scanning TEM/energy-dispersive X-ray spectroscopy (STEM/EDX), showing the atomic structure of the metallic layer. Three-point bending tests are also carried out using an atomic force microscope (AFM) and supported by finite element method (FEM) simulation with COMSOL Multiphysics allowing the characterization of the mechanical behavior and the estimation of the stiffness of the resulting NS. The information obtained on the structural and mechanical properties of the NS is discussed for future nano-electro-mechanical system (NEMS) applications.

Simulation of Nitrogen and Phosphorus Losses in Loess Landforms of Northern Iran

NASA Astrophysics Data System (ADS)

Kiani, F.; Behtarinejad, B.; Najafinejad, A.; Kaboli, R.

2018-02-01

Population growth, urban expansion and intensive agriculture and thus increased use of fertilizers aimed at increasing the production capacity cause extensive loss of nutrients such as nitrogen and phosphorus and lead to reduced quality of soil and water. Therefore, identification of nutrients in the soil and their potential are essential. The aim of this study was to evaluate the capability of the SWAT model in simulating runoff, sediment, and nitrogen and phosphorus losses in Tamer catchment. Runoff and sediment measured at Tamar gauging station were used to calibrate and validate the model. Simulated values were generally consistent with the data observed during calibration and validation period (0.6 < R 2 and 0.5 < NS). In the case of nitrogen loss, the model performed an almost good simulation (0.6 < R 2 and 0.47 < NS), but phosphorus simulation yielded better results (0.76 < R 2 and 0.66 < NS). The results showed that cultivated lands had higher loss of nitrogen and phosphorus than other types of land use. Among the various forms of nitrogen and phosphorus, the loss of organic nitrogen and nitrate and soluble phosphorus and mineral phosphorus attached to the sediments showed the greatest sensitivity to the type of land use. Results also showed that the average nutrient loss caused by erosion in this catchment, was 6.99 kg/ha for nitrogen, 0.35 kg/ha for nitrate, 1.3 kg/ha for organic phosphorus, 0.015 kg/ha for soluble phosphorus, and 0.45 kg/ha for mineral phosphorus.

Sub-nanosecond resolution electric field measurements during ns pulse breakdown in ambient air

NASA Astrophysics Data System (ADS)

Simeni Simeni, Marien; Goldberg, Ben; Gulko, Ilya; Frederickson, Kraig; Adamovich, Igor V.

2018-01-01

Electric field during ns pulse discharge breakdown in ambient air has been measured by ps four-wave mixing, with temporal resolution of 0.2 ns. The measurements have been performed in a diffuse plasma generated in a dielectric barrier discharge, in plane-to-plane geometry. Absolute calibration of the electric field in the plasma is provided by the Laplacian field measured before breakdown. Sub-nanosecond time resolution is obtained by using a 150 ps duration laser pulse, as well as by monitoring the timing of individual laser shots relative to the voltage pulse, and post-processing four-wave mixing signal waveforms saved for each laser shot, placing them in the appropriate ‘time bins’. The experimental data are compared with the analytic solution for time-resolved electric field in the plasma during pulse breakdown, showing good agreement on ns time scale. Qualitative interpretation of the data illustrates the effects of charge separation, charge accumulation/neutralization on the dielectric surfaces, electron attachment, and secondary breakdown. Comparison of the present data with more advanced kinetic modeling is expected to provide additional quantitative insight into air plasma kinetics on ~ 0.1-100 ns scales.

Variable neutron star free precession in Hercules X-1 from evolution of RXTE X-ray pulse profiles with phase of the 35-d cycle

NASA Astrophysics Data System (ADS)

Postnov, K.; Shakura, N.; Staubert, R.; Kochetkova, A.; Klochkov, D.; Wilms, J.

2013-10-01

Accretion of matter on to the surface of a freely precessing neutron star (NS) with a complex non-dipole magnetic field can explain the change of X-ray pulse profiles of Her X-1 observed by RXTE with the phase of the 35-d cycle. We demonstrate this using all available measurements of X-ray pulse profiles in the 9-13 keV energy range obtained with the RXTE/Proportional Counter Array (PCA). The measured profiles guided the elaboration of a geometrical model and the definition of locations of emitting poles, arcs and spots on the NS surface which satisfactorily reproduce the observed pulse profiles and their dependence on free precession phase. We have found that the observed trend of the times of the 35-d turn-ons on the O-C diagram, which can be approximated by a collection of consecutive linear segments around the mean value, can be described by our model by assuming a variable free precession period, with a fractional period change of about a few per cent. Under this assumption and using our model, we have found that the times of phase zero of the NS free precession (which we identify with the maximum separation of the brightest spot on the NS surface with the NS spin axis) occur about 1.6 d after the mean turn-on times inside each `stable' epoch, producing a linear trend on the O-C diagram with the same slope as the observed times of turn-ons. We propose that the 2.5 per cent changes in the free precession period that occur on time scales of several to tens of 35-d cycles can be related to wandering of the principal inertia axis of the NS body due to variations in the patterns of accretion on to the NS surface. The closeness of periods of the disc precession and the NS free precession can be explained by the presence of a synchronization mechanism in the system, which modulates the dynamical interaction of the gas streams and the accretion disc with the NS free precession period.

Self-assembly formation of palm-based esters nano-emulsion: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Abdul Rahman, Mohd. Basyaruddin; Huan, Qiu-Yi; Tejo, Bimo A.; Basri, Mahiran; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Abdul

2009-10-01

Palm-oil esters (POEs) are unsaturated and non-ionic esters that can be prepared by enzymatic synthesis from palm oil. Their nano-emulsion properties possess great potential to act as drug carrier for transdermal drug delivery system. A ratio of 75:5:20 (water/POEs/Span20) was chosen from homogenous region in the phase diagram of our previous experimental work to undergo molecular dynamics simulation. A 15 ns molecular dynamics simulation of nano-emulsion system (water/POEs/Span20) was carried out using OPLS-AA force field. The aggregations of the oil and surfactant molecules are observed throughout the simulation. After 8 ns of simulation, the molecules start to aggregate to form one spherical micelle where the POEs molecules are surrounded by the non-ionic surfactant (Span20) molecules with an average size of 4.2 ± 0.05 nm. The size of the micelle and the ability of palm-based nano-emulsion to self-assemble suggest that this nano-emulsion can potentially use in transdermal drug delivery system.

Bimolecular Recombination Kinetics of an Exciton-Trion Gas

DTIC Science & Technology

2015-07-01

3-D systems. Whereas a linear time-dependent system of first-order differential equations has only trivial steady- state solutions (all carrier...derivatives to zero, which reduces the system (Eq. 9) to the following set of 3 algebraic equations: ( ) ( ) ( ) ( ) 1 2 210 2 110...crossover around 20 ns. The exciton curve is nearly linear over a wide range from 10 ns to 50 ns. Fig. 2 Time dependence of carrier species for Λ = 4

Atomistic simulation of shocks in single crystal and polycrystalline Ta

NASA Astrophysics Data System (ADS)

Bringa, E. M.; Higginbotham, A.; Park, N.; Tang, Y.; Suggit, M.; Mogni, G.; Ruestes, C. J.; Hawreliak, J.; Erhart, P.; Meyers, M. A.; Wark, J. S.

2011-06-01

Non-equilibrium molecular dynamics (MD) simulations of shocks in Ta single crystals and polycrystals were carried out using up to 360 million atoms. Several EAM and FS type potentials were tested up to 150 GPa, with varying success reproducing the Hugoniot and the behavior of elastic constants under pressure. Phonon modes were studied to exclude possible plasticity nucleation by soft-phonon modes, as observed in MD simulations of Cu crystals. The effect of loading rise time in the resulting microstructure was studied for ramps up to 0.2 ns long. Dislocation activity was not observed in single crystals, unless there were defects acting as dislocation sources above a certain pressure. E.M.B. was funded by CONICET, Agencia Nacional de Ciencia y Tecnología (PICT2008-1325), and a Royal Society International Joint Project award.

Fission-neutrons source with fast neutron-emission timing

NASA Astrophysics Data System (ADS)

Rusev, G.; Baramsai, B.; Bond, E. M.; Jandel, M.

2016-05-01

A neutron source with fast timing has been built to help with detector-response measurements. The source is based on the neutron emission from the spontaneous fission of 252Cf. The time is provided by registering the fission fragments in a layer of a thin scintillation film with a signal rise time of 1 ns. The scintillation light output is measured by two silicon photomultipliers with rise time of 0.5 ns. Overall time resolution of the source is 0.3 ns. Design of the source and test measurements using it are described. An example application of the source for determining the neutron/gamma pulse-shape discrimination by a stilbene crystal is given.

Evaluation and hydrological application of satellite-based precipitation datasets in driving hydrological models over the Huifa river basin in Northeast China

NASA Astrophysics Data System (ADS)

Zhu, Honglei; Li, Ying; Huang, Yanwei; Li, Yingchen; Hou, Cuicui; Shi, Xiaoliang

2018-07-01

Satellite-based precipitation estimates with high spatial and temporal resolution and large areal coverage have provided hydrologists a potential alternative source for hydrological applications since the last few years, especially for ungauged regions. This study evaluates five satellite-based precipitation datasets, namely, Fengyun, TRMM 3B42, TRMM 3B42RT, CMORPH_BLD and CMORPH_RAW, against gauge observations for streamflow simulation with a distributed hydrological model (SWAT) over the Huifa river basin, Northeast China. Results show that, by comparing the statistical indices (MA, M5P, STDE, ME, BIAS and CC) and inter-annual precipitation, it is demonstrated that Fengyun TRMM 3B42 and CMORPH_BLD show better agreement with gauge precipitation data than CMORPH_RAW and TRMM 3B42RT. When the SWAT model for each dataset calibrated and validated individually, satisfactory model performances (defined as: NS > 0.5) are achieved at daily scale for Fengyun, TRMM 3B42 and gauge-driven model, and very good performances (defined as: NS > 0.75) are achieved at monthly scale for Fengyun and gauge-driven model, respectively. The CMORPH_BLD forced daily simulations also yield higher values of NS and R2 than CMORPH_RAW and TRMM 3B42RT at daily and monthly step. From the uncertainty results, variations of P-factor values and frequency distribution curves of NS suggest that the simulation uncertainty increase when operating the Fengyun, 3B42RT, CMORPH_BLD and CMORPH_RAW-driven model with best fitted parameters for rain gauge SWAT model. The results also indicate that the influence of parameter uncertainty on model simulation results may be greater than the effect of input data accuracy. It is noted that uncertainty analysis is necessary to evaluate the hydrological applications of satellite-based precipitation datasets.

General-relativistic Large-eddy Simulations of Binary Neutron Star Mergers

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

Radice, David, E-mail: dradice@astro.princeton.edu

The flow inside remnants of binary neutron star (NS) mergers is expected to be turbulent, because of magnetohydrodynamics instability activated at scales too small to be resolved in simulations. To study the large-scale impact of these instabilities, we develop a new formalism, based on the large-eddy simulation technique, for the modeling of subgrid-scale turbulent transport in general relativity. We apply it, for the first time, to the simulation of the late-inspiral and merger of two NSs. We find that turbulence can significantly affect the structure and survival time of the merger remnant, as well as its gravitational-wave (GW) and neutrinomore » emissions. The former will be relevant for GW observation of merging NSs. The latter will affect the composition of the outflow driven by the merger and might influence its nucleosynthetic yields. The accretion rate after black hole formation is also affected. Nevertheless, we find that, for the most likely values of the turbulence mixing efficiency, these effects are relatively small and the GW signal will be affected only weakly by the turbulence. Thus, our simulations provide a first validation of all existing post-merger GW models.« less

Energy Deposition and Condition of the Metal Core in Exploding Wire Experiments

NASA Astrophysics Data System (ADS)

Sarkisov, G. S.; Rosenthal, S. E.; Struve, K. W.; McDaniel, D. H.; Waisman, E. M.; Sasorov, P. V.

2002-11-01

Measurements of the Joule energy deposition into exploding wire and its relation with condition of the expanding wire core are presented. Wires of nine different metals with diameters of 10-30 microns, have been exploded by fast 150A/ns and slow 20A/ns pulses, in vacuum and in air. It has been shown by interferometry and light emission that expanding wire core has different conditions. The substances with small atomization enthalpy (Ag, Al, Cu, Au) demonstrate full vaporization of the wire core. The refractory metals (Ti, Pt, Mo, W) demonstrates that core consists from vapor and small and hot microparticles. In this case we observe "firework effect" when large radiation from the wire exceed the energy deposition time in a three order of magnitude. For non-refractory metals radiation dropping fast in 100 ns time scale due to effective adiabatic cooling. It is possible if main part of the metal core was vaporized. The interferometrical investigation of the refraction coefficient of expanding metal core is proof this conclusion. It has been shown that energy deposition before surface breakdown dependent strongly from current rate, surface coatings, environment, wire diameter and radial electric field. The regime of wire explosion in vacuum without shunting plasma shell has been realized for fast exploding mode. In this case we observe anomaly high energy deposition in to the wire core exceeding regular value in almost 20 times. The experimental results for Al wire have been compared with ALEGRA 2D MHD simulations. *Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL8500.

Dressing control of biphoton waveform transitions

NASA Astrophysics Data System (ADS)

Li, Xinghua; Zhang, Dan; Zhang, Da; Hao, Ling; Chen, Haixia; Wang, Zhiguo; Zhang, Yanpeng

2018-05-01

We experimentally realize and theoretically analyze narrow-band biphotons generated in a hot rubidium vapor cell by four-wave-mixing processing. A dressing laser beam is used to alternate both linear and nonlinear susceptibilities of the vapor, thereby modifying the biphoton's temporal correlation function. Most notably, the correlation time is increased from 6 to 165 ns. The biphoton shape is also shown to change as a result of the coupled-states dressing. We observed Rabi oscillations and optical precursors in hot atomic vapor cells. We also theoretically simulated biphoton correlation times as influenced by dressing-laser detuning and power, the results of which are consistent with our experiments.

Alteration of time-resolved autofluorescence properties of rat aorta, induced by diabetes mellitus

NASA Astrophysics Data System (ADS)

Uherek, M.; Uličná, O.; Vančová, O.; Muchová, J.; Ďuračková, Z.; Šikurová, L.; Chorvát, D.

2016-10-01

Changes in autofluorescence properties of isolated rat aorta, induced by diabetes mellitus, were detected using time-resolved fluorescence spectroscopy with pulsed ultraviolet (UV) laser excitation. We demonstrated that time-resolved spectroscopy was able to detect changes in aorta tissues related to diabetes and unambiguously discriminate diabetic (τ 1 0.63  ±  0.05 ns, τ 2 3.66  ±  0.10 ns) samples from the control (τ 1 0.76  ±  0.03 ns, τ 2 4.48  ±  0.15 ns) group. We also report changes in the ratio of relative amplitudes of the two lifetime component in aorta tissue during diabetes, most likely related to the pseudohypoxic state with altered NADH homeostasis.

Photoacoustic simulation study of chirp excitation response from different size absorbers

NASA Astrophysics Data System (ADS)

Jnawali, K.; Chinni, B.; Dogra, V.; Rao, N.

2017-03-01

Photoacoustic (PA) imaging is a hybrid imaging modality that integrates the strength of optical and ultrasound imaging. Nanosecond (ns) pulsed lasers used in current PA imaging systems are expensive, bulky and they often waste energy. We propose and evaluate, through simulations, the use of a continuous wave (CW) laser whose amplitude is linear frequency modulated (chirp) for PA imaging. The chirp signal provides signal-to-side-lobe ratio (SSR) improvement potential and full control over PA signal frequencies excited in the sample. The PA signal spectrum is a function of absorber size and the time frequencies present in the chirp. A mismatch between the input chirp spectrum and the output PA signal spectrum can affect the compressed pulse that is recovered from cross-correlating the two. We have quantitatively characterized this effect. The k-wave Matlab tool box was used to simulate PA signals in three dimensions for absorbers ranging in size from 0.1 mm to 0.6 mm, in response to laser excitation amplitude that is linearly swept from 0.5 MHz to 4 MHz. This sweep frequency range was chosen based on the spectrum analysis of a PA signal generated from ex-vivo human prostate tissue samples. In comparison, the energy wastage by a ns laser pulse was also estimated. For the chirp methodology, the compressed pulse peak amplitude, pulse width and side lobe structure parameters were extracted for different size absorbers. While the SSR increased 6 fold with absorber size, the pulse width decreased by 25%.

Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Malek, Kourosh; Odijk, Theo; Coppens, Marc-Olivier

2005-07-01

The dynamics of water and sodium counter-ions (Na+) in a C2221 orthorhombic β-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. The effect of the fluctuation of the protein atoms on the motion of water and sodium ions is studied by comparing simulations in a rigid and in a flexible lattice. The electrostatic interactions of sodium ions with the positively charged LYS residues inside the crystal channels significantly influence the ionic motion. According to our results, water molecules close to the protein surface undergo an anomalous diffusive motion. On the other hand, the motion of water molecules further away from the protein surface is normal diffusive. Protein fluctuations affect the diffusion constant of water, which increases from 0.646 ± 0.108 to 0.887 ± 0.41 nm2 ns-1, when protein fluctuations are taken into account. The pore size (0.63-1.05 nm) and the water diffusivities are in good agreement with previous experimental results. The dynamics of sodium ions is disordered. LYS residues inside the pore are the main obstacles to the motion of sodium ions. However, the simulation time is still too short for providing a precise description of anomalous diffusion of sodium ions. The results are not only of interest for studying ion and water transport through biological nanopores, but may also elucidate water-protein and ion-protein interactions in protein crystals.

The effect of curcumin and its nanoformulation on adjuvant-induced arthritis in rats.

PubMed

Zheng, Zhaoling; Sun, YanHua; Liu, Ziliang; Zhang, Mingqin; Li, Chunqing; Cai, Hui

2015-01-01

Rheumatoid arthritis (RA), induced by the prolonged inappropriate inflammatory responses, is one of the most prevalent of all chronic inflammatory joint diseases. Curcumin (CM), a yellow hydrophobic polyphenol derived from the herb turmeric, has various pharmacological activities against many chronic diseases and acts by inhibiting cell proliferation and metastasis and downregulating various factors, including nuclear factor kappa B, interleukin-1β and TNF-α. Given the pathogenesis of RA, we hypothesized that the drug also has antiarthritic effects. The aims of the present study included the following: 1) examining the therapeutic effect of CM administered via intravenous (iv) injection on RA and 2) formulating the drug into oil-water nanoemulsions (Ns) to overcome the low oral bioavailability of CM and achieve oral delivery of the drug. The effect of CM administered through iv injection on adjuvant-induced arthritis in rats was studied in terms of paw swelling, weight indices of the thymus and spleen, and pathological changes in nuclear factor kappa B expression and inflammatory cytokines. Methotrexate was used as a positive control. The CM-Ns were prepared using a high-pressure homogenizing method and characterized with respect to the particle size and morphology. The stability of the CM-Ns in simulated gastrointestinal (GI) fluids and in vitro release were also investigated. A pharmacokinetic study of the CM-Ns and suspensions in which the plasma levels were determined using an high performance liquid chromatography method and the pharmacokinetic parameters were calculated based on a statistical moment theory was also performed in rats. CM administered via iv injection had a therapeutic effect on RA similar to methotrexate. CM-Ns with a diameter of approximately 150 nm were successfully prepared, and the drug was well encapsulated into the Ns without degradation in simulated GI conditions. The area under the curve (AUC) and Cmax for the CM-Ns were more than threefold greater than those for the suspensions; moreover, similar decreases in the levels of TNF-α and interleukin-1β in both synovial fluid and blood serum were obtained from oral administration of CM-Ns and iv injection. CM was an effective antiarthritic agent, and the present N formulation appeared to be a promising system that allowed RA therapy with CM to be converted from iv to oral administration.

Unprecented syntonization and syncronization accuracy via simultaneous viewing with GPS receivers: Construction characteristics of an NBS/GPS receiver

NASA Technical Reports Server (NTRS)

Davis, D. D.; Weiss, M.; Clements, A.; Allan, D. W.

1982-01-01

The National Bureau of Standards/Global Positioning System (NBS/GPS) receiver is discussed. It is designed around the concept of obtaining high accuracy, low cost time and frequency comparisons between remote frequency standards and clocks with the intent to aid international time and frequency coordination. Preliminary tests of this comparison technique between Boulder, CO and Washington, D.C indicate the ability to do accurate time transfer to better that 10 ns, and frequency measurements to better than 1 part in 10 to the 14th power. The hardware and software of the receiver is detailed. The receiver is fully automatic with a built-in 0.1 ns resolution time interval counter. A microprocessor does data processing. Satellite signal stabilities are routinely at the 5 ns level for 15 s averages, and the internal receiver stabilities are at the 1 ns level.

Refractory Sampling Links Efficiency and Costs of Sensory Encoding to Stimulus Statistics

PubMed Central

Song, Zhuoyi

2014-01-01

Sensory neurons integrate information about the world, adapting their sampling to its changes. However, little is understood mechanistically how this primary encoding process, which ultimately limits perception, depends upon stimulus statistics. Here, we analyze this open question systematically by using intracellular recordings from fly (Drosophila melanogaster and Coenosia attenuata) photoreceptors and corresponding stochastic simulations from biophysically realistic photoreceptor models. Recordings show that photoreceptors can sample more information from naturalistic light intensity time series (NS) than from Gaussian white-noise (GWN), shuffled-NS or Gaussian-1/f stimuli; integrating larger responses with higher signal-to-noise ratio and encoding efficiency to large bursty contrast changes. Simulations reveal how a photoreceptor's information capture depends critically upon the stochastic refractoriness of its 30,000 sampling units (microvilli). In daylight, refractoriness sacrifices sensitivity to enhance intensity changes in neural image representations, with more and faster microvilli improving encoding. But for GWN and other stimuli, which lack longer dark contrasts of real-world intensity changes that reduce microvilli refractoriness, these performance gains are submaximal and energetically costly. These results provide mechanistic reasons why information sampling is more efficient for natural/naturalistic stimulation and novel insight into the operation, design, and evolution of signaling and code in sensory neurons. PMID:24849356

Hydrogen and Ethene Plasma Assisted Ignition by NS discharge at Elevated Temperatures

NASA Astrophysics Data System (ADS)

Starikovskiy, Andrey

2015-09-01

The kinetics of ignition in lean H2:O2:Ar and C2H4:O2:Ar mixtures has been studied experimentally and numerically after a high-voltage nanosecond discharge. The ignition delay time behind a reflected shock wave was measured with and without the discharge. It was shown that the initiation of the discharge with a specific deposited energy of 10 - 30 mJ/cm3 leads to an order of magnitude decrease in the ignition delay time. Discharge processes and following chain chemical reactions with energy release were simulated. The generation of atoms, radicals and excited and charged particles was numerically simulated using the measured time - resolved discharge current and electric field in the discharge phase. The calculated densities of the active particles were used as input data to simulate plasma-assisted ignition. Good agreement was obtained between the calculated ignition delay times and the experimental data. It follows from the analysis of the calculated results that the main mechanism of the effect of gas discharge on the ignition of hydrocarbons is the electron impact dissociation of O2 molecules in the discharge phase. Detailed kinetic mechanism for plasma assisted ignition of hydrogen and ethene is elaborated and verified.

Three-dimensional GRMHD Simulations of Neutrino-cooled Accretion Disks from Neutron Star Mergers

NASA Astrophysics Data System (ADS)

Siegel, Daniel M.; Metzger, Brian D.

2018-05-01

Merging binaries consisting of two neutron stars (NSs) or an NS and a stellar-mass black hole typically form a massive accretion torus around the remnant black hole or long-lived NS. Outflows from these neutrino-cooled accretion disks represent an important site for r-process nucleosynthesis and the generation of kilonovae. We present the first three-dimensional, general-relativistic magnetohydrodynamic (GRMHD) simulations including weak interactions and a realistic equation of state of such accretion disks over viscous timescales (380 ms). We witness the emergence of steady-state MHD turbulence, a magnetic dynamo with an ∼20 ms cycle, and the generation of a “hot” disk corona that launches powerful thermal outflows aided by the energy released as free nucleons recombine into α-particles. We identify a self-regulation mechanism that keeps the midplane electron fraction low (Y e ∼ 0.1) over viscous timescales. This neutron-rich reservoir, in turn, feeds outflows that retain a sufficiently low value of Y e ≈ 0.2 to robustly synthesize third-peak r-process elements. The quasi-spherical outflows are projected to unbind 40% of the initial disk mass with typical asymptotic escape velocities of 0.1c and may thus represent the dominant mass ejection mechanism in NS–NS mergers. Including neutrino absorption, our findings agree with previous hydrodynamical α-disk simulations that the entire range of r-process nuclei from the first to the third r-process peak can be synthesized in the outflows, in good agreement with observed solar system abundances. The asymptotic escape velocities and quantity of ejecta, when extrapolated to moderately higher disk masses, are consistent with those needed to explain the red kilonova emission following the NS merger GW170817.

How directions of route descriptions influence orientation specificity: the contribution of spatial abilities.

PubMed

Meneghetti, Chiara; Muffato, Veronica; Varotto, Diego; De Beni, Rossana

2017-03-01

Previous studies found mental representations of route descriptions north-up oriented when egocentric experience (given by the protagonist's initial view) was congruent with the global reference system. This study examines: (a) the development and maintenance of representations derived from descriptions when the egocentric and global reference systems are congruent or incongruent; and (b) how spatial abilities modulate these representations. Sixty participants (in two groups of 30) heard route descriptions of a protagonist's moves starting from the bottom of a layout and headed mainly northwards (SN description) in one group, and headed south from the top (NS description, the egocentric view facing in the opposite direction to the canonical north) in the other. Description recall was tested with map drawing (after hearing the description a first and second time; i.e. Time 1 and 2) and South-North (SN) or North-South (NS) pointing tasks; and spatial objective tasks were administered. The results showed that: (a) the drawings were more rotated in NS than in SN descriptions, and performed better at Time 2 than at Time 1 for both types of description; SN pointing was more accurate than NS pointing for the SN description, while SN and NS pointing accuracy did not differ for the NS description; (b) spatial (rotation) abilities were related to recall accuracy for both types of description, but were more so for the NS ones. Overall, our results showed that the way in which spatial information is conveyed (with/without congruence between the egocentric and global reference systems) and spatial abilities influence the development and maintenance of mental representations.

Brightening X-Ray/Optical/Radio Emission of GW170817/SGRB 170817A: Evidence for an Electron–Positron Wind from the Central Engine?

NASA Astrophysics Data System (ADS)

Geng, Jin-Jun; Dai, Zi-Gao; Huang, Yong-Feng; Wu, Xue-Feng; Li, Long-Biao; Li, Bing; Meng, Yan-Zhi

2018-04-01

Recent follow-up observations of the binary neutron star (NS) merging event GW170817/SGRB 170817A reveal that its X-ray/optical/radio emissions are brightening continuously up to ∼100 days post-merger. This late-time brightening is unexpected from the kilonova model or the off-axis top-hat jet model for gamma-ray burst (SGRB) afterglows. In this Letter, by assuming that the merger remnant is a long-lived NS, we propose that the interaction between an electron–positron-pair (e + e ‑) wind from the central NS and the jet could produce a long-lived reverse shock, from which a new emission component would rise and can interpret current observations well. The magnetic-field-induced ellipticity of the NS is taken to be 4 × 10‑5 in our modeling, so that the braking of the NS is mainly through the gravitational wave (GW) radiation rather than the magnetic dipole radiation, and the emission luminosity at early times would not exceed the observational limits. In our scenario, because the peak time of the brightening is roughly equal to the spin-down timescale of the NS, the accurate peak time may help constrain the ellipticity of the remnant NS. We suggest that radio polarization observations of the brightening would help to distinguish our scenario from other scenarios. Future observations on a large sample of short gamma-ray burst afterglows or detections of GW signals from merger remnants would test our scenario.

Dynamic response of polyurea subjected to nanosecond rise-time stress waves

NASA Astrophysics Data System (ADS)

Youssef, George; Gupta, Vijay

2012-08-01

Shaped charges and explosively formed projectiles used in modern warfare can attain speeds as high as 30,000 ft/s. Impacts from these threats are expected to load the armor materials in the 10 to 100 ns timeframe. During this time, the material strains are quite limited but the strain rates are extremely high. To develop armors against such threats it is imperative to understand the dynamic constitutive behavior of materials in the tens of nanoseconds timeframe. Material behavior in this parameter space cannot be obtained by even the most sophisticated plate-impact and split-Hopkinson bar setups that exist within the high energy materials field today. This paper introduces an apparatus and a test method that are based on laser-generated stress waves to obtain such material behaviors. Although applicable to any material system, the test procedures are demonstrated on polyurea which shows unusual dynamic properties. Thin polyurea layers were deformed using laser-generated stress waves with 1-2 ns rise times and 16 ns total duration. The total strain in the samples was less than 3%. Because of the transient nature of the stress wave, the strain rate varied throughout the deformation history of the sample. A peak value of 1.1×105 s-1 was calculated. It was found that the stress-strain characteristics, determined from experimentally recorded incident and transmitted wave profiles, matched satisfactorily with those computed from a 2D wave mechanics simulation in which the polyurea was modeled as a linearly viscoelastic solid with constants derived from the quasi-static experiments. Thus, the test data conformed to the Time-Temperature Superposition (TTS) principle even at extremely high strain rates of our test. This then extends the previous observations of Zhao et al. (Mech. Time-Depend. Mater. 11:289-308, 2007) who showed the applicability of the TTS principle for polyurea in the linearly viscoelastic regime up to peak strain rates of 1200 s-1.

Hardware simulator for optical correlation spectroscopy with Gaussian statistics and arbitrary correlation functions.

PubMed

Molteni, Matteo; Weigel, Udo M; Remiro, Francisco; Durduran, Turgut; Ferri, Fabio

2014-11-17

We present a new hardware simulator (HS) for characterization, testing and benchmarking of digital correlators used in various optical correlation spectroscopy experiments where the photon statistics is Gaussian and the corresponding time correlation function can have any arbitrary shape. Starting from the HS developed in [Rev. Sci. Instrum. 74, 4273 (2003)], and using the same I/O board (PCI-6534 National Instrument) mounted on a modern PC (Intel Core i7-CPU, 3.07GHz, 12GB RAM), we have realized an instrument capable of delivering continuous streams of TTL pulses over two channels, with a time resolution of Δt = 50ns, up to a maximum count rate of 〈I〉 ∼ 5MHz. Pulse streams, typically detected in dynamic light scattering and diffuse correlation spectroscopy experiments were generated and measured with a commercial hardware correlator obtaining measured correlation functions that match accurately the expected ones.

Equilibration and analysis of first-principles molecular dynamics simulations of water

NASA Astrophysics Data System (ADS)

Dawson, William; Gygi, François

2018-03-01

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

PubMed

Dawson, William; Gygi, François

2018-03-28

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

The Generalized Born solvation model: What is it?

NASA Astrophysics Data System (ADS)

Onufriev, Alexey

2004-03-01

Implicit solvation models provide, for many applications, an effective way of describing the electrostatic effects of aqueous solvation. Here we outline the main approximations behind the popular Generalized Born solvation model. We show how its accuracy, relative to the Poisson-Boltzmann treatment, can be significantly improved in a computationally inexpensive manner to make the model useful in the studies of large-scale conformational transitions at the atomic level. The improved model is tested in a molecular dynamics simulation of folding of a 46-residue (three helix bundle) protein. Starting from an extended structure at 450K, the protein folds to the lowest energy conformation within 6 ns of simulation time, and the predicted structure differs from the native one by 2.4 A (backbone RMSD).

Protein dynamics observed by tunable mid-IR quantum cascade lasers across the time range from 10ns to 1s.

PubMed

Schultz, Bernd-Joachim; Mohrmann, Hendrik; Lorenz-Fonfria, Victor A; Heberle, Joachim

2018-01-05

We have developed a spectrometer based on tunable quantum cascade lasers (QCLs) for recording time-resolved absorption spectra of proteins in the mid-infrared range. We illustrate its performance by recording time-resolved difference spectra of bacteriorhodopsin in the carboxylic range (1800-1700cm -1 ) and on the CO rebinding reaction of myoglobin (1960-1840cm -1 ), at a spectral resolution of 1cm -1 . The spectrometric setup covers the time range from 4ns to nearly a second with a response time of 10-15ns. Absorption changes as low as 1×10 -4 are detected in single-shot experiments at t>1μs, and of 5×10 -6 in kinetics obtained after averaging 100 shots. While previous time-resolved IR experiments have mostly been conducted on hydrated films of proteins, we demonstrate here that the brilliance of tunable quantum cascade lasers is superior to perform ns time-resolved experiments even in aqueous solution (H 2 O). Copyright © 2017 Elsevier B.V. All rights reserved.

Spatiotemporal temperature and density characterization of high-power atmospheric flashover discharges over inert poly(methyl methacrylate) and energetic pentaerythritol tetranitrate dielectric surfaces

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

Tang, V.; Grant, C. D.; McCarrick, J. F.

2012-03-01

A flashover arc source that delivered up to 200 mJ on the 100s-of-ns time-scale to the arc and a user-selected dielectric surface was characterized for studying high-explosive kinetics under plasma conditions. The flashover was driven over thin pentaerythritol tetranitrate (PETN) and poly(methyl methacrylate) (PMMA) dielectric films and the resultant plasma was characterized in detail. Time- and space-resolved temperatures and electron densities of the plasma were obtained using atomic emission spectroscopy. The hydrodynamics of the plasma was captured through fast, visible imaging. Fourier transform infrared spectroscopy (FTIR) was used to characterize the films pre- and post-shot for any chemical alterations. Time-resolvedmore » infrared spectroscopy (TRIR) provided PETN depletion data during the plasma discharge. For both types of films, temperatures of 1.6-1.7 eV and electron densities of {approx}7-8 x 10{sup 17}/cm{sup 3}{approx}570 ns after the start of the discharge were observed with temperatures of 0.6-0.7 eV persisting out to 15 {mu}s. At 1.2 {mu}s, spatial characterization showed flat temperature and density profiles of 1.1-1.3 eV and 2-2.8 x 10{sup 17}/cm{sup 3} for PETN and PMMA films, respectively. Images of the plasma showed an expanding hot kernel starting from radii of {approx}0.2 mm at {approx}50 ns and reaching {approx}1.1 mm at {approx}600 ns. The thin films ablated or reacted several hundred nm of material in response to the discharge. First TRIR data showing the in situ reaction or depletion of PETN in response to the flashover arc were successfully obtained, and a 2-{mu}s, 1/e decay constant was measured. Preliminary 1 D simulations compared reasonably well with the experimentally determined plasma radii and temperatures. These results complete the first steps to resolving arc-driven PETN reaction pathways and their associated kinetic rates using in situ spectroscopy techniques.« less

Particle-in-cell simulations with charge-conserving current deposition on graphic processing units

NASA Astrophysics Data System (ADS)

Ren, Chuang; Kong, Xianglong; Huang, Michael; Decyk, Viktor; Mori, Warren

2011-10-01

Recently using CUDA, we have developed an electromagnetic Particle-in-Cell (PIC) code with charge-conserving current deposition for Nvidia graphic processing units (GPU's) (Kong et al., Journal of Computational Physics 230, 1676 (2011). On a Tesla M2050 (Fermi) card, the GPU PIC code can achieve a one-particle-step process time of 1.2 - 3.2 ns in 2D and 2.3 - 7.2 ns in 3D, depending on plasma temperatures. In this talk we will discuss novel algorithms for GPU-PIC including charge-conserving current deposition scheme with few branching and parallel particle sorting. These algorithms have made efficient use of the GPU shared memory. We will also discuss how to replace the computation kernels of existing parallel CPU codes while keeping their parallel structures. This work was supported by U.S. Department of Energy under Grant Nos. DE-FG02-06ER54879 and DE-FC02-04ER54789 and by NSF under Grant Nos. PHY-0903797 and CCF-0747324.

Near-Space TOPSAR Large-Scene Full-Aperture Imaging Scheme Based on Two-Step Processing

PubMed Central

Zhang, Qianghui; Wu, Junjie; Li, Wenchao; Huang, Yulin; Yang, Jianyu; Yang, Haiguang

2016-01-01

Free of the constraints of orbit mechanisms, weather conditions and minimum antenna area, synthetic aperture radar (SAR) equipped on near-space platform is more suitable for sustained large-scene imaging compared with the spaceborne and airborne counterparts. Terrain observation by progressive scans (TOPS), which is a novel wide-swath imaging mode and allows the beam of SAR to scan along the azimuth, can reduce the time of echo acquisition for large scene. Thus, near-space TOPS-mode SAR (NS-TOPSAR) provides a new opportunity for sustained large-scene imaging. An efficient full-aperture imaging scheme for NS-TOPSAR is proposed in this paper. In this scheme, firstly, two-step processing (TSP) is adopted to eliminate the Doppler aliasing of the echo. Then, the data is focused in two-dimensional frequency domain (FD) based on Stolt interpolation. Finally, a modified TSP (MTSP) is performed to remove the azimuth aliasing. Simulations are presented to demonstrate the validity of the proposed imaging scheme for near-space large-scene imaging application. PMID:27472341

The light-yield response of a NE-213 liquid-scintillator detector measured using 2-6 MeV tagged neutrons

NASA Astrophysics Data System (ADS)

Scherzinger, J.; Al Jebali, R.; Annand, J. R. M.; Fissum, K. G.; Hall-Wilton, R.; Kanaki, K.; Lundin, M.; Nilsson, B.; Perrey, H.; Rosborg, A.; Svensson, H.

2016-12-01

The response of a NE-213 liquid-scintillator detector has been measured using tagged neutrons from 2 to 6 MeV originating from an Am/Be neutron source. The neutron energies were determined using the time-of-flight technique. Pulse-shape discrimination was employed to discern between gamma-rays and neutrons. The behavior of both the fast (35 ns) and the combined fast and slow (475 ns) components of the neutron scintillation-light pulses were studied. Three different prescriptions were used to relate the neutron maximum energy-transfer edges to the corresponding recoil-proton scintillation-light yields, and the results were compared to simulations. The overall normalizations of parametrizations which predict the fast or total light yield of the scintillation pulses were also tested. Our results agree with both existing data and existing parametrizations. We observe a clear sensitivity to the portion and length of the neutron scintillation-light pulse considered.

Investigation of surface evolution for stainless steel electrode under pulsed megagauss magnetic field

NASA Astrophysics Data System (ADS)

Zou, Wenkang; Dan, Jiakun; Wang, Guilin; Duan, Shuchao; Wei, Bing; Zhang, Hengdi; Huang, Xianbin; Zhang, Zhaohui; Guo, Fan; Gong, Boyi; Chen, Lin; Wang, Meng; Feng, Shuping; Xie, Weiping; Deng, Jianjun

2018-02-01

Surface evolution for a conductor electrode under pulsed megagauss (MG) magnetic field was investigated. Stainless steel rods with 3 mm diameter were driven by 8 MA, 130 ns (10%-90%) current pulse in a series of shots on the Primary Test Stand. Experimental data from two complementary diagnostic systems and simulation results from one-dimensional magneto-hydrodynamics code reveal a transition phase for instability development. The transition, which begins as the conductor surface starts to expand, lasts about 40 ns in the pulse. It ends after the thermal plasma is formed, and striation electrothermal instability growth stops but magneto-Rayleigh-Taylor instability (MRTI) starts to develop. An expanding velocity which grows to about 2.0 km/s during the transition phase was directly measured for the first time. The threshold magnetic field for thermal plasma formation on the stainless steel surface was inferred to be 3.3 MG under a rising rate of about 66 MG/μs, and after that MRTI becomes predominant for amplitude growth in surface perturbation.

Development of a Nomarski-type multi-frame interferometer as a time and space resolving diagnostics for the free electron density of laser-generated plasma

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

Boerner, M.; Frank, A.; Pelka, A.

2012-04-15

This article reports on the development and set-up of a Nomarski-type multi-frame interferometer as a time and space resolving diagnostics of the free electron density in laser-generated plasma. The interferometer allows the recording of a series of 4 images within 6 ns of a single laser-plasma interaction. For the setup presented here, the minimal accessible free electron density is 5 x 10{sup 18} cm{sup -3}, the maximal one is 2 x 10{sup 20} cm{sup -3}. Furthermore, it provides a resolution of the electron density in space of 50 {mu}m and in time of 0.5 ns for one image with amore » customizable magnification in space for each of the 4 images. The electron density was evaluated from the interferograms using an Abel inversion algorithm. The functionality of the system was proven during first experiments and the experimental results are presented and discussed. A ray tracing procedure was realized to verify the interferometry pictures taken. In particular, the experimental results are compared to simulations and show excellent agreement, providing a conclusive picture of the evolution of the electron density distribution.« less

Minority Carrier Lifetime Spectroscopy | Photovoltaic Research | NREL

Science.gov Websites

electronically. It examines the return of photoexcited carriers back to equilibrium as a function of time and time-correlated single-photon counting or time-resolved photoluminescence provides exceptionally fast bandgap materials. The 5-ns time resolution for the µPCD systems (7 and 20 GHz) and ~ 50-ns resolution

Prediction of functionally significant single nucleotide polymorphisms in PTEN tumor suppressor gene: An in silico approach.

