Explicit high-order symplectic integrators for charged particles in general electromagnetic fields
Tao, Molei
2016-01-01
This article considers non-relativistic charged particle dynamics in both static and non-static electromagnetic fields, which are governed by nonseparable, possibly time-dependent Hamiltonians. For the first time, explicit symplectic integrators of arbitrary high-orders are constructed for accurate and efficient simulations of such mechanical systems. Performances superior to the standard non-symplectic method of Runge-Kutta are demonstrated on two examples: the first is on the confined motio...
High-order nodal discontinuous Galerkin particle-in-cell method on unstructured grids
Jacobs, G. B.; Hesthaven, J. S.
2006-05-01
We present a high-order particle-in-cell (PIC) algorithm for the simulation of kinetic plasmas dynamics. The core of the algorithm utilizes an unstructured grid discontinuous Galerkin Maxwell field solver combining high-order accuracy with geometric flexibility. We introduce algorithms in the Lagrangian framework that preserve the favorable properties of the field solver in the PIC solver. Fast full-order interpolation and effective search algorithms are used for tracking individual particles on the general grid and smooth particle shape functions are introduced to ensure low noise in the charge and current density. A pre-computed levelset distance function is employed to represent the geometry and facilitates complex particle-boundary interaction. To enforce charge conservation we consider two different techniques, one based on projection and one on hyperbolic cleaning. Both are found to work well, although the latter is found be too expensive when used with explicit time integration. Examples of simple plasma phenomena, e.g., plasma waves, instabilities, and Landau damping are shown to agree well with theoretical predictions and/or results found by other computational methods. We also discuss generic well known problems such as numerical Cherenkov radiation and grid heating before presenting a few two-dimensional tests, showing the potential of the current method to handle fully relativistic plasma dynamics in complex geometries.
Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems
Energy Technology Data Exchange (ETDEWEB)
Xiao, Jianyuan [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Qin, Hong [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543, USA; Liu, Jian [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; He, Yang [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Zhang, Ruili [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Sun, Yajuan [LSEC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, P.O. Box 2719, Beijing 100190, China
2015-11-01
Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithms conserve a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a structure-preserving splitting method discovered by He et al. [preprint arXiv: 1505.06076 (2015)], which produces five exactly soluble sub-systems, and high-order structure-preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom on massively parallel supercomputers. The algorithms have been tested and verified by the two physics problems, i.e., the nonlinear Landau damping and the electron Bernstein wave. (C) 2015 AIP Publishing LLC.
Yu, Mei Ping; Han, Yi Ping; Cui, Zhi Wei; Chen, An Tao
2017-07-01
This study investigates the electromagnetic scattering of a high-order Bessel vortex beam by multiple dielectric particles of arbitrary shape based on the surface integral equation (SIE) method. In Cartesian coordinates, the mathematical formulas are given for characterizing the electromagnetic field components of an arbitrarily incident high-order Bessel vortex beam. By using the SIE, a numerical scheme is formulated to find solutions for characterizing the electromagnetic scattering by multiple homogeneous particles of arbitrary shape and a home-made FORTRAN program is written. The presented theoretical derivations as well as the home-made program are validated by comparing to the scattering results of a Zero-Order Bessel Beam by the Generalized Lorenz-Mie theory. From our simulations, the beam's order, half-cone angles, and the ways of particles' arrangement have a great influence upon the differential scattering cross section (DSCS) for multiple particles. Furthermore, for a better understanding of the scattering characteristic in three dimension (3-D) space, the 3-D distribution of the DSCS for different cases is presented. It is anticipated that these results can be helpful to understand the scattering mechanisms of a high-order Bessel vortex beam on multiple dielectric particles of arbitrary shape.
Yu, Jianbo
2015-12-01
Prognostics is much efficient to achieve zero-downtime performance, maximum productivity and proactive maintenance of machines. Prognostics intends to assess and predict the time evolution of machine health degradation so that machine failures can be predicted and prevented. A novel prognostics system is developed based on the data-model-fusion scheme using the Bayesian inference-based self-organizing map (SOM) and an integration of logistic regression (LR) and high-order particle filtering (HOPF). In this prognostics system, a baseline SOM is constructed to model the data distribution space of healthy machine under an assumption that predictable fault patterns are not available. Bayesian inference-based probability (BIP) derived from the baseline SOM is developed as a quantification indication of machine health degradation. BIP is capable of offering failure probability for the monitored machine, which has intuitionist explanation related to health degradation state. Based on those historic BIPs, the constructed LR and its modeling noise constitute a high-order Markov process (HOMP) to describe machine health propagation. HOPF is used to solve the HOMP estimation to predict the evolution of the machine health in the form of a probability density function (PDF). An on-line model update scheme is developed to adapt the Markov process changes to machine health dynamics quickly. The experimental results on a bearing test-bed illustrate the potential applications of the proposed system as an effective and simple tool for machine health prognostics.
Kamina, Anyango D; Williams, Noreen
2017-01-01
RNA binding proteins are involved in many aspects of RNA metabolism. In Trypanosoma brucei, our laboratory has identified two trypanosome-specific RNA binding proteins P34 and P37 that are involved in the maturation of the 60S subunit during ribosome biogenesis. These proteins are part of the T. brucei 5S ribonucleoprotein particle (5S RNP) and P34 binds to 5S ribosomal RNA (rRNA) and ribosomal protein L5 through its N-terminus and its RNA recognition motif (RRM) domains. We generated truncated P34 proteins to determine these domains' interactions with 5S rRNA and L5. Our analyses demonstrate that RRM1 of P34 mediates the majority of binding with 5S rRNA and the N-terminus together with RRM1 contribute the most to binding with L5. We determined that the consensus ribonucleoprotein (RNP) 1 and 2 sequences, characteristic of canonical RRM domains, are not fully conserved in the RRM domains of P34. However, the aromatic amino acids previously described to mediate base stacking interactions with their RNA target are conserved in both of the RRM domains of P34. Surprisingly, mutation of these aromatic residues did not disrupt but instead enhanced 5S rRNA binding. However, we identified four arginine residues located in RRM1 of P34 that strongly impact L5 binding. These mutational analyses of P34 suggest that the binding site for 5S rRNA and L5 are near each other and specific residues within P34 regulate the formation of the 5S RNP. These studies show the unique way that the domains of P34 mediate binding with the T. brucei 5S RNP.
Tomkuvienė, Miglė; Ličytė, Janina; Olendraitė, Ingrida; Liutkevičiūtė, Zita; Clouet-d'Orval, Béatrice; Klimašauskas, Saulius
2017-09-01
Archaeal fibrillarin (aFib) is a well-characterized S-adenosyl methionine (SAM)-dependent RNA 2'-O-methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a box C/D guide RNA. In the reaction, the guide RNA serves to direct the methylation reaction to a specific site in tRNA or rRNA by sequence complementarity. Here we show that a Pyrococcus abyssi aFib-Nop5 heterodimer can alone perform SAM-dependent 2'-O-methylation of 16S and 23S ribosomal RNAs in vitro independently of L7Ae and C/D guide RNAs. Using tritium-labeling, mass spectrometry, and reverse transcription analysis, we identified three in vitro 2'-O-methylated positions in the 16S rRNA of P. abyssi, positions lying outside of previously reported pyrococcal C/D RNP methylation sites. This newly discovered stand-alone activity of aFib-Nop5 may provide an example of an ancestral activity retained in enzymes that were recruited to larger complexes during evolution. © 2017 Tomkuvienė et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Synthesis of highly ordered 30 nm NiFe2O4 particles by the microwave-combustion method
Mahmoud, M. H.; Elshahawy, A. M.; Makhlouf, Salah A.; Hamdeh, H. H.
2014-11-01
NiFe2O4 of 30 nm average size was synthesized by microwave combustion and subsequent solid state reaction at 1273 K. The materials were characterized by X-ray diffraction, TEM, vibrating sample magnetometery and Mössbauer spectroscopy. The microwave combustion produced materials were comprised chemically of ferrites and a smaller amount of hematite. The NiFe2O4 particles have the cubic spinel structure with crystallites of sizes less than 10 nm, and were found to have low magnetization, and essentially no hysteresis loop; characteristics of superparamagnetism. Upon annealing at temperatures 973 K and below, crystallite growth was accompanied by increase in both coercive field and magnetization. The coercive field was a maximum for the sample annealed at 973 K. On the other hand, crystallite growth at higher annealing temperatures yielded mainly ferrites and improvement in soft magnetic properties. Mössbauer and magnetization measurements indicate that the fine NiFe2O4 particles produced at the annealing temperature of 1273 K are in good chemical and magnetic order, excluding the spins arrangement at the surface of the particles which show spin glass-like behavior.
DEFF Research Database (Denmark)
Jønson, Lars; Nielsen, Finn Cilius; Christiansen, Jan
2011-01-01
be regarded as a supramolecular assembly of RNA and protein, probably representing several overlapping post-transcriptional operons. The present protocol describes how RNP granules may be isolated by the transgenic expression of a 3X FLAG version of an RNA-binding protein under tetracycline control via...
Mukherjee, Nillohit; Jana, Sumanta; Gopal Khan, Gobinda; Mondal, Anup
2012-12-01
Visible light induced frequency switching behavior, exhibited by the electrochemically deposited thin films of polyvinylpyrrolidone (PVP) encapsulated Ag2S nanosphere (core-shell) is shown here. A low frequency (˜40 Hz) pulse was found to be generated upon illumination with 1 Sun due to excitonic transition, which also showed good switching behavior with the "on" and "off" state of the light. Capping of the semiconductor surface by a polymer like PVP reduces the surface states and thus lowers the built in barrier height and the width of depletion region. So, the number of photo generated but non recombining electron-hole pairs (excitons) increases, which put their signature in some unique physical properties like increase in photoluminescence (PL) intensity, light induced frequency switching behavior due to free exciton generation, etc. Here, the depositions were carried out on indium tin oxide coated glass substrates from an aqueous solution of AgNO3, thioacetamide, and PVP. The films were structurally characterized using high resolution X-ray diffraction, field emission scanning electron microscopy, and high resolution transmission electron microscopic techniques. The deposited particles were regular in shape with significantly high order of size distribution. Furrier transform infrared spectroscopy confirmed the presence of PVP as the encapsulating agent. Optical characterization, viz., UV - vis - NIR and NIR-PL revealed noteworthy amount of NIR emission from the deposited material.
Nuclear surveillance of mRNP formation
DEFF Research Database (Denmark)
Jensen, Torben Heick
Proper formation of mRNP requires co-transcriptional loading of proteins onto nascent transcripts. Mutations in several genes involved in mRNA processing, mRNP assembly and nuclear export lead to production of aberrant mRNPs that are retained in transcription site-associated foci. Retention...... and degradation of transcripts depend on the nuclear exosome of 3’-5’ exonucleases.We have studied connections between mRNP assembly and quality control in the yeast S. cerevisiae using mutants of the THO complex. THO is implicated in co-transcriptional mRNP assembly, but its precise role is not known. Genetic...... and biochemical data now show that a defective THO complex negatively impacts mRNA 3’-end processing. We are currently trying to understand the relationship between this phenomenon and mRNP quality control. Retention of mRNP in THO mutants is dependent on the nuclear exosome component Rrp6p. Using the solved...
Efficient Unsteady Flow Visualization with High-Order Access Dependencies
Energy Technology Data Exchange (ETDEWEB)
Zhang, Jiang; Guo, Hanqi; Yuan, Xiaoru
2016-04-19
We present a novel high-order access dependencies based model for efficient pathline computation in unsteady flow visualization. By taking longer access sequences into account to model more sophisticated data access patterns in particle tracing, our method greatly improves the accuracy and reliability in data access prediction. In our work, high-order access dependencies are calculated by tracing uniformly-seeded pathlines in both forward and backward directions in a preprocessing stage. The effectiveness of our proposed approach is demonstrated through a parallel particle tracing framework with high-order data prefetching. Results show that our method achieves higher data locality and hence improves the efficiency of pathline computation.
Golas, Monika M; Sander, Bjoern; Will, Cindy L; Lührmann, Reinhard; Stark, Holger
2005-03-18
In some eukaryotes, a minor class of introns is removed by the U12-dependent spliceosome, which contains the small nuclear ribonucleoprotein (snRNP) heterodimer U11/U12. The U11/U12 di-snRNP forms a molecular bridge that functionally pairs the intron ends of the pre-mRNA. We have determined the three-dimensional (3D) structure of the human U11/U12 di-snRNP by single particle electron cryomicroscopy using angular reconstitution and random conical tilt. SF3b, a heteromeric protein complex functionally important for branch site recognition, was located in the U11/U12 di-snRNP by antibody labeling and by identification of structural domains of SF3b155, SF3b49, and p14. The conformation of SF3b bound to the U11/U12 di-snRNP differs from that of isolated SF3b: upon integration into the di-snRNP, SF3b rearranges into a more open form. The manner in which SF3b is integrated in the U11/U12 di-snRNP has important implications for branch site recognition. Furthermore, a putative model of the pre-mRNA binding to the U11/U12 di-snRNP is proposed.
A high order solver for the unbounded Poisson equation
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Rasmussen, Johannes Tophøj; Chatelain, Philippe
In mesh-free particle methods a high order solution to the unbounded Poisson equation is usually achieved by constructing regularised integration kernels for the Biot-Savart law. Here the singular, point particles are regularised using smoothed particles to obtain an accurate solution with an order...... of convergence consistent with the moments conserved by the applied smoothing function. In the hybrid particle-mesh method of Hockney and Eastwood (HE) the particles are interpolated onto a regular mesh where the unbounded Poisson equation is solved by a discrete non-cyclic convolution of the mesh values...... and the integration kernel. In this work we show an implementation of high order regularised integration kernels in the HE algorithm for the unbounded Poisson equation to formally achieve an arbitrary high order convergence. We further present a quantitative study of the convergence rate to give further insight...
Directory of Open Access Journals (Sweden)
Benjamin Dombert
Full Text Available Spinal muscular atrophy (SMA is caused by deficiency of the ubiquitously expressed survival motoneuron (SMN protein. SMN is crucial component of a complex for the assembly of spliceosomal small nuclear ribonucleoprotein (snRNP particles. Other cellular functions of SMN are less characterized so far. SMA predominantly affects lower motoneurons, but the cellular basis for this relative specificity is still unknown. In contrast to nonneuronal cells where the protein is mainly localized in perinuclear regions and the nucleus, Smn is also present in dendrites, axons and axonal growth cones of isolated motoneurons in vitro. However, this distribution has not been shown in vivo and it is not clear whether Smn and hnRNP R are also present in presynaptic axon terminals of motoneurons in postnatal mice. Smn also associates with components not included in the classical SMN complex like RNA-binding proteins FUS, TDP43, HuD and hnRNP R which are involved in RNA processing, subcellular localization and translation. We show here that Smn and hnRNP R are present in presynaptic compartments at neuromuscular endplates of embryonic and postnatal mice. Smn and hnRNP R are localized in close proximity to each other in axons and axon terminals both in vitro and in vivo. We also provide new evidence for a direct interaction of Smn and hnRNP R in vitro and in vivo, particularly in the cytosol of motoneurons. These data point to functions of SMN beyond snRNP assembly which could be crucial for recruitment and transport of RNA particles into axons and axon terminals, a mechanism which may contribute to SMA pathogenesis.
High-order epistasis shapes evolutionary trajectories.
Sailer, Zachary R.; Harms, Michael J.
2017-01-01
High-order epistasis-where the effect of a mutation is determined by interactions with two or more other mutations-makes small, but detectable, contributions to genotype-fitness maps. While epistasis between pairs of mutations is known to be an important determinant of evolutionary trajectories, the evolutionary consequences of high-order epistasis remain poorly understood. To determine the effect of high-order epistasis on evolutionary trajectories, we computationally removed high-order epis...
High-order epistasis shapes evolutionary trajectories
Sailer, Zachary R.
2017-01-01
High-order epistasis?where the effect of a mutation is determined by interactions with two or more other mutations?makes small, but detectable, contributions to genotype-fitness maps. While epistasis between pairs of mutations is known to be an important determinant of evolutionary trajectories, the evolutionary consequences of high-order epistasis remain poorly understood. To determine the effect of high-order epistasis on evolutionary trajectories, we computationally removed high-order epis...
The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress.
Sloan, Katherine E; Bohnsack, Markus T; Watkins, Nicholas J
2013-10-17
Several proto-oncogenes and tumor suppressors regulate the production of ribosomes. Ribosome biogenesis is a major consumer of cellular energy, and defects result in p53 activation via repression of mouse double minute 2 (MDM2) homolog by the ribosomal proteins RPL5 and RPL11. Here, we report that RPL5 and RPL11 regulate p53 from the context of a ribosomal subcomplex, the 5S ribonucleoprotein particle (RNP). We provide evidence that the third component of this complex, the 5S rRNA, is critical for p53 regulation. In addition, we show that the 5S RNP is essential for the activation of p53 by p14(ARF), a protein that is activated by oncogene overexpression. Our data show that the abundance of the 5S RNP, and therefore p53 levels, is determined by factors regulating 5S complex formation and ribosome integration, including the tumor suppressor PICT1. The 5S RNP therefore emerges as the critical coordinator of signaling pathways that couple cell proliferation with ribosome production. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.
Calviño, Fabiola R.; Kharde, Satyavati; Ori, Alessandro; Hendricks, Astrid; Wild, Klemens; Kressler, Dieter; Bange, Gert; Hurt, Ed; Beck, Martin; Sinning, Irmgard
2015-04-01
During 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is not known. Here we report the crystal structure of a ternary symportin Syo1-RpL5-N-RpL11 complex and provide biochemical and structural insights into 5S RNP assembly. Syo1 guards the 25S RNA-binding surface on RpL11 and competes with H84 for binding. Pull-down experiments show that H84 releases RpL11 from the ternary complex, but not in the presence of 5S RNA. Crosslinking mass spectrometry visualizes structural rearrangements on incorporation of 5S RNA into the Syo1-RpL5-RpL11 complex supporting the formation of a pre-5S RNP. Our data underline the dual role of Syo1 in ribosomal protein transport and as an assembly platform for 5S RNP.
Calviño, Fabiola R; Kharde, Satyavati; Ori, Alessandro; Hendricks, Astrid; Wild, Klemens; Kressler, Dieter; Bange, Gert; Hurt, Ed; Beck, Martin; Sinning, Irmgard
2015-04-07
During 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is not known. Here we report the crystal structure of a ternary symportin Syo1-RpL5-N-RpL11 complex and provide biochemical and structural insights into 5S RNP assembly. Syo1 guards the 25S RNA-binding surface on RpL11 and competes with H84 for binding. Pull-down experiments show that H84 releases RpL11 from the ternary complex, but not in the presence of 5S RNA. Crosslinking mass spectrometry visualizes structural rearrangements on incorporation of 5S RNA into the Syo1-RpL5-RpL11 complex supporting the formation of a pre-5S RNP. Our data underline the dual role of Syo1 in ribosomal protein transport and as an assembly platform for 5S RNP.
High-order epistasis shapes evolutionary trajectories.
Sailer, Zachary R; Harms, Michael J
2017-05-01
High-order epistasis-where the effect of a mutation is determined by interactions with two or more other mutations-makes small, but detectable, contributions to genotype-fitness maps. While epistasis between pairs of mutations is known to be an important determinant of evolutionary trajectories, the evolutionary consequences of high-order epistasis remain poorly understood. To determine the effect of high-order epistasis on evolutionary trajectories, we computationally removed high-order epistasis from experimental genotype-fitness maps containing all binary combinations of five mutations. We then compared trajectories through maps both with and without high-order epistasis. We found that high-order epistasis strongly shapes the accessibility and probability of evolutionary trajectories. A closer analysis revealed that the magnitude of epistasis, not its order, predicts is effects on evolutionary trajectories. We further find that high-order epistasis makes it impossible to predict evolutionary trajectories from the individual and paired effects of mutations. We therefore conclude that high-order epistasis profoundly shapes evolutionary trajectories through genotype-fitness maps.
High order harmonic generation in rare gases
Energy Technology Data Exchange (ETDEWEB)
Budil, Kimberly Susan [Univ. of California, Davis, CA (United States)
1994-05-01
The process of high order harmonic generation in atomic gases has shown great promise as a method of generating extremely short wavelength radiation, extending far into the extreme ultraviolet (XUV). The process is conceptually simple. A very intense laser pulse (I ~10^{13}-10^{14} W/cm^{2}) is focused into a dense (~10^{17} particles/cm^{3}) atomic medium, causing the atoms to become polarized. These atomic dipoles are then coherently driven by the laser field and begin to radiate at odd harmonics of the laser field. This dissertation is a study of both the physical mechanism of harmonic generation as well as its development as a source of coherent XUV radiation. Recently, a semiclassical theory has been proposed which provides a simple, intuitive description of harmonic generation. In this picture the process is treated in two steps. The atom ionizes via tunneling after which its classical motion in the laser field is studied. Electron trajectories which return to the vicinity of the nucleus may recombine and emit a harmonic photon, while those which do not return will ionize. An experiment was performed to test the validity of this model wherein the trajectory of the electron as it orbits the nucleus or ion core is perturbed by driving the process with elliptically, rather than linearly, polarized laser radiation. The semiclassical theory predicts a rapid turn-off of harmonic production as the ellipticity of the driving field is increased. This decrease in harmonic production is observed experimentally and a simple quantum mechanical theory is used to model the data. The second major focus of this work was on development of the harmonic "source". A series of experiments were performed examining the spatial profiles of the harmonics. The quality of the spatial profile is crucial if the harmonics are to be used as the source for experiments, particularly if they must be refocused.
Essential Assembly Factor Rpf2 Forms Novel Interactions within the 5S RNP in Trypanosoma brucei.
Kamina, Anyango D; Jaremko, Daniel; Christen, Linda; Williams, Noreen
2017-01-01
Ribosome biogenesis is a highly complex and conserved cellular process that is responsible for making ribosomes. During this process, there are several assembly steps that function as regulators to ensure proper ribosome formation. One of these steps is the assembly of the 5S ribonucleoprotein particle (5S RNP) in the central protuberance of the 60S ribosomal subunit. In eukaryotes, the 5S RNP is composed of 5S rRNA, ribosomal proteins L5 and L11, and assembly factors Rpf2 and Rrs1. Our laboratory previously showed that in Trypanosoma brucei, the 5S RNP is composed of 5S rRNA, L5, and trypanosome-specific RNA binding proteins P34 and P37. In this study, we characterize an additional component of the 5S RNP, the T. brucei homolog of Rpf2. This is the first study to functionally characterize interactions mediated by Rpf2 in an organism other than fungi. T. brucei Rpf2 (TbRpf2) was identified from tandem affinity purification using extracts prepared from protein A-tobacco etch virus (TEV)-protein C (PTP)-tagged L5, P34, and P37 cell lines, followed by mass spectrometry analysis. We characterized the binding interactions between TbRpf2 and the previously characterized members of the T. brucei 5S RNP. Our studies show that TbRpf2 mediates conserved binding interactions with 5S rRNA and L5 and that TbRpf2 also interacts with trypanosome-specific proteins P34 and P37. We performed RNA interference (RNAi) knockdown of TbRpf2 and showed that this protein is essential for the survival of the parasites and is critical for proper ribosome formation. These studies provide new insights into a critical checkpoint in the ribosome biogenesis pathway in T. brucei. IMPORTANCETrypanosoma brucei is the parasitic protozoan that causes African sleeping sickness. Ribosome assembly is essential for the survival of this parasite through the different host environments it encounters during its life cycle. The assembly of the 5S ribonucleoprotein particle (5S RNP) functions as one of the
High-Order Frequency-Locked Loops
DEFF Research Database (Denmark)
Golestan, Saeed; Guerrero, Josep M.; Quintero, Juan Carlos Vasquez
2017-01-01
In very recent years, some attempts for designing high-order frequency-locked loops (FLLs) have been made. Nevertheless, the advantages and disadvantages of these structures, particularly in comparison with a standard FLL and high-order phase-locked loops (PLLs), are rather unclear. This lack...... study, and its small-signal modeling, stability analysis, and parameter tuning are presented. Finally, to gain insight about advantages and disadvantages of high-order FLLs, a theoretical and experimental performance comparison between the designed second-order FLL and a standard FLL (first-order FLL...
Energy Technology Data Exchange (ETDEWEB)
Cervera, J.; Baguena-Cervellera, R.; Martinez, A.
1985-12-01
The effects of zinc on the ribonucleoprotein (RNP) constituents of HEp-2 cells have been analyzed. Pulse-chase autoradiographic experiments show a preferential inhibition of nucleolar RNA synthesis and a block in the transport of nucleolar and extranucleolar RNA in zinc-treated cells. Concomitantly with the disturbance in RNA metabolism and in protein synthesis, nucleolar condensation, accumulation of perichromatin granules and fibrils, condensation of interchromatin fibrils, and appearance of dense granular bodies occur. Accumulation of perichromatin fibrils and condensation of interchromatin fibrils appear to be related to the block in the transport of heterogeneous nuclear RNA. Depletion of certain proteins required for the assembly of RNP particles could share in the abnormal behavior of RNA and lead to the accumulation of perichromatin granules and the appearance of dense granular bodies.
Theoretical study on high order interior tomography
Yang, Jiansheng; Cong, Wenxiang; Jiang, Ming; Wang, Ge
2013-01-01
In this paper, we study a new type of high order interior problems characterized by high order differential phase shift measurement. This problem is encountered in local x-ray phase-contrast tomography. Here we extend our previous theoretical framework from interior CT to interior differential phase-contrast tomography, and establish the solution uniqueness in this context. We employ the analytic continuation method and high order total variation minimization which we developed in our previous work for interior CT, and prove that an image in a region of interest (ROI) can be uniquely reconstructed from truncated high order differential projection data if the image is known a priori in a sub-region of the ROI or the image is piecewise polynomial in the ROI. Preliminary numerical experiments support the theoretical finding. PMID:23324783
Jaako, P; Ugale, A; Wahlestedt, M; Velasco-Hernandez, T; Cammenga, J; Lindström, M S; Bryder, D
2017-01-01
Mutations resulting in constitutive activation of signaling pathways that regulate ribosome biogenesis are among the most common genetic events in acute myeloid leukemia (AML). However, whether ribosome biogenesis presents as a therapeutic target to treat AML remains unexplored. Perturbations in ribosome biogenesis trigger the 5S ribonucleoprotein particle (RNP)-Mdm2-p53 ribosomal stress pathway, and induction of this pathway has been shown to have therapeutic efficacy in Myc-driven lymphoma. In the current study we address the physiological and therapeutic role of the 5S RNP-Mdm2-p53 pathway in AML. By utilizing mice that have defective ribosome biogenesis due to downregulation of ribosomal protein S19 (Rps19), we demonstrate that induction of the 5S RNP-Mdm2-p53 pathway significantly delays the initiation of AML. However, even a severe Rps19 deficiency that normally results in acute bone marrow failure has no consistent efficacy on already established disease. Finally, by using mice that harbor a mutation in the Mdm2 gene disrupting its binding to 5S RNP, we show that loss of the 5S RNP-Mdm2-p53 pathway is dispensable for development of AML. Our study suggests that induction of the 5S RNP-Mdm2-p53 ribosomal stress pathway holds limited potential as a single-agent therapy in the treatment of AML.
Sabath, Ivan; Skrajna, Aleksandra; Yang, Xiao-cui; Dadlez, Michał; Marzluff, William F.; Dominski, Zbigniew
2013-01-01
3′-End cleavage of animal replication-dependent histone pre-mRNAs is controlled by the U7 snRNP. Lsm11, the largest component of the U7-specific Sm ring, interacts with FLASH, and in mammalian nuclear extracts these two proteins form a platform that recruits the CPSF73 endonuclease and other polyadenylation factors to the U7 snRNP. FLASH is limiting, and the majority of the U7 snRNP in mammalian extracts exists as a core particle consisting of the U7 snRNA and the Sm ring. Here, we purified the U7 snRNP from Drosophila nuclear extracts and characterized its composition by mass spectrometry. In contrast to the mammalian U7 snRNP, a significant fraction of the Drosophila U7 snRNP contains endogenous FLASH and at least six subunits of the polyadenylation machinery: symplekin, CPSF73, CPSF100, CPSF160, WDR33, and CstF64. The same composite U7 snRNP is recruited to histone pre-mRNA for 3′-end processing. We identified a motif in Drosophila FLASH that is essential for the recruitment of the polyadenylation complex to the U7 snRNP and analyzed the role of other factors, including SLBP and Ars2, in 3′-end processing of Drosophila histone pre-mRNAs. SLBP that binds the upstream stem–loop structure likely recruits a yet-unidentified essential component(s) to the processing machinery. In contrast, Ars2, a protein previously shown to interact with FLASH in mammalian cells, is dispensable for processing in Drosophila. Our studies also demonstrate that Drosophila symplekin and three factors involved in cleavage and polyadenylation—CPSF, CstF, and CF Im—are present in Drosophila nuclear extracts in a stable supercomplex. PMID:24145821
High order Poisson Solver for unbounded flows
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Rasmussen, Johannes Tophøj; Chatelain, Philippe
2015-01-01
This paper presents a high order method for solving the unbounded Poisson equation on a regular mesh using a Green’s function solution. The high order convergence was achieved by formulating mollified integration kernels, that were derived from a filter regularisation of the solution field....... The method was implemented on a rectangular domain using fast Fourier transforms (FFT) to increase computational efficiency. The Poisson solver was extended to directly solve the derivatives of the solution. This is achieved either by including the differential operator in the integration kernel...... or by performing the differentiation as a multiplication of the Fourier coefficients. In this way, differential operators such as the divergence or curl of the solution field could be solved to the same high order convergence without additional computational effort. The method was applied and validated using...
High-Order Thermal Radiative Transfer
Energy Technology Data Exchange (ETDEWEB)
Woods, Douglas Nelson [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cleveland, Mathew Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wollaeger, Ryan Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Warsa, James S. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2017-09-18
The objective of this research is to asses the sensitivity of the linearized thermal radiation transport equations to finite element order on unstructured meshes and to investigate the sensitivity of the nonlinear TRT equations due to evaluating the opacities and heat capacity at nodal temperatures in 2-D using high-order finite elements.
High-Order Adaptive Galerkin Methods
Canuto, C.; Nochetto, R.H.; Stevenson, R.; Verani, M.; Kirby, R.M.; Berzins, M.; Hesthaven, J.S.
2015-01-01
We design adaptive high-order Galerkin methods for the solution of linear elliptic problems and study their performance. We first consider adaptive Fourier-Galerkin methods and Legendre-Galerkin methods, which offer unlimited approximation power only restricted by solution and data regularity. Their
Stuparevic, Igor; Mosrin-Huaman, Christine; Hervouet-Coste, Nadège; Remenaric, Mateja; Rahmouni, A Rachid
2013-11-01
The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated. Using an experimental approach in which mRNP formation in yeast is disturbed by the action of the bacterial Rho helicase, we have shown previously that the targeting of Rho-induced aberrant mRNPs is mediated by Rrp6p, which is recruited cotranscriptionally in association with Nrd1p following Rho action. Here we investigated the specific involvement in this quality control process of different cofactors associated with the nuclear RNA degradation machinery. We show that, in addition to the main hydrolytic action of the exonuclease Rrp6p, the cofactors Rrp47p, Mpp6p as well as the Trf-Air-Mtr4 polyadenylation (TRAMP) components Trf4p, Trf5p, and Air2p contribute significantly by stimulating the degradation process upon their cotranscriptional recruitment. Trf4p and Trf5p are apparently recruited in two distinct TRAMP complexes that both contain Air2p as component. Surprisingly, Rrp47p appears to play an important role in mutual protein stabilization with Rrp6p, which highlights a close association between the two partners. Together, our results provide an integrated view of how different cofactors of the RNA degradation machinery cooperate to target and eliminate aberrant mRNPs.
Stuparevic, Igor; Mosrin-Huaman, Christine; Hervouet-Coste, Nadège; Remenaric, Mateja; Rahmouni, A. Rachid
2013-01-01
The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated. Using an experimental approach in which mRNP formation in yeast is disturbed by the action of the bacterial Rho helicase, we have shown previously that the targeting of Rho-induced aberrant mRNPs is mediated by Rrp6p, which is recruited cotranscriptionally in association with Nrd1p following Rho action. Here we investigated the specific involvement in this quality control process of different cofactors associated with the nuclear RNA degradation machinery. We show that, in addition to the main hydrolytic action of the exonuclease Rrp6p, the cofactors Rrp47p, Mpp6p as well as the Trf-Air-Mtr4 polyadenylation (TRAMP) components Trf4p, Trf5p, and Air2p contribute significantly by stimulating the degradation process upon their cotranscriptional recruitment. Trf4p and Trf5p are apparently recruited in two distinct TRAMP complexes that both contain Air2p as component. Surprisingly, Rrp47p appears to play an important role in mutual protein stabilization with Rrp6p, which highlights a close association between the two partners. Together, our results provide an integrated view of how different cofactors of the RNA degradation machinery cooperate to target and eliminate aberrant mRNPs. PMID:24047896
HuR-Regulated mRNAs Associated with Nuclear hnRNP A1-RNP Complexes
Directory of Open Access Journals (Sweden)
Apostolia Guialis
2013-10-01
Full Text Available Post-transcriptional regulatory networks are dependent on the interplay of many RNA-binding proteins having a major role in mRNA processing events in mammals. We have been interested in the concerted action of the two RNA-binding proteins hnRNP A1 and HuR, both stable components of immunoselected hnRNP complexes and having a major nuclear localization. Specifically, we present here the application of the RNA-immunoprecipitation (RIP-Chip technology to identify a population of nuclear transcripts associated with hnRNP A1-RNPs as isolated from the nuclear extract of either HuR WT or HuR-depleted (KO mouse embryonic fibroblast (MEF cells. The outcome of this analysis was a list of target genes regulated via HuR for their association (either increased or reduced with the nuclear hnRNP A1-RNP complexes. Real time PCR analysis was applied to validate a selected number of nuclear mRNA transcripts, as well as to identify pre-spliced transcripts (in addition to their mature mRNA counterpart within the isolated nuclear hnRNP A1-RNPs. The differentially enriched mRNAs were found to belong to GO categories relevant to biological processes anticipated for hnRNP A1 and HuR (such as transport, transcription, translation, apoptosis and cell cycle indicating their concerted function in mRNA metabolism.
Dbp5, Gle1-IP6 and Nup159: a working model for mRNP export.
Folkmann, Andrew W; Noble, Kristen N; Cole, Charles N; Wente, Susan R
2011-01-01
Gene expression is a stepwise process involving distinct cellular processes including transcription, mRNA (mRNA) processing, mRNA export, and translation. As mRNAs are being synthesized, proteins associate with the RNA to form messenger ribonucleoprotein particles (mRNPs). Previous studies have demonstrated that the RNA-binding protein composition of these mRNPs is dynamic, changing as the mRNP moves through the different steps of gene expression, and playing a critical role in these events. An important step during this maturation process occurs at the cytoplasmic face of the nuclear pore complex (NPC) where the export protein Gle1 bound to inositol hexakisphosphate (IP 6) spatially activates the ATP-hydrolysis and mRNP-remodeling activity of the DEAD-box protein Dbp5. Recent work from our laboratory and others has provided important insights into the function and regulation of Dbp5. These include a more detailed explanation of the mechanism of Dbp5 RNP remodeling, the role of Gle1-IP6 in stimulating Dbp5 ATPase activity, and the identification of a novel paradigm for regulation of Dbp5 by Nup159. Based on in vitro biochemical assays, X-ray crystallography, and corresponding in vivo phenotypes, we propose here an updated model of the Dbp5 cycle during mRNP export through the NPC. This takes into account all available data and provides a platform for future studies.
High order path integrals made easy.
Kapil, Venkat; Behler, Jörg; Ceriotti, Michele
2016-12-21
The precise description of quantum nuclear fluctuations in atomistic modelling is possible by employing path integral techniques, which involve a considerable computational overhead due to the need of simulating multiple replicas of the system. Many approaches have been suggested to reduce the required number of replicas. Among these, high-order factorizations of the Boltzmann operator are particularly attractive for high-precision and low-temperature scenarios. Unfortunately, to date, several technical challenges have prevented a widespread use of these approaches to study the nuclear quantum effects in condensed-phase systems. Here we introduce an inexpensive molecular dynamics scheme that overcomes these limitations, thus making it possible to exploit the improved convergence of high-order path integrals without having to sacrifice the stability, convenience, and flexibility of conventional second-order techniques. The capabilities of the method are demonstrated by simulations of liquid water and ice, as described by a neural-network potential fitted to the dispersion-corrected hybrid density functional theory calculations.
High order path integrals made easy
Kapil, Venkat; Behler, Jörg; Ceriotti, Michele
2016-12-01
The precise description of quantum nuclear fluctuations in atomistic modelling is possible by employing path integral techniques, which involve a considerable computational overhead due to the need of simulating multiple replicas of the system. Many approaches have been suggested to reduce the required number of replicas. Among these, high-order factorizations of the Boltzmann operator are particularly attractive for high-precision and low-temperature scenarios. Unfortunately, to date, several technical challenges have prevented a widespread use of these approaches to study the nuclear quantum effects in condensed-phase systems. Here we introduce an inexpensive molecular dynamics scheme that overcomes these limitations, thus making it possible to exploit the improved convergence of high-order path integrals without having to sacrifice the stability, convenience, and flexibility of conventional second-order techniques. The capabilities of the method are demonstrated by simulations of liquid water and ice, as described by a neural-network potential fitted to the dispersion-corrected hybrid density functional theory calculations.
Mosrin-Huaman, Christine; Honorine, Romy; Rahmouni, A Rachid
2009-08-01
In eukaryotic cells, the nascent pre-mRNA molecule is coated sequentially with a large set of processing and binding proteins that mediate its transformation into an export-competent ribonucleoprotein particle (mRNP) that is ready for translation in the cytoplasm. We have implemented an original assay that monitors the dynamic interplay between transcription and mRNP biogenesis and that allows the screening for new factors linking mRNA synthesis to translation in Saccharomyces cerevisiae. The assay is based on the perturbation of gene expression induced by the bacterial Rho factor, an RNA-dependent helicase/translocase that acts as a competitor at one or several steps of mRNP biogenesis in yeast. We show that the expression of Rho in yeast leads to a dose-dependent growth defect that stems from its action on RNA polymerase II-mediated transcription. Rho expression induces the production of aberrant transcripts that are degraded by the nuclear exosome. A screen for dosage suppressors of the Rho-induced growth defect identified several genes that are involved in the different steps of mRNP biogenesis and export, as well as other genes with both known functions in transcription regulation and unknown functions. Our results provide evidence for an extensive cross talk between transcription, mRNP biogenesis, and export. They also uncover new factors that potentially are involved in these interconnected events.
Mosrin-Huaman, Christine; Honorine, Romy; Rahmouni, A. Rachid
2009-01-01
In eukaryotic cells, the nascent pre-mRNA molecule is coated sequentially with a large set of processing and binding proteins that mediate its transformation into an export-competent ribonucleoprotein particle (mRNP) that is ready for translation in the cytoplasm. We have implemented an original assay that monitors the dynamic interplay between transcription and mRNP biogenesis and that allows the screening for new factors linking mRNA synthesis to translation in Saccharomyces cerevisiae. The assay is based on the perturbation of gene expression induced by the bacterial Rho factor, an RNA-dependent helicase/translocase that acts as a competitor at one or several steps of mRNP biogenesis in yeast. We show that the expression of Rho in yeast leads to a dose-dependent growth defect that stems from its action on RNA polymerase II-mediated transcription. Rho expression induces the production of aberrant transcripts that are degraded by the nuclear exosome. A screen for dosage suppressors of the Rho-induced growth defect identified several genes that are involved in the different steps of mRNP biogenesis and export, as well as other genes with both known functions in transcription regulation and unknown functions. Our results provide evidence for an extensive cross talk between transcription, mRNP biogenesis, and export. They also uncover new factors that potentially are involved in these interconnected events. PMID:19451224
Jaako, P; Debnath, S; Olsson, K; Zhang, Y; Flygare, J; Lindström, M S; Bryder, D; Karlsson, S
2015-11-01
Diamond-Blackfan anemia (DBA) is a congenital erythroid hypoplasia caused by haploinsufficiency of genes encoding ribosomal proteins (RPs). Perturbed ribosome biogenesis in DBA has been shown to induce a p53-mediated ribosomal stress response. However, the mechanisms of p53 activation and its relevance for the erythroid defect remain elusive. Previous studies have indicated that activation of p53 is caused by the inhibition of mouse double minute 2 (Mdm2), the main negative regulator of p53, by the 5S ribonucleoprotein particle (RNP). Meanwhile, it is not clear whether this mechanism solely mediates the p53-dependent component found in DBA. To approach this question, we crossed our mouse model for RPS19-deficient DBA with Mdm2(C305F) knock-in mice that have a disrupted 5S RNP-Mdm2 interaction. Upon induction of the Rps19 deficiency, Mdm2(C305F) reversed the p53 response and improved expansion of hematopoietic progenitors in vitro, and ameliorated the anemia in vivo. Unexpectedly, disruption of the 5S RNP-Mdm2 interaction also led to selective defect in erythropoiesis. Our findings highlight the sensitivity of erythroid progenitor cells to aberrations in p53 homeostasis mediated by the 5S RNP-Mdm2 interaction. Finally, we provide evidence indicating that physiological activation of the 5S RNP-Mdm2-p53 pathway may contribute to functional decline of the hematopoietic system in a cell-autonomous manner over time.
Early Targets of nRNP Humoral Autoimmunity in Human Systemic Lupus Erythematosus
Poole, Brian D.; Schneider, Rebecca I.; Guthridge, Joel M.; Velte, Cathy A.; Reichlin, Morris; Harley, John B.; James, Judith A.
2009-01-01
Objective: The U1 small nuclear ribonucleoproteins (nRNPs) are common targets of autoantibodies in lupus and other autoimmune diseases. However, the etiology and progression of autoimmune responses directed against these antigens are not well understood. Using a unique collection of serial human samples from before and after nRNP antibody development, we investigated early humoral events in the development of anti-nRNP autoimmunity. Methods: Lupus patients with sera available from both before and after nRNP antibody precipitin development were identified from the Oklahoma Clinical Immunology Serum Repository. Antibodies in the serial samples were analyzed by ELISA, Western blotting, solid-phase epitope mapping and competition assays. Results: The first detected nRNP antibodies targeted 6 common initial epitopes in nRNP A, 2 in nRNP C and 9 in nRNP 70K. The initial epitopes of nRNP A and nRNP C were significantly enriched for proline (p=0.0004, p=0.048) and shared up to 95% sequence homology. The initial nRNP 70K humoral epitopes differed from nRNP A and C. The initial antibodies to nRNP A and nRNP C were cross-reactive with the Sm B′-derived peptide PPPGMRPP. Antibody binding against all three nRNP subunits diversified significantly over time. Conclusions: nRNP A and nRNP C autoantibodies initially targeted restricted, proline-rich motifs. Antibody binding subsequently spread to other epitopes. The similarity and cross-reactivity between the initial targets of nRNP and Sm autoantibodies identifies a likely commonality in etiology and a focal point for intermolecular epitope spreading. PMID:19248110
Tunable Intense High-Order Vortex Generation.
Zhang, Xiaomei; Shen, Baifei
2017-10-01
In 2015, we found the scheme to generate intense high-order optical vortices that carry OAM in the extreme ultraviolet region based on relativistic harmonics from the surface of a solid target. The topological charge of the harmonics scales with its order. These results have been confirmed in recent experiments. In the two incident beams case, we produced relativistic intense harmonics with expected frequency and optical vortex. When two counter-propagating LG laser pulses impinge on a solid thin foil and interact with each other, the contribution of each input pulse in producing harmonics can be distinguished with the help of angular momentum conservation of photons, which is almost impossible for harmonic generation without optical vortex. The generation of tunable, intense vortex harmonics with different photon topological charge is predicted based on the theoretical analysis and 3D PIC simulations. This work was supported by the National Natural Science Foundation of China (Grant Nos. 11374319, 11674339).
Iron oxide nanoparticles stabilized inside highly ordered ...
Indian Academy of Sciences (India)
.Rm; 81.07.Bc; 81.16.Be; 82.35.Np. 1. Introduction. Developments in the field of uniform nanometer sized particles have been studied extensively in recent times because of their technological and fundamental scien- tific importance [1].
High-order nonuniformly correlated beams
Wu, Dan; Wang, Fei; Cai, Yangjian
2018-02-01
We have introduced a class of partially coherent beams with spatially varying correlations named high-order nonuniformly correlated (HNUC) beams, as an extension of conventional nonuniformly correlated (NUC) beams. Such beams bring a new parameter (mode order) which is used to tailor the spatial coherence properties. The behavior of the spectral density of the HNUC beams on propagation has been investigated through numerical examples with the help of discrete model decomposition and fast Fourier transform (FFT) algorithm. Our results reveal that by selecting the mode order appropriately, the more sharpened intensity maxima can be achieved at a certain propagation distance compared to that of the NUC beams, and the lateral shift of the intensity maxima on propagation is closed related to the mode order. Furthermore, analytical expressions for the r.m.s width and the propagation factor of the HNUC beams on free-space propagation are derived by means of Wigner distribution function. The influence of initial beam parameters on the evolution of the r.m.s width and the propagation factor, and the relation between the r.m.s width and the occurring of the sharpened intensity maxima on propagation have been studied and discussed in detail.
hnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene.
Directory of Open Access Journals (Sweden)
Indrani Talukdar
Full Text Available Exon 11 of the insulin receptor gene (INSR is alternatively spliced in a developmentally and tissue-specific manner. Linker scanning mutations in a 5' GA-rich enhancer in intron 10 identified AGGGA sequences that are important for enhancer function. Using RNA-affinity purification and mass spectrometry, we identified hnRNP F and hnRNP A1 binding to these AGGGA sites and also to similar motifs at the 3' end of the intron. The hnRNPs have opposite functional effects with hnRNP F promoting and hnRNP A1 inhibiting exon 11 inclusion, and deletion of the GA-rich elements eliminates both effects. We also observed specific binding of hnRNP A1 to the 5' splice site of intron 11. The SR protein SRSF1 (SF2/ASF co-purified on the GA-rich enhancer and, interestingly, also competes with hnRNP A1 for binding to the splice site. A point mutation -3U→C decreases hnRNP A1 binding, increases SRSF1 binding and renders the exon constitutive. Lastly, our data point to a functional interaction between hnRNP F and SRSF1 as a mutant that eliminates SRSF1 binding to exon 11, or a SRSF1 knockdown, which prevents the stimulatory effect of hnRNP F over expression.
A high-order SPH method by introducing inverse kernels
Directory of Open Access Journals (Sweden)
Le Fang
2017-02-01
Full Text Available The smoothed particle hydrodynamics (SPH method is usually expected to be an efficient numerical tool for calculating the fluid-structure interactions in compressors; however, an endogenetic restriction is the problem of low-order consistency. A high-order SPH method by introducing inverse kernels, which is quite easy to be implemented but efficient, is proposed for solving this restriction. The basic inverse method and the special treatment near boundary are introduced with also the discussion of the combination of the Least-Square (LS and Moving-Least-Square (MLS methods. Then detailed analysis in spectral space is presented for people to better understand this method. Finally we show three test examples to verify the method behavior.
High-order harmonic generation by polyatomic molecules
Odžak, S.; Hasović, E.; Milošević, D. B.
2017-04-01
We present a theory of high-order harmonic generation by arbitrary polyatomic molecules based on the molecular strong-field approximation (MSFA) in the framework of the S-matrix theory. A polyatomic molecule is modeled by an (N + 1)-particle system, which consists of N heavy atomic (ionic) centers and an electron. We derived various versions (with or without the dressing of the initial and/or final molecular state) of the MSFA. The general expression for the T-matrix element takes a simple form for neutral polyatomic molecules. We show the existence of the interference minima in the harmonic spectrum and explain these minima as a multiple-slit type of interference. This is illustrated by numerical examples for the nitrous oxide (N2O) molecule exposed to strong linearly polarized laser field.
Nishimura, Kazuho; Kumazawa, Takuya; Kuroda, Takao; Katagiri, Naohiro; Tsuchiya, Mai; Goto, Natsuka; Furumai, Ryohei; Murayama, Akiko; Yanagisawa, Junn; Kimura, Keiji
2015-03-03
The 5S ribonucleoprotein particle (RNP) complex, consisting of RPL11, RPL5, and 5S rRNA, is implicated in p53 regulation under ribotoxic stress. Here, we show that the 5S RNP contributes to p53 activation and promotes cellular senescence in response to oncogenic or replicative stress. Oncogenic stress accelerates rRNA transcription and replicative stress delays rRNA processing, resulting in RPL11 and RPL5 accumulation in the ribosome-free fraction, where they bind MDM2. Experimental upregulation of rRNA transcription or downregulation of rRNA processing, mimicking the nucleolus under oncogenic or replicative stress, respectively, also induces RPL11-mediated p53 activation and cellular senescence. We demonstrate that exogenous expression of certain rRNA-processing factors rescues the processing defect, attenuates p53 accumulation, and increases replicative lifespan. To summarize, the nucleolar-5S RNP-p53 pathway functions as a senescence inducer in response to oncogenic and replicative stresses. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
Directory of Open Access Journals (Sweden)
Kazuho Nishimura
2015-03-01
Full Text Available The 5S ribonucleoprotein particle (RNP complex, consisting of RPL11, RPL5, and 5S rRNA, is implicated in p53 regulation under ribotoxic stress. Here, we show that the 5S RNP contributes to p53 activation and promotes cellular senescence in response to oncogenic or replicative stress. Oncogenic stress accelerates rRNA transcription and replicative stress delays rRNA processing, resulting in RPL11 and RPL5 accumulation in the ribosome-free fraction, where they bind MDM2. Experimental upregulation of rRNA transcription or downregulation of rRNA processing, mimicking the nucleolus under oncogenic or replicative stress, respectively, also induces RPL11-mediated p53 activation and cellular senescence. We demonstrate that exogenous expression of certain rRNA-processing factors rescues the processing defect, attenuates p53 accumulation, and increases replicative lifespan. To summarize, the nucleolar-5S RNP-p53 pathway functions as a senescence inducer in response to oncogenic and replicative stresses.