PubMed

Khan, Imran; Ansari, Irfan A; Singh, Pratichi; Dass J, Febin Prabhu

2017-09-01

The phosphatase and tensin homolog (PTEN) gene plays a crucial role in signal transduction by negatively regulating the PI3K signaling pathway. It is the most frequent mutated gene in many human-related cancers. Considering its critical role, a functional analysis of missense mutations of PTEN gene was undertaken in this study. Thirty five nonsynonymous single nucleotide polymorphisms (nsSNPs) within the coding region of the PTEN gene were selected for our in silico investigation, and five nsSNPs (G129E, C124R, D252G, H61D, and R130G) were found to be deleterious based on combinatorial predictions of different computational tools. Moreover, molecular dynamics (MD) simulation was performed to investigate the conformational variation between native and all the five mutant PTEN proteins having predicted deleterious nsSNPs. The results of MD simulation of all mutant models illustrated variation in structural attributes such as root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and total energy; which depicts the structural stability of PTEN protein. Furthermore, mutant PTEN protein structures also showed a significant variation in the solvent accessible surface area and hydrogen bond frequencies from the native PTEN structure. In conclusion, results of this study have established the deleterious effect of the all the five predicted nsSNPs on the PTEN protein structure. Thus, results of the current study can pave a new platform to sort out nsSNPs that can be undertaken for the confirmation of their phenotype and their correlation with diseased status in case of control studies. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

The C-terminal 50 amino acid residues of dengue NS3 protein are important for NS3-NS5 interaction and viral replication.

PubMed

Tay, Moon Y F; Saw, Wuan Geok; Zhao, Yongqian; Chan, Kitti W K; Singh, Daljit; Chong, Yuwen; Forwood, Jade K; Ooi, Eng Eong; Grüber, Gerhard; Lescar, Julien; Luo, Dahai; Vasudevan, Subhash G

2015-01-23

Dengue virus multifunctional proteins NS3 protease/helicase and NS5 methyltransferase/RNA-dependent RNA polymerase form part of the viral replication complex and are involved in viral RNA genome synthesis, methylation of the 5'-cap of viral genome, and polyprotein processing among other activities. Previous studies have shown that NS5 residue Lys-330 is required for interaction between NS3 and NS5. Here, we show by competitive NS3-NS5 interaction ELISA that the NS3 peptide spanning residues 566-585 disrupts NS3-NS5 interaction but not the null-peptide bearing the N570A mutation. Small angle x-ray scattering study on NS3(172-618) helicase and covalently linked NS3(172-618)-NS5(320-341) reveals a rigid and compact formation of the latter, indicating that peptide NS5(320-341) engages in specific and discrete interaction with NS3. Significantly, NS3:Asn-570 to alanine mutation introduced into an infectious DENV2 cDNA clone did not yield detectable virus by plaque assay even though intracellular double-stranded RNA was detected by immunofluorescence. Detection of increased negative-strand RNA synthesis by real time RT-PCR for the NS3:N570A mutant suggests that NS3-NS5 interaction plays an important role in the balanced synthesis of positive- and negative-strand RNA for robust viral replication. Dengue virus infection has become a global concern, and the lack of safe vaccines or antiviral treatments urgently needs to be addressed. NS3 and NS5 are highly conserved among the four serotypes, and the protein sequence around the pinpointed amino acids from the NS3 and NS5 regions are also conserved. The identification of the functionally essential interaction between the two proteins by biochemical and reverse genetics methods paves the way for rational drug design efforts to inhibit viral RNA synthesis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

The shock/shear platform for planar radiation-hydrodynamics experiments on the National Ignition Facility

DOE PAGES

Doss, F. W.; Kline, J. L.; Flippo, K. A.; ...

2015-04-17

An indirectly-driven shock tube experiment fielded on the National Ignition Facility (NIF) was used to create a high-energy-density hydrodynamics platform at unprecedented scale. Scaling up a shear-induced mixing experiment previously fielded at OMEGA, the NIF shear platform drives 130 μm/ns shocks into a CH foam-filled shock tube (~ 60 mg/cc) with interior dimensions of 1.5 mm diameter and 5 mm length. The pulse-shaping capabilities of the NIF are used to extend the drive for >10 ns, and the large interior tube volumes are used to isolate physics-altering edge effects from the region of interest. The scaling of the experiment tomore » the NIF allows for considerable improvement in maximum driving time of hydrodynamics, in fidelity of physics under examination, and in diagnostic clarity. Details of the experimental platform and post-shot simulations used in the analysis of the platform-qualifying data are presented. Hydrodynamic scaling is used to compare shear data from OMEGA with that from NIF, suggesting a possible change in the dimensionality of the instability at late times from one platform to the other.« less

Feeding of Nigella sativa during neonatal and juvenile growth improves learning and memory of rats

PubMed Central

Beheshti, Farimah; Hosseini, Mahmoud; Vafaee, Farzaneh; Shafei, Mohammad Naser; Soukhtanloo, Mohammad

2015-01-01

The positive roles of antioxidants on brain development and learning and memory have been suggested. Nigella sativa (NS) has been suggested to have antioxidant and neuroprotective effects. This study was done to investigate the effects of feeding by the hydro-alcoholic extract of NS during neonatal and juvenile growth on learning and memory of rats. The pregnant rats were kept in separate cages. After delivery, they were randomly divided into four Groups including: (1) control; (2) NS 100 mg/kg (NS 100); (3) NS 200 mg/kg (NS 200); and (4) NS 400 mg/kg (NS 400). Rats in the control group (Group 1) received normal drinking water, whereas Groups 2, 3, and 4 received the same drinking water supplemented with the hydro-alcoholic extract of NS (100 mg/kg, 200 mg/kg, and 400 mg/kg, respectively) from the 1st day after birth through the first 8 weeks of life. After 8 weeks, 10 male offspring from each group were randomly selected and tested in the Morris water maze (MWM) and passive avoidance (PA) test. Finally, the brains were removed and total thiol groups and malondialdehyde (MDA) concentrations were determined. In the MWM, treatment by 400 mg/kg extract reduced both the time latency and the distance traveled to reach the platform compared to the control group (p < 0.05–p < 0.01). Both 200 mg/kg and 400 mg/kg of the extract increased the time spent in the target quadrant (p < 0.05–p < 0.01). In the PA test, the treatment of the animals by 200 mg/kg and 400 mg/kg of NS extract significantly increased the time latency for entering the dark compartment (p < 0.05–p < 0.001). Pretreatment of the animals with 400 mg/kg of NS extract decreased the MDA concentration in hippocampal tissues whereas it increased the thiol content compared to the control group (p < 0.001). These results allow us to propose that feeding of the rats by the hydro-alcoholic extract of NS during neonatal and juvenile growth has positive effects on learning and memory. The effects might be due to the antioxidant effects. PMID:27114937

Traumatic brain injury in mice and pentadecapeptide BPC 157 effect.

PubMed

Tudor, Mario; Jandric, Ivan; Marovic, Anton; Gjurasin, Miroslav; Perovic, Darko; Radic, Bozo; Blagaic, Alenka Boban; Kolenc, Danijela; Brcic, Luka; Zarkovic, Kamelija; Seiwerth, Sven; Sikiric, Predrag

2010-02-25

Gastric pentadecapeptide BPC 157 (GEPPPGKPADDAGLV, an anti-ulcer peptide, efficient in inflammatory bowel disease trials (PL 14736), no toxicity reported, improved muscle crush injury. After an induced traumatic brain injury (TBI) in mice by a falling weight, BPC 157 regimens (10.0microg, 10.0ng/kgi.p.) demonstrated a marked attenuation of damage with an improved early outcome and a minimal postponed mortality throughout a 24h post-injury period. Ultimately, the traumatic lesions (subarachnoidal and intraventricular haemorrhage, brain laceration, haemorrhagic laceration) were less intense and consecutive brain edema had considerably improved. Given prophylactically (30 min before TBI) the improved conscious/unconscious/death ratio in TBI-mice was after force impulses of 0.068 Ns, 0.093 Ns, 0.113 Ns, 0.130 Ns, 0.145 Ns, and 0.159 Ns. Counteraction (with a reduction of unconsciousness, lower mortality) with both microg- and ng-regimens included the force impulses of 0.068-0.145 Ns. A higher regimen presented effectiveness also against the maximal force impulse (0.159 Ns). Furthermore, BPC 157 application immediately prior to injury was beneficial in mice subjected to force impulses of 0.093 Ns-TBI. For a more severe force impulse (0.130 Ns, 0.145 Ns, or 0159 Ns), the time-relation to improve the conscious/unconscious/death ratio was: 5 min (0.130 Ns-TBI), 20 min (0.145 Ns-TBI) or 30 min (0.159 Ns-TBI). Copyright 2009 Elsevier B.V. All rights reserved.

Suppression of the Transit -Time Instability in Large-Area Electron Beam Diodes

NASA Astrophysics Data System (ADS)

Myers, Matthew C.; Friedman, Moshe; Swanekamp, Stephen B.; Chan, Lop-Yung; Ludeking, Larry; Sethian, John D.

2002-12-01

Experiment, theory, and simulation have shown that large-area electron-beam diodes are susceptible to the transit-time instability. The instability modulates the electron beam spatially and temporally, producing a wide spread in electron energy and momentum distributions. The result is gross inefficiency in beam generation and propagation. Simulations indicate that a periodic, slotted cathode structure that is loaded with resistive elements may be used to eliminate the instability. Such a cathode has been fielded on one of the two opposing 60 cm × 200 cm diodes on the NIKE KrF laser at the Naval Research Laboratory. These diodes typically deliver 600 kV, 500 kA, 250 ns electron beams to the laser cell in an external magnetic field of 0.2 T. We conclude that the slotted cathode suppressed the transit-time instability such that the RF power was reduced by a factor of 9 and that electron transmission efficiency into the laser gas was improved by more than 50%.

Radionuclide transport from soil to air, native vegetation, kangaroo rats and grazing cattle on the Nevada test site

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

Gilbert, R.O.; Shinn, J.H.; Essington, E.H.

Between 1970 and 1986 the Nevada Applied Ecology Group (NAEG), U.S. Department of Energy, conducted environmental radionuclide studies at weapons-testing sites on or adjacent to the Nevada Test Site. In this paper, NAEG studies conducted at two nuclear (fission) sites (NS201, NS219) and two nonnuclear (nonfission) sites (Area 13 (Project 57) and Clean Slate 2) are reviewed, synthesized and compared regarding (1) soil particle-size distribution and physical-chemical characteristics of 239 + 240Pu-bearing radioactive particles, (2) 239 + 240Pu resuspension rates and (3) transuranic and fission-product radionuclide transfers from soil to native vegetation, kangaroo rats and grazing cattle. The data indicatemore » that transuranic radionuclides were transferred more readily on the average from soil to air, the external surfaces of native vegetation and to tissues of kangaroo rats at Area 13 than at NS201 or NS219. The 239 + 240Pu resuspension factor for undisturbed soil at Area 13 was three to four orders-of-magnitude larger than at NS201 and NS219, the geometric mean (GM) vegetation-over-soil 239 + 240Pu concentration ratio was from ten to 100 times larger than at NS201, and the GM GI-over-soil, carcass-over-soil and pelt-over-soil 239 + 240Pu ratios for kangaroo rats were about ten times larger than at NS201. These results are consistent with the finding that Area 13, compared with NS201 or NS219, has a higher percentage of radioactivity associated with smaller soil particles and a larger percentage of resuspendable and respirable soil. However, the resuspension factor increased by a factor of 27 at NS201 when the surface soil was disturbed, and by a factor of 12 at NS219 following a wildfire.« less

Electropermeabilization by uni- or bipolar nanosecond electric pulses: The impact of extracellular conductivity.

PubMed

Gianulis, Elena C; Casciola, Maura; Xiao, Shu; Pakhomova, Olga N; Pakhomov, Andrei G

2018-02-01

Cellular effects caused by nanosecond electric pulses (nsEP) can be reduced by an electric field reversal, a phenomenon known as bipolar cancellation. The reason for this cancellation effect remains unknown. We hypothesized that assisted membrane discharge is the mechanism for bipolar cancellation. CHO-K1 cells bathed in high (16.1mS/cm; HCS) or low (1.8mS/cm; LCS) conductivity solutions were exposed to either one unipolar (300-ns) or two opposite polarity (300+300-ns; bipolar) nsEP (4-40kV/cm) with increasing interpulse intervals (0.1-50μs). Time-lapse YO-PRO-1 (YP) uptake revealed enhanced membrane permeabilization in LCS compared to HCS at all tested voltages. The time-dependence of bipolar cancellation was similar in both solutions, using either identical (22kV/cm) or isoeffective nsEP treatments (12 and 32kV/cm for LCS and HCS, respectively). However, cancellation was significantly stronger in LCS when the bipolar nsEP had no, or very short (<1μs), interpulse intervals. Finally, bipolar cancellation was still present with interpulse intervals as long as 50μs, beyond the time expected for membrane discharge. Our findings do not support assisted membrane discharge as the mechanism for bipolar cancellation. Instead they exemplify the sustained action of nsEP that can be reversed long after the initial stimulus. Copyright © 2017 Elsevier B.V. All rights reserved.

Black hole-neutron star binary merger: Dependence on black hole spin orientation and equation of state

NASA Astrophysics Data System (ADS)

Kawaguchi, Kyohei; Kyutoku, Koutarou; Nakano, Hiroyuki; Okawa, Hirotada; Shibata, Masaru; Taniguchi, Keisuke

2015-07-01

We systematically performed numerical-relativity simulations for black hole-neutron star (BH-NS) binary mergers with a variety of the BH spin orientation and nuclear-theory-based equations of state (EOS) of the NS. The initial misalignment angles of the BH spin measured from the direction of the orbital angular momentum are chosen in the range of itilt,0≈30 ° -90 ° . We employed four models of nuclear-theory-based zero-temperature EOS for the NS in which the compactness of the NS is in the range of C =MNS/RNS=0.138 -0.180 , where MNS and RNS are the mass and the radius of the NS, respectively. The mass ratio of the BH to the NS, Q =MBH/MNS , and the dimensionless spin parameter of the BH, χ , are chosen to be Q =5 and χ =0.75 , together with MNS=1.35 M⊙ so that the BH spin misalignment has a significant effect on tidal disruption of the NS. We obtain the following results: (i) The inclination angles of itilt,0<70 ° and itilt,0<50 ° are required for the formation of a remnant disk with its mass larger than 0.1 M⊙ for the cases C =0.140 and C =0.160 , respectively, while the disk mass is always smaller than 0.1 M⊙ for C ≳0.175 . The ejecta with its mass larger than 0.01 M⊙ is obtained for itilt,0<85 ° with C =0.140 , for itilt,0<65 ° with C =0.160 , and for itilt,0<30 ° with C =0.175 . (ii) The rotational axis of the dense part of the remnant disk with its rest-mass density larger than 109 g /cm3 is approximately aligned with the remnant BH spin for itilt,0≈30 ° . On the other hand, the disk axis is misaligned initially with ˜30 ° for itilt,0≈60 ° , and the alignment with the remnant BH spin is achieved at ˜50 - 60 ms after the onset of merger. The accretion time scale of the remnant disk is typically ˜100 ms and depends only weakly on the misalignment angle and the EOS. (iii) The ejecta velocity is typically ˜0.2 - 0.3 c and depends only weakly on the misalignment angle and the EOS of the NS, while the morphology of the ejecta depends on its mass. (iv) The gravitational-wave spectra contains the information of the NS compactness in the cutoff frequency for itilt,0≲60 ° .

Raising the avermectins production in Streptomyces avermitilis by utilizing nanosecond pulsed electric fields (nsPEFs)

NASA Astrophysics Data System (ADS)

Guo, Jinsong; Ma, Ruonan; Su, Bo; Li, Yinglong; Zhang, Jue; Fang, Jing

2016-05-01

Avermectins, a group of anthelmintic and insecticidal agents produced from Streptomyces avermitilis, are widely used in agricultural, veterinary, and medical fields. This study presents the first report on the potential of using nanosecond pulsed electric fields (nsPEFs) to improve avermectin production in S. avermitilis. The results of colony forming units showed that 20 pulses of nsPEFs at 10 kV/cm and 20 kV/cm had a significant effect on proliferation, while 100 pulses of nsPEFs at 30 kV/cm exhibited an obvious effect on inhibition of agents. Ultraviolet spectrophotometry assay revealed that 20 pulses of nsPEFs at 15 kV/cm increased avermectin production by 42% and reduced the time for reaching a plateau in fermentation process from 7 days to 5 days. In addition, the decreased oxidation reduction potential (ORP) and increased temperature of nsPEFs-treated liquid were evidenced to be closely associated with the improved cell growth and fermentation efficiency of avermectins in S. avermitilis. More importantly, the real-time RT-PCR analysis showed that nsPEFs could remarkably enhance the expression of aveR and malE in S. avermitilis during fermentation, which are positive regulator for avermectin biosynthesis. Therefore, the nsPEFs technology presents an alternative strategy to be developed to increase avermectin output in fermentation industry.

Nanosecond retinal structure changes in K-590 during the room-temperature bacteriorhodopsin photocycle: picosecond time-resolved coherent anti-stokes Raman spectroscopy.

PubMed

Weidlich, O; Ujj, L; Jäger, F; Atkinson, G H

1997-05-01

Time-resolved vibrational spectra are used to elucidate the structural changes in the retinal chromophore within the K-590 intermediate that precedes the formation of the L-550 intermediate in the room-temperature (RT) bacteriorhodopsin (BR) photocycle. Measured by picosecond time-resolved coherent anti-Stokes Raman scattering (PTR/CARS), these vibrational data are recorded within the 750 cm-1 to 1720 cm-1 spectral region and with time delays of 50-260 ns after the RT/BR photocycle is optically initiated by pulsed (< 3 ps, 1.75 nJ) excitation. Although K-590 remains structurally unchanged throughout the 50-ps to 1-ns time interval, distinct structural changes do appear over the 1-ns to 260-ns period. Specifically, comparisons of the 50-ps PTR/CARS spectra with those recorded with time delays of 1 ns to 260 ns reveal 1) three types of changes in the hydrogen-out-of-plane (HOOP) region: the appearance of a strong, new feature at 984 cm-1; intensity decreases for the bands at 957 cm-1, 952 cm-1, and 939 cm-1; and small changes intensity and/or frequency of bands at 855 cm-1 and 805 cm-1; and 2) two types of changes in the C-C stretching region: the intensity increase in the band at 1196 cm-1 and small intensity changes and/or frequency shifts for bands at 1300 cm-1 and 1362 cm-1. No changes are observed in the C = C stretching region, and no bands assignable to the Schiff base stretching mode (C = NH+) mode are found in any of the PTR/CARS spectra assignable to K-590. These PTR/CARS data are used, together with vibrational mode assignments derived from previous work, to characterize the retinal structural changes in K-590 as it evolves from its 3.5-ps formation (ps/K-590) through the nanosecond time regime (ns/K-590) that precedes the formation of L-550. The PTR/CARS data suggest that changes in the torsional modes near the C14-C15 = N bonds are directly associated with the appearance of ns/K-590, and perhaps with the KL intermediate proposed in earlier studies. These vibrational data can be primarily interpreted in terms of the degree of twisting of the C14-C15 retinal bond. Such twisting may be accompanied by changes in the adjacent protein. Other smaller, but nonetheless clear, spectral changes indicate that alterations along the retinal polyene chain also occur. The changes in the retinal structure are preliminary to the deprotonation of the Schiff base nitrogen during the formation of M-412. The time constant for the ps/ns K-590 transformation is estimated from the amplitude change of four vibrational bands in the HOOP region to be 40-70 ns.

XAS Characterization of the Zn Site of Non-structural Protein 3 (NS3) from Hepatitis C Virus

NASA Astrophysics Data System (ADS)

Ascone, I.; Nobili, G.; Benfatto, M.; Congiu-Castellano, A.

2007-02-01

XANES spectra of non structural protein 3 (NS3) have been calculated using 4 Zn coordination models from three crystallographic structures in the Protein Data Base (PDB): 1DY9, subunit B, 1CU1 subunit A and B, and 1JXP subunit B. Results indicate that XANES is an appropriate tool to distinguish among them. Experimental XANES spectra have been simulated refining crystallographic data. The model obtained by XAS is compared with the PDB models.

First Results of GPS Time Transfer to Australia

NASA Technical Reports Server (NTRS)

Mck.luck, J.; Woodger, J. R.; Wells, J. E.; Churchill, P. N.; Clements, P. A.

1984-01-01

A global positioning system (GPS) time transfer unit was installed at Tidbinbilla Deep Space Communications Complex of the DSN in June 1983. It was used to estimate the relationship to UTC(USNO MC) of the Tidbinbilla frequency and time system TID(FTS) based on a hydrogen maser, and to estimate the performance of the Australian free-running time scale UTC(AUS). Data from the first 3 months were analyzed three ways: by two-hop common view using JPL as intermediary; by long-arc interpolation of measurements against space vehicle clocks; and by long arc interpolation of GPS-Time results. Residuals from a single quadratic fit through 3 months of UTC(USNO MC) -TID(FTS) results were white noise with standard error 15 ns, and a flying clock measurement gave 70 ns agreement. A straight line fit through results UTC(USNO MC) - UTC(AUS) gave 90 ns standard error and 120 ns agreement. It is proposed to use the GPS measurements to steer UTC(AUS) to UTC(BIH), and to rename the existing time scale TA(AUS).

Impact of the ceramide subspecies on the nanostructure of stratum corneum lipids using neutron scattering and molecular dynamics simulations. Part I: impact of CER[NS].

PubMed

Schmitt, Thomas; Gupta, Rakesh; Lange, Stefan; Sonnenberger, Stefan; Dobner, Bodo; Hauß, Thomas; Rai, Beena; Neubert, Reinhard H H

2018-05-30

For this study mixtures based on the ceramides [NS] (NS = non-hydroxy-sphingosine) and [AP] (AP = α-hydroxy-phytosphingosine) in a 2:1 and 1:2 ratio, together with cholesterol and lignoceric acid, were investigated. These mixtures are modelling the uppermost skin layer, the stratum corneum. Neutron diffraction, utilizing specifically deuterated ceramide molecules, was used to obtain a maximum amount of experimental detail. Highly detailed molecular dynamics simulations were used to generate even more information from the experimental data. It was possible to observe a single lamellar phase for both systems. They had a lamellar repeat distance of 5.43 ± 0.05 nm for the [NS]/[AP] 2:1 and a slightly shorter one of 5.34 ± 0.05 nm for the 1:2 system. The structure and water content was uninfluenced by excess humidity. Both the experimental and simulation data indicated slightly tilted ceramides, with their C24 chains overlapping in the lamellar mid-plane. This arrangement is well comparable to systems investigated before. The structure of both systems, except for the differing repeat distance, looks similar at first. However, on a smaller scale there were various distinct differences, demonstrating only low redundancy between the different ceramide species, despite only minor chemical differences. The mainly ceramide [AP] determined 1:2 system has a slightly smaller repeat distance. This is a result of a tighter arrangement of the lipids chain along the bilayer normal and increased overlapping of the long chains in the lamellar middle. For the CER[NS] some novel features could be shown, despite it being the overall most investigated ceramide. These include the low adaptability to changed lateral interactions, leading to an increased chain opening. This effect could explain its low miscibility with other lipids. The investigated model systems allows it to directly compare results from the literature which have used ceramide [NS] to the most recent studies using the phytosphingosine ceramides such as ceramide [AP]. Copyright © 2018 Elsevier B.V. All rights reserved.

A graphite based STT-RAM cell with reduction in switching current

NASA Astrophysics Data System (ADS)

Varghani, Ali; Peiravi, Ali

2015-10-01

Spin Transfer Torque Random Access Memory (STT-RAM) is a serious candidate for "universal memory" because of its non-volatility, fast access time, high density, good scalability, high endurance and relatively low power dissipation. However, problems with low write speed and large write current are important existing challenges in STT-RAM design and there is a tradeoff between them and data retention time. In this study, a novel STT-RAM cell structure which uses perfect graphite based Magnetic Tunnel Junction (MTJ) is proposed. First, the cross-section of the structure is selected to be an ellipse of 45 nm and 180 nm dimensions and a six-layer graphite is used as tunnel barrier. By passing a lateral current with a short pulse width (before applying STT current and independent of it) through four middle graphene layers of the tunnel barrier, a 27% reduction in the amplitude of the switching current (for fast switching time of 2 ns) or a 58% reduction in its pulse width is achieved without any reduction in data retention time. Finally, the effect of downscaling of technology on the proposed structure is evaluated. A reduction of 31.6% and 9% in switching current is achieved for 90 and 22 nm cell width respectively by passing sufficient current (100 μA with 0.1 ns pulse width) through the tunnel barrier. Simulations are done using Object Oriented Micro Magnetic Framework (OOMMF).

Roles of p53 and caspases in induction of apoptosis in MCF- 7 breast cancer cells treated with a methanolic extract of Nigella sativa seeds.

PubMed

Alhazmi, Mohammed I; Hasan, Tarique N; Shafi, Gowhar; Al-Assaf, Abdullah H; Alfawaz, Mohammed A; Alshatwi, Ali A

2014-01-01

Nigella Sativa (NS) is an herb from the Ranunculaceae family that exhibits numerous medicinal properties and has been used as important constituent of many complementary and alternative medicines (CAMs). The ability of NS to kill cancer cells such as PC3, HeLa and hepatoma cells is well established. However, our understanding of the mode of death caused by NS remains nebulous. The objective of this study was to gain further insight into the mode and mechanism of death caused by NS in breast cancer MCF-7 cells. Human breast cancer cells (MCF-7) were treated with a methanolic extract of NS, and a dose- and time-dependent study was performed. The IC50 was calculated using a Cell Titer Blue® viability assay assay, and evidence for DNA fragmentation was obtained by fluorescence microscopy TUNEL assay. Gene expression was also profiled for a number of apoptosis-related genes (Caspase-3, -8, -9 and p53 genes) through qPCR. The IC50 of MCF-7 cells was 62.8 μL/mL. When MCF-7 cells were exposed to 50 μL/mL and 100 μL/mL NS for 24 h, 48 h and 72 h, microscopic examination (TUNEL assay) revealed a dose- and time-dependent increase in apoptosis. Similarly, the expression of the Caspase-3, -8, -9 and p53 genes increased significantly according to the dose and time. NS induced apoptosis in MCF-7 cells through both the p53 and caspase pathways. NS could potentially represent an alternative source of medicine for breast cancer therapy.

Dynamical Tidal Response of a Rotating Neutron Star

NASA Astrophysics Data System (ADS)

Landry, Philippe; Poisson, Eric

2017-01-01

The gravitational wave phase of a neutron star (NS) binary is sensitive to the deformation of the NS that results from its companion's tidal influence. In a perturbative treatment, the tidal deformation can be characterized by a set of dimensionless constants, called Love numbers, which depend on the NS equation of state. For static NSs, one type of Love number encodes the response to gravitoelectric tidal fields (associated with mass multipole moments), while another does likewise for gravitomagnetic fields (associated with mass currents). A NS subject to a gravitomagnetic tidal field develops internal fluid motions through gravitomagnetic induction; the fluid motions are irrotational, provided the star is non-rotating. When the NS is allowed to rotate, the situation is complicated by couplings between the tidal field and the star's spin. The problem becomes tractable in the slow-rotation limit. In this case, the fluid motions induced by an external gravitomagnetic field are fully dynamical, even if the tidal field is stationary: interior metric and fluid variables are time-dependent, and vary on the timescale of the rotation period. Remarkably, the exterior geometry of the NS remains time-independent.

Intrafascial versus interfascial nerve sparing in radical prostatectomy for localized prostate cancer: a systematic review and meta-analysis.

PubMed

Weng, Hong; Zeng, Xian-Tao; Li, Sheng; Meng, Xiang-Yu; Shi, Ming-Jun; He, Da-Lin; Wang, Xing-Huan

2017-09-13

The present study aimed to systematically evaluate the effectiveness and safety of the intrafascial and interfascial nerve sparing (ITR-NS and ITE-NS) radical prostatectomy. PubMed, Embase, and Cochrane Library databases were searched for eligible studies. Meta-analysis with random-effects model was performed. Six comparative trials were selected and embraced in this research, including one randomized controlled trial, three prospective comparative trials, and two retrospective comparative trials. With regard to perioperative parameters, no significant association of operative time, blood loss, transfusion rates, duration of catheterization, and hospital stay existed between ITR-NS and ITE-NS. With respect to the functional results, ITR-NS had advantages in terms of both continence and potency recovery compared with ITE-NS. In reference to the oncologic results, the ITR-NS showed lower overall positive surgical margin (PSM) compared with ITE-NS but pT2 PSM and biochemical recurrence free rates were similar to the two surgical types. This study demonstrates that ITR-NS has better continence at 6 mo and 36 mo and better potency recovery at 6 mo and 12 mo postoperatively, regardless of the surgical technique. The cancer control of ITR-NS was also better than that of ITE-NS. This may be explained by the fact that patients in ITE-NS group present higher risk cancer than patients in ITR-NS group.

Design of fast signal processing readout front-end electronics implemented in CMOS 40 nm technology

NASA Astrophysics Data System (ADS)

Kleczek, Rafal

2016-12-01

The author presents considerations on the design of fast readout front-end electronics implemented in a CMOS 40 nm technology with an emphasis on the system dead time, noise performance and power dissipation. The designed processing channel consists of a charge sensitive amplifier with different feedback types (Krummenacher, resistive and constant current blocks), a threshold setting block, a discriminator and a counter with logic circuitry. The results of schematic and post-layout simulations with randomly generated input pulses in a time domain according to the Poisson distribution are presented and analyzed. Dead time below 20 ns is possible while keeping noise ENC ≈ 90 e- for a detector capacitance CDET = 160 fF.

Investigation of digital timing resolution and further improvement by using constant fraction signal time marker slope for fast scintillator detectors

NASA Astrophysics Data System (ADS)

Singh, Kundan; Siwal, Davinder

2018-04-01

A digital timing algorithm is explored for fast scintillator detectors, viz. LaBr3, BaF2, and BC501A. Signals were collected with CAEN 250 mega samples per second (MSPS) and 500 MSPS digitizers. The zero crossing time markers (TM) were obtained with a standard digital constant fraction timing (DCF) method. Accurate timing information is obtained using cubic spline interpolation of a DCF transient region sample points. To get the best time-of-flight (TOF) resolution, an optimization of DCF parameters is performed (delay and constant fraction) for each pair of detectors: (BaF2-LaBr3), (BaF2-BC501A), and (LaBr3-BC501A). In addition, the slope information of an interpolated DCF signal is extracted at TM position. This information gives a new insight to understand the broadening in TOF, obtained for a given detector pair. For a pair of signals having small relative slope and interpolation deviations at TM, leads to minimum time broadening. However, the tailing in TOF spectra is dictated by the interplay between the interpolation error and slope variations. Best TOF resolution achieved at the optimum DCF parameters, can be further improved by using slope parameter. Guided by the relative slope parameter, events selection can be imposed which leads to reduction in TOF broadening. While the method sets a trade-off between timing response and coincidence efficiency, it provides an improvement in TOF. With the proposed method, the improved TOF resolution (FWHM) for the aforementioned detector pairs are; 25% (0.69 ns), 40% (0.74 ns), 53% (0.6 ns) respectively, obtained with 250 MSPS, and corresponds to 12% (0.37 ns), 33% (0.72 ns), 35% (0.69 ns) respectively with 500 MSPS digitizers. For the same detector pair, event survival probabilities are; 57%, 58%, 51% respectively with 250 MSPS and becomes 63%, 57%, 68% using 500 MSPS digitizers.

Molecular modeling, simulation and virtual screening of MurD ligase protein from Salmonella typhimurium LT2.

PubMed

Samal, Himanshu Bhusan; Das, Jugal Kishore; Mahapatra, Rajani Kanta; Suar, Mrutyunjay

2015-01-01

The Mur enzymes of the peptidoglycan biosynthesis pathway constitute ideal targets for the design of new classes of antimicrobial inhibitors in Gram-negative bacteria. We built a homology model of MurD of Salmonella typhimurium LT2 using MODELLER (9v12) software. 'The homology model was subjected to energy minimization by molecular dynamics (MD) simulation study with GROMACS software for a simulation time of 20 ns in water environment. The model was subjected for virtual screening study from the Zinc Database using Dockblaster software. Inhibition assay for the best inhibitor, 3-(amino methyl)-n-(4-methoxyphenyl) aniline, by flow cytometric analysis revealed the effective inhibition of peptidoglycan biosynthesis. Results from this study provide new insights for the molecular understanding and development of new antibacterial drugs against the pathogen. Copyright © 2015 Elsevier Inc. All rights reserved.

The first measurements of soft x-ray flux from ignition scale Hohlraums at the national ignition facility using DANTE

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

Kline, John L; Glenzer, S H; Olson, Rick

2010-01-01

The first 96 and 192 beam vacuum hohlraum have been fielded at the National Ignition Facility demonstrating radiation temperatures up to 340 eV and fluxes of 20 TW/sr representing a 20 times flux increase over NOVA/Omega scale hohlraums. The vacuum hohlraums were irradiated with 2 ns square pulses with energies between 150 - 635 kJ. They produced nearly Planckian spectra with about 30 {+-} 10% more flux than predicted by the current radiation hydrodynamic simulations after careful verification of all component calibrations (which included an {approx} 10% downward correction to Center X-Ray Optics opacities just below the Cu L edgemore » at 50-750 eV), cable deconvolution, and analysis software routines. To corroborate these results, first a half hohlraum experiment was conducted using a single 2 ns-long axial quad with an irradiance of {approx} 1-2 x 10{sup 15} W/cm{sup 2} for comparison with NIF Early Light experiments completed in 2004. Second, we completed a conversion efficiency test using a 128-beam nearly uniformly illuminated gold sphere with intensities kept low (at 1 x 10{sup 14} W/cm{sup 2} over 5 ns) to avoid sensitivity to modeling uncertainties for non-local heat conduction and non-linear absorption mechanisms, to compare with similar intensity, 3 ns OMEGA sphere results. The 2004 and 2009 NIF half-hohlraums agreed to 10% in flux, but more importantly, the 2006 OMEGA Au Sphere, the 2009 NIF Au sphere and the calculated Au conversion efficiency agree to {+-}5% in flux, which is estimated to be the absolute calibration accuracy of the DANTEs. Hence we concluded the 30 {+-} 10% higher than expected radiation fluxes from the 96 and 192 beam vacuum hohlraums are attributable to differences in physics when we transitioned to large hot hohlraums. Specifically, using variants in the atomic physics models and electron heat conduction, newer simulations show that nonlocalization of energy deposition leads to less energy being stored in the coronal plasma leading to higher x-ray conversion efficiency. Since the larger volume-to-area ratio hohlraums have large coronal plasmas which scale volumetrically, the reduction in energy losses to the corona become more pronounced than for smaller NOVA/Omega scale hohlraums. The higher conversion efficiencies are also consistent with observations from other 1 ns gold sphere experiments conducted at Omega with 1 x 10{sup 15} W/cm{sup 2} laser irradiances.« less

The effect of wide swathing on wilting times and nutritive value of alfalfa haylage.

PubMed

Kung, L; Stough, E C; McDonell, E E; Schmidt, R J; Hofherr, M W; Reich, L J; Klingerman, C M

2010-04-01

On 3 consecutive cuttings, alfalfa from a single field was mowed with a John Deere 946 mower-conditioner (4-m cut width; Moline, IL) to leave narrow swaths (NS) ranging from 1.2 to 1.52 m wide (30-37% of cutter bar width) and wide swaths (WS) ranging from 2.44 to 2.74 m wide (62-67% of cutter bar width). Samples were collected from windrows and dry matter (DM) was monitored during wilting until a target of 43 to 45% DM was obtained. Forage from random windrows (n=4-6) was harvested by hand, chopped through a forage harvester before being packed in replicated vacuum-sealed bags, and allowed to ensile for 65 d. There was no swath width x cutting interaction for any parameter tested. Over all cuttings, the resulting silage DM was not different between the NS silage (43.8%) and the WS silage (44.9%). However, wide swathing greatly reduced the time of wilting before making silage. The hours of wilting time needed to reach the targeted DM for the NS silage compared with the WS silage at cuttings 1, 2, and 3 were 50 versus 29, 54 versus 28, and 25 versus 6, respectively. At the time of ensiling, the WS silage had more water-soluble carbohydrates (5.1%) than did the NS silage (3.7%). The WS silage had a lower pH (4.58) than did the NS silage (4.66), but swath width did not affect fermentation end products (lactic acid, acetic acid, and ethanol). The NS silage had more NH(3)-N (0.26%) than did the WS silage (0.21%). Wide swathing did not affect the concentration of ash or the digestibility of NDF, but it lowered the N content (NS=3.45%; WS=3.23%) and increased the ADF content (NS=39.7%; WS=40.9%) of the resulting silage. Wide swathing can markedly reduce the time that alfalfa must wilt before it can be chopped for silage, but under good conditions, as in this study, the resulting silage quality was generally not improved. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Stellar encounters involving neutron stars in globular cluster cores

NASA Technical Reports Server (NTRS)

Davies, M. B.; Benz, W.; Hills, J. G.

1992-01-01

Encounters between a 1.4 solar mass neutron star and a 0.8 solar mass red giant (RG) and between a 1.4 solar mass neutron star (NS) and an 0.8 solar mass main-sequence (MS) star have been successfully simulated. In the case of encounters involving an RG, bound systems are produced when the separation at periastron passage R(MIN) is less than about 2.5 R(RG). At least 70 percent of these bound systems are composed of the RG core and NS forming a binary engulfed in a common envelope of what remains of the former RG envelope. Once the envelope is ejected, a tight white dwarf-NS binary remains. For MS stars, encounters with NSs will produce bound systems when R(MIN) is less than about 3.5 R(MS). Some 50 percent of these systems will be single objects with the NS engulfed in a thick disk of gas almost as massive as the original MS star. The ultimate fate of such systems is unclear.

The effect of intravenous lactated Ringer's solution versus 0.9% sodium chloride solution on serum osmolality in human volunteers.

PubMed

Williams, E L; Hildebrand, K L; McCormick, S A; Bedel, M J

1999-05-01

Animal studies have shown that large volumes of IV lactated Ringer's solution (LR) decrease serum osmolality, thereby increasing cerebral water. These studies have led to recommendations to limit LR to avoid cerebral edema in neurosurgical patients. Eighteen healthy human volunteers aged 20-48 yr received 50 mL/kg LR over 1 h on one occasion and 0.9% sodium chloride (NS) on another. Venous samples were taken at baseline (T1), at infusion end (T2), and 1 h after T2 (T3). Time until first urination was noted. With LR, serum osmolality decreased by 4+/-3 mOsm/kg from T1 to T2 and increased insignificantly with NS. At T3, osmolality returned almost to baseline in the LR group. Blood pH increased from T1 to T2 with LR by 0.04+/-0.04 and decreased with NS by 0.04+/-0.04. These pH changes persisted at T3. Subjective mental changes occurred only with NS. Abdominal discomfort was more common with NS. Time until first urination was longer with NS (106+/-11 min) than with LR (75+/-10 min) (P < 0.001). In healthy humans, an infusion of large volumes of LR, but not NS, transiently decreased serum osmolality, whereas acidosis associated with NS persisted and urinary output was slower with NS. Large volumes of lactated Ringer's solution administered to healthy humans produced small transient changes in serum osmolality. Large volumes of sodium chloride did not change osmolality but resulted in lower pH.

[Down-regulatory effect of Nucleostemin expression on signal molecule of PI3K/AKT/mTOR pathway in HL-60 cells].

PubMed

Jia, Yu; Wei, Yuan-Yu; Zhang, Fan; Li, Zhao-Bo; Liu, Shuai; Yue, Bao-Hong

2014-02-01

This study was purpose to explore the down-regulatory effect of nucleostemin (NS) expression on signal molecules of PI3K/AKT/mTOR pathway belonged to candidate ways of p53-independent signal pathway in the leukemia cells. The expression of NS was interfered by using recombinant lentivirus expression vector NS-RNAi-GV248 to transfect HL-60 cells of p53 deficiency. The expression of NS and signal molecules of PI3K/AKT/mTOR pathway were detected by using Real-time PCR. The results of showed that the HL-60 cells were transfected by recombinant lentivirus vector NS-RNAi-GV248 successfully and with transfection rate up to 80%. According to results of Real-time PCR detection, the inhibition rate of NS gene was 56.5% in HL-60 cells. And the expression levels of PI3K,AKT and GβL mRNA (0.491 ± 0.084,0.398 ± 0.164, 0.472 ± 0.097 respectively) were obviously down-regulated by silencing NS, and showed statistical difference (P < 0.05) in comparison with control (1.002 ± 0.171, 1.000 ± 0.411, 1.001 ± 0.206 respectively) . It is concluded that the changes of signal molecules of PI3K/AKT/mTOR pathway positively correlate with NS down-regulation, which provides evidence for confirming PI3K/AKT/mTOR signal pathway possible as a type of NS p53-independent pathway.

Structural Study of the C-Terminal Domain of Nonstructural Protein 1 from Japanese Encephalitis Virus.