Directory of Open Access Journals (Sweden)
Shanye Yin
2017-06-01
Full Text Available Hexanucleotide repeat expansion in the C9ORF72 gene results in production of dipeptide repeat (DPR proteins that may disrupt pre-mRNA splicing in amyotrophic lateral sclerosis (ALS and frontotemporal dementia (FTD patients. At present, the mechanisms underlying this mis-splicing are not understood. Here, we show that addition of proline-arginine (PR and glycine-arginine (GR toxic DPR peptides to nuclear extracts blocks spliceosome assembly and splicing, but not other types of RNA processing. Proteomic and biochemical analyses identified the U2 small nuclear ribonucleoprotein particle (snRNP as a major interactor of PR and GR peptides. In addition, U2 snRNP, but not other splicing factors, mislocalizes from the nucleus to the cytoplasm both in C9ORF72 patient induced pluripotent stem cell (iPSC-derived motor neurons and in HeLa cells treated with the toxic peptides. Bioinformatic studies support a specific role for U2-snRNP-dependent mis-splicing in C9ORF72 patient brains. Together, our data indicate that DPR-mediated dysfunction of U2 snRNP could account for as much as ∼44% of the mis-spliced cassette exons in C9ORF72 patient brains.
HnRNP L and hnRNP LL antagonistically modulate PTB-mediated splicing suppression of CHRNA1 pre-mRNA.
Rahman, Mohammad Alinoor; Masuda, Akio; Ohe, Kenji; Ito, Mikako; Hutchinson, David O; Mayeda, Akila; Engel, Andrew G; Ohno, Kinji
2013-10-14
CHRNA1 gene, encoding the muscle nicotinic acetylcholine receptor alpha subunit, harbors an inframe exon P3A. Inclusion of exon P3A disables assembly of the acetylcholine receptor subunits. A single nucleotide mutation in exon P3A identified in congenital myasthenic syndrome causes exclusive inclusion of exon P3A. The mutation gains a de novo binding affinity for a splicing enhancing RNA-binding protein, hnRNP LL, and displaces binding of a splicing suppressing RNA-binding protein, hnRNP L. The hnRNP L binds to another splicing repressor PTB through the proline-rich region and promotes PTB binding to the polypyrimidine tract upstream of exon P3A, whereas hnRNP LL lacking the proline-rich region cannot bind to PTB. Interaction of hnRNP L with PTB inhibits association of U2AF(65) and U1 snRNP with the upstream and downstream of P3A, respectively, which causes a defect in exon P3A definition. HnRNP L and hnRNP LL thus antagonistically modulate PTB-mediated splicing suppression of exon P3A.
High-order harmonic generation from eld-distorted orbitals
DEFF Research Database (Denmark)
Spiewanowski, Maciek; Etches, Adam; Madsen, Lars Bojer
We investigate the eect on high-order harmonic generation of the distortion of molecular orbitals by the driving laser eld. Calculations for high-order harmonic generation including orbital distortion are performed for N2 (high polarizability). Our results allow us to suggest that field...... of the minimum in the high-order harmonic spectra. This is in agreement with experiment....
Structured non-coding RNAs and the RNP Renaissance
Hogg, J. Robert; Collins, Kathleen
2009-01-01
Summary Non-protein-coding (nc) RNAs are diverse in their modes of synthesis, processing, assembly, and function. The inventory of transcripts known or suspected to serve their biological roles as RNA has increased dramatically in recent years. Although studies of ncRNA function are only beginning to match the pace of ncRNA discovery, some principles are emerging. Here we focus on a framework for understanding functions of ncRNAs that have evolved in a protein-rich cellular environment, as distinct from ncRNAs that arose originally in the ancestral RNA World. The folding and function of ncRNAs in the context of ribonucleoprotein (RNP) complexes provide myriad opportunities for ncRNA gain of function, leading to a modern-day RNP Renaissance. PMID:18950732
Dbp5, Gle1-IP6 and Nup159: A working model for mRNP export
Folkmann, Andrew W.; Noble, Kristen N.; Cole, Charles N.; Wente, Susan R.
2011-01-01
Gene expression is a stepwise process involving distinct cellular processes including transcription, mRNA (mRNA) processing, mRNA export, and translation. As mRNAs are being synthesized, proteins associate with the RNA to form messenger ribonucleoprotein particles (mRNPs). Previous studies have demonstrated that the RNA-binding protein composition of these mRNPs is dynamic, changing as the mRNP moves through the different steps of gene expression, and playing a critical role in these events. ...
Reconstitution of a functional 7SK snRNP
Brogie, John E.
2017-01-01
Abstract The 7SK small nuclear ribonucleoprotein (snRNP) plays a central role in RNA polymerase II elongation control by regulating the availability of active P-TEFb. We optimized conditions for analyzing 7SK RNA by SHAPE and demonstrated a hysteretic effect of magnesium on 7SK folding dynamics including a 7SK GAUC motif switch. We also found evidence that the 5΄ end pairs alternatively with two different regions of 7SK giving rise to open and closed forms that dictate the state of the 7SK motif. We then used recombinant P-TEFb, HEXIM1, LARP7 and MEPCE to reconstruct a functional 7SK snRNP in vitro. Stably associated P-TEFb was highly inhibited, but could still be released and activated by HIV-1 Tat. Notably, P-TEFb association with both in vitro-reconstituted and cellular snRNPs led to similar changes in SHAPE reactivities, confirming that 7SK undergoes a P-TEFb-dependent structural change. We determined that the xRRM of LARP7 binds to the 3΄ stem loop of 7SK and inhibits the methyltransferase activity of MEPCE through a C-terminal MEPCE interaction domain (MID). Inhibition of MEPCE is dependent on the structure of the 3΄ stem loop and the closed form of 7SK RNA. This study provides important insights into intramolecular interactions within the 7SK snRNP. PMID:28431135
Ubiquitin and assembly of export competent mRNP.
Babour, Anna; Dargemont, Catherine; Stutz, Françoise
2012-06-01
The production of mature and export competent mRNP (mRNA ribonucleoprotein) complexes depends on a series of highly coordinated processing reactions. RNA polymerase II (RNAPII) plays a central role in this process by mediating the sequential recruitment of mRNA maturation and export factors to transcribing genes, thereby establishing a strong functional link between transcription and export through nuclear pore complexes (NPC). Growing evidence indicates that post-translational modifications participate in the dynamic association of processing and export factors with mRNAs ensuring that the transitions and rearrangements undergone by the mRNP occur at the right time and place. This review mainly focuses on the role of ubiquitin conjugation in controlling mRNP assembly and quality control from transcription down to export through the NPC. It emphasizes the central role of ubiquitylation in organizing the chronology of events along this highly dynamic pathway. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing. Copyright © 2012 Elsevier B.V. All rights reserved.
Plasma channel undulator excited by high-order laser modes
Wang, Jingwei; Schroeder, Carl; Zepf, Matt; Rykovanov, Sergey
2017-10-01
The possibility of utilizing plasma undulators and plasma accelerators to produce compact and economical ultraviolet and X-ray radiation sources has attracted considerable interest for a few decades. This interest has been driven by the great potential to decrease the threshold for accessing such sources, which are now mainly provided by a very few dedicated large-scale synchrotron or free-electron laser (FEL) facilities. However, the typically broad radiation bandwidth of such plasma devices limits the source brightness and makes it difficult for the FEL instability to develop. Here, using multi-dimensional electromagnetic particle-in-cell simulations, we demonstrate that a plasma undulator generated by the beating of a mixture of high-order laser modes propagating inside a plasma channel, leads to a few percent radiation bandwidth. The strength of the undulator can reach unity, the period can be less than a millimeter, and the total number of undulator periods can be significantly increased by a phase locking technique based on the longitudinal density modulation. According to analytical estimates and simulations, in the fully beam loaded regime, the electron current in the undulator can reach 0.3 kA, making such an undulator a potential candidate towards a table-top FEL.
Giant poly(A)-rich RNP aggregates form at terminal regions of avian lampbrush chromosomes.
Kulikova, T; Chervyakova, D; Zlotina, A; Krasikova, A; Gaginskaya, E
2016-09-01
The cell nucleus comprises a number of chromatin-associated domains. Certain chromatin-associated domains are nucleated by nascent RNA and accumulate non-nascent transcripts in the form of ribonucleoprotein (RNP) aggregates. In the transcriptionally active nucleus of the growing avian oocyte, RNP-rich structures, here termed giant terminal RNP aggregates (GITERA), form at the termini of lampbrush chromosomes. Using GITERA as an example, we aimed to explore mechanisms of RNP aggregate formation at certain chromosomal loci to establish whether they accumulate non-nascent RNA and to analyze protein composition in RNP aggregates. We found that GITERA on chicken and pigeon lampbrush chromosomes do not contain nascent transcripts. At the same time, RNA fluorescent in situ hybridization (FISH) and in situ reverse transcription demonstrated that GITERA accumulate poly(A)-rich RNA. Moreover, subtelomere chromosome regions adjacent to GITERA are transcriptionally active as shown by detection of incorporated BrUTP and the elongating form of RNA polymerase II. GITERA on both chicken and pigeon lampbrush chromosomes are enriched in splicing factors but not in heterogeneous nuclear RNP (hnRNP) L and K. A subtype of GITERA concentrates hnRNP I/PTB and p54nrb/NonO. Interestingly, hnRNP I/PTB and p54nrb/NonO in such subtype of GITERA were revealed in long threads. The resemblance of these threads to amyloid-like fibers is discussed. Our data suggest that transcription of subtelomeric sequences serves as a seeding event for accumulation of non-nascent RNA and associated RNP proteins. Such accumulation leads to GITERA formation in terminal chromosomal regions in avian oocyte nucleus. 3'-processed transcripts derived from other chromosomal loci may be attracted to GITERA by binding to the same RNP proteins or to their interaction partners.
High-order-harmonic generation from field-distorted orbitals
DEFF Research Database (Denmark)
Spiewanowski, Maciek; Etches, Adam; Madsen, Lars Bojer
2013-01-01
We investigate the effect on high-order-harmonic generation of the distortion of molecular orbitals by the driving laser field. Calculations for high-order-harmonic generation including orbital distortion are performed for N2. Our results allow us to suggest that field distortion is the reason why...
Li, Xiaoze; Johansson, Cecilia; Glahder, Jacob; Mossberg, Ann-Kristin; Schwartz, Stefan
2013-01-01
Human papillomavirus type 16 (HPV-16) 5′-splice site SD3632 is used exclusively to produce late L1 mRNAs. We identified a 34-nt splicing inhibitory element located immediately upstream of HPV-16 late 5′-splice site SD3632. Two AUAGUA motifs located in these 34 nt inhibited SD3632. Two nucleotide substitutions in each of the HPV-16 specific AUAGUA motifs alleviated splicing inhibition and induced late L1 mRNA production from episomal forms of the HPV-16 genome in primary human keratinocytes. The AUAGUA motifs bind specifically not only to the heterogeneous nuclear RNP (hnRNP) D family of RNA-binding proteins including hnRNP D/AUF, hnRNP DL and hnRNP AB but also to hnRNP A2/B1. Knock-down of these proteins induced HPV-16 late L1 mRNA expression, and overexpression of hnRNP A2/B1, hnRNP AB, hnRNP DL and the two hnRNP D isoforms hnRNP D37 and hnRNP D40 further suppressed L1 mRNA expression. This inhibition may allow HPV-16 to hide from the immune system and establish long-term persistent infections with enhanced risk at progressing to cancer. There is an inverse correlation between expression of hnRNP D proteins and hnRNP A2/B1 and HPV-16 L1 production in the cervical epithelium, as well as in cervical cancer, supporting the conclusion that hnRNP D proteins and A2/B1 inhibit HPV-16 L1 mRNA production. PMID:24013563
Chiou, Ni-ting; Shankarling, Ganesh; Lynch, Kristen W.
2013-01-01
Pre-mRNA splicing is catalyzed through the activity of the spliceosome, a dynamic enzymatic complex. Forcing aberrant interactions within the spliceosome can reduce splicing efficiency and alter splice site choice; however, it is unknown whether such alterations are naturally exploited mechanisms of splicing regulation. Here we demonstrate that hnRNP L represses CD45 exon 4 by recruiting hnRNP A1 to a sequence upstream of the 5’ splice site. Together, hnRNP L and A1 induce extended contacts between the 5’ splice site-bound U1 snRNA and neighboring exonic sequences which, in turn, inhibit stable association of U6 snRNA and subsequent catalysis. Importantly, analysis of several exons regulated by hnRNP L shows a clear relationship between the potential for binding of hnRNP A1 and U1 snRNA, and the effect of hnRNP L on splicing. Together our results demonstrate conformational perturbations within the spliceosome are a naturally occurring and generalizable mechanism for controlling alternative splicing decisions. PMID:23394998
The high-order Boltzmann machine: learned distribution and topology.
Albizuri, F X; Danjou, A; Grana, M; Torrealdea, J; Hernandez, M C
1995-01-01
In this paper we give a formal definition of the high-order Boltzmann machine (BM), and extend the well-known results on the convergence of the learning algorithm of the two-order BM. From the Bahadur-Lazarsfeld expansion we characterize the probability distribution learned by the high order BM. Likewise a criterion is given to establish the topology of the BM depending on the significant correlations of the particular probability distribution to be learned.
Electrochemical Hydrogen Storage in a Highly Ordered Mesoporous Carbon
Dan eLiu; Chao eZeng; Haolin eTan; Dong eZheng; Rong eLi; Deyu eQu; zhizhong eXie; Jiahen eLei; Liang eXiao; Deyang eQu
2014-01-01
A highly ordered mesoporous carbon (HOMC) has been synthesized through a strongly acidic, aqueous cooperative assembly route. The structure and morphology of the carbon material were investigated using TEM, SEM, and nitrogen adsorption–desorption isotherms. The carbon was proven to be meso-structural and consisted of graphitic micro-domain with larger interlayer space. Active carbon impedance and electrochemical measurements reveal that the synthesized highly ordered mesoporous carbon (HOMC) ...
Directory of Open Access Journals (Sweden)
Bastian Linder
Full Text Available Pre-mRNA splicing by the spliceosome is an essential step in the maturation of nearly all human mRNAs. Mutations in six spliceosomal proteins, PRPF3, PRPF4, PRPF6, PRPF8, PRPF31 and SNRNP200, cause retinitis pigmentosa (RP, a disease characterized by progressive photoreceptor degeneration. All splicing factors linked to RP are constituents of the U4/U6.U5 tri-snRNP subunit of the spliceosome, suggesting that the compromised function of this particle may lead to RP. Here, we report the identification of the p.R192H variant of the tri-snRNP factor PRPF4 in a patient with RP. The mutation affects a highly conserved arginine residue that is crucial for PRPF4 function. Introduction of a corresponding mutation into the zebrafish homolog of PRPF4 resulted in a complete loss of function in vivo. A series of biochemical experiments suggested that p.R192H disrupts the binding interface between PRPF4 and its interactor PRPF3. This interferes with the ability of PRPF4 to integrate into the tri-snRNP, as shown in a human cell line and in zebrafish embryos. These data suggest that the p.R192H variant of PRPF4 represents a functional null allele. The resulting haploinsufficiency of PRPF4 compromises the function of the tri-snRNP, reinforcing the notion that this spliceosomal particle is of crucial importance in the physiology of the retina.
The importance of ribosome production, and the 5S RNP-MDM2 pathway, in health and disease.
Pelava, Andria; Schneider, Claudia; Watkins, Nicholas J
2016-08-15
Ribosomes are abundant, large RNA-protein complexes that are the source of all protein synthesis in the cell. The production of ribosomes is an extremely energetically expensive cellular process that has long been linked to human health and disease. More recently, it has been shown that ribosome biogenesis is intimately linked to multiple cellular signalling pathways and that defects in ribosome production can lead to a wide variety of human diseases. Furthermore, changes in ribosome production in response to nutrient levels in the diet lead to metabolic re-programming of the liver. Reduced or abnormal ribosome production in response to cellular stress or mutations in genes encoding factors critical for ribosome biogenesis causes the activation of the tumour suppressor p53, which leads to re-programming of cellular transcription. The ribosomal assembly intermediate 5S RNP (ribonucleoprotein particle), containing RPL5, RPL11 and the 5S rRNA, accumulates when ribosome biogenesis is blocked. The excess 5S RNP binds to murine double minute 2 (MDM2), the main p53-suppressor in the cell, inhibiting its function and leading to p53 activation. Here, we discuss the involvement of ribosome biogenesis in the homoeostasis of p53 in the cell and in human health and disease. © 2016 The Author(s).
Electrochemical Hydrogen Storage in a Highly Ordered Mesoporous Carbon
Directory of Open Access Journals (Sweden)
Dan eLiu
2014-10-01
Full Text Available A highly order mesoporous carbon has been synthesized through a strongly acidic, aqueous cooperative assembly route. The structure and morphology of the carbon material were investigated using TEM, SEM and nitrogen adsorption-desorption isotherms. The carbon was proven to be meso-structural and consisted of graphitic micro-domain with larger interlayer space. AC impedance and electrochemical measurements reveal that the synthesized highly ordered mesoporous carbon exhibits a promoted electrochemical hydrogen insertion process and improved capacitance and hydrogen storage stability. The meso-structure and enlarged interlayer distance within the highly ordered mesoporous carbon are suggested as possible causes for the enhancement in hydrogen storage. Both hydrogen capacity in the carbon and mass diffusion within the matrix were improved.
A high order solver for the unbounded Poisson equation
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Rasmussen, Johannes Tophøj; Chatelain, Philippe
2013-01-01
. The method is extended to directly solve the derivatives of the solution to Poissonʼs equation. In this way differential operators such as the divergence or curl of the solution field can be solved to the same high order convergence without additional computational effort. The method, is applied...... and validated, however not restricted, to the equations of fluid mechanics, and can be used in many applications to solve Poissonʼs equation on a rectangular unbounded domain.......A high order converging Poisson solver is presented, based on the Greenʼs function solution to Poissonʼs equation subject to free-space boundary conditions. The high order convergence is achieved by formulating regularised integration kernels, analogous to a smoothing of the solution field...
Dynamic Stability Analysis Using High-Order Interpolation
Directory of Open Access Journals (Sweden)
Juarez-Toledo C.
2012-10-01
Full Text Available A non-linear model with robust precision for transient stability analysis in multimachine power systems is proposed. The proposed formulation uses the interpolation of Lagrange and Newton's Divided Difference. The High-Order Interpolation technique developed can be used for evaluation of the critical conditions of the dynamic system.The technique is applied to a 5-area 45-machine model of the Mexican interconnected system. As a particular case, this paper shows the application of the High-Order procedure for identifying the slow-frequency mode for a critical contingency. Numerical examples illustrate the method and demonstrate the ability of the High-Order technique to isolate and extract temporal modal behavior.
Use of high order, periodic orbits in the PIES code
Monticello, Donald; Reiman, Allan
2010-11-01
We have implemented a version of the PIES code (Princeton Iterative Equilibrium SolverootnotetextA. Reiman et al 2007 Nucl. Fusion 47 572) that uses high order periodic orbits to select the surfaces on which straight magnetic field line coordinates will be calculated. The use of high order periodic orbits has increase the robustness and speed of the PIES code. We now have more uniform treatment of in-phase and out-of-phase islands. This new version has better convergence properties and works well with a full Newton scheme. We now have the ability to shrink islands using a bootstrap like current and this includes the m=1 island in tokamaks.
Airfoil noise computation use high-order schemes
DEFF Research Database (Denmark)
Zhu, Wei Jun; Shen, Wen Zhong; Sørensen, Jens Nørkær
2007-01-01
) finite difference schemes and optimized high-order compact finite difference schemes are applied for acoustic computation. Acoustic equations are derived using so-called splitting technique by separating the compressible NS equations into viscous (flow equation) and inviscid (acoustic equation) parts......High-order finite difference schemes with at least 4th-order spatial accuracy are used to simulate aerodynamically generated noise. The aeroacoustic solver with 4th-order up to 8th-order accuracy is implemented into the in-house flow solver, EllipSys2D/3D. Dispersion-Relation-Preserving (DRP...
A high order solver for the unbounded Poisson equation
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Rasmussen, Johannes Tophøj; Chatelain, Philippe
2012-01-01
This work improves upon Hockney and Eastwood's Fourier-based algorithm for the unbounded Poisson equation to formally achieve arbitrary high order of convergence without any additional computational cost. We assess the methodology on the kinematic relations between the velocity and vorticity fields....
High-Order CESE Methods for Solving Hyperbolic PDEs (Preprint)
2011-05-03
system of coupled hyperbolic PDE’s with arbitrarily high-order con- vergence . Numerical results show that the extended algorithm can achieve higher...Velocity- Stress Equations for Waves in Solids of Hexagonal Symmetry Solved by the Space-Time CESE Method. ASME Journal of Vibration and Acoustics, 133 (2
Enhanced high-order harmonic generation from Argon-clusters
Tao, Yin; Hagmeijer, Rob; Bastiaens, Hubertus M.J.; Goh, S.J.; van der Slot, P.J.M.; Biedron, S.; Milton, S.; Boller, Klaus J.
2017-01-01
High-order harmonic generation (HHG) in clusters is of high promise because clusters appear to offer an increased optical nonlinearity. We experimentally investigate HHG from Argon clusters in a supersonic gas jet that can generate monomer-cluster mixtures with varying atomic number density and
The Development of High Order Methods for Real World Applications
2015-12-03
three-stage 3rd order Runge-Kutta scheme Gottlieb and Shu [43] is used as the temporal discretization. Here we give a brief description. Rewrite the...Science and Engineering. Springer Berlin Heidelberg, pp. 47–95. [43] Gottlieb , S., Shu, C.-W., 2011. Strong stability-preserving high-order time dis
The effect of O-GlcNAcylation on hnRNP A1 translocation and interaction with transportin1
Energy Technology Data Exchange (ETDEWEB)
Roth, Shira; Khalaila, Isam, E-mail: isam@bgu.ac.il
2017-01-01
The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a major pre-mRNA binding protein involved in transcription and translation. Although predominantly nuclear, hnRNP A1 shuttles rapidly between the nucleus and the cytosol, delivering its anchored pre-mRNA for further processing. Translocation is important for hnRNP A1 to accomplish its transcriptional and translational roles. Transportin1 (Trn1), a translocation protein, facilitates the translocation of hnRNP A1 back to the nucleus. Moreover, phosphorylation of serine residues at hnRNP A1 C-terminal domain affects its translocation. In this study, we found that phosphorylation is not the only modification that hnRNP A1 undergoes, but also O-linked N-acetylglucosaminylation (O-GlcNAcylation) could occur. Several putative novel O-GlcNAcylation and phosphorylation sites in hnRNP A1 were mapped. Whereas enhanced O-GlcNAcylation increased hnRNP A1 interaction with Trn1, enhanced phosphorylation reduced the interaction between the proteins. In addition, elevated O-GlcNAcylation resulted in hnRNP A1 seclusion in the nucleus, whereas elevated phosphorylation resulted in its accumulation in the cytosol. These findings suggest that a new player, i.e., O-GlcNAcylation, regulates hnRNP A1 translocation and interaction with Trn1, possibly affecting its function. There is a need for further study, to elucidate the role of O-GlcNAcylation in the regulation of the specific activities of hnRNP A1 in transcription and translation. - Highlights: • O-GlcNAcylation regulates hnRNP A1 translocation and interaction with Trn1. • Reciprocity between phosphorylation and O-GlcNAcylation in hnRNP A1 is proposed. • Novel O-GlcNAcylation and phosphorylation sites on hnRNPA1 were identified.
Energy Technology Data Exchange (ETDEWEB)
Dobrev, Veselin A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kolev, Tzanio V. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Rieben, Robert N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2012-09-20
The numerical approximation of the Euler equations of gas dynamics in a movingLagrangian frame is at the heart of many multiphysics simulation algorithms. Here, we present a general framework for high-order Lagrangian discretization of these compressible shock hydrodynamics equations using curvilinear finite elements. This method is an extension of the approach outlined in [Dobrev et al., Internat. J. Numer. Methods Fluids, 65 (2010), pp. 1295--1310] and can be formulated for any finite dimensional approximation of the kinematic and thermodynamic fields, including generic finite elements on two- and three-dimensional meshes with triangular, quadrilateral, tetrahedral, or hexahedral zones. We discretize the kinematic variables of position and velocity using a continuous high-order basis function expansion of arbitrary polynomial degree which is obtained via a corresponding high-order parametric mapping from a standard reference element. This enables the use of curvilinear zone geometry, higher-order approximations for fields within a zone, and a pointwise definition of mass conservation which we refer to as strong mass conservation. Moreover, we discretize the internal energy using a piecewise discontinuous high-order basis function expansion which is also of arbitrary polynomial degree. This facilitates multimaterial hydrodynamics by treating material properties, such as equations of state and constitutive models, as piecewise discontinuous functions which vary within a zone. To satisfy the Rankine--Hugoniot jump conditions at a shock boundary and generate the appropriate entropy, we introduce a general tensor artificial viscosity which takes advantage of the high-order kinematic and thermodynamic information available in each zone. Finally, we apply a generic high-order time discretization process to the semidiscrete equations to develop the fully discrete numerical algorithm. Our method can be viewed as the high-order generalization of the so-called staggered
Intronic binding sites for hnRNP A/B and hnRNP F/H proteins stimulate pre-mRNA splicing.
Directory of Open Access Journals (Sweden)
Rebeca Martinez-Contreras
2006-02-01
Full Text Available hnRNP A/B proteins modulate the alternative splicing of several mammalian and viral pre-mRNAs, and are typically viewed as proteins that enforce the activity of splicing silencers. Here we show that intronic hnRNP A/B-binding sites (ABS can stimulate the in vitro splicing of pre-mRNAs containing artificially enlarged introns. Stimulation of in vitro splicing could also be obtained by providing intronic ABS in trans through the use of antisense oligonucleotides containing a non-hybridizing ABS-carrying tail. ABS-tailed oligonucleotides also improved the in vivo inclusion of an alternative exon flanked by an enlarged intron. Notably, binding sites for hnRNP F/H proteins (FBS replicate the activity of ABS by improving the splicing of an enlarged intron and by modulating 5' splice-site selection. One hypothesis formulated to explain these effects is that bound hnRNP proteins self-interact to bring in closer proximity the external pair of splice sites. Consistent with this model, positioning FBS or ABS at both ends of an intron was required to stimulate splicing of some pre-mRNAs. In addition, a computational analysis of the configuration of putative FBS and ABS located at the ends of introns supports the view that these motifs have evolved to support cooperative interactions. Our results document a positive role for the hnRNP A/B and hnRNP F/H proteins in generic splicing, and suggest that these proteins may modulate the conformation of mammalian pre-mRNAs.
Intronic Binding Sites for hnRNP A/B and hnRNP F/H Proteins Stimulate Pre-mRNA Splicing.
Directory of Open Access Journals (Sweden)
2006-01-01
Full Text Available hnRNP A/B proteins modulate the alternative splicing of several mammalian and viral pre-mRNAs, and are typically viewed as proteins that enforce the activity of splicing silencers. Here we show that intronic hnRNP A/B-binding sites (ABS can stimulate the in vitro splicing of pre-mRNAs containing artificially enlarged introns. Stimulation of in vitro splicing could also be obtained by providing intronic ABS in trans through the use of antisense oligonucleotides containing a non-hybridizing ABS-carrying tail. ABS-tailed oligonucleotides also improved the in vivo inclusion of an alternative exon flanked by an enlarged intron. Notably, binding sites for hnRNP F/H proteins (FBS replicate the activity of ABS by improving the splicing of an enlarged intron and by modulating 5' splice-site selection. One hypothesis formulated to explain these effects is that bound hnRNP proteins self-interact to bring in closer proximity the external pair of splice sites. Consistent with this model, positioning FBS or ABS at both ends of an intron was required to stimulate splicing of some pre-mRNAs. In addition, a computational analysis of the configuration of putative FBS and ABS located at the ends of introns supports the view that these motifs have evolved to support cooperative interactions. Our results document a positive role for the hnRNP A/B and hnRNP F/H proteins in generic splicing, and suggest that these proteins may modulate the conformation of mammalian pre-mRNAs.
Directory of Open Access Journals (Sweden)
Stephanie C. Huelga
2012-02-01
Full Text Available Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS in human cells. Using splicing-sensitive microarrays, crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and autoregulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells.
Huelga, Stephanie C; Vu, Anthony Q; Arnold, Justin D; Liang, Tiffany Y; Liu, Patrick P; Yan, Bernice Y; Donohue, John Paul; Shiue, Lily; Hoon, Shawn; Brenner, Sydney; Ares, Manuel; Yeo, Gene W
2012-02-23
Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq), and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and autoregulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells.
Differential effects of hnRNP D/AUF1 isoforms on HIV-1 gene expression
Lund, Nicole; Milev, Miroslav P.; Wong, Raymond; Sanmuganantham, Tharmila; Woolaway, Kathryn; Chabot, Benoit; Abou Elela, Sherif; Mouland, Andrew J.; Cochrane, Alan
2012-01-01
Control of RNA processing plays a major role in HIV-1 gene expression. To explore the role of several hnRNP proteins in this process, we carried out a siRNA screen to examine the effect of depletion of hnRNPs A1, A2, D, H, I and K on HIV-1 gene expression. While loss of hnRNPs H, I or K had little effect, depletion of A1 and A2 increased expression of viral structural proteins. In contrast, reduced hnRNP D expression decreased synthesis of HIV-1 Gag and Env. Loss of hnRNP D induced no changes in viral RNA abundance but reduced the accumulation of HIV-1 unspliced and singly spliced RNAs in the cytoplasm. Subsequent analyses determined that hnRNP D underwent relocalization to the cytoplasm upon HIV-1 infection and was associated with Gag protein. Screening of the four isoforms of hnRNP D determined that, upon overexpression, they had differential effects on HIV-1 Gag expression, p45 and p42 isoforms increased viral Gag synthesis while p40 and p37 suppressed it. The differential effect of hnRNP D isoforms on HIV-1 expression suggests that their relative abundance could contribute to the permissiveness of cell types to replicate the virus, a hypothesis subsequently confirmed by selective depletion of p45 and p42. PMID:22187150
Parallel preconditioners and high order elements for microwave imaging
Bonazzoli, M; Rapetti, F; Tournier, P -H
2016-01-01
This paper combines the use of high order finite element methods with parallel preconditioners of domain decomposition type for solving electromagnetic problems arising from brain microwave imaging. The numerical algorithms involved in such complex imaging systems are computationally expensive since they require solving the direct problem of Maxwell's equations several times. Moreover, wave propagation problems in the high frequency regime are challenging because a sufficiently high number of unknowns is required to accurately represent the solution. In order to use these algorithms in practice for brain stroke diagnosis, running time should be reasonable. The method presented in this paper, coupling high order finite elements and parallel preconditioners, makes it possible to reduce the overall computational cost and simulation time while maintaining accuracy.
High-order harmonic generation in laser plasma plumes
Ganeev, Rashid A
2013-01-01
This book represents the first comprehensive treatment of high-order harmonic generation in laser-produced plumes, covering the principles, past and present experimental status and important applications. It shows how this method of frequency conversion of laser radiation towards the extreme ultraviolet range matured over the course of multiple studies and demonstrated new approaches in the generation of strong coherent short-wavelength radiation for various applications. Significant discoveries and pioneering contributions of researchers in this field carried out in various laser scientific centers worldwide are included in this first attempt to describe the important findings in this area of nonlinear spectroscopy. "High-Order Harmonic Generation in Laser Plasma Plumes" is a self-contained and unified review of the most recent achievements in the field, such as the application of clusters (fullerenes, nanoparticles, nanotubes) for efficient harmonic generation of ultrashort laser pulses in cluster-containin...
High-Order Modulation for Optical Fiber Transmission
Seimetz, Matthias
2009-01-01
Catering to the current interest in increasing the spectral efficiency of optical fiber networks by the deployment of high-order modulation formats, this monograph describes transmitters, receivers and performance of optical systems with high-order phase and quadrature amplitude modulation. In the first part of the book, the author discusses various transmitter implementation options as well as several receiver concepts based on direct and coherent detection, including designs of new structures. Hereby, both optical and electrical parts are considered, allowing the assessment of practicability and complexity. In the second part, a detailed characterization of optical fiber transmission systems is presented, regarding a wide range of modulation formats. It provides insight in the fundamental behavior of different formats with respect to relevant performance degradation effects and identifies the major trends in system performance.
High-order harmonic generation from polar molecules
DEFF Research Database (Denmark)
Etches, Adam
When a molecule is submitted to a very intense laser pulse it emits coherent bursts of light in each optical half-cycle of the laser field. This process is known as high-order harmonic generation because the spectrum consists of many peaks at energies corresponding to an integer amount of laser...... photons. The harmonics contain information about the wave function of the loosest bound electron on an Ångström length scale and attosecond time scale. However, accurate theoretical models are needed in order to extract this information. In this thesis the most widely used model of high-order harmonic...... generation is extended to polar molecules by including the laser-induced Stark shift of each molecular orbitals. The Stark shift is shown to have a major influence on the relative strength of harmonic bursts in neighbouring half-cycles, as well as leaving an imprint on the phase of the harmonics...
Full quantum trajectories resolved high-order harmonic generation.
Ye, Peng; He, Xinkui; Teng, Hao; Zhan, Minjie; Zhong, Shiyang; Zhang, Wei; Wang, Lifeng; Wei, Zhiyi
2014-08-15
We use a carrier-envelope-phase stabilized sub-2-cycle laser pulse to generate high-order harmonics and study how the two-dimensional spectrum of harmonics, with the resolutions in temporal frequency and spatial frequency, is shaped by the laser phase. An arrowlike spectrum obtained experimentally when the gas cell is located in front of the laser focus point shows a resolution of full quantum trajectories; i.e., harmonics from different trajectories stand on different positions in this spectrum. In particular, due to the laser phase combined with the classical-like action, the harmonics from short and long trajectories differ maximally in their curvatures of wave fronts in the generation area, and so occupy very different ranges of spatial frequency at the far field. The result directly gives a full map of quantum trajectories in high-order harmonic generation. The conclusion is supported by an analytical model and quantum mechanics simulations.
Development of high-order segmented MEMS deformable mirrors
Helmbrecht, Michael A.; He, Min; Kempf, Carl J.
2012-03-01
The areas of biological microscopy, ophthalmic research, and atmospheric turbulence correction require high-order DMs to obtain diffraction-limited images. Iris AO has been developing high-order MEMS DMs to address these requirements. Recent development has resulted in fully functional 489-actuator DMs capable of 9.5 µm stroke. For laser applications, the DMs were modified to make them compatible with high-reflectance dielectric coatings. Experimental results for the 489-actuator DMs with dielectric coatings shows they can be made with superb optical quality λ/93.3 rms (11.4 nm rms) and λ/75.9 rms (20.3 nm rms) for 1064 nm and 1540 nm coatings. Laser testing has demonstrated 300 W/cm2 power handling with off-the-shelf packaging. Power handling of 2800 W/cm2 is projected when incorporating packaging optimized for heat transfer.
A High-Order CFS Algorithm for Clustering Big Data
Fanyu Bu; Zhikui Chen; Peng Li; Tong Tang; Ying Zhang
2016-01-01
With the development of Internet of Everything such as Internet of Things, Internet of People, and Industrial Internet, big data is being generated. Clustering is a widely used technique for big data analytics and mining. However, most of current algorithms are not effective to cluster heterogeneous data which is prevalent in big data. In this paper, we propose a high-order CFS algorithm (HOCFS) to cluster heterogeneous data by combining the CFS clustering algorithm and the dropout deep learn...
Discrete nonlinear Schrodinger equations with arbitrarily high-order nonlinearities
DEFF Research Database (Denmark)
Khare, A.; Rasmussen, Kim Ø; Salerno, M.
2006-01-01
A class of discrete nonlinear Schrodinger equations with arbitrarily high-order nonlinearities is introduced. These equations are derived from the same Hamiltonian using different Poisson brackets and include as particular cases the saturable discrete nonlinear Schrodinger equation and the Ablowitz......-Ladik equation. As a common property, these equations possess three kinds of exact analytical stationary solutions for which the Peierls-Nabarro barrier is zero. Several properties of these solutions, including stability, discrete breathers, and moving solutions, are investigated....
High order numerical methods for myxobacteria pattern formation
Glavan, Ana Maria
2015-01-01
Rippling patterns of myxobacteria appear in starving colonies before they aggregate to form fruiting bodies. These periodic traveling cell density waves arise from the coordination of individual cell reversals, resulting from an internal clock regulating them, and from contact signaling during bacterial collisions. Our main interest in this research is the numerical approximation with high order accuracy in space of the solutions of mathematical models proposed for myxobacteria rippling. We r...
Separation of High Order Harmonics with Fluoride Windows
Energy Technology Data Exchange (ETDEWEB)
Allison, Tom; van Tilborg, Jeroen; Wright, Travis; Hertlein, Marcus; Falcone, Roger; Belkacem, Ali
2010-08-02
The lower orders produced in high order harmonic generation can be effciently temporally separated into monochromatic pulses by propagation in a Fluoride window while still preserving their femtosecond pulse duration. We present calculations for MgF2, CaF2, and LiF windows for the third, fifth, and seventh harmonics of 800 nm. We demonstrate the use of this simple and inexpensive technique in a femtosecond pump/probe experiment using the fifth harmonic.
International Conference on Spectral and High-Order Methods
Dumont, Ney; Hesthaven, Jan
2017-01-01
This book features a selection of high-quality papers chosen from the best presentations at the International Conference on Spectral and High-Order Methods (2016), offering an overview of the depth and breadth of the activities within this important research area. The carefully reviewed papers provide a snapshot of the state of the art, while the extensive bibliography helps initiate new research directions.
High-order harmonic generation via multicolor beam superposition
Sarikhani, S.; Batebi, S.
2017-09-01
In this article, femtosecond pulses, especially designed by multicolor beam superposition are used for high-order harmonic generation. To achieve this purpose, the spectral difference between the beams, and their width are taken to be small values, i.e., less than 1 nm. Applying a Gaussian distribution to the beam intensities leads to a more distinct pulses. Also, it is seen that these pulses have an intrinsic linear chirp. By changing the width of the Gaussian distributions, we can have several pulses with different bandwidths and hence various pulse duration. Thus, the study of these broadband pulse influences, in contrast with monochromatic pulses, on the atomic or molecular targets was achievable. So, we studied numerically the effect of these femtosecond pulses on behavior of the high-order harmonics generated after interaction between the pulse and the atomic hydrogen. For this study, we adjusted the beam intensities so that the produced pulse intensity be in the over-barrier ionization region. This makes the power spectrum of high-order harmonics more extensive. Cutoff frequency of the power spectrum along with the first harmonic intensity and its shift from the incident pulse are investigated. Additionally, maximum ionization probability with respect to the pulse bandwidth was also studied.
HOKF: High Order Kalman Filter for Epilepsy Forecasting Modeling.
Nguyen, Ngoc Anh Thi; Yang, Hyung-Jeong; Kim, Sunhee
2017-08-01
Epilepsy forecasting has been extensively studied using high-order time series obtained from scalp-recorded electroencephalography (EEG). An accurate seizure prediction system would not only help significantly improve patients' quality of life, but would also facilitate new therapeutic strategies to manage epilepsy. This paper thus proposes an improved Kalman Filter (KF) algorithm to mine seizure forecasts from neural activity by modeling three properties in the high-order EEG time series: noise, temporal smoothness, and tensor structure. The proposed High-Order Kalman Filter (HOKF) is an extension of the standard Kalman filter, for which higher-order modeling is limited. The efficient dynamic of HOKF system preserves the tensor structure of the observations and latent states. As such, the proposed method offers two main advantages: (i) effectiveness with HOKF results in hidden variables that capture major evolving trends suitable to predict neural activity, even in the presence of missing values; and (ii) scalability in that the wall clock time of the HOKF is linear with respect to the number of time-slices of the sequence. The HOKF algorithm is examined in terms of its effectiveness and scalability by conducting forecasting and scalability experiments with a real epilepsy EEG dataset. The results of the simulation demonstrate the superiority of the proposed method over the original Kalman Filter and other existing methods. Copyright © 2017 Elsevier B.V. All rights reserved.
Hyperspectral target detection using regularized high-order matched filter
Shi, Zhenwei; Yang, Shuo; Jiang, Zhiguo
2011-05-01
Automatic target detection is an important application in the hyperspectral image processing field. Most statistics-based detection algorithms use second-order statistics to construct detectors. However, for target detection in a real hyperspectral image, targets of interest usually occupy a few pixels with small population. In this case, high-order statistics could characterize targets more effectively than second-order statistics. Also, the inherent variation of spectra of targets is an obstacle to successful target detection. In this paper, we propose a regularized high-order matched filter (RHF) which uses high-order statistics to build an objective function and uses a regularized term to make the algorithm robust to target spectral variation. A gradient descent method is used to solve this optimization problem, and we obtain the convergence properties of the RHF. According to the experimental hyperspectral data, the results have shown that the proposed algorithm performed better than those classical second-order statistics-based algorithms and some kernel-based methods.
Hybrid RANS-LES using high order numerical methods
Henry de Frahan, Marc; Yellapantula, Shashank; Vijayakumar, Ganesh; Knaus, Robert; Sprague, Michael
2017-11-01
Understanding the impact of wind turbine wake dynamics on downstream turbines is particularly important for the design of efficient wind farms. Due to their tractable computational cost, hybrid RANS/LES models are an attractive framework for simulating separation flows such as the wake dynamics behind a wind turbine. High-order numerical methods can be computationally efficient and provide increased accuracy in simulating complex flows. In the context of LES, high-order numerical methods have shown some success in predictions of turbulent flows. However, the specifics of hybrid RANS-LES models, including the transition region between both modeling frameworks, pose unique challenges for high-order numerical methods. In this work, we study the effect of increasing the order of accuracy of the numerical scheme in simulations of canonical turbulent flows using RANS, LES, and hybrid RANS-LES models. We describe the interactions between filtering, model transition, and order of accuracy and their effect on turbulence quantities such as kinetic energy spectra, boundary layer evolution, and dissipation rate. This work was funded by the U.S. Department of Energy, Exascale Computing Project, under Contract No. DE-AC36-08-GO28308 with the National Renewable Energy Laboratory.
Vector wave analysis of an electromagnetic high-order Bessel vortex beam of fractional type α.
Mitri, F G
2011-03-01
The scalar wave theory of nondiffracting electromagnetic (EM) high-order Bessel vortex beams of fractional type α has been recently explored, and their novel features and promising applications have been revealed. However, complete characterization of the properties for this new type of beam requires a vector analysis to determine the fields' components in space because scalar wave theory is inadequate to describe such beams, especially when the central spot is comparable to the wavelength (k(r)/k≈1, where k(r) is the radial component of the wavenumber k). Stemming from Maxwell's vector equations and the Lorenz gauge condition, a full vector wave analysis for the electric and magnetic fields is presented. The results are of particular importance in the study of EM wave scattering of a high-order Bessel vortex beam of fractional type α by particles.
Intrinsic origin of the high order angular momentum terms in a nuclear rotation Hamiltonian
Energy Technology Data Exchange (ETDEWEB)
Minkov, N [Institute of Nuclear Research and Nuclear Energy, 72 Tzarigrad Road, Sofia 1784 (Bulgaria); Yotov, P [Institute of Nuclear Research and Nuclear Energy, 72 Tzarigrad Road, Sofia 1784 (Bulgaria); Jolos, R V [Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Scheid, W [Institut fuer Theoretische Physik der Justus-Liebig-Universitaet, Heinrich-Buff-Ring 16, D-35392 Giessen (Germany)
2007-02-15
A nuclear Hamiltonian with high order terms in the collective angular momentum operators is constructed by applying the method of contact transformations to a Hamiltonian including intrinsic particle motion and Coriolis interaction. In the space of intrinsic variables, the coefficients of the transformed Hamiltonian appear as matrix elements depending on the intrinsic angular momentum. Their transformation properties under the time reversal assure the time-reversal invariance of the Hamiltonian in the collective space. It is shown that the intrinsic matrix elements correspond to the coefficients in the point-symmetry-based quadrupole-octupole rotation Hamiltonian. In this framework, the developed formalism gives an insight into the intrinsic origin of the high order effects in the rotation motion of complex-deformed nuclei.
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm
A regularisation method for solving the Poisson equation using Green’s functions is presented.The method is shown to obtain a convergence rate which corresponds to the design of the regularised Green’s function and a spectral-like convergence rate is obtained using a spectrally ideal regularisation....... It is shown that the regularised Poisson solver can be extended to handle mixed periodic and free-space boundary conditions. This is done by solving the equation spectrally in the periodic directions which yields a modified Helmholtz equation for the free-space directions which in turn is solved by deriving...... the appropriate regularised Green’s functions. Using an analogy to the particle-particle particle-mesh method, a framework for calculating multi-resolution solutions using local refinement patches is presented. The regularised Poisson solver is shown to maintain a high order converging solution for different...
DEFF Research Database (Denmark)
Krüger, Asger Christian; Raarup, Merete Krog; Nielsen, Morten Muhlig
2010-01-01
the interaction of hnRNP A1 with G-quadruplex DNA structures containing the human telomere repeat (TTAGGG) by gel retardation assays, ensemble fluorescence energy transfer (FRET) spectroscopy, and single molecule FRET microscopy. Our biochemical experiments show that hnRNP A1 binds well to the G......-quadruplex telomeric DNA. Ensemble and single molecule FRET measurements provide further insight into molecular conformation: the telomeric DNA overhang is found to be in a folded state in the absence of hnRNP A1 and to remain predominantly in a compact state when complexed with hnRNP A1. This finding is in contrast...
Directory of Open Access Journals (Sweden)
Estruch Francisco
2012-09-01
Full Text Available Abstract Background The various steps of mRNP biogenesis (transcription, processing and export are interconnected. It has been shown that the transcription machinery plays a pivotal role in mRNP assembly, since several mRNA export factors are recruited during transcription and physically interact with components of the transcription machinery. Although the shuttling DEAD-box protein Dbp5p is concentrated on the cytoplasmic fibrils of the NPC, previous studies demonstrated that it interacts physically and genetically with factors involved in transcription initiation. Results We investigated the effect of mutations affecting various components of the transcription initiation apparatus on the phenotypes of mRNA export mutant strains. Our results show that growth and mRNA export defects of dbp5 and mex67 mutant strains can be suppressed by mutation of specific transcription initiation components, but suppression was not observed for mutants acting in the very first steps of the pre-initiation complex (PIC formation. Conclusions Our results indicate that mere reduction in the amount of mRNP produced is not sufficient to suppress the defects caused by a defective mRNA export factor. Suppression occurs only with mutants affecting events within a narrow window of the mRNP biogenesis process. We propose that reducing the speed with which transcription converts from initiation and promoter clearance to elongation may have a positive effect on mRNP formation by permitting more effective recruitment of partially-functional mRNP proteins to the nascent mRNP.
Yeast hnRNP-related proteins contribute to the maintenance of telomeres
Energy Technology Data Exchange (ETDEWEB)
Lee-Soety, Julia Y., E-mail: jlee04@sju.edu [Department of Biology, Saint Joseph' s University, PA 19131 (United States); Jones, Jennifer; MacGibeny, Margaret A.; Remaly, Erin C.; Daniels, Lynsey; Ito, Andrea; Jean, Jessica; Radecki, Hannah; Spencer, Shannon [Department of Biology, Saint Joseph' s University, PA 19131 (United States)
2012-09-14
Highlights: Black-Right-Pointing-Pointer Yeast hnRNP-related proteins are able to prevent faster senescence in telomerase-null cells. Black-Right-Pointing-Pointer The conserved RRMs in Npl3 are important for telomere maintenance. Black-Right-Pointing-Pointer Human hnRNP A1 is unable to complement the lack of NPL3 in yeast. Black-Right-Pointing-Pointer Npl3 and Cbc2 may work as telomere capping proteins. -- Abstract: Telomeres protect the ends of linear chromosomes, which if eroded to a critical length can become uncapped and lead to replicative senescence. Telomerase maintains telomere length in some cells, but inappropriate expression facilitates the immortality of cancer cells. Recently, proteins involved in RNA processing and ribosome assembly, such as hnRNP (heterogeneous nuclear ribonucleoprotein) A1, have been found to participate in telomere maintenance in mammals. The Saccharomyces cerevisiae protein Npl3 shares significant amino acid sequence similarities with hnRNP A1. We found that deleting NPL3 accelerated the senescence of telomerase null cells. The highly conserved RNA recognition motifs (RRM) in Npl3 appear to be important for preventing faster senescence. Npl3 preferentially binds telomere sequences in vitro, suggesting that Npl3 may affect telomeres directly. Despite similarities between the two proteins, human hnRNP A1 is unable to complement the lack of Npl3 to rescue accelerated senescence in tlc1 npl3 cells. Deletion of CBC2, which encodes another hnRNP-related protein that associates with Npl3, also accelerates senescence. Potential mechanisms by which hnRNP-related proteins maintain telomeres are discussed.
Effect of Under-Resolved Grids on High Order Methods
Yee, H. C.; Sjoegreen, B.; Mansour, Nagi (Technical Monitor)
2001-01-01
There has been much discussion on verification and validation processes for establishing the credibility of CFD simulations. Since the early 1990s, many of the aeronautical and mechanical engineering related reference journals mandated that any accepted articles in numerical simulations (without known solutions to compared with) need to perform a minimum of one level of grid refinement and time step reduction. Due to the difficulty in analysis, the effect of under-resolved grids and the nonlinear behavior of available spatial discretizations, are scarcely discussed in the literature. Here, an under-resolved numerical simulation is one where the grid spacing being used is too coarse to resolve the smallest physically relevant scales of the chosen continuum governing equations that are of interest to the numerical modeler. With the advent of new developments in fourth-order or higher spatial schemes, it has become common to regard high order schemes as more accurate, reliable and require less grid points. The danger comes when one tries to perform computations with the coarsest grid possible while still hoping to maintain numerical results sufficiently accurate for complex flows, and especially, data-limited problems. On one hand, high order methods when applies to highly coupled multidimensional complex nonlinear problems might have different stability, convergence and reliability behavior than their well studied low order counterparts, especially for nonlinear schemes such as TVD, MUSCL with limiters, ENO, WENO and discrete Galerkin. On the other hand, high order methods involve more operation counts and systematic grid convergence study can be time consuming and prohibitively expansive. At the same time it is difficult to fully understand or categorize the different nonlinear behavior of finite discretizations, especially at the limits of under-resolution when different types of bifurcation phenomena might occur, depending on the combination of grid spacings, time
Efficiency of High Order Spectral Element Methods on Petascale Architectures
Hutchinson, Maxwell
2016-06-14
High order methods for the solution of PDEs expose a tradeoff between computational cost and accuracy on a per degree of freedom basis. In many cases, the cost increases due to higher arithmetic intensity while affecting data movement minimally. As architectures tend towards wider vector instructions and expect higher arithmetic intensities, the best order for a particular simulation may change. This study highlights preferred orders by identifying the high order efficiency frontier of the spectral element method implemented in Nek5000 and NekBox: the set of orders and meshes that minimize computational cost at fixed accuracy. First, we extract Nek’s order-dependent computational kernels and demonstrate exceptional hardware utilization by hardware-aware implementations. Then, we perform productionscale calculations of the nonlinear single mode Rayleigh-Taylor instability on BlueGene/Q and Cray XC40-based supercomputers to highlight the influence of the architecture. Accuracy is defined with respect to physical observables, and computational costs are measured by the corehour charge of the entire application. The total number of grid points needed to achieve a given accuracy is reduced by increasing the polynomial order. On the XC40 and BlueGene/Q, polynomial orders as high as 31 and 15 come at no marginal cost per timestep, respectively. Taken together, these observations lead to a strong preference for high order discretizations that use fewer degrees of freedom. From a performance point of view, we demonstrate up to 60% full application bandwidth utilization at scale and achieve ≈1PFlop/s of compute performance in Nek’s most flop-intense methods.
Pumping RNA: nuclear bodybuilding along the RNP pipeline.
Matera, A Gregory; Shpargel, Karl B
2006-06-01
Cajal bodies (CBs) are nuclear subdomains involved in the biogenesis of several classes of small ribonucleoproteins (RNPs). A number of recent advances highlight progress in the understanding of the organization and dynamics of CB components. For example, a class of small Cajal body-specific (sca) RNPs has been discovered. Localization of scaRNPs to CBs was shown to depend on a conserved RNA motif. Intriguingly, this motif is also present in mammalian telomerase RNA and the evidence suggests that assembly of the active form of telomerase RNP occurs in and around CBs during S phase. Important steps in the assembly and modification of spliceosomal RNPs have also been shown to take place in CBs. Additional experiments have revealed the existence of kinetically distinct subclasses of CB components. Finally, the recent identification of novel markers for CBs in both Drosophila and Arabidopsis not only lays to rest questions about the evolutionary conservation of these nuclear suborganelles, but also should enable forward genetic screens for the identification of new components and pathways involved in their assembly, maintenance and function.
On high-order perturbative calculations at finite density
Energy Technology Data Exchange (ETDEWEB)
Ghişoiu, Ioan, E-mail: ioan.ghisoiu@helsinki.fi [Helsinki Institute of Physics and Department of Physics, University of Helsinki (Finland); Gorda, Tyler, E-mail: tyler.gorda@helsinki.fi [Helsinki Institute of Physics and Department of Physics, University of Helsinki (Finland); Department of Physics, University of Colorado Boulder, Boulder, CO (United States); Kurkela, Aleksi, E-mail: aleksi.kurkela@cern.ch [Theoretical Physics Department, CERN, Geneva (Switzerland); Faculty of Science and Technology, University of Stavanger, Stavanger (Norway); Romatschke, Paul, E-mail: paul.romatschke@colorado.edu [Department of Physics, University of Colorado Boulder, Boulder, CO (United States); Center for Theory of Quantum Matter, University of Colorado, Boulder, CO (United States); Säppi, Matias, E-mail: matias.sappi@helsinki.fi [Helsinki Institute of Physics and Department of Physics, University of Helsinki (Finland); Vuorinen, Aleksi, E-mail: aleksi.vuorinen@helsinki.fi [Helsinki Institute of Physics and Department of Physics, University of Helsinki (Finland)
2017-02-15
We discuss the prospects of performing high-order perturbative calculations in systems characterized by a vanishing temperature but finite density. In particular, we show that the determination of generic Feynman integrals containing fermionic chemical potentials can be reduced to the evaluation of three-dimensional phase space integrals over vacuum on-shell amplitudes — a result reminiscent of a previously proposed “naive real-time formalism” for vacuum diagrams. Applications of these rules are discussed in the context of the thermodynamics of cold and dense QCD, where it is argued that they facilitate an extension of the Equation of State of cold quark matter to higher perturbative orders.
High-order harmonic generation in laser plasma: Recent achievements
Ganeev, R. A.
2012-07-01
Recent studies of high-order harmonic generation of laser radiation in laser-produced plasma show new attractive developments in this field. Those include generation of extended harmonics in plasma plumes, new approaches in application of two-color pump, generation of extremely broadened harmonics, further developments in harmonic generation in clusters (fullerenes, carbon nanotubes, in-situ produced nanoparticles), destructive interference of harmonics from different emitters, resonance-induced enhancement of harmonics, applications of high pulse repetition rate lasers for the enhancement of average power of generating harmonics, observation of quantum path signatures, etc. We review some of these recent developments.
Plasma high-order-harmonic generation from ultraintense laser pulses
Tang, Suo; Kumar, Naveen; Keitel, Christoph H.
2017-05-01
Plasma high-order-harmonic generation from an extremely intense short-pulse laser is explored by including the effects of ion motion, electron-ion collisions, and radiation reaction force in the plasma dynamics. The laser radiation pressure induces plasma ion motion through the hole-boring effect, resulting in frequency shifting and widening of the harmonic spectra. The classical radiation reaction force slightly mitigates the frequency broadening caused by the ion motion. Based on the results and physical considerations, parameter maps highlighting the optimum regions for generating a single intense attosecond pulse and coherent XUV radiation are presented.
High-order harmonic generation in a capillary discharge
Rocca, Jorge J.; Kapteyn, Henry C.; Mumane, Margaret M.; Gaudiosi, David; Grisham, Michael E.; Popmintchev, Tenio V.; Reagan, Brendan A.
2010-06-01
A pre-ionized medium created by a capillary discharge results in more efficient use of laser energy in high-order harmonic generation (HHG) from ions. It extends the cutoff photon energy, and reduces the distortion of the laser pulse as it propagates down the waveguide. The observed enhancements result from a combination of reduced ionization energy loss and reduced ionization-induced defocusing of the driving laser as well as waveguiding of the driving laser pulse. The discharge plasma also provides a means to spectrally tune the harmonics by tailoring the initial level of ionization of the medium.
Spatial Mode Control of High-Order Harmonics
Energy Technology Data Exchange (ETDEWEB)
Mercer, I.; Mevel, E.; Zerne, R.; LHuillier, A.; Antoine, P.; Wahlstroem, C. [Department of Physics, Lund Institute of Technology, S-221 00 Lund (Sweden)]|[Commissariat a l`Energie Atomique, DSM/DRECAM/SPAM, Centre d`Etudes de Saclay, 91191 Gif-sur-Yvette (France)
1996-08-01
We demonstrate that the spatial mode of high-order harmonics can be continuously controlled. The control is achieved by spatially modulating the degree of elliptical polarization of the fundamental field using birefringent optics. A highly sensitive relationship between the efficiency of harmonic generation and the degree of laser elliptical polarization leads to atoms emitting harmonics only in regions of linear polarization. The harmonics are emitted as annular beams whose angles of divergence can be continuously varied. {copyright} {ital 1996 The American Physical Society.}
Generation of high order geometry representations in Octree meshes
Directory of Open Access Journals (Sweden)
Harald G. Klimach
2015-11-01
Full Text Available We propose a robust method to convert triangulated surface data into polynomial volume data. Such polynomial representations are required for high-order partial differential solvers, as low-order surface representations would diminish the accuracy of their solution. Our proposed method deploys a first order spatial bisection algorithm to find robustly an approximation of given geometries. The resulting voxelization is then used to generate Legendre polynomials of arbitrary degree. By embedding the locally defined polynomials in cubical elements of a coarser mesh, this method can reliably approximate even complex structures, like porous media. It thereby is possible to provide appropriate material definitions for high order discontinuous Galerkin schemes. We describe the method to construct the polynomial and how it fits into the overall mesh generation. Our discussion includes numerical properties of the method and we show some results from applying it to various geometries. We have implemented the described method in our mesh generator Seeder, which is publically available under a permissive open-source license.
Study of high-order harmonic generation from nanoparticles
Energy Technology Data Exchange (ETDEWEB)
Singhal, H; Naik, P A; Srivastava, A K; Singh, A; Chari, R; Khan, R A; Chakera, J A; Gupta, P D [Raja Ramanna Centre for Advanced Technology, Indore 452 013 (India); Ganeev, R A, E-mail: himanshu@rrcat.gov.i [Institute of Electronics, Uzbekistan Academy of Sciences, Tashkent 100125 (Uzbekistan)
2010-01-28
An experimental study on high-order harmonic generation from the interaction of 45 fs Ti:sapphire laser pulses with preformed plasma plumes of metal nanoparticles was carried out. Highly efficient harmonic generation in the range of 9th order to 19th order was observed for Ag nanoparticles. The stability of harmonic generation was enhanced by utilizing special target fabrication techniques and through optimizing the conditions of plasma plume formation. Broadband harmonic generation was observed through the optimization of femtosecond laser intensity and through the use of spectrally broadened laser pulses. The harmonic generation was compared for various target materials (nano and bulk) and for Ag nanoparticle targets prepared from different fabrication techniques. Efficient generation of even- and odd-order harmonics was observed through the use of two-colour pulses. The observations can be explained qualitatively from symmetry breaking of high-order harmonic generation through the introduction of second harmonic pulses. The spectral broadening and shift of harmonic radiation can be understood from the self-modulation of the laser and harmonic radiation in the plasma.
Accelerating experimental high-order spatial statistics calculations using GPUs
Li, Xue; Huang, Tao; Lu, De-Tang; Niu, Cong
2014-09-01
High-order spatial statistics have been widely used to describe the spatial phenomena in the field of geology science. Spatial statistics are subject to extremely heavy computational burden for large geostatistical models. To improve the computational efficiency, a parallel approach based on GPU (Graphics Processing Unit) is proposed for the calculation of high-order spatial statistics. The parallel scheme is achieved by utilizing a two-stage method to calculate the replicate of a moment for a given template simultaneously termed as the node-stage parallelism, and transform the spatial moments to cumulants for all lags of a template simultaneously termed as the template-stage parallelism. Also, a series of optimization strategies are proposed to take full advantage of the computational capabilities of GPUs, including the appropriate task allocation to the CUDA (Compute Unified Device Architecture) threads, proper organization of the GPU physical memory, and optimal improvement of the existed parallel routines. Tests are carried out on two training images to compare the performance of the GPU-based method with that of the serial implementation. Error analysis results indicate that the proposed parallel method can generate accurate cumulant maps, and the performance comparisons on various examples show that all the speedups for third-order, fourth-order and fifth-order cumulants calculation are over 17 times.
High-order regularization in lattice-Boltzmann equations
Mattila, Keijo K.; Philippi, Paulo C.; Hegele, Luiz A.
2017-04-01
A lattice-Boltzmann equation (LBE) is the discrete counterpart of a continuous kinetic model. It can be derived using a Hermite polynomial expansion for the velocity distribution function. Since LBEs are characterized by discrete, finite representations of the microscopic velocity space, the expansion must be truncated and the appropriate order of truncation depends on the hydrodynamic problem under investigation. Here we consider a particular truncation where the non-equilibrium distribution is expanded on a par with the equilibrium distribution, except that the diffusive parts of high-order non-equilibrium moments are filtered, i.e., only the corresponding advective parts are retained after a given rank. The decomposition of moments into diffusive and advective parts is based directly on analytical relations between Hermite polynomial tensors. The resulting, refined regularization procedure leads to recurrence relations where high-order non-equilibrium moments are expressed in terms of low-order ones. The procedure is appealing in the sense that stability can be enhanced without local variation of transport parameters, like viscosity, or without tuning the simulation parameters based on embedded optimization steps. The improved stability properties are here demonstrated using the perturbed double periodic shear layer flow and the Sod shock tube problem as benchmark cases.
High order variational solutions of time dependent neutron transport problems
Energy Technology Data Exchange (ETDEWEB)
Wilson, B.C.
1985-01-01
High order numerical solutions of the time-dependent one speed neutron transport equation are developed using cubic hermite polynomial trial functions, variational techniques, and exponential matrix operators. Two new numerical solutions are developed that are high order with respect to both time and space variables. In the first method, the time-dependent P/sub N/ equations are transformed into Generalized Telegrapher's Equations (GTE) that are valid for any order P/sub N/ approximation. The Generalized Telegrapher's Equations form a coupled set of second order differential equations with respect to both time and space. In the second method, the time-dependent P/sub N/ equations are transformed into coupled Transport Diffusion Equations (TDE), keeping the additional terms that maintain the transport nature of the solution. The Transport Diffusion Equations are first order in time and second order in space. Numerically evaluated time-dependent analytic solutions are also developed for homogeneous media transport problems in the P/sub 1/ and P/sub 3/ approximations via Laplace Transforms in order to validate the variational GTE and TDE solutions. The analytic solutions allow anisotropic scattering, up to the appropriate P/sub N/ order. The analytic solutions are not limited to the non-precise extrapolation boundary condition, like many time-dependent analytic P/sub N/ solutions, but allow any of the standard transport vacuum boundary condition approximations.
A High-Order CFS Algorithm for Clustering Big Data
Directory of Open Access Journals (Sweden)
Fanyu Bu
2016-01-01
Full Text Available With the development of Internet of Everything such as Internet of Things, Internet of People, and Industrial Internet, big data is being generated. Clustering is a widely used technique for big data analytics and mining. However, most of current algorithms are not effective to cluster heterogeneous data which is prevalent in big data. In this paper, we propose a high-order CFS algorithm (HOCFS to cluster heterogeneous data by combining the CFS clustering algorithm and the dropout deep learning model, whose functionality rests on three pillars: (i an adaptive dropout deep learning model to learn features from each type of data, (ii a feature tensor model to capture the correlations of heterogeneous data, and (iii a tensor distance-based high-order CFS algorithm to cluster heterogeneous data. Furthermore, we verify our proposed algorithm on different datasets, by comparison with other two clustering schemes, that is, HOPCM and CFS. Results confirm the effectiveness of the proposed algorithm in clustering heterogeneous data.
Efficient high-order suppression system for a metrology beamline.
Sokolov, A; Sertsu, M G; Gaupp, A; Lüttecke, M; Schäfers, F
2018-01-01
High-quality metrology with synchrotron radiation requires in particular a very high spectral purity of the incident beam. This is usually achieved by a set of transmission filters with suitable absorption edges to suppress high-order radiation of the monochromator. The at-wavelength metrology station at a BESSY-II bending-magnet collimated plane-grating monochromator (c-PGM) beamline has recently commissioned a high-order suppression system (HiOS) based on four reflections from mirrors which can be inserted into the beam path. Two pairs of mirrors are aligned parallel so as not to disturb the original beam path and are rotated clockwise and counter-clockwise. Three sets of coatings are available for the different energy ranges and the incidence angle is freely tunable to find the optimum figure of merit for maximum suppression at maximum transmission for each photon energy required. Measured performance results of the HiOS for the EUV and XUV range are compared with simulations, and applications are discussed.
High-order finite element methods for cardiac monodomain simulations
Directory of Open Access Journals (Sweden)
Kevin P Vincent
2015-08-01
Full Text Available Computational modeling of tissue-scale cardiac electrophysiology requires numerically converged solutions to avoid spurious artifacts. The steep gradients inherent to cardiac action potential propagation necessitate fine spatial scales and therefore a substantial computational burden. The use of high-order interpolation methods has previously been proposed for these simulations due to their theoretical convergence advantage. In this study, we compare the convergence behavior of linear Lagrange, cubic Hermite, and the newly proposed cubic Hermite-style serendipity interpolation methods for finite element simulations of the cardiac monodomain equation. The high-order methods reach converged solutions with fewer degrees of freedom and longer element edge lengths than traditional linear elements. Additionally, we propose a dimensionless number, the cell Thiele modulus, as a more useful metric for determining solution convergence than element size alone. Finally, we use the cell Thiele modulus to examine convergence criteria for obtaining clinically useful activation patterns for applications such as patient-specific modeling where the total activation time is known a priori.
High-order finite element methods for cardiac monodomain simulations
Vincent, Kevin P.; Gonzales, Matthew J.; Gillette, Andrew K.; Villongco, Christopher T.; Pezzuto, Simone; Omens, Jeffrey H.; Holst, Michael J.; McCulloch, Andrew D.
2015-01-01
Computational modeling of tissue-scale cardiac electrophysiology requires numerically converged solutions to avoid spurious artifacts. The steep gradients inherent to cardiac action potential propagation necessitate fine spatial scales and therefore a substantial computational burden. The use of high-order interpolation methods has previously been proposed for these simulations due to their theoretical convergence advantage. In this study, we compare the convergence behavior of linear Lagrange, cubic Hermite, and the newly proposed cubic Hermite-style serendipity interpolation methods for finite element simulations of the cardiac monodomain equation. The high-order methods reach converged solutions with fewer degrees of freedom and longer element edge lengths than traditional linear elements. Additionally, we propose a dimensionless number, the cell Thiele modulus, as a more useful metric for determining solution convergence than element size alone. Finally, we use the cell Thiele modulus to examine convergence criteria for obtaining clinically useful activation patterns for applications such as patient-specific modeling where the total activation time is known a priori. PMID:26300783
Cluster size dependence of high-order harmonic generation
Tao, Y; Bastiaens, H M J; van der Slot, P J M; Biedron, S G; Milton, S V; Boller, K -J
2016-01-01
We investigate high-order harmonic generation (HHG) from noble gas clusters in a supersonic gas jet. To identify the contribution of harmonic generation from clusters versus that from gas monomers, we measure the high-order harmonic output over a broad range of the total atomic number density in the jet (from 3x10^{16} cm^{-3} to 3x10^{18} cm^{-3}) at two different reservoir temperatures (303 K and 363 K). For the first time in the evaluation of the harmonic yield in such measurements, the variation of the liquid mass fraction, g, versus pressure and temperature is taken into consideration, which we determine, reliably and consistently, to be below 20% within our range of experimental parameters. Based on measurements with a thin jet where significant variations in reabsorption and the phase matching conditions can be neglected, we conclude that atoms in the form of small clusters (average cluster size < 1000 atoms) provide the same higher-order nonlinear response as single-atoms. This implies that HHG in ...
GLD-2/RNP-8 cytoplasmic poly(A) polymerase is a broad-spectrum regulator of the oogenesis program
Wilson, Tracy L.; Kimble, Judith
2010-01-01
Regulated polyadenylation is a broadly conserved mechanism that controls key events during oogenesis. Pivotal to that mechanism is GLD-2, a catalytic subunit of cytoplasmic poly(A) polymerase (PAP). Caenorhabditis elegans GLD-2 forms an active PAP with multiple RNA-binding partners to regulate diverse aspects of germline and early embryonic development. One GLD-2 partner, RNP-8, was previously shown to influence oocyte fate specification. Here we use a genomic approach to identify transcripts selectively associated with both GLD-2 and RNP-8. Among the 335 GLD-2/RNP-8 potential targets, most were annotated as germline mRNAs and many as maternal mRNAs. These targets include gld-2 and rnp-8 themselves, suggesting autoregulation. Removal of either GLD-2 or RNP-8 resulted in shortened poly(A) tails and lowered abundance of four target mRNAs (oma-2, egg-1, pup-2, and tra-2); GLD-2 depletion also lowered the abundance of most GLD-2/RNP-8 putative target mRNAs when assayed on microarrays. Therefore, GLD-2/RNP-8 appears to polyadenylate and stabilize its target mRNAs. We also provide evidence that rnp-8 influences oocyte development; rnp-8 null mutants have more germ cell corpses and fewer oocytes than normal. Furthermore, RNP-8 appears to work synergistically with another GLD-2–binding partner, GLD-3, to ensure normal oogenesis. We propose that the GLD-2/RNP-8 enzyme is a broad-spectrum regulator of the oogenesis program that acts within an RNA regulatory network to specify and produce fully functional oocytes. PMID:20855596
Directory of Open Access Journals (Sweden)
Wu Xiaobing
2011-01-01
Full Text Available Abstract Background Influenza A virus can infect a wide variety of animal species including humans, pigs, birds and other species. Viral ribonucleoprotein (vRNP was involved in genome replication, transcription and host adaptation. Currently, firefly luciferase (Fluc reporter system was used in vRNP functional assay. However, its limitation for the testing by virus infection resulted in an increased need for rapid, sensitive, and biosafe techniques. Here, an influenza A virus UTR-driven gene reporter for vRNP assay based on secreted Gaussia luciferase (Gluc activity was evaluated. Results By measuring Gluc levels in supernatants, reporter gene activity could be detected and quantitated after either reconstitution of influenza A virus polymerase complex or viral infection of 293T and A549 cells, respectively. As compared with Fluc reporter, Gluc-based reporter was heat-tolerant (65°C for 30 min and produced 50-fold higher bioluminescent activity at 24 h posttransfection. Signals generated by Gluc reporter gene could be detected as early as 6 h post-infection and accumulated with time. Testing by viral infection, stronger signals were detected by Gluc reporter at a MOI of 0.001 than that of 1 and the effects of PB2-627K/E or amantadine on influenza vRNP activity were elucidated more effectively by the Gluc reporter system. Conclusions This approach provided a rapid, sensitive, and biosafe assay of influenza vRNP function, particularly for the highly pathogenic avian influenza viruses.
High order harmonic generation with femtosecond mid-infrared laser
Lin, Jinpu; Nees, John; Krushelnick, Karl; Dollar, Franklin; Nguyen, Tam
2017-10-01
There has been growing interest in high order harmonic generation (HHG) from laser-solid interactions as a compact source of coherent x-rays. The ponderomotive potential in laser-plasma interactions increases with longer laser wavelength, so there may be significant differences in the physics of harmonic generation and other phenomena when experiments are conducted with mid-infrared lasers. Previous experiments, however, have been done almost exclusively with near-infrared lasers. In this work, we report the results of experiments performed with millijoule, 40 fs, 2 µm laser pulses generated by an optical parametric amplifier (OPA) which are focused onto solid targets such as silicon and glass. The HHG efficiency, polarization dependence, and x-ray emission are studied and compared to measurements with near-infrared lasers. Funded by AFOSR MURI.
Improving the Accuracy of High-Order Nodal Transport Methods
Energy Technology Data Exchange (ETDEWEB)
Azmy, Y.Y.; Buscaglia, G.C.; Zamonsky, O.M.
1999-09-27
This paper outlines some recent advances towards improving the accuracy of neutron transport calculations using the Arbitrarily High Order Transport-Nodal (AHOT-N) Method. These advances consist of several contributions: (a) A formula for the spatial weights that allows for the polynomial order to be raised arbitrarily high without suffering adverse effects from round-off error; (b) A reconstruction technique for the angular flux, based upon a recursive formula, that reduces the pointwise error by one ordeq (c) An a posterior error indicator that estimates the true error and its distribution throughout the domain, so that it can be used for adaptively refining the approximation. Present results are mainly for ID, extension to 2D-3D is in progress.
Improving the Accuracy of High-Order Nodal Transport Methods
Energy Technology Data Exchange (ETDEWEB)
Azmy, Y.Y.; Buscaglia, G.C.; Zamonsky, O.M.
1999-09-27
This paper outlines some recent advances towards improving the accuracy of neutron calculations using the Arbitrarily High Order Transport-Nodal (AHOT-N) Method. These transport advances consist of several contributions: (a) A formula for the spatial weights that allows for the polynomial order to be raised arbitrarily high without suffering from pollution from round-off, error; (b) A reconstruction technique for the angular flux, based upon a recursive formula, that reduces the pointwise error by one order; (c) An a posterior error indicator that estimates the true error and its distribution throughout the domain, so that it can be used for adaptively reftig the approximation. Present results are mainly for ID, extension to 2D-3D is in progress.
High-order total variation minimization for interior SPECT
Yang, Jiansheng; Yu, Hengyong; Jiang, Ming; Wang, Ge
2011-01-01
Recently, we developed an approach for solving the computed tomography (CT) interior problem based on the high-order TV (HOT) minimization, assuming that a region-of-interest (ROI) is piecewise polynomial. In this paper, we generalize this finding from the CT field to the single-photon emission computed tomography (SPECT) field, and prove that if an ROI is piecewise polynomial, then the ROI can be uniquely reconstructed from the SPECT projection data associated with the ROI through the HOT minimization. Also, we propose a new formulation of HOT, which has an explicit formula for any n-order piecewise polynomial function, while the original formulation has no explicit formula for n ≥ 2. Finally, we verify our theoretical results in numerical simulation, and discuss relevant issues. PMID:22215932
High-Order Sparse Linear Predictors for Audio Processing
DEFF Research Database (Denmark)
Giacobello, Daniele; van Waterschoot, Toon; Christensen, Mads Græsbøll
2010-01-01
of interesting features that make the idea of using it in audio processing not far fetched, e.g., the strong ability of modeling the spectral peaks that play a dominant role in perception. In this paper, we provide some preliminary conjectures and experiments on the use of high-order sparse linear predictors......Linear prediction has generally failed to make a breakthrough in audio processing, as it has done in speech processing. This is mostly due to its poor modeling performance, since an audio signal is usually an ensemble of different sources. Nevertheless, linear prediction comes with a whole set...... in audio processing. These predictors, successfully implemented in modeling the short-term and long-term redundancies present in speech signals, will be used to model tonal audio signals, both monophonic and polyphonic. We will show how the sparse predictors are able to model efﬁciently the different...
High order integral equation method for diffraction gratings.
Lu, Wangtao; Lu, Ya Yan
2012-05-01
Conventional integral equation methods for diffraction gratings require lattice sum techniques to evaluate quasi-periodic Green's functions. The boundary integral equation Neumann-to-Dirichlet map (BIE-NtD) method in Wu and Lu [J. Opt. Soc. Am. A 26, 2444 (2009)], [J. Opt. Soc. Am. A 28, 1191 (2011)] is a recently developed integral equation method that avoids the quasi-periodic Green's functions and is relatively easy to implement. In this paper, we present a number of improvements for this method, including a revised formulation that is more stable numerically, and more accurate methods for computing tangential derivatives along material interfaces and for matching boundary conditions with the homogeneous top and bottom regions. Numerical examples indicate that the improved BIE-NtD map method achieves a high order of accuracy for in-plane and conical diffractions of dielectric gratings. © 2012 Optical Society of America
A high order theory for uniform and laminated plates
Lo, K. H.; Christensen, R. M.; Wu, E. M.
1976-01-01
A theory of plate deformation is derived which accounts for the effects of transverse shear deformation, transverse normal strain, and a nonlinear distribution of the in-plane displacements with respect to the thickness coordinate. The theory is compared with lower order plate theories through application to a particular problem involving a plate acted upon by a sinusoidal surface pressure. Comparison is also made with exact elasticity solution of this problem. It is found that when the ratio of the characteristic length of the load pattern to the plate thickness is of the order of unity, lower order theories are inadequate and the present high order theory is required to give meaningful results. Results are given for the bending of symmetric cross-ply and angle-ply laminates. Comparison with exact elasticity solutions indicates that the present plate theory is sufficiently accurate for predicting the behavior of thick laminates.
On high-order polynomial heat-balance integral implementations
Directory of Open Access Journals (Sweden)
Wood Alastair S.
2009-01-01
Full Text Available This article reconsiders aspects of the analysis conventionally used to establish accuracy, performance and limitations of the heat balance integral method: theoretical and practical rates of convergence are confirmed for a familiar piecewise heat-balance integral based upon mesh refinement, and the use of boundary conditions is discussed with respect to fixed and moving boundaries. Alternates to mesh refinement are increased order of approximation or non-polynomial approximants. Here a physically intuitive high-order polynomial heat balance integral formulation is described that exhibits high accuracy, rapid convergence, and desirable qualitative solution properties. The simple approach combines a global approximant of prescribed degree with spatial sub-division of the solution domain. As a variational-type method, it can be argued that heat-balance integral is simply 'one amongst many'. The approach is compared with several established variational formulations and performance is additionally assessed in terms of 'smoothness'.
XAO coronagraphy with the High-Order Test bench
Directory of Open Access Journals (Sweden)
Kasper M.
2011-07-01
Full Text Available Extreme adaptive optics systems dedicated to the search for extra solar planets are currently being developed for 8–10 meter class telescopes. The High-Order Test bench (HOT is a high-contrast imaging adaptive optics bench developed at ESO. Its objective is to test and optimize different techniques and technologies (e.g. wave front sensors, coronagraphs, speckle calibration methods…. It mimics realistic conditions at a telescope (e.g. VLT, including turbulence generator, XAO, and various near-IR coronagraphs. Here we provide a short overview of the system, and present results of recent AO-closed loop coronagraphic runs obtained with an Apodized Pupil Lyot Coronagraph (APLC.
Role of Rydberg States In High-order Harmonic Generation
Beaulieu, Samuel; Comby, Antoine; Wanie, Vincent; Petit, Stéphane; Légaré, François; Catoire, Fabrice; Mairesse, Yann
2016-01-01
The role of Rydberg states in strong field physics has known a renewed interest in the past few years with the study of resonant high-order harmonic generation. In addition to its fundamental in- terest, this process could create bright sources of coherent vacuum and extreme ultraviolet radiation with controlled polarization state. We investigate the spectral, spatial and temporal characteristics of the radiation produced near the ionization threshold of argon by few-cycle laser pulses. The intensity-dependence of the emission shows that two different pathways interfere to populate the Rydberg states. Furthermore, we show that the population of Rydberg states can lead to different emission mecanisms: either direct emission through XUV Free Induction Decay, or sequentially with absorption of additional photons, in processes similar to resonance-enhanced multiphoton above- threshold ionization. Last, using the attosecond lighthouse technique we show that the resonant emission from Rydberg states is not temporal...
High-Order Wave Propagation Algorithms for Hyperbolic Systems
Ketcheson, David I.
2013-01-22
We present a finite volume method that is applicable to hyperbolic PDEs including spatially varying and semilinear nonconservative systems. The spatial discretization, like that of the well-known Clawpack software, is based on solving Riemann problems and calculating fluctuations (not fluxes). The implementation employs weighted essentially nonoscillatory reconstruction in space and strong stability preserving Runge--Kutta integration in time. The method can be extended to arbitrarily high order of accuracy and allows a well-balanced implementation for capturing solutions of balance laws near steady state. This well-balancing is achieved through the $f$-wave Riemann solver and a novel wave-slope WENO reconstruction procedure. The wide applicability and advantageous properties of the method are demonstrated through numerical examples, including problems in nonconservative form, problems with spatially varying fluxes, and problems involving near-equilibrium solutions of balance laws.
High-order hydrodynamic algorithms for exascale computing
Energy Technology Data Exchange (ETDEWEB)
Morgan, Nathaniel Ray [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2016-02-05
Hydrodynamic algorithms are at the core of many laboratory missions ranging from simulating ICF implosions to climate modeling. The hydrodynamic algorithms commonly employed at the laboratory and in industry (1) typically lack requisite accuracy for complex multi- material vortical flows and (2) are not well suited for exascale computing due to poor data locality and poor FLOP/memory ratios. Exascale computing requires advances in both computer science and numerical algorithms. We propose to research the second requirement and create a new high-order hydrodynamic algorithm that has superior accuracy, excellent data locality, and excellent FLOP/memory ratios. This proposal will impact a broad range of research areas including numerical theory, discrete mathematics, vorticity evolution, gas dynamics, interface instability evolution, turbulent flows, fluid dynamics and shock driven flows. If successful, the proposed research has the potential to radically transform simulation capabilities and help position the laboratory for computing at the exascale.
Stable switching among high-order modes in polariton condensates
Sun, Yongbao; Yoon, Yoseob; Khan, Saeed; Ge, Li; Steger, Mark; Pfeiffer, Loren N.; West, Ken; Türeci, Hakan E.; Snoke, David W.; Nelson, Keith A.
2018-01-01
We report multistate optical switching among high-order bouncing-ball modes ("ripples") and whispering-gallery modes ("petals") of exciton-polariton condensates in a laser-generated annular trap. By tailoring the diameter and power of the annular trap, the polariton condensate can be switched among different trapped modes, accompanied by redistribution of spatial densities and superlinear increase in the emission intensities, implying that polariton condensates in this geometry could be exploited for an all-optical multistate switch. A model based on non-Hermitian modes of the generalized Gross-Pitaevskii equation reveals that this mode switching arises from competition between pump-induced gain and in-plane polariton loss. The parameters for reproducible switching among trapped modes have been measured experimentally, giving us a phase diagram for mode switching. Taken together, the experimental result and theoretical modeling advance our fundamental understanding of the spontaneous emergence of coherence and move us toward its practical exploitation.
High order accurate finite difference schemes based on symmetry preservation
Ozbenli, Ersin; Vedula, Prakash
2017-11-01
In this paper, we present a mathematical approach that is based on modified equations and the method of equivariant moving frames for construction of high order accurate invariant finite difference schemes that preserve Lie symmetry groups of underlying partial differential equations (PDEs). In the proposed approach, invariant (or symmetry preserving) numerical schemes with a desired (or fixed) order of accuracy are constructed from some non-invariant (base) numerical schemes. Modified forms of PDEs are used to improve the order of accuracy of existing schemes and these modified forms are obtained through addition of defect correction terms to the original forms of PDEs. These defect correction terms of modified PDEs that are noted from truncation error analysis are either completely removed from schemes or their representation is significantly simplified by considering convenient moving frames. This feature of the proposed method can especially be useful to avoid cumbersome numerical representations when high order schemes are developed from low order ones via the method of modified equations. The proposed method is demonstrated via construction of invariant numerical schemes with fixed (and higher) order of accuracy for some common linear and nonlinear problems (including the linear advection-diffusion equation in 1D and 2D, inviscid Burgers' equation, and viscous Burgers' equation) and the performance of these invariant numerical schemes is further evaluated. Our results indicate that such invariant numerical schemes obtained from existing base numerical schemes have the potential to significantly improve the quality of results not only in terms of desired higher order accuracy but also in the context of preservation of appropriate symmetry properties of underlying PDEs.
Cluster size dependence of high-order harmonic generation
Tao, Y.; Hagmeijer, R.; Bastiaens, H. M. J.; Goh, S. J.; van der Slot, P. J. M.; Biedron, S. G.; Milton, S. V.; Boller, K.-J.
2017-08-01
We investigate high-order harmonic generation (HHG) from noble gas clusters in a supersonic gas jet. To identify the contribution of harmonic generation from clusters versus that from gas monomers, we measure the high-order harmonic output over a broad range of the total atomic number density in the jet (from 3×1016 to 3 × 1018 {{cm}}-3) at two different reservoir temperatures (303 and 363 K). For the first time in the evaluation of the harmonic yield in such measurements, the variation of the liquid mass fraction, g, versus pressure and temperature is taken into consideration, which we determine, reliably and consistently, to be below 20% within our range of experimental parameters. By comparing the measured harmonic yield from a thin jet with the calculated corresponding yield from monomers alone, we find an increased emission of the harmonics when the average cluster size is less than 3000. Using g, under the assumption that the emission from monomers and clusters add up coherently, we calculate the ratio of the average single-atom response of an atom within a cluster to that of a monomer and find an enhancement of around 100 for very small average cluster size (∼200). We do not find any dependence of the cut-off frequency on the composition of the cluster jet. This implies that HHG in clusters is based on electrons that return to their parent ions and not to neighboring ions in the cluster. To fully employ the enhanced average single-atom response found for small average cluster sizes (∼200), the nozzle producing the cluster jet must provide a large liquid mass fraction at these small cluster sizes for increasing the harmonic yield. Moreover, cluster jets may allow for quasi-phase matching, as the higher mass of clusters allows for a higher density contrast in spatially structuring the nonlinear medium.
HnRNP A1 is Involved in Deep Vein Thrombosis Patients with Behçet's Disease.
Chen, Peng; Zhang, Chunyan; Liu, Chen; Zhang, Liyun; Yang, Chunhe; Chen, Guangyu; Ma, Dan; Tian, Yaping; Du, Hongwu
2016-04-01
The aim of this study was to verify the hypothesis originated from bioinformatics and literature reviews that hnNRP A1 may be a new immune target of Behçet's disease (BD). First, bioinformatics was used to show the correlation between hnRNP A1 and A2/B1 in amino acid sequences and three dimensional structures. Second, hnRNP A1 was expressed, purified, and immunologically confirmed by systematic immunology methods including: Western blotting, immunoprecipitation and Dot-ELISA. Then, ELISA was used to screen the anti-hnRNP A1 autoantibodies in newly confirmed clinical samples and the clinical significance was compared between anti-hnRNP A1 antibody positive and negative groups. Finally, the endothelial cells antigen profile of one anti-hnRNP A1 antibody positive BD patient was detected using immunoprecipitation with liquid chromatography tandem mass spectrometry (LC-TMS). In total 720 subjects enrolled and tested in this study. Our results demonstrated hnRNP A1 as a new immune target of BD. The reactivity of BD serum IgG antibodies against hnRNP A1 was significantly higher than healthy controls (P<0.0001), and deep vein thrombosis (DVT) showed a significant higher in the anti-hnRNP A1 antibodies positive group (P<0.05). Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.
factor high order fuzzy time series with applications to temperature ...
African Journals Online (AJOL)
HOD
Kuo et al in [10] proposed a new Master Voting scheme to derive forecasts. Mohammed et al [1] adopted weighted sum of centroids to obtain forecasts using particle swarm optimization. In this study, fuzzy C-means clustering was used, in the fuzzification process, to determine valid and useful unequal length of intervals for ...
Mode of conception of triplets and high order multiple pregnancies.
LENUS (Irish Health Repository)
Basit, I
2012-03-01
A retrospective audit was performed of all high order multiple pregnancies (HOMPs) delivered in three maternity hospitals in Dublin between 1999 and 2008. The mode of conception for each pregnancy was established with a view to determining means of reducing their incidence. A total of 101 HOMPs occurred, 93 triplet, 7 quadruplet and 1 quintuplet. Information regarding the mode of conception was available for 78 (81%) pregnancies. Twenty eight (27.7%) were spontaneous, 34 (33.7%) followedlVF\\/ICSI\\/FET treatment (in-vitro fertilisation, intracytoplasmic sperm injection, frozen embryo transfer), 16 (15.8%) resulted from Clomiphene Citrate treatment and 6 (6%) followed ovulation induction with gonadotrophins. Triplet and HOMPs are a major cause of maternal, feta land neonatal morbidity. Many are iatrogenic, arising from fertility treatments including Clomiphene. Reducing the numbers of embryos transferred will address IVF\\/ICSI\\/FET-related multiple pregnancy rates and this is currently happening in Ireland. Clomiphene and gonadotrophins should only be prescribed when appropriate resources are available to monitor patients adequately.
High-order WENO scheme for polymerization-type equations*
Directory of Open Access Journals (Sweden)
Gabriel Pierre
2010-12-01
Full Text Available Polymerization of proteins is a biochemical process involved in different diseases. Mathematically, it is generally modeled by aggregation-fragmentation-type equations. In this paper we consider a general polymerization model and propose a high-order numerical scheme to investigate the behavior of the solution. An important property of the equation is the mass conservation. The WENO scheme is built to preserve the total mass of proteins along time. Le processus biophysique de polymérisation de protéines entre en jeu dans différentes maladies. Mathématiquement, ceci est généralement modélisé par des équations de type agrégation-fragmentation. Dans cet article nous considérons un modèle général de polymérisation et proposons un schéma d’ordre élevé pour sa résolution numérique. Une propriété importante de l’équation est la conservation de la masse. Le schéma WENO est construit pour conserver la masse totale de protéines au cours du temps.
Stirling Analysis Comparison of Commercial vs. High-Order Methods
Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.; Demko, Rikako
2007-01-01
Recently, three-dimensional Stirling engine simulations have been accomplished utilizing commercial Computational Fluid Dynamics software. The validations reported can be somewhat inconclusive due to the lack of precise time accurate experimental results from engines, export control/ proprietary concerns, and the lack of variation in the methods utilized. The last issue may be addressed by solving the same flow problem with alternate methods. In this work, a comprehensive examination of the methods utilized in the commercial codes is compared with more recently developed high-order methods. Specifically, Lele's Compact scheme and Dyson s Ultra Hi-Fi method will be compared with the SIMPLE and PISO methods currently employed in CFD-ACE, FLUENT, CFX, and STAR-CD (all commercial codes which can in theory solve a three-dimensional Stirling model although sliding interfaces and their moving grids limit the effective time accuracy). We will initially look at one-dimensional flows since the current standard practice is to design and optimize Stirling engines with empirically corrected friction and heat transfer coefficients in an overall one-dimensional model. This comparison provides an idea of the range in which commercial CFD software for modeling Stirling engines may be expected to provide accurate results. In addition, this work provides a framework for improving current one-dimensional analysis codes.
Stirling Analysis Comparison of Commercial Versus High-Order Methods
Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.; Demko, Rikako
2005-01-01
Recently, three-dimensional Stirling engine simulations have been accomplished utilizing commercial Computational Fluid Dynamics software. The validations reported can be somewhat inconclusive due to the lack of precise time accurate experimental results from engines, export control/proprietary concerns, and the lack of variation in the methods utilized. The last issue may be addressed by solving the same flow problem with alternate methods. In this work, a comprehensive examination of the methods utilized in the commercial codes is compared with more recently developed high-order methods. Specifically, Lele's compact scheme and Dyson's Ultra Hi-Fi method will be compared with the SIMPLE and PISO methods currently employed in CFD-ACE, FLUENT, CFX, and STAR-CD (all commercial codes which can in theory solve a three-dimensional Stirling model with sliding interfaces and their moving grids limit the effective time accuracy). We will initially look at one-dimensional flows since the current standard practice is to design and optimize Stirling engines with empirically corrected friction and heat transfer coefficients in an overall one-dimensional model. This comparison provides an idea of the range in which commercial CFD software for modeling Stirling engines may be expected to provide accurate results. In addition, this work provides a framework for improving current one-dimensional analysis codes.
Recursive regularization step for high-order lattice Boltzmann methods
Coreixas, Christophe; Wissocq, Gauthier; Puigt, Guillaume; Boussuge, Jean-François; Sagaut, Pierre
2017-09-01
A lattice Boltzmann method (LBM) with enhanced stability and accuracy is presented for various Hermite tensor-based lattice structures. The collision operator relies on a regularization step, which is here improved through a recursive computation of nonequilibrium Hermite polynomial coefficients. In addition to the reduced computational cost of this procedure with respect to the standard one, the recursive step allows to considerably enhance the stability and accuracy of the numerical scheme by properly filtering out second- (and higher-) order nonhydrodynamic contributions in under-resolved conditions. This is first shown in the isothermal case where the simulation of the doubly periodic shear layer is performed with a Reynolds number ranging from 104 to 106, and where a thorough analysis of the case at Re=3 ×104 is conducted. In the latter, results obtained using both regularization steps are compared against the Bhatnagar-Gross-Krook LBM for standard (D2Q9) and high-order (D2V17 and D2V37) lattice structures, confirming the tremendous increase of stability range of the proposed approach. Further comparisons on thermal and fully compressible flows, using the general extension of this procedure, are then conducted through the numerical simulation of Sod shock tubes with the D2V37 lattice. They confirm the stability increase induced by the recursive approach as compared with the standard one.
Design and high order optimization of the ATF2 lattices
Marin, E; Woodley, M; Kubo, K; Okugi, T; Tauchi, T; Urakawa, J; Tomas, R
2013-01-01
The next generation of future linear colliders (LC) demands nano-meter beam sizes at the interaction point (IP) in order to reach the required luminosity. The final focus system (FFS) of a LC is meant to deliver such small beam sizes. The Accelerator Test Facility (ATF) aims to test the feasibility of the new local chromaticity correction scheme which the future LCs are based on. To this end the ATF2 nominal and ultra-low beta* lattices are design to vertically focus the beam at the IP to 37nm and 23nm, respectively if error-free lattices are considered. However simulations show that the measured field errors of the ATF2 magnets preclude to reach the mentioned spot sizes. This paper describes the optimization of high order aberrations of the ATF2 lattices in order to minimize the detrimental effect of the measured multipole components for both ATF2 lattices. Specifically three solutions are studied, the replacement of the last focusing quadrupole (QF1FF), insertion of octupole magnets and optics modification....
A Novel QAM Technique for High Order QAM Signaling
Directory of Open Access Journals (Sweden)
A. Ozen
2011-09-01
Full Text Available The paper proposes a novel spread quadrature amplitude modulation (S-QAM technique with high SNR improvement for high-order QAM channels. Simulated and experimental bit error rate (BER performance analyses of the proposed technique in blind and non-blind equalizers are obtained by using single carrier (SC WiMAX (IEEE 802.16-2004 radio. Instead of using any one particular type of channel profile, this study concentrates on true frequency selective Rayleigh fading channels in the real-time WiMAX radio environment around 3.5 GHz. The Constant Modulus Algorithm (CMA blind equalizer has been compared with the popular non-blind equalizers, Recursive Least Squares (RLS and Least Mean Squares (LMS algorithm, as benchmarks. It has been proven in experimental and simulated channels that CMA blind equalizer, using the proposed technique, can be considered as a low complexity, spectrum efficient and high performance time domain equalizations to be embedded in a transceiver for the next generation communications. Furthermore the proposed technique has also reduced approximately till 5 dB and 7.5 dB performance differences between non-blind and blind equalizers for 16-QAM and 64-QAM, respectively. The simulation results have demonstrated that the simulated and experimental studies of the proposed technique are compatible with each other and extremely satisfying.
High order shear horizontal modes for minimum remnant thickness.
Belanger, Pierre
2014-04-01
Thickness mapping in aging structures suffering from corrosion is challenging especially when the structure is only partially accessible. In plates the high order shear horizontal guided wave modes all have a cutoff frequency thickness product below which they cannot propagate. This property is potentially attractive to estimate the minimum remnant thickness between two transducers. When using a source and a sensor array it is possible to control the number of modes being excited and the size of the region interrogated by the technique. Finite element simulations were used to show that by exciting multiple guided wave modes simultaneously and identifying which modes are received by a sensor array it is possible to estimate the minimum remaining thickness along the propagation path. Initial experimental results showed excellent agreement with the finite element simulations when the plate is uniform and with a thickness reduction between the source and the sensor arrays the minimum remnant thickness was underestimated by approximately 20%. Copyright © 2014 Elsevier B.V. All rights reserved.
Integrated high-order surface diffraction gratings for diode lasers
Energy Technology Data Exchange (ETDEWEB)
Zolotarev, V V; Leshko, A Yu; Pikhtin, N A; Slipchenko, S O; Sokolova, Z N; Lubyanskiy, Ya V; Voronkova, N V; Tarasov, I S [Ioffe Physicotechnical Institute, Russian Academy of Sciences, St. Petersburg (Russian Federation)
2015-12-31
High-order surface diffraction gratings acting as a distributed Bragg reflector (DBR) in mesa stripe semiconductor lasers (λ = 1030 nm) have been studied theoretically and experimentally. Higher order interfering radiation modes (IRMs), which propagate off the plane of the waveguide, have been shown to have a crucial effect on the reflection and transmission spectra of the DBR. The decrease in the reflectivity of the DBR in response to the increase in the diffraction efficiency of these modes may reach 80% and more. According to theoretical analysis results, the intensity of the higher order IRMs is determined by the geometry of the DBR groove profile. Experimental data demonstrate that the noncavity modes are responsible for parasitic light leakage losses in the laser cavity. It has been shown that, in the case of nonoptimal geometry of the grating groove profile, the overall external differential quantum efficiency of the parasitic laser emission may exceed 45%, which is more than half of the laser output power. The optimal geometry of the DBR groove profile is trapezoidal, with the smallest possible lower base. Experimental evidence has been presented that this geometry considerably reduces the power of the higher order IRMs and minimises the parasitic light leakage loss. (lasers)
Global Monte Carlo Simulation with High Order Polynomial Expansions
Energy Technology Data Exchange (ETDEWEB)
William R. Martin; James Paul Holloway; Kaushik Banerjee; Jesse Cheatham; Jeremy Conlin
2007-12-13
The functional expansion technique (FET) was recently developed for Monte Carlo simulation. The basic idea of the FET is to expand a Monte Carlo tally in terms of a high order expansion, the coefficients of which can be estimated via the usual random walk process in a conventional Monte Carlo code. If the expansion basis is chosen carefully, the lowest order coefficient is simply the conventional histogram tally, corresponding to a flat mode. This research project studied the applicability of using the FET to estimate the fission source, from which fission sites can be sampled for the next generation. The idea is that individual fission sites contribute to expansion modes that may span the geometry being considered, possibly increasing the communication across a loosely coupled system and thereby improving convergence over the conventional fission bank approach used in most production Monte Carlo codes. The project examined a number of basis functions, including global Legendre polynomials as well as “local” piecewise polynomials such as finite element hat functions and higher order versions. The global FET showed an improvement in convergence over the conventional fission bank approach. The local FET methods showed some advantages versus global polynomials in handling geometries with discontinuous material properties. The conventional finite element hat functions had the disadvantage that the expansion coefficients could not be estimated directly but had to be obtained by solving a linear system whose matrix elements were estimated. An alternative fission matrix-based response matrix algorithm was formulated. Studies were made of two alternative applications of the FET, one based on the kernel density estimator and one based on Arnoldi’s method of minimized iterations. Preliminary results for both methods indicate improvements in fission source convergence. These developments indicate that the FET has promise for speeding up Monte Carlo fission source
High-order-harmonic generation in atomic and molecular systems
Suárez, Noslen; Chacón, Alexis; Pérez-Hernández, Jose A.; Biegert, Jens; Lewenstein, Maciej; Ciappina, Marcelo F.