PubMed

Poonsiri, Thanalai; Wright, Gareth S A; Diamond, Michael S; Turtle, Lance; Solomon, Tom; Antonyuk, Svetlana V

2018-04-01

Japanese encephalitis virus (JEV) is a mosquito-transmitted flavivirus that is closely related to other emerging viral pathogens, including dengue virus (DENV), West Nile virus (WNV), and Zika virus (ZIKV). JEV infection can result in meningitis and encephalitis, which in severe cases cause permanent brain damage and death. JEV occurs predominantly in rural areas throughout Southeast Asia, the Pacific Islands, and the Far East, causing around 68,000 cases of infection worldwide each year. In this report, we present a 2.1-Å-resolution crystal structure of the C-terminal β-ladder domain of JEV nonstructural protein 1 (NS1-C). The surface charge distribution of JEV NS1-C is similar to those of WNV and ZIKV but differs from that of DENV. Analysis of the JEV NS1-C structure, with in silico molecular dynamics simulation and experimental solution small-angle X-ray scattering, indicates extensive loop flexibility on the exterior of the protein. This, together with the surface charge distribution, indicates that flexibility influences the protein-protein interactions that govern pathogenicity. These factors also affect the interaction of NS1 with the 22NS1 monoclonal antibody, which is protective against West Nile virus infection. Liposome and heparin binding assays indicate that only the N-terminal region of NS1 mediates interaction with membranes and that sulfate binding sites common to NS1 structures are not glycosaminoglycan binding interfaces. This report highlights several differences between flavivirus NS1 proteins and contributes to our understanding of their structure-pathogenic function relationships. IMPORTANCE JEV is a major cause of viral encephalitis in Asia. Despite extensive vaccination, epidemics still occur. Nonstructural protein 1 (NS1) plays a role in viral replication, and, because it is secreted, it can exhibit a wide range of interactions with host proteins. NS1 sequence and protein folds are conserved within the Flavivirus genus, but variations in NS1 protein-protein interactions among viruses likely contribute to differences in pathogenesis. Here, we compared characteristics of the C-terminal β-ladder domain of NS1 between flaviviruses, including surface charge, loop flexibility, epitope cross-reactivity, membrane adherence, and glycosaminoglycan binding. These structural features are central to NS1 functionality and may provide insight into the development of diagnostic tests and therapeutics. Copyright © 2018 American Society for Microbiology.

Kilonova from post-merger ejecta as an optical and near-Infrared counterpart of GW170817

NASA Astrophysics Data System (ADS)

Tanaka, Masaomi; Utsumi, Yousuke; Mazzali, Paolo A.; Tominaga, Nozomu; Yoshida, Michitoshi; Sekiguchi, Yuichiro; Morokuma, Tomoki; Motohara, Kentaro; Ohta, Kouji; Kawabata, Koji S.; Abe, Fumio; Aoki, Kentaro; Asakura, Yuichiro; Baar, Stefan; Barway, Sudhanshu; Bond, Ian A.; Doi, Mamoru; Fujiyoshi, Takuya; Furusawa, Hisanori; Honda, Satoshi; Itoh, Yoichi; Kawabata, Miho; Kawai, Nobuyuki; Kim, Ji Hoon; Lee, Chien-Hsiu; Miyazaki, Shota; Morihana, Kumiko; Nagashima, Hiroki; Nagayama, Takahiro; Nakaoka, Tatsuya; Nakata, Fumiaki; Ohsawa, Ryou; Ohshima, Tomohito; Okita, Hirofumi; Saito, Tomoki; Sumi, Takahiro; Tajitsu, Akito; Takahashi, Jun; Takayama, Masaki; Tamura, Yoichi; Tanaka, Ichi; Terai, Tsuyoshi; Tristram, Paul J.; Yasuda, Naoki; Zenko, Tetsuya

2017-12-01

Recent detection of gravitational waves from a neutron star (NS) merger event GW170817 and identification of an electromagnetic counterpart provide a unique opportunity to study the physical processes in NS mergers. To derive properties of ejected material from the NS merger, we perform radiative transfer simulations of kilonova, optical and near-infrared emissions powered by radioactive decays of r-process nuclei synthesized in the merger. We find that the observed near-infrared emission lasting for >10 d is explained by 0.03 M⊙ of ejecta containing lanthanide elements. However, the blue optical component observed at the initial phases requires an ejecta component with a relatively high electron fraction (Ye). We show that both optical and near-infrared emissions are simultaneously reproduced by the ejecta with a medium Ye of ˜0.25. We suggest that a dominant component powering the emission is post-merger ejecta, which exhibits that the mass ejection after the first dynamical ejection is quite efficient. Our results indicate that NS mergers synthesize a wide range of r-process elements and strengthen the hypothesis that NS mergers are the origin of r-process elements in the Universe.

Nanosecond pulsed electric fields and the cell cycle

NASA Astrophysics Data System (ADS)

Mahlke, Megan A.

Exposure to nanosecond pulsed electrical fields (nsPEFs) can cause poration of external and internal cell membranes, DNA damage, and disassociation of cytoskeletal components, all of which are capable of disrupting a cell's ability to replicate. The phase of the cell cycle at the time of exposure is linked to differential sensitivities to nsPEFs across cell lines, as DNA structure, membrane elasticity, and cytoskeletal structure change dramatically during the cell cycle. Additionally, nsPEFs are capable of activating cell cycle checkpoints, which could lead to apoptosis or slow population growth. NsPEFs are emerging as a method for treating tumors via apoptotic induction; therefore, investigating the relevance of nsPEFs and the cell cycle could translate into improved efficacy in tumor treatment. Populations of Jurkat and Chinese Hamster Ovary (CHO) cells were examined post-exposure (10 ns pulse trains at 150kV/cm) by analysis of DNA content via propidium iodide staining and flow cytometric analysis at various time points (1, 6, and 12h post-exposure) to determine population distribution in cell cycle phases. Additionally, CHO and Jurkat cells were synchronized in G1/S and G2/M phases, pulsed, and analyzed to evaluate the role of cell cycle phase in survival of nsPEFs. CHO populations appeared similar to sham populations post-nsPEFs but exhibited arrest in the G1 phase at 6h after exposure. Jurkat cells exhibited increased cell death after nsPEFs compared to CHO cells but did not exhibit checkpoint arrest at any observed time point. The G1/S phase checkpoint is partially controlled by the action of p53; the lack of an active p53 response in Jurkat cells could contribute to their ability to pass this checkpoint and resist cell cycle arrest. Both cell lines exhibited increased sensitivity to nsPEFs in G2/M phase. Live imaging of CHO cells after nsPEF exposure supports the theory of G1/S phase arrest, as a reduced number of cells undergo mitosis within 24 h when compared to sham treated cells. CHO cells undergoing mitosis after exposure also exhibit improper separation of chromatids which could indicate loss of function of the mitotic spindle checkpoint. Activation and loss of function of checkpoints in CHO but not Jurkat cells after nsPEF exposure suggests that activation of cell cycle checkpoints could be important in defining the character of cell line specific recovery after nsPEF exposure. Moreover, the increased sensitivity in G2/M phase exhibited by both cell lines indicates that cell cycle phase is an important consideration during nsPEF exposure, particularly when aiming to induce apoptosis.

Expanding the potential of standard flow cytometry by extracting fluorescence lifetimes from cytometric pulse shifts

PubMed Central

Cao, Ruofan; Naivar, Mark A; Wilder, Mark; Houston, Jessica P

2014-01-01

Fluorescence lifetime measurements provide information about the fluorescence relaxation, or intensity decay, of organic fluorophores, fluorescent proteins, and other inorganic molecules that fluoresce. The fluorescence lifetime is emerging in flow cytometry and is helpful in a variety of multiparametric, single cell measurements because it is not impacted by nonlinearity that can occur with fluorescence intensity measurements. Yet time-resolved cytometry systems rely on major hardware modifications making the methodology difficult to reproduce. The motivation of this work is, by taking advantage of the dynamic nature of flow cytometry sample detection and applying digital signal processing methods, to measure fluorescence lifetimes using an unmodified flow cytometer. We collect a new lifetime-dependent parameter, referred to herein as the fluorescence-pulse-delay (FPD), and prove it is a valid representation of the average fluorescence lifetime. To verify we generated cytometric pulses in simulation, with light emitting diode (LED) pulsation, and with true fluorescence measurements of cells and microspheres. Each pulse is digitized and used in algorithms to extract an average fluorescence lifetime inherent in the signal. A range of fluorescence lifetimes is measurable with this approach including standard organic fluorophore lifetimes (∼1 to 22 ns) as well as small, simulated shifts (0.1 ns) under standard conditions (reported herein). This contribution demonstrates how digital data acquisition and signal processing can reveal time-dependent information foreshadowing the exploitation of full waveform analysis for quantification of similar photo-physical events within single cells. © 2014 The Authors. Published by Wiley Periodicals, Inc. PMID:25274073

Increased shell entropy as an explanation for observed decreased shell areal densities in OMEGA implosions

NASA Astrophysics Data System (ADS)

Hoffman, Nelson; Herrmann, Hans; Kim, Yongho

2014-10-01

A reduced ion-kinetic (RIK) model used in hydrodynamic simulations has had some success in explaining time- and space-averaged observables characterizing the fusion fuel in hot low-density ICF capsule implosions driven by 1-ns 60-beam laser pulses at OMEGA. But observables characterizing the capsule shell, e.g., the areal density of 12C in a plastic shell, have proved harder to explain. Recently we have found that assuming the shell has higher entropy than expected in a 1D laser-driven RIK simulation allows an explanation of the observed values of 12C areal density, and its dependence on initial shell thickness in a set of DT-filled plastic capsules. If, for example, a 15- μm CH shell implodes on an adiabat two to three times higher than predicted in a typical unmodified RIK simulation, the calculated burn-averaged shell areal density decreases from ~80 mg/cm2 in the unmodified simulation to the observed value of ~25 mg/cm2. We discuss possible mechanisms that could lead to increased entropy in such implosions. Research supported by U.S. Department of Energy under Contract DE-AC52-06NA25396.

Simulation of the High Performance Time to Digital Converter for the ATLAS Muon Spectrometer trigger upgrade

NASA Astrophysics Data System (ADS)

Meng, X. T.; Levin, D. S.; Chapman, J. W.; Zhou, B.

2016-09-01

The ATLAS Muon Spectrometer endcap thin-Resistive Plate Chamber trigger project compliments the New Small Wheel endcap Phase-1 upgrade for higher luminosity LHC operation. These new trigger chambers, located in a high rate region of ATLAS, will improve overall trigger acceptance and reduce the fake muon trigger incidence. These chambers must generate a low level muon trigger to be delivered to a remote high level processor within a stringent latency requirement of 43 bunch crossings (1075 ns). To help meet this requirement the High Performance Time to Digital Converter (HPTDC), a multi-channel ASIC designed by CERN Microelectronics group, has been proposed for the digitization of the fast front end detector signals. This paper investigates the HPTDC performance in the context of the overall muon trigger latency, employing detailed behavioral Verilog simulations in which the latency in triggerless mode is measured for a range of configurations and under realistic hit rate conditions. The simulation results show that various HPTDC operational configurations, including leading edge and pair measurement modes can provide high efficiency (>98%) to capture and digitize hits within a time interval satisfying the Phase-1 latency tolerance.

Stochastic Estimation and Control of Queues Within a Computer Network

DTIC Science & Technology

2009-03-01

3]. And NS-2 is a network simulator developed at UC Berkely and is a well known, free, powerful network simulator tool. As will be more discussed...HA011118931033.aspx 7. James Trulove , “Broadband Networking”, CRC Press, 2nd edition, 2000 8. Jonathan Pengelly “MONTE CARLO METHODS” University of Otago

Nigella sativa seed extract attenuates the fatigue induced by exhaustive swimming in rats

PubMed Central

Rahman, Mahbubur; Yang, Dong Kwon; Kim, Gi-Beum; Lee, Sei-Jin; Kim, Shang-Jin

2017-01-01

In previous studies, Nigella sativa (NS) has been studied due to its various physiological and pharmacological activities. However, evidence on the effects of NS on physical fatigue following exhaustive swimming remains limited. In the present study, the authors evaluated the potential beneficial effects of NS against the fatigue activity following exhaustive swimming. Rats were orally administered with NS extract (2 g/kg/day) for 21 days, and the anti-fatigue effect was assessed by exhaustive swimming exercise. The presented results indicated that pre-treatment of NS extract significantly increased the time to exhaustion. In hemodynamic parameters, NS extract increased blood pO2 and O2sat, but decreased pCO2. For underlying mechanisms, NS extract protected depletion of energy, indicated by increased levels of blood pH, glucose and tissue glycogen contents, and decreased levels of blood lactate, tissue lactic dehydrogenase and creatine kinase, when the NS extract was pre-treated. In addition, the NS extract inhibited oxidative stress following exhaustive swimming, as reflected by the results of increased levels of superoxide dismutase and redox ratio, and decreased the level of malondialdehyde when the NS extract was pre-treated. Collectively, the present study demonstrated that NS extract has an anti-fatigue activity against exhaustive swimming by energy restoration and oxidative-stress defense. PMID:28413647

Molecular dynamics study of methane hydrate formation at a water/methane interface.

PubMed

Zhang, Junfang; Hawtin, R W; Yang, Ye; Nakagava, Edson; Rivero, M; Choi, S K; Rodger, P M

2008-08-28

We present molecular dynamics simulation results of a liquid water/methane interface, with and without an oligomer of poly(methylaminoethylmethacrylate), PMAEMA. PMAEMA is an active component of a commercial low dosage hydrate inhibitor (LDHI). Simulations were performed in the constant NPT ensemble at temperatures of 220, 235, 240, 245, and 250 K and a pressure of 300 bar. The simulations show the onset of methane hydrate growth within 30 ns for temperatures below 245 K in the methane/water systems; at 240 K there is an induction period of ca. 20 ns, but at lower temperatures growth commences immediately. The simulations were analyzed to calculate hydrate content, the propensity for hydrogen bond formation, and how these were affected by both temperature and the presence of the LDHI. As expected, both the hydrogen bond number and hydrate content decreased with increasing temperature, though little difference was observed between the lowest two temperatures considered. In the presence of PMAEMA, the temperature below which sustained hydrate growth occurred was observed to decrease. Some of the implications for the role of PMAEMA in LDHIs are discussed.

The interdomain interface in bifunctional enzyme protein 3/4A (NS3/4A) regulates protease and helicase activities.

PubMed

Aydin, Cihan; Mukherjee, Sourav; Hanson, Alicia M; Frick, David N; Schiffer, Celia A

2013-12-01

Hepatitis C (HCV) protein 3/4A (NS3/4A) is a bifunctional enzyme comprising two separate domains with protease and helicase activities, which are essential for viral propagation. Both domains are stable and have enzymatic activity separately, and the relevance and implications of having protease and helicase together as a single protein remains to be explored. Altered in vitro activities of isolated domains compared with the full-length NS3/4A protein suggest the existence of interdomain communication. The molecular mechanism and extent of this communication was investigated by probing the domain-domain interface observed in HCV NS3/4A crystal structures. We found in molecular dynamics simulations that the two domains of NS3/4A are dynamically coupled through the interface. Interestingly, mutations designed to disrupt this interface did not hinder the catalytic activities of either domain. In contrast, substrate cleavage and DNA unwinding by these mutants were mostly enhanced compared with the wild-type protein. Disrupting the interface did not significantly alter RNA unwinding activity; however, the full-length protein was more efficient in RNA unwinding than the isolated protease domain, suggesting a more direct role in RNA processing independent of the interface. Our findings suggest that HCV NS3/4A adopts an "extended" catalytically active conformation, and interface formation acts as a switch to regulate activity. We propose a unifying model connecting HCV NS3/4A conformational states and protease and helicase function, where interface formation and the dynamic interplay between the two enzymatic domains of HCV NS3/4A potentially modulate the protease and helicase activities in vivo. © 2013 The Protein Society.

Exploring the Lead Compounds for Zika Virus NS2B-NS3 Protein: an e-Pharmacophore-Based Approach.

PubMed

Rohini, K; Agarwal, Pratika; Preethi, B; Shanthi, V; Ramanathan, K

2018-06-18

The rapid spread of the Zika virus and its association with the abnormal brain development constitute a global health emergency. With a continuing spread of the mosquito vector, the exposure is expected to accelerate in the coming years. Despite number of efforts, there is still no proper vaccine or medicine to combat this virus. Of note, the NS2B-NS3 protein is proven to be the potential target for the Zika virus therapeutics. Hence, e-pharmacophore-based drug design strategy was employed to identify potent inhibitors of NS2B-NS3 protein from ASINEX database consisting of 467,802 molecules. A 3D e-pharmacophore model was generated using PHASE module of Schrödinger Suite. The generated model consists of one hydrogen bond acceptor (A), two hydrogen bond donors (D), and two aromatic rings (R), ADDRR. The model was further evaluated for its ability to screen actives using enrichment analysis. Subsequently, high-throughput virtual screening protocol was employed, and the resultant hit molecules were also examined for its binding free energies and ADME properties using Prime MM-GBSA and Qikprop module of Schrodinger packages, respectively. Finally, the screened hit molecule was subjected to molecular dynamics simulation to examine its stability. Overall, the results from our analysis suggest that compound BAS 19192837 could be a potent inhibitor for the NS2B-NS3 protein of the Zika virus. It is also noteworthy to mention that our results are in good agreement with literature evidences. We hope that this result is of immense importance in designing potential drug molecules to combat the spread of Zika virus in the near future.

Structural Insights into the Regulation of Foreign Genes in Salmonella by the Hha/H-NS Complex*

PubMed Central

Ali, Sabrina S.; Whitney, John C.; Stevenson, James; Robinson, Howard; Howell, P. Lynne; Navarre, William Wiley

2013-01-01

The bacterial nucleoid-associated proteins Hha and H-NS jointly repress horizontally acquired genes in Salmonella, including essential virulence loci encoded within Salmonella pathogenicity islands. Hha is known to interact with the N-terminal dimerization domain of H-NS; however, the manner in which this interaction enhances transcriptional silencing is not understood. To further understand this process, we solved the x-ray crystal structure of Hha in complex with the N-terminal dimerization domain of H-NS (H-NS(1–46)) to 3.2 Å resolution. Two monomers of Hha bind to symmetrical sites on either side of the H-NS(1–46) dimer. Disruption of the Hha/H-NS interaction by the H-NS site-specific mutation I11A results in increased expression of the Hha/H-NS co-regulated gene hilA without affecting the expression levels of proV, a target gene repressed by H-NS in an Hha-independent fashion. Examination of the structure revealed a cluster of conserved basic amino acids that protrude from the surface of Hha on the opposite side of the Hha/H-NS(1–46) interface. Hha mutants with a diminished positively charged surface maintain the ability to interact with H-NS but can no longer regulate hilA. Increased expression of the hilA locus did not correspond to significant depletion of H-NS at the promoter region in chromatin immunoprecipitation assays. However, in vitro, we find Hha improves H-NS binding to target DNA fragments. Taken together, our results show for the first time how Hha and H-NS interact to direct transcriptional repression and reveal that a positively charged surface of Hha enhances the silencing activity of H-NS nucleoprotein filaments. PMID:23515315

Analysis of Hepatitis C Virus Genotype 1b Resistance Variants in Japanese Patients Treated with Paritaprevir-Ritonavir and Ombitasvir.

PubMed

Krishnan, Preethi; Schnell, Gretja; Tripathi, Rakesh; Beyer, Jill; Reisch, Thomas; Zhang, Xinyan; Setze, Carolyn; Rodrigues, Lino; Burroughs, Margaret; Redman, Rebecca; Chayama, Kazuaki; Kumada, Hiromitsu; Collins, Christine; Pilot-Matias, Tami

2016-02-01

Treatment of HCV genotype 1b (GT1b)-infected Japanese patients with paritaprevir (NS3/4A inhibitor boosted with ritonavir) and ombitasvir (NS5A inhibitor) in studies M12-536 and GIFT-I demonstrated high sustained virologic response (SVR) rates. The virologic failure rate was 3% (13/436) across the two studies. Analyses were conducted to evaluate the impact of baseline resistance-associated variants (RAVs) on treatment outcome and the emergence and persistence of RAVs in patients experiencing virologic failure. Baseline paritaprevir resistance-conferring variants in NS3 were infrequent, while Y93H in NS5A was the most prevalent ombitasvir resistance-conferring variant at baseline. A comparison of baseline prevalence of polymorphisms in Japanese and western patients showed that Q80L and S122G in NS3 and L28M, R30Q, and Y93H in NS5A were significantly more prevalent in Japanese patients. In the GIFT-I study, the prevalence of Y93H in NS5A varied between 13% and 21% depending on the deep-sequencing detection threshold. Among patients with Y93H comprising <1%, 1 to 40%, or >40% of their preexisting viral population, the 24-week SVR (SVR24) rates were >99% (276/277), 93% (38/41), and 76% (25/33), respectively, indicating that the prevalence of Y93H within a patient's viral population is a good predictor of treatment response. The predominant RAVs at the time of virologic failure were D168A/V in NS3 and Y93H alone or in combination with other variants in NS5A. While levels of NS3 RAVs declined over time, NS5A RAVs persisted through posttreatment week 48. Results from these analyses are informative in understanding the resistance profile of an ombitasvir- plus paritaprevir/ritonavir-based regimen in Japanese GT1b-infected patients. Copyright © 2016 Krishnan et al.

NEUTRON-STAR MERGER EJECTA AS OBSTACLES TO NEUTRINO-POWERED JETS OF GAMMA-RAY BURSTS

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

Just, O.; Janka, H.-T.; Schwarz, N.

2016-01-10

We present the first special relativistic, axisymmetric hydrodynamic simulations of black hole-torus systems (approximating general relativistic gravity) as remnants of binary-neutron star (NS–NS) and neutron star–black hole (NS–BH) mergers, in which the viscously driven evolution of the accretion torus is followed with self-consistent energy-dependent neutrino transport and the interaction with the cloud of dynamical ejecta expelled during the NS–NS merging is taken into account. The modeled torus masses, BH masses and spins, and the ejecta masses, velocities, and spatial distributions are adopted from relativistic merger simulations. We find that energy deposition by neutrino annihilation can accelerate outflows with initially highmore » Lorentz factors along polar low-density funnels, but only in mergers with extremely low baryon pollution in the polar regions. NS–BH mergers, where polar mass ejection during the merging phase is absent, provide sufficiently baryon-poor environments to enable neutrino-powered, ultrarelativistic jets with terminal Lorentz factors above 100 and considerable dynamical collimation, favoring short gamma-ray bursts (sGRBs), although their typical energies and durations might be too small to explain the majority of events. In the case of NS–NS mergers, however, neutrino emission of the accreting and viscously spreading torus is too short and too weak to yield enough energy for the outflows to break out from the surrounding ejecta shell as highly relativistic jets. We conclude that neutrino annihilation alone cannot power sGRBs from NS–NS mergers.« less

Advanced Radiation Theory Support Annual Report 2004

DTIC Science & Technology

2005-04-29

100 0 100 2W 30 Time (ns) Fig. 3. Timing reference for hologram analyzed here (-70 ns) relative to Plasma Return Flashcard current waveform and...experiments. sufficient preionization was provided by UV radiation from the If photoionization and ionization process associated with the flashcard , in at

The first measurements of soft x-ray flux from ignition scale Hohlraums at the National Ignition Facility using DANTE (invited)

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

Kline, J. L.; Widmann, K.; Warrick, A.

2010-10-15

The first 96 and 192 beam vacuum Hohlraum target experiments have been fielded at the National Ignition Facility demonstrating radiation temperatures up to 340 eV and fluxes of 20 TW/sr as viewed by DANTE representing an {approx}20 times flux increase over NOVA/Omega scale Hohlraums. The vacuum Hohlraums were irradiated with 2 ns square laser pulses with energies between 150 and 635 kJ. They produced nearly Planckian spectra with about 30{+-}10% more flux than predicted by the preshot radiation hydrodynamic simulations. To validate these results, careful verification of all component calibrations, cable deconvolution, and software analysis routines has been conducted. Inmore » addition, a half Hohlraum experiment was conducted using a single 2 ns long axial quad with an irradiance of {approx}2x10{sup 15} W/cm{sup 2} for comparison with NIF Early Light experiments completed in 2004. We have also completed a conversion efficiency test using a 128-beam nearly uniformly illuminated gold sphere with intensities kept low (at 1x10{sup 14} W/cm{sup 2} over 5 ns) to avoid sensitivity to modeling uncertainties for nonlocal heat conduction and nonlinear absorption mechanisms, to compare with similar intensity, 3 ns OMEGA sphere results. The 2004 and 2009 NIF half-Hohlraums agreed to 10% in flux, but more importantly, the 2006 OMEGA Au Sphere, the 2009 NIF Au sphere, and the calculated Au conversion efficiency agree to {+-}5% in flux, which is estimated to be the absolute calibration accuracy of the DANTEs. Hence we conclude that the 30{+-}10% higher than expected radiation fluxes from the 96 and 192 beam vacuum Hohlraums are attributable to differences in physics of the larger Hohlraums.« less

North Alabama Lightning Mapping Array (LMA): VHF Source Retrieval Algorithm and Error Analyses

NASA Technical Reports Server (NTRS)

Koshak, W. J.; Solakiewicz, R. J.; Blakeslee, R. J.; Goodman, S. J.; Christian, H. J.; Hall, J.; Bailey, J.; Krider, E. P.; Bateman, M. G.; Boccippio, D.

2003-01-01

Two approaches are used to characterize how accurately the North Alabama Lightning Mapping Array (LMA) is able to locate lightning VHF sources in space and in time. The first method uses a Monte Carlo computer simulation to estimate source retrieval errors. The simulation applies a VHF source retrieval algorithm that was recently developed at the NASA Marshall Space Flight Center (MSFC) and that is similar, but not identical to, the standard New Mexico Tech retrieval algorithm. The second method uses a purely theoretical technique (i.e., chi-squared Curvature Matrix Theory) to estimate retrieval errors. Both methods assume that the LMA system has an overall rms timing error of 50 ns, but all other possible errors (e.g., multiple sources per retrieval attempt) are neglected. The detailed spatial distributions of retrieval errors are provided. Given that the two methods are completely independent of one another, it is shown that they provide remarkably similar results. However, for many source locations, the Curvature Matrix Theory produces larger altitude error estimates than the (more realistic) Monte Carlo simulation.

Self-consistent molecular dynamics formulation for electric-field-mediated electrolyte transport through nanochannels

NASA Astrophysics Data System (ADS)

Raghunathan, A. V.; Aluru, N. R.

2007-07-01

A self-consistent molecular dynamics (SCMD) formulation is presented for electric-field-mediated transport of water and ions through a nanochannel connected to reservoirs or baths. The SCMD formulation is compared with a uniform field MD approach, where the applied electric field is assumed to be uniform, for 2nm and 3.5nm wide nanochannels immersed in a 0.5M KCl solution. Reservoir ionic concentrations are maintained using the dual-control-volume grand canonical molecular dynamics technique. Simulation results with varying channel height indicate that the SCMD approach calculates the electrostatic potential in the simulation domain more accurately compared to the uniform field approach, with the deviation in results increasing with the channel height. The translocation times and ionic fluxes predicted by uniform field MD can be substantially different from those predicted by the SCMD approach. Our results also indicate that during a 2ns simulation time K+ ions can permeate through a 1nm channel when the applied electric field is computed self-consistently, while the permeation is not observed when the electric field is assumed to be uniform.

Multistage reaction pathways in detonating high explosives

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; CACS Collaboration; ALCF Team

2015-06-01

Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N2 and H2O within 10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct uni-molecular and intermolecular reaction pathways, respectively, for the rapid N2 and H2O productions. This work was supported by the Office of Naval Research Grant No. N000014-12-1-0555 and the Basic Research Program of Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-08-1-0036. All the simulations were performed at USC and Argonne LCF.

Dependence of Initial Oxygen Concentration on Ozone Yield Using Inductive Energy Storage System Pulsed Power Generator

NASA Astrophysics Data System (ADS)

Go, Tomio; Tanaka, Yasushi; Yamazaki, Nobuyuki; Mukaigawa, Seiji; Takaki, Koichi; Fujiwara, Tamiya

Dependence of initial oxygen concentration on ozone yield using streamer discharge reactor driven by an inductive energy storage system pulsed power generator is described in this paper. Fast recovery type diodes were employed as semiconductor opening switch to interrupt a circuit current within 100 ns. This rapid current change produced high-voltage short pulse between a secondary energy storage inductor. The repetitive high-voltage short pulse was applied to a 1 mm diameter center wire electrode placed in a cylindrical pulse corona reactor. The streamer discharge successfully occurred between the center wire electrode and an outer cylinder ground electrode of 2 cm inner diameter. The ozone was produced with the streamer discharge and increased with increasing pulse repetition rate. The ozone yield changed in proportion to initial oxygen concentration contained in the injected gas mixture at 800 ns forward pumping time of the current. However, the decrease of the ozone yield by decreasing oxygen concentration in the gas mixture at 180 ns forward pumping time of the current was lower than the decrease at 800 ns forward pumping time of the current. This dependence of the initial oxygen concentration on ozone yield at 180 ns forward pumping time is similar to that of dielectric barrier discharge reactor.

A hydrophobic patch surrounding Trp154 in human neuroserpin controls the helix F dynamics with implications in inhibition and aggregation

NASA Astrophysics Data System (ADS)

Ali, Mohammad Farhan; Kaushik, Abhinav; Kapil, Charu; Gupta, Dinesh; Jairajpuri, Mohamad Aman

2017-02-01

Neuroserpin (NS) mediated inhibition of tissue-type plasminogen activator (tPA) is important for brain development, synapse formation and memory. Aberrations in helix F and β-sheet A movement during inhibition can directly lead to epilepsy or dementia. Conserved W154 residue in a hydrophobic patch between helix F and β-sheet A is ideally placed to control their movement during inhibition. Molecular Dynamics (MD) simulation on wild type (WT) NS and its two variants (W154A and W154P) demonstrated partial deformation in helix F and conformational differences in strands 1A and 2A only in W154P. A fluorescence and Circular Dichroism (CD) analysis with purified W154 variants revealed a significant red-shift and an increase in α-helical content in W154P as compared to W154A and WT NS. Kinetics of tPA inhibition showed a decline in association rates (ka) for W154A as compared to WT NS with indication of complex formation. Appearance of cleaved without complex formation in W154P indicates that the variant acts as substrate due to conformational misfolding around helix F. Both the variants however showed increased rate of aggregation as compared to WT NS. The hydrophobic patch identified in this study may have importance in helix F dynamics of NS.

A single-chip 32-channel analog beamformer with 4-ns delay resolution and 768-ns maximum delay range for ultrasound medical imaging with a linear array transducer.

PubMed

Um, Ji-Yong; Kim, Yoon-Jee; Cho, Seong-Eun; Chae, Min-Kyun; Kim, Byungsub; Sim, Jae-Yoon; Park, Hong-June

2015-02-01

A single-chip 32-channel analog beamformer is proposed. It achieves a delay resolution of 4 ns and a maximum delay range of 768 ns. It has a focal-point based architecture, which consists of 7 sub-analog beamformers (sub-ABF). Each sub-ABF performs a RX focusing operation for a single focal point. Seven sub-ABFs perform a time-interleaving operation to achieve the maximum delay range of 768 ns. Phase interpolators are used in sub-ABFs to generate sampling clocks with the delay resolution of 4 ns from a low frequency system clock of 5 MHz. Each sub-ABF samples 32 echo signals at different times into sampling capacitors, which work as analog memory cells. The sampled 32 echo signals of each sub-ABF are originated from one target focal point at one instance. They are summed at one instance in a sub-ABF to perform the RX focusing for the target focal point. The proposed ABF chip has been fabricated in a 0.13- μ m CMOS process with an active area of 16 mm (2). The total power consumption is 287 mW. In measurement, the digital echo signals from a commercial ultrasound medical imaging machine were applied to the fabricated chip through commercial DAC chips. Due to the speed limitation of the DAC chips, the delay resolution was relaxed to 10 ns for the real-time measurement. A linear array transducer with no steering operation is used in this work.

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

PubMed

Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

2017-10-12

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

Final Report, Fundamental Mechanisms of Transient States in Materials Quantified by DTEM

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

Campbell, G. H.; McKeown, J. T.

At the project’s inception, there was growing evidence that the time domain for in situ observations of material evolution held great promise for allowing measurements to be made in never previously contemplated regimes. Also, central to the development of the project was the knowledge that phase transformations are of central importance to the development of materials microstructure and hence properties. We addressed this opportunity by developing a transmission electron microscope that could be operated in the pulsed mode (DTEM), with exposure times down to 20 ns and interframe times down to 20 ns in the nine-frame movie mode, designed withmore » the intent of performing in situ experiments. This unprecedented capability allowed us to investigate structural phase transformations, intermetallic formation reactions, crystallization from the amorphous phase, rapid solidification of liquid metals, transformations in phase change materials, and catalyst nanoparticles. The ability of the electron microscope to create images with high spatial resolution allows for the accurate measurement of position. Common to all of the transformations mentioned above is the presence of a distinct interface between the old phase and the growing new phase. Measuring the position of the interface as a function of time, combined with the ability to count nucleation sites as a function of time, allowed for the exceptionally accurate measure of transformation kinetics. These measurements were used to guide and constrain the development of models and simulation methods for the classes of transformations studied.« less

Utility of dengue NS1 antigen rapid diagnostic test for use in difficult to reach areas and its comparison with dengue NS1 ELISA and qRT-PCR.

PubMed

Shukla, Mohan K; Singh, Neeru; Sharma, Ravendra K; Barde, Pradip V

2017-07-01

The objective of this study was to demonstrate the utility of dengue virus (DENV) non structural protein 1 (NS1) based rapid diagnostic test (RDT) for use in tribal and difficult to reach areas for early dengue (DEN) diagnosis in acute phase patients and evaluate its sensitivity and specificity against DENV NS1 enzyme linked immune sorbent assay (ELISA) and real time reverse transcriptase polymerase chain reaction (qRT-PCR). The DENV NS1 RDT was used for preliminary diagnosis during outbreaks in difficult to reach rural and tribal areas. The diagnosis was confirmed by DENV NS1 ELISA in the laboratory. The samples were also tested and serotyped by qRT-PCR. The results were evaluated using statistical tests. The DENV NS1 RDT showed 99.2% sensitivity and 96.0% specificity when analyzed using DENV NS1 ELISA as standard. The specificity and sensitivity of the RDT when compared with qRT-PCR was 93.6% and 91.1%, respectively. The serotype specific evaluation showed more than 90% sensitivity and specificity for DENV-1, 2, and 3. The RDT proved a good diagnostic tool in difficult to reach rural and tribal areas. Further evaluation studies with different commercially available RDTs in different field conditions are essential, that will help clinicians and patients for treatment and programme managers for timely intervention. © 2017 Wiley Periodicals, Inc.

Disassembly time of deuterium-cluster-fusion plasma irradiated by an intense laser pulse.

PubMed

Bang, W

2015-07-01

Energetic deuterium ions from large deuterium clusters (>10nm diameter) irradiated by an intense laser pulse (>10(16)W/cm(2)) produce DD fusion neutrons for a time interval determined by the geometry of the resulting fusion plasma. We present an analytical solution of this time interval, the plasma disassembly time, for deuterium plasmas that are cylindrical in shape. Assuming a symmetrically expanding deuterium plasma, we calculate the expected fusion neutron yield and compare with an independent calculation of the yield using the concept of a finite confinement time at a fixed plasma density. The calculated neutron yields agree quantitatively with the available experimental data. Our one-dimensional simulations indicate that one could expect a tenfold increase in total neutron yield by magnetically confining a 10-keV deuterium fusion plasma for 10ns.

Analysis of hydrodynamic fluctuations in heterogeneous adjacent multidomains in shear flow

NASA Astrophysics Data System (ADS)

Bian, Xin; Deng, Mingge; Tang, Yu-Hang; Karniadakis, George Em

2016-03-01

We analyze hydrodynamic fluctuations of a hybrid simulation under shear flow. The hybrid simulation is based on the Navier-Stokes (NS) equations on one domain and dissipative particle dynamics (DPD) on the other. The two domains overlap, and there is an artificial boundary for each one within the overlapping region. To impose the artificial boundary of the NS solver, a simple spatial-temporal averaging is performed on the DPD simulation. In the artificial boundary of the particle simulation, four popular strategies of constraint dynamics are implemented, namely the Maxwell buffer [Hadjiconstantinou and Patera, Int. J. Mod. Phys. C 08, 967 (1997), 10.1142/S0129183197000837], the relaxation dynamics [O'Connell and Thompson, Phys. Rev. E 52, R5792 (1995), 10.1103/PhysRevE.52.R5792], the least constraint dynamics [Nie et al., J. Fluid Mech. 500, 55 (2004), 10.1017/S0022112003007225; Werder et al., J. Comput. Phys. 205, 373 (2005), 10.1016/j.jcp.2004.11.019], and the flux imposition [Flekkøy et al., Europhys. Lett. 52, 271 (2000), 10.1209/epl/i2000-00434-8], to achieve a target mean value given by the NS solver. Going beyond the mean flow field of the hybrid simulations, we investigate the hydrodynamic fluctuations in the DPD domain. Toward that end, we calculate the transversal autocorrelation functions of the fluctuating variables in k space to evaluate the generation, transport, and dissipation of fluctuations in the presence of a hybrid interface. We quantify the unavoidable errors in the fluctuations, due to both the truncation of the domain and the constraint dynamics performed in the artificial boundary. Furthermore, we compare the four methods of constraint dynamics and demonstrate how to reduce the errors in fluctuations. The analysis and findings of this work are directly applicable to other hybrid simulations of fluid flow with thermal fluctuations.

Scheduling with hop-by-hop priority increasing in meshed optical burst-switched network

NASA Astrophysics Data System (ADS)

Chang, Hao; Luo, Jiangtao; Zhang, Zhizhong; Xia, Da; Gong, Jue

2006-09-01

In OBS, JET (Just-Enough-Time) is the classical wavelength reservation scheme. But there is a phenomenon that the burst priority decreasing hop-by-hop in multi-hop networks that will waste the bandwidth that was used in the upstream. Based on the HPI (Hop-by-hop Priority Increasing) proposed in the former research, this paper will do an unprecedented simulation in 4×4 meshed topology, which is closer to the real network environment with the help of a NS2-based OBSN simulation platform constructed by ourselves. By contrasting, the drop probability and throughput on one of the longest end-to-end path lengths in the whole networks, it shows that the HPI scheme can improve the utilance of bandwidth better.

Cavitation-induced fragmentation of an acoustically-levitated droplet

NASA Astrophysics Data System (ADS)

Gonzalez Avila, Silvestre Roberto; Ohl, Claus-Dieter

2015-12-01

In this paper we investigate the initial sequence of events that lead to the fragmentation of a millimetre sized water droplets when interacting with a focused ns-laser pulse. The experimental results show complex processes that result from the reflection of an initial shock wave from plasma generation with the soft boundary of the levitating droplet; furthermore, when the reflected waves from the walls of the droplet refocus they leave behind a trail of microbubbles that later act as cavitation inception regions. Numerical simulations of a shock wave impacting and reflecting from a soft boundary are also reported; the simulated results show that the lowest pressure inside the droplet occurs at the equatorial plane. The results of the numerical model display good agreement with the experimental results both in time and in space.

The effect of Nigella sativa Linn. seed on memory, attention and cognition in healthy human volunteers.

PubMed

Bin Sayeed, Muhammad Shahdaat; Asaduzzaman, Md; Morshed, Helal; Hossain, Md Monir; Kadir, Mohammad Fahim; Rahman, Md Rezowanur

2013-07-30

Experimental evidences have demonstrated that Nigella sativa Linn. seed (NS) has positive modulation effects on aged rats with memory impairments, prevents against hippocampal pyramidal cell loss and enhances consolidation of recall capability of stored information and spatial memory in rats. NS has neuroprotective, nephroprotective, lung protective, cardioprotective, hepatoprotective activities as established by previous studies on animals. Several clinical trials with NS on human have also demonstrated beneficial effect. The present study was designed to investigate the effects of NS on memory, attention and cognition in healthy elderly volunteers. Furthermore, safety profile of NS was assessed during the nine-week study period. Forty elderly volunteers were recruited and divided randomly into group A and group B--each consisting of 20 volunteers. The treatment procedure for group A was 500 mg NS capsule twice daily for nine weeks and Group B received placebo instead of NS in the similar manner. All the volunteers were assessed for neuropsychological state and safety profile twice before treatment and after nine weeks. The neuropsychological tests were logical memory test, digit span test, Rey-Osterrieth complex figure test, letter cancellation test, trail making test and stroop test. Safety profile was assessed by measuring biochemical markers of Cardiac (total cholesterol, triglycerides and high density lipoprotein cholesterol, very low density lipoprotein, low density lipoprotein cholesterol, creatine kinase-MB); Liver (aspartate aminotransferase, alanin aminotransferase, alkaline phosphatase, total protein, albumin, bilirubin) and Kidney (creatinine and blood urea nitrogen) through using commercial kits. There was significant difference (p<0.05) in the score of logical memory test-I and II, total score of digit span, 30 min delayed-recall, percent score in Rey-Osterrieth complex figure test, time taken to complete letter cancellation test, time taken in trail making test-A and test-B, score in part C of stroop test due to ingestion of NS for nine weeks. There were not statistically significant changes (p>0.05) in any of the biochemical markers of cardiac, liver, kidney function during this nine-week study period. The current study demonstrates the role of NS in enhancing memory, attention and cognition. Therefore, whether NS could be considered as potential food supplement for preventing or slow progressing of Alzheimer disease needs further investigations. However, study with Alzheimer's patients with large population size for longer period of time is recommended before using NS daily and extensive phytochemical investigations are recommended for novel drug discovery from NS for treating cognitive disorders. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Associations among hypothalamus-pituitary-adrenal axis function, novelty seeking, and retention in methadone maintenance therapy for heroin dependency.

PubMed

Lin, Shih-Hsien; Chen, Wei Tseng; Chen, Kao Chin; Lee, Sheng-Yu; Lee, I Hui; Chen, Po See; Yeh, Tzung Lieh; Lu, Ru-Band; Yang, Yen Kuang

2013-01-01

The efficacy of methadone maintenance therapy for heroin dependence is compromised by the low retention rate. Hypothalamus-pituitary-adrenal (HPA) axis function, which is associated with stress response, and novelty seeking (NS), a personality trait associated with low dopaminergic activity, may play roles in retention. We conducted a prospective study in which HPA axis function and NS were assessed by the dexamethasone suppression test and the Tridimensional Personality Questionnaire at baseline, respectively. The retention rate was assessed at the half- and 1-year points of methadone maintenance therapy. A low suppression rate of dexamethasone suppression test (D%) was associated with a high level of NS. A low D% was associated with half-year dropout, whereas a high level of NS was associated with 1-year dropout. Survival analysis confirmed that D% and NS were significant time-dependent covariates for retention. The findings showed that HPA axis function and NA were associated with retention at different time points.

Development of a Computational Assay for the Estrogen Receptor

DTIC Science & Technology

2006-07-01

University Ashley Deline, Senior Thesis in chemistry, " Molecular Dynamic Simulations of a Glycoform and its Constituent Parts Related to Rheumatoid Arthritis...involves running a long molecular dynamics (MD) simulation of the uncoupled receptor in order to sample the protein’s unique conformations. The second...Receptor binding domain. * Performed several long molecular dynamics simulations (800 ps - 3 ns) on the ligand-ER system using ligands with known

A multi-layer steganographic method based on audio time domain segmented and network steganography

NASA Astrophysics Data System (ADS)

Xue, Pengfei; Liu, Hanlin; Hu, Jingsong; Hu, Ronggui

2018-05-01

Both audio steganography and network steganography are belong to modern steganography. Audio steganography has a large capacity. Network steganography is difficult to detect or track. In this paper, a multi-layer steganographic method based on the collaboration of them (MLS-ATDSS&NS) is proposed. MLS-ATDSS&NS is realized in two covert layers (audio steganography layer and network steganography layer) by two steps. A new audio time domain segmented steganography (ATDSS) method is proposed in step 1, and the collaboration method of ATDSS and NS is proposed in step 2. The experimental results showed that the advantage of MLS-ATDSS&NS over others is better trade-off between capacity, anti-detectability and robustness, that means higher steganographic capacity, better anti-detectability and stronger robustness.

Towards a portable Raman spectrometer using a concave grating and a time-gated CMOS SPAD.

PubMed

Li, Zhiyun; Deen, M Jamal

2014-07-28

A low-cost, compact Raman spectrometer suitable for the on-line water monitoring applications is explored. A custom-designed concave grating for wavelength selection was fabricated and tested. The detection of the Raman signal is accomplished with a time-gated single photon avalanche diode (TG-SPAD). A fixed gate window of 3.5ns is designed and applied to the TG-SPAD. The temporal resolution of the SPAD was ~60ps when tested with a 7ps, 532nm solid-state laser. To test the efficiency of the gating in fluorescence signal suppression, different detection windows (3ns-0.25ns) within the 3.5ns gate window are used to measure the Raman spectra of Rhodamine B. Strong Raman peaks are resolved with this low-cost system.

Laser propagation measurements in long-scale-length underdense plasmas relevant to magnetized liner inertial fusion.

PubMed

Harvey-Thompson, A J; Sefkow, A B; Wei, M S; Nagayama, T; Campbell, E M; Blue, B E; Heeter, R F; Koning, J M; Peterson, K J; Schmitt, A

2016-11-01

We report experimental results and simulations showing efficient laser energy coupling into plasmas at conditions relevant to the magnetized liner inertial fusion (MagLIF) concept. In MagLIF, to limit convergence and increase the hydrodynamic stability of the implosion, the fuel must be efficiently preheated. To determine the efficiency and physics of preheating by a laser, an Ar plasma with n_{e}/n_{crit}∼0.04 is irradiated by a multi-ns, multi-kJ, 0.35-μm, phase-plate-smoothed laser at spot-averaged intensities ranging from 1.0×10^{14} to 2.5×10^{14}W/cm^{2} and pulse widths from 2 to 10 ns. Time-resolved x-ray images of the laser-heated plasma are compared to two-dimensional radiation-hydrodynamic simulations that show agreement with the propagating emission front, a comparison that constrains laser energy deposition to the plasma. The experiments show that long-pulse, modest-intensity (I=1.5×10^{14}W/cm^{2}) beams can efficiently couple energy (∼82% of the incident energy) to MagLIF-relevant long-length (9.5 mm) underdense plasmas. The demonstrated heating efficiency is significantly higher than is thought to have been achieved in early integrated MagLIF experiments [A. B. Sefkow et al., Phys. Plasmas 21, 072711 (2014)10.1063/1.4890298].

Laser propagation measurements in long-scale-length underdense plasmas relevant to magnetized liner inertial fusion

NASA Astrophysics Data System (ADS)

Harvey-Thompson, A. J.; Sefkow, A. B.; Wei, M. S.; Nagayama, T.; Campbell, E. M.; Blue, B. E.; Heeter, R. F.; Koning, J. M.; Peterson, K. J.; Schmitt, A.

2016-11-01

We report experimental results and simulations showing efficient laser energy coupling into plasmas at conditions relevant to the magnetized liner inertial fusion (MagLIF) concept. In MagLIF, to limit convergence and increase the hydrodynamic stability of the implosion, the fuel must be efficiently preheated. To determine the efficiency and physics of preheating by a laser, an Ar plasma with ne/nc r i t˜0.04 is irradiated by a multi-ns, multi-kJ, 0.35-μm, phase-plate-smoothed laser at spot-averaged intensities ranging from 1.0 ×1014 to 2.5 ×1014W /c m2 and pulse widths from 2 to 10 ns. Time-resolved x-ray images of the laser-heated plasma are compared to two-dimensional radiation-hydrodynamic simulations that show agreement with the propagating emission front, a comparison that constrains laser energy deposition to the plasma. The experiments show that long-pulse, modest-intensity (I =1.5 ×1014W /c m2 ) beams can efficiently couple energy (˜82 % of the incident energy) to MagLIF-relevant long-length (9.5 mm) underdense plasmas. The demonstrated heating efficiency is significantly higher than is thought to have been achieved in early integrated MagLIF experiments [A. B. Sefkow et al., Phys. Plasmas 21, 072711 (2014), 10.1063/1.4890298].

Laser propagation measurements in long-scale-length underdense plasmas relevant to magnetized liner inertial fusion

DOE PAGES

Harvey-Thompson, A. J.; Sefkow, A. B.; Wei, M. S.; ...

2016-11-02

Here, we report experimental results and simulations showing efficient laser energy coupling into plasmas at conditions relevant to the magnetized liner inertial fusion (MagLIF) concept. In MagLIF, to limit convergence and increase the hydrodynamic stability of the implosion, the fuel must be efficiently preheated. To determine the efficiency and physics of preheating by a laser, an Ar plasma with n e / n c r i t ~ 0.04 is irradiated by a multi-ns, multi-kJ, 0.35-μm, phase-plate-smoothed laser at spot-averaged intensities ranging from 1.0 × 10 14 to 2.5 × 10 14 W / c m 2 andmore » pulse widths from 2 to 10 ns. Time-resolved x-ray images of the laser-heated plasma are compared to two-dimensional radiation-hydrodynamic simulations that show agreement with the propagating emission front, a comparison that constrains laser energy deposition to the plasma. The experiments show that long-pulse, modest-intensity ( I = 1.5 × 10 14 W / c m 2 ) beams can efficiently couple energy ( ~ 82 % of the incident energy) to MagLIF-relevant long-length (9.5 mm) underdense plasmas. The heating efficiency we demonstrate is significantly higher than it was thought to have been achieved in early integrated MagLIF experiments [A. B. Sefkow et al., Phys. Plasmas 21, 072711 (2014)].« less

Laser propagation measurements in long-scale-length underdense plasmas relevant to magnetized liner inertial fusion

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

Harvey-Thompson, A. J.; Sefkow, A. B.; Wei, M. S.

Here, we report experimental results and simulations showing efficient laser energy coupling into plasmas at conditions relevant to the magnetized liner inertial fusion (MagLIF) concept. In MagLIF, to limit convergence and increase the hydrodynamic stability of the implosion, the fuel must be efficiently preheated. To determine the efficiency and physics of preheating by a laser, an Ar plasma with n e / n c r i t ~ 0.04 is irradiated by a multi-ns, multi-kJ, 0.35-μm, phase-plate-smoothed laser at spot-averaged intensities ranging from 1.0 × 10 14 to 2.5 × 10 14 W / c m 2 andmore » pulse widths from 2 to 10 ns. Time-resolved x-ray images of the laser-heated plasma are compared to two-dimensional radiation-hydrodynamic simulations that show agreement with the propagating emission front, a comparison that constrains laser energy deposition to the plasma. The experiments show that long-pulse, modest-intensity ( I = 1.5 × 10 14 W / c m 2 ) beams can efficiently couple energy ( ~ 82 % of the incident energy) to MagLIF-relevant long-length (9.5 mm) underdense plasmas. The heating efficiency we demonstrate is significantly higher than it was thought to have been achieved in early integrated MagLIF experiments [A. B. Sefkow et al., Phys. Plasmas 21, 072711 (2014)].« less

Time concurrency/phase-time synchronization in digital communications networks

NASA Technical Reports Server (NTRS)

Kihara, Masami; Imaoka, Atsushi

1990-01-01

Digital communications networks have the intrinsic capability of time synchronization which makes it possible for networks to supply time signals to some applications and services. A practical estimation method for the time concurrency on terrestrial networks is presented. By using this method, time concurrency capability of the Nippon Telegraph and Telephone Corporation (NTT) digital communications network is estimated to be better than 300 ns rms at an advanced level, and 20 ns rms at final level.

Analysis of 440 GeV proton beam-matter interaction experiments at the High Radiation Materials test facility at CERN

NASA Astrophysics Data System (ADS)

Burkart, F.; Schmidt, R.; Raginel, V.; Wollmann, D.; Tahir, N. A.; Shutov, A.; Piriz, A. R.

2015-08-01

In a previous paper [Schmidt et al., Phys. Plasmas 21, 080701 (2014)], we presented the first results on beam-matter interaction experiments that were carried out at the High Radiation Materials test facility at CERN. In these experiments, extended cylindrical targets of solid copper were irradiated with beam of 440 GeV protons delivered by the Super Proton Synchrotron (SPS). The beam comprised of a large number of high intensity proton bunches, each bunch having a length of 0.5 ns with a 50 ns gap between two neighboring bunches, while the length of this entire bunch train was about 7 μs. These experiments established the existence of the hydrodynamic tunneling phenomenon the first time. Detailed numerical simulations of these experiments were also carried out which were reported in detail in another paper [Tahir et al., Phys. Rev. E 90, 063112 (2014)]. Excellent agreement was found between the experimental measurements and the simulation results that validate our previous simulations done using the Large Hadron Collider (LHC) beam of 7 TeV protons [Tahir et al., Phys. Rev. Spec. Top.--Accel. Beams 15, 051003 (2012)]. According to these simulations, the range of the full LHC proton beam and the hadronic shower can be increased by more than an order of magnitude due to the hydrodynamic tunneling, compared to that of a single proton. This effect is of considerable importance for the design of machine protection system for hadron accelerators such as SPS, LHC, and Future Circular Collider. Recently, using metal cutting technology, the targets used in these experiments have been dissected into finer pieces for visual and microscopic inspection in order to establish the precise penetration depth of the protons and the corresponding hadronic shower. This, we believe will be helpful in studying the very important phenomenon of hydrodynamic tunneling in a more quantitative manner. The details of this experimental work together with a comparison with the numerical simulations are presented in this paper.

Commercial counterboard for 10 ns software correlator for photon and fluorescence correlation spectroscopy.

PubMed

Molteni, Matteo; Ferri, Fabio

2016-11-01

A 10 ns time resolution, multi-tau software correlator, capable of computing simultaneous autocorrelation (A-A, B-B) and cross (A-B) correlation functions at count rates up to ∼10 MHz, with no data loss, has been developed in LabVIEW and C++ by using the National Instrument timer/counterboard (NI PCIe-6612) and a fast Personal Computer (PC) (Intel Core i7-4790 Processor 3.60 GHz ). The correlator works by using two algorithms: for large lag times (τ ≳ 1 μs), a classical time-mode scheme, based on the measure of the number of pulses per time interval, is used; differently, for τ ≲ 1 μs a photon-mode (PM) scheme is adopted and the correlation function is retrieved from the sequence of the photon arrival times. Single auto- and cross-correlation functions can be processed online in full real time up to count rates of ∼1.8 MHz and ∼1.2 MHz, respectively. Two autocorrelation (A-A, B-B) and a cross correlation (A-B) functions can be simultaneously processed in full real time only up to count rates of ∼750 kHz. At higher count rates, the online processing takes place in a delayed modality, but with no data loss. When tested with simulated correlation data and latex spheres solutions, the overall performances of the correlator appear to be comparable with those of commercial hardware correlators, but with several nontrivial advantages related to its flexibility, low cost, and easy adaptability to future developments of PC and data acquisition technology.

Commercial counterboard for 10 ns software correlator for photon and fluorescence correlation spectroscopy

NASA Astrophysics Data System (ADS)

Molteni, Matteo; Ferri, Fabio

2016-11-01

A 10 ns time resolution, multi-tau software correlator, capable of computing simultaneous autocorrelation (A-A, B-B) and cross (A-B) correlation functions at count rates up to ˜10 MHz, with no data loss, has been developed in LabVIEW and C++ by using the National Instrument timer/counterboard (NI PCIe-6612) and a fast Personal Computer (PC) (Intel Core i7-4790 Processor 3.60 GHz ). The correlator works by using two algorithms: for large lag times (τ ≳ 1 μs), a classical time-mode scheme, based on the measure of the number of pulses per time interval, is used; differently, for τ ≲ 1 μs a photon-mode (PM) scheme is adopted and the correlation function is retrieved from the sequence of the photon arrival times. Single auto- and cross-correlation functions can be processed online in full real time up to count rates of ˜1.8 MHz and ˜1.2 MHz, respectively. Two autocorrelation (A-A, B-B) and a cross correlation (A-B) functions can be simultaneously processed in full real time only up to count rates of ˜750 kHz. At higher count rates, the online processing takes place in a delayed modality, but with no data loss. When tested with simulated correlation data and latex spheres solutions, the overall performances of the correlator appear to be comparable with those of commercial hardware correlators, but with several nontrivial advantages related to its flexibility, low cost, and easy adaptability to future developments of PC and data acquisition technology.

All-atomic Molecular Dynamic Studies of Human CDK8: Insight into the A-loop, Point Mutations and Binding with Its Partner CycC

PubMed Central

Xu, Wu; Amire-Brahimi, Benjamin; Xie, Xiao-Jun; Huang, Liying; Ji, Jun-Yuan

2014-01-01

The Mediator, a conserved multisubunit protein complex in eukaryotic organisms, regulates gene expression by bridging sequence-specific DNA-binding transcription factors to the general RNA polymerase II machinery. In yeast, Mediator complex is organized in three core modules (head, middle and tail) and a separable ‘CDK8 submodule’ consisting of four subunits including Cyclin-dependent kinase CDK8 (CDK8), Cyclin C (CycC), MED12, and MED13. The 3-D structure of human CDK8-CycC complex has been recently experimentally determined. To take advantage of this structure and the improved theoretical calculation methods, we have performed molecular dynamic simulations to study dynamics of CDK8 and two CDK8 point mutations (D173A and D189N), which have been identified in human cancers, with and without full length of the A-loop as well as the binding between CDK8 and CycC. We found that CDK8 structure gradually loses two helical structures during the 50-ns molecular dynamic simulation, likely due to the presence of the full-length A-loop. In addition, our studies showed the hydrogen bond occupation of the CDK8 A-loop increases during the first 20-ns MD simulation and stays stable during the later 30-ns MD simulation. Four residues in the A-loop of CDK8 have high hydrogen bond occupation, while the rest residues have low or no hydrogen bond occupation. The hydrogen bond dynamic study of the A-loop residues exhibits three types of changes: increasing, decreasing, and stable. Furthermore, the 3-D structures of CDK8 point mutations D173A, D189N, T196A and T196D have been built by molecular modeling and further investigated by 50-ns molecular dynamic simulations. D173A has the highest average potential energy, while T196D has the lowest average potential energy, indicating that T196D is the most stable structure. Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex. Taken together, these analyses will improve our understanding of the exact functions of CDK8 and the interaction with its partner CycC. PMID:24754906

Value of Nephrometry Score Constituents on Perioperative Outcomes and Split Renal Function in Patients Undergoing Minimally Invasive Partial Nephrectomy.

PubMed

Watts, Kara L; Ghosh, Propa; Stein, Solomon; Ghavamian, Reza

2017-01-01

To assess the relationship between individual nephrometry score (NS) constituents (RENAL) on perioperative outcomes and renal function of the surgical kidney in patients undergoing laparoscopic partial nephrectomy or robotic-assisted partial nephrectomy. Two hundred forty-five patients who underwent laparoscopic partial nephrectomy or robotic-assisted partial nephrectomy between 2005 and 2014 were retrospectively reviewed. Each renal mass' NS was calculated from preoperative computed tomography imaging. Multivariate regression analysis was used to evaluate the effect of NS variables on perioperative outcomes and change in overall renal function (as estimated by glomerular filtration rate) from preoperative to 1-year postoperative. A cohort analysis assessed the effect of NS variables on change in split renal function of the surgical kidney from pre- to postoperative based on nuclear medicine renal scintigraphy. Tumor radius (R), endophytic nature (E), and nearness to collecting system (N) variables significantly and incrementally predicted a longer operative time and warm ischemia time. Overall renal function based on glomerular filtration rate was not affected by any NS variable. However, percent function of the surgical kidney by renal scintigraphy significantly decreased postoperatively as R and E values increased. R, E, and N were associated with significant changes in warm ischemia time and operative time. R and E were associated with a significant decrease in split renal function of the surgical kidney at 1 year after surgery but not with overall renal function. R, E, and N are the NS constituents most relevant to perioperative outcomes and postoperative differential renal function after partial nephrectomy. Copyright © 2016. Published by Elsevier Inc.

Emergency Radiology Practice Patterns: Shifts, Schedules, and Job Satisfaction.

PubMed

Hanna, Tarek N; Shekhani, Haris; Lamoureux, Christine; Mar, Hanna; Nicola, Refky; Sliker, Clint; Johnson, Jamlik-Omari

2017-03-01

To assess the practice environment of emergency radiologists with a focus on schedule, job satisfaction, and self-perception of health, wellness, and diagnostic accuracy. A survey drawing from prior radiology and health care shift-work literature was distributed via e-mail to national societies, teleradiology groups, and private practices. The survey remained open for 4 weeks in 2016, with one reminder. Data were analyzed using hypothesis testing and logistic regression modeling. Response rate was 29.6% (327/1106); 69.1% of respondents (n = 226) were greater than 40 years old, 73% (n = 240) were male, and 87% (n = 284) practiced full time. With regard to annual overnight shifts (NS): 36% (n = 118) did none, 24.9% (n = 81) did 182 or more, and 15.6% (n = 51) did 119. There was a significant association between average NS worked per year and both perceived negative health effects (P < .01) and negative impact on memory (P < .01). There was an inverse association between overall job enjoyment and number of annual NS (P < .05). The odds of agreeing to the statement "I enjoy my job" for radiologists who work no NS is 2.21 times greater than for radiologists who work at least 119 NS, when shift length is held constant. Radiologists with 11+ years of experience who work no NS or 1 to 100 NS annually have lower odds of feeling overwhelmed when compared with those working the same number of NS with <10 years' experience. There is significant variation in emergency radiology practice patterns. Annual NS burden is associated with lower job satisfaction and negative health self-perception. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Absolute comparison of simulated and experimental protein-folding dynamics

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Nguyen, Houbi; Pande, Vijay S.; Gruebele, Martin

2002-11-01

Protein folding is difficult to simulate with classical molecular dynamics. Secondary structure motifs such as α-helices and β-hairpins can form in 0.1-10µs (ref. 1), whereas small proteins have been shown to fold completely in tens of microseconds. The longest folding simulation to date is a single 1-µs simulation of the villin headpiece; however, such single runs may miss many features of the folding process as it is a heterogeneous reaction involving an ensemble of transition states. Here, we have used a distributed computing implementation to produce tens of thousands of 5-20-ns trajectories (700µs) to simulate mutants of the designed mini-protein BBA5. The fast relaxation dynamics these predict were compared with the results of laser temperature-jump experiments. Our computational predictions are in excellent agreement with the experimentally determined mean folding times and equilibrium constants. The rapid folding of BBA5 is due to the swift formation of secondary structure. The convergence of experimentally and computationally accessible timescales will allow the comparison of absolute quantities characterizing in vitro and in silico (computed) protein folding.

Fundamental Mechanisms, Predictive Modeling, and Novel Aerospace Applications of Plasma Assisted Combustion

DTIC Science & Technology

2013-10-22

0.0, pulse #10 Front view: T0=500 K, ϕ=0.3 Front view: T0=300 K, ϕ=0.0 200 Torr DBD Discharges : 20 kV, 10kHz ICCD gate 50 ns. P = 20 Torr #5...0.60 19,050 49 ppm 0.47 10,820 Non-diffusive hybrid scheme for simulation of filamentary discharges AVALANCHE TO STREAMER TRANSITION IN...Specific Deposited Discharge Energy and Energy Deposited in First Pulse С2Н2:О2:Ar = 17:83:900 (φ = 0.5) Ignition delay time in С2Н2:О2:Ar

The Effect of the Dental Operating Microscope on the Outcome of Nonsurgical Root Canal Treatment: A Retrospective Case-control Study.

PubMed

Khalighinejad, Navid; Aminoshariae, Anita; Kulild, James C; Williams, Kristin A; Wang, Jeannie; Mickel, Andre

2017-05-01

The aim of the current investigation was to assess the effect of the use of a dental operating microscope on the outcome of nonsurgical root canal treatment (NS RCT) while treating the mesiobuccal (MB) root of the maxillary first molar. This retrospective investigation included endodontically treated maxillary first molars (ETMs) with apparent adequate previous NS RCT and restorations referred for endodontic retreatment at the endodontic graduate clinic. Inclusion criteria were ETMs that were diagnosed with irreversible pulpitis and normal periapical tissues before the initial NS RCT and ETMs that presented with a minimum of 1 identifiable periapical lesion (PAR) at 1 of the roots at the time of retreatment. One hundred ninety-five ETMs were included and divided into 2 groups: (1) the initial NS RCT had been performed using a microscope (n = 83) and (2) NS RCT had been performed without the use of a microscope (n = 112). Data extracted were whether the second MB (MB2) canal was located initially and the presence of an MB PAR at the time of retreatment. Data were statistically analyzed using binary logistic regression (α = 0.05). The MB root was 3 times more likely to present with a PAR at the time of retreatment if the initial NS RCT was performed without the use of a microscope (P < .05, odds ratio = 3.1). There was a significant association between a missed MB2 canal and an MB PAR in the group in which the initial NS RCT was performed without the use of a microscope (P < .05, odds ratio = 5.1). However, in cases in which the initial NS RCT was performed using a microscope, a missed MB2 canal was not associated with the presence of an MB PAR. With proper education, dentists can gain further insight into recognizing limitations in treating cases that require advanced training and advanced optics such as a microscope. Based on this strategy, it would appear that the outcome of NS RCT can be improved. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Reservoir computing with a single time-delay autonomous Boolean node

NASA Astrophysics Data System (ADS)

Haynes, Nicholas D.; Soriano, Miguel C.; Rosin, David P.; Fischer, Ingo; Gauthier, Daniel J.

2015-02-01

We demonstrate reservoir computing with a physical system using a single autonomous Boolean logic element with time-delay feedback. The system generates a chaotic transient with a window of consistency lasting between 30 and 300 ns, which we show is sufficient for reservoir computing. We then characterize the dependence of computational performance on system parameters to find the best operating point of the reservoir. When the best parameters are chosen, the reservoir is able to classify short input patterns with performance that decreases over time. In particular, we show that four distinct input patterns can be classified for 70 ns, even though the inputs are only provided to the reservoir for 7.5 ns.

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.

PubMed

Csaszar, K; Spacková, N; Stefl, R; Sponer, J; Leontis, N B

2001-11-09

Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion of solvent and counterions. In all, 33 ns of simulation were carried out, including 10 ns of the native structure with protonation of the crucial cytosine residue, C8(N3+). The native structure exhibited stable trajectories retaining all Watson-Crick and tertiary base-pairs, except for fluctuations or transient disruptions at specific sites. The most significant fluctuations involved the change or disruption of hydrogen-bonding between C8(N3+) and bases G12, A25, and C26, as well as disruption of the water bridges linking C8(N3+) with A25 and C26. To increase sampling of rare events, the native simulation was continued at 400 K. A partial, irreversible unfolding of the molecule was initiated by slippage of C8(N3+) relative to G12 and continued by sudden concerted changes in hydrogen-bonding involving A23, A24, and A25. These events were followed by a gradual loss of stacking interactions in loop 2. Of the Watson-Crick base-pairs, only the 5'-terminal pair of stem 1 dissociated at 400 K, while the trans sugar-edge/sugar-edge A20.G4 interaction remained surprisingly stable. Four additional room-temperature simulations were carried out to obtain insights into the structural and dynamic effects of selected mutations. In two of these, C8 was left unprotonated. Considerable local rearrangements occurred that were not observed in the crystal structure, thus confirming N3-protonation of C8 in the native molecule. We also investigated the effect of mutating C8(N3+) to U8, to correlate with experimental and phylogenetic studies, and of changing the G4 x C17 base-pair to A4 x U17 to weaken the trans sugar-edge interaction between positions 4 and 20 and to test models of unfolding. The simulations indicate that the C8 x G12 x C26 base-triple at the junction is the most labile region of the frame-shifting pseudoknot. They provide insights into the roles of the other non-Watson-Crick base-pairs in the early stages of unfolding of the pseudoknot, which must occur to allow readthrough of the message by the ribosome. The simulations revealed several critical, highly ordered hydration sites with close to 100 % occupancies and residency times of individual water molecules of up to 5 ns. Sodium cation coordination sites with occupancies above 50 % were also observed. Copyright 2001 Academic Press.

Time gating for energy selection and scatter rejection: High-energy pulsed neutron imaging at LANSCE

NASA Astrophysics Data System (ADS)

Swift, Alicia; Schirato, Richard; McKigney, Edward; Hunter, James; Temple, Brian

2015-09-01

The Los Alamos Neutron Science Center (LANSCE) is a linear accelerator in Los Alamos, New Mexico that accelerates a proton beam to 800 MeV, which then produces spallation neutron beams. Flight path FP15R uses a tungsten target to generate neutrons of energy ranging from several hundred keV to ~600 MeV. The beam structure has micropulses of sub-ns width and period of 1.784 ns, and macropulses of 625 μs width and frequency of either 50 Hz or 100 Hz. This corresponds to 347 micropulses per macropulse, or 1.74 x 104 micropulses per second when operating at 50 Hz. Using a very fast, cooled ICCD camera (Princeton Instruments PI-Max 4), gated images of various objects were obtained on FP15R in January 2015. Objects imaged included blocks of lead and borated polyethylene; a tungsten sphere; and a tungsten, polyethylene, and steel cylinder. Images were obtained in 36 min or less, with some in as little as 6 min. This is novel because the gate widths (some as narrow as 10 ns) were selected to reject scatter and other signal not of interest (e.g. the gamma flash that precedes the neutron pulse), which has not been demonstrated at energies above 14 MeV. This proof-of-principle experiment shows that time gating is possible above 14MeV and is useful for selecting neutron energy and reducing scatter, thus forming clearer images. Future work (simulation and experimental) is being undertaken to improve camera shielding and system design and to precisely determine optical properties of the imaging system.

Hanle measurements of electrodeposited Fe/GaAs spin tunnel contacts

NASA Astrophysics Data System (ADS)

Majumder, Sarmita; Hohertz, Donna; McNeil, James; SpringThorpe, Anthony; Kavanagh, Karen L.

2014-03-01

We report spin transport in electrodeposited Fe/n-GaAs tunnel diodes via three-terminal Hanle measurements. For temperatures between 20 K and 150 K, the spin resistance was up to 20 times higher than expected from theoretical calculations and 1000 times larger compared to a vacuum-deposited counterpart. This higher spin resistance was correlated with a higher contact resistance, and a higher concentration of oxygen impurities in the electrodeposited Fe film and interface, as detected via x-ray photoelectron and Auger spectroscopies, and inferred from Fe film nucleation rates. These results can be explained via a small effective tunnel-contact area of 5%, but extra spin filtering via interfacial states or magnetic oxide layers cannot be ruled out. The spin diffusion times (8.5 ± 0.4 ns to 1.8 ± 0.4 ns, for 20 K to 150 K) extracted from Lorentzian fits were in good agreement with values obtained from earlier 4-terminal Hanle measurements (7.8 ± 0.4 ns to 3.2 ± 0.4 ns, for 25 K to 77 K), both 10 times slower than reported vacuum-deposited contacts.

Background estimation of cosmic-ray induced neutrons in Chooz site water veto tank for possible future Ricochet Deployment

NASA Astrophysics Data System (ADS)

Silva, James

2017-09-01

The Ricochet experiment seeks to measure Coherent (neutral-current) Elastic Neutrino-Nucleus Scattering (CE νNS) using metallic superconducting and germanium semi-conducting detectors with sub-keV thresholds placed near a neutrino source such as the Chooz Nuclear Reactor Complex. In this poster, we present an estimate of the flux of cosmic-ray induced neutrons, which represent an important background in any (CE νNS) search, based on reconstructed cosmic ray data from the Chooz Site. We have simulated a possible Ricochet deployment at the Chooz site in GEANT4 focusing on the spallation neutrons generated when cosmic rays interact with the water tank veto that would surround our detector. We further simulate and discuss the effectiveness of various shielding configurations for optimizing the background levels for a future Ricochet deployment.

Generation of nanosecond neutron pulses in vacuum accelerating tubes

NASA Astrophysics Data System (ADS)

Didenko, A. N.; Shikanov, A. E.; Rashchikov, V. I.; Ryzhkov, V. I.; Shatokhin, V. L.

2014-06-01

The generation of neutron pulses with a duration of 1-100 ns using small vacuum accelerating tubes is considered. Two physical models of acceleration of short deuteron bunches in pulse neutron generators are described. The dependences of an instantaneous neutron flux in accelerating tubes on the parameters of pulse neutron generators are obtained using computer simulation. The results of experimental investigation of short-pulse neutron generators based on the accelerating tube with a vacuum-arc deuteron source, connected in the circuit with a discharge peaker, and an accelerating tube with a laser deuteron source, connected according to the Arkad'ev-Marx circuit, are given. In the experiments, the neutron yield per pulse reached 107 for a pulse duration of 10-100 ns. The resultant experimental data are in satisfactory agreement with the results of computer simulation.

Enhanced charge transport and photovoltaic performance of PBDTTT-C-T/PC70BM solar cells via UV-ozone treatment.

PubMed

Adhikary, Prajwal; Venkatesan, Swaminathan; Adhikari, Nirmal; Maharjan, Purna P; Adebanjo, Olusegun; Chen, Jihua; Qiao, Qiquan

2013-10-21

In this work, the electron transport layer of PBDTTT-C-T/PC70BM polymer solar cells were subjected to UV-ozone treatment, leading to improved cell performances from 6.46% to 8.34%. The solar cell efficiency reached a maximum of 8.34% after an optimal 5 minute UV-ozone treatment, and then decreased if treated for a longer time. To the best of our knowledge, the mechanism behind the effects of UV-ozone treatment on the improvement of charge transport and cell performance is not fully understood. We have developed a fundamental understanding of the UV-ozone treatment mechanism, which explains both the enhancements in charge transport and photovoltaic performance at an optimal treatment time, and also the phenomenon whereby further treatment time leads to a drop in cell efficiency. Transient photocurrent measurements indicated that the cell charge transport times were 1370 ns, 770 ns, 832 ns, 867 ns, and 1150 ns for the 0 min, 5 min, 10 min, 15 min, and 20 min UV-ozone treatment times, respectively. Therefore the 5 min UV-ozone treatment time led to the shortest transport time and the most efficient charge transport in the cells. The 5 min UV-ozone treated sample exhibited the highest peak intensity (E2) in the Raman spectra of the treated films, at about 437 cm(-1), indicating that it possessed the best wurtzite phase crystallinity of the ZnO films. Further increasing the UV-ozone treatment time from 5 to 20 min induced the formation of p-type defects (e.g. interstitial oxygen atoms), pushing the ZnO Fermi-level further away from the vacuum level, and decreasing the wurtzite crystallinity.

Is bacteriostatic saline superior to normal saline as an echocardiographic contrast agent?

PubMed

Cardozo, Shaun; Gunasekaran, Prasad; Patel, Hena; McGorisk, Timothy; Toosi, Mehrdad; Faraz, Haroon; Zalawadiya, Sandip; Alesh, Issa; Kottam, Anupama; Afonso, Luis

2014-12-01

Objective data on the performance characteristics and physical properties of commercially available saline formulations [normal saline (NS) vs. bacteriostatic normal saline (bNS)] are sparse. This study sought to compare the in vitro physical properties and in vivo characteristics of two commonly employed echocardiographic saline contrast agents in an attempt to assess superiority. Nineteen patients undergoing transesophageal echocardiograms were each administered agitated regular NS and bNS injections in random order and in a blinded manner according to a standardized protocol. Video time-intensity (TI) curves were constructed from a representative region of interest, placed paraseptally within the right atrium, in the bicaval view. TI curves were analyzed for maximal plateau acoustic intensity (Vmax, dB) and dwell time (DT, s), defined as time duration between onset of Vmax and decay of video intensity below clinically useful levels, reflecting the duration of homogenous opacification of the right atrium. To further characterize the physical properties of the bubbles in vitro, fixed aliquots of similarly agitated saline were injected into a glass well slide-cover slip assembly and examined using an optical microscope to determine bubble diameter in microns (µm) and concentration [bubble count/high power field (hpf)]. A higher acoustic intensity (a less negative dB level), higher bubble concentration and longer DT were considered properties of a superior contrast agent. For statistical analysis, a paired t test was conducted to evaluate the differences in means of Vmax and DT. Compared to NS, bNS administration was associated with superior opacification (video intensity -8.69 ± 4.7 vs. -10.46 ± 4.1 dB, P = 0.002), longer DT (17.3 ± 6.1 vs. 10.2 ± 3.7 s) in vivo and smaller mean bubble size (43.4 vs. 58.6 μm) and higher bubble concentration (1,002 vs. 298 bubble/hpf) in vitro. bNS provides higher intensity and more sustained opacification of the right atrium compared to NS. Higher bubble concentration and stability appear to be additional desirable rheological characteristics favoring bNS as a contrast agent.

Comparison of nonstructural protein-1 antigen detection by rapid and enzyme-linked immunosorbent assay test and its correlation with polymerase chain reaction for early diagnosis of dengue

PubMed Central

Gaikwad, Seema; Sawant, Sandhya S.; Shastri, Jayanthi S.

2017-01-01

INTRODUCTION: Early diagnosis of dengue is important for appropriate clinical management and vector control. Different serological tests based on the principle of immunochromatography and enzyme-linked immunosorbent assay (ELISA) are commonly used for detection of antigen and antibodies of dengue virus. The performance of these tests depends on the sensitivity and specificity. Hence, the study was undertaken to compare nonstructural protein-1 (NS1) antigen detection by rapid and ELISA with real-time polymerase chain reaction (RT-PCR) for diagnosis of dengue. MATERIALS AND METHODS: Prospective laboratory study was carried out on sera samples (n = 200) from clinically suspected cases of dengue. The sera samples were subjected for NS1 antigen detection test by rapid test, NS1 ELISA, and RT-PCR. The results of rapid and ELISA tests were compared with real Time PCR. RESULTS: The sensitivity, specificity, positive, and negative predictive value of rapid dengue NS1 antigen test were 81.5%, 66.7%, 78.2%, and 71.1%, respectively whereas that of NS1 ELISA were 89.9%, 100%, 100%, and 94%, respectively. Concordance of Rapid NS1 and NS1 ELISA with PCR was 75.5% and 94%. DISCUSSION AND CONCLUSION: NS1 antigen ELISA can be implemented in diagnostic laboratories for diagnosis of dengue in the acute phase of illness. The test also has great potential value for use in epidemic situations, as it could facilitate the early screening of patients and limit disease expansion. PMID:28706387

Isomers in the excited state of electron-transferring flavoprotein from Megasphaera elsdenii: spectral resolution from the time-resolved fluorescence spectra.

PubMed

Sato, Kyosuke; Nishina, Yasuzo; Shiga, Kiyoshi; Tanaka, Fumio

2008-02-27

Electron-transferring flavoprotein (Holo-ETF) from Megasphaera elsdenii contains two FAD's, one of which easily dissociates to form Iso-ETF (contains one FAD). Time-resolved fluorescence of FAD in Iso-ETF, and Holo-ETF were measured at 5 degrees C and 25 degrees C. Wavelength-dependent fluorescence decays of the both ETF at 5 degrees C and 25 degrees C were analyzed to resolve them into two independent spectra. It was found that Iso-ETF displayed two spectra with lifetime of 0.605 ns (emission peak, 508 nm) and with lifetime of 1.70 ns (emission peak, 540 nm) at 5 degrees C, and with lifetime of 0.693 ns (emission peak, 508 nm) and with lifetime of 2.75 ns (emission peak, 540 nm) at 25 degrees C. Holo-ETF displayed two spectra with lifetime of 0.739 ns (emission peak, 508 nm) and with lifetime of 2.06 ns (emission peak, 545 nm) at 5 degrees C, and with lifetime of 0.711 ns (emission peak, 527 nm) and with lifetime of 3.08 ns (emission peak, 540 nm) at 25 degrees C. Thus fluorescence lifetimes of every spectrum increased upon elevating temperature. Emission peaks Iso-ETF did not change much upon elevating temperature. Activation enthalpy changes, activation entropy changes and activation Gibbs energy changes of quenching rates all displayed negative. Two emission species in the both ETF may be hydrogen-bonding isomers, because isoalloxazine ring of FAD contains four hydrogen acceptors and one donor.

Identification of antigenic domains in the non-structural protein of Muscovy duck parvovirus.

PubMed

Yu, Tian-Fei; Li, Ming; Yan, Bing; Shao, Shu-Li; Fan, Xing-Dong; Wang, Jia; Wang, Dan-Na

2016-08-01

Muscovy duck parvovirus (MDPV) infection is widespread in many Muscovy-duck-farming countries, leading to a huge economic loss. By means of overlapping peptides expressed in Escherichia coli in combination with Western blot, antigenic domains on the non-structural protein (NSP) of MDPV were identified for the first time. On the Western blot, the fragments NS(481-510), NS (501-530), NS (521-550), NS (541-570), NS (561-590), NS (581-610) and NS (601-627) were positive (the numbers in parentheses indicate the location of amino acids), and other fragments were negative. These seven fragments were also reactive in an indirect enzyme-linked immunosorbent assay (i-ELISA). We therefore conclude that a linear antigenic domain of the NSP is located at its C-terminal end (amino acid residues 481-627). These results may facilitate future investigations into the function of NSP of MDPV and the development of immunoassays for the diagnosis of MDPV infection.

Antagonistic effect of Pseudomonas graminis CPA-7 against foodborne pathogens in fresh-cut apples under simulated commercial conditions.

PubMed

Alegre, Isabel; Viñas, Inmaculada; Usall, Josep; Anguera, Marina; Altisent, Rosa; Abadias, Maribel

2013-04-01

Recently, we reported that the application of the strain CPA-7 of Pseudomonas graminis, previously isolated from apple, could reduce the population of foodborne pathogens on minimally processed (MP) apples and peaches under laboratory conditions. Therefore, the objective of the present work was to find an antioxidant treatment and a packaging atmosphere condition to improve CPA-7 efficacy in reducing a cocktail of four Salmonella and five Listeria monocytogenes strains on MP apples under simulated commercial processing. The effect of CPA-7 application on apple quality and its survival to simulated gastric stress were also evaluated. Ascorbic acid (2%, w/v) and N-acetyl-l-cysteine (1%, w/v) as antioxidant treatments reduced Salmonella, L. monocytogenes and CPA-7 recovery, meanwhile no reduction was observed with NatureSeal(®) AS1 (NS, 6%, w/v). The antagonistic strain was effective on NS-treated apple wedges stored at 10 °C with or without modified atmosphere packaging (MAP). Then, in a semi-commercial assay, efficacy of CPA-7 inoculated at 10(5) and 10(7) cfu mL(-1) against Salmonella and L. monocytogenes strains on MP apples with NS and MAP and stored at 5 and 10 °C was evaluated. Although high CPA-7 concentrations/populations avoided Salmonella growth at 10 °C and lowered L. monocytogenes population increases were observed at both temperatures, the effect was not instantaneous. No effect on apple quality was detected and CPA-7 did not survived to simulated gastric stress throughout storage. Therefore, CPA-7 could avoid pathogens growth on MP apples during storage when use as part of a hurdle technology in combination with disinfection techniques, low storage temperature and MAP. Copyright © 2012 Elsevier Ltd. All rights reserved.

Particle velocity measurements of the reaction zone in nitromethane

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

Sheffield, S. A.; Engelke, R. P.; Alcon, R. R.

2002-01-01

The detonation reaction-zone length in neat, deuterated, and chemically sensitized nitromethane (NM) has been measured by using several different laser-based velocity interferometry systems. The experiments involved measuring the particle velocity history at a NM/PMMA (polymethylmethacrylate) window interface during the time a detonation in the NM interacted with the interface. Initially, Fabry-Perot interferometry was used, but, because of low time resolution (>5 ns), several different configurations of VISAR interferometry were subsequently used. Early work was done with VISARs with a time resolution of about 3 ns. By making changes to the recording system, we were able to improve this to {approx}1more » ns. Profiles measured at the NM/PMMA interface agree with the ZND theory, in that a spike ({approx}2.45 mm/{micro}s) is measured that is consistent with an extrapolated reactant NM Hugoniot matched to the PMMA window. The spike is rather sharp, followed by a rapid drop in particle velocity over a time of 5 to 10 ns; this is evidence of early fast reactions. Over about 50 ns, a much slower particle velocity decrease occurs to the assumed CJ condition - indicating a total reaction zone length of {approx}300 {micro}m. When the NM is chemically changed, such as replacing the hydrogen atoms with deuterium or chemically sensitizing with a base, some changes are observed in the early part of the reaction zone.« less

Wolfgang Bargmann (1906-1978) and Heinrich von Hayek (1900-1969): careers in anatomy continuing through German National Socialism to postwar leadership.