2017-03-01
High-order-harmonic generation (HHG) results from the interaction of ultrashort laser pulses with matter. It configures an invaluable tool to produce attosecond pulses, moreover, to extract electron structural and dynamical information of the target, i.e., atoms, molecules, and solids. In this contribution, we introduce an analytical description of atomic and molecular HHG, that extends the well-established theoretical strong-field approximation (SFA). Our approach involves two innovative aspects: (i) First, the bound-continuum and rescattering matrix elements can be analytically computed for both atomic and multicenter molecular systems, using a nonlocal short range model, but separable, potential. When compared with the standard models, these analytical derivations make possible to directly examine how the HHG spectra depend on the driven media and laser-pulse features. Furthermore, we can turn on and off contributions having distinct physical origins or corresponding to different mechanisms. This allows us to quantify their importance in the various regions of the HHG spectra. (ii) Second, as reported recently [N. Suárez et al., Phys. Rev. A 94, 043423 (2016), 10.1103/PhysRevA.94.043423], the multicenter matrix elements in our theory are free from nonphysical gauge- and coordinate-system-dependent terms; this is accomplished by adapting the coordinate system to the center from which the corresponding time-dependent wave function originates. Our SFA results are contrasted, when possible, with the direct numerical integration of the time-dependent Schrödinger equation in reduced and full dimensionality. Very good agreement is found for single and multielectronic atomic systems, modeled under the single active electron approximation, and for simple diatomic molecular systems. Interference features, ubiquitously present in every strong-field phenomenon involving a multicenter target, are also captured by our model.
De Basabe, Jonás D.
2010-04-01
We investigate the stability of some high-order finite element methods, namely the spectral element method and the interior-penalty discontinuous Galerkin method (IP-DGM), for acoustic or elastic wave propagation that have become increasingly popular in the recent past. We consider the Lax-Wendroff method (LWM) for time stepping and show that it allows for a larger time step than the classical leap-frog finite difference method, with higher-order accuracy. In particular the fourth-order LWM allows for a time step 73 per cent larger than that of the leap-frog method; the computational cost is approximately double per time step, but the larger time step partially compensates for this additional cost. Necessary, but not sufficient, stability conditions are given for the mentioned methods for orders up to 10 in space and time. The stability conditions for IP-DGM are approximately 20 and 60 per cent more restrictive than those for SEM in the acoustic and elastic cases, respectively. © 2010 The Authors Journal compilation © 2010 RAS.
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Wang, Zhenyu, E-mail: wzy72609@163.com [Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030 (China); Zhao, Xiuyang, E-mail: xiuzh@psb.vib-ugent.be [Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030 (China); Wang, Bing, E-mail: wangbing@ibcas.ac.cn [Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030 (China); Liu, Erlong, E-mail: liuel14@lzu.edu.cn [Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030 (China); Chen, Ni, E-mail: 63710156@qq.com [Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030 (China); Zhang, Wei, E-mail: wzhang1216@yahoo.com [Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444 (China); Liu, Heng, E-mail: hengliu@lzu.edu.cn [Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030 (China)
2016-04-01
Heterogeneous nuclear ribonucleoproteins (hnRNPs) participate in diverse regulations of plant growth and environmental stress responses. In this work, an Arabidopsis hnRNP of unknown function, AtRNP1, was investigated. We found that AtRNP1 gene is highly expressed in rosette and cauline leaves, and slightly induced under drought, salt, osmotic and ABA stresses. AtRNP1 protein is localized to both the nucleus and cytoplasm. We performed homologous overexpression of AtRNP1 and found that the transgenic plants showed shortened root length and plant height, and accelerated flowering. In addition, the transgenic plants also showed reduced tolerance to drought, salt, osmotic and ABA stresses. Further studies revealed that under both normal and stress conditions, the proline contents in the transgenic plants are markedly decreased, associated with reduced expression levels of a proline synthase gene and several stress-responsive genes. These results suggested that the overexpression of AtRNP1 negatively affects plant growth and abiotic stress tolerance. - Highlights: • AtRNP1 is a widely expressed gene and its expression is slightly induced under abiotic stresses. • AtRNP1 protein is localized to both the nucleus and cytoplasm. • Overexpression of AtRNP1 affects plant growth. • Overexpression of AtRNP1 reduces plant tolerance to drought and salt stresses. • AtRNP1 overexpression plants show decreased proline accumulation and stress-responsive gene expressions.
U3 snoRNP associates with fibrillarin a component of the scleroderma clumpy nucleolar domain
DEFF Research Database (Denmark)
Herrera-Esparza, Rafael; Kruse, Lars; von Essen, Marina
2002-01-01
Serum from patients with scleroderma recognizes the clumpy autoantigen. The present studies addressed the issue as to whether the clumpy nucleolar autoantigen recognized by scleroderma serum is fibrillarin-U3 snoRNP. Clones encoding for clumpy autoantigen were immunodetected from a lambdagt11 HeL...
Novel inhibitors of Staphylococcus aureus RnpA that synergize with mupirocin.
Lounsbury, Nicole; Eidem, Tess; Colquhoun, Jennifer; Mateo, George; Abou-Gharbia, Magid; Dunman, Paul M; Childers, Wayne E
2018-01-31
We recently discovered RnpA as a promising new drug discovery target for methicillin-resistant S. aureus (MRSA). RnpA is an essential protein that is thought to perform two required cellular processes. As part of the RNA degrasome Rnpa mediates RNA degradation. In combination with rnpB it forms RNase P haloenzymes which are required for tRNA maturation. A high throughput screen identified RNPA2000 as an inhibitor of both RnpA-associated activities that displayed antibacterial activity against clinically relevant strains of S. aureus, including MRSA. Structure-activity studies aimed at improving potency and replacing the potentially metabotoxic furan moiety led to the identification of a number of more potent analogs. Many of these new analogs possessed overt cellular toxicity that precluded their use as antibiotics but two derivatives, including compound 5o, displayed an impressive synergy with mupirocin, an antibiotic used for decolonizing MSRA whose effectiveness has recently been jeopardized by bacterial resistance. Based on our results, compounds like 5o may ultimately find use in resensitizing mupirocin-resistant bacteria to mupirocin. Copyright © 2018 Elsevier Ltd. All rights reserved.
Fritz, Melanie; Vanselow, Jens; Sauer, Nadja; Lamer, Stephanie; Goos, Carina; Siegel, T Nicolai; Subota, Ines; Schlosser, Andreas; Carrington, Mark; Kramer, Susanne
2015-09-18
RNP granules are ribonucleoprotein assemblies that regulate the post-transcriptional fate of mRNAs in all eukaryotes. Their exact function remains poorly understood, one reason for this is that RNP granule purification has not yet been achieved. We have exploited a unique feature of trypanosomes to prepare a cellular fraction highly enriched in starvation stress granules. First, granules remain trapped within the cage-like, subpellicular microtubule array of the trypanosome cytoskeleton while soluble proteins are washed away. Second, the microtubules are depolymerized and the granules are released. RNA sequencing combined with single molecule mRNA FISH identified the short and highly abundant mRNAs encoding ribosomal mRNAs as being excluded from granules. By mass spectrometry we have identified 463 stress granule candidate proteins. For 17/49 proteins tested by eYFP tagging we have confirmed the localization to granules, including one phosphatase, one methyltransferase and two proteins with a function in trypanosome life-cycle regulation. The novel method presented here enables the unbiased identification of novel RNP granule components, paving the way towards an understanding of RNP granule function. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Spinal Muscular Atrophy: From Defective Chaperoning of snRNP Assembly to Neuromuscular Dysfunction
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Maia Lanfranco
2017-06-01
Full Text Available Spinal Muscular Atrophy (SMA is a neuromuscular disorder that results from decreased levels of the survival motor neuron (SMN protein. SMN is part of a multiprotein complex that also includes Gemins 2–8 and Unrip. The SMN-Gemins complex cooperates with the protein arginine methyltransferase 5 (PRMT5 complex, whose constituents include WD45, PRMT5 and pICln. Both complexes function as molecular chaperones, interacting with and assisting in the assembly of an Sm protein core onto small nuclear RNAs (snRNAs to generate small nuclear ribonucleoproteins (snRNPs, which are the operating components of the spliceosome. Molecular and structural studies have refined our knowledge of the key events taking place within the crowded environment of cells and the numerous precautions undertaken to ensure the faithful assembly of snRNPs. Nonetheless, it remains unclear whether a loss of chaperoning in snRNP assembly, considered as a “housekeeping” activity, is responsible for the selective neuromuscular phenotype in SMA. This review thus shines light on in vivo studies that point toward disturbances in snRNP assembly and the consequential transcriptome abnormalities as the primary drivers of the progressive neuromuscular degeneration underpinning the disease. Disruption of U1 snRNP or snRNP assembly factors other than SMN induces phenotypes that mirror aspects of SMN deficiency, and splicing defects, described in numerous SMA models, can lead to a DNA damage and stress response that compromises the survival of the motor system. Restoring the correct chaperoning of snRNP assembly is therefore predicted to enhance the benefit of SMA therapeutic modalities based on augmenting SMN expression.
High Order Finite Volume Nonlinear Schemes for the Boltzmann Transport Equation
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Bihari, B L; Brown, P N
2005-03-29
The authors apply the nonlinear WENO (Weighted Essentially Nonoscillatory) scheme to the spatial discretization of the Boltzmann Transport Equation modeling linear particle transport. The method is a finite volume scheme which ensures not only conservation, but also provides for a more natural handling of boundary conditions, material properties and source terms, as well as an easier parallel implementation and post processing. It is nonlinear in the sense that the stencil depends on the solution at each time step or iteration level. By biasing the gradient calculation towards the stencil with smaller derivatives, the scheme eliminates the Gibb's phenomenon with oscillations of size O(1) and reduces them to O(h{sup r}), where h is the mesh size and r is the order of accuracy. The current implementation is three-dimensional, generalized for unequally spaced meshes, fully parallelized, and up to fifth order accurate (WENO5) in space. For unsteady problems, the resulting nonlinear spatial discretization yields a set of ODE's in time, which in turn is solved via high order implicit time-stepping with error control. For the steady-state case, they need to solve the non-linear system, typically by Newton-Krylov iterations. There are several numerical examples presented to demonstrate the accuracy, non-oscillatory nature and efficiency of these high order methods, in comparison with other fixed-stencil schemes.
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Ziaei, Samira, E-mail: ziaeisamira@gmail.com [City College of New York, City University of New York, New York, NY (United States); The Graduate School and University Center of CUNY, New York, NY (United States); Shimada, Naoko, E-mail: lensdev@yahoo.co.jp [City College of New York, City University of New York, New York, NY (United States); Kucharavy, Herman, E-mail: veterduy@yahoo.com [City College of New York, City University of New York, New York, NY (United States); Hubbard, Karen, E-mail: khubbard@sci.ccny.cuny.edu [City College of New York, City University of New York, New York, NY (United States); The Graduate School and University Center of CUNY, New York, NY (United States)
2012-03-10
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is an RNA-binding protein that modulates splice site usage, polyadenylation, and cleavage efficiency. This protein has also been implicated in mRNA stability and transport from the nucleus. We have previously demonstrated that hnRNP A1 had diminished protein levels and showed cytoplasmic accumulation in senescent human diploid fibroblasts. Furthermore, we have shown that inhibition of p38 MAPK, a key regulator of cellular senescence, elevated hnRNP A1 protein levels and inhibited hnRNP A1 cytoplasmic localization. In this study, we have explored the possible involvement of MNK1, one of the downstream effector of p38 MAPK, in the regulation of hnRNP A1. We have demonstrated that pharmacological inhibition of MNK1 by CGP 57380 decreased the phosphorylation levels of hnRNP A1 in young and senescent fibroblast cells and blocked the cytoplasmic accumulation of hnRNP A1 in senescent cells. In addition, MNK1 formed a complex with hnRNP A1 in vivo. The expression levels of MNK1, phospho-MNK1, and phospho-eIF4E proteins were found to be elevated in senescent cells. These data suggest that MNK1 regulates the phosphorylation and the subcellular distribution of hnRNP A1 and that MNK1 may play a role in the induction of senescence. -- Highlights: Black-Right-Pointing-Pointer MNK1 and not MAPKAPK2 phosphorylates hnRNP A1. Black-Right-Pointing-Pointer MNK1 has elevated levels in senescent cells, this has not been reported previously. Black-Right-Pointing-Pointer MNK1 activity induces cytoplasmic accumulation of hnRNP A1 in senescent cells. Black-Right-Pointing-Pointer Altered cytoplasmic localization of hnRNP A1 may alter gene expression patterns. Black-Right-Pointing-Pointer Our studies may increase our understanding of RNA metabolism during cellular aging.
Inclusion of poorly soluble drugs in highly ordered mesoporous silica nanoparticles.
Thomas, M J K; Slipper, I; Walunj, A; Jain, A; Favretto, M E; Kallinteri, P; Douroumis, D
2010-03-15
Silica nanoparticles (MSNs) with a highly ordered mesoporous structures (103A) with cubic Im3 m have been synthesized using triblock copolymers with high poly(alkylene oxide) (EO) segments in acid media. The produced nanoparticles displayed large specific surface area (approximately 765 cm(2)/g) with an average particles size of 120 nm. The loading efficiency was assessed by incorporating three major antiepileptic active substances via passive loading and it was found to varying from 17 to 25%. The state of the adsorbed active agents was further analyzed using differential scanning calorimetry (DSC) and X-ray powder diffraction (XRPD). Dissolution studies revealed rapid release profiles within the first 3 h. The viability of 3T3 endothelial cells was not affected in the presence of MSNs indicating negligible cytotoxicity. 2009 Elsevier B.V. All rights reserved.
Decrease in hnRNP A/B expression during erythropoiesis mediates a pre-mRNA splicing switch
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Hou, Victor C.; Lersch, Robert; Gee, Sherry L.; Ponthier, Julie L.; Lo, Annie J.; Wu, Michael; Turck, Chris W.; Koury, Mark; Krainer, Adrian R.; Mayeda, Akila; Conboy, John G.
2002-10-17
A physiologically important alternative pre-mRNA splicing switch, involving activation of protein 4.1R exon 16 (E16) splicing, is required for establishing proper mechanical integrity of the erythrocyte membrane during erythropoiesis. Here we identify a conserved exonic splicing silencer element (CE16) in E16 that interacts with hnRNP A/B proteins and plays a role in repression of E16 splicing during early erythropoiesis. Experiments with model pre-mRNAs showed that CE16 can repress splicing of upstream introns, and that mutagenesis or replacement of CE16 can relieve this inhibition. An affinity selection assay with biotinylated CE16 RNA demonstrated specific binding of hnRNP A/B proteins. Depletion of hnRNP A/B proteins from nuclear extract significantly increased E16 inclusion, while repletion with recombinant hnRNP A/B restored E16 silencing. Most importantly, differentiating mouse erythroblasts exhibited a stage-specific activation of the E16 splicing switch in concert with a drama tic and specific down-regulation of hnRNP A/B protein expression. These findings demonstrate that natural developmental changes in hnRNP A/B proteins can effect physiologically important switches in pre-mRNA splicing.
HnRNP Q Has a Suppressive Role in the Translation of Mouse Cryptochrome1.
Directory of Open Access Journals (Sweden)
Ilgye Lim
Full Text Available Precise regulation of gene expression is especially important for circadian timekeeping which is maintained by the proper oscillation of the mRNA and protein of clock genes and clock-controlled genes. As a main component of the core negative arm feedback loops in the circadian clock, the Cry1 gene contributes to the maintenance of behavioral and molecular rhythmicity. Despite the central role of Cry1, the molecular mechanisms regulating expression levels of Cry1 mRNA and protein are not well defined. In particular, the post-transcriptional regulation of Cry1 mRNA fate decisions is unclear. Here, we demonstrate that hnRNP Q binds to mCry1 mRNA via the 5'UTR. Furthermore, hnRNP Q inhibits the translation of mCry1 mRNA, leading to altered rhythmicity in the mCRY1 protein profile.
TERRA, hnRNP A1, and DNA-PKcs Interactions at Human Telomeres.
Le, Phuong N; Maranon, David G; Altina, Noelia H; Battaglia, Christine L R; Bailey, Susan M
2013-01-01
Maintenance of telomeres, repetitive elements at eukaryotic chromosomal termini, and the end-capping structure and function they provide, are imperative for preserving genome integrity and stability. The discovery that telomeres are transcribed into telomere repeat containing RNA (TERRA) has revolutionized our view of this repetitive, rather unappreciated region of the genome. We have previously shown that the non-homologous end-joining, shelterin associated DNA dependent protein kinase catalytic subunit (DNA-PKcs) participates in mammalian telomeric end-capping, exclusively at telomeres created by leading-strand synthesis. Here, we explore potential roles of DNA-PKcs and its phosphorylation target heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) in the localization of TERRA at human telomeres. Evaluation of co-localized foci utilizing RNA-FISH and three-dimensional (3D) reconstruction strategies provided evidence that both inhibition of DNA-PKcs kinase activity and siRNA depletion of hnRNP A1 result in accumulation of TERRA at individual telomeres; depletion of hnRNP A1 also resulted in increased frequencies of fragile telomeres. These observations are consistent with previous demonstrations that decreased levels of the nonsense RNA-mediated decay factors SMG1 and UPF1 increase TERRA at telomeres and interfere with replication of leading-strand telomeres. We propose that hTR mediated stimulation of DNA-PKcs and subsequent phosphorylation of hnRNP A1 influences the cell cycle dependent distribution of TERRA at telomeres by contributing to the removal of TERRA from telomeres, an action important for progression of S-phase, and thereby facilitating efficient telomere replication and end-capping.
Stiffened yeast telomerase RNA supports RNP function in vitro and in vivo
Lebo, Kevin J.; Zappulla, David C.
2012-01-01
The 1157-nt Saccharomyces cerevisiae telomerase RNA, TLC1, in addition to providing a 16-nt template region for reverse transcription, has been proposed to act as a scaffold for protein subunits. Although accessory subunits of the telomerase ribonucleoprotein (RNP) complex function even when their binding sites are relocated on the yeast telomerase RNA, the physical nature of the RNA scaffold has not been directly analyzed. Here we explore the structure–function organization of the yeast telomerase RNP by extensively stiffening the three long arms of TLC1, which connect essential and important accessory protein subunits Ku, Est1, and Sm7, to its central catalytic hub. This 956-nt triple-stiff-arm TLC1 (TSA-T) reconstitutes active telomerase with TERT (Est2) in vitro. Furthermore, TSA-T functions in vivo, even maintaining longer telomeres than TLC1 on a per RNA basis. We also tested functional contributions of each stiffened arm within TSA-T and found that the stiffened Est1 and Ku arms contribute to telomere lengthening, while stiffening the terminal arm reduces telomere length and telomerase RNA abundance. The fact that yeast telomerase tolerates significant stiffening of its RNA subunit in vivo advances our understanding of the architectural and functional organization of this RNP and, more broadly, our conception of the world of lncRNPs. PMID:22850424
The relationship between dendritic branch dynamics and CPEB-labeled RNP granules captured in vivo
Directory of Open Access Journals (Sweden)
Jennifer E Bestman
2009-01-01
Full Text Available Cytoplasmic Polyadenylation Element Binding protein (CPEB is an RNA binding protein involved in dendritic delivery of mRNA and activity-dependent, polyadenylation-induced translation of mRNAs in the dendritic arbor. CPEB affects learning and memory and impacts neuronal morphological and synaptic plasticity. In neurons, CPEB is concentrated in ribonucleoprotein (RNP granules that distribute throughout the dendritic arbor and localize near synapses. We tagged full-length CPEB and an inactive mutant CPEB, that is incapable of triggering activity-induced mRNA translation, with fluorescent protein, then imaged rapid dendritic branch dynamics and RNP distribution using 2-photon time-lapse microscopy of neurons in the optic tectum of living Xenopus laevis tadpoles. The density of CPEB-containing RNP granules in dendrites is high and the distribution of granules does not correlate with sites of rapid dendritic branch dynamics. Nevertheless, inactive CPEB accumulates in granules in terminal dendritic branches, supporting the hypothesis that upon activation CPEB and its mRNA cargo are released from granules and are then available for dendritic translation.
Haploinsufficiency of hnRNP U Changes Activity Pattern and Metabolic Rhythms.
Lai, Beibei; Zou, Jianghuan; Lin, Zhaoyu; Qu, Zhipeng; Song, Anying; Xu, Ying; Gao, Xiang
2018-01-01
The neuropeptides arginine vasopressin (Avp) and vasoactive intestinal polypeptide (Vip) are critical for the communication and coupling of suprachiasmatic nucleus neurons, which organize daily rhythms of physiology and behavior in mammals. However, how these peptides are regulated remains uncharacterized. We found that heterogeneous nuclear ribonucleoprotein U (hnRNP U) is essential for the expression of Avp and Vip. Loss of one copy of the Hnrnpu gene resulted in fragmented locomotor activities and disrupted metabolic rhythms. Hnrnpu +/- mice were more active than wild-type mice in the daytime but more inactive at night. These phenotypes were partially rescued by microinfusion of Avp and Vip into free-moving animals. In addition, hnRNP U modulated Avp and Vip via directly binding to their promoters together with brain and muscle Arnt-like protein-1/circadian locomotor output cycles kaput heterodimers. Our work identifies hnRNP U as a novel regulator of the circadian pacemaker and provides new insights into the mechanism of rhythm output. Copyright © 2018 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.
Characterization of transcription site-associated mRNP retention in Saccharomyces cerevisiae
DEFF Research Database (Denmark)
Jensen, Torben Heick
In a variety of S. cerevisiae mutants with defective mRNP maturation and/or export, heat shock (hs) mRNPs are retained at or near their sites of transcription. For example, mutants of the THO complex display an intense hs-mRNA FISH signal, which co-localizes with the hs-gene after transcriptional...... induction. The THO complex is implicated in co-transcriptional mRNP assembly, but its precise role is still unclear. Transcriptional run-on analysis as well as genetic interaction data suggest that the function of the THO complex is linked to 3’-end processing. Chromatin immunoprecipitation (ChIP) assays...... underrepresented in recovered fractions from mutant cells. This bias is abolished when a THO mutation is combined with a second site mutation alleviating the mRNA export block. Thus, the bias parallels transcription-site retention of the mRNP and suggests the existence of a complex specifically formed at the 3...
The Survival of Motor Neuron Protein Acts as a Molecular Chaperone for mRNP Assembly
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Paul G. Donlin-Asp
2017-02-01
Full Text Available Spinal muscular atrophy (SMA is a motor neuron disease caused by reduced levels of the survival of motor neuron (SMN protein. SMN is part of a multiprotein complex that facilitates the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs. SMN has also been found to associate with mRNA-binding proteins, but the nature of this association was unknown. Here, we have employed a combination of biochemical and advanced imaging methods to demonstrate that SMN promotes the molecular interaction between IMP1 protein and the 3′ UTR zipcode region of β-actin mRNA, leading to assembly of messenger ribonucleoprotein (mRNP complexes that associate with the cytoskeleton to facilitate trafficking. We have identified defects in mRNP assembly in cells and tissues from SMA disease models and patients that depend on the SMN Tudor domain and explain the observed deficiency in mRNA localization and local translation, providing insight into SMA pathogenesis as a ribonucleoprotein (RNP-assembly disorder.
U2 snRNP is required for expression of the 3' end of genes.
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Mitsunori Koga
Full Text Available Pre-mRNA in eukaryotes is subjected to mRNA processing, which includes capping, polyadenylation, and splicing. Transcription and mRNA processing are coupled, and this coupling stimulates mRNA processing; however, the effects of mRNA processing on transcription are not fully understood. In this study, we found that inhibition of U2 snRNP by a splicing inhibitor, spliceostatin A (SSA, or by an antisense oligonucleotide to U2 snRNA, caused gene-specific 3'-end down-regulation. Removal of SSA from the culture media restored expression of the 3' ends of genes, suggesting that U2 snRNP is required for expression of the 3' end of genes. Finally, we found that SSA treatment caused accumulation of Pol II near the 5' end of 3'-end down regulated genes, such as CDK6, SMEK2 and EGFR, indicating that SSA treatment led to transcription elongation arrest on these genes. These findings suggest that U2 snRNP is important for production of full length mRNA probably through regulation of transcription elongation, and that a novel checkpoint mechanism prevents pre-mRNA from accumulating as a result of splicing deficiencies, and thereby prevents production of aberrant proteins that might be translated from pre-mRNAs through the arrest of transcription elongation.
Chen, Zhe; Gui, Bin; Zhang, Yu; Xie, Guojia; Li, Wanjin; Liu, Shumeng; Xu, Bosen; Wu, Chongyang; He, Lin; Yang, Jianguo; Yi, Xia; Yang, Xiaohan; Sun, Luyang; Liang, Jing; Shang, Yongfeng
2017-11-03
The de novo assembly and post-splicing reassembly of the U4/U6.U5 tri-snRNP remain to be investigated. We report here that ZIP, a protein containing a CCCH-type zinc finger and a G-patch domain, as characterized by us previously, regulates pre-mRNA splicing independent of RNA binding. We found that ZIP physically associates with the U4/U6.U5 tri-small nuclear ribonucleoprotein (tri-snRNP). Remarkably, the ZIP-containing tri-snRNP, which has a sedimentation coefficient of ∼35S, is a tri-snRNP that has not been described previously. We also found that the 35S tri-snRNP contains hPrp24, indicative of a state in which the U4/U6 di-snRNP is integrating with the U5 snRNP. We found that the 35S tri-snRNP is enriched in the Cajal body, indicating that it is an assembly intermediate during 25S tri-snRNP maturation. We showed that the 35S tri-snRNP also contains hPrp43, in which ATPase/RNA helicase activities are stimulated by ZIP. Our study identified, for the first time, a tri-snRNP intermediate, shedding new light on the de novo assembly and recycling of the U4/U6.U5 tri-snRNP. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
hnRNP-Q1 represses nascent axon growth in cortical neurons by inhibiting Gap-43 mRNA translation.
Williams, Kathryn R; McAninch, Damian S; Stefanovic, Snezana; Xing, Lei; Allen, Megan; Li, Wenqi; Feng, Yue; Mihailescu, Mihaela Rita; Bassell, Gary J
2016-02-01
Posttranscriptional regulation of gene expression by mRNA-binding proteins is critical for neuronal development and function. hnRNP-Q1 is an mRNA-binding protein that regulates mRNA processing events, including translational repression. hnRNP-Q1 is highly expressed in brain tissue, suggesting a function in regulating genes critical for neuronal development. In this study, we have identified Growth-associated protein 43 (Gap-43) mRNA as a novel target of hnRNP-Q1 and have demonstrated that hnRNP-Q1 represses Gap-43 mRNA translation and consequently GAP-43 function. GAP-43 is a neuronal protein that regulates actin dynamics in growth cones and facilitates axonal growth. Previous studies have identified factors that regulate Gap-43 mRNA stability and localization, but it remains unclear whether Gap-43 mRNA translation is also regulated. Our results reveal that hnRNP-Q1 knockdown increased nascent axon length, total neurite length, and neurite number in mouse embryonic cortical neurons and enhanced Neuro2a cell process extension; these phenotypes were rescued by GAP-43 knockdown. Additionally, we have identified a G-quadruplex structure in the 5' untranslated region of Gap-43 mRNA that directly interacts with hnRNP-Q1 as a means to inhibit Gap-43 mRNA translation. Therefore hnRNP-Q1-mediated repression of Gap-43 mRNA translation provides an additional mechanism for regulating GAP-43 expression and function and may be critical for neuronal development. © 2016 Williams et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
Sander, Bjoern; Golas, Monika M; Makarov, Evgeny M; Brahms, Hero; Kastner, Berthold; Lührmann, Reinhard; Stark, Holger
2006-10-20
In eukaryotes, pre-mRNA exons are interrupted by large noncoding introns. Alternative selection of exons and nucleotide-exact removal of introns are performed by the spliceosome, a highly dynamic macromolecular machine. U4/U6.U5 tri-snRNP is the largest and most conserved building block of the spliceosome. By 3D electron cryomicroscopy and labeling, the exon-aligning U5 snRNA loop I is localized at the center of the tetrahedrally shaped tri-snRNP reconstructed to approximately 2.1 nm resolution in vitrified ice. Independent 3D reconstructions of its subunits, U4/U6 and U5 snRNPs, show how U4/U6 and U5 combine to form tri-snRNP and, together with labeling experiments, indicate a close proximity of the spliceosomal core components U5 snRNA loop I and U4/U6 at the center of tri-snRNP. We suggest that this central tri-snRNP region may be the site to which the prespliceosomal U2 snRNA has to approach closely during formation of the catalytic core of the spliceosome.
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Arroyo Gómez, José J. [Instituto de Ingeniería Electroquímica y Corrosión (INIEC ), Departamento de Ingeniería Química, Universidad Nacional del Sur, Avda. Alem 1253, 8000 Bahía Blanca (Argentina); Zubieta, Carolina; Ferullo, Ricardo M. [INQUISUR , Departamento de Química, Universidad Nacional del Sur, Avda. Alem 1253, 8000 Bahía Blanca (Argentina); García, Silvana G., E-mail: sgarcia@criba.edu.ar [Instituto de Ingeniería Electroquímica y Corrosión (INIEC ), Departamento de Ingeniería Química, Universidad Nacional del Sur, Avda. Alem 1253, 8000 Bahía Blanca (Argentina)
2016-02-15
Graphical abstract: - Highlights: • The electrodeposition of Au on HOPG tends to follow the response predicted for a 3D instantaneous nucleation mechanism in the potential range considered. • By choosing suitable nucleation and growth pulses, one-dimensional deposits were possible, preferentially located on step edges of the HOPG substrate. • Quantum-mechanical calculations confirmed the tendency of Au atoms to join selectively on the HOPG step edges, at the early stages of Au electrodeposition. - Abstract: The electrochemical formation of Au nanoparticles on a highly ordered pyrolytic graphite (HOPG) substrate using conventional electrochemical techniques and ex-situ AFM is reported. From the potentiostatic current transients studies, the Au electrodeposition process on HOPG surfaces was described, within the potential range considered, by a model involving instantaneous nucleation and diffusion controlled 3D growth, which was corroborated by the microscopic analysis. Initially, three-dimensional (3D) hemispherical nanoparticles distributed on surface defects (step edges) of the substrate were observed, with increasing particle size at more negative potentials. The double potential pulse technique allowed the formation of rounded deposits at low deposition potentials, which tend to form lines of nuclei aligned in defined directions leading to 3D ordered structures. By choosing suitable nucleation and growth pulses, one-dimensional (1D) deposits were possible, preferentially located on step edges of the HOPG substrate. Quantum-mechanical calculations confirmed the tendency of Au atoms to join selectively on surface defects, such as the HOPG step edges, at the early stages of Au electrodeposition.
High order Fuchsian equations for the square lattice Ising model: {chi}-tilde{sup (5)}
Energy Technology Data Exchange (ETDEWEB)
Bostan, A [INRIA Paris-Rocquencourt, Domaine de Voluceau, B.P. 105 78153 Le Chesnay, Cedex (France); Boukraa, S [LPTHIRM and Departement d' Aeronautique, Universite de Blida (Algeria); Guttmann, A J; Jensen, I [ARC Centre of Excellence for Mathematics and Statistics of Complex Systems, Department of Mathematics and Statistics, University of Melbourne, Victoria 3010 (Australia); Hassani, S; Zenine, N [Centre de Recherche Nucleaire d' Alger, 2 Bd. Frantz Fanon, BP 399, 16000 Alger (Algeria); Maillard, J-M [LPTMC, UMR 7600 CNRS, Universite de Paris, Tour 24, 4eme etage, case 121, 4 Place Jussieu, 75252 Paris Cedex 05 (France)], E-mail: alin.bostan@inria.fr, E-mail: boukraa@mail.univ-blida.dz, E-mail: tonyg@ms.unimelb.edu.au, E-mail: I.Jensen@ms.unimelb.edu.au, E-mail: maillard@lptmc.jussieu.fr, E-mail: maillard@lptl.jussieu.fr, E-mail: njzenine@yahoo.com
2009-07-10
We consider the Fuchsian linear differential equation obtained (modulo a prime) for {chi}-tilde{sup (5)}, the five-particle contribution to the susceptibility of the square lattice Ising model. We show that one can understand the factorization of the corresponding linear differential operator from calculations using just a single prime. A particular linear combination of {chi}-tilde{sup (1)} and {chi}-tilde{sup (3)} can be removed from {chi}-tilde{sup (5)} and the resulting series is annihilated by a high order globally nilpotent linear ODE. The corresponding (minimal order) linear differential operator, of order 29, splits into factors of small orders. A fifth-order linear differential operator occurs as the left-most factor of the 'depleted' differential operator and it is shown to be equivalent to the symmetric fourth power of L{sub E}, the linear differential operator corresponding to the elliptic integral E. This result generalizes what we have found for the lower order terms {chi}-tilde{sup (3)} and {chi}-tilde{sup (4)}. We conjecture that a linear differential operator equivalent to a symmetric (n - 1) th power of L{sub E} occurs as a left-most factor in the minimal order linear differential operators for all {chi}-tilde{sup (n)}'s.
Energy Technology Data Exchange (ETDEWEB)
Zheng, Zi-Zheng; Sun, Yuan-Yuan; Zhao, Min; Huang, Hui [National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian 361005 (China); School of Life Sciences, Xiamen University, Xiamen, Fujian 361005 (China); Zhang, Jun; Xia, Ning-Shao [National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian 361005 (China); School of Life Sciences, Xiamen University, Xiamen, Fujian 361005 (China); School of Public Health, Xiamen University, Xiamen, Fujian 361005 (China); Miao, Ji, E-mail: jmiao@xmu.edu.cn [National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian 361005 (China); School of Life Sciences, Xiamen University, Xiamen, Fujian 361005 (China); Zhao, Qinjian, E-mail: qinjian_zhao@xmu.edu.cn [National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian 361005 (China); School of Public Health, Xiamen University, Xiamen, Fujian 361005 (China)
2013-01-18
Highlights: ► The RNA-binding hnRNP H regulates late viral gene expression. ► hnRNP H activity was inhibited by a late viral protein. ► Specific interaction between HPV L1 and hnRNP H was demonstrated. ► Co-localization of HPV L1 and hnRNP H inside cells was observed. ► Viral capsid protein production, enabling rapid capsid assembly, was implicated. -- Abstract: Heterogeneous nuclear ribonucleoproteins (hnRNPs), including hnRNP H, are RNA-binding proteins that function as splicing factors and are involved in downstream gene regulation. hnRNP H, which binds to G triplet regions in RNA, has been shown to play an important role in regulating the staged expression of late proteins in viral systems. Here, we report that the specific association between hnRNP H and a late viral capsid protein, human papillomavirus (HPV) L1 protein, leads to the suppressed function of hnRNP H in the presence of the L1 protein. The direct interaction between the L1 protein and hnRNP H was demonstrated by complex formation in solution and intracellularly using a variety of biochemical and immunochemical methods, including peptide mapping, specific co-immunoprecipitation and confocal fluorescence microscopy. These results support a working hypothesis that a late viral protein HPV16 L1, which is down regulated by hnRNP H early in the viral life cycle may provide an auto-regulatory positive feedback loop that allows the rapid production of HPV capsid proteins through suppression of the function of hnRNP H at the late stage of the viral life cycle. In this positive feedback loop, the late viral gene products that were down regulated earlier themselves disable their suppressors, and this feedback mechanism could facilitate the rapid production of capsid proteins, allowing staged and efficient viral capsid assembly.
Practical aspects of spherical near-field antenna measurements using a high-order probe
DEFF Research Database (Denmark)
Laitinen, Tommi; Pivnenko, Sergey; Nielsen, Jeppe Majlund
2006-01-01
Two practical aspects related to accurate antenna pattern characterization by probe-corrected spherical near-field antenna measurements with a high-order probe are examined. First, the requirements set by an arbitrary high-order probe on the scanning technique are pointed out. Secondly, a channel...... balance calibration procedure for a high-order dual-port probe with non-identical ports is presented, and the requirements set by this procedure for the probe are discussed....
High-order evolving surface finite element method for parabolic problems on evolving surfaces
Kovács, Balázs
2016-01-01
High-order spatial discretisations and full discretisations of parabolic partial differential equations on evolving surfaces are studied. We prove convergence of the high-order evolving surface finite element method, by showing high-order versions of geometric approximation errors and perturbation error estimates and by the careful error analysis of a modified Ritz map. Furthermore, convergence of full discretisations using backward difference formulae and implicit Runge-Kutta methods are als...
A high order multi-resolution solver for the Poisson equation with application to vortex methods
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Spietz, Henrik Juul; Walther, Jens Honore
A high order method is presented for solving the Poisson equation subject to mixed free-space and periodic boundary conditions by using fast Fourier transforms (FFT). The high order convergence is achieved by deriving mollified Green’s functions from a high order regularization function which...... provides a correspondingly smooth solution to the Poisson equation.The high order regularization function may be obtained analogous to the approximate deconvolution method used in turbulence models and strongly relates to deblurring algorithms used in image processing. At first we show that the regularized...
DEFF Research Database (Denmark)
Nielsen, Klaus H; Valásek, Leos; Sykes, Caroah
2006-01-01
We found that mutating the RNP1 motif in the predicted RRM domain in yeast eukaryotic initiation factor 3 (eIF3) subunit b/PRT1 (prt1-rnp1) impairs its direct interactions in vitro with both eIF3a/TIF32 and eIF3j/HCR1. The rnp1 mutation in PRT1 confers temperature-sensitive translation initiation...... in vivo and reduces 40S-binding of eIF3 to native preinitiation complexes. Several findings indicate that the rnp1 lesion decreases recruitment of eIF3 to the 40S subunit by HCR1: (i) rnp1 strongly impairs the association of HCR1 with PRT1 without substantially disrupting the eIF3 complex; (ii) rnp1......) hcr1Delta impairs 40S binding of eIF3 in otherwise wild-type cells. Interestingly, rnp1 also reduces the levels of 40S-bound eIF5 and eIF1 and increases leaky scanning at the GCN4 uORF1. Thus, the PRT1 RNP1 motif coordinates the functions of HCR1 and TIF32 in 40S binding of eIF3 and is needed...
A Function for the hnRNP A1/A2 Proteins in Transcription Elongation.
Directory of Open Access Journals (Sweden)
Bruno Lemieux
Full Text Available The hnRNP A1 and A2 proteins regulate processes such as alternative pre-mRNA splicing and mRNA stability. Here, we report that a reduction in the levels of hnRNP A1 and A2 by RNA interference or their cytoplasmic retention by osmotic stress drastically increases the transcription of a reporter gene. Based on previous work, we propose that this effect may be linked to a decrease in the activity of the transcription elongation factor P-TEFb. Consistent with this hypothesis, the transcription of the reporter gene was stimulated when the catalytic component of P-TEFb, CDK9, was inhibited with DRB. While low levels of A1/A2 stimulated the association of RNA polymerase II with the reporter gene, they also increased the association of CDK9 with the repressor 7SK RNA, and compromised the recovery of promoter-distal transcription on the Kitlg gene after the release of pausing. Transcriptome analysis revealed that more than 50% of the genes whose expression was affected by the siRNA-mediated depletion of A1/A2 were also affected by DRB. RNA polymerase II-chromatin immunoprecipitation assays on DRB-treated and A1/A2-depleted cells identified a common set of repressed genes displaying increased occupancy of polymerases at promoter-proximal locations, consistent with pausing. Overall, our results suggest that lowering the levels of hnRNP A1/A2 elicits defective transcription elongation on a fraction of P-TEFb-dependent genes, hence favoring the transcription of P-TEFb-independent genes.
Efficiency Benchmarking of an Energy Stable High-Order Finite Difference Discretization
van der Weide, Edwin Theodorus Antonius; Giangaspero, G.; Svärd, M
2015-01-01
In this paper, results are presented for a number of benchmark cases, proposed at the 2nd International Workshop on High-Order CFD Methods in Cologne, Germany, in 2013. A robust high-order-accurate finite difference method was used that was developed during the last 10–15 years. The robustness stems
Derivation and test of high order fluid model for streamer discharges
A. Markosyan (Aram); S. Dujko (Sasa); U. Ebert (Ute); A. Blaszczyk; R. Hiptmair; P. Leuchtmann; J. Ostrowski
2012-01-01
textabstractA high order fluid model for streamer dynamics is developed by closing the system after the 4th moment of the Boltzmann equation in local mean energy approximation. This is done by approximating the high order pressure tensor in the heat flux equation through the previous moments.
Energy Technology Data Exchange (ETDEWEB)
Choi, I. W.; Kim, I J.; Pae, K. H.; Nam, K. H.; Lee, C.-L.; Yun, H.; Kim, H. T.; Lee, S. K.; Yu, T. J.; Sung, J. H.; Lee, J. [Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of); Pirozhkov, A. S.; Ogura, K.; Orimo, S.; Daido, H. [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kizugawa, Kyoto 619-0215 (Japan)
2011-10-31
We report the manufacturing of an (ultra-)thin foil target made of conjugated polymer, poly(9,9'-dioctylfluorene-co-benzothiadiazole) (F8BT), and the simultaneous observation of laser-accelerated ions and second harmonic radiation, when irradiated with ultrahigh-contrast laser pulse at a maximum intensity of 4 x 10{sup 19 }W/cm{sup 2}. Maximum proton energy of 8 MeV is achieved along the target normal direction. Strong second harmonic with over 6% energy ratio compared to fundamental is emitted along the specular direction. Two-dimensional particle-in-cell simulations confirm the simultaneous generation of protons and high-order harmonics, which demonstrates the feasibility of applications requiring particle and radiation sources at once, effectively using the same laser and target.
Extended Galilean transformations for high-order systems in two integrable hierarchies
Energy Technology Data Exchange (ETDEWEB)
Zhang Dajun; Chen Dengyuan; Hu Liufeng, E-mail: djzhang@staff.shu.edu.cn [Department of Mathematics, Shanghai University, Shanghai 200444 (China)
2011-04-15
For some integrable hierarchies, there is no Galilean transformation that keeps a high-order equation in these hierarchies invariant, although the first one or two lower-order members admit Galilean invariance. However, the case might be changed if we redefine a high-order system. The redefined system consists of the considered high-order equation itself and all the lower-order members in their hierarchy, and each member of the hierarchy is numbered by introducing temporal coordinates (t{sub 0}, t{sub 1}, t{sub 2}, ...) to replace the uniform t. For such a redefined high-order system, one may construct an extended Galilean transformation that keeps the system invariant. Two examples, the high-order Burgers system and the Korteweg-de Vries system, are employed for demonstrating our point.
A Systematic Approach to Design High-Order Phase-Locked Loops
DEFF Research Database (Denmark)
Golestan, Saeed; Fernandez, Francisco Daniel Freijedo; Guerrero, Josep M.
2015-01-01
A basic approach to improve the performance of phase-locked loop (PLL) under adverse grid condition is to incorporate a first-order low-pass filter (LPF) into its control loop. The first-order LPF, however, has a limited ability to suppress grid disturbances. A natural thought to further improve...... the disturbance rejection capability of PLL is to use high order LPFs, resulting in high order PLLs. Application of high order LPFs, however, results in high order PLLs, which rather complicates the PLL analysis and design procedure. To overcome this challenge, a systematic method to design high order PLLs...... is presented in this letter. The suggested approach has a general theme, which means it can be applied to design the PLL control parameters regardless of the order of in-loop LPF. The effectiveness of suggested design method is confirmed through different design cases....
Pang, Jinli; Zhou, Guowei; Liu, Ruirui; Li, Tianduo
2016-02-01
Mesoporous silica nanoparticles with a wrinkled structure (wrinkled silica nanoparticles, WSNs) having highly ordered, radially oriented mesochannels were synthesized by a solvothermal method. The method used a mixture of cyclohexane, ethanol, and water as solvent, tetraethoxysilane (TEOS) as source of inorganic silica, ammonium hydroxide as hydrolysis additive, cetyltrimethylammonium bromide (CTAB) as surfactant, and polyvinylpyrrolidone (PVP) as stabilizing agent of particle growth. Particle size (240nm to 540nm), specific surface areas (490m(2)g(-1) to 634m(2)g(-1)), surface morphology (radial wrinkled structures), and pore structure (radially oriented mesochannels) of WSN samples were varied using different molar ratios of CTAB to PVP. Using synthesized WSN samples with radially oriented mesochannels as support, we prepared immobilized Candida rugosa lipase (CRL) as a new biocatalyst for biodiesel production through the esterification of oleic acid with methanol. These results suggest that WSNs with highly ordered, radially oriented mesochannels have promising applications in biocatalysis, with the highest oleic acid conversion rate of about 86.4% under the optimum conditions. Copyright © 2015 Elsevier B.V. All rights reserved.
Connections between transcription, mRNP assembly and quality control in S. cerevisiae
DEFF Research Database (Denmark)
Jensen, Torben Heick
-competent mRNP. We show that a transcription-defective allele of the Rad3p helicase, a component of the TFIIH transcription initiation factor, suppress several export-related phenotypes linked to mutation of Rna14p and members of the THO complex. Biochemical and genetic data indicate that mutation of Rad3p...... in the context of THO and rna14-3 mutants improves mRNP quality by acting upstream of transcription-site retention and nuclear degradation of the transcripts. As Rad3p mutant effects can be phenocopied by other mutations known to affect transcription and by the addition of transcription elongation drugs, our...... the role(s) of the THO complex, we have searched for mutant alleles that exhibit a genetic interaction with a strain carrying a deletion of the THO complex component MFT1. Our results suggest that the THO complex is functionally connected to the 3’end formation/mRNA export step. High...
Pseudosubstrate regulation of the SCF(beta-TrCP) ubiquitin ligase by hnRNP-U
DEFF Research Database (Denmark)
Davis, Matti; Hatzubai, Ada; Andersen, Jens S
2002-01-01
beta-TrCP/E3RS (E3RS) is the F-box protein that functions as the receptor subunit of the SCF(beta-TrCP) ubiquitin ligase (E3). Surprisingly, although its two recognized substrates, IkappaB(alpha) and beta-catenin, are present in the cytoplasm, we have found that E3RS is located predominantly...... by competition with a pIkappaB(alpha) peptide, or by a specific point mutation in the E3RS WD region, indicating an E3-substrate-type interaction. However, unlike pI(kappa)Balpha, which is targeted by SCF(beta-TrCP) for degradation, the E3-bound hnRNP-U is stable and is, therefore, a pseudosubstrate....... Consequently, hnRNP-U engages a highly neddylated active SCF(beta-TrCP), which dissociates in the presence of a high-affinity substrate, resulting in ubiquitination of the latter. Our study points to a novel regulatory mechanism, which secures the localization, stability, substrate binding threshold...
HiSeeker: Detecting High-Order SNP Interactions Based on Pairwise SNP Combinations
Directory of Open Access Journals (Sweden)
Jie Liu
2017-05-01
Full Text Available Detecting single nucleotide polymorphisms’ (SNPs interaction is one of the most popular approaches for explaining the missing heritability of common complex diseases in genome-wide association studies. Many methods have been proposed for SNP interaction detection, but most of them only focus on pairwise interactions and ignore high-order ones, which may also contribute to complex traits. Existing methods for high-order interaction detection can hardly handle genome-wide data and suffer from low detection power, due to the exponential growth of search space. In this paper, we proposed a flexible two-stage approach (called HiSeeker to detect high-order interactions. In the screening stage, HiSeeker employs the chi-squared test and logistic regression model to efficiently obtain candidate pairwise combinations, which have intermediate or significant associations with the phenotype for interaction detection. In the search stage, two different strategies (exhaustive search and ant colony optimization-based search are utilized to detect high-order interactions from candidate combinations. The experimental results on simulated datasets demonstrate that HiSeeker can more efficiently and effectively detect high-order interactions than related representative algorithms. On two real case-control datasets, HiSeeker also detects several significant high-order interactions, whose individual SNPs and pairwise interactions have no strong main effects or pairwise interaction effects, and these high-order interactions can hardly be identified by related algorithms.
Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps.
Sailer, Zachary R; Harms, Michael J
2017-03-01
High-order epistasis has been observed in many genotype-phenotype maps. These multi-way interactions between mutations may be useful for dissecting complex traits and could have profound implications for evolution. Alternatively, they could be a statistical artifact. High-order epistasis models assume the effects of mutations should add, when they could in fact multiply or combine in some other nonlinear way. A mismatch in the "scale" of the epistasis model and the scale of the underlying map would lead to spurious epistasis. In this article, we develop an approach to estimate the nonlinear scales of arbitrary genotype-phenotype maps. We can then linearize these maps and extract high-order epistasis. We investigated seven experimental genotype-phenotype maps for which high-order epistasis had been reported previously. We find that five of the seven maps exhibited nonlinear scales. Interestingly, even after accounting for nonlinearity, we found statistically significant high-order epistasis in all seven maps. The contributions of high-order epistasis to the total variation ranged from 2.2 to 31.0%, with an average across maps of 12.7%. Our results provide strong evidence for extensive high-order epistasis, even after nonlinear scale is taken into account. Further, we describe a simple method to estimate and account for nonlinearity in genotype-phenotype maps. Copyright © 2017 Sailer and Harms.
High-order fractional partial differential equation transform for molecular surface construction.
Hu, Langhua; Chen, Duan; Wei, Guo-Wei
2013-01-01
Fractional derivative or fractional calculus plays a significant role in theoretical modeling of scientific and engineering problems. However, only relatively low order fractional derivatives are used at present. In general, it is not obvious what role a high fractional derivative can play and how to make use of arbitrarily high-order fractional derivatives. This work introduces arbitrarily high-order fractional partial differential equations (PDEs) to describe fractional hyperdiffusions. The fractional PDEs are constructed via fractional variational principle. A fast fractional Fourier transform (FFFT) is proposed to numerically integrate the high-order fractional PDEs so as to avoid stringent stability constraints in solving high-order evolution PDEs. The proposed high-order fractional PDEs are applied to the surface generation of proteins. We first validate the proposed method with a variety of test examples in two and three-dimensional settings. The impact of high-order fractional derivatives to surface analysis is examined. We also construct fractional PDE transform based on arbitrarily high-order fractional PDEs. We demonstrate that the use of arbitrarily high-order derivatives gives rise to time-frequency localization, the control of the spectral distribution, and the regulation of the spatial resolution in the fractional PDE transform. Consequently, the fractional PDE transform enables the mode decomposition of images, signals, and surfaces. The effect of the propagation time on the quality of resulting molecular surfaces is also studied. Computational efficiency of the present surface generation method is compared with the MSMS approach in Cartesian representation. We further validate the present method by examining some benchmark indicators of macromolecular surfaces, i.e., surface area, surface enclosed volume, surface electrostatic potential and solvation free energy. Extensive numerical experiments and comparison with an established surface model
Directory of Open Access Journals (Sweden)
Siswoyo Siswoyo
2017-06-01
Full Text Available Abstract This study investigated the implementation of High Order Thinking Skills in high school physics teaching focused on the analysis of the questions that were developed by teachers in Jakarta. Data obtained in training physics teachers in Jakarta. Teachers followed training on how to develop the learning of physics to develop higher order thinking skills. Then the teachers were asked to develop physics problems test as an instrument measuring tool of learning physics at school. Problems that have been made and then analyzed based on the general criteria and the criteria of making about a matter that meets the requirements of high-order thinking skills. Based on the analysis it can be concluded that to devise a matter of meeting the requirements of high order thinking skills required considerable time and good skills especially can apply Bloom's taxonomy in merumsukan indicators of competence to be measured. Keywords: High order thingking skills, physics, Bloom Taxonomy. Abstrak Penelitian ini mengkaji penerapan High Order Thinking Skills dalam pembelajaran fisika di SMA yang difokuskan pada analisis soal-soal yang dikembangkan oleh guru-guru DKI Jakarta. Data diperoleh dalam pelatihan guru fisika di DKI Jakarta. Sebelum membuat soal guru-guru mendapatkan pelatihan bagaimana mengembangkan pembelajaran fisika yang dapat mengembangkan keterampilan berpikir tingkat tinggi (high order thinking skills. Kemudian guru-guru diminta untuk mengembangkan soal-soal fisika sebagai instrumen alat ukur pembelajaran fisika di sekolahnya. Soal-soal yang telah dibuat kemudian dianalisis berdasarkan kriteria umum pembuatan soal dan kriteria soal yang memenuhi persyaratan high order thinking skills. Berdasarkan hasil analisis dapat disimpulkan bahwa untuk dapat menyusun soal yang memenuhi persyaratan high order thinking skills dibutuhkan waktu yang cukup lama dan keterampilan yang baik terutama dapat menerapkan taksonomi Bloom dalam merumsukan indikator
High-Order Calderón Preconditioned Time Domain Integral Equation Solvers
Valdes, Felipe
2013-05-01
Two high-order accurate Calderón preconditioned time domain electric field integral equation (TDEFIE) solvers are presented. In contrast to existing Calderón preconditioned time domain solvers, the proposed preconditioner allows for high-order surface representations and current expansions by using a novel set of fully-localized high-order div-and quasi curl-conforming (DQCC) basis functions. Numerical results demonstrate that the linear systems of equations obtained using the proposed basis functions converge rapidly, regardless of the mesh density and of the order of the current expansion. © 1963-2012 IEEE.
A new design of a directional coupler for high order mode multiplexing in few mode fibers
Trichili, Abderrahmen; Ben Salem, Amine; Cherif, Rim; Zghal, Mourad; Forbes, Andrew
2014-05-01
We propose a new and versatile design of a directional coupler able to generate and multiplex high order modes in few mode fibers. The designed device can selectively generate five high order modes and multiplex them in a few mode fiber with an overall insertion loss not exceeding 3dB at the telecommunication wavelength λ = 1550 nm. The mode dependent loss is found to be weakly dependent to the wavelength. The proposed device is very promising for high order mode multiplexing and suitable for high bit-rate optical communication systems.
High order SSB modulation and its application for advanced optical comb generation based on RFS
Sun, Lin; Du, Jiangbing; Li, Lu; He, Zuyuan
2015-11-01
In this work, a method for high-order single sideband (SSB) modulation is demonstrated. Extended frequency shifting can be obtained based on the high-order SSB modulator. The design of the 2nd and 3rd order SSB modulators are presented and investigated based on simulations. The demonstrated high-order SSB modulators can be used for advanced optical comb generation when they are configured in recirculating frequency shifter (RFS). Optical comb with significantly enlarged carrier-to-carrier spacing can be obtained and thus applications including wavelength division multiplexing (WDM) communication, optical frequency domain reflectometry (OFDR) and so on can be benefited.
Lupus autoantibodies to native DNA cross-react with the A and D SnRNP polypeptides
National Research Council Canada - National Science Library
Reichlin, M; Martin, A; Taylor-Albert, E; Tsuzaka, K; Zhang, W; Reichlin, M W; Koren, E; Ebling, F M; Tsao, B; Hahn, B H
1994-01-01
Antibodies to native DNA (nDNA) in sera from patients with systemic lupus erythematosus have been found to frequently correlate with antibodies to the A and D SnRNP proteins measured in Western blot assays. 40 of 54 SLE (74.1...
High Order Wavelet-Based Multiresolution Technology for Airframe Noise Prediction Project
National Aeronautics and Space Administration — An integrated framework is proposed for efficient prediction of rotorcraft and airframe noise. A novel wavelet-based multiresolution technique and high-order...
ASYMPTOTICALLY OPTIMAL HIGH-ORDER ACCURATE ALGORITHMS FOR THE SOLUTION OF CERTAIN ELLIPTIC PDEs
Energy Technology Data Exchange (ETDEWEB)
Leonid Kunyansky, PhD
2008-11-26
The main goal of the project, "Asymptotically Optimal, High-Order Accurate Algorithms for the Solution of Certain Elliptic PDE's" (DE-FG02-03ER25577) was to develop fast, high-order algorithms for the solution of scattering problems and spectral problems of photonic crystals theory. The results we obtained lie in three areas: (1) asymptotically fast, high-order algorithms for the solution of eigenvalue problems of photonics, (2) fast, high-order algorithms for the solution of acoustic and electromagnetic scattering problems in the inhomogeneous media, and (3) inversion formulas and fast algorithms for the inverse source problem for the acoustic wave equation, with applications to thermo- and opto- acoustic tomography.
Finite-Bandwidth Resonances of High-Order Axial Modes (HOAM) in a Gyrotron Cavity
Sabchevski, Svilen; IDEHARA, Toshitaka
2014-01-01
Finite-bandwidth resonances of high-order axial modes (HOAM) in an open gyrotron cavity are studied numerically using the GYROSIM problem-oriented software package for modelling, simulation and computer-aided design (CAD) of gyrotron tubes.
Technical Training on High-Order Spectral Analysis and Thermal Anemometry Applications
Maslov, A. A.; Shiplyuk, A. N.; Sidirenko, A. A.; Bountin, D. A.
2003-01-01
The topics of thermal anemometry and high-order spectral analyses were the subject of the technical training. Specifically, the objective of the technical training was to study: (i) the recently introduced constant voltage anemometer (CVA) for high-speed boundary layer; and (ii) newly developed high-order spectral analysis techniques (HOSA). Both CVA and HOSA are relevant tools for studies of boundary layer transition and stability.
Decay of high order optical vortices in anisotropic nonlinear optical media
DEFF Research Database (Denmark)
Mamaev, A.V.; Saffman, M.; Zozulya, A.A.
1997-01-01
We present an experimental and theoretical study of the decay of high order optical vortices in media with an anisotropic nonlocal nonlinearity. Vortices with charge n decay into an aligned array of n vortices of unit charge.......We present an experimental and theoretical study of the decay of high order optical vortices in media with an anisotropic nonlocal nonlinearity. Vortices with charge n decay into an aligned array of n vortices of unit charge....
High-order ionospheric effects on electron density estimation from Fengyun-3C GPS radio occultation
Li, Junhai; Jin, Shuanggen
2017-03-01
GPS radio occultation can estimate ionospheric electron density and total electron content (TEC) with high spatial resolution, e.g., China's recent Fengyun-3C GPS radio occultation. However, high-order ionospheric delays are normally ignored. In this paper, the high-order ionospheric effects on electron density estimation from the Fengyun-3C GPS radio occultation data are estimated and investigated using the NeQuick2 ionosphere model and the IGRF12 (International Geomagnetic Reference Field, 12th generation) geomagnetic model. Results show that the high-order ionospheric delays have large effects on electron density estimation with up to 800 el cm-3, which should be corrected in high-precision ionospheric density estimation and applications. The second-order ionospheric effects are more significant, particularly at 250-300 km, while third-order ionospheric effects are much smaller. Furthermore, the high-order ionospheric effects are related to the location, the local time, the radio occultation azimuth and the solar activity. The large high-order ionospheric effects are found in the low-latitude area and in the daytime as well as during strong solar activities. The second-order ionospheric effects have a maximum positive value when the radio occultation azimuth is around 0-20°, and a maximum negative value when the radio occultation azimuth is around -180 to -160°. Moreover, the geomagnetic storm also affects the high-order ionospheric delay, which should be carefully corrected.
Cho, S B; Zheng, Z; Cho, S; Ahn, K J; Choi, M J; Kim, D-Y; Lee, K H; Bang, D
2013-01-01
Heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 has been identified as a target antigen of anti-endothelial cell immunglobulin (Ig)A antibodies in patients with Behçet's disease (BD). The aim was to investigate the effects of the sera from BD patients and Streptococcus sanguis on the subcellular expression of hnRNP A2/B1 in human dermal microvascular endothelial cells (HDMECs). The sera of BD patients and healthy controls (HC) as well as cultured S. sanguis were used to stimulate HDMECs. Subcellular fractions were obtained from stimulated HDMECs and were subjected to immunoblot analyses. The distribution of hnRNP A2/B1 was investigated by immunocytochemistry and direct immunofluorescence study was performed in biopsy specimens of mucosal ulcers from BD patients. BD patients' sera increased the membrane expression of hnRNP A2/B1 in HDMECs after 12 and 24 h of incubation compared with HDMECs incubated with endothelial cell culture media and HC sera. S. sanguis also increased hnRNP A2/B1 in the cellular membrane. hnRNP A2/B1 mRNA level was also significantly upregulated in HDMECs incubated with BD patients' sera and S. sanguis. Immunocytochemistry demonstrated marked expression of hnRNP A2/B1 in the cytoplasm and cellular membrane of HDMECs incubated with BD patients' sera or S. sanguis. In addition, direct immunofluorescence experiments revealed the co-localization of serum IgA antibodies and monoclonal antibodies (mAbs) against hnRNP A2/B1 in tissue sections from ulcers of BD patients. Our data indicate that both the sera of BD patients with active disease and S. sanguis infection are inflammatory stimuli that can induce membranous hnRNP A2/B1 expression in HDMECs.
Chen, Xiaobo; Zhang, Han; Lee, Seong-Whan; Shen, Dinggang
2017-07-01
Conventional Functional connectivity (FC) analysis focuses on characterizing the correlation between two brain regions, whereas the high-order FC can model the correlation between two brain region pairs. To reduce the number of brain region pairs, clustering is applied to group all the brain region pairs into a small number of clusters. Then, a high-order FC network can be constructed based on the clustering result. By varying the number of clusters, multiple high-order FC networks can be generated and the one with the best overall performance can be finally selected. However, the important information contained in other networks may be simply discarded. To address this issue, in this paper, we propose to make full use of the information contained in all high-order FC networks. First, an agglomerative hierarchical clustering technique is applied such that the clustering result in one layer always depends on the previous layer, thus making the high-order FC networks in the two consecutive layers highly correlated. As a result, the features extracted from high-order FC network in each layer can be decomposed into two parts (blocks), i.e., one is redundant while the other might be informative or complementary, with respect to its previous layer. Then, a selective feature fusion method, which combines sequential forward selection and sparse regression, is developed to select a feature set from those informative feature blocks for classification. Experimental results confirm that our novel method outperforms the best single high-order FC network in diagnosis of mild cognitive impairment (MCI) subjects.
Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities.
Fiorini, Francesca; Bagchi, Debjani; Le Hir, Hervé; Croquette, Vincent
2015-07-03
RNA helicases are implicated in most cellular RNA-dependent events. In eukaryotes however, only few have been functionally characterized. Upf1 is a RNA helicase essential for nonsense-mediated mRNA decay (NMD). Here, using magnetic tweezers and bulk assays, we observe that human Upf1 is able to translocate slowly over long single-stranded nucleic acids with a processivity >10 kb. Upf1 efficiently translocates through double-stranded structures and protein-bound sequences, demonstrating that Upf1 is an efficient ribonucleoprotein complex remodeler. Our observation of processive unwinding by an eukaryotic RNA helicase reveals that Upf1, once recruited onto NMD mRNA targets, can scan the entire transcript to irreversibly remodel the mRNP, facilitating its degradation by the NMD machinery.
Gao, Ran; Shah, Navjot; Lee, Jung-Sun; Katiyar, Shashank P; Li, Ling; Oh, Eonju; Sundar, Durai; Yun, Chae-Ok; Wadhwa, Renu; Kaul, Sunil C
2014-12-01
Ashwagandha is an important herb used in the Indian system of traditional home medicine, Ayurveda. Alcoholic extract (i-Extract) from its leaves and its component, withanone, were previously shown to possess anticancer activity. In the present study, we developed a combination of withanone and withaferin A, major withanolides in the i-Extract, that retained the selective cancer cell killing activity and found that it also has significant antimigratory, -invasive, and -angiogenic activities, in both in vitro and in vivo assays. Using bioinformatics and biochemical approaches, we demonstrate that these phytochemicals caused downregulation of migration-promoting proteins hnRNP-K, VEGF, and metalloproteases and hence are candidate natural drugs for metastatic cancer therapy. ©2014 American Association for Cancer Research.
Leblanc, A.; Quéré, F.
2018-01-01
Measuring the spatial properties of high-order harmonic beams produced by high-intensity laser-matter interactions directly in the target plane is very challenging due to the extreme physical conditions at stake in the interaction area. A measurement scheme has been recently developed to obtain this information experimentally, which consists in adapting a lensless imaging method known as ptychography. In this paper, we present a theoretical validation of this method in the case of harmonic generation from plasma mirrors, using a combination of simple modeling and 2D Particle-In-Cell simulations. This study investigates the concept of in situ ptychography and supports the analysis of experimental measurements presented in previous publications.
High-order harmonic generation using a high-repetition-rate turnkey laser
Lorek, Eleonora; Heyl, Christoph Michael; Carlström, Stefanos; Paleček, David; Zigmantas, Donatas; Mauritsson, Johan
2014-01-01
We generate high-order harmonics at high pulse repetition rates using a turnkey laser. High-order harmonics at 400 kHz are observed when argon is used as target gas. In neon we achieve generation of photons with energies exceeding 90 eV ($\\sim$13 nm) at 20 kHz. We measure a photon flux of 4.4$\\cdot10^{10}$ photons per second per harmonic in argon at 100 kHz. Many experiments employing high-order harmonics would benefit from higher repetition rates, and the user-friendly operation opens up for applications of coherent extreme ultra-violet pulses in new research areas.
DEFF Research Database (Denmark)
Madsen, Christian Bruun; Abu-Samha, Mahmoud; Madsen, Lars Bojer
2010-01-01
as a nuclear correlation function. We express the nuclear correlation function in terms of Franck-Condon factors, which allows us to decompose nuclear motion into modes and identify the modes that are dominant in the high-order harmonic generation process. We show results for the isotopes CH4 and CD4......We present a generic approach for treating the effect of nuclear motion in high-order harmonic generation from polyatomic molecules. Our procedure relies on a separation of nuclear and electron dynamics where we account for the electronic part using the Lewenstein model and nuclear motion enters...... and thereby provide direct theoretical support for a recent experiment [S. Baker et al., Science 312, 424 (2006)] that uses high-order harmonic generation to probe the ultrafast structural nuclear rearrangement of ionized methane....
High-order conservative discretizations for some cases of the rigid body motion
Energy Technology Data Exchange (ETDEWEB)
Kozlov, Roman [Department of Mathematics, University of Bergen, Johannes Brunsgate 12, 5008 Bergen (Norway)], E-mail: roman.kozlov@mi.uib.no
2008-12-22
Modified vector fields can be used to construct high-order structure-preserving numerical integrators for ordinary differential equations. In the present Letter we consider high-order integrators based on the implicit midpoint rule, which conserve quadratic first integrals. It is shown that these integrators are particularly suitable for the rigid body motion with an additional quadratic first integral. In this case high-order integrators preserve all four first integrals of motion. The approach is illustrated on the Lagrange top (a rotationally symmetric rigid body with a fixed point on the symmetry axis). The equations of motion are considered in the space fixed frame because in this frame Lagrange top admits a neat description. The Lagrange top motion includes the spherical pendulum and the planar pendulum, which swings in a vertical plane, as particular cases.
Giant Faraday Rotation of High-Order Plasmonic Modes in Graphene-Covered Nanowires.
Kuzmin, Dmitry A; Bychkov, Igor V; Shavrov, Vladimir G; Temnov, Vasily V
2016-07-13
Plasmonic Faraday rotation in nanowires manifests itself in the rotation of the spatial intensity distribution of high-order surface plasmon polariton (SPP) modes around the nanowire axis. Here we predict theoretically the giant Faraday rotation for SPPs propagating on graphene-coated magneto-optically active nanowires. Upon the reversal of the external magnetic field pointing along the nanowire axis some high-order plasmonic modes may be rotated by up to ∼100° on the length scale of about 500 nm at mid-infrared frequencies. Tuning the carrier concentration in graphene by chemical doping or gate voltage allows for controlling SPP-properties and notably the rotation angle of high-order azimuthal modes. Our results open the door to novel plasmonic applications ranging from nanowire-based Faraday isolators to the magnetic control in quantum-optical applications.
National Research Council Canada - National Science Library
Koren, E; Koscec, M; Wolfson-Reichlin, M; Ebling, FM; Tsao, B; Hahn, BH; Reichlin, M
1995-01-01
.... Murine monoclonal and human affinity-purified Abs to native DNA (anti- nDNA) that cross-react with the A and D SnRNP polypeptides were analyzed for direct injurious effects against cultured pig kidney (PK15...
Neurodynamics-Based Robust Pole Assignment for High-Order Descriptor Systems.
Le, Xinyi; Wang, Jun
2015-11-01
In this paper, a neurodynamic optimization approach is proposed for synthesizing high-order descriptor linear systems with state feedback control via robust pole assignment. With a new robustness measure serving as the objective function, the robust eigenstructure assignment problem is formulated as a pseudoconvex optimization problem. A neurodynamic optimization approach is applied and shown to be capable of maximizing the robust stability margin for high-order singular systems with guaranteed optimality and exact pole assignment. Two numerical examples and vehicle vibration control application are discussed to substantiate the efficacy of the proposed approach.
Development of high-order harmonic focusing system based on ellipsoidal mirror
Energy Technology Data Exchange (ETDEWEB)
Motoyama, H.; Takei, Y.; Kume, T.; Egawa, S.; Mimura, H., E-mail: mimura@edm.t.u-tokyo.ac.jp [Department of Precision Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkuyo-ku, Tokyo 113-8656 (Japan); Sato, T.; Iwasaki, A.; Yamanouchi, K. [Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Hiraguri, K.; Hashizume, H. [Natsume Optical Corp., 3461 Kamichaya, Kanae, Iida, Nagano 395-0808 (Japan)
2016-05-15
We have developed a focusing system for extreme ultraviolet light produced by high-order harmonic generation. An ellipsoidal mirror with a precise surface shape was fabricated and installed into the focusing system. A rigid mirror manipulator and a beam profiler were employed to perform precise and stable mirror alignment. As a demonstration of the focusing performance, high-order harmonics in the wavelength range of 13.5–19.5 nm were successfully focused into a 2.4 × 2.3 μm{sup 2} spot.
High-Order Entropy Stable Finite Difference Schemes for Nonlinear Conservation Laws: Finite Domains
Fisher, Travis C.; Carpenter, Mark H.
2013-01-01
Developing stable and robust high-order finite difference schemes requires mathematical formalism and appropriate methods of analysis. In this work, nonlinear entropy stability is used to derive provably stable high-order finite difference methods with formal boundary closures for conservation laws. Particular emphasis is placed on the entropy stability of the compressible Navier-Stokes equations. A newly derived entropy stable weighted essentially non-oscillatory finite difference method is used to simulate problems with shocks and a conservative, entropy stable, narrow-stencil finite difference approach is used to approximate viscous terms.
Energy Technology Data Exchange (ETDEWEB)
R. M. Ferrer; Y. Y. Azmy
2009-05-01
We present a robust arbitrarily high order transport method of the characteristic type for unstructured tetrahedral grids. Previously encountered difficulties have been addressed through the reformulation of the method based on coordinate transformations, evaluation of the moments balance relation as a linear system of equations involving the expansion coefficients of the projected basis, and the asymptotic expansion of the integral kernels in the thin cell limit. The proper choice of basis functions for the high-order spatial expansion of the solution is discussed and its effect on problems involving scattering discussed. Numerical tests are presented to illustrate the beneficial effect of these improvements, and the improved robustness they yield.
Propagation and power flow of high-order three-Airy beams
Liang, Yi; Chen, Yingkang; Wan, Lingyu
2017-12-01
We demonstrate experimentally propagation and evolution of high-order three-Airy beams in this letter. Our results show clearly that, a high-order three-Airy beam tends to evolve into a Laguerre-Gaussian-like beam, in consistence with previous prediction. Moreover, by analyzing the internal transverse power flow of three-Airy beams during propagation, we found that, as the order of three-Airy beams goes higher, the initial beam intensity distributes more in the "side lobes", and it takes longer propagation for the beams to reach a maximum peak intensity and then transform into patterns of corresponding Laguerre-Gaussian-like modes.
Convergence of high order perturbative expansions in open system quantum dynamics.
Xu, Meng; Song, Linze; Song, Kai; Shi, Qiang
2017-02-14
We propose a new method to directly calculate high order perturbative expansion terms in open system quantum dynamics. They are first written explicitly in path integral expressions. A set of differential equations are then derived by extending the hierarchical equation of motion (HEOM) approach. As two typical examples for the bosonic and fermionic baths, specific forms of the extended HEOM are obtained for the spin-boson model and the Anderson impurity model. Numerical results are then presented for these two models. General trends of the high order perturbation terms as well as the necessary orders for the perturbative expansions to converge are analyzed.
A high-order statistical tensor based algorithm for anomaly detection in hyperspectral imagery.
Geng, Xiurui; Sun, Kang; Ji, Luyan; Zhao, Yongchao
2014-11-04
Recently, high-order statistics have received more and more interest in the field of hyperspectral anomaly detection. However, most of the existing high-order statistics based anomaly detection methods require stepwise iterations since they are the direct applications of blind source separation. Moreover, these methods usually produce multiple detection maps rather than a single anomaly distribution image. In this study, we exploit the concept of coskewness tensor and propose a new anomaly detection method, which is called COSD (coskewness detector). COSD does not need iteration and can produce single detection map. The experiments based on both simulated and real hyperspectral data sets verify the effectiveness of our algorithm.
Dynamical evolution of space debris on high-elliptical orbits near high-order resonance zones
Kuznetsov, Eduard; Zakharova, Polina
2015-08-01
Both analytical and numerical results are used to study high-order resonance regions in the vicinity of Molniya-type orbits. Based on data of numerical simulations, long-term orbital evolution are studied for HEO objects depending on their AMR. The Poynting-Robertson effect causes a secular decrease in the semi-major axis of a spherically symmetrical satellite. Under the Poynting-Robertson effect, objects pass through the regions of high-order resonances. The Poynting-Robertson effect and secular perturbations of the semi-major axis lead to the formation of weak stochastic trajectories.
Directory of Open Access Journals (Sweden)
Vojislav S. Milosavljević
2010-01-01
Full Text Available Radi što adekvatnijeg odgovora na najnovije izazove tržišta vazdušnog prevoza javila se ideja da se aerodrom 'Batajnica' otvori i za civilni saobraćaj. Time bi se znatno promenila situacija u terminalnom vazdušnom prostoru, pa je potrebno razmotriti nove okolnosti i prema njima optimizovati terminalni prostor. Znatan deo optimizacije čini i definisanje procedura za prilaz i sletanje, kao i strateško razdvajanje prilaznih tokova. Predložene procedure konstruisane su primenom savremenih koncepcija i rešenja u civilnoj avijaciji: Performance-Based Navigation, Baro-VNAV i CDA, koja se vrlo uspešno već primenjuju širom sveta. / Introduction Numerous advantages of Performance-Based Navigation should be applied in reorganizing the terminal airspace around Belgrade after the opening of 'Batajnica' airport for civil operations. The concept of Performance-Based Navigation Contrary to conventional navigation which relies on navigation signals from ground navaids, PBN is predominantly based upon satellite navigation. RNP - Required Navigation Performance RNP is defined as a set of standards which specify required navigation performance accuracy of an aircraft in certain airspace. Some of its key features are monitoring of actually achieved navigational performances and navigation containment. Benefits and possible issues with RNP implementation Implementation of RNP leads to significant savings in fuel and time, it increases the efficiency of airspace and capacity, reduces ATC workload while on the other hand there are a number of issues that still should be addressed. Barometric Vertical Navigation (Baro-VNAV The essence of Baro-VNAV is calculation of the vertical component of a 3D flight path that aircraft should follow based on measured static pressure. CDA - Continuous Descent Approach By CDA, approach is flown with a constant gradient at minimal thrust instead of alternating descent and level flight with increased thrust as it is flown in
Masuda, Akio; Shen, Xin-Ming; Ito, Mikako; Matsuura, Tohru; Engel, Andrew G; Ohno, Kinji
2008-12-15
In humans and great apes, CHRNA1 encoding the muscle nicotinic acetylcholine receptor alpha subunit carries an inframe exon P3A, the inclusion of which yields a nonfunctional alpha subunit. In muscle, the P3A(-) and P3A(+) transcripts are generated in a 1:1 ratio but the functional significance and regulation of the alternative splicing remain elusive. An intronic mutation (IVS3-8G>A), identified in a patient with congenital myasthenic syndrome, disrupts an intronic splicing silencer (ISS) and results in exclusive inclusion of the downstream P3A exon. We found that the ISS-binding splicing trans-factor was heterogeneous nuclear ribonucleoprotein (hnRNP) H and the mutation attenuated the affinity of hnRNP for the ISS approximately 100-fold. We next showed that direct placement of hnRNP H to the 3' end of intron 3 silences, and siRNA-mediated downregulation of hnRNP H enhances recognition of exon P3A. Analysis of the human genome suggested that the hnRNPH-binding UGGG motif is overrepresented close to the 3' ends of introns. Pursuing this clue, we showed that alternative exons of GRIP1, FAS, VPS13C and NRCAM are downregulated by hnRNP H. Our findings imply that the presence of the hnRNP H-binding motif close to the 3' end of an intron is an essential but underestimated splicing regulator of the downstream exon.
A hierarchy of high-order theories for modes in an elastic layer
DEFF Research Database (Denmark)
Sorokin, Sergey V.; Chapman, C. John
2015-01-01
A hierarchy of high-order theories for symmetric and skew-symmetric modes in an infinitely long elastic layer of the constant thickness is derived. For each member of the hierarchy, boundary conditions for layers of the finite length are formulated. The forcing problems at several approximation...
Overlay control methodology comparison: field-by-field and high-order methods
Huang, Chun-Yen; Chiu, Chui-Fu; Wu, Wen-Bin; Shih, Chiang-Lin; Huang, Chin-Chou Kevin; Huang, Healthy; Choi, DongSub; Pierson, Bill; Robinson, John C.
2012-03-01
Overlay control in advanced integrated circuit (IC) manufacturing is becoming one of the leading lithographic challenges in the 3x and 2x nm process nodes. Production overlay control can no longer meet the stringent emerging requirements based on linear composite wafer and field models with sampling of 10 to 20 fields and 4 to 5 sites per field, which was the industry standard for many years. Methods that have emerged include overlay metrology in many or all fields, including the high order field model method called high order control (HOC), and field by field control (FxFc) methods also called correction per exposure. The HOC and FxFc methods were initially introduced as relatively infrequent scanner qualification activities meant to supplement linear production schemes. More recently, however, it is clear that production control is also requiring intense sampling, similar high order and FxFc methods. The added control benefits of high order and FxFc overlay methods need to be balanced with the increased metrology requirements, however, without putting material at risk. Of critical importance is the proper control of edge fields, which requires intensive sampling in order to minimize signatures. In this study we compare various methods of overlay control including the performance levels that can be achieved.
Highly ordered three-dimensional macroporous carbon spheres for determination of heavy metal ions
Energy Technology Data Exchange (ETDEWEB)
Zhang, Yuxiao; Zhang, Jianming [Institute of Functional Nano and Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123 (China); Liu, Yang, E-mail: yangl@suda.edu.cn [Institute of Functional Nano and Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123 (China); Huang, Hui [Institute of Functional Nano and Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123 (China); Kang, Zhenhui, E-mail: zhkang@suda.edu.cn [Institute of Functional Nano and Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123 (China)
2012-04-15
Highlights: Black-Right-Pointing-Pointer Highly ordered three dimensional macroporous carbon spheres (MPCSs) were prepared. Black-Right-Pointing-Pointer MPCS was covalently modified by cysteine (MPCS-CO-Cys). Black-Right-Pointing-Pointer MPCS-CO-Cys was first time used in electrochemical detection of heavy metal ions. Black-Right-Pointing-Pointer Heavy metal ions such as Pb{sup 2+} and Cd{sup 2+} can be simultaneously determined. -- Abstract: An effective voltammetric method for detection of trace heavy metal ions using chemically modified highly ordered three dimensional macroporous carbon spheres electrode surfaces is described. The highly ordered three dimensional macroporous carbon spheres were prepared by carbonization of glucose in silica crystal bead template, followed by removal of the template. The highly ordered three dimensional macroporous carbon spheres were covalently modified by cysteine, an amino acid with high affinities towards some heavy metals. The materials were characterized by physical adsorption of nitrogen, scanning electron microscopy, and transmission electron microscopy techniques. While the Fourier-transform infrared spectroscopy was used to characterize the functional groups on the surface of carbon spheres. High sensitivity was exhibited when this material was used in electrochemical detection (square wave anodic stripping voltammetry) of heavy metal ions due to the porous structure. And the potential application for simultaneous detection of heavy metal ions was also investigated.
STUDY OF SAMPLE AND HOLD DIGITAL-ANALOG CONVERTER WITH HIGH ORDER JITTER NOISE SHAPING
北原, 義大; KITAHARA, Yoshihiro
2014-01-01
In this paper, present sample hold DAC with high order jitter noise shaping using 2nd order architecture or feed-forward 2nd order architecture. Performance improvements of sample hold DAC can be expected by using higher order jitter noise shaping. The effectiveness of presented architecture is confirmed by MATLAB simulation results and SPICE simulation results.
2017-01-09
19b. TELEPHONE NUMBER (Include area code) 01/09/2017 Briefing Charts 01 January 2017 - 31 January 2017 Isolating Flow -field Discontinuities while...Unclassified Unclassified Unclassified SAR 18 V. Sanakaran N/A Isolating Flow -field Discontinuities while Preserving Monotonicity and High-order
Laser-induced bound-state phases in high-order harmonic generation
DEFF Research Database (Denmark)
Etches, Adam; B. Gaarde, Mette; Bojer Madsen, Lars
2012-01-01
We present single-molecule and macroscopic calculations showing that laser-induced Stark shifts contribute significantly to the phase of high-order harmonics from polar molecules. This is important for orbital tomography, where phases of field-free dipole matrix elements are needed in order...
Stability predictions for high-order ΣΔ modulators based on quasilinear modeling
DEFF Research Database (Denmark)
Risbo, Lars
1994-01-01
This paper introduces a novel interpretation of the instability mechanisms in high-order one-bit Sigma-Delta modulators. Furthermore, it is demonstrated how the maximum stable amplitude range can be predicted very well. The results are obtained using an extension of the well known quasilinear...
2007-12-06
high order well-balanced schemes to a class of hyperbolic systems with source terms, Boletin de la Sociedad Espanola de Matematica Aplicada, v34 (2006...schemes to a class of hyperbolic systems with source terms, Boletin de la Sociedad Espanola de Matematica Aplicada, v34 (2006), pp.69-80. 39. Y. Xu and C.-W
High-order equations of motion in quantum mechanics and Galilean relativity
Energy Technology Data Exchange (ETDEWEB)
Fushchych, W.I. [Department of Mathematics, UMIST, Manchester (United Kingdom); Symenoh, Z.I. [Institute of Mathematics of the National Academy of Sciences of Ukraina, Kyiv (Ukraine)
1997-03-21
Linear partial differential equations of arbitrary order invariant under the Galilei transformations are described. Symmetry classification of potentials for these equations in two-dimensional space is carried out. High-order nonlinear partial differential equations invariant under the Galilei, extended Galilei and full Galilei algebras are studied. (author). Letter-to-the-editor.
The Development of High-Order Methods for Real World Applications
2015-12-03
three-stage 3rd order Runge-Kutta scheme Gottlieb and Shu [43] is used as the temporal discretization. Here we give a brief description. Rewrite the...Science and Engineering. Springer Berlin Heidelberg, pp. 47–95. [43] Gottlieb , S., Shu, C.-W., 2011. Strong stability-preserving high-order time dis
Construction of Low Dissipative High Order Well-Balanced Filter Schemes for Non-Equilibrium Flows
Wang, Wei; Yee, H. C.; Sjogreen, Bjorn; Magin, Thierry; Shu, Chi-Wang
2009-01-01
The goal of this paper is to generalize the well-balanced approach for non-equilibrium flow studied by Wang et al. [26] to a class of low dissipative high order shock-capturing filter schemes and to explore more advantages of well-balanced schemes in reacting flows. The class of filter schemes developed by Yee et al. [30], Sjoegreen & Yee [24] and Yee & Sjoegreen [35] consist of two steps, a full time step of spatially high order non-dissipative base scheme and an adaptive nonlinear filter containing shock-capturing dissipation. A good property of the filter scheme is that the base scheme and the filter are stand alone modules in designing. Therefore, the idea of designing a well-balanced filter scheme is straightforward, i.e., choosing a well-balanced base scheme with a well-balanced filter (both with high order). A typical class of these schemes shown in this paper is the high order central difference schemes/predictor-corrector (PC) schemes with a high order well-balanced WENO filter. The new filter scheme with the well-balanced property will gather the features of both filter methods and well-balanced properties: it can preserve certain steady state solutions exactly; it is able to capture small perturbations, e.g., turbulence fluctuations; it adaptively controls numerical dissipation. Thus it shows high accuracy, efficiency and stability in shock/turbulence interactions. Numerical examples containing 1D and 2D smooth problems, 1D stationary contact discontinuity problem and 1D turbulence/shock interactions are included to verify the improved accuracy, in addition to the well-balanced behavior.
The hnRNP 2H9 gene, which is involved in the splicing reaction, is a multiply spliced gene
DEFF Research Database (Denmark)
Honoré, B
2000-01-01
transcripts: hnRNPs 2H9, 2H9A, 2H9B, 2H9C, 2H9D and 2H9E predicting proteins containing 346, 331, 297, 215, 145 and 139 amino acids, respectively. The hnRNP 2H9A cDNA sequence was used to obtain a genomic BAC clone and the structure of the hnRNP 2H9 gene was revealed by sequencing two subclones together...... indicates that the alternatively spliced transcripts give rise to different sets and levels of proteins expressed among various human cells and tissues. Due to their great structural variations the different proteins may thus possess different functions in the splicing reaction. Udgivelsesdato: 2000-Jun-21...
DEFF Research Database (Denmark)
Laursen, Lisbeth Schmidt; Chan, Colin W; ffrench-Constant, Charles
2011-01-01
of protein synthesis represents one mechanism used to control the different requirements for myelin sheath at each axo–glia interaction. Prior work has established that β1-integrins are involved in the axoglial interactions that initiate myelination. Here, we show that integrin activation regulates...... translation of a key sheath protein, myelin basic protein (MBP), by reversing the inhibitory effect of the mRNA 3′UTR. During oligodendrocyte differentiation and myelination α6β1-integrin interacts with hnRNP-K, an mRNA-binding protein, which binds to MBP mRNA and translocates from the nucleus to the myelin...... sheath. Furthermore, knockdown of hnRNP-K inhibits MBP protein synthesis during myelination. Together, these results identify a novel pathway by which axoglial adhesion molecules coordinate MBP synthesis with myelin sheath formation...
Genome-wide analysis of KAP1, the 7SK snRNP complex, and RNA polymerase II
Directory of Open Access Journals (Sweden)
Ryan P. McNamara
2016-03-01
Full Text Available The transition of RNA polymerase II (Pol II from transcription initiation into productive elongation in eukaryotic cells is regulated by the P-TEFb kinase, which phosphorylates the C-terminal domain of paused Pol II at promoter-proximal regions. Our recent study found that P-TEFb (in an inhibited state bound to the 7SK snRNP complex interacts with the KAP1/TRIM28 transcriptional regulator, and that KAP1 and the 7SK snRNP co-occupy most gene promoters containing paused Pol II. Here we provide a detailed experimental description and analysis of the ChIP-seq datasets that have been deposited into Gene Expression Omnibus (GEO: GS72622, so that independent groups can replicate and expand upon these findings. We propose these datasets would provide valuable information for researchers studying mechanisms of transcriptional regulation including Pol II pausing and pause release.
Qin, Wanwan; Yang, Jianjun
2017-07-01
We report a new one-step maskless method to fabricate high-order nanoarray metal structures comprising periodic grooves and particle chains on a single-crystal Cu surface using femtosecond laser pulses at the central wavelength of 400 nm. Remarkably, when a circularly polarized infrared femtosecond laser pulse (spectrally centered at 800 nm) pre-irradiates the sample surface, the geometric dimensions of the composite structure can be well controlled. With increasing the energy fluence of the infrared laser pulse, both the groove width and particle diameter are observed to reduce, while the measured spacing-to-diameter ratio of the nanoparticles tends to present an increasing tendency. A physical scenario is proposed to elucidate the underlying mechanisms: as the infrared femtosecond laser pulse pre-irradiates the target, the copper surface is triggered to display anomalous transient physical properties, on which the subsequently incident Gaussian blue laser pulse is spatially modulated into fringe-like energy depositions via the excitation of ultrafast surface plasmon. During the following relaxation processes, the periodically heated thin-layer regions can be transferred into the metastable liquid rivulets and then they break up into nanodroplet arrays owing to the modified Rayleigh-like instability. This investigation indicates a simple integrated approach for active designing and large-scale assembly of complexed functional nanostructures on bulk materials.
DEFF Research Database (Denmark)
Baggesen, Jan Conrad; Madsen, Lars Bojer
2011-01-01
On the dipole, velocity and acceleration forms in high-order harmonic generation from a single atom or molecule......On the dipole, velocity and acceleration forms in high-order harmonic generation from a single atom or molecule...
40LoVe and Samba are involved in Xenopus neural development and functionally distinct from hnRNP AB.
Directory of Open Access Journals (Sweden)
Maria Andreou
Full Text Available Heterogeneous nuclear ribonucleoproteins (hnRNPs comprise a large group of modular RNA-binding proteins classified according to their conserved domains. This modular nature, coupled with a large choice of alternative splice variants generates functional diversity. Here, we investigate the biological differences between 40LoVe, its splice variant Samba and its pseudoallele hnRNP AB in neural development. Loss of function experiments lead to defects in neural development with reduction of eye size, which stem primarily from increased apoptosis and reduced proliferation in neural tissues. Despite very high homology between 40LoVe/Samba and hnRNP AB, these proteins display major differences in localization, which appear to be in part responsible for functional differences. Specifically, we show that the 40Love/Samba carboxy-terminal domain (GRD enables nucleocytoplasmic shuttling behavior. This domain is slightly different in hnRNP AB, leading to nuclear-restricted localization. Finally, we show that shuttling is required for 40LoVe/Samba function in neural development.
A high-order spatial filter for a cubed-sphere spectral element model
Kang, Hyun-Gyu; Cheong, Hyeong-Bin
2017-04-01
A high-order spatial filter is developed for the spectral-element-method dynamical core on the cubed-sphere grid which employs the Gauss-Lobatto Lagrange interpolating polynomials (GLLIP) as orthogonal basis functions. The filter equation is the high-order Helmholtz equation which corresponds to the implicit time-differencing of a diffusion equation employing the high-order Laplacian. The Laplacian operator is discretized within a cell which is a building block of the cubed sphere grid and consists of the Gauss-Lobatto grid. When discretizing a high-order Laplacian, due to the requirement of C0 continuity along the cell boundaries the grid-points in neighboring cells should be used for the target cell: The number of neighboring cells is nearly quadratically proportional to the filter order. Discrete Helmholtz equation yields a huge-sized and highly sparse matrix equation whose size is N*N with N the number of total grid points on the globe. The number of nonzero entries is also almost in quadratic proportion to the filter order. Filtering is accomplished by solving the huge-matrix equation. While requiring a significant computing time, the solution of global matrix provides the filtered field free of discontinuity along the cell boundaries. To achieve the computational efficiency and the accuracy at the same time, the solution of the matrix equation was obtained by only accounting for the finite number of adjacent cells. This is called as a local-domain filter. It was shown that to remove the numerical noise near the grid-scale, inclusion of 5*5 cells for the local-domain filter was found sufficient, giving the same accuracy as that obtained by global domain solution while reducing the computing time to a considerably lower level. The high-order filter was evaluated using the standard test cases including the baroclinic instability of the zonal flow. Results indicated that the filter performs better on the removal of grid-scale numerical noises than the explicit
Decomposition of conditional probability for high-order symbolic Markov chains
Melnik, S. S.; Usatenko, O. V.
2017-07-01
The main goal of this paper is to develop an estimate for the conditional probability function of random stationary ergodic symbolic sequences with elements belonging to a finite alphabet. We elaborate on a decomposition procedure for the conditional probability function of sequences considered to be high-order Markov chains. We represent the conditional probability function as the sum of multilinear memory function monomials of different orders (from zero up to the chain order). This allows us to introduce a family of Markov chain models and to construct artificial sequences via a method of successive iterations, taking into account at each step increasingly high correlations among random elements. At weak correlations, the memory functions are uniquely expressed in terms of the high-order symbolic correlation functions. The proposed method fills the gap between two approaches, namely the likelihood estimation and the additive Markov chains. The obtained results may have applications for sequential approximation of artificial neural network training.
Learning High-Order Filters for Efficient Blind Deconvolution of Document Photographs
Xiao, Lei
2016-09-16
Photographs of text documents taken by hand-held cameras can be easily degraded by camera motion during exposure. In this paper, we propose a new method for blind deconvolution of document images. Observing that document images are usually dominated by small-scale high-order structures, we propose to learn a multi-scale, interleaved cascade of shrinkage fields model, which contains a series of high-order filters to facilitate joint recovery of blur kernel and latent image. With extensive experiments, we show that our method produces high quality results and is highly efficient at the same time, making it a practical choice for deblurring high resolution text images captured by modern mobile devices. © Springer International Publishing AG 2016.
A multiresolution method for solving the Poisson equation using high order regularization
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Walther, Jens Honore
2016-01-01
We present a novel high order multiresolution Poisson solver based on regularized Green's function solutions to obtain exact free-space boundary conditions while using fast Fourier transforms for computational efficiency. Multiresolution is a achieved through local refinement patches and regulari......We present a novel high order multiresolution Poisson solver based on regularized Green's function solutions to obtain exact free-space boundary conditions while using fast Fourier transforms for computational efficiency. Multiresolution is a achieved through local refinement patches...... and regularized Green's functions corresponding to the difference in the spatial resolution between the patches. The full solution is obtained utilizing the linearity of the Poisson equation enabling super-position of solutions. We show that the multiresolution Poisson solver produces convergence rates...
Highly ordered palladium nanodots and nanowires from switchable block copolymer thin films
Bhoje Gowd, E.; Nandan, Bhanu; Vyas, Mukesh Kumar; Bigall, Nadja C.; Eychmüller, Alexander; Schlörb, Heike; Stamm, Manfred
2009-10-01
We demonstrate a new approach to fabricate highly ordered arrays of nanoscopic palladium dots and wires using switchable block copolymer thin films. The surface-reconstructed block copolymer templates were directly deposited with palladium nanoparticles from a simple aqueous solution. The preferential interaction of the nanoparticles with one of the blocks is mainly responsible for the lateral arrangement of the nanoparticles inside the pores of the templates in addition to the capillary forces. A subsequent stabilization by UV-irradiation followed by pyrolysis in air at 450 °C removes the polymer to produce highly ordered metallic nanostructures. We extended this approach to micellar films to obtain metallic nanostructures. This method is highly versatile as the procedure used here is simple, eco-friendly and provides a simple approach to fabricate a broad range of nanoscaled architectures with tunable lateral spacing, and can be extended to systems with even smaller dimensions.
Energy stable and high-order-accurate finite difference methods on staggered grids
O'Reilly, Ossian; Lundquist, Tomas; Dunham, Eric M.; Nordström, Jan
2017-10-01
For wave propagation over distances of many wavelengths, high-order finite difference methods on staggered grids are widely used due to their excellent dispersion properties. However, the enforcement of boundary conditions in a stable manner and treatment of interface problems with discontinuous coefficients usually pose many challenges. In this work, we construct a provably stable and high-order-accurate finite difference method on staggered grids that can be applied to a broad class of boundary and interface problems. The staggered grid difference operators are in summation-by-parts form and when combined with a weak enforcement of the boundary conditions, lead to an energy stable method on multiblock grids. The general applicability of the method is demonstrated by simulating an explosive acoustic source, generating waves reflecting against a free surface and material discontinuity.
High order aberrations calculation of a hexapole corrector using a differential algebra method
Energy Technology Data Exchange (ETDEWEB)
Kang, Yongfeng, E-mail: yfkang@mail.xjtu.edu.cn [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi' an Jiaotong University, Xi' an 710049 (China); Liu, Xing [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi' an Jiaotong University, Xi' an 710049 (China); Zhao, Jingyi, E-mail: jingyi.zhao@foxmail.com [School of Science, Chang’an University, Xi’an 710064 (China); Tang, Tiantong [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi' an Jiaotong University, Xi' an 710049 (China)
2017-02-21
A differential algebraic (DA) method is proved as an unusual and effective tool in numerical analysis. It implements conveniently differentiation up to arbitrary high order, based on the nonstandard analysis. In this paper, the differential algebra (DA) method has been employed to compute the high order aberrations up to the fifth order of a practical hexapole corrector including round lenses and hexapole lenses. The program has been developed and tested as well. The electro-magnetic fields of arbitrary point are obtained by local analytic expressions, then field potentials are transformed into new forms which can be operated in the DA calculation. In this paper, the geometric and chromatic aberrations up to fifth order of a practical hexapole corrector system are calculated by the developed program.
Level set methods for detonation shock dynamics using high-order finite elements
Energy Technology Data Exchange (ETDEWEB)
Dobrev, V. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Grogan, F. C. [Univ. of California, San Diego, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kolev, T. V. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Rieben, R [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Tomov, V. Z. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2017-05-26
Level set methods are a popular approach to modeling evolving interfaces. We present a level set ad- vection solver in two and three dimensions using the discontinuous Galerkin method with high-order nite elements. During evolution, the level set function is reinitialized to a signed distance function to maintain ac- curacy. Our approach leads to stable front propagation and convergence on high-order, curved, unstructured meshes. The ability of the solver to implicitly track moving fronts lends itself to a number of applications; in particular, we highlight applications to high-explosive (HE) burn and detonation shock dynamics (DSD). We provide results for two- and three-dimensional benchmark problems as well as applications to DSD.
High-Order Ghost-Fluid Method for Compressible Flow in Complex Geometry
Al Marouf, Mohamad; Samtaney, Ravi
2014-11-01
We present a high-order embedded boundary method for numerical solutions of the Compressible Navier Stokes (CNS) equations in arbitrary domains. A high-order ghost fluid method based on the PDEs multidimensional extrapolation approach of Aslam (J. Comput. Phys. 2003) is utilized to extrapolate the solution across the fluid-solid interface to impose boundary conditions. A fourth order accurate numerical time integration for the CNS is achieved by fourth order Runge-Kutta scheme, and a fourth order conservative finite volume scheme by McCorquodale & Colella (Comm. in App. Math. & Comput. Sci. 2011) is used to evaluate the fluxes. Resolution at the embedded boundary and high gradient regions is accomplished by applying block-structured adaptive mesh refinement. A number of numerical examples with different Reynolds number for a low Mach number flow over an airfoil and circular cylinder will be presented. Supported by OCRF-CRG grant at KAUST.