PubMed

Hildebrandt, Sabine

2013-07-01

None of the existing studies on the history of anatomy in National Socialism (NS) has yet explored the careers of those younger anatomists, whose professional development continued through NS times and who attained prominence in postwar German and Austrian anatomy. As they became modern anatomists' teachers and role models, the revelation that men like Wolfgang Bargmann and Heinrich von Hayek had used bodies of the executed for research in their early careers has recently led to some consternation. This study contributes to the analysis of the moral challenges inherent to a science that relies on work with "material" from human bodies and its interaction with its political environment. The results reveal that Bargmann and Hayek behaved like most other anatomists at the time, in that they used bodies of the executed for research and in that they joined the NS party or other NS political groups. As ambitious and successful young anatomists they may have felt that an early joining of NS affiliations was inevitable for the advancement of their careers. They and most of their colleagues became in some measure complicit with the NS regime. The complicated biographical realities of such luminous postwar figures as Bargmann and Hayek should lead modern anatomists to the questioning of their own ethical and political decisions in politically less demanding times. Copyright © 2013 Elsevier GmbH. All rights reserved.

Exploration of structural stability in deleterious nsSNPs of the XPA gene: A molecular dynamics approach.

PubMed

Nagasundaram, N; Priya Doss, C George

2011-01-01

Distinguishing the deleterious from the massive number of non-functional nsSNPs that occur within a single genome is a considerable challenge in mutation research. In this approach, we have used the existing in silico methods to explore the mutation-structure-function relationship in the XPAgene. We used the Sorting Intolerant From Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen), I-Mutant 2.0, and the Protein Analysis THrough Evolutionary Relationships methods to predict the effects of deleterious nsSNPs on protein function and evaluated the impact of mutation on protein stability by Molecular Dynamics simulations. By comparing the scores of all the four in silico methods, nsSNP with an ID rs104894131 at position C108F was predicted to be highly deleterious. We extended our Molecular dynamics approach to gain insight into the impact of this non-synonymous polymorphism on structural changes that may affect the activity of the XPAgene. Based on the in silico methods score, potential energy, root-mean-square deviation, and root-mean-square fluctuation, we predict that deleterious nsSNP at position C108F would play a significant role in causing disease by the XPA gene. Our approach would present the application of in silicotools in understanding the functional variation from the perspective of structure, evolution, and phenotype.

Development of in situ time-resolved Raman spectroscopy facility for dynamic shock loading in materials

NASA Astrophysics Data System (ADS)

Chaurasia, S.; Rastogi, V.; Rao, U.; Sijoy, C. D.; Mishra, V.; Deo, M. N.

2017-11-01

The transient state of excitation and relaxation processes in materials under shock compression can be investigated by coupling the laser driven shock facility with Raman spectroscopy. For this purpose, a time resolved Raman spectroscopy setup has been developed to monitor the physical and the chemical changes such as phase transitions, chemical reactions, molecular kinetics etc., under shock compression with nanosecond time resolution. This system consist of mainly three parts, a 2 J/8 ns Nd:YAG laser system used for generation of pump and probe beams, a Raman spectrometer with temporal and spectral resolution of 1.2 ns and 3 cm-1 respectively and a target holder in confinement geometry assembly. Detailed simulation for the optimization of confinement geometry targets is performed. Time resolved measurement of polytetrafluoroethylene (PTFE) targets at focused laser intensity of 2.2 GW/cm2 has been done. The corresponding pressure in the Aluminum and PTFE are 3.6 and 1.7 GPa respectively. At 1.7 GPa in PTFE, a red shift of 5 cm-1 is observed for the CF2 twisting mode (291 cm-1). Shock velocity in PTFE is calculated by measuring rate of change of ratios of the intensity of Raman lines scattered from shocked volume to total volume of sample in the laser focal spot along the laser axis. The calculated shock velocity in PTFE is found to be 1.64 ± 0.16 km/s at shock pressure of 1.7 GPa, for present experimental conditions.

Novel graphene-based biosensor for early detection of Zika virus infection.

PubMed

Afsahi, Savannah; Lerner, Mitchell B; Goldstein, Jason M; Lee, Joo; Tang, Xiaoling; Bagarozzi, Dennis A; Pan, Deng; Locascio, Lauren; Walker, Amy; Barron, Francie; Goldsmith, Brett R

2018-02-15

We have developed a cost-effective and portable graphene-enabled biosensor to detect Zika virus with a highly specific immobilized monoclonal antibody. Field Effect Biosensing (FEB) with monoclonal antibodies covalently linked to graphene enables real-time, quantitative detection of native Zika viral (ZIKV) antigens. The percent change in capacitance in response to doses of antigen (ZIKV NS1) coincides with levels of clinical significance with detection of antigen in buffer at concentrations as low as 450pM. Potential diagnostic applications were demonstrated by measuring Zika antigen in a simulated human serum. Selectivity was validated using Japanese Encephalitis NS1, a homologous and potentially cross-reactive viral antigen. Further, the graphene platform can simultaneously provide the advanced quantitative data of nonclinical biophysical kinetics tools, making it adaptable to both clinical research and possible diagnostic applications. The speed, sensitivity, and selectivity of this first-of-its-kind graphene-enabled Zika biosensor make it an ideal candidate for development as a medical diagnostic test. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Beneficial Effect of Post-Deposition Treatment in High-Efficiency Cu(In,Ga)Se2 Solar Cells through Reduced Potential Fluctuations

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

Jensen, Soren A.; Glynn, Stephen; Kanevce, Ana

World-record power conversion efficiencies for Cu(In,Ga)Se2 (CIGS) solar cells have been achieved via a post-deposition treatment with alkaline metals, which increases the open-circuit voltage and fill factor. We explore the role of the potassium fluoride (KF) post-deposition treatment in CIGS by employing energy- and time-resolved photoluminescence spectroscopy and electrical characterization combined with numerical modeling. The bulk carrier lifetime is found to increase with post-deposition treatment from 255 ns to 388 ns, which is the longest charge carrier lifetime reported for CIGS, and within ~40% of the radiative limit. We find evidence that the post-deposition treatment causes a decrease in themore » electronic potential fluctuations. These potential fluctuations have previously been shown to reduce the open-circuit voltage and the device efficiency in CIGS. Additionally, numerical simulations based on the measured carrier lifetimes and mobilities show a diffusion length of ~10 um, which is ~4 times larger than the film thickness. Thus, carrier collection in the bulk is not a limiting factor for device efficiency. By considering differences in doping, bandgap, and potential fluctuations, we present a possible explanation for the voltage difference between KF-treated and untreated samples.« less

Interferometric and schlieren characterization of the plasmas and shock wave dynamics during laser-triggered discharge in atmospheric air

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

Wei, Wenfu; Li, Xingwen, E-mail: xwli@mail.xjtu.edu.cn; Wu, Jian

2014-08-15

This paper describes our efforts to reveal the underlying physics of laser-triggered discharges in atmospheric air using a Mach-Zehnder interferometer and schlieren photography. Unlike the hemispherical shock waves that are produced by laser ablation, bell-like morphologies are observed during laser-triggered discharges. Phase shifts are recovered from the interferograms at a time of 1000 ns by the 2D fast Fourier transform method, and then the values of the refractive index are deduced using the Abel inversion. An abundance of free electrons is expected near the cathode surface. The schlieren photographs visualize the formation of stagnation layers at ∼600 ns in the interaction zonesmore » of the laser- and discharge-produced plasmas. Multiple reflected waves are observed at later times with the development of shock wave propagations. Estimations using the Taylor-Sedov self-similar solution indicated that approximately 45.8% and 51.9% of the laser and electrical energies are transferred into the gas flow motions, respectively. Finally, numerical simulations were performed, which successfully reproduced the main features of the experimental observations, and provided valuable insights into the plasma and shock wave dynamics during the laser-triggered discharge.« less

Design and implementation of fast bipolar clock drivers for CCD imaging systems in space applications

NASA Astrophysics Data System (ADS)

Jayarajan, Jayesh; Kumar, Nishant; Verma, Amarnath; Thaker, Ramkrishna

2016-05-01

Drive electronics for generating fast, bipolar clocks, which can drive capacitive loads of the order of 5-10nF are indispensable for present day Charge Coupled Devices (CCDs). Design of these high speed bipolar clocks is challenging because of the capacitive loads that have to be driven and a strict constraint on the rise and fall times. Designing drive electronics circuits for space applications becomes even more challenging due to limited number of available discrete devices, which can survive in the harsh radiation prone space environment. This paper presents the design, simulations and test results of a set of such high speed, bipolar clock drivers. The design has been tested under a thermal cycle of -15 deg C to +55 deg C under vacuum conditions and has been designed using radiation hardened components. The test results show that the design meets the stringent rise/fall time requirements of 50+/-10ns for Multiple Vertical CCD (VCCD) clocks and 20+/-5ns for Horizontal CCD (HCCD) clocks with sufficient design margins across full temperature range, with a pixel readout rate of 6.6MHz. The full design has been realized in flexi-rigid PCB with package volume of 140x160x50 mm3.

Analysis of optical route in a micro high-speed magneto-optic switch

NASA Astrophysics Data System (ADS)

Weng, Zihua; Yang, Guoguang; Huang, Yuanqing; Chen, Zhimin; Zhu, Yun; Wu, Jinming; Lin, Shufen; Mo, Weiping

2005-02-01

A novel micro high-speed 2x2 magneto-optic switch and its optical route, which is used in high-speed all-optical communication network, is designed and analyzed in this paper. The study of micro high-speed magneto-optic switch mainly involves the optical route and high-speed control technique design. The optical route design covers optical route design of polarization in optical switch, the performance analysis and material selection of magneto-optic crystal and magnetic path design in Faraday rotator. The research of high-speed control technique involves the study of nanosecond pulse generator, high-speed magnetic field and its control technique etc. High-speed current transients from nanosecond pulse generator are used to switch the magnetization of the magneto-optic crystal, which propagates a 1550nm optical beam. The optical route design schemes and electronic circuits of high-speed control technique are both simulated on computer and test by the experiments respectively. The experiment results state that the nanosecond pulse generator can output the pulse with rising edge time 3~35ns, voltage amplitude 10~90V and pulse width 10~100ns. Under the control of CPU singlechip, the optical beam can be stably switched and the switching time is less than 1μs currently.

Cellular automata model for traffic flow at intersections in internet of vehicles

NASA Astrophysics Data System (ADS)

Zhao, Han-Tao; Liu, Xin-Ru; Chen, Xiao-Xu; Lu, Jian-Cheng

2018-03-01

Considering the effect of the front vehicle's speed, the influence of the brake light and the conflict of the traffic flow, we established a cellular automata model called CE-NS for traffic flow at the intersection in the non-vehicle networking environment. According to the information interaction of Internet of Vehicles (IoV), introducing parameters describing the congestion and the accurate speed of the front vehicle into the CE-NS model, we improved the rules of acceleration, deceleration and conflict, and finally established a cellular automata model for traffic flow at intersections of IoV. The relationship between traffic parameters such as vehicle speed, flow and average travel time is obtained by numerical simulation of two models. Based on this, we compared the traffic situation of the non-vehicle networking environment with conditions of IoV environment, and analyzed the influence of the different degree of IoV on the traffic flow. The results show that the traffic speed is increased, the travel time is reduced, the flux of intersections is increased and the traffic flow is more smoothly under IoV environment. After the vehicle which achieves IoV reaches a certain proportion, the operation effect of the traffic flow begins to improve obviously.

Ionization of Xenon to the Nickel-Like Stage and Beyond in Micro-Capillary Plasma Columns Heated by Ultrafast Current Pulses

NASA Astrophysics Data System (ADS)

Avaria, G.; Grisham, M.; Li, J.; Tomasel, F. G.; Shlyapstsev, V. N.; Busquet, M.; Woolston, M.; Rocca, J. J.

Homogeneous plasma columns with ionization levels typical of MA discharges were created by rapidly heating gas-filled 520 µm diameter channels with ns rise-time current pulses of unusually low amplitude, 40 kA. These conditions allow the generation of high aspect ratio (eg. > 300:1) plasma columns with very high degrees of ionization (e.g. Ni-like Xenon) of interest for soft x-ray lasers below λ = 10 nm. Spectra and simulations of plasmas generated in 520 µm diameter alumina capillaries driven by 35-40 kA current pulses with 4 ns rise time were obtained for discharges in Xenon and Neon discharges. The first shows the presence of lines corresponding to ionization stages up to Fe-like Xe. The latter show that Al impurities from the walls are ionized to the H-like and He-like stages. He-like Al spectra containing the resonance line significantly broaden by opacity, the intercombination line, and Li-like satellites are analyzed. For Xenon discharges, the spectral lines from the Ni-like transitions the 3d94d (3/2, 3/2)J = 0 to the 3d94p(5/2, 3/2)J = 1 and to 3d94p(3/2, 1/2)J = 1 are observed.

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

NASA Astrophysics Data System (ADS)

Naritomi, Yusuke; Fuchigami, Sotaro

2011-02-01

Protein dynamics on a long time scale was investigated using all-atom molecular dynamics (MD) simulation and time-structure based independent component analysis (tICA). We selected the lysine-, arginine-, ornithine-binding protein (LAO) as a target protein and focused on its domain motions in the open state. A MD simulation of the LAO in explicit water was performed for 600 ns, in which slow and large-amplitude domain motions of the LAO were observed. After extracting domain motions by rigid-body domain analysis, the tICA was applied to the obtained rigid-body trajectory, yielding slow modes of the LAO's domain motions in order of decreasing time scale. The slowest mode detected by the tICA represented not a closure motion described by a largest-amplitude mode determined by the principal component analysis but a twist motion with a time scale of tens of nanoseconds. The slow dynamics of the LAO were well described by only the slowest mode and were characterized by transitions between two basins. The results show that tICA is promising for describing and analyzing slow dynamics of proteins.

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: the case of domain motions.

PubMed

Naritomi, Yusuke; Fuchigami, Sotaro

2011-02-14

Protein dynamics on a long time scale was investigated using all-atom molecular dynamics (MD) simulation and time-structure based independent component analysis (tICA). We selected the lysine-, arginine-, ornithine-binding protein (LAO) as a target protein and focused on its domain motions in the open state. A MD simulation of the LAO in explicit water was performed for 600 ns, in which slow and large-amplitude domain motions of the LAO were observed. After extracting domain motions by rigid-body domain analysis, the tICA was applied to the obtained rigid-body trajectory, yielding slow modes of the LAO's domain motions in order of decreasing time scale. The slowest mode detected by the tICA represented not a closure motion described by a largest-amplitude mode determined by the principal component analysis but a twist motion with a time scale of tens of nanoseconds. The slow dynamics of the LAO were well described by only the slowest mode and were characterized by transitions between two basins. The results show that tICA is promising for describing and analyzing slow dynamics of proteins.

A robust and high-performance queue management controller for large round trip time networks

NASA Astrophysics Data System (ADS)

Khoshnevisan, Ladan; Salmasi, Farzad R.

2016-05-01

Congestion management for transmission control protocol is of utmost importance to prevent packet loss within a network. This necessitates strategies for active queue management. The most applied active queue management strategies have their inherent disadvantages which lead to suboptimal performance and even instability in the case of large round trip time and/or external disturbance. This paper presents an internal model control robust queue management scheme with two degrees of freedom in order to restrict the undesired effects of large and small round trip time and parameter variations in the queue management. Conventional approaches such as proportional integral and random early detection procedures lead to unstable behaviour due to large delay. Moreover, internal model control-Smith scheme suffers from large oscillations due to the large round trip time. On the other hand, other schemes such as internal model control-proportional integral and derivative show excessive sluggish performance for small round trip time values. To overcome these shortcomings, we introduce a system entailing two individual controllers for queue management and disturbance rejection, simultaneously. Simulation results based on Matlab/Simulink and also Network Simulator 2 (NS2) demonstrate the effectiveness of the procedure and verify the analytical approach.

Flow strength of highly hydrated Mg- and Na-sulfate hydrate salts, pure and in mixtures with water ice, with application to Europa

USGS Publications Warehouse

Durham, W.B.; Stern, L.A.; Kubo, T.; Kirby, S.H.

2005-01-01

We selected two Europan-ice-shell candidate highly hydrated sulfate salts for a laboratory survey of ductile flow properties: MgSO4 ?? 7H2O (epsomite) and Na2SO4 ?? 10H2O (mirabilite), called MS7 and NS10, respectively. Polycrystalline samples in pure form and in mixtures with water ice I were tested using our cryogenic high-pressure creep apparatus at temperatures 232 ??? T ??? 294 K, confining pressures P = 50 and 100 MPa, and strain rates 4 ?? 10-8 ??? ???dot;e ??? 7 ?? 10-5 s-1. Grain size of NS10 samples was > 100 ??m. The flow strength ?? of pure MS7 was over 100 times that of polycrystalline ice I at comparable conditions; that of pure NS10 over 20 times that of ice. In terms of the creep law ???dot;e = A??n e-Q/RT, where R is the gas constant, we determine parameter values of A = 1012.1 MPa-ns-1, n = 5.4, and Q = 128 kJ/mol for pure NS10. Composites of ice I and NS10 of volume fraction ?? NS10 have flow strength ??c = [??NS10??NS10J + (1 - ?? NS10)??iceIJ]1/J where J ??? -0.5, making the effect on the flow of ice with low volume fractions of NS10 much like that of virtually undeformable hard rock inclusions. Being much stronger and denser than ice, massive sulfate inclusions in the warmer, ductile layer of the Europan ice shell are less likely to be entrained in convective ice flow and more likely to be drawn to the base of the ice shell by gravitational forces and eventually expelled. With only smaller, dispersed sulfate inclusions, at probable sulfate ?? < 0.2, the shell may be treated rheologically as pure, polycrystalline ice, with boundary conditions perhaps influenced by the high density and low thermal conductivity of the hydrated salts. Copyright 2005 by the American Geophysical Union.

The High Field Ultra Low Aspect Ratio Tokamak (HF-ULART)

NASA Astrophysics Data System (ADS)

Ribeiro, Celso

2017-10-01

Recently, a medium-size HF-ULART has been proposed. The major objective is to explore the high beta and pressure under the high toroidal field, using present day technology. This might be one of pathway scenarios for a potential ultra-compact pulsed neutron source (UCP-NS) based on the spherical tokamak (ST) concept, which may lead to more steady-state NS or even to a fusion reactor, via realistic design scaling. The HF-ULART pulsed mode operation is created by quasi-simultaneous adiabatic compression (AC) in both minor and major radius of a very high beta plasma, possibly with further help of passive-wall stabilization, as envisaged in the RULART concept. This may help the revival of the studies of the AC technique in tokamaks, alongside the less compact and more complex ST-40 device, currently under construction. In addition, by similarities, studies in HF-ULART as a UCP-NS may also help to test the feasibility of the compact NS via the spheromak concept, which also uses the AC technique. Simulations of AC in HF-ULART plasmas will be presented.

The r-process nucleosynthesis and related challenges

NASA Astrophysics Data System (ADS)

Goriely, Stephane; Bauswein, Andreas; Janka, Hans-Thomas; Just, Oliver; Pllumbi, Else

2018-01-01

The rapid neutron-capture process, or r-process, is known to be of fundamental importance for explaining the origin of approximately half of the A > 60 stable nuclei observed in nature. Recently, special attention has been paid to neutron star (NS) mergers following the confirmation by hydrodynamic simulations that a non-negligible amount of matter can be ejected and by nucleosynthesis calculations combined with the predicted astrophysical event rate that such a site can account for the majority of r-material in our Galaxy. We show here that the combined contribution of both the dynamical (prompt) ejecta expelled during binary NS or NS-black hole (BH) mergers and the neutrino and viscously driven outflows generated during the post-merger remnant evolution of relic BH-torus systems can lead to the production of r-process elements from mass number A ≳ 90 up to actinides. The corresponding abundance distribution is found to reproduce the solar distribution extremely well. It can also account for the elemental distributions observed in low-metallicity stars. However, major uncertainties still affect our understanding of the composition of the ejected matter. These concern (i) the β-interactions of electron (anti)neutrinos with free neutrons and protons, as well as their inverse reactions, which may affect the neutron-richness of the matter at the early phase of the ejection, and (ii) the nuclear physics of exotic neutron-rich nuclei, including nuclear structure as well as nuclear interaction properties, which impact the calculated abundance distribution. Both aspects are discussed in the light of recent hydrodynamical simulations of NS mergers and microscopic calculations of nuclear decay and reaction probabilities.

Recent progress of the improved magnetically insulated transmission line oscillator.

PubMed

Fan, Yu-Wei; Zhong, Hui-Huang; Li, Zhi-Qiang; Shu, Ting; Zhang, Jian-De; Liu, Jin-Liang; Yang, Jian-Hua; Zhang, Jun; Yuan, Cheng-Wei; Luo, Ling

2008-03-01

The improved magnetically insulated transmission line oscillator (MILO) is a gigawatt-class L-band high power microwave tube driven by a 550 kV, 57 kA, 50 ns electron beam. It has allowed us to generate 2.4 GW pulse of 22 ns duration. The recent progress of the improved MILO is presented in this paper. First, a field shaper cathode is introduced into the improved MILO to avoid the cathode flares in the triple point region. The experimental results show that the cathode flares are avoided, so the lifetime of the velvet cathode is longer than that of the taper cathode. Furthermore, the shot-to-shot reproducibility is better than that of the taper cathode. Second, In order to prolong the pulse duration and increase the radiated microwave power, a self-built 600 kV, 10 Omega, 80 ns pulser: SPARK-03 is employed to drive the improved MILO. Simulation and experimental investigation are performed. In simulation, when the improved MILO is driven by a 600 kV, 57 kA electron beam, high-power microwave is generated with output power of 4.15 GW, frequency of 1.76 GHz, and relevant power conversion efficiency of 12.0%. In experiments, when the diode voltage is 550 kV and current is 54 kA, the measured results are that the radiated microwave power is above 3.1 GW, the pulse duration is above 40 ns, the microwave frequency is about 1.755 GHz, and the power conversion efficiency is about 10.4%.

Validation of a Laser-Ray Package in an Eulerian Code

NASA Astrophysics Data System (ADS)

Bradley, Paul; Hall, Mike; McKenty, Patrick; Collins, Tim; Keller, David

2014-10-01

A laser-ray absorption package was recently installed in the RAGE code by the Laboratory for Laser Energetics (LLE). In this presentation, we describe our use of this package to implode Omega 60 beam symmetric direct drive capsules. The capsules have outer diameters of about 860 microns, CH plastic shell thicknesses between 8 and 32 microns, DD or DT gas fills between 5 and 20 atmospheres, and a 1 ns square pulse of 23 to 27 kJ. These capsule implosions were previously modeled with a calibrated energy source in the outer layer of the capsule, where we matched bang time and burn ion temperature well, but the simulated yields were two to three times higher than the data. We will run simulations with laser ray energy deposition to the experiments and the results to the yield and spectroscopic data. Work performed by Los Alamos National Laboratory under Contract DE-AC52-06NA25396 for the National Nuclear Security Administration of the U.S. Department of Energy.

A Review of Staphylococcal Cassette Chromosome mec (SCCmec) Types in Coagulase-Negative Staphylococci (CoNS) Species.

PubMed

Saber, Huda; Jasni, Azmiza Syawani; Jamaluddin, Tengku Zetty Maztura Tengku; Ibrahim, Rosni

2017-10-01

Coagulase-negative staphylococci (CoNS) are considered low pathogenic organisms. However, they are progressively causing more serious infections with time because they have adapted well to various antibiotics owing to their ability to form biofilms. Few studies have been conducted on CoNS in both, hospital and community-acquired settings, especially in Malaysia. Thus, it is important to study their species and gene distributions. A mobile genetic element, staphylococcal cassette chromosome mec (SCC mec ), plays an important role in staphylococci pathogenesis. Among CoNS, SCC mec has been studied less frequently than Staphylococcus aureus (coagulase-positive staphylococci). A recent study (8) conducted in Malaysia successfully detected SCC mec type I to VIII as well as several new combination patterns in CoNS species, particularly Staphylococcus epidermidis . However, data are still limited, and further research is warranted. This paper provides a review on SCC mec types among CoNS species.

Timing performance of the silicon PET insert probe

PubMed Central

Studen, A.; Burdette, D.; Chesi, E.; Cindro, V.; Clinthorne, N. H.; Cochran, E.; Grošičar, B.; Kagan, H.; Lacasta, C.; Linhart, V.; Mikuž, M.; Stankova, V.; Weilhammer, P.; Žontar, D.

2010-01-01

Simulation indicates that PET image could be improved by upgrading a conventional ring with a probe placed close to the imaged object. In this paper, timing issues related to a PET probe using high-resistivity silicon as a detector material are addressed. The final probe will consist of several (four to eight) 1-mm thick layers of silicon detectors, segmented into 1 × 1 mm2 pads, each pad equivalent to an independent p + nn+ diode. A proper matching of events in silicon with events of the external ring can be achieved with a good timing resolution. To estimate the timing performance, measurements were performed on a simplified model probe, consisting of a single 1-mm thick detector with 256 square pads (1.4 mm side), coupled with two VATAGP7s, application-specific integrated circuits. The detector material and electronics are the same that will be used for the final probe. The model was exposed to 511 keV annihilation photons from an 22Na source, and a scintillator (LYSO)–PMT assembly was used as a timing reference. Results were compared with the simulation, consisting of four parts: (i) GEANT4 implemented realistic tracking of electrons excited by annihilation photon interactions in silicon, (ii) calculation of propagation of secondary ionisation (electron–hole pairs) in the sensor, (iii) estimation of the shape of the current pulse induced on surface electrodes and (iv) simulation of the first electronics stage. A very good agreement between the simulation and the measurements were found. Both indicate reliable performance of the final probe at timing windows down to 20 ns. PMID:20215445

Timing performance of the silicon PET insert probe.

PubMed

Studen, A; Burdette, D; Chesi, E; Cindro, V; Clinthorne, N H; Cochran, E; Grosicar, B; Kagan, H; Lacasta, C; Linhart, V; Mikuz, M; Stankova, V; Weilhammer, P; Zontar, D

2010-01-01

Simulation indicates that PET image could be improved by upgrading a conventional ring with a probe placed close to the imaged object. In this paper, timing issues related to a PET probe using high-resistivity silicon as a detector material are addressed. The final probe will consist of several (four to eight) 1-mm thick layers of silicon detectors, segmented into 1 x 1 mm(2) pads, each pad equivalent to an independent p + nn+ diode. A proper matching of events in silicon with events of the external ring can be achieved with a good timing resolution. To estimate the timing performance, measurements were performed on a simplified model probe, consisting of a single 1-mm thick detector with 256 square pads (1.4 mm side), coupled with two VATAGP7s, application-specific integrated circuits. The detector material and electronics are the same that will be used for the final probe. The model was exposed to 511 keV annihilation photons from an (22)Na source, and a scintillator (LYSO)-PMT assembly was used as a timing reference. Results were compared with the simulation, consisting of four parts: (i) GEANT4 implemented realistic tracking of electrons excited by annihilation photon interactions in silicon, (ii) calculation of propagation of secondary ionisation (electron-hole pairs) in the sensor, (iii) estimation of the shape of the current pulse induced on surface electrodes and (iv) simulation of the first electronics stage. A very good agreement between the simulation and the measurements were found. Both indicate reliable performance of the final probe at timing windows down to 20 ns.

A study of the cross-correlation and time lag in black hole X-ray binary XTE J1859+226

NASA Astrophysics Data System (ADS)

Pei, Songpeng; Ding, Guoqiang; Li, Zhibing; Lei, Yajuan; Yuen, Rai; Qu, Jinlu

2017-07-01

With Rossi X-ray Timing Explorer (RXTE) data, we systematically study the cross-correlation and time lag in all spectral states of black hole X-ray binary (BHXB) XTE J1859+226 in detail during its entire 1999-2000 outburst that lasted for 166 days. Anti-correlations and positive correlations and their respective soft and hard X-ray lags are only detected in the first 100 days of the outburst when the luminosity is high. This suggests that the cross-correlations may be related to high luminosity. Positive correlations are detected in every state of XTE J1859+226, viz., hard state, hard-intermediate state (HIMS), soft-intermediate state (SIMS) and soft state. However, anti-correlations are only detected in HIMS and SIMS, anti-correlated hard lags are only detected in SIMS, while anti-correlated soft lags are detected in both HIMS and SIMS. Moreover, the ratio of the observations with anti-correlated soft lags to hard lags detected in XTE J1859+226 is significantly different from that in neutron star low-mass X-ray binaries (NS LMXBs). So far, anti-correlations are never detected in the soft state of BHXBs but detected in every branch or state of NS LMXBs. This may be due to the origin of soft seed photons in BHXBs is confined to the accretion disk and, for NS LMXBs, from both accretion disk and the surface of the NS. We notice that the timescale of anti-correlated time lags detected in XTE J1859+226 is similar with that of other BHXBs and NS LMXBs. We suggest that anti-correlated soft lag detected in BHXB may result from fluctuation in the accretion disk as well as NS LMXB.

Computer simulations suggest direct and stable tip to tip interaction between the outer membrane channel TolC and the isolated docking domain of the multidrug RND efflux transporter AcrB.

PubMed

Schmidt, Thomas H; Raunest, Martin; Fischer, Nadine; Reith, Dirk; Kandt, Christian

2016-07-01

One way by which bacteria achieve antibiotics resistance is preventing drug access to its target molecule for example through an overproduction of multi-drug efflux pumps of the resistance nodulation division (RND) protein super family of which AcrAB-TolC in Escherichia coli is a prominent example. Although representing one of the best studied efflux systems, the question of how AcrB and TolC interact is still unclear as the available experimental data suggest that either both proteins interact in a tip to tip manner or do not interact at all but are instead connected by a hexamer of AcrA molecules. Addressing the question of TolC-AcrB interaction, we performed a series of 100 ns - 1 µs-molecular dynamics simulations of membrane-embedded TolC in presence of the isolated AcrB docking domain (AcrB(DD)). In 5/6 simulations we observe direct TolC-AcrB(DD) interaction that is only stable on the simulated time scale when both proteins engage in a tip to tip manner. At the same time we find TolC opening and closing freely on extracellular side while remaining closed at the inner periplasmic bottleneck region, suggesting that either the simulated time is too short or additional components are required to unlock TolC. Copyright © 2016 Elsevier B.V. All rights reserved.

Room temperature deposition of silicon nanodot clusters by plasma-enhanced chemical vapor deposition.

PubMed

Kim, Jae-Kwan; Kim, Jun Young; Yoon, Jae-Sik; Lee, Ji-Myon

2013-10-01

The formation of nanometer-scale (ns)-Si dots and clusters on p-GaN layers has been studied by controlling the early stage of growth during plasma-enhanced chemical vapor deposition (PECVD) at room temperature. We found that ns-Si dots and clusters formed on the p-GaN surface, indicating that growth was the Volmer-Weber mode. The deposition parameters such as radio frequency (RF) power and processing time mainly influenced the size of the ns-Si dots (40 nm-160 nm) and the density of the ns-Si dot clusters.

Generation of large-area and glow-like surface discharge in atmospheric pressure air

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

Song, Ying; Bi, Zhenhua; Wang, Xueyang

2016-08-15

A large-area (6 cm × 6 cm) air surface dielectric barrier discharge has been generated at atmospheric pressure by using well-aligned and micron-sized dielectric tubes with tungsten wire electrodes. Intensified CCD images with an exposure time of 5 ns show that the uniform surface air discharge can be generated during the rising and falling time of pulsed DC voltage. Current and voltage and optical measurements confirm the formation of glow-like air discharges on the surface of micron-sized dielectric tubes. Simulation results indicate that the microelectrode configuration contributes to the formation of strong surface electric field and plays an important role in the generation of uniformmore » surface air discharge.« less

Discrete time modeling and stability analysis of TCP Vegas

NASA Astrophysics Data System (ADS)

You, Byungyong; Koo, Kyungmo; Lee, Jin S.

2007-12-01

This paper presents an analysis method for TCP Vegas network model with single link and single source. Some papers showed global stability of several network models, but those models are not a dual problem where dynamics both exist in sources and links such as TCP Vegas. Other papers studied TCP Vegas as a dual problem, but it did not fully derive an asymptotic stability region. Therefore we analyze TCP Vegas with Jury's criterion which is necessary and sufficient condition. So we use state space model in discrete time and by using Jury's criterion, we could find an asymptotic stability region of TCP Vegas network model. This result is verified by ns-2 simulation. And by comparing with other results, we could know our method performed well.

GESPA: classifying nsSNPs to predict disease association.

PubMed

Khurana, Jay K; Reeder, Jay E; Shrimpton, Antony E; Thakar, Juilee

2015-07-25

Non-synonymous single nucleotide polymorphisms (nsSNPs) are the most common DNA sequence variation associated with disease in humans. Thus determining the clinical significance of each nsSNP is of great importance. Potential detrimental nsSNPs may be identified by genetic association studies or by functional analysis in the laboratory, both of which are expensive and time consuming. Existing computational methods lack accuracy and features to facilitate nsSNP classification for clinical use. We developed the GESPA (GEnomic Single nucleotide Polymorphism Analyzer) program to predict the pathogenicity and disease phenotype of nsSNPs. GESPA is a user-friendly software package for classifying disease association of nsSNPs. It allows flexibility in acceptable input formats and predicts the pathogenicity of a given nsSNP by assessing the conservation of amino acids in orthologs and paralogs and supplementing this information with data from medical literature. The development and testing of GESPA was performed using the humsavar, ClinVar and humvar datasets. Additionally, GESPA also predicts the disease phenotype associated with a nsSNP with high accuracy, a feature unavailable in existing software. GESPA's overall accuracy exceeds existing computational methods for predicting nsSNP pathogenicity. The usability of GESPA is enhanced by fast SQL-based cloud storage and retrieval of data. GESPA is a novel bioinformatics tool to determine the pathogenicity and phenotypes of nsSNPs. We anticipate that GESPA will become a useful clinical framework for predicting the disease association of nsSNPs. The program, executable jar file, source code, GPL 3.0 license, user guide, and test data with instructions are available at http://sourceforge.net/projects/gespa.

Histopathology of normal skin and melanomas after nanosecond pulsed electric field treatment.

PubMed

Chen, Xinhua; James Swanson, R; Kolb, Juergen F; Nuccitelli, Richard; Schoenbach, Karl H

2009-12-01

Nanosecond pulsed electric fields (nsPEFs) can affect the intracellular structures of cells in vitro. This study shows the direct effects of nsPEFs on tumor growth, tumor volume, and histological characteristics of normal skin and B16-F10 melanoma in SKH-1 mice. A melanoma model was set up by injecting B16-F10 into female SKH-1 mice. After a 100-pulse treatment with an nsPEF (40-kV/cm field strength; 300-ns duration; 30-ns rise time; 2-Hz repetition rate), tumor growth and histology were studied using transillumination, light microscopy with hematoxylin and eosin stain and transmission electron microscopy. Melanin and iron within the melanoma tumor were also detected with specific stains. After nsPEF treatment, tumor development was inhibited with decreased volumes post-nsPEF treatment compared with control tumors (P<0.05). The nsPEF-treated tumor volume was reduced significantly compared with the control group (P<0.01). Hematoxylin and eosin stain and transmission electron microscopy showed morphological changes and nuclear shrinkage in the tumor. Fontana-Masson stain indicates that nsPEF can externalize the melanin. Iron stain suggested nsPEF caused slight hemorrhage in the treated tissue. Histology confirmed that repeated applications of nsPEF disrupted the vascular network. nsPEF treatment can significantly disrupt the vasculature, reduce subcutaneous murine melanoma development, and produce tumor cell contraction and nuclear shrinkage while concurrently, but not permanently, damaging peripheral healthy skin tissue in the treated area, which we attribute to the highly localized electric fields surrounding the needle electrodes.

Structural insight and flexible features of NS5 proteins from all four serotypes of Dengue virus in solution

PubMed Central

Saw, Wuan Geok; Tria, Giancarlo; Grüber, Ardina; Subramanian Manimekalai, Malathy Sony; Zhao, Yongqian; Chandramohan, Arun; Srinivasan Anand, Ganesh; Matsui, Tsutomu; Weiss, Thomas M.; Vasudevan, Subhash G.; Grüber, Gerhard

2015-01-01

Infection by the four serotypes of Dengue virus (DENV-1 to DENV-4) causes an important arthropod-borne viral disease in humans. The multifunctional DENV nonstructural protein 5 (NS5) is essential for capping and replication of the viral RNA and harbours a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. In this study, insights into the overall structure and flexibility of the entire NS5 of all four Dengue virus serotypes in solution are presented for the first time. The solution models derived revealed an arrangement of the full-length NS5 (NS5FL) proteins with the MTase domain positioned at the top of the RdRP domain. The DENV-1 to DENV-4 NS5 forms are elongated and flexible in solution, with DENV-4 NS5 being more compact relative to NS5 from DENV-1, DENV-2 and DENV-3. Solution studies of the individual MTase and RdRp domains show the compactness of the RdRp domain as well as the contribution of the MTase domain and the ten-residue linker region to the flexibility of the entire NS5. Swapping the ten-residue linker between DENV-4 NS5FL and DENV-3 NS5FL demonstrated its importance in MTase–RdRp communication and in concerted interaction with viral and host proteins, as probed by amide hydrogen/deuterium mass spectrometry. Conformational alterations owing to RNA binding are presented. PMID:26527147

Structural insight and flexible features of NS5 proteins from all four serotypes of Dengue virus in solution

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

Saw, Wuan Geok; Tria, Giancarlo; Grüber, Ardina

Infection by the four serotypes ofDengue virus(DENV-1 to DENV-4) causes an important arthropod-borne viral disease in humans. The multifunctional DENV nonstructural protein 5 (NS5) is essential for capping and replication of the viral RNA and harbours a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. In this study, insights into the overall structure and flexibility of the entire NS5 of all fourDengue virusserotypes in solution are presented for the first time. The solution models derived revealed an arrangement of the full-length NS5 (NS5FL) proteins with the MTase domain positioned at the top of the RdRP domain. The DENV-1more » to DENV-4 NS5 forms are elongated and flexible in solution, with DENV-4 NS5 being more compact relative to NS5 from DENV-1, DENV-2 and DENV-3. Solution studies of the individual MTase and RdRp domains show the compactness of the RdRp domain as well as the contribution of the MTase domain and the ten-residue linker region to the flexibility of the entire NS5. Swapping the ten-residue linker between DENV-4 NS5FL and DENV-3 NS5FL demonstrated its importance in MTase–RdRp communication and in concerted interaction with viral and host proteins, as probed by amide hydrogen/deuterium mass spectrometry. Conformational alterations owing to RNA binding are presented.« less

Anomalous diffusion of water molecules at grain boundaries in ice Ih.

PubMed

Moreira, Pedro Augusto Franco Pinheiro; Veiga, Roberto Gomes de Aguiar; Ribeiro, Ingrid de Almeida; Freitas, Rodrigo; Helfferich, Julian; de Koning, Maurice

2018-05-23

Using ab initio and classical molecular dynamics simulations, we study pre-melting phenomena in pristine coincident-site-lattice grain boundaries (GBs) in proton-disordered hexagonal ice Ih at temperatures just below the melting point Tm. Concerning pre-melt-layer thicknesses, the results are consistent with the available experimental estimates for low-disorder impurity-free GBs. With regard to molecular mobility, the simulations provide a key new insight: the translational motion of the water molecules is found to be subdiffusive for time scales from ∼10 ns up to at least 0.1 μs. Moreover, the fact that the anomalous diffusion occurs even at temperatures just below Tm where the bulk supercooled liquid still diffuses normally suggests that it is related to the confinement of the GB pre-melt layers by the surrounding crystalline environment. Furthermore, we show that this behavior can be characterized by continuous-time random walk models in which the waiting-time distributions decay according to power-laws that are very similar to those describing dynamics in glass-forming systems.

Serotype-specific differences in dengue virus non-structural protein 5 nuclear localization.

PubMed

Hannemann, Holger; Sung, Po-Yu; Chiu, Han-Chen; Yousuf, Amjad; Bird, Jim; Lim, Siew Pheng; Davidson, Andrew D

2013-08-02

The four serotypes of dengue virus (DENV-1 to -4) cause the most important arthropod-borne viral disease of humans. DENV non-structural protein 5 (NS5) contains enzymatic activities required for capping and replication of the viral RNA genome that occurs in the host cytoplasm. However, previous studies have shown that DENV-2 NS5 accumulates in the nucleus during infection. In this study, we examined the nuclear localization of NS5 for all four DENV serotypes. We demonstrate for the first time that there are serotypic differences in NS5 nuclear localization. Whereas the DENV-2 and -3 proteins accumulate in the nucleus, DENV-1 and -4 NS5 are predominantly if not exclusively localized to the cytoplasm. Comparative studies on the DENV-2 and -4 NS5 proteins revealed that the difference in DENV-4 NS5 nuclear localization was not due to rapid nuclear export but rather the lack of a functional nuclear localization sequence. Interaction studies using DENV-2 and -4 NS5 and human importin-α isoforms failed to identify an interaction that supported the differential nuclear localization of NS5. siRNA knockdown of the human importin-α isoform KPNA2, corresponding to the murine importin-α isoform previously shown to bind to DENV-2 NS5, did not substantially affect DENV-2 NS5 nuclear localization, whereas knockdown of importin-β did. The serotypic differences in NS5 nuclear localization did not correlate with differences in IL-8 gene expression. The results show that NS5 nuclear localization is not strictly required for virus replication but is more likely to have an auxiliary function in the life cycle of specific DENV serotypes.