High Order Adjoint Derivatives using ESDIRK Methods for Oil Reservoir Production Optimization
DEFF Research Database (Denmark)
Capolei, Andrea; Stenby, Erling Halfdan; Jørgensen, John Bagterp
2012-01-01
In production optimization, computation of the gradients is the computationally expensive step. We improve the computational efficiency of such algorithms by improving the gradient computation using high-order ESDIRK (Explicit Singly Diagonally Implicit Runge-Kutta) temporal integration methods...... and continuous adjoints . The high order integration scheme allows larger time steps and therefore faster solution times. We compare gradient computation by the continuous adjoint method to the discrete adjoint method and the finite-difference method. The methods are implemented for a two phase flow reservoir...... the time steps are controlled in a certain range, the continuous adjoint method produces gradients sufficiently accurate for the optimization algorithm and somewhat faster than the discrete adjoint method....
A Reconstruction Approach to High-Order Schemes Including Discontinuous Galerkin for Diffusion
Huynh, H. T.
2009-01-01
We introduce a new approach to high-order accuracy for the numerical solution of diffusion problems by solving the equations in differential form using a reconstruction technique. The approach has the advantages of simplicity and economy. It results in several new high-order methods including a simplified version of discontinuous Galerkin (DG). It also leads to new definitions of common value and common gradient quantities at each interface shared by the two adjacent cells. In addition, the new approach clarifies the relations among the various choices of new and existing common quantities. Fourier stability and accuracy analyses are carried out for the resulting schemes. Extensions to the case of quadrilateral meshes are obtained via tensor products. For the two-point boundary value problem (steady state), it is shown that these schemes, which include most popular DG methods, yield exact common interface quantities as well as exact cell average solutions for nearly all cases.
Directory of Open Access Journals (Sweden)
Daniel Ketteler
2012-01-01
Full Text Available Due to the deficits of schizophrenic patients regarding the understanding of vague meanings (D. Ketteler and S. Ketteler (2010 we develop a special test battery called HOLF (high order linguistic function test, which should be able to detect subtle linguistic performance deficits in schizophrenic patients. HOLF was presented to 40 schizophrenic patients and controls, focussing on linguistic features such as ambiguity, synonymy, hypero-/hyponymy, antinomy, and adages. Using the HOLF test battery we found that schizophrenic patients showed significant difficulties in discriminating ambiguities, hypero- and hyponymy, or synonymy compared to healthy controls. Antonyms and adages showed less significant results in comparing both groups. The more difficult a linguistic task was, the more confusion was measured in the schizophrenic group while healthy controls did not show significant problems in processing high order language tasks.
Ab initio multiscale simulation of high-order harmonic generation in solids
Floss, Isabella; Lemell, Christoph; Wachter, Georg; Smejkal, Valerie; Sato, Shunsuke A.; Tong, Xiao-Min; Yabana, Kazuhiro; Burgdörfer, Joachim
2018-01-01
High-order-harmonic generation by a highly nonlinear interaction of infrared laser fields with matter allows for the generation of attosecond pulses in the XUV spectral regime. This process, well established for atoms, has been recently extended to the condensed phase. Remarkably well-pronounced harmonics up to order ˜30 have been observed for dielectrics. We establish a route toward an ab initio multiscale simulation of solid-state high-order-harmonic generation. We find that mesoscopic effects of the extended system, in particular the realistic sampling of the entire Brillouin zone, the pulse propagation in the dense medium, and the inhomogeneous illumination of the crystal, have a strong effect on the harmonic spectra. Our results provide an explanation for the formation of clean harmonics and have implications for a wide range of nonlinear optical processes in dense media.
Quantum Key Distribution with High Order Fibonacci-like Orbital Angular Momentum States
Pan, Ziwen; Cai, Jiarui; Wang, Chuan
2017-08-01
The coding space in quantum communication could be expanded to high-dimensional space by using orbital angular momentum (OAM) states of photons, as both the capacity of the channel and security are enhanced. Here we present a novel approach to realize high-capacity quantum key distribution (QKD) by exploiting OAM states. The innovation of the proposed approach relies on a unique type of entangled-photon source which produces entangled photons with OAM randomly distributed among high order Fiboncci-like numbers and a new physical mechanism for efficiently sharing keys. This combination of entanglement with mathematical properties of high order Fibonacci sequences provides the QKD protocol immunity to photon-number-splitting attacks and allows secure generation of long keys from few photons. Unlike other protocols, reference frame alignment and active modulation of production and detection bases are unnecessary.
Duru, Kenneth
2014-12-01
© 2014 Elsevier Inc. In this paper, we develop a stable and systematic procedure for numerical treatment of elastic waves in discontinuous and layered media. We consider both planar and curved interfaces where media parameters are allowed to be discontinuous. The key feature is the highly accurate and provably stable treatment of interfaces where media discontinuities arise. We discretize in space using high order accurate finite difference schemes that satisfy the summation by parts rule. Conditions at layer interfaces are imposed weakly using penalties. By deriving lower bounds of the penalty strength and constructing discrete energy estimates we prove time stability. We present numerical experiments in two space dimensions to illustrate the usefulness of the proposed method for simulations involving typical interface phenomena in elastic materials. The numerical experiments verify high order accuracy and time stability.
Radial index of Laguerre-Gaussian modes in high-order-harmonic generation
Géneaux, Romain; Chappuis, Céline; Auguste, Thierry; Beaulieu, Samuel; Gorman, Timothy T.; Lepetit, Fabien; DiMauro, Louis F.; Ruchon, Thierry
2017-05-01
High-order-harmonic generation (HHG) is a tabletop and tunable source of extreme ultraviolet (XUV) light. Its flexibility was lately evidenced by the production of Laguerre-Gaussian (LG) modes in the XUV with a known azimuthal index. Here we investigate the role of the radial index of LG modes in HHG. We show both numerically and experimentally that the mode content of the emitted XUV radiation can be tuned by controlling the weight of the different quantum trajectories involved in the process. The appearance of high-order radial modes is finally linked to the atomic dipole phase of HHG. These results extend the capabilities of shaping the spatial mode of ultrashort XUV pulses of light.
Retrieval of interatomic separations of molecules from laser-induced high-order harmonic spectra
Energy Technology Data Exchange (ETDEWEB)
Le, Van-Hoang; Nguyen, Ngoc-Ty [Department of Physics, University of Pedagogy, 280 An Duong Vuong, Ward 5, Ho Chi Minh City (Viet Nam); Jin, C; Le, Anh-Thu; Lin, C D [J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS 66506 (United States)
2008-04-28
We illustrate an iterative method for retrieving the internuclear separations of N{sub 2}, O{sub 2} and CO{sub 2} molecules using the high-order harmonics generated from these molecules by intense infrared laser pulses. We show that accurate results can be retrieved with a small set of harmonics and with one or few alignment angles of the molecules. For linear molecules the internuclear separations can also be retrieved from harmonics generated using isotropically distributed molecules. By extracting the transition dipole moment from the high-order harmonic spectra, we further demonstrated that it is preferable to retrieve the interatomic separation iteratively by fitting the extracted dipole moment. Our results show that time-resolved chemical imaging of molecules using infrared laser pulses with femtosecond temporal resolutions is possible.
Broadband high-order mode pass filter based on mode conversion.
Ahmmed, Kazi Tanvir; Chan, Hau Ping; Li, Binghui
2017-09-15
We report a unique concept to implement a high-order mode pass filter using mode converters. Our proposed design method implements a high-order mode pass filter of any order, uses different mode converters available, and applies to a variety of planar lightwave circuit material platforms. We fabricate a broadband fundamental mode filter device using a Mach-Zehnder interferometer and Y-junctions to demonstrate our idea. The performance of the fabricated device is demonstrated experimentally in the wavelength range of 1.530-1.565 μm (C-band). This filter exhibits a simulated extinction ratio of 37 dB with an excess loss of 0.52 dB for the first-order mode transmission.
High-order dispersion control of 10-petawatt Ti:sapphire laser facility.
Li, Shuai; Wang, Cheng; Liu, Yanqi; Xu, Yi; Li, Yanyan; Liu, Xingyan; Gan, Zebiao; Yu, Lianghong; Liang, Xiaoyan; Leng, Yuxin; Li, Ruxin
2017-07-24
A grism pair is utilized to control the high-order dispersion of the Shanghai Superintense Ultrafast Lasers Facility, which is a large-scale project aimed at delivering 10-PW laser pulses. We briefly present the characteristics of the laser system and calculate the cumulative B-integral, which determines the nonlinear phase shift influence on material dispersion. Three parameters are selected, grism separation, angle of incidence and slant distance of grating compressor, to determine their optimal values through an iterative searching procedure. Both the numerical and experimental results confirm that the spectral phase distortion is controlled, and the recompressed pulse with a duration of 24 fs is obtained in the single-shot mode. The distributions and stabilities of the pulse duration at different positions of the recompressed beam are also investigated. This approach offers a new feasible solution for the high-order dispersion compensation of femtosecond petawatt laser systems.
European Workshop on High Order Nonlinear Numerical Schemes for Evolutionary PDEs
Beaugendre, Héloïse; Congedo, Pietro; Dobrzynski, Cécile; Perrier, Vincent; Ricchiuto, Mario
2014-01-01
This book collects papers presented during the European Workshop on High Order Nonlinear Numerical Methods for Evolutionary PDEs (HONOM 2013) that was held at INRIA Bordeaux Sud-Ouest, Talence, France in March, 2013. The central topic is high order methods for compressible fluid dynamics. In the workshop, and in this proceedings, greater emphasis is placed on the numerical than the theoretical aspects of this scientific field. The range of topics is broad, extending through algorithm design, accuracy, large scale computing, complex geometries, discontinuous Galerkin, finite element methods, Lagrangian hydrodynamics, finite difference methods and applications and uncertainty quantification. These techniques find practical applications in such fields as fluid mechanics, magnetohydrodynamics, nonlinear solid mechanics, and others for which genuinely nonlinear methods are needed.
High-order finite elements for material and geometric nonlinear finite strain problems
Heisserer, Ulrich
2008-01-01
For the simulation of geometric and material nonlinear problems implicit high-order (p-version) displacement-based finite elements are applied. Besides hyperelastic materials a finite strain viscoplasticity model with internal variables is considered. We apply the combination of Backward-Euler integration and Multilevel-Newton algorithm to solve the system of differential-algebraic equations resulting from the space-discretized weak form. For an efficient modeling of the cold isostatic pressi...
Time implicit high-order discontinuous galerkin method with reduced evaluation cost
Renac, Florent; Marmignon, Claude; Coquel, Frédéric
2012-01-01
International audience; Abstract: An efficient and robust time integration procedure for a high-order discontinuous Galerkin method is introduced for solving nonlinear second-order partial differential equations. The time discretization is based on an explicit formulation for the hyperbolic term and an implicit formulation for the parabolic term. The procedure uses an iterative algorithm with reduced evaluation cost. The size of the linear system to be solved is greatly reduced thanks to par...
Entropy Viscosity Method for High-Order Approximations of Conservation Laws
Guermond, J. L.
2010-09-17
A stabilization technique for conservation laws is presented. It introduces in the governing equations a nonlinear dissipation function of the residual of the associated entropy equation and bounded from above by a first order viscous term. Different two-dimensional test cases are simulated - a 2D Burgers problem, the "KPP rotating wave" and the Euler system - using high order methods: spectral elements or Fourier expansions. Details on the tuning of the parameters controlling the entropy viscosity are given. © 2011 Springer.
Calculation and manipulation of the chirp rates of high-order harmonics
Murakami, M.; Mauritsson, Johan; L'Huillier, Anne; Schafer, KJ; Gaarde, Mette
2005-01-01
We calculate the linear chirp rates of high-order harmonics in argon, generated by intense, 810 nm laser pulses, and explore the dependence of the chirp rate on harmonic order, driving laser intensity, and pulse duration. By using a time-frequency representation of the harmonic fields we can identify several different linear chirp contributions. to the plateau harmonics. Our results, which are based on numerical integration of the time-dependent Schrodinger equation, are in good agreement wit...
Phenylthiourea Modified Highly Ordered Nanoporous Silica for Heavy Metal Ion (Hg2+ Trapping
Directory of Open Access Journals (Sweden)
A. R. Badiei
2012-03-01
Full Text Available The phenylthiourea-substituted triethoxysilane as a silane agent was synthesized and grafted on highly ordered nanoporous silica (LUS- 1 with a textured morphology and hexagonal array. This material (Tu-LUS-1 contained 0.8 mmol/g of soft base phenylthiourea group and surface area 760 m2 g-1 and was able to adsorb 0.75 mmolHg/g of TU-LUS-1 in endothermic reaction.
10th International Conference on Spectral and High-Order Methods
Berzins, Martin; Hesthaven, Jan
2015-01-01
The book contains a selection of high quality papers, chosen among the best presentations during the International Conference on Spectral and High-Order Methods (2014), and provides an overview of the depth and breadth of the activities within this important research area. The carefully reviewed selection of papers will provide the reader with a snapshot of the state-of-the-art and help initiate new research directions through the extensive biography.
Tsunami wave propagation using a high-order well-balanced finite volume scheme
Castro, Cristóbal E.
2010-05-01
In this work we present a new numerical tool suitable for tsunami wave propagation simulations. We developed a finite volume high-order well-balanced numerical method on unstructured meshes based on the ADER-FV scheme [1]. We use the ADER-FV[2,3] scheme to solve with arbitrary accuracy in space and time the shallow water equation with non-constant bathymetry. In order to properly simulate a tsunami wave propagation we introduce the well-balanced or C-property[4] in the high-order numerical solution. In this presentation we address two important issues that appear when one tries to solve a tsunami propagation problem. First, when small gravity waves are propagated for hundred of wave-lengths, the accuracy in space and time of the numerical method is fundamental to preserve the amplitude. In this presentation we study the propagation of small perturbations over long distances, relating the order of accuracy, the mesh dimension and the wave amplitude. Second, as we deal with high-order schemes we can naturally use polynomial representation of the bathymetry. Here we try to understand the influence of the bathymetry representation in the final solution. [1] C. E. Castro et al. "ADER scheme on unstructured meshes for shallow water: simulation of tsunami waves", submitted [2] E. F. Toro et al. "Towards very high order godunov schemes". In E. F. Toro, editor, Godunov methods; Theory and applications, pages 907--940, Oxford, 2001. Kluwer Academic Plenum Publishers. [3] E. F. Toro and V. A. Titarev. "Solution of the generalized Riemann problem for advection-reaction equations". Proc. Roy. Soc. London, pages 271--281, 2002. [4] A. Bermúdez and M. E. Vázquez. "Upwind methods for hyperbolic conservation laws with source terms". Computer and Fluids, 23(8):1049--1071, 1994.
Nonlinear wave-structure interactions with a high-order Boussinesq model
DEFF Research Database (Denmark)
Fuhrman, David R.; Bingham, Harry; Madsen, Per A.
2005-01-01
on a structurally divided domain, and it is shown that exterior corner points pose potential stability problems, as well as other numerical difficulties. These are mainly due to the discretization of high-order mixed-derivative terms near these points, where the flow is theoretically singular. Fortunately......, and highly nonlinear deep water wave run-up on a vertical plate. These cases demonstrate the applicability of the model over a wide range of water depth and nonlinearity....
High-Order Sliding Mode Control for DFIG-Based Wind Turbine Fault Ride-Through
Benbouzid, Mohamed; Beltran, Brice; Amirat, Yassine; Gang, Yao; Jingang, Han; Mangel, Hervé
2013-01-01
International audience; This paper deals with the Fault Ride-Through (FRT) capability assessment of a Doubly-Fed Induction Generator (DFIG)-based Wind Turbine (WT) using High-Order Sliding Mode (HOSM) control. Indeed, it has been recently suggested that sliding mode control is a solution of choice to the FRT problem. In this context, this paper proposes HOSM as an improved solution that handle the classical sliding mode chattering problem. Indeed, the main and attractive features of HOSMs are...
A high-order q-difference equation for q-Hahn multiple orthogonal polynomials
DEFF Research Database (Denmark)
Arvesú, J.; Esposito, Chiara
2012-01-01
A high-order linear q-difference equation with polynomial coefficients having q-Hahn multiple orthogonal polynomials as eigenfunctions is given. The order of the equation coincides with the number of orthogonality conditions that these polynomials satisfy. Some limiting situations when are studie....... Indeed, the difference equation for Hahn multiple orthogonal polynomials given in Lee [J. Approx. Theory (2007), ), doi: 10.1016/j.jat.2007.06.002] is obtained as a limiting case....
Lattice Boltzmann model for high-order nonlinear partial differential equations
Chai, Zhenhua; He, Nanzhong; Guo, Zhaoli; Shi, Baochang
2018-01-01
In this paper, a general lattice Boltzmann (LB) model is proposed for the high-order nonlinear partial differential equation with the form ∂tϕ +∑k=1mαk∂xkΠk(ϕ ) =0 (1 ≤k ≤m ≤6 ), αk are constant coefficients, Πk(ϕ ) are some known differential functions of ϕ . As some special cases of the high-order nonlinear partial differential equation, the classical (m)KdV equation, KdV-Burgers equation, K (n ,n ) -Burgers equation, Kuramoto-Sivashinsky equation, and Kawahara equation can be solved by the present LB model. Compared to the available LB models, the most distinct characteristic of the present model is to introduce some suitable auxiliary moments such that the correct moments of equilibrium distribution function can be achieved. In addition, we also conducted a detailed Chapman-Enskog analysis, and found that the high-order nonlinear partial differential equation can be correctly recovered from the proposed LB model. Finally, a large number of simulations are performed, and it is found that the numerical results agree with the analytical solutions, and usually the present model is also more accurate than the existing LB models [H. Lai and C. Ma, Sci. China Ser. G 52, 1053 (2009), 10.1007/s11433-009-0149-3; H. Lai and C. Ma, Phys. A (Amsterdam) 388, 1405 (2009), 10.1016/j.physa.2009.01.005] for high-order nonlinear partial differential equations.
High-order-harmonic generation in gas with a flat-top laser beam
Energy Technology Data Exchange (ETDEWEB)
Boutu, W.; Auguste, T.; Binazon, L.; Gobert, O.; Carre, B. [Service des Photons, Atomes et Molecules, CEA-Saclay, FR-91191 Gif-sur-Yvette Cedex (France); Boyko, O.; Valentin, C. [Laboratoire d' Optique Appliquee, UMR 7639 ENSTA/CNRS/Ecole Polytechnique, FR-91761 Palaiseau (France); Sola, I.; Constant, E.; Mevel, E. [Universite de Bordeaux, CEA, CNRS UMR 5107, CELIA (Centre Lasers Intenses et Applications), FR-33400 Talence (France); Balcou, Ph. [Laboratoire d' Optique Appliquee, UMR 7639 ENSTA/CNRS/Ecole Polytechnique, FR-91761 Palaiseau (France); Universite de Bordeaux, CEA, CNRS UMR 5107, CELIA (Centre Lasers Intenses et Applications), FR-33400 Talence (France); Merdji, H. [Service des Photons, Atomes et Molecules, CEA-Saclay, FR-91191 Gif-sur-Yvette Cedex (France); PULSE Institute for Ultrafast Energy Science, Stanford Linear Accelerator Center, Stanford University, 2575 Sand Hill Road, Menlo Park, California 94025 (United States)
2011-12-15
We present experimental and numerical results on high-order-harmonic generation with a flat-top laser beam. We show that a simple binary tunable phase plate, made of two concentric glass plates, can produce a flat-top profile at the focus of a Gaussian infrared beam. Both experiments and numerical calculations show that there is a scaling law between the harmonic generation efficiency and the increase of the generation volume.
Low-frequency approximation for high-order harmonic generation by a bicircular laser field
Milošević, D. B.
2018-01-01
We present low-frequency approximation (LFA) for high-order harmonic generation (HHG) process. LFA represents the lowest-order term of an expansion of the final-state interaction matrix element in powers of the laser-field frequency ω . In this approximation the plane-wave recombination matrix element which appears in the strong-field approximation is replaced by the exact laser-free recombination matrix element calculated for the laser-field dressed electron momenta. First, we have shown that the HHG spectra obtained using the LFA agree with those obtained solving the time-dependent Schrödinger equation. Next, we have applied this LFA to calculate the HHG rate for inert gases exposed to a bicircular field. The bicircular field, which consists of two coplanar counter-rotating fields having different frequencies (usually ω and 2 ω ), is presently an important subject of scientific research since it enables efficient generation of circularly polarized high-order harmonics (coherent soft x rays). Analyzing the photorecombination matrix element we have found that the HHG rate can efficiently be calculated using the angular momentum basis with the states oriented in the direction of the bicircular field components. Our numerical results show that the HHG rate for atoms having p ground state, for higher high-order harmonic energies, is larger for circularly polarized harmonics having the helicity -1 . For lower energies the harmonics having helicity +1 prevails. The transition between these two harmonic energy regions can appear near the Cooper minimum, which, in the case of Ar atoms, makes the selection of high-order harmonics having the same helicity much easier. This is important for applications (for example, for generation of attosecond pulse trains of circularly polarized harmonics).
Research on Appraisal System of Procurator Performance by Using High-Order CFA Model
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Yong-mao Huang
2014-01-01
Full Text Available The prosecutor is the main body of procuratorial organs. The performance appraisal system plays an important role in promoting the work efficiency of procurator. In this paper, we establish the performance appraisal system of procurators by high-order confirmatory factor analysis method and evaluate procurators’ performance by fuzzy comprehensive evaluation method based on the 360 degrees. The results have some help to performance management of procuratorial organs.
Laser-induced versus shock wave induced transformation of highly ordered pyrolytic graphite
Pezeril, T.; Bulou, A.; Veysset, David Georges; Kooi, Steven E.; Nelson, Keith Adam
2015-01-01
We demonstrate that in-plane 2D propagation and focusing of a laser-induced shock wave result in enhanced nano-crystallization of highly ordered pyrolytic graphite. Throughout the 2D shock focusing technique, which enables to clearly distinguish between the laser-induced and the shock-induced transformation/transition, our findings establish the role of the shock wave during the transformation/transition process. This configuration could open the way to an alternative path for laser shock fab...
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L. Iaccarino
2011-09-01
Full Text Available Objective: To investigate the reliability of the immunoblot method in the detection of serum immunoreactivity towards the B/B’ polypeptides of U small nuclear ribonucleoproteins (UsnRNP and to assess the significance of these antibodies in connective tissue disease (CTD patients. Methods: We tested the sera of 348 patients with CTD (101 SLE, 51 systemic sclerosis, 53 primary Sjogren’s syndrome, 27 poly/dermatomyositis, 15 rheumatoid arthritis and 101 overlap CTD, of 31 matched healthy subjects and 13 patients with primary Epstein-Barr virus (EBV infection with high titre IgG anti-EBV antibodies. IgG anti-UsnRNP antibodies were determined by immunoblotting on nuclear extract from Raji cells (an EBV-immortalised human B lymphoid cell line and Jurkat cells (a human T lymphoid cell line. Anti-dsDNA antibodies were detected by indirect immunofluorescence on Crithidia luciliae and anti-ENA by counterimmunoelectrophoresis. Anti-dsDNA activity and avidity were measured in SLE sera by ELISA with Scatchard analysis. Results were statistically analysed by chi-square and Mann-Whitney tests. Results: A high frequency of anti-B/B’ antibodies was found in the sera of CTD patients, confined to SLE (54.4% and overlap CTD with SLE features (55,2%. Anti-B/B’ immune reactivity was closely associated with other anti-UsnRNP specificities, gel precipitating anti-nRNP and anti-P antibodies. Nine out of 15 (60% anti-B/B’ positive/anti-ENA negative lupus sera on Raji blots were confirmed to be positive also on Jurkat blots. The sera from patients with EBV infection provided, on Raji blots, completely different band patterns from those obtained with auto-immune sera. Conclusions. The Sm B/B’ proteins are the predominant or, at least, the most frequently targeted antigens of the UsnRNP auto-immune response in SLE and “lupus-like” overlap CTD. Moreover, anti-B/B’ is diagnostically specific for CTD with SLE features. Immunoblotting on human B lymphoid cells
A high-order model of rotating stall in axial compressors with inlet distortion
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Peng LIN
2017-06-01
Full Text Available In this paper, a high-order distortion model is proposed for analyzing the rotating stall inception process induced by inlet distortion in axial compressors. A distortion-generating screen in the compressor inlet is considered. By assuming a quadratic function for the local flow total pressure-drop, the existing Mansoux model is extended to include the effects of static inlet distortion, and a new high-order distortion model is derived. To illustrate the effectiveness of the distortion model, numerical simulations are performed on an eighteenth-order model. It is demonstrated that long length-scale disturbances emerge out of the distorted background flow, and further induce the onset of rotating stall in advance. In addition, the circumferential non-uniform distribution and time evolution of the axial flow are also shown to be consistent with the existing features. It is thus shown that the high-order distortion model is capable of describing the transient behavior of stall inception and will contribute further to stall detection under inlet distortion.
Tanaka, Satoshi; Yoshikawa, Kohji; Minoshima, Takashi; Yoshida, Naoki
2017-11-01
We develop new numerical schemes for Vlasov–Poisson equations with high-order accuracy. Our methods are based on a spatially monotonicity-preserving (MP) scheme and are modified suitably so that the positivity of the distribution function is also preserved. We adopt an efficient semi-Lagrangian time integration scheme that is more accurate and computationally less expensive than the three-stage TVD Runge–Kutta integration. We apply our spatially fifth- and seventh-order schemes to a suite of simulations of collisionless self-gravitating systems and electrostatic plasma simulations, including linear and nonlinear Landau damping in one dimension and Vlasov–Poisson simulations in a six-dimensional phase space. The high-order schemes achieve a significantly improved accuracy in comparison with the third-order positive-flux-conserved scheme adopted in our previous study. With the semi-Lagrangian time integration, the computational cost of our high-order schemes does not significantly increase, but remains roughly the same as that of the third-order scheme. Vlasov–Poisson simulations on {128}3× {128}3 mesh grids have been successfully performed on a massively parallel computer.
Impact of leakage delay on bifurcation in high-order fractional BAM neural networks.
Huang, Chengdai; Cao, Jinde
2018-02-01
The effects of leakage delay on the dynamics of neural networks with integer-order have lately been received considerable attention. It has been confirmed that fractional neural networks more appropriately uncover the dynamical properties of neural networks, but the results of fractional neural networks with leakage delay are relatively few. This paper primarily concentrates on the issue of bifurcation for high-order fractional bidirectional associative memory(BAM) neural networks involving leakage delay. The first attempt is made to tackle the stability and bifurcation of high-order fractional BAM neural networks with time delay in leakage terms in this paper. The conditions for the appearance of bifurcation for the proposed systems with leakage delay are firstly established by adopting time delay as a bifurcation parameter. Then, the bifurcation criteria of such system without leakage delay are successfully acquired. Comparative analysis wondrously detects that the stability performance of the proposed high-order fractional neural networks is critically weakened by leakage delay, they cannot be overlooked. Numerical examples are ultimately exhibited to attest the efficiency of the theoretical results. Copyright © 2017 Elsevier Ltd. All rights reserved.
Minimum in the high-order harmonic generation spectrum from molecules: role of excited states
DEFF Research Database (Denmark)
Han, Yong-Chang; Madsen, Lars Bojer
2010-01-01
that the coherent laser coupling induced between the 2Σ+g(1sσg) ground state and the first excited 2Σ+u(2pσu) state leads to two dominating amplitudes for the high-order harmonic generation that may interfere: amplitudes describing recombination back into the σg and σu states, respectively. These two amplitudes may......We model the process of high-order harmonic generation by solving the time-dependent Schrödinger equation for H+2 in the fixed nuclei approximation including full 3D electron motion for nonvanishing angles between the nuclear axis and the linear polarization of the driving pulse. We show...... interfere destructively or constructively. The effect of a destructive interference is very clear through the occurrence of a minimum in the high-order harmonic spectrum. We show cases where such a minimum in the spectrum is approximately at the position predicted by the simple two-centre interference...
Energy Technology Data Exchange (ETDEWEB)
Wang, Guanghui, E-mail: gsnuwgh@163.com; Zhang, Weifeng; Lu, Jiahui; Zhao, Huijun
2016-08-12
We analytically study dispersion properties and optical gradient forces of different-order transverse magnetic (TM) modes in two coupled hyperbolic metamaterial waveguides (HMMWs). According to Maxwell's equations, we obtain the dispersion relation of symmetric and antisymmetric modes, and calculate optical gradient forces of different-order modes by using Maxwell stress tensor. Numerical results show that the dispersion properties are dependent on the filling ratio, and the optical gradient forces of high-order TM modes are larger than the fundamental mode when the gap between two HMMWs is very narrow, but they weaken much faster than the case of low-order TM modes with the gap width increasing. In addition, the effects of the dielectric surrounding of waveguides on the coupling effect and optical gradient force are clarified. These properties offer an avenue for various optomechanical applications in optical sensors and actuators. - Highlights: • The dependence of dispersion properties in hyperbolic metamaterials on the filling ratio is analyzed. • It is possible that the optical gradient forces of high-order modes are larger than the fundamental mode. • Optical gradient forces of high-order modes weaken much faster than the case of low-order modes. • The influence of the dielectric surrounding on the coupling effect and optical gradient force are clarified.
Narrow-bandwidth high-order harmonics driven by long-duration hot spots
Kozlov, Maxim; Kfir, Ofer; Fleischer, Avner; Kaplan, Alex; Carmon, Tal; Schwefel, Harald G. L.; Bartal, Guy; Cohen, Oren
2012-06-01
We predict and investigate the emission of high-order harmonics by atoms that cross intense laser hot spots that last for a nanosecond or longer. An atom that moves through a nanometer-scale hot spot at characteristic thermal velocity can emit high-order harmonics in a similar fashion to an atom that is irradiated by a short-duration (picosecond-scale) laser pulse. We analyze the collective emission from a thermal gas and from a jet of atoms. In both cases, the line shape of a high-order harmonic exhibits a narrow spike with spectral width that is determined by the bandwidth of the driving laser. Finally, we discuss a scheme for producing long-duration laser hot spots with intensity in the range of the intensity threshold for high-harmonic generation. In the proposed scheme, the hot spot is produced by a long laser pulse that is consecutively coupled to a high-quality micro-resonator and a metallic nano-antenna. This system may be used for generating ultra-narrow bandwidth extreme-ultraviolet radiation through frequency up-conversion of a low-cost compact pump laser.
Energy Technology Data Exchange (ETDEWEB)
Rieben, Robert N. [Univ. of California, Davis, CA (United States)
2004-01-01
The goal of this dissertation is two-fold. The first part concerns the development of a numerical method for solving Maxwell's equations on unstructured hexahedral grids that employs both high order spatial and high order temporal discretizations. The second part involves the use of this method as a computational tool to perform high fidelity simulations of various electromagnetic devices such as optical transmission lines and photonic crystal structures to yield a level of accuracy that has previously been computationally cost prohibitive. This work is based on the initial research of Daniel White who developed a provably stable, charge and energy conserving method for solving Maxwell's equations in the time domain that is second order accurate in both space and time. The research presented here has involved the generalization of this procedure to higher order methods. High order methods are capable of yielding far more accurate numerical results for certain problems when compared to corresponding h-refined first order methods , and often times at a significant reduction in total computational cost. The first half of this dissertation presents the method as well as the necessary mathematics required for its derivation. The second half addresses the implementation of the method in a parallel computational environment, its validation using benchmark problems, and finally its use in large scale numerical simulations of electromagnetic transmission devices.
New Stability Criteria for High-Order Neural Networks with Proportional Delays
Xu, Chang-Jin; Li, Pei-Luan
2017-03-01
This paper is concerned with high-order neural networks with proportional delays. The proportional delay is a time-varying unbounded delay which is different from the constant delay, bounded time-varying delay and distributed delay. By the nonlinear transformation {y}i(t)={u}i({{{e}}}t){{ }}(i=1,2,\\ldots ,n), we transform a class of high-order neural networks with proportional delays into a class of high-order neural networks with constant delays and time-varying coefficients. With the aid of Brouwer fixed point theorem and constructing the delay differential inequality, we obtain some delay-independent and delay-dependent sufficient conditions to ensure the existence, uniqueness and global exponential stability of equilibrium of the network. Two examples with their simulations are given to illustrate the theoretical findings. Our results are new and complement previously known results. Supported by National Natural Science Foundation of China under Grant Nos. 61673008 and 11261010, and Project of High-level Innovative Talents of Guizhou Province ([2016]5651)
A high-order 3D spectral difference solver for simulating flows about rotating geometries
Zhang, Bin; Liang, Chunlei
2017-11-01
Fluid flows around rotating geometries are ubiquitous. For example, a spinning ping pong ball can quickly change its trajectory in an air flow; a marine propeller can provide enormous amount of thrust to a ship. It has been a long-time challenge to accurately simulate these flows. In this work, we present a high-order and efficient 3D flow solver based on unstructured spectral difference (SD) method and a novel sliding-mesh method. In the SD method, solution and fluxes are reconstructed using tensor products of 1D polynomials and the equations are solved in differential-form, which leads to high-order accuracy and high efficiency. In the sliding-mesh method, a computational domain is decomposed into non-overlapping subdomains. Each subdomain can enclose a geometry and can rotate relative to its neighbor, resulting in nonconforming sliding interfaces. A curved dynamic mortar approach is designed for communication on these interfaces. In this approach, solutions and fluxes are projected from cell faces to mortars to compute common values which are then projected back to ensures continuity and conservation. Through theoretical analysis and numerical tests, it is shown that this solver is conservative, free-stream preservative, and high-order accurate in both space and time.
Time-Frequency Analysis Using Warped-Based High-Order Phase Modeling
Directory of Open Access Journals (Sweden)
Ioana Cornel
2005-01-01
Full Text Available The high-order ambiguity function (HAF was introduced for the estimation of polynomial-phase signals (PPS embedded in noise. Since the HAF is a nonlinear operator, it suffers from noise-masking effects and from the appearance of undesired cross-terms when multicomponents PPS are analyzed. In order to improve the performances of the HAF, the multi-lag HAF concept was proposed. Based on this approach, several advanced methods (e.g., product high-order ambiguity function (PHAF have been recently proposed. Nevertheless, performances of these new methods are affected by the error propagation effect which drastically limits the order of the polynomial approximation. This phenomenon acts especially when a high-order polynomial modeling is needed: representation of the digital modulation signals or the acoustic transient signals. This effect is caused by the technique used for polynomial order reduction, common for existing approaches: signal multiplication with the complex conjugated exponentials formed with the estimated coefficients. In this paper, we introduce an alternative method to reduce the polynomial order, based on the successive unitary signal transformation, according to each polynomial order. We will prove that this method reduces considerably the effect of error propagation. Namely, with this order reduction method, the estimation error at a given order will depend only on the performances of the estimation method.
Schreiber, Claire A; Sakuma, Toshie; Izumiya, Yoshihiro; Holditch, Sara J; Hickey, Raymond D; Bressin, Robert K; Basu, Upamanyu; Koide, Kazunori; Asokan, Aravind; Ikeda, Yasuhiro
2015-08-01
Adeno-associated viruses (AAV) have evolved to exploit the dynamic reorganization of host cell machinery during co-infection by adenoviruses and other helper viruses. In the absence of helper viruses, host factors such as the proteasome and DNA damage response machinery have been shown to effectively inhibit AAV transduction by restricting processes ranging from nuclear entry to second-strand DNA synthesis. To identify host factors that might affect other key steps in AAV infection, we screened an siRNA library that revealed several candidate genes including the PHD finger-like domain protein 5A (PHF5A), a U2 snRNP-associated protein. Disruption of PHF5A expression selectively enhanced transgene expression from AAV by increasing transcript levels and appears to influence a step after second-strand synthesis in a serotype and cell type-independent manner. Genetic disruption of U2 snRNP and associated proteins, such as SF3B1 and U2AF1, also increased expression from AAV vector, suggesting the critical role of U2 snRNP spliceosome complex in this host-mediated restriction. Notably, adenoviral co-infection and U2 snRNP inhibition appeared to target a common pathway in increasing expression from AAV vectors. Moreover, pharmacological inhibition of U2 snRNP by meayamycin B, a potent SF3B1 inhibitor, substantially enhanced AAV vector transduction of clinically relevant cell types. Further analysis suggested that U2 snRNP proteins suppress AAV vector transgene expression through direct recognition of intact AAV capsids. In summary, we identify U2 snRNP and associated splicing factors, which are known to be affected during adenoviral infection, as novel host restriction factors that effectively limit AAV transgene expression. Concurrently, we postulate that pharmacological/genetic manipulation of components of the spliceosomal machinery might enable more effective gene transfer modalities with recombinant AAV vectors.
mRNP assembly, axonal transport, and local translation in neurodegenerative diseases.
Khalil, Bilal; Morderer, Dmytro; Price, Phillip L; Liu, Feilin; Rossoll, Wilfried
2018-02-17
The development, maturation, and maintenance of the mammalian nervous system rely on complex spatiotemporal patterns of gene expression. In neurons, this is achieved by the expression of differentially localized isoforms and specific sets of mRNA-binding proteins (mRBPs) that regulate RNA processing, mRNA trafficking, and local protein synthesis at remote sites within dendrites and axons. There is growing evidence that axons contain a specialized transcriptome and are endowed with the machinery that allows them to rapidly alter their local proteome via local translation and protein degradation. This enables axons to quickly respond to changes in their environment during development, and to facilitate axon regeneration and maintenance in adult organisms. Aside from providing autonomy to neuronal processes, local translation allows axons to send retrograde injury signals to the cell soma. In this review, we discuss evidence that disturbances in mRNP transport, granule assembly, axonal localization, and local translation contribute to pathology in various neurodegenerative diseases, including spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease (AD). Copyright © 2018. Published by Elsevier B.V.
Ganeev, R. A.
2017-06-01
Various recently emerged applications of mid-infrared pulses for high-order harmonic generation in laser plasmas produced on the surfaces of various materials are reviewed. Among them are (a) the highorder harmonic generation in Ag, Sn, fullerene, and graphene nanoparticle-containing plasmas using tunable two-color mid-infrared pulses, (b) efficiency dependence on the generating particle properties in the case of two-color high-harmonic generation of the longer-wavelength radiation in the plasmas, and (c) high-order sum and difference frequency generation using tunable two- and three-color commensurate and incommensurate mid-infrared pumps of graphite plasma. These studies demonstrate the perspectives of the frequency conversion of mid-infrared radiation in the extended laser-produced plasmas.
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Bing Wei
Full Text Available Based on high order hierarchical basis function and the ideal of shift operator, shift operator discontinuous Galerkin time domain (SO-DGTD technique for dealing with weakly ionized dusty plasma electromagnetic problems is proposed. Lagrange interpolation is used to transform the metallic blunt cone aircraft with weakly ionized dusty plasma sheath from geometric model built by COMSOL to electromagnetic computational model. In the case of two-dimensional transverse magnetic (TM wave, the electromagnetic wave propagation in weakly ionized dusty plasma sheath is calculated by SO-DGTD technique. And then, the influence of dust particle concentration and dust radius on the radio wave transmission is analyzed, and the radio wave propagation characteristics pass through the sheath is compared with the flight speed and height change. Keywords: SO-DGTD, Weakly ionized dusty plasma sheath, High order hierarchical basis function
An improved 2D MoF method by using high order derivatives
Chen, Xiang; Zhang, Xiong
2017-11-01
The MoF (Moment of Fluid) method is one of the most accurate approaches among various interface reconstruction algorithms. Alike other second order methods, the MoF method needs to solve an implicit optimization problem to obtain the optimal approximate interface, so an iteration process is inevitable under most circumstances. In order to solve the optimization efficiently, the properties of the objective function are worthy of studying. In 2D problems, the first order derivative has been deduced and applied in the previous researches. In this paper, the high order derivatives of the objective function are deduced on the convex polygon. We show that the nth (n ≥ 2) order derivatives are discontinuous, and the number of the discontinuous points is two times the number of the polygon edge. A rotation algorithm is proposed to successively calculate these discontinuous points, thus the target interval where the optimal solution is located can be determined. Since the high order derivatives of the objective function are continuous in the target interval, the iteration schemes based on high order derivatives can be used to improve the convergence rate. Moreover, when iterating in the target interval, the value of objective function and its derivatives can be directly updated without explicitly solving the volume conservation equation. The direct update makes a further improvement of the efficiency especially when the number of edges of the polygon is increasing. The Halley's method, which is based on the first three order derivatives, is applied as the iteration scheme in this paper and the numerical results indicate that the CPU time is about half of the previous method on the quadrilateral cell and is about one sixth on the decagon cell.
Liu, Xiaolin; Lauer, Kathryn K; Ward, Barney D; Rao, Stephen M; Li, Shi-Jiang; Hudetz, Anthony G
2012-10-01
Current theories suggest that disrupting cortical information integration may account for the mechanism of general anesthesia in suppressing consciousness. Human cognitive operations take place in hierarchically structured neural organizations in the brain. The process of low-order neural representation of sensory stimuli becoming integrated in high-order cortices is also known as cognitive binding. Combining neuroimaging, cognitive neuroscience, and anesthetic manipulation, we examined how cognitive networks involved in auditory verbal memory are maintained in wakefulness, disrupted in propofol-induced deep sedation, and re-established in recovery. Inspired by the notion of cognitive binding, an functional magnetic resonance imaging-guided connectivity analysis was utilized to assess the integrity of functional interactions within and between different levels of the task-defined brain regions. Task-related responses persisted in the primary auditory cortex (PAC), but vanished in the inferior frontal gyrus (IFG) and premotor areas in deep sedation. For connectivity analysis, seed regions representing sensory and high-order processing of the memory task were identified in the PAC and IFG. Propofol disrupted connections from the PAC seed to the frontal regions and thalamus, but not the connections from the IFG seed to a set of widely distributed brain regions in the temporal, frontal, and parietal lobes (with exception of the PAC). These later regions have been implicated in mediating verbal comprehension and memory. These results suggest that propofol disrupts cognition by blocking the projection of sensory information to high-order processing networks and thus preventing information integration. Such findings contribute to our understanding of anesthetic mechanisms as related to information and integration in the brain. Copyright © 2011 Wiley Periodicals, Inc.
Lin, Zhiqun; Byun, Myunghwan; Hong, Suck Won
2009-03-01
We demonstrate a robust, one-step method of evaporating polymer solutions in curve-on-flat geometries to create versatile, highly regular microstructures in a precisely controlled environment, as well as offering a comprehensive study of the influence of different upper surfaces on complex structure formation via controlled evaporation. Our method further enhances current fabrication approaches to creating highly ordered structures in a simple and cost-effective manner, with the potential to be tailored for use in photonics, electronics, optoelectronics, microfluidic devices, nanotechnology, and biotechnology.
HIERtalker: A default hierarchy of high order neural networks that learns to read English aloud
Energy Technology Data Exchange (ETDEWEB)
An, Z.G.; Mniszewski, S.M.; Lee, Y.C.; Papcun, G.; Doolen, G.D.
1988-01-01
A new learning algorithm based on a default hierarchy of high order neural networks has been developed that is able to generalize as well as handle exceptions. It learns the ''building blocks'' or clusters of symbols in a stream that appear repeatedly and convey certain messages. The default hierarchy prevents a combinatoric explosion of rules. A simulator of such a hierarchy, HIERtalker, has been applied to the conversion of English words to phonemes. Achieved accuracy is 99% for trained words and ranges from 76% to 96% for sets of new words. 8 refs., 4 figs., 1 tab.
High-order FDTD methods for transverse electromagnetic systems in dispersive inhomogeneous media.
Zhao, Shan
2011-08-15
This Letter introduces a novel finite-difference time-domain (FDTD) formulation for solving transverse electromagnetic systems in dispersive media. Based on the auxiliary differential equation approach, the Debye dispersion model is coupled with Maxwell's equations to derive a supplementary ordinary differential equation for describing the regularity changes in electromagnetic fields at the dispersive interface. The resulting time-dependent jump conditions are rigorously enforced in the FDTD discretization by means of the matched interface and boundary scheme. High-order convergences are numerically achieved for the first time in the literature in the FDTD simulations of dispersive inhomogeneous media. © 2011 Optical Society of America
XUV digital in-line holography using high-order harmonics
Genoud, G.; Guilbaud, O.; Mengotti, E.; Pettersson, S.-G.; Georgiadou, E.; Pourtal, E.; Wahlström, C.-G.; L'Huillier, A.
2008-03-01
A step towards a successful implementation of time-resolved digital in-line holography with extreme ultraviolet (XUV) radiation is presented. Ultra-short XUV pulses are produced as high-order harmonics of a femtosecond laser and a Schwarzschild objective is used to focus harmonic radiation at 38 nm and to produce a strongly divergent reference beam for holographic recording. Experimental holograms of thin wires are recorded and the objects reconstructed. Descriptions of the simulation and reconstruction theory and algorithms are also given. Spatial resolution of a few hundreds of nanometers is potentially achievable, and the micrometer resolution range is demonstrated.
Distributed Finite-Time Cooperative Control of Multiple High-Order Nonholonomic Mobile Robots.
Du, Haibo; Wen, Guanghui; Cheng, Yingying; He, Yigang; Jia, Ruting
2017-12-01
The consensus problem of multiple nonholonomic mobile robots in the form of high-order chained structure is considered in this paper. Based on the model features and the finite-time control technique, a finite-time cooperative controller is explicitly constructed which guarantees that the states consensus is achieved in a finite time. As an application of the proposed results, finite-time formation control of multiple wheeled mobile robots is studied and a finite-time formation control algorithm is proposed. To show effectiveness of the proposed approach, a simulation example is given.
Nodal DG-FEM solution of high-order Boussinesq-type equations
DEFF Research Database (Denmark)
Engsig-Karup, Allan Peter; Hesthaven, Jan S.; Bingham, Harry B.
2006-01-01
We present a discontinuous Galerkin finite element method (DG-FEM) solution to a set of high-order Boussinesq-type equations for modelling highly nonlinear and dispersive water waves in one and two horizontal dimensions. The continuous equations are discretized using nodal polynomial basis...... and convergence of the model with both h (grid size) and p (order) refinement are verified for the linearized equations, and calculations are provided for two nonlinear test cases in one horizontal dimension: harmonic generation over a submerged bar; and reflection of a steep solitary wave from a vertical wall...
Photoemission with high-order harmonics: A tool for time-resolved core-level spectroscopy
DEFF Research Database (Denmark)
Christensen, Bjarke Holl; Raarup, Merete Krog; Balling, Peter
2010-01-01
A setup for femtosecond time-resolved photoelectron spectroscopy of solid surfaces is presented. The photon energies for core-level spectroscopy experiments are created by high-order harmonic generation from infrared 120-femtosecond laser pulses focused in a Ne gas jet. The present experimental...... realization allows the sample, located in an ultrahigh-vacuum chamber, to be illuminated by 106 65-eV photons per laser pulse at a 10 Hz repetition rate. The spectral width of a single harmonic is 0.77 eV (FWHM), and a few harmonics are selected by specially designed Mo/Si multi-layer mirrors. Photoelectrons...
Rigorous study of supercontinuum generation by high-order optical modes
Ben Salem, Amine; Trichili, Abderrahmen; Cherif, Rim; Zghal, Mourad
2016-09-01
We numerically study the supercontinuum (SC) generation in a six modes photonic crystal fiber (PCF). By solving the multimode generalised Schrdinger equation, we demonstrate the generation of SC by initially exciting the fundamental mode or one of the higher order modes and then observe the energy transfer to the other high order modes. We analyze the energy transfer between degenerate modes during propagation through the few mode PCF. A detailed investigation of the nonlinear effects on the SC process through linear and nonlinear coupling is provided which confirms the energy transfer between optical degenerate modes during propagation inside the few- mode fiber.
Discrete-time adaptive backstepping nonlinear control via high-order neural networks.
Alanis, Alma Y; Sanchez, Edgar N; Loukianov, Alexander G
2007-07-01
This paper deals with adaptive tracking for discrete-time multiple-input-multiple-output (MIMO) nonlinear systems in presence of bounded disturbances. In this paper, a high-order neural network (HONN) structure is used to approximate a control law designed by the backstepping technique, applied to a block strict feedback form (BSFF). This paper also includes the respective stability analysis, on the basis of the Lyapunov approach, for the whole controlled system, including the extended Kalman filter (EKF)-based NN learning algorithm. Applicability of the scheme is illustrated via simulation for a discrete-time nonlinear model of an electric induction motor.
High-order Boussinesq-type modelling of nonlinear wave phenomena in deep and shallow water
DEFF Research Database (Denmark)
Madsen, Per A.; Fuhrman, David R.
2010-01-01
In this work, we start with a review of the development of Boussinesq theory for water waves covering the period from 1872 to date. Previous reviews have been given by Dingemans,1 Kirby,2,3 and Madsen & Schäffer.4 Next, we present our most recent high-order Boussinesq-type formulation valid...... for fully nonlinear and highly dispersive waves traveling over a rapidly varying bathymetry. Finally, we cover applications of this Boussinesq model, and we study a number of nonlinear wave phenomena in deep and shallow water. These include (1) Kinematics in highly nonlinear progressive deep-water waves; (2...
Synchronization of a coupled Hodgkin-Huxley neurons via high order sliding-mode feedback
Energy Technology Data Exchange (ETDEWEB)
Aguilar-Lopez, R. [Division de Ciencias Basicas e Ingenieria, Universidad Autonoma Metropolitana, Av. San Pablo No. 180, Reynosa-Tamaulipas, 02200 Azcapotzalco, Mexico, D.F. (Mexico)], E-mail: raguilar@correo.azc.uam.mx; Martinez-Guerra, R. [Departamento de Control Automatico, CINVESTAV-IPN, Apartado Postal 14-740, Mexico, D.F. C.P. 07360 (Mexico)], E-mail: rguerra@ctrl.cinvestav.mx
2008-07-15
This work deals with the synchronizations of two both coupled Hodgkin-Huxley (H-H) neurons, where the master neuron posses inner noise and the slave neuron is considered in a resting state, (without inner noise) and an exciting state (with inner noise). The synchronization procedure is done via a feedback control, considering a class of high order sliding-mode controller which provides chattering reduction and finite time synchronization convergence, with a satisfactory performance. Theoretical analysis is done in order to show the closed-loop stability of the proposed controller and the calculated finite time for convergence. The main results are illustrated via numerical experiments.
Prediction model of sinoatrial node field potential using high order partial least squares.
Feng, Yu; Cao, Hui; Zhang, Yanbin
2015-01-01
High order partial least squares (HOPLS) is a novel data processing method. It is highly suitable for building prediction model which has tensor input and output. The objective of this study is to build a prediction model of the relationship between sinoatrial node field potential and high glucose using HOPLS. The three sub-signals of the sinoatrial node field potential made up the model's input. The concentration and the actuation duration of high glucose made up the model's output. The results showed that on the premise of predicting two dimensional variables, HOPLS had the same predictive ability and a lower dispersion degree compared with partial least squares (PLS).
Simulation of vesicle using level set method solved by high order finite element
Directory of Open Access Journals (Sweden)
Doyeux Vincent
2013-01-01
Full Text Available We present a numerical method to simulate vesicles in fluid flows. This method consists of writing all the properties of the membrane as interfacial forces between two fluids. The main advantage of this approach is that the vesicle and the fluid models may be decoupled easily. A level set method has been implemented to track the interface. Finite element discretization has been used with arbitrarily high order polynomial approximation. Several polynomial orders have been tested in order to get a better accuracy. A validation on equilibrium shapes and “tank treading” motion of vesicle have been presented.
High Order Sliding Mode Control of Doubly-fed Induction Generator under Unbalanced Grid Faults
DEFF Research Database (Denmark)
Zhu, Rongwu; Chen, Zhe; Wu, Xiaojie
2013-01-01
This paper deals with a doubly-fed induction generator-based (DFIG) wind turbine system under grid fault conditions such as: unbalanced grid voltage, three-phase grid fault, using a high order sliding mode control (SMC). A second order sliding mode controller, which is robust with respect...... to matched internal or external disturbances, fast transient response and finite reaching time, is employed to reduce chattering phenomenon caused by high frequency switching of SMC, which serious exists in lower order SMC, and to overcome parameter dependence of traditional proportional integral (PI...
Comparison of high order modes damping techniques for 800 MHz single cell superconducting cavities
Shashkov, Ya V; Zobov, M M
2014-01-01
Currently, applications of 800 MHz harmonic cavities in both bunch lengthening and shortening regimes are under consideration and discussion in the framework of the High Luminosity LHC project. In this paper we study electromagnetic characteristics of high order modes (HOM) for a single cell 800 MHz superconducting cavity and arrays of such cavities connected by drifts tubes. Different techniques for the HOM damping such as beam pipe grooves, coaxial-notch loads, fluted beam pipes etc. are investigated and compared. The influence of the sizes and geometry of the drift tubes on the HOM damping is analyzed.
Panourgias, Konstantinos T.; Ekaterinaris, John A.
2016-12-01
The nonlinear filter introduced by Yee et al. (1999) [27] and extensively used in the development of low dissipative well-balanced high order accurate finite-difference schemes is adapted to the finite element context of discontinuous Galerkin (DG) discretizations. The filter operator is constructed in the canonical computational domain for the standard cubical element where it is applied to the computed conservative variables in a direction per direction basis. Filtering becomes possible for all element types in unstructured meshes using collapsed coordinate transformations. The performance of the proposed nonlinear filter for DG discretizations is demonstrated and evaluated for different orders of expansions for one-dimensional and multidimensional problems with exact solutions. It is shown that for higher order discretizations discontinuity resolution within the cell is achieved and the design order of accuracy is preserved. The filter is applied for a number of standard inviscid flow test problems including strong shocks interactions to demonstrate that the proposed dissipative mechanism for DG discretizations yields superior results compared to the results obtained with the total variation bounded (TVB) limiter and high-order hierarchical limiting. The proposed approach is suitable for p-adaptivity in order to locally enhance resolution of three-dimensional flow simulations that include discontinuities and complex flow features.
Mei, Peng; Pramanik, Malay; Lee, Jaewoo; Ide, Yusuke; Alothman, Zeid Abdullah; Kim, Jung Ho; Yamauchi, Yusuke
2017-03-28
Highly ordered mesostructured vanadium phosphonates (VP) have been synthesized in the presence of cetyltrimethylammonium bromide (CTAB) as a structure-directing agent. Nitrilotris(methylene)triphosphonic acid (NMPA) and (ammonium/sodium) metavanadate (NH4 VO3 /NaVO3 ) have been used for the construction of pore walls. The CTAB templates are removed from the materials by an extraction process without destroying the parent mesostructure. The formation mechanism for the ordered mesoporous structure and its impact on electrochemical application in lithium ion batteries (LIBs) are explained by considering the structural and electrochemical stability of the framework. The results demonstrate that the counter cations (NH4+ /Na+ ) of the metavanadate precursors have a crucial role in stabilizing the mesoporous structure of the mesoporous VP materials. Mesoporous VP materials with highly ordered structure have great applicability as high-performance electrode materials in LIBs due to the advantages of their large contact area with electrolyte and short transport paths for lithium ions. Mesoporous VP electrodes exhibit high reversible specific capacity with superb cycling stability (100 cycles) and excellent retention of capacity (92 %). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Highly Ordered Block Copolymer Templates for the Generation of Nanostructured Materials
Bhoje Gowd, E.; Nandan, Bhanu; Bigall, Nadja C.; Eychmuller, Alexander; Stamm, Manfred
2009-03-01
Among many different types of self-assembled materials, block copolymers have attracted immense interest for applications in nanotechnology. Block copolymer thin film can be used as a template for patterning of hard inorganic materials such as metal nanoparticles. In the present work, we demonstrate a new approach to fabricate highly ordered arrays of nanoscopic inorganic dots and wires using switchable block copolymer thin films. Various inorganic nanoparticles from a simple aqueous solution were directly deposited on the surface reconstructed block copolymer templates. The preferential interaction of the nanoparticles with one of the blocks is mainly responsible for the lateral distribution of the nanoparticles in addition to the capillary forces. Subsequent stabilization by UV-irradiation followed by pyrolysis in air at 450 ^oC removes the polymer to produce highly ordered metallic nanostructures. This method is highly versatile as the procedure used here is simple, eco-friendly and provides a facile approach to fabricate a broad range of nanoscaled architectures with tunable lateral spacing.
Chahrour, Khaled M.; Ahmed, Naser M.; Hashim, M. R.; Elfadill, Nezar G.; Qaeed, M. A.
2014-09-01
In this work, simple fabrication of hexagonally highly ordered porous anodic aluminum oxide (AAO) of Al thin film (1 μm) on Si substrate is described using two-step anodization method for electrochemical synthesis of nanostructures. In this method, the templates were prepared under the controllable conditions of the parameters, which give rise to the possibility of highly ordered nanopore arrays with a well aspect ratio. Pore widening was then fulfilled in 5 wt% phosphoric acid solution at 25 °C. The pore diameter and spacing are proportional to the applied voltage, which is due to the mechanical stress associated with the volume expansion of the aluminum during the anodization according to the mechanical stress model. Pore-widening solution adjusted the pore diameter and thinned the AAO barrier layer at room temperature under the control of etching time. As an application, Cu nanorods arrays embedded in anodic alumina (AAO) template were fabricated by dc electrodeposition. The characterization of the AAO templates and the Cu nanorods produced was made by X-ray diffraction, field emission scanning microscope, energy dispersive X-ray spectroscopy and atomic force microscope (AFM). The images of AFM show that porous AAO template under constant voltage is 40 V which presents the optimum ordering.
High-order mode based dispersion compensating modules using spatial mode conversion
Tur, M.; Menashe, D.; Japha, Y.; Danziger, Y.
High-Order Mode Dispersion Compensating Modules (HOM-DCM) using spatial optical transformations for mode conversion are reviewed. It is shown that mode transformers using this technology can be designed to transform the LP01 mode of SMF fibers to the LP02 mode of specially designed dispersion compensating High-Order Mode Fiber (HOMF), with typical insertion loss of ~1 dB, and typical extinction ratio to other modes less than -20 dB.TheHOMFitself can provide high negative dispersion [typically in the range of 400-600 ps/(nm km)], and high negative dispersion slope, allowing efficient compensation of all types of transmission fiber. Combining two mode transformers with HOMF and possibly trim fiber for fine-tuning, results, for example, in a HOM-DCM that compensates 100 km LEAF R ® fiber, with Insertion loss mode transformers and fiber coupling within the HOMF. MPI values of < -36 dB have been shown to allow error free transmission of 10 Gb/s signals over up to 6000 km. Finally, a number of applications well suited to the properties of HOM-DCMs are reviewed.
Shah, Syed Awais Wahab
2017-11-24
This paper addresses the problem of blind demixing of instantaneous mixtures in a multiple-input multiple-output communication system. The main objective is to present efficient blind source separation (BSS) algorithms dedicated to moderate or high-order QAM constellations. Four new iterative batch BSS algorithms are presented dealing with the multimodulus (MM) and alphabet matched (AM) criteria. For the optimization of these cost functions, iterative methods of Givens and hyperbolic rotations are used. A pre-whitening operation is also utilized to reduce the complexity of design problem. It is noticed that the designed algorithms using Givens rotations gives satisfactory performance only for large number of samples. However, for small number of samples, the algorithms designed by combining both Givens and hyperbolic rotations compensate for the ill-whitening that occurs in this case and thus improves the performance. Two algorithms dealing with the MM criterion are presented for moderate order QAM signals such as 16-QAM. The other two dealing with the AM criterion are presented for high-order QAM signals. These methods are finally compared with the state of art batch BSS algorithms in terms of signal-to-interference and noise ratio, symbol error rate and convergence rate. Simulation results show that the proposed methods outperform the contemporary batch BSS algorithms.
Multi-Block Computation by Characteristic Interface Conditions with High-Order Interpolation
Sumi, Takahiro; Kurotaki, Takuji; Hiyama, Jun
In the previous study, the authors proposed the generalized characteristic interface conditions (GCIC) for high-order finite difference multi-block computation in the structured grid system. The GCIC can realize single point connection between adjacent blocks, and allows metric discontinuities on the block interface, however, the grid points of the adjacent blocks have to be collocated correspondingly on the block interface. In this study, in order to enhance the flexibility of the GCIC, by incorporating the high-order interpolation method such as the Lagrange or B-spline interpolation, the GCIC+I (GCIC with Interpolation) are newly developed and introduced. The GCIC+I can solve multi-block problem with non-uniform staggered grid connection on the block interface, and the grid resolution can be arbitrarily changed in each block. In this article, their theoretical concept is briefly presented, and suitable numerical test analysis of inviscid or viscous flow is conducted in order to validate the proposed theory. As a result, the successful functions of the GCIC+I are confirmed.
Optimal Design of High-Order Passive-Damped Filters for Grid-Connected Applications
DEFF Research Database (Denmark)
Beres, Remus Narcis; Wang, Xiongfei; Blaabjerg, Frede
2016-01-01
Harmonic stability problems caused by the resonance of high-order filters in power electronic systems are ever increasing. The use of passive damping does provide a robust solution to address these issues, but at the price of reduced efficiency due to the presence of additional passive components...... filter resonance. The passive filters are designed, built and validated both analytically and experimentally for verification........ Hence, a new method is proposed in this paper to optimally design the passive damping circuit for the LCL filters and LCL with multi-tuned LC traps. In short, the optimization problem reduces to the proper choice of the multi-split capacitors or inductors in the high-order filter. Compared to existing...... design procedures, the proposed method simplifies the iterative design of the overall filter while ensuring the minimum resonance peak with a lower damping capacitor and a lower rated resistor. It is shown that there is only one optimal value of the damping resistor or quality factor to achieve a minimum...
The hnRNP-Q protein LIF2 participates in the plant immune response.
Directory of Open Access Journals (Sweden)
Clémentine Le Roux
Full Text Available Eukaryotes have evolved complex defense pathways to combat invading pathogens. Here, we investigated the role of the Arabidopsis thaliana heterogeneous nuclear ribonucleoprotein (hnRNP-Q LIF2 in the plant innate immune response. We show that LIF2 loss-of-function in A. thaliana leads to changes in the basal expression of the salicylic acid (SA- and jasmonic acid (JA- dependent defense marker genes PR1 and PDF1.2, respectively. Whereas the expression of genes involved in SA and JA biosynthesis and signaling was also affected in the lif2-1 mutant, no change in SA and JA hormonal contents was detected. In addition, the composition of glucosinolates, a class of defense-related secondary metabolites, was altered in the lif2-1 mutant in the absence of pathogen challenge. The lif2-1 mutant exhibited reduced susceptibility to the hemi-biotrophic pathogen Pseudomonas syringae and the necrotrophic ascomycete Botrytis cinerea. Furthermore, the lif2-1 sid2-2 double mutant was less susceptible than the wild type to P. syringae infection, suggesting that the lif2 response to pathogens was independent of SA accumulation. Together, our data suggest that lif2-1 exhibits a basal primed defense state, resulting from complex deregulation of gene expression, which leads to increased resistance to pathogens with various infection strategies. Therefore, LIF2 may function as a suppressor of cell-autonomous immunity. Similar to its human homolog, NSAP1/SYNCRIP, a trans-acting factor involved in both cellular processes and the viral life cycle, LIF2 may regulate the conflicting aspects of development and defense programs, suggesting that a conserved evolutionary trade-off between growth and defense pathways exists in eukaryotes.
Bradrick, Shelton S.; Nagyal, Simardeep; Novatt, Hilary
2013-01-01
Micro(mi)RNAs are 21- to 23-nt RNAs that regulate multiple biological processes. In association with Argonaute (Ago) proteins and other factors that form the RNA-induced silencing complex (RISC), miRNAs typically bind mRNA 3′ untranslated regions (UTRs) and repress protein production through antagonizing translation and transcript stability. For a given mRNA–miRNA interaction, cis-acting RNA elements and trans-acting RNA-binding proteins (RBPs) may influence mRNA fate. This is particularly true of the hepatitis C virus (HCV) genome which interacts with miR-122, an abundant liver miRNA. miR-122 binding to HCV RNA considerably stimulates virus replication in cultured cells and primates, but the mechanism(s) and associated host factors required for enhancement of HCV replication have not been fully elucidated. We recapitulated miR-122–HCV RNA interactions in a cell-free translation system derived from cells that express miR-122. Specifically, lysates produced from HEK-293 cells that inducibly transcribe and process pri-miR-122 were characterized alongside those from isogenic cells lacking miR-122 expression. We observed a stimulatory effect of miR-122 on HCV reporter mRNAs in a manner that depended on expression of miR-122 and intact target sites within the HCV 5′ UTR. We took advantage of this system to affinity-purify miR-122-HCV RNP complexes. Similar to functional assays, we found that association of immobilized HCV internal ribosome entry site (IRES) RNA with endogenous Ago2 requires both miR-122 expression and intact miR-122 target sites in cis. This combined approach may be generalizable to affinity purification of miRNP complexes for selected target mRNAs, allowing identification of miRNP components and RBPs that may contribute to regulation. PMID:23793894
Linc-RoR promotes c-Myc expression through hnRNP I and AUF1.
Huang, Jianguo; Zhang, Ali; Ho, Tsui-Ting; Zhang, Ziqiang; Zhou, Nanjiang; Ding, Xianfeng; Zhang, Xu; Xu, Min; Mo, Yin-Yuan
2016-04-20
Linc-RoR was originally identified to be a regulator for induced pluripotent stem cells in humans and it has also been implicated in tumorigenesis. However, the underlying mechanism of Linc-RoR-mediated gene expression in cancer is poorly understood. The present study demonstrates that Linc-RoR plays an oncogenic role in part through regulation of c-Myc expression. Linc-RoR knockout (KO) suppresses cell proliferation and tumor growth. In particular, Linc-RoR KO causes a significant decrease in c-Myc whereas re-expression of Linc-RoR in the KO cells restores the level of c-Myc. Mechanistically, Linc-RoR interacts with heterogeneous nuclear ribonucleoprotein (hnRNP) I and AU-rich element RNA-binding protein 1 (AUF1), respectively, with an opposite consequence to their interaction with c-Myc mRNA. While Linc-RoR is required for hnRNP I to bind to c-Myc mRNA, interaction of Linc-RoR with AUF1 inhibits AUF1 to bind to c-Myc mRNA. As a result, Linc-RoR may contribute to the increased stability of c-Myc mRNA. Although hnRNP I and AUF1 can interact with many RNA species and regulate their functions, with involvement of Linc-RoR they would be able to selectively regulate mRNA stability of specific genes such as c-Myc. Together, these results support a role for Linc-RoR in c-Myc expression in part by specifically enhancing its mRNA stability, leading to cell proliferation and tumorigenesis. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Energy Technology Data Exchange (ETDEWEB)
Leder, Verena [Molecular Cell Physiology, Faculty of Biology, Bielefeld University (Germany); Biomolecular Photonics, Faculty of Physics, Bielefeld University (Germany); Lummer, Martina [Molecular Cell Physiology, Faculty of Biology, Bielefeld University (Germany); Tegeler, Kathrin [Molecular Cell Physiology, Faculty of Biology, Bielefeld University (Germany); Biomolecular Photonics, Faculty of Physics, Bielefeld University (Germany); Humpert, Fabian [Biomolecular Photonics, Faculty of Physics, Bielefeld University (Germany); Lewinski, Martin [Molecular Cell Physiology, Faculty of Biology, Bielefeld University (Germany); Schüttpelz, Mark [Biomolecular Photonics, Faculty of Physics, Bielefeld University (Germany); Staiger, Dorothee, E-mail: dorothee.staiger@uni-bielefeld.de [Molecular Cell Physiology, Faculty of Biology, Bielefeld University (Germany)
2014-10-10
Highlights: • We use FCS to investigate binding site requirements for the hnRNP-like protein AtGRP7. • We identify three nucleotides critical for AtGRP7 binding to its own intron. • Mutation of the conserved R{sup 49} abolishes binding altogether. • The paralogue AtGRP8 binds to an overlapping motif with different sequence requirement. • The glycine-rich stretch of a plant hnRNP-like protein contributes to binding. - Abstract: Arabidopsis thaliana glycine-rich RNA binding protein 7 (AtGRP7) is part of a negative feedback loop through which it regulates alternative splicing and steady-state abundance of its pre-mRNA. Here we use fluorescence correlation spectroscopy to investigate the requirements for AtGRP7 binding to its intron using fluorescently-labelled synthetic oligonucleotides. By systematically introducing point mutations we identify three nucleotides that lead to an increased K{sub d} value when mutated and thus are critical for AtGRP7 binding. Simultaneous mutation of all three residues abrogates binding. The paralogue AtGRP8 binds to an overlapping motif but with a different sequence preference, in line with overlapping but not identical functions of this protein pair. Truncation of the glycine-rich domain reduces the binding affinity of AtGRP7, showing for the first time that the glycine-rich stretch of a plant hnRNP-like protein contributes to binding. Mutation of the conserved R{sup 49} that is crucial for AtGRP7 function in pathogen defence and splicing abolishes binding.
Energy Technology Data Exchange (ETDEWEB)
Verschaeve, Joris C. G.
2011-07-01
The present thesis focuses on two distinct topics of computational fluid dynamics. The first one, treated in part I, focuses on the no-slip boundary conditions for the lattice Boltzmann method, whereas the second one, presented in part II, proposes a high order accurate description of the interface in two-phase flow computations for volume tracking in two dimensions.Part I of the present thesis presents an important issue in the framework of the lattice Boltzmann method, namely no-slip boundary conditions. Since the central object of the lattice Boltzmann method is the particle distribution function, the implementation of the no-slip boundary condition, although straightforward for continuum Navier Stokes solvers, is more involved. Additional physical arguments for the no-slip boundary condition at straight walls are presented. This leads to an alternative formulation of the no-slip boundary condition for the lattice Boltzmann method. This boundary condition is second order accurate with respect to the grid spacing and conserves mass. The origin of numerical instabilities observed for a variety of other boundary conditions is investigated, and it is shown how these can be removed leading to stable boundary conditions. Some arguments unifying different formulations of the no-slip boundary condition are presented. In addition to straight boundary conditions, the question of curved boundary conditions is treated. These represent an elevated level of complexity, since the lattice Boltzmann method is only defined for equidistant Cartesian grids. The curved boundary condition in the present thesis conserves the second order accuracy of the lattice Boltzmann method.Due to the complexity of two-phase flow problems, the majority of numerical methods in this field displays a rather low order of accuracy. In part II of the present thesis, a subproblem of the two-phase flow problem, namely the tracking of the interface is treated. Two different interface descriptions allowing
Liu, Yen; Vinokur, Marcel; Wang, Z. J.
2004-01-01
A three-dimensional, high-order, conservative, and efficient discontinuous spectral volume (SV) method for the solutions of Maxwell's equations on unstructured grids is presented. The concept of discontinuous 2nd high-order loca1 representations to achieve conservation and high accuracy is utilized in a manner similar to the Discontinuous Galerkin (DG) method, but instead of using a Galerkin finite-element formulation, the SV method is based on a finite-volume approach to attain a simpler formulation. Conventional unstructured finite-volume methods require data reconstruction based on the least-squares formulation using neighboring cell data. Since each unknown employs a different stencil, one must repeat the least-squares inversion for every cell at each time step, or to store the inversion coefficients. In a high-order, three-dimensional computation, the former would involve impractically large CPU time, while for the latter the memory requirement becomes prohibitive. In the SV method, one starts with a relatively coarse grid of triangles or tetrahedra, called spectral volumes (SVs), and partition each SV into a number of structured subcells, called control volumes (CVs), that support a polynomial expansion of a desired degree of precision. The unknowns are cell averages over CVs. If all the SVs are partitioned in a geometrically similar manner, the reconstruction becomes universal as a weighted sum of unknowns, and only a few universal coefficients need to be stored for the surface integrals over CV faces. Since the solution is discontinuous across the SV boundaries, a Riemann solver is thus necessary to maintain conservation. In the paper, multi-parameter and symmetric SV partitions, up to quartic for triangle and cubic for tetrahedron, are first presented. The corresponding weight coefficients for CV face integrals in terms of CV cell averages for each partition are analytically determined. These discretization formulas are then applied to the integral form of
Pabis, Marta; Neufeld, Noa; Steiner, Michaela C.; Bojic, Teodora; Shav-Tal, Yaron; Neugebauer, Karla M.
2013-01-01
The nuclear cap-binding complex (CBC) binds to the 7-methyl guanosine cap present on every RNA polymerase II transcript. CBC has been implicated in many aspects of RNA biogenesis; in addition to roles in miRNA biogenesis, nonsense-mediated decay, 3′-end formation, and snRNA export from the nucleus, CBC promotes pre-mRNA splicing. An unresolved question is how CBC participates in splicing. To investigate CBC’s role in splicing, we used mass spectrometry to identify proteins that copurify with mammalian CBC. Numerous components of spliceosomal snRNPs were specifically detected. Among these, three U4/U6·U5 snRNP proteins (hBrr2, hPrp4, and hPrp31) copurified with CBC in an RNA-independent fashion, suggesting that a significant fraction of CBC forms a complex with the U4/U6·U5 snRNP and that the activity of CBC might be associated with snRNP recruitment to pre-mRNA. To test this possibility, CBC was depleted from HeLa cells by RNAi. Chromatin immunoprecipitation and live-cell imaging assays revealed decreased cotranscriptional accumulation of U4/U6·U5 snRNPs on active transcription units, consistent with a requirement for CBC in cotranscriptional spliceosome assembly. Surprisingly, recruitment of U1 and U2 snRNPs was also affected, indicating that RNA-mediated interactions between CBC and snRNPs contribute to splicing. On the other hand, CBC depletion did not impair snRNP biogenesis, ruling out the possibility that decreased snRNP recruitment was due to changes in nuclear snRNP concentration. Taken together, the data support a model whereby CBC promotes pre-mRNA splicing through a network of interactions with and among spliceosomal snRNPs during cotranscriptional spliceosome assembly. PMID:23793891
Zerbe, Laura K; Pino, Irene; Pio, Ruben; Cosper, Pippa F; Dwyer-Nield, Lori D; Meyer, Amy M; Port, J David; Montuenga, Luis M; Malkinson, Alvin M
2004-12-01
Pre-mRNA processing is an important mechanism for globally modifying cellular protein composition during tumorigenesis. To understand this process during lung cancer, expression of two key pre-mRNA alternative splicing factors was compared in a mouse model of early lung carcinogenesis and during regenerative growth following reversible lung injury. Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 and alternative splicing factor/splicing factor 2 (ASF/SF2) act antagonistically to modulate splice site selection. Both hnRNP A1 and ASF/SF2 contents rose in adenomas and during injury-induced hyperplasia compared to control lungs, as measured by immunoblotting. While both proteins increased similarly during compensatory hyperplasia, hnRNP A1 increased to a much greater extent than ASF/SF2 in tumors, resulting in a 6-fold increase of the hnRNP A1 to ASF/SF2 ratio. Immunohistochemical analysis showed that hnRNP A1 localized exclusively within tumor nuclei, while ASF/SF2 appeared in cytoplasm and/or nuclei, depending on the growth pattern of the tumor cells. We also demonstrated cancer-associated changes in the pre-mRNA alternative splicing of CD44, a membrane glycoprotein involved in cell-cell and cell-extracellular matrix interactions. hnRNP A1 and ASF/SF2 expression is thus differentially altered in neoplastic lung cells by mechanisms that do not strictly arise from increased cell division. These changes are influenced by tumor histology and may be associated with production of variant CD44 mRNA isoforms. (c) 2004 Wiley-Liss, Inc.
Directory of Open Access Journals (Sweden)
Aleksey Maslyanskiy
2014-01-01
Full Text Available Heterogeneous nuclear ribonucleoproteins (hnRNPs are potent autoantigenic targets in systemic autoimmune rheumatic diseases (SARD. Loss of tolerance to the RA33 complex consisting of hnRNP A2 and its alternatively spliced variants B1 and B2 has been the interest of rheumatologists. A novel ELISA for the detection of anti-hnRNP B1 autoantibodies has been developed to investigate the prevalence thereof in 397 patients with SARD, including patients with rheumatoid arthritis (RA, spondyloarthropathy (SPA, juvenile chronic arthritis, systemic lupus erythematosus (SLE, systemic sclerosis (SSc, and Sjögren’s syndrome (SS, in comparison to 174 controls. Anti-hnRNP B1 autoantibodies were significantly more prevalent in patients with SARD than controls (47/397, 11.8% versus 2/174, 1.1%; P<0.001. In particular, anti-hnRNP B1 were found more frequently in the disease cohorts than in the controls and were present in 24/165 (14.5% patients with RA, 6/58 (10.3% SPA, 11/65 (16.9% SSc, and 4/50 (8.0% SLE. In RA patients, anti-hnRNP B1 autoantibodies correlated significantly with C-reactive protein levels and erythrocyte sedimentation rate, while in patients with SSc it was associated with features of arterial wall stiffness and presence of hypertension. Anti-hnRNP B1 autoantibodies occur in SARD and seem to be correlated with distinct clinical characteristics in patients with RA and SSc.
Directory of Open Access Journals (Sweden)
Valeria Rimoldi
Full Text Available Most pathological pseudoexon inclusion events originate from single activating mutations, suggesting that many intronic sequences are on the verge of becoming exons. However, the precise mechanisms controlling pseudoexon definition are still largely unexplored. Here, we investigated the cis-acting elements and trans-acting regulatory factors contributing to the regulation of a previously described fibrinogen gamma-chain (FGG pseudoexon, which is activated by a deep-intronic mutation (IVS6-320A>T. This pseudoexon contains several G-run elements, which may be bound by heterogeneous nuclear ribonucleoproteins (hnRNPs F and H. To explore the effect of these proteins on FGG pseudoexon inclusion, both silencing and overexpression experiments were performed in eukaryotic cells. While hnRNP H did not significantly affect pseudoexon splicing, hnRNP F promoted pseudoexon inclusion, indicating that these two proteins have only partially redundant functions. To verify the binding of hnRNP F and the possible involvement of other trans-acting splicing modulators, pulldown experiments were performed on the region of the pseudoexon characterized by both a G-run and enrichment for exonic splicing enhancers. This 25-bp-long region strongly binds hnRNP F/H and weakly interacts with Serine/Arginine-rich protein 40, which however was demonstrated to be dispensable for FGG pseudoexon inclusion in overexpression experiments. Deletion analysis, besides confirming the splicing-promoting role of the G-run within this 25-bp region, demonstrated that two additional hnRNP F binding sites might instead function as silencer elements. Taken together, our results indicate a major role of hnRNP F in regulating FGG pseudoexon inclusion, and strengthen the notion that G-runs may function either as splicing enhancers or silencers of the same exon.
Rimoldi, Valeria; Soldà, Giulia; Asselta, Rosanna; Spena, Silvia; Stuani, Cristiana; Buratti, Emanuele; Duga, Stefano
2013-01-01
Most pathological pseudoexon inclusion events originate from single activating mutations, suggesting that many intronic sequences are on the verge of becoming exons. However, the precise mechanisms controlling pseudoexon definition are still largely unexplored. Here, we investigated the cis-acting elements and trans-acting regulatory factors contributing to the regulation of a previously described fibrinogen gamma-chain (FGG) pseudoexon, which is activated by a deep-intronic mutation (IVS6-320A>T). This pseudoexon contains several G-run elements, which may be bound by heterogeneous nuclear ribonucleoproteins (hnRNPs) F and H. To explore the effect of these proteins on FGG pseudoexon inclusion, both silencing and overexpression experiments were performed in eukaryotic cells. While hnRNP H did not significantly affect pseudoexon splicing, hnRNP F promoted pseudoexon inclusion, indicating that these two proteins have only partially redundant functions. To verify the binding of hnRNP F and the possible involvement of other trans-acting splicing modulators, pulldown experiments were performed on the region of the pseudoexon characterized by both a G-run and enrichment for exonic splicing enhancers. This 25-bp-long region strongly binds hnRNP F/H and weakly interacts with Serine/Arginine-rich protein 40, which however was demonstrated to be dispensable for FGG pseudoexon inclusion in overexpression experiments. Deletion analysis, besides confirming the splicing-promoting role of the G-run within this 25-bp region, demonstrated that two additional hnRNP F binding sites might instead function as silencer elements. Taken together, our results indicate a major role of hnRNP F in regulating FGG pseudoexon inclusion, and strengthen the notion that G-runs may function either as splicing enhancers or silencers of the same exon.
Directory of Open Access Journals (Sweden)
Henrik Gross
Full Text Available The Epstein-Barr Virus (EBV -encoded EBNA2 protein, which is essential for the in vitro transformation of B-lymphocytes, interferes with cellular processes by binding to proteins via conserved sequence motifs. Its Arginine-Glycine (RG repeat element contains either symmetrically or asymmetrically di-methylated arginine residues (SDMA and ADMA, respectively. EBNA2 binds via its SDMA-modified RG-repeat to the survival motor neurons protein (SMN and via the ADMA-RG-repeat to the NP9 protein of the human endogenous retrovirus K (HERV-K (HML-2 Type 1. The hypothesis of this work was that the methylated RG-repeat mimics an epitope shared with cellular proteins that is used for interaction with target structures. With monoclonal antibodies against the modified RG-repeat, we indeed identified cellular homologues that apparently have the same surface structure as methylated EBNA2. With the SDMA-specific antibodies, we precipitated the Sm protein D3 (SmD3 which, like EBNA2, binds via its SDMA-modified RG-repeat to SMN. With the ADMA-specific antibodies, we precipitated the heterogeneous ribonucleoprotein K (hnRNP K. Specific binding of the ADMA- antibody to hnRNP K was demonstrated using E. coli expressed/ADMA-methylated hnRNP K. In addition, we show that EBNA2 and hnRNP K form a complex in EBV- infected B-cells. Finally, hnRNP K, when co-expressed with EBNA2, strongly enhances viral latent membrane protein 2A (LMP2A expression by an unknown mechanism as we did not detect a direct association of hnRNP K with DNA-bound EBNA2 in gel shift experiments. Our data support the notion that the methylated surface of EBNA2 mimics the surface structure of cellular proteins to interfere with or co-opt their functional properties.
Castruccio, Stefano
2016-01-01
In multivariate or spatial extremes, inference for max-stable processes observed at a large collection of points is a very challenging problem and current approaches typically rely on less expensive composite likelihoods constructed from small subsets of data. In this work, we explore the limits of modern state-of-the-art computational facilities to perform full likelihood inference and to efficiently evaluate high-order composite likelihoods. With extensive simulations, we assess the loss of information of composite likelihood estimators with respect to a full likelihood approach for some widely used multivariate or spatial extreme models, we discuss how to choose composite likelihood truncation to improve the efficiency, and we also provide recommendations for practitioners. This article has supplementary material online.
Rad-Hydro with a High-Order, Low-Order Method
Energy Technology Data Exchange (ETDEWEB)
Wollaber, Allan Benton [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Park, HyeongKae [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lowrie, Robert Byron [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rauenzahn, Rick M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cleveland, Mathew Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2015-08-04
Moment-based acceleration via the development of “high-order, low-order” (HO-LO) algorithms has provided substantial accuracy and efficiency enhancements for solutions of the nonlinear, thermal radiative transfer equations by CCS-2 and T-3 staff members. Accuracy enhancements over traditional, linearized methods are obtained by solving a nonlinear, timeimplicit HO-LO system via a Jacobian-free Newton Krylov procedure. This also prevents the appearance of non-physical maximum principle violations (“temperature spikes”) associated with linearization. Efficiency enhancements are obtained in part by removing “effective scattering” from the linearized system. In this highlight, we summarize recent work in which we formally extended the HO-LO radiation algorithm to include operator-split radiation-hydrodynamics.
Elassy, Kareem S.; Rafat, Nadia H.; Khedr, Mohamed E.; Aly, Moustafa H.
2014-05-01
Metamaterials have effective properties that are distinct from their composites as they consist of engineered-designed properties that are not in nature. In order to be able to design a metamaterial, we should establish sufficient understanding of the properties of the constituents. This will enable us to engineer new effective parameters of the metamaterial. We shall perform a detailed analytical study for the effective parameters and the constituents' parameters of silver-silica metamaterial. This will define the optical response of the mixture at different sizes of the inclusions' and different volume fractions of the silver and silica. Also an optimum value of the volume fraction is proposed to achieve a broadened resonance optical response. Finally, we propose the design technique and constraints of a non-magnetic optical cloaking device, based on high-order transformation optics with different volume fractions of silver and silica.
Mignone, A
2014-01-01
High-order reconstruction schemes for the solution of hyperbolic conservation laws in orthogonal curvilinear coordinates are revised in the finite volume approach. The formulation employs a piecewise polynomial approximation to the zone-average values to reconstruct left and right interface states from within a computational zone to arbitrary order of accuracy by inverting a Vandermonde-like linear system of equations with spatially varying coefficients. The approach is general and can be used on uniform and non-uniform meshes although explicit expressions are derived for polynomials from second to fifth degree in cylindrical and spherical geometries with uniform grid spacing. It is shown that, in regions of large curvature, the resulting expressions differ considerably from their Cartesian counterparts and that the lack of such corrections can severely degrade the accuracy of the solution close to the coordinate origin. Limiting techniques and monotonicity constraints are revised for conventional reconstruct...
Performance Prediction of Double-Binary Turbo Codes with High Order Modulations in AWGN Channel
Directory of Open Access Journals (Sweden)
BALTA, H.
2014-11-01
Full Text Available In this paper, we present a method for turbo codes (TC performance prediction, in terms of bit error rate (BER and frame error rate (FER versus signal to noise ratio (SNR, when they are used with high-order modulations (HOM. The method is based on two simplifying hypotheses and assumes that the BER/FER vs. SNR performance, in the case of BPSK modulation, is known. For the simulations we have chosen the double-binary turbo codes (DBTC used in the DVB-RCS standard. The experimental results confirm the good accuracy of the proposed prediction method and validate our assumptions. The method has been applied in the case of 16-Quadrature Amplitude Modulation (16-QAM, but it can be easily extended to any other type of modulation.
The high-order cyclotron modes in Fermi liquid of Q2D layered conductors
Directory of Open Access Journals (Sweden)
O.V.Kirichenko
2005-01-01
Full Text Available The propagation of electromagnetic waves in layered conductors at the presence of an external magnetic field is investigated theoretically. At certain orientations of a magnetic field concerning the layers of the conductor the collisionless absorption is absent and weakly damping collective modes can propagate even under the strong spatial dispersion. In a short-wave limit the existence of electromagnetic waves with frequencies near the cyclotron resonances is possible at an arbitrary orientation of the wave vector with respect to an external magnetic field. We have obtained the spectrum of waves with the frequencies near the cyclotron resonances of high order with regard to the Fermi-liquid interaction of the electrons.
Polarization shaping of high-order harmonics in laser-aligned molecules
Skantzakis, E.; Chatziathanasiou, S.; Carpeggiani, P. A.; Sansone, G.; Nayak, A.; Gray, D.; Tzallas, P.; Charalambidis, D.; Hertz, E.; Faucher, O.
2016-12-01
The present work reports on the generation of short-pulse coherent extreme ultraviolet radiation of controlled polarization. The proposed strategy is based on high-order harmonics generated in pre-aligned molecules. Field-free molecular alignment produced by a short linearly-polarized infrared laser pulse is used to break the isotropy of a gas medium. Driving the aligned molecules by a circularly-polarized infrared pulse allows to transfer the anisotropy of the medium to the polarization of the generated harmonic light. The ellipticity of the latter is controlled by adjusting the angular distribution of the molecules at the time they interact with the driving pulse. Extreme ultraviolet radiation produced with high degree of ellipticity (close to circular) is demonstrated.
Superconducting linac beam dynamics with high-order maps for RF resonators
Geraci, A A; Pardo, R C; 10.1016/j.nima.2003.11.177
2004-01-01
The arbitrary-order map beam optics code COSY Infinity has recently been adapted to calculate accurate high-order ion-optical maps for electrostatic and radio-frequency accelerating structures. The beam dynamics of the superconducting low-velocity positive-ion injector linac for the ATLAS accelerator at Argonne National Lab is used to demonstrate some advantages of the new simulation capability. The injector linac involves four different types of superconducting accelerating structures and has a total of 18 resonators. The detailed geometry for each of the accelerating cavities is included, allowing an accurate representation of the on- and off-axis electric fields. The fields are obtained within the code from a Poisson-solver for cylindrically symmetric electrodes of arbitrary geometry. The transverse focusing is done with superconducting solenoids. A detailed comparison of the transverse and longitudinal phase space is made with the conventional ray-tracing code LINRAY. The two codes are evaluated for ease ...
Highly-ordered vertical Si nanowire/nanowall decorated solar cells.
Wang, Jian; Li, Zhenhua; Singh, Navab; Lee, Sungjoo
2011-11-07
Highly-ordered vertical nanowire and nanowall arrays are studied on Si solar cell surface. The nanowall textured solar cell is found to be more effective in reducing the overall optical reflectance, resulting in higher short circuit current (Jsc = 24.9 mA/cm²) over nanowire structured (Jsc = 23.3 mA/cm²) and planar (Jsc = 17.5 mA/cm²) solar cells. The extracted energy conversion efficiency (η) from planar solar cell is 7.1%, while nanowire/nanowall cells show efficiency of 8.2% and 6.3%, respectively. If corrected with series resistance (Rs), nanowall solar cell exhibits the highest η of 9.8% in this experiment. A careful study of the series resistance from different types of the nanostructures is also presented.
Wang, Jie; Zong, Qun; Su, Rui; Tian, Bailing
2014-05-01
This paper investigates the problem of tracking control with uncertainties for a flexible air-breathing hypersonic vehicle (FAHV). In order to overcome the analytical intractability of this model, an Input-Output linearization model is constructed for the purpose of feedback control design. Then, the continuous finite time convergence high order sliding mode controller is designed for the Input-Output linearization model without uncertainties. In addition, a nonlinear disturbance observer is applied to estimate the uncertainties in order to compensate the controller and disturbance suppression, where disturbance observer and controller synthesis design is obtained. Finally, the synthesis of controller and disturbance observer is used to achieve the tracking for the velocity and altitude of the FAHV and simulations are presented to illustrate the effectiveness of the control strategies. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.
A Modified AH-FDTD Unconditionally Stable Method Based on High-Order Algorithm
Directory of Open Access Journals (Sweden)
Zheng Pan
2017-01-01
Full Text Available The unconditionally stable method, Associated-Hermite FDTD, has attracted more and more attentions in computational electromagnetic for its time-frequency compact property. Because of the fewer orders of AH basis needed in signal reconstruction, the computational efficiency can be improved further. In order to further improve the accuracy of the traditional AH-FDTD, a high-order algorithm is introduced. Using this method, the dispersion error induced by the space grid can be reduced, which makes it possible to set coarser grid. The simulation results show that, on the condition of coarse grid, the waveforms obtained from the proposed method are matched well with the analytic result, and the accuracy of the proposed method is higher than the traditional AH-FDTD. And the efficiency of the proposed method is higher than the traditional FDTD method in analysing 2D waveguide problems with fine-structure.
A fast algorithm for high order total variation minimization based interior tomography.
Zhao, Zhenhua; Yang, Jiansheng; Jiang, Ming
2015-01-01
Interior tomography as a promising X-ray imaging technique has received increasing attention in medical imaging field. In our previous works, we proposed a high-order total variation (HOT) minimization method for interior tomography and proved that the region of interest (ROI) can be reconstructed accurately by minimizing the HOT if the object image is piecewise polynomial within the ROI. In this paper, we propose a modified HOT (MHOT) and develop a fast MHOT minimization algorithm for interior tomography, based on split Bregman iteration and ordered-subset simultaneous algebraic reconstruction techniques (OS-SART). Numerical simulation demonstrates that our algorithm is computationally efficient and can be applied to obtain high-quality reconstructed image.
Carrier-wave Rabi-flopping signatures in high-order harmonic generation for alkali atoms.
Ciappina, M F; Pérez-Hernández, J A; Landsman, A S; Zimmermann, T; Lewenstein, M; Roso, L; Krausz, F
2015-04-10
We present a theoretical investigation of carrier-wave Rabi flopping in real atoms by employing numerical simulations of high-order harmonic generation (HHG) in alkali species. Given the short HHG cutoff, related to the low saturation intensity, we concentrate on the features of the third harmonic of sodium (Na) and potassium (K) atoms. For pulse areas of 2π and Na atoms, a characteristic unique peak appears, which, after analyzing the ground state population, we correlate with the conventional Rabi flopping. On the other hand, for larger pulse areas, carrier-wave Rabi flopping occurs, and is associated with a more complex structure in the third harmonic. These characteristics observed in K atoms indicate the breakdown of the area theorem, as was already demonstrated under similar circumstances in narrow band gap semiconductors.
Probe of Multi-electron Dynamics in Xenon by Caustics in High Order Harmonic Generation
Faccialà, Davide; Bruner, Barry D; Ciriolo, Anna G; De Silvestri, Sandro; Devetta, Michele; Negro, Matteo; Soifer, Hadas; Stagira, Salvatore; Dudovich, Nirit; Vozzi, Caterina
2016-01-01
We investigated the giant resonance in Xenon by high-order harmonic generation spectroscopy driven by a two-color field. The addition of a non-perturbative second harmonic component parallel to the driving field breaks the symmetry between neighboring sub-cycles resulting in the appearance of spectral caustics at two distinct cut-off energies. By controlling the phase delay between the two color components it is possible to tailor the harmonic emission in order to amplify and isolate the spectral feature of interest. In this paper we demonstrate how this control scheme can be used to investigate the role of electron correlations that give birth to the giant resonance in Xenon. The collective excitations of the giant dipole resonance in Xenon combined with the spectral manipulation associated with the two color driving field allow to see features that are normally not accessible and to obtain a quantitative good agreement between the experimental results and the theoretical predictions.
DEFF Research Database (Denmark)
Han, Yong-Chang; Madsen, Lars Bojer
2010-01-01
We solve the time-dependent Schrödinger equation for atomic hydrogen in an intense field using spherical coordinates with a radial grid and a spherical harmonic basis for the angular part. We present the high-order harmonic spectra based on three different forms, the dipole, dipole velocity......, and acceleration forms, and two gauges, the length and velocity gauges. The relationships among the harmonic phases obtained from the Fourier transform of the three forms are discussed in detail. Although quantum mechanics is gauge invariant and the length and velocity gauges should give identical results, the two...... gauges present different computation efficiencies, which reflects the different behavior in terms of characteristics of the physical couplings acting in the two gauges. In order to obtain convergence, more angular momentum states are required in the length gauge, while more grid points are required...
Efficient simulation of cardiac electrical propagation using high order finite elements.
Arthurs, Christopher J; Bishop, Martin J; Kay, David
2012-05-20
We present an application of high order hierarchical finite elements for the efficient approximation of solutions to the cardiac monodomain problem. We detail the hurdles which must be overcome in order to achieve theoretically-optimal errors in the approximations generated, including the choice of method for approximating the solution to the cardiac cell model component. We place our work on a solid theoretical foundation and show that it can greatly improve the accuracy in the approximation which can be achieved in a given amount of processor time. Our results demonstrate superior accuracy over linear finite elements at a cheaper computational cost and thus indicate the potential indispensability of our approach for large-scale cardiac simulation.
Tran, Giang; Shi, Yonggang
2013-01-01
Diffusion imaging data from the Human Connectome Project (HCP) provides a great opportunity to map the whole brain white matter connectivity to unprecedented resolution in vivo. In this paper we develop a novel method for accurately reconstruct fiber orientation distribution from cutting-edge diffusion data by solving the spherical deconvolution problem as a constrained convex optimization problem. With a set of adaptively selected constraints, our method allows the use of high order spherical harmonics to reliably resolve crossing fibers with small separation angles. In our experiments, we demonstrate on simulated data that our algorithm outperforms a popular spherical deconvolution method in resolving fiber crossings. We also successfully applied our method to the multi-shell and diffusion spectrum imaging (DSI) data from HCP to demonstrate its ability in using state-of-the-art diffusion data to study complicated fiber structures.
High Order Numerical Simulation of Sound Generated by the Kirchhoff Vortex
Mueller, Bernhard; Yee, H. C.
2001-01-01
An improved high order finite difference method for low Mach number computational aeroacoustics (CAA) is described. The improvements involve the conditioning of the Euler equations in perturbation form to minimize numerical cancellation error, and the use of a stable non-dissipative sixth-order central spatial differencing for the interior points and third-order at the boundary points. The spatial difference operator satisfies the summation-by-parts property to guarantee strict stability for linear hyperbolic systems. Spurious high frequency oscillations are damped by a third-order characteristic-based filter. The objective of this paper is to apply these improvements in the simulation of sound generated by the Kirchhoff vortex.
A high-order language for a system of closely coupled processing elements
Feyock, S.; Collins, W. R.
1986-01-01
The research reported in this paper was occasioned by the requirements on part of the Real-Time Digital Simulator (RTDS) project under way at NASA Lewis Research Center. The RTDS simulation scheme employs a network of CPUs running lock-step cycles in the parallel computations of jet airplane simulations. Their need for a high order language (HOL) that would allow non-experts to write simulation applications and that could be implemented on a possibly varying network can best be fulfilled by using the programming language Ada. We describe how the simulation problems can be modeled in Ada, how to map a single, multi-processing Ada program into code for individual processors, regardless of network reconfiguration, and why some Ada language features are particulary well-suited to network simulations.
Multi-dimensional high-order numerical schemes for Lagrangian hydrodynamics
Energy Technology Data Exchange (ETDEWEB)
Dai, William W [Los Alamos National Laboratory; Woodward, Paul R [Los Alamos National Laboratory
2009-01-01
An approximate solver for multi-dimensional Riemann problems at grid points of unstructured meshes, and a numerical scheme for multi-dimensional hydrodynamics have been developed in this paper. The solver is simple, and is developed only for the use in numerical schemes for hydrodynamics. The scheme is truely multi-dimensional, is second order accurate in both space and time, and satisfies conservation laws exactly for mass, momentum, and total energy. The scheme has been tested through numerical examples involving strong shocks. It has been shown that the scheme offers the principle advantages of high-order Codunov schemes; robust operation in the presence of very strong shocks and thin shock fronts.
Attosecond dynamics of light-induced resonant hole transfer in high-order-harmonic generation
You, Jhih-An; Dahlström, Jan Marcus; Rohringer, Nina
2017-02-01
We present a study of high-order-harmonic generation (HHG) assisted by extreme ultraviolet (XUV) attosecond pulses, which can lead to the excitation of inner-shell electrons and the generation of a second HHG plateau. With the treatment of a one-dimensional model of krypton, based on time-dependent configuration interaction singles (TDCIS) of an effective two-electron system, we show that the XUV-assisted HHG spectrum reveals the duration of the semiclassical electron trajectories. The results are interpreted by the strong-field approximation (SFA) and the importance of the hole transfer during the tunneling process is emphasized. Finally, coherent population transfer between the inner and outer holes with attosecond pulse trains is discussed.
High-order Composite Likelihood Inference for Max-Stable Distributions and Processes
Castruccio, Stefano
2015-09-29
In multivariate or spatial extremes, inference for max-stable processes observed at a large collection of locations is a very challenging problem in computational statistics, and current approaches typically rely on less expensive composite likelihoods constructed from small subsets of data. In this work, we explore the limits of modern state-of-the-art computational facilities to perform full likelihood inference and to efficiently evaluate high-order composite likelihoods. With extensive simulations, we assess the loss of information of composite likelihood estimators with respect to a full likelihood approach for some widely-used multivariate or spatial extreme models, we discuss how to choose composite likelihood truncation to improve the efficiency, and we also provide recommendations for practitioners. This article has supplementary material online.
Resonance enhanced high-order harmonic generation in H2+ by two sequential laser pulses.