Serotype-specific Differences in Dengue Virus Non-structural Protein 5 Nuclear Localization*

PubMed Central

Hannemann, Holger; Sung, Po-Yu; Chiu, Han-Chen; Yousuf, Amjad; Bird, Jim; Lim, Siew Pheng; Davidson, Andrew D.

2013-01-01

The four serotypes of dengue virus (DENV-1 to -4) cause the most important arthropod-borne viral disease of humans. DENV non-structural protein 5 (NS5) contains enzymatic activities required for capping and replication of the viral RNA genome that occurs in the host cytoplasm. However, previous studies have shown that DENV-2 NS5 accumulates in the nucleus during infection. In this study, we examined the nuclear localization of NS5 for all four DENV serotypes. We demonstrate for the first time that there are serotypic differences in NS5 nuclear localization. Whereas the DENV-2 and -3 proteins accumulate in the nucleus, DENV-1 and -4 NS5 are predominantly if not exclusively localized to the cytoplasm. Comparative studies on the DENV-2 and -4 NS5 proteins revealed that the difference in DENV-4 NS5 nuclear localization was not due to rapid nuclear export but rather the lack of a functional nuclear localization sequence. Interaction studies using DENV-2 and -4 NS5 and human importin-α isoforms failed to identify an interaction that supported the differential nuclear localization of NS5. siRNA knockdown of the human importin-α isoform KPNA2, corresponding to the murine importin-α isoform previously shown to bind to DENV-2 NS5, did not substantially affect DENV-2 NS5 nuclear localization, whereas knockdown of importin-β did. The serotypic differences in NS5 nuclear localization did not correlate with differences in IL-8 gene expression. The results show that NS5 nuclear localization is not strictly required for virus replication but is more likely to have an auxiliary function in the life cycle of specific DENV serotypes. PMID:23770669

Disassembly time of deuterium-cluster-fusion plasma irradiated by an intense laser pulse

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

Bang, W.

Energetic deuterium ions from large deuterium clusters (>10 nm diameter) irradiated by an intense laser pulse (>10¹⁶ W/cm²) produce DD fusion neutrons for a time interval determined by the geometry of the resulting fusion plasma. We show an analytical solution of this time interval, the plasma disassembly time, for deuterium plasmas that are cylindrical in shape. Assuming a symmetrically expanding deuterium plasma, we calculate the expected fusion neutron yield and compare with an independent calculation of the yield using the concept of a finite confinement time at a fixed plasma density. The calculated neutron yields agree quantitatively with the availablemore » experimental data. Our one-dimensional simulations indicate that one could expect a tenfold increase in total neutron yield by magnetically confining a 10 - keV deuterium fusion plasma for 10 ns.« less

Disassembly time of deuterium-cluster-fusion plasma irradiated by an intense laser pulse

DOE PAGES

Bang, W.

2015-07-02

Energetic deuterium ions from large deuterium clusters (>10 nm diameter) irradiated by an intense laser pulse (>10¹⁶ W/cm²) produce DD fusion neutrons for a time interval determined by the geometry of the resulting fusion plasma. We show an analytical solution of this time interval, the plasma disassembly time, for deuterium plasmas that are cylindrical in shape. Assuming a symmetrically expanding deuterium plasma, we calculate the expected fusion neutron yield and compare with an independent calculation of the yield using the concept of a finite confinement time at a fixed plasma density. The calculated neutron yields agree quantitatively with the availablemore » experimental data. Our one-dimensional simulations indicate that one could expect a tenfold increase in total neutron yield by magnetically confining a 10 - keV deuterium fusion plasma for 10 ns.« less

3D streamers simulation in a pin to plane configuration using massively parallel computing

NASA Astrophysics Data System (ADS)

Plewa, J.-M.; Eichwald, O.; Ducasse, O.; Dessante, P.; Jacobs, C.; Renon, N.; Yousfi, M.

2018-03-01

This paper concerns the 3D simulation of corona discharge using high performance computing (HPC) managed with the message passing interface (MPI) library. In the field of finite volume methods applied on non-adaptive mesh grids and in the case of a specific 3D dynamic benchmark test devoted to streamer studies, the great efficiency of the iterative R&B SOR and BiCGSTAB methods versus the direct MUMPS method was clearly demonstrated in solving the Poisson equation using HPC resources. The optimization of the parallelization and the resulting scalability was undertaken as a function of the HPC architecture for a number of mesh cells ranging from 8 to 512 million and a number of cores ranging from 20 to 1600. The R&B SOR method remains at least about four times faster than the BiCGSTAB method and requires significantly less memory for all tested situations. The R&B SOR method was then implemented in a 3D MPI parallelized code that solves the classical first order model of an atmospheric pressure corona discharge in air. The 3D code capabilities were tested by following the development of one, two and four coplanar streamers generated by initial plasma spots for 6 ns. The preliminary results obtained allowed us to follow in detail the formation of the tree structure of a corona discharge and the effects of the mutual interactions between the streamers in terms of streamer velocity, trajectory and diameter. The computing time for 64 million of mesh cells distributed over 1000 cores using the MPI procedures is about 30 min ns-1, regardless of the number of streamers.

Inactivation of Ricin Toxin by Nanosecond Pulsed Electric Fields Including Evidences from Cell and Animal Toxicity.

PubMed

Wei, Kai; Li, Wei; Gao, Shan; Ji, Bin; Zang, Yating; Su, Bo; Wang, Kaile; Yao, Maosheng; Zhang, Jue; Wang, Jinglin

2016-01-05

Ricin is one of the most toxic and easily produced plant protein toxin extracted from the castor oil plant, and it has been classified as a chemical warfare agent. Here, nanosecond pulsed electric fields (nsPEFs) at 30 kV/cm (pulse durations: 10 ns, 100 ns, and 300 ns) were applied to inactivating ricin up to 4.2 μg/mL. To investigate the efficacy, cells and mice were tested against the ricin treated by the nsPEFs via direct intraperitoneal injection and inhalation exposure. Results showed that nsPEFs treatments can effectively reduce the toxicity of the ricin. Without the nsPEFs treatment, 100% of mice were killed upon the 4 μg ricin injection on the first day, however 40% of the mice survived the ricin treated by the nsPEFs. Compared to injection, inhalation exposure even with higher ricin dose required longer time to observe mice fatality. Pathological observations revealed damages to heart, lung, kidney, and stomach after the ricin exposure, more pronounced for lung and kidney including severe bleeding. Sodium dodecyl sulfate polyacrylamide gel electrophoresis(SDS-PAGE) and circular dichroism (CD) analyses revealed that although the primary structure of ricin was not altered, its secondary structures (beta-sheet and beta-turn) underwent transition upon the nsPEFs treatment.

Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water.

PubMed

Daidone, Isabella; Amadei, Andrea; Di Nola, Alfredo

2005-05-15

The folding of the amyloidogenic H1 peptide MKHMAGAAAAGAVV taken from the syrian hamster prion protein is explored in explicit aqueous solution at 300 K using long time scale all-atom molecular dynamics simulations for a total simulation time of 1.1 mus. The system, initially modeled as an alpha-helix, preferentially adopts a beta-hairpin structure and several unfolding/refolding events are observed, yielding a very short average beta-hairpin folding time of approximately 200 ns. The long time scale accessed by our simulations and the reversibility of the folding allow to properly explore the configurational space of the peptide in solution. The free energy profile, as a function of the principal components (essential eigenvectors) of motion, describing the main conformational transitions, shows the characteristic features of a funneled landscape, with a downhill surface toward the beta-hairpin folded basin. However, the analysis of the peptide thermodynamic stability, reveals that the beta-hairpin in solution is rather unstable. These results are in good agreement with several experimental evidences, according to which the isolated H1 peptide adopts very rapidly in water beta-sheet structure, leading to amyloid fibril precipitates [Nguyen et al., Biochemistry 1995;34:4186-4192; Inouye et al., J Struct Biol 1998;122:247-255]. Moreover, in this article we also characterize the diffusion behavior in conformational space, investigating its relations with folding/unfolding conditions. Copyright 2005 Wiley-Liss, Inc.

A novel low-jitter plasma-jet triggered gas switch operated at a low working coefficient.

PubMed

Tie, Weihao; Liu, Shanhong; Liu, Xuandong; Zhang, Qiaogen; Pang, Lei; Liu, Longchen

2014-02-01

In this paper, we described the fabrication and testing of a novel plasma-jet triggered gas switch (PJTGS) operated at extremely low working coefficients with excellent triggered jitters. While the structure of the PJTGS is similar to that of a traditional three-electrode field-distortion gas switch, to improve its triggered performance we used a conical micro-plasma-gun with a needle-to-plate spark gap embedded in the trigger electrode. Applying a nanosecond pulse to the trigger electrode caused a spark discharge in the micro-plasma-gun. The electric field drove the discharge plasma to spray into the spark gap of the gas switch, causing fast breakdown. We tested the PJTGS with charging voltages of ±25 kV and a trigger voltage of +80 kV (5 ns rise time and 80 ns full width at half maximum) in two working modes. The PJTGS operated in Mode II had a lower triggered jitter and could be operated over a wider range of working coefficients than in Mode I under the same conditions. At working coefficients higher than 70%, we obtained sub-ns triggered jitters (<0.89 ns) from the PJTGS, at working coefficients lower than 50%, we obtained triggered jitters of 1.6-3.5 ns without no-fires or pre-fires. Even at a working coefficient of 27.4%, the PJTGS could still be triggered reliably with a delay time of 96.1 ns and a triggered jitter of 3.5 ns, respectively.

Development of Electrothermal Pulsed Plasma Thrusters for Osaka-Institute-of-Technology Electric-Rocket-Engine onboard Small Space Ship

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

Ishii, Yushuke; Yamamoto, Tsuyoshi; Yamada, Minetsugu

2008-12-31

The Project of Osaka-Institute-of-Technology Electric-Rocket-Engine onboard Small Space Ship (PROITERES) was started at Osaka Institute of Technology. In PROITERES, a 10-kg small satellite with electrothermal pulsed plasma thrusters (PPTs), named JOSHO, will be launched in 2010. The main mission is powered flight of small satellite by electric thruster itself. Electrothermal PPTs were studied with both experiments and numerical simulations. An electrothermal PPT with a side-fed propellant feeding mechanism achieved a total impulse of 3.6 Ns with a repetitive 10000-shot operation. An unsteady numerical simulation showed the existence of considerable amount of ablation delaying to the discharge. However, it was alsomore » shown that this phenomenon should not be regarded as the 'late time ablation' for electrothermal PPTs.« less

Phagocytosis: studies by optical tweezers and time-resolved microspectrofluorometry

NASA Astrophysics Data System (ADS)

Schneckenburger, Herbert; Sailer, Reinhard; Hendinger, Anita; Gschwend, Michael H.; Bauer, Manfred; Strauss, Wolfgang S. L.

1999-01-01

Cellular uptake of transparent Latex particles by J774A.1 mouse macrophages has been studied: First, single beads were kept within an optical light trap and located in close vicinity to individual cells. Uptake of the beads was visualized, and intrinsic fluorescence was detected in the spectral range of 420 - 530 nm. Second, time-gated fluorescence spectra of single cells were recorded at pre- selected times during one hour after cellular uptake. A rapid increase of autofluorescence and a subsequent decrease to the level of control cells within about 10 min. was measured within a time gate of 0 - 5 ns after the exciting laser pulses, and attributed to the 'free' coenzyme NAD(P)H. In contrast, fluorescence increase of NAD(P)H bound to proteins (measured within time gates of 5 - 10 ns or 10 - 15 ns) was less pronounced, and the subsequent decrease occurred within a longer period (about one hour).

Interfacial Microstructure Evolution due to Strain Path Changes in Sliding Contacts.

PubMed

Eder, Stefan J; Cihak-Bayr, Ulrike; Gachot, Carsten; Rodriguez Ripoll, Manel

2018-06-22

We performed large-scale molecular dynamics (MD) simulations to study the transient softening stage that has been observed experimentally in sliding interfaces subject to strain path changes. The occurrence of this effect can be of crucial importance for the energy efficiency and wear resistance of systems that experience changes in sliding direction, such as bearings or gears in wind parks, piston rings in combustion engines, or wheel--rail contacts for portal cranes. We therefore modeled the sliding of a rough counterbody against two polycrystalline substrates of fcc copper and bcc iron with initial near-surface grain sizes of 40 nm. The microstructural development of these substrates was monitored and quantified as a function of time, depth, and applied pressure during unidirectional sliding for 7 ns. The results were then compared to the case of sliding in one direction for 5 ns and reversing the sliding direction for an additional 2 ns. We observed the generation of partial dislocations, grain refinement and rotation, as well as twinning (for fcc) in the near-surface region. All microstructures were increasingly affected by these processes when maintaining the sliding direction, but recovered to a great extent upon sliding reversal up to applied pressures of 0.4 GPa in the case of fcc Cu and 1.5 GPa for bcc Fe. We discuss the applicability and limits of our polycrystalline MD model for reproducing well-known bulk phenomena such as the Bauschinger effect in interfacial processes.

Prediction of Protein-Peptide Interactions: Application of the XPairIT to Anthrax Lethal Factor and Substrates

DTIC Science & Technology

2013-09-01

hydrogen bonds in Tyrosine-containing peptides. Dalkas et al[7] used docking and molecular dynamics simulations to study a variety of MAPKK-based... simulated using NAMD molecular dynamics and the CHARMM[20] forcefield at 300K and employing the Generalized Born Implicit Solvent (GBIS[21]) with the...which were reported in Section 2. Specifically, after a ~10ns molecular dynamics simulation in TIP3 explicit water, significant motion of domains III

NovaSil clay does not affect the concentrations of vitamins A and E and nutrient minerals in serum samples from Ghanaians at high risk for aflatoxicosis.

PubMed

Afriyie-Gyawu, E; Wang, Z; Ankrah, N-A; Xu, L; Johnson, N M; Tang, L; Guan, H; Huebner, H J; Jolly, P E; Ellis, W O; Taylor, R; Brattin, B; Ofori-Adjei, D; Williams, J H; Wang, J-S; Phillips, T D

2008-07-01

To assess the potential interference of NovaSil (NS) clay with micronutrients in humans, vitamins A and E and minerals (15 nutrient and 15 non-nutrient minerals) were measured in serum samples from a 3-month intervention trial with NS. Participants (n = 177) were randomly divided into three groups that received 3.0 g NS day(-1) (high dose, HD), 1.5 g NS day(-1) (low dose, LD), or placebo (PL). Levels of vitamins A and E in serum were comparable among the three study groups at baseline, 1 month and 3 months of NS intervention. Gender-stratified non-parametric mixed-effect model analysis showed no significant effects of dose and dose-time interaction for levels of vitamins A and E. A significant time effect was detected; however, it was limited to an increase in vitamin E in the male participants over the course of the study. No significant differences were found in levels of the nutrient and non-nutrient minerals between the HD and PL groups at baseline and 3 months of NS intervention, except for strontium levels. Strontium was significantly increased (p < 0.001) in the HD group (male = 113.65 +/- 28.00 microg l(-1); female = 116.40 +/- 24.26 microg l(-1)) compared with the PL group (male = 83.55 +/- 39.90 microg l(-1); female = 90.47 +/- 25.68 microg l(-1)) following the 3-month intervention with NS. These results, combined with safety and efficacy data, confirm that NS clay is highly effective in reducing aflatoxin exposure and acts as a selective enterosorbent that does not affect the serum concentrations of important vitamins and nutrient minerals in humans.

Noise sensitivity, rather than noise level, predicts the non-auditory effects of noise in community samples: a population-based survey.

PubMed

Park, Jangho; Chung, Seockhoon; Lee, Jiho; Sung, Joo Hyun; Cho, Seung Woo; Sim, Chang Sun

2017-04-12

Excessive noise affects human health and interferes with daily activities. Although environmental noise may not directly cause mental illness, it may accelerate and intensify the development of latent mental disorders. Noise sensitivity (NS) is considered a moderator of non-auditory noise effects. In the present study, we aimed to assess whether NS is associated with non-auditory effects. We recruited a community sample of 1836 residents residing in Ulsan and Seoul, South Korea. From July to November 2015, participants were interviewed regarding their demographic characteristics, socioeconomic status, medical history, and NS. The non-auditory effects of noise were assessed using the Center of Epidemiologic Studies Depression, Insomnia Severity index, State Trait Anxiety Inventory state subscale, and Stress Response Inventory-Modified Form. Individual noise levels were recorded from noise maps. A three-model multivariate logistic regression analysis was performed to identify factors that might affect psychiatric illnesses. Participants ranged in age from 19 to 91 years (mean: 47.0 ± 16.1 years), and 37.9% (n = 696) were male. Participants with high NS were more likely to have been diagnosed with diabetes and hyperlipidemia and to use psychiatric medication. The multivariable analysis indicated that even after adjusting for noise-related variables, sociodemographic factors, medical illness, and duration of residence, subjects in the high NS group were more than 2 times more likely to experience depression and insomnia and 1.9 times more likely to have anxiety, compared with those in the low NS group. Noise exposure level was not identified as an explanatory value. NS increases the susceptibility and hence moderates there actions of individuals to noise. NS, rather than noise itself, is associated with an elevated susceptibility to non-auditory effects.

Rationalization of reduced penetration of drugs through ceramide gel phase membrane.

PubMed

Paloncýová, Markéta; DeVane, Russell H; Murch, Bruce P; Berka, Karel; Otyepka, Michal

2014-11-25

Since computing resources have advanced enough to allow routine molecular simulation studies of drug molecules interacting with biologically relevant membranes, a considerable amount of work has been carried out with fluid phospholipid systems. However, there is very little work in the literature on drug interactions with gel phase lipids. This poses a significant limitation for understanding permeation through the stratum corneum where the primary pathway is expected to be through a highly ordered lipid matrix. To address this point, we analyzed the interactions of p-aminobenzoic acid (PABA) and its ethyl (benzocaine) and butyl (butamben) esters with two membrane bilayers, which differ in their fluidity at ambient conditions. We considered a dioleoylphosphatidylcholine (DOPC) bilayer in a fluid state and a ceramide 2 (CER2, ceramide NS) bilayer in a gel phase. We carried out unbiased (100 ns long) and biased z-constraint molecular dynamics simulations and calculated the free energy profiles of all molecules along the bilayer normal. The free energy profiles converged significantly slower for the gel phase. While the compounds have comparable affinities for both membranes, they exhibit penetration barriers almost 3 times higher in the gel phase CER2 bilayer. This elevated barrier and slower diffusion in the CER2 bilayer, which are caused by the high ordering of CER2 lipid chains, explain the low permeability of the gel phase membranes. We also compared the free energy profiles from MD simulations with those obtained from COSMOmic. This method provided the same trends in behavior for the guest molecules in both bilayers; however, the penetration barriers calculated by COSMOmic did not differ between membranes. In conclusion, we show how membrane fluid properties affect the interaction of drug-like molecules with membranes.

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

PubMed

Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

2010-05-11

A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

Molecular Dynamics based on a Generalized Born solvation model: application to protein folding

NASA Astrophysics Data System (ADS)

Onufriev, Alexey

2004-03-01

An accurate description of the aqueous environment is essential for realistic biomolecular simulations, but may become very expensive computationally. We have developed a version of the Generalized Born model suitable for describing large conformational changes in macromolecules. The model represents the solvent implicitly as continuum with the dielectric properties of water, and include charge screening effects of salt. The computational cost associated with the use of this model in Molecular Dynamics simulations is generally considerably smaller than the cost of representing water explicitly. Also, compared to traditional Molecular Dynamics simulations based on explicit water representation, conformational changes occur much faster in implicit solvation environment due to the absence of viscosity. The combined speed-up allow one to probe conformational changes that occur on much longer effective time-scales. We apply the model to folding of a 46-residue three helix bundle protein (residues 10-55 of protein A, PDB ID 1BDD). Starting from an unfolded structure at 450 K, the protein folds to the lowest energy state in 6 ns of simulation time, which takes about a day on a 16 processor SGI machine. The predicted structure differs from the native one by 2.4 A (backbone RMSD). Analysis of the structures seen on the folding pathway reveals details of the folding process unavailable form experiment.

The impact of CFD on development test facilities - A National Research Council projection. [computational fluid dynamics

NASA Technical Reports Server (NTRS)

Korkegi, R. H.

1983-01-01

The results of a National Research Council study on the effect that advances in computational fluid dynamics (CFD) will have on conventional aeronautical ground testing are reported. Current CFD capabilities include the depiction of linearized inviscid flows and a boundary layer, initial use of Euler coordinates using supercomputers to automatically generate a grid, research and development on Reynolds-averaged Navier-Stokes (N-S) equations, and preliminary research on solutions to the full N-S equations. Improvements in the range of CFD usage is dependent on the development of more powerful supercomputers, exceeding even the projected abilities of the NASA Numerical Aerodynamic Simulator (1 BFLOP/sec). Full representation of the Re-averaged N-S equations will require over one million grid points, a computing level predicted to be available in 15 yr. Present capabilities allow identification of data anomalies, confirmation of data accuracy, and adequateness of model design in wind tunnel trials. Account can be taken of the wall effects and the Re in any flight regime during simulation. CFD can actually be more accurate than instrumented tests, since all points in a flow can be modeled with CFD, while they cannot all be monitored with instrumentation in a wind tunnel.

Urinary and sexual outcomes in long-term (5+ years) prostate cancer disease free survivors after radical prostatectomy

PubMed Central

2009-01-01

Background After long term disease free follow up (FUp) patients reconsider quality of life (QOL) outcomes. Aim of this study is assess QoL in prostate cancer patients who are disease-free at least 5 years after radical prostatectomy (RP). Methods 367 patients treated with RP for clinically localized pCa, without biochemical failure (PSA ≤ 0.2 ng/mL) at the follow up ≥ 5 years were recruited. Urinary (UF) and Sexual Function (SF), Urinary (UB) and Sexual Bother (SB) were assessed by using UCLA-PCI questionnaire. UF, UB, SF and SB were analyzed according to: treatment timing (age at time of RP, FUp duration, age at time of FUp), tumor characteristics (preoperative PSA, TNM stage, pathological Gleason score), nerve sparing (NS) procedure, and hormonal treatment (HT). We calculated the differences between 93 NS-RP without HT (group A) and 274 non-NS-RP or NS-RP with HT (group B). We evaluated the correlation between function and bother in group A according to follow-up duration. Results Time since prostatectomy had a negative effect on SF and a positive effect SB (both p < 0.001). Elderly men at follow up experienced worse UF and SF (p = 0.02 and p < 0.001) and better SB (p < 0.001). Higher stage PCa negatively affected UB, SF, and SB (all: p ≤ 0.05). NS was associated with better UB, SF and SB (all: p ≤ 0.05); conversely, HT was associated with worse UF, SF and SB (all: p ≤ 0.05). More than 8 years after prostatectomy SF of group A and B were similar. Group A subjects (NS-RP without HT) demonstrated worsening SF, but improved SB, suggesting dissociation of the correlation between SF and SB over time. Conclusion Older age at follow up and higher pathological stage were associated with worse QoL outcomes after RP. The direct correlation between UF and age at follow up, with no correlation between UF and age at time of RP suggests that other issues (i.e: vascular or neurogenic disorders), subsequent to RP, are determinant on urinary incontinence. After NS-RP without HT the correlation between SF and SB is maintained for 7 years, after which function and bother appear to have divergent trajectories. PMID:19912640

Metastable liquid lamellar structures in binary and ternary mixtures of Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Díaz-Herrera, Enrique; Ramírez-Santiago, Guillermo; Moreno Razo, José A.

2004-03-01

We have carried out extensive equilibrium MD simulations to investigate the Liquid-Vapor coexistence in partially miscible binary and ternary mixtures LJ fluids. We have studied in detail the time evolution of the density profiles and the interfacial properties in a temperature region of the phase diagram where the condensed phase is demixed. The composition of the mixtures are fixed, 50% for the binary mixture and 33.33% for the ternary mixture. The results of the simulations clearly indicate that in the range of temperatures 78 < T < 102 ^oK,--in the scale of argon-- the system evolves towards a metastable alternated liquid-liquid lamellar state in coexistence with its vapor phase. These states can be achieved if the initial configuration is fully disordered, that is, when the particles of the fluids are randomly placed on the sites of an FCC crystal or the system is completely mixed. As temperature decreases these states become very well defined and more stable in time. We find that below 90 ^oK, the alternated liquid-liquid lamellar state remains alive for 80 ns, in the scale of argon, the longest simulation we have carried out. Nonetheless, we believe that in this temperature region these states will be alive for even much longer times.

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

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

None, None

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

DOE PAGES

None, None

2016-03-22

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Molecular dynamics simulations of lysozyme-lipid systems: probing the early steps of protein aggregation.

PubMed

Trusova, Valeriya M; Gorbenko, Galyna P

2017-07-10

Using the molecular dynamics simulation, the role of lipids in the lysozyme transition into the aggregation-competent conformation has been clarified. Analysis of the changes of lysozyme secondary structure upon its interactions with the model bilayer membranes composed of phosphatidylcholine and its mixtures with phosphatidylglycerol (10, 40, and 80 mol%) within the time interval of 100 ns showed that lipid-bound protein is characterized by the increased content of β-structures. Along with this, the formation of protein-lipid complexes was accompanied by the increase in the gyration radius and the decrease in RMSD of polypeptide chain. The results obtained were interpreted in terms of the partial unfolding of lysozyme molecule on the lipid matrix, with the magnitude of this effect being increased with increasing the fraction of anionic lipids. Based on the results of molecular dynamics simulation, a hypothetical model of the nucleation of lysozyme amyloid fibrils in a membrane environment was suggested.

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer

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

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas

2009-01-01

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors,more » other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million atom biological systems scale well up to 30k cores, producing 30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.« less

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

PubMed

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas; Smith, Jeremy C

2009-10-13

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors, other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million-atom biological systems scale well up to ∼30k cores, producing ∼30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.

Radionuclide transport from soil to air, native vegetation, kangaroo rats and grazing cattle on the Nevada test site.

PubMed

Gilbert, R O; Shinn, J H; Essington, E H; Tamura, T; Romney, E M; Moor, K S; O'Farrell, T P

1988-12-01

Between 1970 and 1986 the Nevada Applied Ecology Group (NAEG), U.S. Department of Energy, conducted environmental radionuclide studies at weapons-testing sites on or adjacent to the Nevada Test Site. In this paper, NAEG studies conducted at two nuclear (fission) sites (NS201, NS219) and two nonnuclear (nonfission) sites (Area 13 [Project 57] and Clean Slate 2) are reviewed, synthesized and compared regarding (1) soil particle-size distribution and physical-chemical characteristics of 239 + 240Pu-bearing radioactive particles, (2) 239 + 240Pu resuspension rates and (3) transuranic and fission-product radionuclide transfers from soil to native vegetation, kangaroo rats and grazing cattle. The data indicate that transuranic radionuclides were transferred more readily on the average from soil to air, the external surfaces of native vegetation and to tissues of kangaroo rats at Area 13 than at NS201 or NS219. The 239 + 240Pu resuspension factor for undisturbed soil at Area 13 was three to four orders-of-magnitude larger than at NS201 and NS219, the geometric mean (GM) vegetation-over-soil 239 + 240Pu concentration ratio was from ten to 100 times larger than at NS201, and the GM GI-over-soil, carcass-over-soil and pelt-over-soil 239 + 240Pu ratios for kangaroo rats were about ten times larger than at NS201. These results are consistent with the finding that Area 13, compared with NS201 or NS219, has a higher percentage of radioactivity associated with smaller soil particles and a larger percentage of resuspendable and respirable soil. However, the resuspension factor increased by a factor of 27 at NS201 when the surface soil was disturbed, and by a factor of 12 at NS219 following a wildfire. The average (GM) concentration of 239 + 240Pu for the GI (and contents) of Area 13 kangaroo rats and for the rumen contents of beef cattle that grazed Area 13 were very similar (400 vs. 440 Bq kg-1 dry wt, respectively) although the variability between individuals was very large. The GM carcass-over-GI 239 + 240Pu concentration ratio for kangaroo rats at Area 13, Clean Slate 2, and NS201 were similar in value (approximately 2 X 10(-2)), as were the GM GI-over-vegetation concentration ratios (approximately 2 X 10(0)) (no statistical differences).(ABSTRACT TRUNCATED AT 400 WORDS)

A molecular dynamics simulation study of chloroform

NASA Astrophysics Data System (ADS)

Tironi, Ilario G.; van Gunsteren, Wilfred F.

Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

Analysis of direct-drive capsule compression experiments on the Iskra-5 laser facility

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

Gus'kov, S. Yu.; Demchenko, N. N.; Zhidkov, N. V.

2010-09-15

We have analyzed and numerically simulated our experiments on the compression of DT-gas-filled glass capsules under irradiation by a small number of beams on the Iskra-5 facility (12 beams) at the second harmonic of an iodine laser ({lambda} = 0.66 {mu}m) for a laser pulse energy of 2 kJ and duration of 0.5 ns in the case of asymmetric irradiation and compression. Our simulations include the construction of a target illumination map and a histogram of the target surface illumination distribution; 1D capsule compression simulations based on the DIANA code corresponding to various target surface regions; and 2D compression simulationsmore » based on the NUTCY code corresponding to the illumination conditions. We have succeeded in reproducing the shape of the compressed region at the time of maximum compression and the reduction in neutron yield (compared to the 1D simulations) to the experimentally observed values. For the Iskra-5 conditions, we have considered targets that can provide a more symmetric compression and a higher neutron yield.« less

Backbone conformations and side chain flexibility of two somatostatin mimics investigated by molecular dynamics simulations.

PubMed

Interlandi, Gianluca

2009-05-15

Molecular dynamics simulations with two designed somatostatin mimics, SOM230 and SMS 201-995, were performed in explicit water for a total aggregated time of 208 ns. Analysis of the runs with SOM230 revealed the presence of two clusters of conformations. Strikingly, the two sampled conformers correspond to the two main X-ray structures in the asymmetric unit of SMS 201-995. Structural comparison between the residues of SOM230 and SMS 201-995 provides an explanation for the high binding affinity of SOM230 to four of five somatostatin receptors. Similarly, cluster analysis of the simulations with SMS 201-995 shows that the backbone of the peptide interconverts between its two main crystallographic conformers. The conformations of SMS 201-995 sampled in the two clusters violated two different sets of NOE distance constraints in agreement with a previous NMR study. Differences in side chain fluctuations between SOM230 and SMS 201-995 observed in the simulations may contribute to the relatively higher binding affinity of SOM230 to most somatostatin receptors.

Sub-nanosecond time-resolved ambient-pressure X-ray photoelectron spectroscopy setup for pulsed and constant wave X-ray light sources

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

Shavorskiy, Andrey; Slaughter, Daniel S.; Zegkinoglou, Ioannis

2014-09-15

An apparatus for sub-nanosecond time-resolved ambient-pressure X-ray photoelectron spectroscopy studies with pulsed and constant wave X-ray light sources is presented. A differentially pumped hemispherical electron analyzer is equipped with a delay-line detector that simultaneously records the position and arrival time of every single electron at the exit aperture of the hemisphere with ∼0.1 mm spatial resolution and ∼150 ps temporal accuracy. The kinetic energies of the photoelectrons are encoded in the hit positions along the dispersive axis of the two-dimensional detector. Pump-probe time-delays are provided by the electron arrival times relative to the pump pulse timing. An average time-resolution ofmore » (780 ± 20) ps (FWHM) is demonstrated for a hemisphere pass energy E{sub p} = 150 eV and an electron kinetic energy range KE = 503–508 eV. The time-resolution of the setup is limited by the electron time-of-flight (TOF) spread related to the electron trajectory distribution within the analyzer hemisphere and within the electrostatic lens system that images the interaction volume onto the hemisphere entrance slit. The TOF spread for electrons with KE = 430 eV varies between ∼9 ns at a pass energy of 50 eV and ∼1 ns at pass energies between 200 eV and 400 eV. The correlation between the retarding ratio and the TOF spread is evaluated by means of both analytical descriptions of the electron trajectories within the analyzer hemisphere and computer simulations of the entire trajectories including the electrostatic lens system. In agreement with previous studies, we find that the by far dominant contribution to the TOF spread is acquired within the hemisphere. However, both experiment and computer simulations show that the lens system indirectly affects the time resolution of the setup to a significant extent by inducing a strong dependence of the angular spread of electron trajectories entering the hemisphere on the retarding ratio. The scaling of the angular spread with the retarding ratio can be well approximated by applying Liouville's theorem of constant emittance to the electron trajectories inside the lens system. The performance of the setup is demonstrated by characterizing the laser fluence-dependent transient surface photovoltage response of a laser-excited Si(100) sample.« less

Transmembrane Domains of NS2B Contribute to both Viral RNA Replication and Particle Formation in Japanese Encephalitis Virus.

PubMed

Li, Xiao-Dan; Deng, Cheng-Lin; Ye, Han-Qing; Zhang, Hong-Lei; Zhang, Qiu-Yan; Chen, Dong-Dong; Zhang, Pan-Tao; Shi, Pei-Yong; Yuan, Zhi-Ming; Zhang, Bo

2016-06-15

Flavivirus nonstructural protein 2B (NS2B) is a transmembrane protein that functions as a cofactor for viral NS3 protease. The cytoplasmic region (amino acids 51 to 95) alone of NS2B is sufficient for NS3 protease activity, whereas the role of transmembrane domains (TMDs) remains obscure. Here, we demonstrate for the first time that flavivirus NS2B plays a critical role in virion assembly. Using Japanese encephalitis virus (JEV) as a model, we performed a systematic mutagenesis at the flavivirus conserved residues within the TMDs of NS2B. As expected, some mutations severely attenuated (L38A and R101A) or completely destroyed (G12L) viral RNA synthesis. Interestingly, two mutations (G37L and P112A) reduced viral RNA synthesis and blocked virion assembly. None of the mutations affected NS2B-NS3 protease activity. Because mutations G37L and P112A affected virion assembly, we selected revertant viruses for these two mutants. For mutant G37L, replacement with G37F, G37H, G37T, or G37S restored virion assembly. For mutant P112A, insertion of K at position K127 (leading to K127KK) of NS2B rescued virion assembly. A biomolecular fluorescent complementation (BiFC) analysis demonstrated that (i) mutation P112A selectively weakened NS2B-NS2A interaction and (ii) the adaptive mutation K127KK restored NS2B-NS2A interaction. Collectively, our results demonstrate that, in addition to being a cofactor for NS3 protease, flavivirus NS2B also functions in viral RNA replication, as well as virion assembly. Many flaviviruses are important human pathogens. Understanding the molecular mechanisms of the viral infection cycle is essential for vaccine and antiviral development. In this study, we demonstrate that the TMDs of JEV NS2B participate in both viral RNA replication and virion assembly. A viral genetic study and a BiFC assay demonstrated that interaction between NS2B and NS2A may participate in modulating viral assembly in the flavivirus life cycle. Compensatory-mutation analysis confirmed that there was a correlation between viral assembly and NS2B-NS2A interaction. TMDs of NS2B may serve as novel antiviral targets to prevent flavivirus infection, and the structure determination of NS2B will help us to understand the functional mechanism of NS2B in viral RNA replication and assembly. The results have uncovered a new function of flavivirus NS2B in virion assembly, possibly through interaction with the NS2A protein. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Quantifying a cellular automata simulation of electric vehicles

NASA Astrophysics Data System (ADS)

Hill, Graeme; Bell, Margaret; Blythe, Phil

2014-12-01

Within this work the Nagel-Schreckenberg (NS) cellular automata is used to simulate a basic cyclic road network. Results from SwitchEV, a real world Electric Vehicle trial which has collected more than two years of detailed electric vehicle data, are used to quantify the results of the NS automata, demonstrating similar power consumption behavior to that observed in the experimental results. In particular the efficiency of the electric vehicles reduces as the vehicle density increases, due in part to the reduced efficiency of EVs at low speeds, but also due to the energy consumption inherent in changing speeds. Further work shows the results from introducing spatially restricted speed restriction. In general it can be seen that induced congestion from spatially transient events propagates back through the road network and alters the energy and efficiency profile of the simulated vehicles, both before and after the speed restriction. Vehicles upstream from the restriction show a reduced energy usage and an increased efficiency, and vehicles downstream show an initial large increase in energy usage as they accelerate away from the speed restriction.

Modeling elastic wave propagation in kidney stones with application to shock wave lithotripsy.

PubMed

Cleveland, Robin O; Sapozhnikov, Oleg A

2005-10-01

A time-domain finite-difference solution to the equations of linear elasticity was used to model the propagation of lithotripsy waves in kidney stones. The model was used to determine the loading on the stone (principal stresses and strains and maximum shear stresses and strains) due to the impact of lithotripsy shock waves. The simulations show that the peak loading induced in kidney stones is generated by constructive interference from shear waves launched from the outer edge of the stone with other waves in the stone. Notably the shear wave induced loads were significantly larger than the loads generated by the classic Hopkinson or spall effect. For simulations where the diameter of the focal spot of the lithotripter was smaller than that of the stone the loading decreased by more than 50%. The constructive interference was also sensitive to shock rise time and it was found that the peak tensile stress reduced by 30% as rise time increased from 25 to 150 ns. These results demonstrate that shear waves likely play a critical role in stone comminution and that lithotripters with large focal widths and short rise times should be effective at generating high stresses inside kidney stones.

Test beam measurement of the first prototype of the fast silicon pixel monolithic detector for the TT-PET project

NASA Astrophysics Data System (ADS)

Paolozzi, L.; Bandi, Y.; Benoit, M.; Cardarelli, R.; Débieux, S.; Forshaw, D.; Hayakawa, D.; Iacobucci, G.; Kaynak, M.; Miucci, A.; Nessi, M.; Ratib, O.; Ripiccini, E.; Rücker, H.; Valerio, P.; Weber, M.

2018-04-01

The TT-PET collaboration is developing a PET scanner for small animals with 30 ps time-of-flight resolution and sub-millimetre 3D detection granularity. The sensitive element of the scanner is a monolithic silicon pixel detector based on state-of-the-art SiGe BiCMOS technology. The first ASIC prototype for the TT-PET was produced and tested in the laboratory and with minimum ionizing particles. The electronics exhibit an equivalent noise charge below 600 e‑ RMS and a pulse rise time of less than 2 ns , in accordance with the simulations. The pixels with a capacitance of 0.8 pF were measured to have a detection efficiency greater than 99% and, although in the absence of the post-processing, a time resolution of approximately 200 ps .

Ns-scaled time-gated fluorescence lifetime imaging for forensic document examination

NASA Astrophysics Data System (ADS)

Zhong, Xin; Wang, Xinwei; Zhou, Yan

2018-01-01

A method of ns-scaled time-gated fluorescence lifetime imaging (TFLI) is proposed to distinguish different fluorescent substances in forensic document examination. Compared with Video Spectral Comparator (VSC) which can examine fluorescence intensity images only, TFLI can detect questioned documents like falsification or alteration. TFLI system can enhance weak signal by accumulation method. The two fluorescence intensity images of the interval delay time tg are acquired by ICCD and fitted into fluorescence lifetime image. The lifetimes of fluorescence substances are represented by different colors, which make it easy to detect the fluorescent substances and the sequence of handwritings. It proves that TFLI is a powerful tool for forensic document examination. Furthermore, the advantages of TFLI system are ns-scaled precision preservation and powerful capture capability.

Modelling debris and shrapnel generation in inertial confinement fusion experiments

DOE PAGES

Eder, D. C.; Fisher, A. C.; Koniges, A. E.; ...

2013-10-24

Modelling and mitigation of damage are crucial for safe and economical operation of high-power laser facilities. Experiments at the National Ignition Facility use a variety of targets with a range of laser energies spanning more than two orders of magnitude (~14 kJ to ~1.9 MJ). Low-energy inertial confinement fusion experiments are used to study early-time x-ray load symmetry on the capsule, shock timing, and other physics issues. For these experiments, a significant portion of the target is not completely vaporized and late-time (hundreds of ns) simulations are required to study the generation of debris and shrapnel from these targets. Damagemore » to optics and diagnostics from shrapnel is a major concern for low-energy experiments. Here, we provide the first full-target simulations of entire cryogenic targets, including the Al thermal mechanical package and Si cooling rings. We use a 3D multi-physics multi-material hydrodynamics code, ALE-AMR, for these late-time simulations. The mass, velocity, and spatial distribution of shrapnel are calculated for three experiments with laser energies ranging from 14 to 250 kJ. We calculate damage risk to optics and diagnostics for these three experiments. For the lowest energy re-emit experiment, we provide a detailed analysis of the effects of shrapnel impacts on optics and diagnostics and compare with observations of damage sites.« less

Status On Multi-microsecond Prepulse Technique On Sphinx Machine Going From Nested To Single Wire Array For 800 ns Implosion Time Z-pinch

NASA Astrophysics Data System (ADS)

Maury, P.; Calamy, H.; Grunenwald, J.; Lassalle, F.; Zucchini, F.; Loyen, A.; Georges, A.; Morell, A.; Bedoch, J. P.

2009-01-01

The Sphinx machine[1] is a 6 MA, 1 μS driver based on the LTD technology, used for Z-pinch experiments. Important improvements of Sphinx radiation output were recently obtained using a multi-microsecond current prepulse[2]. Total power per unit of length is multiplied by a factor of 6 and FWHM divided by a factor of 2.5. Early breakdown of the wires during the prepulse phase dramatically changes the ablation phase leading to an improvement of axial homogeneity of both the implosion and the final radiating column. As a consequence, the cathode bubble observed on classical shots is definitively removed. The implosion is then centered and zippering effect is reduced, leading to simultaneous x-ray emission of the whole length. A great reproducibility is obtained. Nested arrays were used before to mitigate the Rayleigh-Taylor instabilities during the implosion phase. Further experiments with pre-pulse technique are described here were inner array was removed. The goal of these experiments was to see if long prepulse could give stable enough implosion with single array and at the same time increase the η parameter by reducing the mass of the load. Experimental results of single wire array loads of typical dimension 5 cm in height with implosion time between 700 and 900 ns and diameter varying between 80 and 140 mm are given. Parameters of the loads were varying in term of radius and number of wires. Comparisons with nested wire array loads are done and trends are proposed. Characteristics of both the implosion and the final radiating column are shown. 2D MHD numerical simulations of single wire array become easier as there is no interaction between outer and inner array anymore. A systematic study was done using injection mass model to benchmark simulation with experiments.

Design and development of a chopping and deflecting system for the high current injector at IUAC

NASA Astrophysics Data System (ADS)

Kedia, Sanjay Kumar; Mehta, R.

2018-05-01

The Low Energy Beam Transport (LEBT) section of the High Current Injector (HCI) incorporates a Chopping cum Deflecting System (CDS). The CDS comprises of a deflecting system and a pair of slits that will remove dark current and produce time bunched beam of 60 ns at different repetition rates of 4, 2, 1, 0.5, 0.25 and 0.125 MHz. The distinguishing feature of the design is the use of a multi-plate deflecting structure with low capacitance to optimize the electric field, which in turn results in higher efficiency in terms of achievable ion current. To maximize the effective electric field and its uniformity, the gap between the deflecting plates has been varied and a semi-circular contour has been incorporated on the deflecting plates. Due to this the electric field variation is less than ±0.5% within the plate length. The length of deflecting plates was chosen to maximize the transmission efficiency. Since the velocity of the charged particles in the LEBT section is constant, therefore the separation between two successive sets of deflecting plates has been kept constant to match the ions transient time within the gap which is nearly 32 ns. A square pulse has been chosen, instead of a sinusoidal one, to increase the transmission efficiency and to decrease the tailing effect. The loaded capacitance of the structure was kept <10 pF to achieve fast rise/fall time of the applied voltage signal. A Python code has been developed to verify the various design parameters. The simulation also shows that one can get an efficient deflection of undesired particles resulting in >90% transmission efficiency with in the bunch length. Various simulation codes like Solid Works, TRACE 3D, CST MWS and homebrew Python codes were used to validate the design.

Out-of-Time Beam Extinction in the MU2E Experiment

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

Prebys, E. J.; Werkema, S.

The Mu2e Experiment at Fermilab will search for the conversion of a muon to an electron in the field of an atomic nucleus with unprecedented sensitivity. The experiment requires a beam consisting of proton bunches 250 ns FW long, separated by 1.7more » $$\\mu$$ sec, with no out-of-time protons at the $$10^{10}$$ fractional level. Satisfying this "extinction" requirement is very challenging. The formation of the bunches is expected to result in an extinction on the order of $10^5$. The remaining extinction will be accomplished by a system of resonant magnets and collimators, configured such that only in-time beam is delivered to the experiment. Our simulations show that the total extinction achievable by the system is on the order of $$10^{12}$$, with an efficiency for transmitting in-time beam of 99.6%.« less

Measuring neutron-star properties via gravitational waves from neutron-star mergers.

PubMed

Bauswein, A; Janka, H-T

2012-01-06

We demonstrate by a large set of merger simulations for symmetric binary neutron stars (NSs) that there is a tight correlation between the frequency peak of the postmerger gravitational-wave (GW) emission and the physical properties of the nuclear equation of state (EoS), e.g., expressed by the radius of the maximum-mass Tolman-Oppenheimer-Volkhoff configuration. Therefore, a single measurement of the peak frequency of the postmerger GW signal will constrain the NS EoS significantly. For optimistic merger-rate estimates a corresponding detection with Advanced LIGO is expected to happen within an operation time of roughly a year.

FPGA-based photon-counting phase-modulation fluorometer and a brief comparison with that operated in a pulsed-excitation mode

NASA Astrophysics Data System (ADS)

Iwata, Tetsuo; Taga, Takanori; Mizuno, Takahiko

2018-02-01

We have constructed a high-efficiency, photon-counting phase-modulation fluorometer (PC-PMF) using a field-programmable gate array, which is a modified version of the photon-counting fluorometer (PCF) that works in a pulsed-excitation mode (Iwata and Mizuno in Meas Sci Technol 28:075501, 2017). The common working principle for both is the simultaneous detection of the photoelectron pulse train, which covers 64 ns with a 1.0-ns resolution time (1.0 ns/channel). The signal-gathering efficiency was improved more than 100 times over that of conventional time-correlated single-photon-counting at the expense of resolution time depending on the number of channels. The system dead time for building a histogram was eliminated, markedly shortening the measurement time for fluorescent samples with moderately high quantum yields. We describe the PC-PMF and make a brief comparison with the pulsed-excitation PCF in precision, demonstrating the potential advantage of PC-PMF.

Real-time estimation of BDS/GPS high-rate satellite clock offsets using sequential least squares

NASA Astrophysics Data System (ADS)

Fu, Wenju; Yang, Yuanxi; Zhang, Qin; Huang, Guanwen

2018-07-01

The real-time precise satellite clock product is one of key prerequisites for real-time Precise Point Positioning (PPP). The accuracy of the 24-hour predicted satellite clock product with 15 min sampling interval and an update of 6 h provided by the International GNSS Service (IGS) is only 3 ns, which could not meet the needs of all real-time PPP applications. The real-time estimation of high-rate satellite clock offsets is an efficient method for improving the accuracy. In this paper, the sequential least squares method to estimate real-time satellite clock offsets with high sample rate is proposed to improve the computational speed by applying an optimized sparse matrix operation to compute the normal equation and using special measures to take full advantage of modern computer power. The method is first applied to BeiDou Navigation Satellite System (BDS) and provides real-time estimation with a 1 s sample rate. The results show that the amount of time taken to process a single epoch is about 0.12 s using 28 stations. The Standard Deviation (STD) and Root Mean Square (RMS) of the real-time estimated BDS satellite clock offsets are 0.17 ns and 0.44 ns respectively when compared to German Research Center for Geosciences (GFZ) final clock products. The positioning performance of the real-time estimated satellite clock offsets is evaluated. The RMSs of the real-time BDS kinematic PPP in east, north, and vertical components are 7.6 cm, 6.4 cm and 19.6 cm respectively. The method is also applied to Global Positioning System (GPS) with a 10 s sample rate and the computational time of most epochs is less than 1.5 s with 75 stations. The STD and RMS of the real-time estimated GPS satellite clocks are 0.11 ns and 0.27 ns, respectively. The accuracies of 5.6 cm, 2.6 cm and 7.9 cm in east, north, and vertical components are achieved for the real-time GPS kinematic PPP.

Inactivation of Ricin Toxin by Nanosecond Pulsed Electric Fields Including Evidences from Cell and Animal Toxicity

NASA Astrophysics Data System (ADS)

Wei, Kai; Li, Wei; Gao, Shan; Ji, Bin; Zang, Yating; Su, Bo; Wang, Kaile; Yao, Maosheng; Zhang, Jue; Wang, Jinglin

2016-01-01

Ricin is one of the most toxic and easily produced plant protein toxin extracted from the castor oil plant, and it has been classified as a chemical warfare agent. Here, nanosecond pulsed electric fields (nsPEFs) at 30 kV/cm (pulse durations: 10 ns, 100 ns, and 300 ns) were applied to inactivating ricin up to 4.2 μg/mL. To investigate the efficacy, cells and mice were tested against the ricin treated by the nsPEFs via direct intraperitoneal injection and inhalation exposure. Results showed that nsPEFs treatments can effectively reduce the toxicity of the ricin. Without the nsPEFs treatment, 100% of mice were killed upon the 4 μg ricin injection on the first day, however 40% of the mice survived the ricin treated by the nsPEFs. Compared to injection, inhalation exposure even with higher ricin dose required longer time to observe mice fatality. Pathological observations revealed damages to heart, lung, kidney, and stomach after the ricin exposure, more pronounced for lung and kidney including severe bleeding. Sodium dodecyl sulfate polyacrylamide gel electrophoresis(SDS-PAGE) and circular dichroism (CD) analyses revealed that although the primary structure of ricin was not altered, its secondary structures (beta-sheet and beta-turn) underwent transition upon the nsPEFs treatment.

Inactivation of Ricin Toxin by Nanosecond Pulsed Electric Fields Including Evidences from Cell and Animal Toxicity

PubMed Central

Wei, Kai; Li, Wei; Gao, Shan; Ji, Bin; Zang, Yating; Su, Bo; Wang, Kaile; Yao, Maosheng; Zhang, Jue; Wang, Jinglin

2016-01-01

Ricin is one of the most toxic and easily produced plant protein toxin extracted from the castor oil plant, and it has been classified as a chemical warfare agent. Here, nanosecond pulsed electric fields (nsPEFs) at 30 kV/cm (pulse durations: 10 ns, 100 ns, and 300 ns) were applied to inactivating ricin up to 4.2 μg/mL. To investigate the efficacy, cells and mice were tested against the ricin treated by the nsPEFs via direct intraperitoneal injection and inhalation exposure. Results showed that nsPEFs treatments can effectively reduce the toxicity of the ricin. Without the nsPEFs treatment, 100% of mice were killed upon the 4 μg ricin injection on the first day, however 40% of the mice survived the ricin treated by the nsPEFs. Compared to injection, inhalation exposure even with higher ricin dose required longer time to observe mice fatality. Pathological observations revealed damages to heart, lung, kidney, and stomach after the ricin exposure, more pronounced for lung and kidney including severe bleeding. Sodium dodecyl sulfate polyacrylamide gel electrophoresis(SDS-PAGE) and circular dichroism (CD) analyses revealed that although the primary structure of ricin was not altered, its secondary structures (beta-sheet and beta-turn) underwent transition upon the nsPEFs treatment. PMID:26728251

Changes of ns-soot mixing states and shapes in an urban area during CalNex

NASA Astrophysics Data System (ADS)

Adachi, Kouji; Buseck, Peter R.

2013-05-01

Aerosol particles from megacities influence the regional and global climate as well as the health of their occupants. We used transmission electron microscopes (TEMs) to study aerosol particles collected from the Los Angeles area during the 2010 CalNex campaign. We detected major amounts of ns-soot, defined as consisting of carbon nanospheres, sulfate, sea salt, and organic aerosol (OA) and lesser amounts of brochosome particles from leaf hoppers. Ns-soot-particle shapes, mixing states, and abundances varied significantly with sampling times and days. Within plumes having high CO2 concentrations, much ns-soot was compacted and contained a relatively large number of carbon nanospheres. Ns-soot particles from both CalNex samples and Mexico City, the latter collected in 2006, had a wide range of shapes when mixed with other aerosol particles, but neither sets showed spherical ns-soot nor the core-shell configuration that is commonly used in optical calculations. Our TEM observations and light-absorption calculations of modeled particles indicate that, in contrast to ns-soot particles that are embedded within other materials or have the hypothesized core-shell configurations, those attached to other aerosol particles hardly enhance their light absorption. We conclude that the ways in which ns-soot mixes with other particles explain the observations of smaller light amplification by ns-soot coatings than model calculations during the CalNex campaign and presumably in other areas.

Exploration of structural stability in deleterious nsSNPs of the XPA gene: A molecular dynamics approach

PubMed Central

NagaSundaram, N; Priya Doss, C George

2011-01-01

Background: Distinguishing the deleterious from the massive number of non-functional nsSNPs that occur within a single genome is a considerable challenge in mutation research. In this approach, we have used the existing in silico methods to explore the mutation-structure-function relationship in the XPAgene. Materials and Methods: We used the Sorting Intolerant From Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen), I-Mutant 2.0, and the Protein Analysis THrough Evolutionary Relationships methods to predict the effects of deleterious nsSNPs on protein function and evaluated the impact of mutation on protein stability by Molecular Dynamics simulations. Results: By comparing the scores of all the four in silico methods, nsSNP with an ID rs104894131 at position C108F was predicted to be highly deleterious. We extended our Molecular dynamics approach to gain insight into the impact of this non-synonymous polymorphism on structural changes that may affect the activity of the XPAgene. Conclusion: Based on the in silico methods score, potential energy, root-mean-square deviation, and root-mean-square fluctuation, we predict that deleterious nsSNP at position C108F would play a significant role in causing disease by the XPA gene. Our approach would present the application of in silicotools in understanding the functional variation from the perspective of structure, evolution, and phenotype. PMID:22190868

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

PubMed

Caulfield, Thomas R; Devkota, Batsal; Rollins, Geoffrey C

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

Simulation and comparison of progression-free survival among patients with non-squamous non-small-cell lung cancer receiving sequential therapy.

PubMed

Walzer, Stefan; Chouaid, Christos; Lister, Johanna; Gultyaev, Dmitry; Vergnenegre, Alain; de Marinis, Filippo; Meng, Jie; de Castro Carpeno, Javier; Crott, Ralph; Kleman, Martin; Ngoh, Charles

2015-01-01

In recent years, the treatment landscape in advanced non-squamous non-small-cell lung cancer (nsNSCLC) has changed. New therapies (e.g., bevacizumab indicated in first line) have become available and other therapies (e.g., pemetrexed in first line and second line) moved into earlier lines in the treatment paradigm. While there has been an expansion of the available treatment options, it is still a key research question which therapy sequence results in the best survival outcomes for patients with nsNSCLC. A therapy-sequencing disease model that approximates treatment outcomes in up to five lines of treatment was developed for patients with nsNSCLC. The primary source of data for progression-free survival (PFS) and time to death was published pivotal trial data. All patients were treatment-naïve and in the PFS state, received first-line treatment with either bevacizumab-based therapy or doublet chemotherapy (including the option of pemetrexed + cisplatin). Patients would then progress to a subsequent line of therapy, remain in PFS or die. In case of progression, it was assumed that each survivor would receive a subsequent line of therapy, based on EMA licensed therapies. Weibull distribution curves were fitted to the data. All bevacizumab-based first-line therapy sequences analyzed achieved total PFS of around 15 months. Bevacizumab + carboplatin + paclitaxel (first line) → pemetrexed (second line) → erlotinib (third line) → docetaxel (fourth line) resulted in total mean PFS time of 15.7 months, for instance. Sequences with pemetrexed in combination with cisplatin in first line achieved total PFS times between 12.6 and 12.8 months with a slightly higher total PFS time achieved when assuming pemetrexed continuation therapy in maintenance after pemetrexed + cisplatin in first-line induction. Overall survival results followed the same trend as PFS. The model suggests that treatment-sequencing strategies starting with a bevacizumab-based combination in first line yield better survival outcomes than those starting with pemetrexed-based combinations, a result that is attributable to the possibility of one further line of treatment with first-line bevacizumab-based treatment sequences.

"Twinning procedure" in lung transplantation: influence of graft ischemia on survival and incidence of complications.

PubMed

D'Armini, A M; Boffini, M; Zanotti, G; Pellegrini, C; Rinaldi, M; Abbiate, N; Viganò, M

2004-04-01

The limited number of suitable lung donors is the major obstacle to clinical application of lung transplantation. The "twinning procedure" may represent one strategy to optimize the use of the small pool of available grafts. From November 1991 to May 2003, 99 single lung transplants (SLTx) were performed including 46 (46%) cases of the "twinning procedure." We divided the study population into two groups: group A (recipients of the "first" lung) and group B (recipients of the "second" lung). The ischemia time was significantly different (A: 216 +/- 48 minutes, B: 310 +/- 89 minutes, P <.001). Differences were not observed in the incidence of graft failure (A: 2, B: 0, P = NS), in the length of mechanical ventilation (A: 12.8 +/- 29.4 days, B: 7.8 +/- 15.2 days, P = NS), or ICU stay (A: 18.8 +/- 50.6 days, B: 15.2 +/- 17.1 days, P = NS), or of hospitalization (A: 37.8 +/- 56.8 days, B: 31.4 +/- 31.7 days, P = NS). Three bronchial anastomotic complications occurred in each group. The incidence of infections (A: 0.015 events/patient/month, B: 0.011 events/patient/month, P = NS) and of treated acute rejections (A: 0.011 events/patient/month, B: 0.011 events/patient/month, P = NS) was similar in the two groups. One-year survival rates were 86% +/- 7% and 72% +/- 10% in group A and B patients, respectively (P = NS). In our experience the different ischemia times related to the twinning procedure did not increase the mortality or morbidity in the early and midterm period.

Identification of FGF19 as a prognostic marker and potential driver gene of lung squamous cell carcinomas in Chinese smoking patients

PubMed Central

Xia, Weiliang; Li, Ziming; Niu, Xiaomin; Ji, Wenxiang; Yuan, Hong; Xu, Qiang; Luo, Qingquan; Zhang, Jie; Lu, Shun

2016-01-01

Comprehensive genomic characterizations of lung squamous cell carcinoma (LSCC) have been performed, but the differences between smokers (S-LSCC) and never smokers (NS-LSCC) are not clear, as NS-LSCC could be considered as a different disease from S-LSCC. In this study we delineated genomic alterations in a cohort of 21 NS-LSCC and 16 S-LSCC patients, and identified common gene mutations and amplifications as previously reported. Inclusion of more NS-LSCC patients enabled us to identify unreported S-LSCC- or NS-LSCC-specific alterations. Importantly, an amplification region containing FGF19, FGF3, FGF4 and CCND1 was found five-times more frequent in S-LSCC than in NS-LSCC. Amplification of FGF19 was validated in independent LSCC samples. Furthermore, FGF19 stimulated LSCC cell growth in vitro. These data implicate FGF19 as a potential driver gene in LSCC with clinic characteristics as smoking. PMID:26943773

Identification of FGF19 as a prognostic marker and potential driver gene of lung squamous cell carcinomas in Chinese smoking patients.

PubMed

Tan, Qiang; Li, Fan; Wang, Guan; Xia, Weiliang; Li, Ziming; Niu, Xiaomin; Ji, Wenxiang; Yuan, Hong; Xu, Qiang; Luo, Qingquan; Zhang, Jie; Lu, Shun

2016-04-05

Comprehensive genomic characterizations of lung squamous cell carcinoma (LSCC) have been performed, but the differences between smokers (S-LSCC) and never smokers (NS-LSCC) are not clear, as NS-LSCC could be considered as a different disease from S-LSCC. In this study we delineated genomic alterations in a cohort of 21 NS-LSCC and 16 S-LSCC patients, and identified common gene mutations and amplifications as previously reported. Inclusion of more NS-LSCC patients enabled us to identify unreported S-LSCC- or NS-LSCC-specific alterations. Importantly, an amplification region containing FGF19, FGF3, FGF4 and CCND1 was found five-times more frequent in S-LSCC than in NS-LSCC. Amplification of FGF19 was validated in independent LSCC samples. Furthermore, FGF19 stimulated LSCC cell growth in vitro. These data implicate FGF19 as a potential driver gene in LSCC with clinic characteristics as smoking.

Numerical simulation of time delay Interferometry for LISA with one arm dysfunctional

NASA Astrophysics Data System (ADS)

Ni, Wei-Tou; Dhurandhar, Sanjeev V.; Nayak, K. Rajesh; Wang, Gang

In order to attain the requisite sensitivity for LISA, laser frequency noise must be suppressed below the secondary noises such as the optical path noise, acceleration noise etc. In a previous paper(a), we have found an infinite family of second generation analytic solutions of time delay interferometry and estimated the laser noise due to residual time delay semi-analytically from orbit perturbations due to earth. Since other planets and solar-system bodies also perturb the orbits of LISA spacecraft and affect the time delay interferometry, we simulate the time delay numerically in this paper. To conform to the actual LISA planning, we have worked out a set of 10-year optimized mission orbits of LISA spacecraft using CGC3 ephemeris framework(b). Here we use this numerical solution to calculate the residual errors in the second generation solutions upto n 3 of our previous paper, and compare with the semi-analytic error estimate. The accuracy of this calculation is better than 1 m (or 30 ns). (a) S. V. Dhurandhar, K. Rajesh Nayak and J.-Y. Vinet, time delay Interferometry for LISA with one arm dysfunctional (b) W.-T. Ni and G. Wang, Orbit optimization for 10-year LISA mission orbit starting at 21 June, 2021 using CGC3 ephemeris framework

Ultrafast dynamic response of single-crystal β-HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine)

NASA Astrophysics Data System (ADS)

Zaug, Joseph M.; Austin, Ryan A.; Armstrong, Michael R.; Crowhurst, Jonathan C.; Goldman, Nir; Ferranti, Louis; Saw, Cheng K.; Swan, Raymond A.; Gross, Richard; Fried, Laurence E.

2018-05-01

We report experimental and computational studies of shock wave dynamics in single-crystal β-HMX on an ultrafast time scale. Here, a laser-based compression drive (˜1 ns in duration; stresses of up to ˜40 GPa) is used to propagate shock waves normal to the (110) and (010) lattice planes. Ultrafast time-domain interferometry measurements reveal distinct, time-dependent relationships between the shock wave velocity and particle velocity for each crystal orientation, which suggest evolving physical processes on a sub-nanosecond time scale. To help interpret the experimental data, elastic shock wave response was simulated using a finite-strain model of crystal thermoelasticity. At early propagation times (<500 ps), the model is in agreement with the data, which indicates that the mechanical response is dominated by thermoelastic deformation. The model agreement depends on the inclusion of nonlinear elastic effects in both the spherical and deviatoric stress-strain responses. This is achieved by employing an equation-of-state and a pressure-dependent stiffness tensor, which was computed via atomistic simulation. At later times (>500 ps), the crystal samples exhibit signatures of inelastic deformation, structural phase transformation, or chemical reaction, depending on the direction of wave propagation.

Optical Diagnostic System For Observation Of Laser-Produced Shock Waves

NASA Astrophysics Data System (ADS)

Wilke, Mark D.; Stone, Sidney N.

1980-11-01

Several standard plasma and gas dynamic diagnostic techniques have been integrated into a system for observing the formation and propagation of high-power Nd:glass-laser generated one- and two-dimensional shockwaves in air from 0.1 torr to atmospheric pres-sures. Diagnostics include either single-frame, two-wavelength holographic ruby-laser interferometry or single-frame, single-wavelength interferometry with ten frames of shadow-graphy. Streaks or ten frames of the early luminous shocked region also are taken on all shots, as well as time-resolved luminosity measurements using high-speed biplanar vacuum photodiodes with various wavelength interference filters. Shadowgraphy frames are 200-ns long at 1-μs intervals, while emission frames are variable with a maximum 10-ns exposure and 50-ns interval. Both the streak mode and emission measurements with the vacuum diode allow subnanosecond time resolution. The interferometry provides 20-ns exposures from 500 ns to late times. Methods for reducing and interpreting the data have been, or are currently being, developed. Interactive computer programs for digitizing the fringe patterns provide fringe-shift profiles for Abel inversion. This has provided neutral gas and electron density information in the spherical, one-dimensional cases. Diagrams and photographs of the experiment will be shown as well as examples of the data that have been taken. Methods for data reduction will be outlined and some of the results shown.

Long implosion time (240 ns) Z-pinch experiments with a large diameter (12 cm) double-shell nozzle

NASA Astrophysics Data System (ADS)

Levine, J. S.; Banister, J. W.; Failor, B. H.; Qi, N.; Song, Y.; Sze, H. M.; Fisher, A.

2004-05-01

Recently, an 8 cm diameter double-shell nozzle has produced argon Z pinches with high K-shell yields with implosion time of 210 ns. To produce even longer implosion time Z pinches for facilities such as Decade Quad [D. Price, et al., "Electrical and Mechanical Design of the Decade Quad in PRS Mode," in Proceedings of the 12th IEEE Pulsed Power Conference, Monterey, CA, edited by C. Stallings and H. Kirbie (IEEE, New York, 1999), p. 489] (9 MA short circuit current at 300 ns), a larger nozzle (12 cm outer diameter) was designed and fabricated. During initial testing on Double-EAGLE [P. Sincerny et al., Proceedings of the 5th IEEE Pulsed Power Conference, Arlington, VA, edited by M. F. Rose and P. J. Turchi (IEEE, New York, 1985), p. 151], 9 kJ of argon K-shell radiation in a 6 ns full width at half maximum pulse was produced with a 240 ns implosion. The initial gas distributions produced by various nozzle configurations have been measured and their impact on the final radiative characteristics of the pinch are presented. The addition of a central jet to increase the initial gas density near the axis is observed to enhance the pinch quality, increasing K-shell yield by 17% and power by 40% in the best configuration tested.

Exposure of patient and dental staff to fine and ultrafine particles from scanning spray.

PubMed

Rupf, Stefan; Berger, Hendrik; Buchter, Axel; Harth, Volker; Ong, Mei Fang; Hannig, Matthias

2015-05-01

Sprays containing fine and ultrafine particles are commonly used for optical scanning. The aim of this study was to measure the particle exposure of patient and dentist during application of scanning spray and to evaluate measures for its reduction. A lower molar in a dental simulator was powdered with scanning spray. Patient's particle exposure was measured by a condensation particle counter in the nasal region of the simulator without (P) and with rubber dam (PC). Dentist's exposure (D) was measured behind a surgical mask. Particle concentrations were determined 5-fold without suction (NS), using conventional dental suction (CDS), or high volume evacuation (HVE). Mean background air particle concentrations for the patient were 3.3 × 10(3) and 1.3 × 10(3) pt/cm(3) for the dentist. Particle concentrations increased after spraying; mean cumulated additional particle exposures for the patient were the following: P-NS 7.2 × 10(6), P-CDS 4.6 × 10(6), P-HVE 2.4 × 10(4); using rubber dam: PC-NS 3.6 × 10(6), PC-CDS 3.3 × 10(5), PC-HVE 2.2 × 10(5). The particle exposures of the dentist were the following: D-NS 9.7 × 10(5), D-CDS 1.8 × 10(5), D-HVE 1.6 × 10(4). The use of HVE is recommended to reduce exposure of patients and dental staff to fine and ultrafine particles when using scanning sprays. Effective protection is available for staff and patient by means of high volume evacuation. In patients suffering from obstructive lung diseases, the use of scanning sprays should be avoided altogether.

Deciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations.

PubMed

Méndez-Luna, D; Martínez-Archundia, M; Maroun, Rachid C; Ceballos-Reyes, G; Fragoso-Vázquez, M J; González-Juárez, D E; Correa-Basurto, J

2015-01-01

The G-protein coupled estrogen receptor 1 GPER/GPR30 is a transmembrane seven-helix (7TM) receptor involved in the growth and proliferation of breast cancer. Due to the absence of a crystal structure of GPER/GPR30, in this work, molecular modeling studies have been carried out to build a three-dimensional structure, which was subsequently refined by molecular dynamics (MD) simulations (up to 120 ns). Furthermore, we explored GPER/GPR30's molecular recognition properties by using reported agonist ligands (G1, estradiol (E2), tamoxifen, and fulvestrant) and the antagonist ligands (G15 and G36) in subsequent docking studies. Our results identified the E2 binding site on GPER/GPR30, as well as other receptor cavities for accepting large volume ligands, through GPER/GPR30 π-π, hydrophobic, and hydrogen bond interactions. Snapshots of the MD trajectory at 14 and 70 ns showed almost identical binding motifs for G1 and G15. It was also observed that C107 interacts with the acetyl oxygen of G1 (at 14 ns) and that at 70 ns the residue E275 interacts with the acetyl group and with the oxygen from the other agonist whereas the isopropyl group of G36 is oriented toward Met141, suggesting that both C107 and E275 could be involved in the protein activation. This contribution suggest that GPER1 has great structural changes which explain its great capacity to accept diverse ligands, and also, the same ligand could be recognized in different binding pose according to GPER structural conformations.

Solar radiation and street temperature as function of street orientation. An analysis of the status quo and simulation of future scenarios towards sustainability in Bahrain

NASA Astrophysics Data System (ADS)

Silva, Joao Pinelo

2017-11-01

This paper discusses the contribution of street orientation towards the development of a comfortable microclimate for pedestrians in Bahrain. Increasing walkability is a global agenda to address issues such as a) transportation, b) energy consumption, c) health, and d) air pollution, all of which are topics of the sustainability agenda. Thermal comfort is one of the pre-requisites for walkability. In warm climates, this is a challenging goal. Street design is paramount for pedestrian comfort in warm climates. The roles of street orientation and aspect ratio are of particular importance as they determine the intake of solar radiation into the urban canyon. We investigate the state of affairs in Bahrain, by measuring the frequency with which the street orientations E-W, N-S, NE-SW, and NW-SE, currently occur. Research suggests that the street orientation E-W presents the lesser performance for mitigating the effects of heat gain. The ideal grid orientation would, therefore, be N-S, and NE-SW - NW-SE, avoiding street segments with E-W orientation. A countrywide analysis shows that E-W orientation accounts for the highest overall street length with 37%. The second most frequent orientation is N-S (29%), the best performer. NW-SE and NE-SW both have frequencies of only 17%. Preference for a street grid with N-S, NW-SE, and NE-SW orientation would improve the thermal performance of streets and provide a continuous network of a comfortable pedestrian environment. We simulate two future scenarios based on avoiding new E-W streets, or not. We measure their potential reduction in thermal gain and conclude that a simple policy could reduce solar exposition in 40%.

Usefulness of Multiplex Real-Time PCR for Simultaneous Pathogen Detection and Resistance Profiling of Staphylococcal Bacteremia

PubMed Central

Chung, Yousun; Kim, Taek Soo; Min, Young Gi; Hong, Yun Ji; Park, Jeong Su; Hwang, Sang Mee; Song, Kyoung-Ho; Kim, Eu Suk; Kim, Hong Bin; Song, Junghan; Kim, Eui-Chong

2016-01-01

Staphylococci are the leading cause of nosocomial blood stream infections. Fast and accurate identification of staphylococci and confirmation of their methicillin resistance are crucial for immediate treatment with effective antibiotics. A multiplex real-time PCR assay that targets mecA, femA specific for S. aureus, femA specific for S. epidermidis, 16S rRNA for universal bacteria, and 16S rRNA specific for staphylococci was developed and evaluated with 290 clinical blood culture samples containing Gram-positive cocci in clusters (GPCC). For the 262 blood cultures identified to the species level with the MicroScan WalkAway system (Siemens Healthcare Diagnostics, USA), the direct real-time PCR assay of positive blood cultures showed very good agreement for the categorization of staphylococci into methicillin-resistant S. aureus (MRSA), methicillin-susceptible S. aureus (MSSA), methicillin-resistant S. epidermidis (MRSE), methicillin-susceptible S. epidermidis (MSSE), methicillin-resistant non-S. epidermidis CoNS (MRCoNS), and methicillin-susceptible non-S. epidermidis CoNS (MSCoNS) (κ = 0.9313). The direct multiplex real-time PCR assay of positive blood cultures containing GPCC can provide essential information at the critical point of infection with a turnaround time of no more than 4 h. Further studies should evaluate the clinical outcome of using this rapid real-time PCR assay in glycopeptide antibiotic therapy in clinical settings. PMID:27403436

An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation.

PubMed

Peter, Emanuel K; Shea, Joan-Emma

2017-07-05

In this paper, we present a novel hybrid Molecular Dynamics/kinetic Monte Carlo (MD/kMC) algorithm and apply it to protein folding and aggregation in explicit solvent. The new algorithm uses a dynamical definition of biases throughout the MD component of the simulation, normalized in relation to the unbiased forces. The algorithm guarantees sampling of the underlying ensemble in dependency of one average linear coupling factor 〈α〉 τ . We test the validity of the kinetics in simulations of dialanine and compare dihedral transition kinetics with long-time MD-simulations. We find that for low 〈α〉 τ values, kinetics are in good quantitative agreement. In folding simulations of TrpCage and TrpZip4 in explicit solvent, we also find good quantitative agreement with experimental results and prior MD/kMC simulations. Finally, we apply our algorithm to study growth of the Alzheimer Amyloid Aβ 16-22 fibril by monomer addition. We observe two possible binding modes, one at the extremity of the fibril (elongation) and one on the surface of the fibril (lateral growth), on timescales ranging from ns to 8 μs.

Jet-driven and jet-less fireballs from compact binary mergers

NASA Astrophysics Data System (ADS)

Salafia, O. S.; Ghisellini, G.; Ghirlanda, G.

2018-02-01

During a compact binary merger involving at least one neutron star (NS), a small fraction of the gravitational energy could be liberated in such a way to accelerate a small fraction (˜10-6) of the NS mass in an isotropic or quasi-isotropic way. In presence of certain conditions, a pair-loaded fireball can form, which undergoes accelerated expansion reaching relativistic velocities. As in the standard fireball scenario, internal energy is partly transformed into kinetic energy. At the photospheric radius, the internal radiation can escape, giving rise to a pulse that lasts for a time equal to the delay time since the merger. The subsequent interaction with the interstellar medium can then convert part of the remaining kinetic energy back into radiation in a weak isotropic afterglow at all wavelengths. This scenario does not require the presence of a jet: the associated isotropic prompt and afterglow emission should be visible for all NS-NS and BH-NS mergers within 90 Mpc, independent of their inclination. The prompt emission is similar to that expected from an off-axis jet, either structured or much slower than usually assumed (Γ ˜ 10), or from the jet cocoon. The predicted afterglow emission properties can discriminate among these scenarios.

Characterization of Two Ton NaI Scintillator

NASA Astrophysics Data System (ADS)

Maier, Alleta; Coherent Collaboration

2017-09-01

The COHERENT collaboration is dedicated to measuring Coherent Elastic Neutrino-Nucleus Scattering (CE νNS), an interaction predicted by the standard model that ultimately serves as a background floor for dark matter detection. In the pursuit of observing the N2 scaling predicted, COHERENT is deploying two tons of NaI[Tl] detector to observe CE νNS recoils of sodium nuclei. Before the two tons of this NaI[Tl] scintillator are deployed, however, all crystals and PMTs must be characterized to understand the individual properties vital to precision in the measurement of CE νNS. This detector is also expected to allow COHERENT to observe charged current and CE νNS interactions with 127I. A standard operating procedure is developed to characterize each detector based on seven properties relevant to precision in the measurement of CE νNS: energy scale, energy resolution, low-energy light yield non-linearity, decay time energy dependence, position variance, time variance, and background levels. Crystals will be tested and characterized for these properties in the context of a ton-scale NaI[Tl] detector. Preliminary development of the SOP has allowed for greater understanding of optimization methods needed for characterization for the ton scale detector. TUNL, NSF, Duke University.

The impact of photon flight path on S1 pulse shape analysis in liquid xenon two-phase detectors

NASA Astrophysics Data System (ADS)

Moongweluwan, M.

2016-02-01

The LUX dark matter search experiment is a 350 kg dual-phase xenon time projection chamber located at the 4850 ft level of the Sanford Underground Research Facility in Lead, SD. The success of two-phase xenon detectors for dark matter searches relies on their ability to distinguish electron recoil (ER) background events from nuclear recoil (NR) signal events. Typically, the NR-ER discrimination is obtained from the ratio of the electroluminescence light (S2) to the prompt scintillation light (S1). Analysis of the S1 pulse shape is an additional discrimination technique that can be used to distinguish NR from ER. Pulse-shape NR-ER discrimination can be achieved based on the ratio of the de-excitation processes from singlet and triplet states that generate the S1. The NR S1 is dominated by the de-excitation process from singlet states with a time constant of about 3 ns while the ER S1 is dominated by the de-excitation process from triplet states with a time constant of about 24 ns. As the size of the detectors increases, the variation in the S1 photon flight path can become comparable to these decay constants, reducing the utility of pulse-shape analysis to separate NR from ER. The effect of path length variations in the LUX detector has been studied using the results of simulations and the impact on the S1 pulse shape analysis is discussed.

Kinetic simulation of hydrodynamic equivalent capsule implosions

NASA Astrophysics Data System (ADS)

Kwan, Thomas; Le, Ari; Schmitt, Mark; Herrmann, Hans

2016-10-01

We have carried out simulations of direct-drive hydrodynamic equivalent capsule implosion experiments conducted on Omega laser facility at the Laboratory of Laser Energetics of the University of Rochester. The capsules had a glass shell (SiO2) 4.87 μm with an inner diameter of 1086 μm. One was filled with deuterium (D) and tritium (T) at 6.635 and 2.475 atmospheric pressure respectively. The other capsule with D, T, and He-3 at 2.475, 2.475, and 5.55 atmospheric pressure respectively. The capsules were imploded with 60 laser beams with a square pulse length of 0.6ns of total energy of 15.6 kJ. One-dimensional radiation hydrodynamic calculations with HYDRA and kinetic particle/hybrid simulations with LSP are carried out for the post-shot analysis. HYDRA outputs at 0.6ns are linked to LSP, in which the electrons are treated as a fluid while all the ion dynamics is simulated by the standard particle-in-cell technique. Additionally, simulations with the new photon package in LSP are initiated at the beginning of the implosion to include the implosion phase of the capsule. The simulation results of density, temperature, and velocity profiles of the electrons, D, T, He-3, and SiO2species are compared with HYDRA. Detail comparisons among the kinetic simulations, rad-hydro simulations, and experimental results of neutron yield, yield ratio, fusion burn histories, and shell convergence will be presented to assess plasma kinetic effects. Work performed under the auspices of the US DOE by the Los Alamos National Laboratory under Contract No. W7405-ENG-36.

Hypersonic low-density solutions of the Navier-Stokes equations with chemical nonequilibrium and multicomponent surface slip

NASA Technical Reports Server (NTRS)

Gupta, R. N.; Simmonds, A. L.

1986-01-01

Solutions of the Navier-Stokes equations with chemical nonequilibrium and multicomponent surface slip are presented along the stagnation streamline under low-density hypersonic flight conditions. The conditions analyzed are those encountered by the nose region of the Space Shuttle Orbiter during reentry. A detailed comparison of the Navier-Stokes (NS) results is made with the viscous shock-layer (VSL) and Direct Simulation Monte Carlo (DSMC) predictions. With the inclusion of surface-slip boundary conditions in NS calculations, the surface heat transfer and other flow field quantities adjacent to the surface are predicted favorably with the DSMC calculations from 75 km to 115 km in altitude. Therefore, the practical range for the applicability of Navier-Stokes solutions is much wider than previously thought. This is appealing because the continuum (NS and VSL) methods are commonly used to solve the fluid flow problems and are less demanding in terms of computer resource requirements than the noncontinuum (DSMC) methods. The NS solutions agree well with the VSL results for altitudes less than 92 km. An assessment is made of the frozen flow approximation employed in the VSL calculations.

Perspectives on Ultraluminous X-ray sources after the discovery of Ultraluminous Pulsars

NASA Astrophysics Data System (ADS)

Zampieri, L.; Ambrosi, E.; Fiore, A.; Pintore, F.; Turolla, R.; Israel, GL.; Stella, L.; Casella, P.; Papitto, A.; Rodriguez Castillo, G. A.; De Luca, A.; Tiengo, A.; Belfiore, A.; Esposito, P.; Marelli, M.; Novara, G.; Salvaterra, R.; Salvetti, D.; Mereghetti, S.; Wolter, A.

2017-10-01

Ultraluminous X-ray sources (ULXs) are observationally defined as non-nuclear extragalactic X-ray point sources with inferred (isotropic) luminosity exceeding the Eddington limit for a ˜ 10 M_{⊙} compact object. While in the past few years a certain evidence (and a general consensus) has been gathered in favour of the existence of black hole (BH) remnants in ULXs, the recent discovery of three Ultraluminous X-ray Pulsars has unexpectedly revealed what is likely to be a significant population of neutron star (NS) ULXs. These findings challenge more than ever our present understanding of these sources, their accretion mechanism/history, and their formation pathways. After reviewing some of these intriguing observational facts, we will summarize some perspective studies that we are carrying out to model the multiwavelength variability and broadband spectra of ULXs, including the contribution of an accretion column for NS systems. We derive the luminosity emitted by the latter assuming that a multipolar component dominates the magnetic field close to the NS. The focus is on comparing the simulated multiwavelength emission properties of stellar-mass/massive BHs to those of NS systems, and on confronting the model predictions with the available observations of Pulsar ULXs.

Renormalization-group study of the Nagel-Schreckenberg model

NASA Astrophysics Data System (ADS)

Teoh, Han Kheng; Yong, Ee Hou

2018-03-01

We study the phase transition from free flow to congested phases in the Nagel-Schreckenberg (NS) model by using the dynamically driven renormalization group (DDRG). The breaking probability p that governs the driving strategy is investigated. For the deterministic case p =0 , the dynamics remain invariant in each renormalization-group (RG) transformation. Two fully attractive fixed points, ρc*=0 and 1, and one unstable fixed point, ρc*=1 /(vmax+1 ) , are obtained. The critical exponent ν which is related to the correlation length is calculated for various vmax. The critical exponent appears to decrease weakly with vmax from ν =1.62 to the asymptotical value of 1.00. For the random case p >0 , the transition rules in the coarse-grained scale are found to be different from the NS specification. To have a qualitative understanding of the effect of stochasticity, the case p →0 is studied with simulation, and the RG flow in the ρ -p plane is obtained. The fixed points p =0 and 1 that govern the driving strategy of the NS model are found. A short discussion on the extension of the DDRG method to the NS model with the open-boundary condition is outlined.

Virtual screening of potential inhibitors from TCM for the CPSF30 binding site on the NS1A protein of influenza A virus.

PubMed

Ai, Haixin; Zhang, Li; Chang, Alan K; Wei, Hongyun; Che, Yuchen; Liu, Hongsheng

2014-03-01

Inhibition of CPSF30 function by the effector domain of influenza A virus of non-structural protein 1 (NS1A) protein plays a critical role in the suppression of host key antiviral response. The CPSF30-binding site of NS1A appears to be a very attractive target for the development of new drugs against influenza A virus. In this study, structure-based molecular docking was utilized to screen more than 30,000 compounds from a Traditional Chinese Medicine (TCM) database. Four drug-like compounds were selected as potential inhibitors for the CPSF30-binding site of NS1A. Docking conformation analysis results showed that these potential inhibitors could bind to the CPSF30-binding site with strong hydrophobic interactions and weak hydrogen bonds. Molecular dynamics simulations and MM-PBSA calculations suggested that two of the inhibitors, compounds 32056 and 31674, could stably bind to the CPSF30-binding site with high binding free energy. These two compounds could be modified to achieve higher binding affinity, so that they may be used as potential leads in the development of new anti-influenza drugs.

The effect of classical swine fever virus NS5A and NS5A mutants on oxidative stress and inflammatory response in swine testicular cells.

PubMed

Dong, Wang; Lv, Huifang; Wang, Yifan; Li, Xiaomeng; Li, Cheng; Wang, Lu; Wang, Chengbao; Guo, Kangkang; Zhang, Yanming

2017-06-01

Infection with classical swine fever virus (CSFV) results in highly significant economic losses; this infection is characterized by being highly contagious and accompanied by hyperthermia and systemic bleeding. Oxidative stress (OS) plays a critical role in the pathological process of viral infection. The function of the nonstructural protein 5A (NS5A) in the pathogenesis of CSFV has not been completely understood. Here, OS and the inflammatory response were studied with NS5A and substitution mutants in swine testicular (ST) cells. ST cell lines stably expressing CSFV NS5A or substitution mutants were established. Reactive oxygen species (ROS) production, antioxidant protein expression and inflammatory response were analyzed by quantitative real-time PCR (qRT-PCR), ELISA and flow cytometry analysis. The results showed that CSFV NS5A did not increase ROS production or the antioxidant protein (Trx, HO-1 and PRDX-6) expression in ST cells. However, NS5A inhibited cyclooxygenase-2 (COX-2) expression, a pro-inflammatory protein related to OS. Further studies have shown that NS5A mutants S15A and S92A increased ROS production and inhibited antioxidant protein expression. S15A, S81A and T274A affected the inflammatory response. This study suggested that CSFV NS5A did not induce OS, and amino acids Ser15 and Ser92 of CSFV NS5A were essential for inhibiting OS. Additionally, Ser15, Ser81 and Thr274 played important roles in the inflammatory response in ST cells. These observations provided insight into the function of CSFV NS5A and the mechanism of CSFV persistent infection in ST cells. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of olmesartan medoxomil optimized nanosuspension using the Box-Behnken design to improve oral bioavailability.

PubMed

Nagaraj, K; Narendar, D; Kishan, V

2017-07-01

The aim of the present investigation was to enhance the oral bioavailability of olmesartan medoxomil by improving its solubility and dissolution rate by preparing nanosuspension (OM-NS), using the Box-Behnken design. In this, four factors were evaluated at three levels. Independent variables include: concentration of drug (X 1 ), concentration of surfactant (X 2 ), concentration of polymer (X 3 ) and number of homogenization cycles (X 4 ). Based on preliminary studies, the size (Y 1 ), zeta potential (ZP) (Y 2 ) and % drug release at 5 min (Y 3 ) were chosen as dependent responses. OM-NS was prepared by high pressure homogenization method. The size, PDI, ZP, assay, in vitro release and morphology of OM-NS were characterized. Further, the pharmacokinetic (PK) behavior of OM-NS was evaluated in male wistar rats. Statistically optimized OM-NS formulation exhibited mean particle size of 492 nm, ZP of -27.9 mV and 99.29% release in 5 min. OM-NS showed more than four times increase in its solubility than pure OM. DSC and XRD analyses indicated that the drug incorporated into OM-NS was in amorphous form. The morphology of OM-NS was found to be nearly spherical with high dispersity by scanning electron microscopic studies. The PK results showed that OM lyophilized nanosuspension (NS) exhibited improved PK properties compared to coarse powder suspension and marketed tablet powder suspension (TS). Oral bioavailability of lyophilized NS was increased by 2.45 and 2.25 folds when compared to marketed TS and coarse powder suspension, respectively. Results of this study lead to conclusion that NS approach was effective in preparing OM formulations with enhanced dissolution and improved oral bioavailability.

Slow light generation in single-mode rectangular core photonic crystal fiber

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

Yadav, Sandeep; Saini, Than Singh; Kumar, Ajeet, E-mail: ajeetdph@gmail.com

2016-05-06

In this paper, we have designed and analyzed a rectangular core photonic crystal fiber (PCF) in Tellurite material. For the designed photonics crystal fiber, we have calculated the values of confinement loss and effective mode area for different values of air filling fraction (d/Λ). For single mode operation of the designed photonic crystal fiber, we have taken d/Λ= 0.4 for the further calculation of stimulated Brillouin scattering based time delay. A maximum time delay of 158 ns has been achieved for input pump power of 39 mW. We feel the detailed theoretical investigations and simulations carried out in the study have themore » potential impact on the design and development of slow light-based photonic devices.« less

Axial magnetic field injection in magnetized liner inertial fusion

NASA Astrophysics Data System (ADS)

Gourdain, P.-A.; Adams, M. B.; Davies, J. R.; Seyler, C. E.

2017-10-01

MagLIF is a fusion concept using a Z-pinch implosion to reach thermonuclear fusion. In current experiments, the implosion is driven by the Z-machine using 19 MA of electrical current with a rise time of 100 ns. MagLIF requires an initial axial magnetic field of 30 T to reduce heat losses to the liner wall during compression and to confine alpha particles during fusion burn. This field is generated well before the current ramp starts and needs to penetrate the transmission lines of the pulsed-power generator, as well as the liner itself. Consequently, the axial field rise time must exceed hundreds of microseconds. Any coil capable of being submitted to such a field for that length of time is inevitably bulky. The space required to fit the coil near the liner, increases the inductance of the load. In turn, the total current delivered to the load decreases since the voltage is limited by driver design. Yet, the large amount of current provided by the Z-machine can be used to produce the required 30 T field by tilting the return current posts surrounding the liner, eliminating the need for a separate coil. However, the problem now is the field penetration time, across the liner wall. This paper discusses why skin effect arguments do not hold in the presence of resistivity gradients. Numerical simulations show that fields larger than 30 T can diffuse across the liner wall in less than 60 ns, demonstrating that external coils can be replaced by return current posts with optimal helicity.

Timed Release of Cerebrolysin Using Drug-Loaded Titanate Nanospheres Reduces Brain Pathology and Improves Behavioral Functions in Parkinson's Disease.

PubMed

Ozkizilcik, Asya; Sharma, Aruna; Muresanu, Dafin F; Lafuente, José V; Tian, Z Ryan; Patnaik, Ranjana; Mössler, Herbert; Sharma, Hari S

2018-01-01

Previous studies from our laboratory show that intraperitoneal injections of 1-metyl-4-phenyl-1,2,3,6-tetrahydropyridin (MPTP, 20 mg/kg) daily within 2-h intervals for 5 days in mice induce Parkinson's disease (PD)-like symptoms on the 8th day. A significant decrease in dopamine (DA) and its metabolites 3,4-dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA) along with a marked decrease in the number of tyrosine hydroxylase (TH)-positive cells in the substantia nigra pars compacta (SNpc) and striatum (STr) confirms the validity of this model for studying PD. Since cerebrolysin (CBL) is a well-balanced composition of several neurotrophic factors and active peptide fragments, in the present investigation we examined the timed release of CBL using titanate nanospheres (TiNS) in treating PD in our mouse model. Our observations show that TiNS-CBL (in a dose of 3 ml/kg, i.v.) given after 2 days of MPTP administration for 5 days resulted in a marked increase in TH-positive cells in the SNpc and STr as compared to normal CBL. Also, TiNS-CBL resulted in significantly higher levels of DA, DOPAC, and HVA in SNpc and STr on the 8th day as compared to normal CBL therapy. TiNS-CBL also thwarted increased α-synuclein levels in the brain and in the cerebrospinal fluid (CSF) as well as neuronal nitric oxide synthase (nNOS) in the in PD brain as compared to untreated group. Behavioral function was also significantly improved in MPTP-treated animals that received TiNS-CBL. These observations are the first to demonstrate that timed release of TiNS-CBL has far more superior neuroprotective effects in PD than normal CBL.

AGILE Observations of the Gravitational-wave Source GW170817: Constraining Gamma-Ray Emission from an NS-NS Coalescence

NASA Astrophysics Data System (ADS)

Verrecchia, F.; Tavani, M.; Donnarumma, I.; Bulgarelli, A.; Evangelista, Y.; Pacciani, L.; Ursi, A.; Piano, G.; Pilia, M.; Cardillo, M.; Parmiggiani, N.; Giuliani, A.; Pittori, C.; Longo, F.; Lucarelli, F.; Minervini, G.; Feroci, M.; Argan, A.; Fuschino, F.; Labanti, C.; Marisaldi, M.; Fioretti, V.; Trois, A.; Del Monte, E.; Antonelli, L. A.; Barbiellini, G.; Caraveo, P.; Cattaneo, P. W.; Colafrancesco, S.; Costa, E.; D'Amico, F.; Ferrari, A.; Giommi, P.; Morselli, A.; Paoletti, F.; Pellizzoni, A.; Picozza, P.; Rappoldi, A.; Soffitta, P.; Vercellone, S.; Baroncelli, L.; Zollino, G.

2017-12-01

The LIGO-Virgo Collaboration (LVC) detected, on 2017 August 17, an exceptional gravitational-wave (GW) event temporally consistent within ˜ 1.7 {{s}} with the GRB 1708117A observed by Fermi-GBM and INTEGRAL. The event turns out to be compatible with a neutron star-neutron star (NS-NS) coalescence that subsequently produced a radio/optical/X-ray transient detected at later times. We report the main results of the observations by the AGILE satellite of the GW170817 localization region (LR) and its electromagnetic (EM) counterpart. At the LVC detection time T 0, the GW170817 LR was occulted by the Earth. The AGILE instrument collected useful data before and after the GW/GRB event because in its spinning observation mode it can scan a given source many times per hour. The earliest exposure of the GW170817 LR by the gamma-ray imaging detector started about 935 s after T 0. No significant X-ray or gamma-ray emission was detected from the LR that was repeatedly exposed over timescales of minutes, hours, and days before and after GW170817, also considering Mini-calorimeter and Super-AGILE data. Our measurements are among the earliest ones obtained by space satellites on GW170817 and provide useful constraints on the precursor and delayed emission properties of the NS-NS coalescence event. We can exclude with high confidence the existence of an X-ray/gamma-ray emitting magnetar-like object with a large magnetic field of {10}15 {{G}}. Our data are particularly significant during the early stage of evolution of the EM remnant.

Differential Mouse Pulmonary Dose and Time Course Responses to Titanium Dioxide Nanospheres and Nanobelts

PubMed Central

Porter, Dale W.

2013-01-01

Three anatase titanium dioxide (TiO2) nanoparticles (NPs) were prepared; nanospheres (NSs), short nanobelts (NB1), and long nanobelts (NB2). These NPs were used to investigate the effect of NP shape and length on lung toxicity. Mice were exposed (0–30 µg per mouse) by pharyngeal aspiration and pulmonary toxicity was assessed over a 112-day time course. Whole lung lavage data indicated that NB1- and NB2-exposed mice, but not NS-exposed mice, had significant dose- and time-dependent pulmonary inflammation and damage. Histopathological analyses at 112 days postexposure determined no interstitial fibrosis in any NS-exposed mice, an increased incidence in 30 µg NB1-exposed mice, and significant interstitial fibrosis in 30 µg NB2-exposed mice. At 112 days postexposure, lung burden of NS was decreased by 96.4% and NB2 by 80.5% from initial deposition levels. At 112 days postexposure, enhanced dark field microscopy determined that alveolar macro- phages were the dominant deposition site, but a fraction of NB1 and NB2 was observed in the alveolar interstitial spaces. For the 30 µg exposure groups at 112 days postexposure, confocal micro- scopy and immunofluorescent staining demonstrated that retained NB2 but not NS were present in the interstitium subjacent to the terminal bronchiole near the normal location of the smallest lymphatic capillaries in the lung. These lymphatic capillaries play a critical role in particle clearance, and the accumulation of NB2, but not NS, suggests possible impaired lymphatic clearance by the high aspect ratio particles. In summary, our data indicate that TiO2 NP shape alters pulmonary responses, with severity of responses being ranked as NS < NB1 < NB2. PMID:22956629

Constraining the Speed of Sound inside Neutron Stars with Chiral Effective Field Theory Interactions and Observations

NASA Astrophysics Data System (ADS)

Tews, I.; Carlson, J.; Gandolfi, S.; Reddy, S.

2018-06-01

The dense matter equation of state (EOS) determines neutron star (NS) structure but can be calculated reliably only up to one to two times the nuclear saturation density, using accurate many-body methods that employ nuclear interactions from chiral effective field theory constrained by scattering data. In this work, we use physically motivated ansatzes for the speed of sound c S at high density to extend microscopic calculations of neutron-rich matter to the highest densities encountered in stable NS cores. We show how existing and expected astrophysical constraints on NS masses and radii from X-ray observations can constrain the speed of sound in the NS core. We confirm earlier expectations that c S is likely to violate the conformal limit of {c}S2≤slant {c}2/3, possibly reaching values closer to the speed of light c at a few times the nuclear saturation density, independent of the nuclear Hamiltonian. If QCD obeys the conformal limit, we conclude that the rapid increase of c S required to accommodate a 2 M ⊙ NS suggests a form of strongly interacting matter where a description in terms of nucleons will be unwieldy, even between one and two times the nuclear saturation density. For typical NSs with masses in the range of 1.2–1.4 M ⊙, we find radii between 10 and 14 km, and the smallest possible radius of a 1.4 M ⊙ NS consistent with constraints from nuclear physics and observations is 8.4 km. We also discuss how future observations could constrain the EOS and guide theoretical developments in nuclear physics.

Postural Stability in Cigarette Smokers and During Abstinence from Alcohol

PubMed Central

Schmidt, Thomas Paul; Pennington, David Louis; Durazzo, Timothy Craig; Meyerhoff, Dieter Johannes

2014-01-01

Background Static postural instability is common in alcohol dependent individuals (ALC). Chronic alcohol consumption has deleterious effects on the neural and perceptual systems subserving postural stability. However, little is known about the effects of chronic cigarette smoking on postural stability and its changes during abstinence from alcohol. Methods A modified Fregly ataxia battery was administered to a total of 115 smoking (sALC) and non-smoking ALC (nsALC) and to 74 smoking (sCON) and non-smoking light/non-drinking controls (nsCON). Subgroups of abstinent ALC were assessed at 3 time points (approximately 1 week, 5 weeks, 34 weeks of abstinence from alcohol); a subset of nsCON was re-tested at 40 weeks. We tested if cigarette smoking affects postural stability in CON and in ALC during extended abstinence from alcohol, and we used linear mixed effects modeling to measure change across time points within ALC. Results Chronic smoking was associated with reduced performance on the Sharpened Romberg eyes-closed task in abstinent ALC at all three time points and in CON. The test performance of nsALC increased significantly between 1 and 32 weeks of abstinence, whereas the corresponding increases for sALC between 1 and 35 weeks was non-significant. With long-term abstinence from alcohol, nsALC recovered into the range of nsCON and sALC recovered into the range of sCON. Static postural stability decreased with age and correlated with smoking variables but not with drinking measures. Conclusions Chronic smoking was associated with reduced static postural stability with eyes closed and with lower increases of postural stability during abstinence from alcohol. Smoking cessation in alcohol dependence treatment may facilitate recovery from static postural instability during abstinence. PMID:24721012

Detecting coupled collective motions in protein by independent subspace analysis

NASA Astrophysics Data System (ADS)

Sakuraba, Shun; Joti, Yasumasa; Kitao, Akio

2010-11-01

Protein dynamics evolves in a high-dimensional space, comprising aharmonic, strongly correlated motional modes. Such correlation often plays an important role in analyzing protein function. In order to identify significantly correlated collective motions, here we employ independent subspace analysis based on the subspace joint approximate diagonalization of eigenmatrices algorithm for the analysis of molecular dynamics (MD) simulation trajectories. From the 100 ns MD simulation of T4 lysozyme, we extract several independent subspaces in each of which collective modes are significantly correlated, and identify the other modes as independent. This method successfully detects the modes along which long-tailed non-Gaussian probability distributions are obtained. Based on the time cross-correlation analysis, we identified a series of events among domain motions and more localized motions in the protein, indicating the connection between the functionally relevant phenomena which have been independently revealed by experiments.

Automation of a N-S S and C Database Generation for the Harrier in Ground Effect

NASA Technical Reports Server (NTRS)

Murman, Scott M.; Chaderjian, Neal M.; Pandya, Shishir; Kwak, Dochan (Technical Monitor)

2001-01-01

A method of automating the generation of a time-dependent, Navier-Stokes static stability and control database for the Harrier aircraft in ground effect is outlined. Reusable, lightweight components arc described which allow different facets of the computational fluid dynamic simulation process to utilize a consistent interface to a remote database. These components also allow changes and customizations to easily be facilitated into the solution process to enhance performance, without relying upon third-party support. An analysis of the multi-level parallel solver OVERFLOW-MLP is presented, and the results indicate that it is feasible to utilize large numbers of processors (= 100) even with a grid system with relatively small number of cells (= 10(exp 6)). A more detailed discussion of the simulation process, as well as refined data for the scaling of the OVERFLOW-MLP flow solver will be included in the full paper.

Investigation of Electric and Self-Generated Magnetic Fields in Implosion Experiments on OMEGA

NASA Astrophysics Data System (ADS)

Igumenshchev, I. V.; Nilson, P. M.; Goncharov, V. N.; Li, C. K.; Zylstra, A. B.; Petrasso, R. D.

2013-10-01

Electric and self-generated magnetic fields in direct-drive implosion experiments on the OMEGA laser were investigated using proton radiography. The experiments use plastic-shell targets with various surface defects (glue spot, wire, and stalk mount) to seed perturbations and generate localized electromagnetic fields at the ablation surface and in the plasma corona surrounding the targets. Proton radiographs show features from these perturbations and quasi-spherical multiple shell structures around the capsules at earlier times of implosions (up to ~700 ps for a 1-ns laser pulse) indicating the development of the fields. Two-dimensional magnetohydrodynamic simulations of these experiments predict the growth of magnetic fields up to several MG. The simulated distributions of electromagnetic fields were used to produce proton images, which show good agreement with experimental radiographs. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

PubMed

Khavrutskii, Ilja V; Wallqvist, Anders

2010-11-09

This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.

Beam-based measurements of long-range transverse wakefields in the Compact Linear Collider main-linac accelerating structure

DOE PAGES

Zha, Hao; Latina, Andrea; Grudiev, Alexej; ...

2016-01-20

The baseline design of CLIC (Compact Linear Collider) uses X-band accelerating structures for its main linacs. In order to maintain beam stability in multibunch operation, long-range transverse wakefields must be suppressed by 2 orders of magnitude between successive bunches, which are separated in time by 0.5 ns. Such strong wakefield suppression is achieved by equipping every accelerating structure cell with four damping waveguides terminated with individual rf loads. A beam-based experiment to directly measure the effectiveness of this long-range transverse wakefield and benchmark simulations was made in the FACET test facility at SLAC using a prototype CLIC accelerating structure. Furthermore,more » the experiment showed good agreement with the simulations and a strong suppression of the wakefields with an unprecedented minimum resolution of 0.1 V/(pC mm m).« less

Direction based Hazard Routing Protocol (DHRP) for disseminating road hazard information using road side infrastructures in VANETs.

PubMed

Berlin, M A; Anand, Sheila

2014-01-01

This paper presents Direction based Hazard Routing Protocol (DHRP) for disseminating information about fixed road hazards such as road blocks, tree fall, boulders on road, snow pile up, landslide, road maintenance work and other obstacles to the vehicles approaching the hazardous location. The proposed work focuses on dissemination of hazard messages on highways with sparse traffic. The vehicle coming across the hazard would report the presence of the hazard. It is proposed to use Road Side fixed infrastructure Units for reliable and timely delivery of hazard messages to vehicles. The vehicles can then take appropriate safety action to avoid the hazardous location. The proposed protocol has been implemented and tested using SUMO simulator to generate road traffic and NS 2.33 network simulator to analyze the performance of DHRP. The performance of the proposed protocol was also compared with simple flooding protocol and the results are presented.

A theoretical and experimental study of calcium, iron, zinc, cadmium, and sodium ions absorption by aspartame.

PubMed

Mahnam, Karim; Raisi, Fatame

2017-03-01

Aspartame (L-Aspartyl-L-phenylalanine methyl ester) is a sweet dipeptide used in some foods and beverages. Experimental studies show that aspartame causes osteoporosis and some illnesses, which are similar to those of copper and calcium deficiency. This raises the issue that aspartame in food may interact with cations and excrete them from the body. This study aimed to study aspartame interaction with calcium, zinc, iron, sodium, and cadmium ions via molecular dynamics simulation (MD) and spectroscopy. Following a 480-ns molecular dynamics simulation, it became clear that the aspartame is able to sequester Fe 2+ , Ca 2+ , Cd 2+ , and Zn 2+ ions for a long time. Complexation led to increasing UV-Vis absorption spectra and emission spectra of the complexes. This study suggests a potential risk of cationic absorption of aspartame. This study suggests that purification of cadmium-polluted water by aspartame needs a more general risk assessment.

Chaos Through-Wall Imaging Radar

NASA Astrophysics Data System (ADS)

Xu, Hang; Wang, Bingjie; Zhang, Jianguo; Liu, Li; Li, Ying; Wang, Yuncai; Wang, Anbang

2017-12-01

We experimentally demonstrate a chaos through-wall imaging radar using ultra-wideband chaotic-pulse-position modulation (CPPM) microwave signal. The CPPM signal based on logistic map with 1-ns pulse width and 1-GHz bandwidth is implemented by a field programmable gate array (FPGA) and then up-converted as the radar transmitting signal. Two-dimensional image of human objects behind obstacles is obtained by correlation method and back projection algorithm. Our experiments successfully perform through-wall imaging for single and multiple human objects through 20-cm thick wall. The down-range resolution of the proposed radar is 15 cm. Furthermore, the anti-jamming properties of the proposed radar in CPPM jamming, linear frequency-modulated jamming, and Gaussian noise jamming environments are demonstrated by electromagnetic simulations using the finite-difference time-domain. The simulation results show the CPPM microwave signal possesses excellent jamming immunity to the noise and radio frequency interference, which makes it perform superbly in multiradar environments.

Hydrodynamics of laser-driven double-foil collisions studied by orthogonal x-ray imaging

NASA Astrophysics Data System (ADS)

Aglitskiy, Y.; Metzler, N.; Karasik, M.; Serlin, V.; Obenschain, S. P.; Schmitt, A. J.; Velikovich, A. L.; Gardner, J. H.; Weaver, J.; Oh, J.

2006-10-01

With this experiment we start the study of the physics of hydrodynamic instability seeding and growth during the deceleration and stagnation phases. Our first targets consisted of two separated parallel plastic foils -- flat and rippled. The flat foil was irradiated by the 4 ns Nike KrF laser pulses at 50 TW/cm^2 and accelerated towards the rippled one. Orthogonal imaging, i. e., a simultaneous side-on and face-on radiography of the targets has been used in these experiments. Side-on x-ray radiography and VISAR data yield shock and target velocities before and after the collision. Face-on streaks revealed well-pronounced oscillatory behavior of the single-mode mass perturbations. Both sets of synchronized data were compared with 1D and 2D simulations. Observed velocities, timing and the peak value of areal mass variation are in good agreement with the simulated ones.

Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors.

PubMed

Peddi, Saikiran Reddy; Sivan, Sree Kanth; Manga, Vijjulatha

2018-02-01

The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔG bind and experimental pIC 50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC 50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC 50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.

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

Saxena, Shailendra K., E-mail: phd1211512@iiti.ac.in; Sahu, Gayatri; Sagdeo, Pankaj R.

Quantum confinement effect has been studied in cheese like silicon nano-structures (Ch-SiNS) fabricated by metal induced chemical etching using different etching times. Scanning electron microscopy is used for the morphological study of these Ch-SiNS. A visible photoluminescence (PL) emission is observed from the samples under UV excitation at room temperature due to quantum confinement effect. The average size of Silicon Nanostructures (SiNS) present in the samples has been estimated by bond polarizability model using Raman Spectroscopy from the red-shift observed from SiNSs as compared to its bulk counterpart. The sizes of SiNS present in the samples decreases as etching timemore » increase from 45 to 75 mintunes.« less

Evolution and Persistence of the Resistance-Associated Substitutions of Hepatitis C Virus after Direct-Acting Antiviral Treatment Failures.

PubMed

Jeong, Yechan; Jin, Bora; Lee, Hye Won; Park, Hye Jung; Park, Jun Yong; Kim, Do Young; Han, Kwang-Hyub; Ahn, Sang Hoon; Kim, Seungtaek

2018-05-16

Daclatasvir plus asunaprevir (DCV+ASV) treatment is an all-oral direct-acting antiviral (DAA) therapy for the genotype 1b HCV-infected patients. In this study, we investigated how resistance-associated substitutions (RASs) evolved after treatment failures and assessed the effect of those substitutions on viral fitness. Sequencing of NS5A and NS3 revealed typical RASs after treatment failures. Interestingly, the RASs of NS3 reverted to the wild-type amino acid within one year after treatment failures. However, the RASs of NS5A were stable and did not change. The effect of NS5A and NS3 RASs on viral RNA replication was assessed after mutagenic substitution in the genotype 1b HCV RNA. Among the single substitutions, the effect of D168V was more substantial than the others and the effect of the triple mutant combination (D168V+L31V+Y93H) was the most severe. The RAS at NS5A Y93 affected both viral RNA replication and virus production. Finally, the effect of trans-complementation of NS5A was demonstrated in our co-transfection experiments and these results suggest that such a trans-complementation effect of NS5A may help maintain the NS5A RASs for a long time even after cessation of the DAA treatment. In conclusion, the results from this investigation would help understand the emergence and persistence of RASs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Identification of human hnRNP C1/C2 as a dengue virus NS1-interacting protein

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

Noisakran, Sansanee; Medical Molecular Biology Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Adulyadejvikrom Building; Sengsai, Suchada

Dengue virus nonstructural protein 1 (NS1) is a key glycoprotein involved in the production of infectious virus and the pathogenesis of dengue diseases. Very little is known how NS1 interacts with host cellular proteins and functions in dengue virus-infected cells. This study aimed at identifying NS1-interacting host cellular proteins in dengue virus-infected cells by employing co-immunoprecipitation, two-dimensional gel electrophoresis, and mass spectrometry. Using lysates of dengue virus-infected human embryonic kidney cells (HEK 293T), immunoprecipitation with an anti-NS1 monoclonal antibody revealed eight isoforms of dengue virus NS1 and a 40-kDa protein, which was subsequently identified by quadrupole time-of-flight tandem mass spectrometrymore » (Q-TOF MS/MS) as human heterogeneous nuclear ribonucleoprotein (hnRNP) C1/C2. Further investigation by co-immunoprecipitation and co-localization confirmed the association of hnRNP C1/C2 and dengue virus NS1 proteins in dengue virus-infected cells. Their interaction may have implications in virus replication and/or cellular responses favorable to survival of the virus in host cells.« less

Intense Ion Pulses for Radiation Effects Research

DTIC Science & Technology

2017-04-01

station; here, the time dependent beam current can be measured with a fast Faraday cup (ə ns time resolution). The transverse distribution of the...focused into a spot with a diameter of about 2 mm [8]. The helium ion current and the integrated charge ver- sus time, measured with the fast Faraday cup...target measured with the fast Faraday cup. The sharp peak in the current measurement shows the beam pulse compression from 1 μs to a few ns. The full

In Silico Design of Smart Binders to Anthrax PA

DTIC Science & Technology

2012-09-01

nanosecond(ns) molecular dynamics simulation in the NPT ensemble (constant particle number, pressure, and temperature) at 300K, with the CHARMM force...protective antigen (PA). Before the docking runs, the DS23 peptide was simulated using molecular dynamics to generate an ensemble of structures...structure), we do not see a large amount of structural change when using molecular dynamics after Rosetta docking. We note that this RMSD does not take

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

Nanosecond-level time synchronization of autonomous radio detector stations for extensive air showers

NASA Astrophysics Data System (ADS)

The Pierre Auger Collaboration

2016-01-01

To exploit the full potential of radio measurements of cosmic-ray air showers at MHz frequencies, a detector timing synchronization within 1 ns is needed. Large distributed radio detector arrays such as the Auger Engineering Radio Array (AERA) rely on timing via the Global Positioning System (GPS) for the synchronization of individual detector station clocks. Unfortunately, GPS timing is expected to have an accuracy no better than about 5 ns. In practice, in particular in AERA, the GPS clocks exhibit drifts on the order of tens of ns. We developed a technique to correct for the GPS drifts, and an independent method is used to cross-check that indeed we reach a nanosecond-scale timing accuracy by this correction. First, we operate a ``beacon transmitter'' which emits defined sine waves detected by AERA antennas recorded within the physics data. The relative phasing of these sine waves can be used to correct for GPS clock drifts. In addition to this, we observe radio pulses emitted by commercial airplanes, the position of which we determine in real time from Automatic Dependent Surveillance Broadcasts intercepted with a software-defined radio. From the known source location and the measured arrival times of the pulses we determine relative timing offsets between radio detector stations. We demonstrate with a combined analysis that the two methods give a consistent timing calibration with an accuracy of 2 ns or better. Consequently, the beacon method alone can be used in the future to continuously determine and correct for GPS clock drifts in each individual event measured by AERA.

Nanosecond-level time synchronization of autonomous radio detector stations for extensive air showers

DOE PAGES

Aab, Alexander

2016-01-29

To exploit the full potential of radio measurements of cosmic-ray air showers at MHz frequencies, a detector timing synchronization within 1 ns is needed. Large distributed radio detector arrays such as the Auger Engineering Radio Array (AERA) rely on timing via the Global Positioning System (GPS) for the synchronization of individual detector station clocks. Unfortunately, GPS timing is expected to have an accuracy no better than about 5 ns. In practice, in particular in AERA, the GPS clocks exhibit drifts on the order of tens of ns. We developed a technique to correct for the GPS drifts, and an independentmore » method used for cross-checks that indeed we reach nanosecond-scale timing accuracy by this correction. First, we operate a “beacon transmitter” which emits defined sine waves detected by AERA antennas recorded within the physics data. The relative phasing of these sine waves can be used to correct for GPS clock drifts. In addition to this, we observe radio pulses emitted by commercial airplanes, the position of which we determine in real time from Automatic Dependent Surveillance Broadcasts intercepted with a software-defined radio. From the known source location and the measured arrival times of the pulses we determine relative timing offsets between radio detector stations. We demonstrate with a combined analysis that the two methods give a consistent timing calibration with an accuracy of 2 ns or better. Consequently, the beacon method alone can be used in the future to continuously determine and correct for GPS clock drifts in each individual event measured by AERA.« less

Gravitational waves from relativistic neutron-star mergers with microphysical equations of state.

PubMed

Oechslin, R; Janka, H-T

2007-09-21

The gravitational wave (GW) emission from a set of relativistic neutron-star (NS) merger simulations is analyzed and characteristic signal features are identified. The distinct peak in the GW energy spectrum that is associated with the formation of a hypermassive merger remnant has a frequency that depends strongly on the properties of the nuclear equation of state (EOS) and on the total mass of the binary system, whereas the mass ratio and the NS spins have a weak influence. If the total mass can be determined from the inspiral chirp signal, the peak frequency of the post-merger signal is a sensitive indicator of the EOS.

Design and fabrication of two kind of SOI-based EA-type VOAs

NASA Astrophysics Data System (ADS)

Yuan, Pei; Wang, Yue; Wu, Yuanda; An, Junming; Hu, Xiongwei

2018-06-01

SOI-based variable optical attenuators based on electro-absorption mechanism are demonstrated in this paper. Two different doping structures are adopted to realize the attenuation: a structure with a single lateral p-i-n diode and a structure with several lateral p-i-n diodes connected in series. The VOAs with lateral p-i-n diodes connected in series (series VOA) can greatly improve the device attenuation efficiency compared to VOAs with a single lateral p-i-n diode structure (single VOA), which is verified by the experimental results that the attenuation efficiency of the series VOA and the single VOA is 3.76 dB/mA and 0.189 dB/mA respectively. The corresponding power consumption at 20 dB attenuation is 202 mW (series VOA) and 424 mW (single VOA) respectively. The raise time is 34.5 ns (single VOA) and 45.5 ns (series VOA), and the fall time is 37 ns (single VOA) and 48.5 ns (series VOA).

Beneficial effect of post-deposition treatment in high-efficiency Cu(In,Ga)Se{sub 2} solar cells through reduced potential fluctuations

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

Jensen, S. A., E-mail: Soren.Jensen@nrel.gov, E-mail: Darius.Kuciauskas@nrel.gov; Glynn, S.; Kanevce, A.

World-record power conversion efficiencies for Cu(In,Ga)Se{sub 2} (CIGS) solar cells have been achieved via a post-deposition treatment with alkaline metals, which increases the open-circuit voltage and fill factor. We explore the role of the potassium fluoride (KF) post-deposition treatment in CIGS by employing energy- and time-resolved photoluminescence spectroscopy and electrical characterization combined with numerical modeling. The bulk carrier lifetime is found to increase with post-deposition treatment from 255 ns to 388 ns, which is the longest charge carrier lifetime reported for CIGS, and within ∼40% of the radiative limit. We find evidence that the post-deposition treatment causes a decrease in the electronicmore » potential fluctuations. These potential fluctuations have previously been shown to reduce the open-circuit voltage and the device efficiency in CIGS. Additionally, numerical simulations based on the measured carrier lifetimes and mobilities show a diffusion length of ∼10 μm, which is ∼4 times larger than the film thickness. Thus, carrier collection in the bulk is not a limiting factor for device efficiency. By considering differences in doping, bandgap, and potential fluctuations, we present a possible explanation for the voltage difference between KF-treated and untreated samples.« less

Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations.

PubMed

Koulgi, Shruti; Sonavane, Uddhavesh; Joshi, Rajendra

2010-11-01

Protein folding studies were carried out by performing microsecond time scale simulations on the ultrafast/fast folding protein Engrailed Homeodomain (EnHD) from Drosophila melanogaster. It is a three-helix bundle protein consisting of 54 residues (PDB ID: 1ENH). The positions of the helices are 8-20 (Helix I), 26-36 (Helix II) and 40-53 (Helix III). The second and third helices together form a Helix-Turn-Helix (HTH) motif which belongs to the family of DNA binding proteins. The molecular dynamics (MD) simulations were performed using replica exchange molecular dynamics (REMD). REMD is a method that involves simulating a protein at different temperatures and performing exchanges at regular time intervals. These exchanges were accepted or rejected based on the Metropolis criterion. REMD was performed using the AMBER FF03 force field with the generalised Born solvation model for the temperature range 286-373 K involving 30 replicas. The extended conformation of the protein was used as the starting structure. A simulation of 600 ns per replica was performed resulting in an overall simulation time of 18 μs. The protein was seen to fold close to the native state with backbone root mean square deviation (RMSD) of 3.16 Å. In this low RMSD structure, the Helix I was partially formed with a backbone RMSD of 3.37 Å while HTH motif had an RMSD of 1.81 Å. Analysis suggests that EnHD folds to its native structure via an intermediate in which the HTH motif is formed. The secondary structure development occurs first followed by tertiary packing. The results were in good agreement with the experimental findings. Copyright © 2010 Elsevier Inc. All rights reserved.

Analysis of 440 GeV proton beam–matter interaction experiments at the High Radiation Materials test facility at CERN

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

Burkart, F.; Schmidt, R.; Wollmann, D.

2015-08-07

In a previous paper [Schmidt et al., Phys. Plasmas 21, 080701 (2014)], we presented the first results on beam–matter interaction experiments that were carried out at the High Radiation Materials test facility at CERN. In these experiments, extended cylindrical targets of solid copper were irradiated with beam of 440 GeV protons delivered by the Super Proton Synchrotron (SPS). The beam comprised of a large number of high intensity proton bunches, each bunch having a length of 0.5 ns with a 50 ns gap between two neighboring bunches, while the length of this entire bunch train was about 7 μs. These experiments established the existencemore » of the hydrodynamic tunneling phenomenon the first time. Detailed numerical simulations of these experiments were also carried out which were reported in detail in another paper [Tahir et al., Phys. Rev. E 90, 063112 (2014)]. Excellent agreement was found between the experimental measurements and the simulation results that validate our previous simulations done using the Large Hadron Collider (LHC) beam of 7 TeV protons [Tahir et al., Phys. Rev. Spec. Top.--Accel. Beams 15, 051003 (2012)]. According to these simulations, the range of the full LHC proton beam and the hadronic shower can be increased by more than an order of magnitude due to the hydrodynamic tunneling, compared to that of a single proton. This effect is of considerable importance for the design of machine protection system for hadron accelerators such as SPS, LHC, and Future Circular Collider. Recently, using metal cutting technology, the targets used in these experiments have been dissected into finer pieces for visual and microscopic inspection in order to establish the precise penetration depth of the protons and the corresponding hadronic shower. This, we believe will be helpful in studying the very important phenomenon of hydrodynamic tunneling in a more quantitative manner. The details of this experimental work together with a comparison with the numerical simulations are presented in this paper.« less

Multiphoton imaging reveals that nanosecond pulsed electric fields collapse tumor and normal vascular perfusion in human glioblastoma xenografts.

PubMed

Bardet, Sylvia M; Carr, Lynn; Soueid, Malak; Arnaud-Cormos, Delia; Leveque, Philippe; O'Connor, Rodney P

2016-10-04

Despite the biomedical advances of the last century, many cancers including glioblastoma are still resistant to existing therapies leaving patients with poor prognoses. Nanosecond pulsed electric fields (nsPEF) are a promising technology for the treatment of cancer that have thus far been evaluated in vitro and in superficial malignancies. In this paper, we develop a tumor organoid model of glioblastoma and apply intravital multiphoton microscopy to assess their response to nsPEFs. We demonstrate for the first time that a single 10 ns, high voltage electric pulse (35-45 kV/cm), collapses the perfusion of neovasculature, and also alters the diameter of capillaries and larger vessels in normal tissue. These results contribute to the fundamental understanding of nsPEF effects in complex tissue environments, and confirm the potential of nsPEFs to disrupt the microenvironment of solid tumors such as glioblastoma.

Synergistic induction of astrocytic differentiation by factors secreted from meninges in the mouse developing brain.

PubMed

Kawamura, Yoichiro; Katada, Sayako; Noguchi, Hirofumi; Yamamoto, Hiroyuki; Sanosaka, Tsukasa; Iihara, Koji; Nakashima, Kinichi

2017-11-01

Astrocytes, which support diverse neuronal functions, are generated from multipotent neural stem/precursor cells (NS/PCs) during brain development. Although many astrocyte-inducing factors have been identified and studied in vitro, the regions and/or cells that produce these factors in the developing brain remain elusive. Here, we show that meninges-produced factors induce astrocytic differentiation of NS/PCs. Consistent with the timing when astrocytic differentiation of NS/PCs increases, expression of astrocyte-inducing factors is upregulated. Meningeal secretion-mimicking combinatorial treatment of NS/PCs with bone morphogenetic protein 4, retinoic acid and leukemia inhibitory factor synergistically activate the promoter of a typical astrocytic marker, glial fibrillary acidic protein. Taken together, our data suggest that meninges play an important role in astrocytic differentiation of NS/PCs in the developing brain. © 2017 Federation of European Biochemical Societies.

Molecular Simulation of the Free Energy for the Accurate Determination of Phase Transition Properties of Molecular Solids

NASA Astrophysics Data System (ADS)

Sellers, Michael; Lisal, Martin; Brennan, John

2015-06-01

Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.

Evaluation of the Abbott RealTime HCV genotype II plus RUO (PLUS) assay with reference to core and NS5B sequencing.

PubMed

Mallory, Melanie A; Lucic, Danijela; Ebbert, Mark T W; Cloherty, Gavin A; Toolsie, Dan; Hillyard, David R

2017-05-01

HCV genotyping remains a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen. Current commercial genotyping assays may have difficulty identifying 1a, 1b and genotype 6. To evaluate the concordance for identifying 1a, 1b, and genotype 6 between two methods: the PLUS assay and core/NS5B sequencing. This study included 236 plasma and serum samples previously genotyped by core/NS5B sequencing. Of these, 25 samples were also previously tested by the Abbott RealTime HCV GT II Research Use Only (RUO) assay and yielded ambiguous results. The remaining 211 samples were routine genotype 1 (n=169) and genotype 6 (n=42). Genotypes obtained from sequence data were determined using a laboratory-developed HCV sequence analysis tool and the NCBI non-redundant database. Agreement between the PLUS assay and core/NS5B sequencing for genotype 1 samples was 95.8% (162/169), with 96% (127/132) and 95% (35/37) agreement for 1a and 1b samples respectively. PLUS results agreed with core/NS5B sequencing for 83% (35/42) of unselected genotype 6 samples, with the remaining seven "not detected" by the PLUS assay. Among the 25 samples with ambiguous GT II results, 15 were concordant by PLUS and core/NS5B sequencing, nine were not detected by PLUS, and one sample had an internal control failure. The PLUS assay is an automated method that identifies 1a, 1b and genotype 6 with good agreement with gold-standard core/NS5B sequencing and can aid in the resolution of certain genotype samples with ambiguous GT II results. Copyright © 2017 Elsevier B.V. All rights reserved.