Wang, Baoning; He, Lixin; Wang, Feng; Yuan, Hua; Zhu, Xiaosong; Lan, Pengfei; Lu, Peixiang
2017-07-24
We investigate high-order harmonic generation in H2+ by using two sequential laser pulses, which consist of a 800-nm pump pulse and a time-delayed 1600-nm probe pulse. Based on the solution of the time-dependent Schrödinger equation, we demonstrate that the harmonic cutoff in our two-pulse scheme is significantly extended compared to that in the 1600-nm probe pulse alone. Meanwhile, the harmonic efficiency is enhanced by 2-3 orders of magnitude due to charge-resonance-enhanced ionization steered by the 800-nm pump pulse. By using a probe pulse with longer wavelength, our scheme can be used for efficient high harmonic generation in the water window region. In addition, the influence of the intensity of the pump pulse and the relative time delay of the two laser pulses on the harmonic generation are also investigated.
Ferré, A.; Boguslavskiy, A. E.; Dagan, M.; Blanchet, V.; Bruner, B. D.; Burgy, F.; Camper, A.; Descamps, D.; Fabre, B.; Fedorov, N.; Gaudin, J.; Geoffroy, G.; Mikosch, J.; Patchkovskii, S.; Petit, S.; Ruchon, T.; Soifer, H.; Staedter, D.; Wilkinson, I.; Stolow, A.; Dudovich, N.; Mairesse, Y.
2015-01-01
High-order harmonic generation in polyatomic molecules generally involves multiple channels of ionization. Their relative contribution can be strongly influenced by the presence of resonances, whose assignment remains a major challenge for high-harmonic spectroscopy. Here we present a multi-modal approach for the investigation of unaligned polyatomic molecules, using SF6 as an example. We combine methods from extreme-ultraviolet spectroscopy, above-threshold ionization and attosecond metrology. Fragment-resolved above-threshold ionization measurements reveal that strong-field ionization opens at least three channels. A shape resonance in one of them is found to dominate the signal in the 20–26 eV range. This resonance induces a phase jump in the harmonic emission, a switch in the polarization state and different dynamical responses to molecular vibrations. This study demonstrates a method for extending high-harmonic spectroscopy to polyatomic molecules, where complex attosecond dynamics are expected. PMID:25608712
Busto, S.; Ferrín, J. L.; Toro, E. F.; Vázquez-Cendón, M. E.
2018-01-01
In this paper the projection hybrid FV/FE method presented in [1] is extended to account for species transport equations. Furthermore, turbulent regimes are also considered thanks to the k-ε model. Regarding the transport diffusion stage new schemes of high order of accuracy are developed. The CVC Kolgan-type scheme and ADER methodology are extended to 3D. The latter is modified in order to profit from the dual mesh employed by the projection algorithm and the derivatives involved in the diffusion term are discretized using a Galerkin approach. The accuracy and stability analysis of the new method are carried out for the advection-diffusion-reaction equation. Within the projection stage the pressure correction is computed by a piecewise linear finite element method. Numerical results are presented, aimed at verifying the formal order of accuracy of the scheme and to assess the performance of the method on several realistic test problems.
Solution of stochastic nonlinear PDEs using Wiener-Hermite expansion of high orders
El Beltagy, Mohamed
2016-01-06
In this work, the Wiener-Hermite Expansion (WHE) is used to solve stochastic nonlinear PDEs excited with noise. The generation of the equivalent set of deterministic integro-differential equations is automated and hence allows for high order terms of WHE. The automation difficulties are discussed, solved and implemented to output the final system to be solved. A numerical Pikard-like algorithm is suggested to solve the resulting deterministic system. The automated WHE is applied to the 1D diffusion equation and to the heat equation. The results are compared with previous solutions obtained with WHEP (WHE with perturbation) technique. The solution obtained using the suggested WHE technique is shown to be the limit of the WHEP solutions with infinite number of corrections. The automation is extended easily to account for white-noise of higher dimension and for general nonlinear PDEs.
Energy Technology Data Exchange (ETDEWEB)
Shin, Yongsoon; Tao, Jinhui; Arey, Bruce W.; Wang, Chongmin; Exarhos, Gregory J.; De Yoreo, James J.; Sushko, Maria L.; Liu, Jun
2016-08-30
Molecular templating and self-assembly are fundamental mechanisms for controlling the morphology of biominerals, while in synthetic two-dimensional layered materials similar levels of control over materials structure can be achieved through the epitaxial relationship with the substrate. In this study these two concepts are combined to provide an approach for the nucleation and growth of three-dimensional ordered mesophases on solid surfaces. A combined experimental and theoretical study revealed how atomic ordering of the substrate controls the structure of surfactant template and the orientation and morphology of the epitaxially grown inorganic material. Such dual epitaxial relationship between the substrate, surfactant template and inorganic mesophase gives rise to a highly ordered porous mesophase with a well-defined cubic lattice of pores. The level of control over material’s three-dimensional architecture achieved in this one-step synthesis is reminiscent to that in biomineralization.
A single-electron approach for many-electron dynamics in high-order harmonic generation
Schild, Axel
2016-01-01
We present a novel ab-initio single-electron approach to correlated electron dynamics in strong laser fields. By writing the electronic wavefunction as a product of a marginal one-electron wavefunction and a conditional wavefunction, we show that the exact harmonic spectrum can be obtained from a single-electron Schr\\"odinger equation. To obtain the one-electron potential in practice, we propose an adiabatic approximation, i.e. a potential is generated that depends only on the position of one electron. This potential, together with the laser interaction, is then used to obtain the dynamics of the system. For a model Helium atom in a laser field, we show that by using our approach, the high-order harmonic generation spectrum can be obtained to a good approximation.
Classification of epilepsy using high-order spectra features and principle component analysis.
Du, Xian; Dua, Sumeet; Acharya, Rajendra U; Chua, Chua Kuang
2012-06-01
The classification of epileptic electroencephalogram (EEG) signals is challenging because of high nonlinearity, high dimensionality, and hidden states in EEG recordings. The detection of the preictal state is difficult due to its similarity to the ictal state. We present a framework for using principal components analysis (PCA) and a classification method for improving the detection rate of epileptic classes. To unearth the nonlinearity and high dimensionality in epileptic signals, we extract principal component features using PCA on the 15 high-order spectra (HOS) features extracted from the EEG data. We evaluate eight classifiers in the framework using true positive (TP) rate and area under curve (AUC) of receiver operating characteristics (ROC). We show that a simple logistic regression model achieves the highest TP rate for class "preictal" at 97.5% and the TP rate on average at 96.8% with PCA variance percentages selected at 100%, which also achieves the most AUC at 99.5%.
Effect of transition dipole phase on high-order-harmonic generation in solid materials
Jiang, Shicheng; Wei, Hui; Chen, Jigen; Yu, Chao; Lu, Ruifeng; Lin, C. D.
2017-11-01
High-order harmonic spectra from solid materials driven by single-color multicycle laser fields sometimes contain even harmonics. In this work we attribute the appearance of even harmonics to the nonzero transition dipole phase (TDP) when the solid system has broken symmetry. By calculating the harmonic efficiency from graphene and gapped graphene by using the semiconductor Bloch equations under the tight-binding approximation, we demonstrate the role of the TDP, which has been ignored for a long time. When the crystal has inversion symmetry, or reflection symmetry with the symmetry plane perpendicular to the laser polarization direction, the TDP can be neglected. Without such symmetry, however, the TDP will lead to the appearance of even harmonics. We further show that the TDP is sensitive to the crystal geometry. To extract the structure information from the harmonic spectra of a solid the TDP cannot be ignored.
Unstructured nodal DG-FEM solution of high-order Boussinesq-type equations
DEFF Research Database (Denmark)
Engsig-Karup, Allan Peter
2007-01-01
The main objective of the present study has been to develop a numerical model and investigate solution techniques for solving the recently derived high-order Boussinesq equations of \\cite{MBL02} in irregular domains in one and two horizontal dimensions. The Boussinesq-type methods are the simplest...... alternative to solving full three-dimensional wave problems by e.g. Navier-Stokes equations, which can capture all the important wave phenomena such as diffraction, refraction, nonlinear wave-wave interactions and interaction with structures. The main goal can be reached by using multi-domain methods...... a highly complex system of coupled equations which put any numerical method to the test. The main problems that need to be overcome to solve the equations are the treatment of strongly nonlinear convection-type terms and spatially varying coefficient terms; efficient and robust solution of the resultant...
High-order parameterization of (un)stable manifolds for hybrid maps: Implementation and applications
Naudot, Vincent; Mireles James, J. D.; Lu, Qiuying
2017-12-01
In this work we study, from a numerical point of view, the (un)stable manifolds of a certain class of dynamical systems called hybrid maps. The dynamics of these systems are generated by a two stage procedure: the first stage is continuous time advection under a given vector field, the second stage is discrete time advection under a given diffeomorphism. Such hybrid systems model physical processes where a differential equation is occasionally kicked by a strong disturbance. We propose a numerical method for computing local (un)stable manifolds, which leads to high order polynomial parameterization of the embedding. The parameterization of the invariant manifold is not the graph of a function and can follow folds in the embedding. Moreover we obtain a representation of the dynamics on the manifold in terms of a simple conjugacy relation. We illustrate the utility of the method by studying a planar example system.
Formation of high-order acoustic Bessel beams by spiral diffraction gratings
Jiménez, Noé; Sánchez-Morcillo, Víctor; Romero-García, Vicent; García-Raffi, Lluis M; Staliunas, Kestutis
2016-01-01
The formation of high-order Bessel beams by a passive acoustic device consisting of an Archimedes' spiral diffraction grating is theoretically, numerically and experimentally reported in this work. These beams are propagation-invariant solutions of the Helmholtz equation and are characterized by an azimuthal variation of the phase along its annular spectrum producing an acoustic vortex in the near field. In our system, the scattering of plane acoustic waves by the spiral grating leads to the formation of the acoustic vortex with zero pressure on-axis and the angular phase dislocations characterized by the spiral geometry. The order of the generated Bessel beam and, as a consequence, the size of the generated vortex can be fixed by the number of arms in the spiral diffraction grating. The obtained results allow to obtain Bessel beams with controllable vorticity by a passive device, which has potential applications in low-cost acoustic tweezers and acoustic radiation force devices.
Carrier-wave Rabi flopping signatures in high-order harmonic generation for alkali atoms
Ciappina, M F; Landsman, A S; Zimmermann, T; Lewenstein, M; Roso, L; Krausz, F
2015-01-01
We present the first theoretical investigation of carrier-wave Rabi flopping in real atoms by employing numerical simulations of high-order harmonic generation (HHG) in alkali species. Given the short HHG cutoff, related to the low saturation intensity, we concentrate on the features of the third harmonic of sodium (Na) and potassium (K) atoms. For pulse areas of 2$\\pi$ and Na atoms, a characteristic unique peak appears, which, after analyzing the ground state population, we correlate with the conventional Rabi flopping. On the other hand, for larger pulse areas, carrier-wave Rabi flopping occurs, and is associated with a more complex structure in the third harmonic. These new characteristics observed in K atoms indicate the breakdown of the area theorem, as was already demonstrated under similar circumstances in narrow band gap semiconductors.
High order sliding mode control of a DFIM supplied by two power inverters
Directory of Open Access Journals (Sweden)
Zinelaabidine Boudjema
2015-06-01
Full Text Available Traditional vector control structures which include proportional-integral (PI regulator for the speed of a doubly fed induction motor (DFIM driven have some disadvantages such as parameter tuning complications, mediocre dynamic performances and reduced robustness. Thus, based on the analysis of the mathematical model of a DFIM supplied by two indirect inverters, this paper addresses a nonlinear control algorithm based on high order sliding mode. The conventional sliding mode control has large chattering on the electromagnetic torque developed by the DFIM. In order to solve this problem, the second order sliding mode technique is used. The simulation results show the effectiveness of the proposed method especially in chattering-free behavior, response to sudden load torque variations and robustness against machine parameters variations.
Intelligent Tracking Control for a Class of Uncertain High-Order Nonlinear Systems.
Zhao, Xudong; Shi, Peng; Zheng, Xiaolong; Zhang, Jianhua
2016-09-01
This brief is concerned with the problem of intelligent tracking control for a class of high-order nonlinear systems with completely unknown nonlinearities. An intelligent adaptive control algorithm is presented by combining the adaptive backstepping technique with the neural networks' approximation ability. It is shown that the practical output tracking performance of the system is achieved using the proposed state-feedback controller under two mild assumptions. In particular, by introducing a parameter in the derivations, the tracking error between the time-varying target signal and the output can be reduced via tuning the controller design parameters. Moreover, in order to solve the problem of overparameterization, which is a common issue in adaptive control design, a controller with one adaptive law is also designed. Finally, simulation results are given to show the effectiveness of the theoretical approaches and the potential of the proposed new design techniques.
Attosecond pulse production using resonantly-enhanced high-order harmonics
Strelkov, V V
2016-01-01
We study theoretically the effect of the giant resonance in Xe on the phase difference between the consecutive high order resonantly-enhanced harmonics and calculate the duration of the attosecond pulses produced by these harmonics. For certain conditions resonantly-induced dephasing compensates the phase difference which is intrinsic for the off-resonance harmonics. We find these conditions analytically and compare them with the numerical results. This harmonic synchronization allows attosecond pulse shortening in conjunction with the resonance-induced intensity increase by more than an order of magnitude; the latter enhancement relaxes the requirements for the UV filtering needed for the attosecond pulse production. Using a two-color driving field allows further increase of the intensity. In particular, a caustic-like feature in the harmonic spectrum leads to the generation efficiency growth up to two orders of magnitude, however accompanied by an elongation of the XUV pulse.
HIGH ORDER FUZZY TIME SERIES MODEL AND ITS APLICATION TO IMKB
Directory of Open Access Journals (Sweden)
Çağdaş Hakan ALADAĞ
2010-12-01
Full Text Available The observations of some real time series such as temperature and stock market can take different values in a day. Instead of representing the observations of these time series by real numbers, employing linguistic values or fuzzy sets can be more appropriate. In recent years, many approaches have been introduced to analyze time series consisting of observations which are fuzzy sets and such time series are called fuzzy time series. In this study, a novel approach is proposed to analyze high order fuzzy time series model. The proposed method is applied to IMKB data and the obtained results are discussed. IMKB data is also analyzed by using some other fuzzy time series methods available in the literature and obtained results are compared to results obtained from the proposed method. As a result of the comparison, it is seen that the proposed method produce accurate forecasts.
High-order sliding mode observer for fractional commensurate linear systems with unknown input
Belkhatir, Zehor
2017-05-20
In this paper, a high-order sliding mode observer (HOSMO) is proposed for the joint estimation of the pseudo-state and the unknown input of fractional commensurate linear systems with single unknown input and a single output. The convergence of the proposed observer is proved using a Lyapunov-based approach. In addition, an enhanced variant of the proposed fractional-HOSMO is introduced to avoid the peaking phenomenon and thus to improve the estimation results in the transient phase. Simulation results are provided to illustrate the performance of the proposed fractional observer in both noise-free and noisy cases. The effect of the observer’s gains on the estimated pseudo-state and unknown input is also discussed.
Resonance-modulated wavelength scaling of high-order-harmonic generation from H2+
Wang, Baoning; He, Lixin; Wang, Feng; Yuan, Hua; Zhu, Xiaosong; Lan, Pengfei; Lu, Peixiang
2018-01-01
Wavelength scaling of high-order harmonic generation (HHG) in a non-Born-Oppenheimer treatment of H2+ is investigated by numerical simulations of the time-dependent Schrödinger equation. The results show that the decrease in the wavelength-dependent HHG yield is reduced compared to that in the fixed-nucleus approximation. This slower wavelength scaling is related to the charge-resonance-enhanced ionization effect, which considerably increases the ionization rate at longer driving laser wavelengths due to the relatively larger nuclear separation. In addition, we find an oscillation structure in the wavelength scaling of HHG from H2+. Upon decreasing the laser intensity or increasing the nuclear mass, the oscillation structure will shift towards a longer wavelength of the laser pulse. These results permit the generation of an efficient harmonic spectrum in the midinfrared regime by manipulating the nuclear dynamics of molecules.
The a(4) Scheme-A High Order Neutrally Stable CESE Solver
Chang, Sin-Chung
2009-01-01
The CESE development is driven by a belief that a solver should (i) enforce conservation laws in both space and time, and (ii) be built from a nondissipative (i.e., neutrally stable) core scheme so that the numerical dissipation can be controlled effectively. To provide a solid foundation for a systematic CESE development of high order schemes, in this paper we describe a new high order (4-5th order) and neutrally stable CESE solver of a 1D advection equation with a constant advection speed a. The space-time stencil of this two-level explicit scheme is formed by one point at the upper time level and two points at the lower time level. Because it is associated with four independent mesh variables (the numerical analogues of the dependent variable and its first, second, and third-order spatial derivatives) and four equations per mesh point, the new scheme is referred to as the a(4) scheme. As in the case of other similar CESE neutrally stable solvers, the a(4) scheme enforces conservation laws in space-time locally and globally, and it has the basic, forward marching, and backward marching forms. Except for a singular case, these forms are equivalent and satisfy a space-time inversion (STI) invariant property which is shared by the advection equation. Based on the concept of STI invariance, a set of algebraic relations is developed and used to prove the a(4) scheme must be neutrally stable when it is stable. Numerically, it has been established that the scheme is stable if the value of the Courant number is less than 1/3
Utilizing liquid crystal phases to obtain highly ordered thin films for organic electronics
Springer, Mike T.
Organic electronic materials offer several advantages when compared to inorganic materials, but they suffer from low charge carrier mobility. Two major factors hindering effective charge transport in organic materials are: 1) effective wavefunction overlap in organic crystals and 2) the domain morphology of thin films. Charge transport in organic materials occurs via a hopping mechanism along the conjugated pi system. Often, rigid, aromatic organic materials crystallize in a herringbone, edge-to-face orientation, limiting pi-pi stacking and decreasing charge carrier mobility. Face-to-face orientation of aromatic rings decreases intermolecular pi-pi distances and increases wavefunction overlap. Control of the crystal structure can be achieved to some extent by tuning structural features of the molecule, like increasing the ratio of carbon atoms to hydrogen atoms in the aromatic rings; this is often achieved by introducing heteroatoms like sulfur and oxygen into the aromatic ring structure. Thin films of organic materials often contain many unaligned domains; this is caused by rapid crystallization. Control of the domain morphology of thin films has been shown to increase charge carrier mobility by 6 orders of magnitude for thin films of the same material. Liquid crystal phases allow a slow process of crystallization, whereby the molecules in a thin film can be slowly aligned into a monodomain before crystallization. The crystal-smectic phases, like smectic E, are particularly attractive for this strategy due to their high degree of intermolecular order. This project describes the synthesis and characterization of organic semiconductors designed to exhibit short pi-pi distances and highly ordered crystal-smectic phases to obtain thin films with high charge carrier mobility. The n,2-OBTTT series contains 15 newly designed and synthesized mesogens. The liquid crystal and solid crystal structures of these mesogens are examined and deposition conditions are optimized for
Direct Simulations of Transition and Turbulence Using High-Order Accurate Finite-Difference Schemes
Rai, Man Mohan
1997-01-01
In recent years the techniques of computational fluid dynamics (CFD) have been used to compute flows associated with geometrically complex configurations. However, success in terms of accuracy and reliability has been limited to cases where the effects of turbulence and transition could be modeled in a straightforward manner. Even in simple flows, the accurate computation of skin friction and heat transfer using existing turbulence models has proved to be a difficult task, one that has required extensive fine-tuning of the turbulence models used. In more complex flows (for example, in turbomachinery flows in which vortices and wakes impinge on airfoil surfaces causing periodic transitions from laminar to turbulent flow) the development of a model that accounts for all scales of turbulence and predicts the onset of transition may prove to be impractical. Fortunately, current trends in computing suggest that it may be possible to perform direct simulations of turbulence and transition at moderate Reynolds numbers in some complex cases in the near future. This seminar will focus on direct simulations of transition and turbulence using high-order accurate finite-difference methods. The advantage of the finite-difference approach over spectral methods is that complex geometries can be treated in a straightforward manner. Additionally, finite-difference techniques are the prevailing methods in existing application codes. In this seminar high-order-accurate finite-difference methods for the compressible and incompressible formulations of the unsteady Navier-Stokes equations and their applications to direct simulations of turbulence and transition will be presented.
Fast motif matching revisited: high-order PWMs, SNPs and indels.
Korhonen, Janne H; Palin, Kimmo; Taipale, Jussi; Ukkonen, Esko
2017-02-15
While the position weight matrix (PWM) is the most popular model for sequence motifs, there is growing evidence of the usefulness of more advanced models such as first-order Markov representations, and such models are also becoming available in well-known motif databases. There has been lots of research of how to learn these models from training data but the problem of predicting putative sites of the learned motifs by matching the model against new sequences has been given less attention. Moreover, motif site analysis is often concerned about how different variants in the sequence affect the sites. So far, though, the corresponding efficient software tools for motif matching have been lacking. We develop fast motif matching algorithms for the aforementioned tasks. First, we formalize a framework based on high-order position weight matrices for generic representation of motif models with dinucleotide or general q -mer dependencies, and adapt fast PWM matching algorithms to the high-order PWM framework. Second, we show how to incorporate different types of sequence variants , such as SNPs and indels, and their combined effects into efficient PWM matching workflows. Benchmark results show that our algorithms perform well in practice on genome-sized sequence sets and are for multiple motif search much faster than the basic sliding window algorithm. Implementations are available as a part of the MOODS software package under the GNU General Public License v3.0 and the Biopython license ( http://www.cs.helsinki.fi/group/pssmfind ). janne.h.korhonen@gmail.com.
Highly ordered Ni–Ti–O nanotubes for non-enzymatic glucose detection
Energy Technology Data Exchange (ETDEWEB)
Hang, Ruiqiang, E-mail: hangruiqiang@tyut.edu.cn [Research Institute of Surface Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Liu, Yanlian [Research Institute of Surface Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Gao, Ang [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong (China); Bai, Long; Huang, Xiaobo; Zhang, Xiangyu; Lin, Naiming [Research Institute of Surface Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Tang, Bin, E-mail: tangbin@tyut.edu.cn [Research Institute of Surface Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Chu, Paul K. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong (China)
2015-06-01
Anodization is used to fabricate Ni–Ti–O nanotube (NT) electrodes for non-enzymatic glucose detection. The morphology, microstructure and composition of the materials are characterized by field emission scanning electron microscopy (FE-SEM), high resolution transmission electron microscopy (HR-TEM) and X-ray photoelectron spectroscopy (XPS). Our results show amorphous and highly ordered NTs with diameter of 50 nm, length of 800 nm, and Ni/Ti ratio (at %) of 0.35 can be fabricated in ethylene glycol electrolyte supplemented with 0.2 wt.% NH{sub 4}F and 0.5 vol.% H{sub 2}O at 30 °C and 25 V for 1 h. Electrochemical experiments indicate that at an applied potential of 0.60 V vs. Ag/AgCl, the electrode exhibits a linear response window for glucose concentrations from 0.002 mM to 0.2 mM with a response time of 10 s, detection limit of 0.13 μM (S/N = 3), and sensitivity of 83 μA mM{sup −1} cm{sup −2}. The excellent performance of the electrode is attributed to its large specific area and fast electron transfer between the NT walls. The good electrochemical performance of the Ni–Ti–O NTs as well as their simple and low-cost preparation method make the strategy promising in non-enzymatic glucose detection. - Highlights: • Highly ordered Ni–Ti–O nanotubes have been fabricated by one-step anodization. • We find H{sub 2}O contents in the electrolyte is critical to successful fabrication of the NTs. • The Ni–Ti–O nanotubes are ideal electrode materials for non-enzymatic glucose detection.
Chen, Tianheng; Shu, Chi-Wang
2017-09-01
It is well known that semi-discrete high order discontinuous Galerkin (DG) methods satisfy cell entropy inequalities for the square entropy for both scalar conservation laws (Jiang and Shu (1994) [39]) and symmetric hyperbolic systems (Hou and Liu (2007) [36]), in any space dimension and for any triangulations. However, this property holds only for the square entropy and the integrations in the DG methods must be exact. It is significantly more difficult to design DG methods to satisfy entropy inequalities for a non-square convex entropy, and/or when the integration is approximated by a numerical quadrature. In this paper, we develop a unified framework for designing high order DG methods which will satisfy entropy inequalities for any given single convex entropy, through suitable numerical quadrature which is specific to this given entropy. Our framework applies from one-dimensional scalar cases all the way to multi-dimensional systems of conservation laws. For the one-dimensional case, our numerical quadrature is based on the methodology established in Carpenter et al. (2014) [5] and Gassner (2013) [19]. The main ingredients are summation-by-parts (SBP) operators derived from Legendre Gauss-Lobatto quadrature, the entropy conservative flux within elements, and the entropy stable flux at element interfaces. We then generalize the scheme to two-dimensional triangular meshes by constructing SBP operators on triangles based on a special quadrature rule. A local discontinuous Galerkin (LDG) type treatment is also incorporated to achieve the generalization to convection-diffusion equations. Extensive numerical experiments are performed to validate the accuracy and shock capturing efficacy of these entropy stable DG methods.
Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET
Hardin, John W.; Warnasooriya, Chandani; Kondo, Yasushi; Nagai, Kiyoshi; Rueda, David
2015-01-01
In large ribonucleoprotein machines, such as ribosomes and spliceosomes, RNA functions as an assembly scaffold as well as a critical catalytic component. Protein binding to the RNA scaffold can induce structural changes, which in turn modulate subsequent binding of other components. The spliceosomal U4/U6 di-snRNP contains extensively base paired U4 and U6 snRNAs, Snu13, Prp31, Prp3 and Prp4, seven Sm and seven LSm proteins. We have studied successive binding of all protein components to the snRNA duplex during di-snRNP assembly by electrophoretic mobility shift assay and accompanying conformational changes in the U4/U6 RNA 3-way junction by single-molecule FRET. Stems I and II of the duplex were found to co-axially stack in free RNA and function as a rigid scaffold during the entire assembly, but the U4 snRNA 5′ stem-loop adopts alternative orientations each stabilized by Prp31 and Prp3/4 binding accounting for altered Prp3/4 binding affinities in presence of Prp31. PMID:26503251
Lupus autoantibodies to native DNA cross-react with the A and D SnRNP polypeptides.
Reichlin, M; Martin, A; Taylor-Albert, E; Tsuzaka, K; Zhang, W; Reichlin, M W; Koren, E; Ebling, F M; Tsao, B; Hahn, B H
1994-01-01
Antibodies to native DNA (nDNA) in sera from patients with systemic lupus erythematosus have been found to frequently correlate with antibodies to the A and D SnRNP proteins measured in Western blot assays. 40 of 54 SLE (74.1%) sera with anti-nDNA bound to A and D proteins, while 9 of 113 sera (8%) without anti-nDNA bound the A and D proteins, P reacted equally with A and D, and two reacted predominantly with D. Two of three murine monoclonal anti-DNA antibodies isolated from NZB/NZW F1 hybrid mice bound A and D equally in Western blot with a titer > 1/40,000. These reactions were directed to the unfolded A and D proteins measurable in Western blot since these monoclonals (and several of the human anti-nDNA populations) failed to react with native U1RNP in ELISA or in RNA immunoprecipitation experiments. These newly recognized cross reactions of anti-nDNA may amplify the immune response to DNA and be part of the original immunogenic drive.
Development of a three-dimensional high-order strand-grids approach
Tong, Oisin
Development of a novel high-order flux correction method on strand grids is presented. The method uses a combination of flux correction in the unstructured plane and summation-by-parts operators in the strand direction to achieve high-fidelity solutions. Low-order truncation errors are cancelled with accurate flux and solution gradients in the flux correction method, thereby achieving a formal order of accuracy of 3, although higher orders are often obtained, especially for highly viscous flows. In this work, the scheme is extended to high-Reynolds number computations in both two and three dimensions. Turbulence closure is achieved with a robust version of the Spalart-Allmaras turbulence model that accommodates negative values of the turbulence working variable, and the Menter SST turbulence model, which blends the k-epsilon and k-o turbulence models for better accuracy. A major advantage of this high-order formulation is the ability to implement traditional finite volume-like limiters to cleanly capture shocked and discontinuous flows. In this work, this approach is explored via a symmetric limited positive (SLIP) limiter. Extensive verification and validation is conducted in two and three dimensions to determine the accuracy and fidelity of the scheme for a number of different cases. Verification studies show that the scheme achieves better than third order accuracy for low and high-Reynolds number flows. Cost studies show that in three-dimensions, the third-order flux correction scheme requires only 30% more walltime than a traditional second-order scheme on strand grids to achieve the same level of convergence. In order to overcome meshing issues at sharp corners and other small-scale features, a unique approach to traditional geometry, coined "asymptotic geometry," is explored. Asymptotic geometry is achieved by filtering out small-scale features in a level set domain through min/max flow. This approach is combined with a curvature based strand shortening
Directory of Open Access Journals (Sweden)
Essadki Mohamed
2016-09-01
Full Text Available Predictive simulation of liquid fuel injection in automotive engines has become a major challenge for science and applications. The key issue in order to properly predict various combustion regimes and pollutant formation is to accurately describe the interaction between the carrier gaseous phase and the polydisperse evaporating spray produced through atomization. For this purpose, we rely on the EMSM (Eulerian Multi-Size Moment Eulerian polydisperse model. It is based on a high order moment method in size, with a maximization of entropy technique in order to provide a smooth reconstruction of the distribution, derived from a Williams-Boltzmann mesoscopic model under the monokinetic assumption [O. Emre (2014 PhD Thesis, École Centrale Paris; O. Emre, R.O. Fox, M. Massot, S. Chaisemartin, S. Jay, F. Laurent (2014 Flow, Turbulence and Combustion 93, 689-722; O. Emre, D. Kah, S. Jay, Q.-H. Tran, A. Velghe, S. de Chaisemartin, F. Laurent, M. Massot (2015 Atomization Sprays 25, 189-254; D. Kah, F. Laurent, M. Massot, S. Jay (2012 J. Comput. Phys. 231, 394-422; D. Kah, O. Emre, Q.-H. Tran, S. de Chaisemartin, S. Jay, F. Laurent, M. Massot (2015 Int. J. Multiphase Flows 71, 38-65; A. Vié, F. Laurent, M. Massot (2013 J. Comp. Phys. 237, 277-310]. The present contribution relies on a major extension of this model [M. Essadki, S. de Chaisemartin, F. Laurent, A. Larat, M. Massot (2016 Submitted to SIAM J. Appl. Math.], with the aim of building a unified approach and coupling with a separated phases model describing the dynamics and atomization of the interface near the injector. The novelty is to be found in terms of modeling, numerical schemes and implementation. A new high order moment approach is introduced using fractional moments in surface, which can be related to geometrical quantities of the gas-liquid interface. We also provide a novel algorithm for an accurate resolution of the evaporation. Adaptive mesh refinement properly scaling on massively
Optimization of accelerator parameters using normal form methods on high-order transfer maps
Energy Technology Data Exchange (ETDEWEB)
Snopok, Pavel [Michigan State Univ., East Lansing, MI (United States)
2007-05-01
Methods of analysis of the dynamics of ensembles of charged particles in collider rings are developed. The following problems are posed and solved using normal form transformations and other methods of perturbative nonlinear dynamics: (1) Optimization of the Tevatron dynamics: (a) Skew quadrupole correction of the dynamics of particles in the Tevatron in the presence of the systematic skew quadrupole errors in dipoles; (b) Calculation of the nonlinear tune shift with amplitude based on the results of measurements and the linear lattice information; (2) Optimization of the Muon Collider storage ring: (a) Computation and optimization of the dynamic aperture of the Muon Collider 50 x 50 GeV storage ring using higher order correctors; (b) 750 x 750 GeV Muon Collider storage ring lattice design matching the Tevatron footprint. The normal form coordinates have a very important advantage over the particle optical coordinates: if the transformation can be carried out successfully (general restrictions for that are not much stronger than the typical restrictions imposed on the behavior of the particles in the accelerator) then the motion in the new coordinates has a very clean representation allowing to extract more information about the dynamics of particles, and they are very convenient for the purposes of visualization. All the problem formulations include the derivation of the objective functions, which are later used in the optimization process using various optimization algorithms. Algorithms used to solve the problems are specific to collider rings, and applicable to similar problems arising on other machines of the same type. The details of the long-term behavior of the systems are studied to ensure the their stability for the desired number of turns. The algorithm of the normal form transformation is of great value for such problems as it gives much extra information about the disturbing factors. In addition to the fact that the dynamics of particles is represented
Hybrid High-Order methods for finite deformations of hyperelastic materials
Abbas, Mickaël; Ern, Alexandre; Pignet, Nicolas
2018-01-01
We devise and evaluate numerically Hybrid High-Order (HHO) methods for hyperelastic materials undergoing finite deformations. The HHO methods use as discrete unknowns piecewise polynomials of order k≥1 on the mesh skeleton, together with cell-based polynomials that can be eliminated locally by static condensation. The discrete problem is written as the minimization of a broken nonlinear elastic energy where a local reconstruction of the displacement gradient is used. Two HHO methods are considered: a stabilized method where the gradient is reconstructed as a tensor-valued polynomial of order k and a stabilization is added to the discrete energy functional, and an unstabilized method which reconstructs a stable higher-order gradient and circumvents the need for stabilization. Both methods satisfy the principle of virtual work locally with equilibrated tractions. We present a numerical study of the two HHO methods on test cases with known solution and on more challenging three-dimensional test cases including finite deformations with strong shear layers and cavitating voids. We assess the computational efficiency of both methods, and we compare our results to those obtained with an industrial software using conforming finite elements and to results from the literature. The two HHO methods exhibit robust behavior in the quasi-incompressible regime.
Structure/Processing Relationships of Highly Ordered Lead Salt Nanocrystal Superlattices
Hanrath, Tobias
2009-10-27
We investigated the influence of processing conditions, nanocrystal/substrate interactions and solvent evaporation rate on the ordering of strongly interacting nanocrystals by synergistically combining electron microscopy and synchrotron-based small-angle X-ray scattering analysis. Spin-cast PbSe nanocrystal films exhibited submicrometer-sized supracrystals with face-centered cubic symmetry and (001)s planes aligned parallel to the substrate. The ordering of drop-cast lead salt nanocrystal films was sensitive to the nature of the substrate and solvent evaporation dynamics. Nanocrystal films drop-cast on rough indium tin oxide substrates were polycrystalline with small grain size and low degree of orientation with respect to the substrate, whereas films drop-cast on flat Si substrates formed highly ordered face-centered cubic supracrystals with close-packed (111)s planes parallel to the substrate. The spatial coherence of nanocrystal films drop-cast in the presence of saturated solvent vapor was significantly improved compared to films drop-cast in a dry environment. Solvent vapor annealing was demonstrated as a postdeposition technique to modify the ordering of nanocrystals in the thin film. Octane vapor significantly improved the long-range order and degree of orientation of initially disordered or polycrystalline nanocrystal assemblies. Exposure to 1,2-ethanedithiol vapor caused partial displacement of surface bound oleic acid ligands and drastically degraded the degree of order in the nanocrystal assembly. © 2009 American Chemical Society.
Fabrication of free-standing copper foils covered with highly-ordered copper nanowire arrays
Zaraska, Leszek; Sulka, Grzegorz D.; Jaskuła, Marian
2012-07-01
The through-hole nanoporous anodic aluminum oxide (AAO) membranes with relatively large surface area (ca. 2 cm2) were employed for fabrication of free-standing and mechanically stable copper foils covered with close-packed and highly-ordered copper nanowire arrays. The home-made AAO membranes with different pore diameters and interpore distances were fabricated via a two-step self-organized anodization of aluminum performed in sulfuric acid, oxalic acid and phosphoric acid followed by the pore opening/widening procedure. The direct current (DC) electrodeposition of copper was performed efficiently on both sides of AAO templates. The bottom side of the AAO templates was not insulated and consequently Cu nanowire arrays on thick Cu layers were obtained. The proposed template-assisted fabrication of free-standing copper nanowire array electrodes is a promising method for synthesis of nanostructured current collectors. The composition of Cu nanowires was confirmed by energy dispersive X-Ray spectroscopy (EDS) and X-ray diffraction (XRD) analyses. The structural features of nanowires were evaluated from field emission scanning electron microscopy (FE-SEM) images and compared with the characteristic parameters of anodic alumina membranes.
Role of high-order aberrations in senescent changes in spatial vision
Energy Technology Data Exchange (ETDEWEB)
Elliot, S; Choi, S S; Doble, N; Hardy, J L; Evans, J W; Werner, J S
2009-01-06
The contributions of optical and neural factors to age-related losses in spatial vision are not fully understood. We used closed-loop adaptive optics to test the visual benefit of correcting monochromatic high-order aberrations (HOAs) on spatial vision for observers ranging in age from 18-81 years. Contrast sensitivity was measured monocularly using a two-alternative forced choice (2AFC) procedure for sinusoidal gratings over 6 mm and 3 mm pupil diameters. Visual acuity was measured using a spatial 4AFC procedure. Over a 6 mm pupil, young observers showed a large benefit of AO at high spatial frequencies, whereas older observers exhibited the greatest benefit at middle spatial frequencies, plus a significantly larger increase in visual acuity. When age-related miosis is controlled, young and old observers exhibited a similar benefit of AO for spatial vision. An increase in HOAs cannot account for the complete senescent decline in spatial vision. These results may indicate a larger role of additional optical factors when the impact of HOAs is removed, but also lend support for the importance of neural factors in age-related changes in spatial vision.
Law, Yan Nei; Lieng, Monica Keiko; Li, Jingmei; Khoo, David Aik-Aun
2014-03-01
Breast cancer is the most common cancer and second leading cause of cancer death among women in the US. The relative survival rate is lower among women with a more advanced stage at diagnosis. Early detection through screening is vital. Mammography is the most widely used and only proven screening method for reliably and effectively detecting abnormal breast tissues. In particular, mammographic density is one of the strongest breast cancer risk factors, after age and gender, and can be used to assess the future risk of disease before individuals become symptomatic. A reliable method for automatic density assessment would be beneficial and could assist radiologists in the evaluation of mammograms. To address this problem, we propose a density classification method which uses statistical features from different parts of the breast. Our method is composed of three parts: breast region identification, feature extraction and building ensemble classifiers for density assessment. It explores the potential of the features extracted from second and higher order statistical information for mammographic density classification. We further investigate the registration of bilateral pairs and time-series of mammograms. The experimental results on 322 mammograms demonstrate that (1) a classifier using features from dense regions has higher discriminative power than a classifier using only features from the whole breast region; (2) these high-order features can be effectively combined to boost the classification accuracy; (3) a classifier using these statistical features from dense regions achieves 75% accuracy, which is a significant improvement from 70% accuracy obtained by the existing approaches.
Lee, Euntaek; Ahn, Hyung Taek; Luo, Hong
2018-02-01
We apply a hyperbolic cell-centered finite volume method to solve a steady diffusion equation on unstructured meshes. This method, originally proposed by Nishikawa using a node-centered finite volume method, reformulates the elliptic nature of viscous fluxes into a set of augmented equations that makes the entire system hyperbolic. We introduce an efficient and accurate solution strategy for the cell-centered finite volume method. To obtain high-order accuracy for both solution and gradient variables, we use a successive order solution reconstruction: constant, linear, and quadratic (k-exact) reconstruction with an efficient reconstruction stencil, a so-called wrapping stencil. By the virtue of the cell-centered scheme, the source term evaluation was greatly simplified regardless of the solution order. For uniform schemes, we obtain the same order of accuracy, i.e., first, second, and third orders, for both the solution and its gradient variables. For hybrid schemes, recycling the gradient variable information for solution variable reconstruction makes one order of additional accuracy, i.e., second, third, and fourth orders, possible for the solution variable with less computational work than needed for uniform schemes. In general, the hyperbolic method can be an effective solution technique for diffusion problems, but instability is also observed for the discontinuous diffusion coefficient cases, which brings necessity for further investigation about the monotonicity preserving hyperbolic diffusion method.
First demonstration of high-order QAM signal amplification in PPLN-based phase sensitive amplifier.
Umeki, T; Tadanaga, O; Asobe, M; Miyamoto, Y; Takenouchi, H
2014-02-10
We demonstrate the phase sensitive amplification of a high-order quadrature amplitude modulation (QAM) signal using non-degenerate parametric amplification in a periodically poled lithium niobate (PPLN) waveguide. The interaction between the pump, signal, and phase-conjugated idler enables us to amplify arbitrary phase components of the signal. The 16QAM signals are amplified without distortion because of the high gain linearity of the PPLN-based phase sensitive amplifier (PSA). Both the phase and amplitude noise reduction capabilities of the PSA are ensured. Phase noise cancellation is achieved by using the interaction with the phase-conjugated idler. A degraded signal-to-noise ratio (SNR) is restored by using the gain difference between a phase-correlated signal-idler pair and uncorrelated excess noise. The applicability of the simultaneous amplification of multi-carrier signals and the amplification of two independent polarization signals are also confirmed with a view to realizing ultra-high spectrally efficient signal amplification.
Investigating parasitic current formation in MITLs through high-order continuum kinetic simulations
Vogman, G. V.; Hammer, J. H.; Farmer, W. A.; Shumlak, U.
2017-10-01
The Z pulsed power facility is designed to deliver more than 20 MA of current to a load through magnetically insulated transmission lines (MITLs), which prevent high voltage arcs. Experimental results show that as much as 10% of the current can be lost due to the unintended formation of low-density plasmas in the MITLs. The configuration of the electric and magnetic fields within the MITL, where the plasma is born, creates conditions in which drift and kinetic instabilities can lead to the formation of parasitic currents. To understand the plasma dynamics that lead to current loss, the MITL configuration is investigated using a high-order continuum kinetic Vlasov-Poisson solver in two spatial and two velocity dimensions. The simulations capture the effects of varying magnetization and yield insights into plasma behavior over the course of current rise and corresponding magnetic field generation. The effects of plasma formation at the cathode versus at the anode are explored in detail. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Quantum interference during high-order harmonic generation from aligned molecules.
Kanai, Tsuneto; Minemoto, Shinichirou; Sakai, Hirofumi
2005-05-26
High-order harmonic generation (HHG) from atoms and molecules offers potential application as a coherent ultrashort radiation source in the extreme ultraviolet and soft X-ray regions. In the three-step model of HHG, an electron tunnels out from the atom and may recombine with the parent ion (emitting a high-energy photon) after undergoing laser-driven motion in the continuum. Aligned molecules can be used to study quantum phenomena in HHG associated with molecular symmetries; in particular, simultaneous observations of both ion yields and harmonic signals under the same conditions serve to disentangle the contributions from the ionization and recombination processes. Here we report evidence for quantum interference of electron de Broglie waves in the recombination process of HHG from aligned CO2 molecules. The interference takes place within a single molecule and within one optical cycle. Characteristic modulation patterns of the harmonic signals measured as a function of the pump-probe delay are explained with simple formulae determined by the valence orbital of the molecules. We propose that simultaneous observations of both ion yields and harmonic signals can serve as a new route to probe the instantaneous structure of molecular systems.
Measurements of High Order Modes in High Phase Advance Damped Detuned Accelerating Structure for NLC
Khabiboulline, N; Carter, H
2004-01-01
The RF Technology Development group at Fermilab is working together with the NLC and JLC groups at SLAC and KEK on developing technology for room temperature X-band accelerating structures for a future linear collider. We have built several series of structures for high gradient tests. We have also built 150° phase advance per cell, 60 cm long, damped and detuned structures (HDDS or FXC series). Some of these structures will be used for the 8-pack test at SLAC by the end of 2004, as part of the JLC/NLC effort to demonstrate the readiness of room temperature RF technology for a linear collider. HDSS structures are very close to the final design for the linear collider, and it was very interesting to study the properties of high order modes in the structures produced by semi-industrial methods. In this study advanced RF technique and methods developed at Fermilab for structure low power testing and tuning have been used. The results of these measurements are presented in this paper.
Martínez-Fonseca, Nadhynee; Castañeda, Luis Ángel; Uranga, Agustín; Luviano-Juárez, Alberto; Chairez, Isaac
2016-05-01
This study addressed the problem of robust control of a biped robot based on disturbance estimation. Active disturbance rejection control was the paradigm used for controlling the biped robot by direct active estimation. A robust controller was developed to implement disturbance cancelation based on a linear extended state observer of high gain class. A robust high-gain scheme was proposed for developing a state estimator of the biped robot despite poor knowledge of the plant and the presence of uncertainties. The estimated states provided by the state estimator were used to implement a feedback controller that was effective in actively rejecting the perturbations as well as forcing the trajectory tracking error to within a small vicinity of the origin. The theoretical convergence of the tracking error was proven using the Lyapunov theory. The controller was implemented by numerical simulations that showed the convergence of the tracking error. A comparison with a high-order sliding-mode-observer-based controller confirmed the superior performance of the controller using the robust observer introduced in this study. Finally, the proposed controller was implemented on an actual biped robot using an embedded hardware-in-the-loop strategy. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.
Yonata, B.; Nasrudin, H.
2018-01-01
A worksheet has to be a set with activity which is help students to arrange their own experiments. For this reason, this research is focused on how to train students’ higher order thinking skills in laboratory activity by developing laboratory activity worksheet on surface chemistry lecture. To ensure that the laboratory activity worksheet already contains aspects of the higher order thinking skill, it requires theoretical and empirical validation. From the data analysis results, it shows that the developed worksheet worth to use. The worksheet is worthy of theoretical and empirical feasibility. This conclusion is based on the findings: 1) Assessment from the validators about the theoretical feasibility aspects in the category is very feasible with an assessment range of 95.24% to 97.92%. 2) students’ higher thinking skill from N Gain values ranges from 0.50 (enough) to 1.00 (high) so it can be concluded that the laboratory activity worksheet on surface chemistry lecture is empirical in terms of worth. The empirical feasibility is supported by the responses of the students in very reasonable categories. It is expected that the laboratory activity worksheet on surface chemistry lecture can train students’ high order thinking skills for students who program surface chemistry lecture.
Hao, Qun; Li, Tengfei; Hu, Yao
2018-01-01
Surface parameters are the properties to describe the shape characters of aspheric surface, which mainly include vertex radius of curvature (VROC) and conic constant (CC). The VROC affects the basic properties, such as focal length of an aspheric surface, while the CC is the basis of classification for aspheric surface. The deviations of the two parameters are defined as surface parameter error (SPE). Precisely measuring SPE is critical for manufacturing and aligning aspheric surface. Generally, SPE of aspheric surface is measured directly by curvature fitting on the absolute profile measurement data from contact or non-contact testing. And most interferometry-based methods adopt null compensators or null computer-generated holograms to measure SPE. To our knowledge, there is no effective way to measure SPE of highorder aspheric surface with non-null interferometry. In this paper, based on the theory of slope asphericity and the best compensation distance (BCD) established in our previous work, we propose a SPE measurement method for high-order aspheric surface in partial compensation interferometry (PCI) system. In the procedure, firstly, we establish the system of two element equations by utilizing the SPE-caused BCD change and surface shape change. Then, we can simultaneously obtain the VROC error and CC error in PCI system by solving the equations. Simulations are made to verify the method, and the results show a high relative accuracy.
Quality metrics for high order meshes: analysis of the mechanical simulation of the heart beat.
Lamata, Pablo; Roy, Ishani; Blazevic, Bojan; Crozier, Andrew; Land, Sander; Niederer, Steven A; Hose, D Rod; Smith, Nicolas P
2013-01-01
The quality of a computational mesh is an important characteristic for stable and accurate simulations. Quality depends on the regularity of the initial mesh, and in mechanical simulations it evolves in time, with deformations causing changes in volume and distortion of mesh elements. Mesh quality metrics are therefore relevant for both mesh personalization and the monitoring of the simulation process. This work evaluates the significance, in meshes with high order interpolation, of four quality metrics described in the literature, applying them to analyse the stability of the simulation of the heart beat. It also investigates how image registration and mesh warping parameters affect the quality and stability of meshes. Jacobian-based metrics outperformed or matched the results of coarse geometrical metrics of aspect ratio or orthogonality, although they are more expensive computationally. The stability of simulations of a complete heart cycle was best predicted with a specificity of 61%, sensitivity of 85%, and only nominal differences were found changing the intra-element and per-element combination of quality values. A compromise between fitting accuracy and mesh stability and quality was found. Generic geometrical quality metrics have a limited success predicting stability, and an analysis of the simulation problem may be required for an optimal definition of quality.
Catalytic properties of highly ordered crystalline nanoporous tungsten oxide in butanol dehydration.
Choi, Hyeonhee; Lee, Eunok; Jin, Mingshi; Park, Young-Kwon; Kim, Ji Man; Jeon, Jong-Ki
2014-11-01
Highly ordered mesoporous tungsten oxide (meso-WO3) was successfully synthesized using mesoporous silica KIT-6 as a hard template via the nanoreplication method. The physicochemical properties of meso-WO3 were characterized by X-ray diffraction, nitrogen adsorption-desorption, transmission electron microscopy, X-ray photoelectron spectroscopy, temperature-programmed desorption of ammonia, and infra-red spectroscopy of adsorbed pyridine. No oxidation state other than WO3 was observed in the meso-WO3 sample. Lewis acid sites were dominant in meso-WO3, which could be confirmed by infra-red spectroscopy of pyridine and temperature-programmed desorption of ammonia. Its catalytic behavior in 2-butanol dehydration was investigated in a fixed bed reactor and compared with that of the WO3/MCM-41 catalyst prepared by the atomic layer deposition method. The meso-WO3 catalyst exhibited higher 2-butanol dehydration activity than that of the WO3/MCM-41 catalyst, which is ascribed to the stronger acidity as well as higher amount of acid sites that are mainly composed of Lewis acid sites in the meso-WO3 catalyst.
Highly ordered nanowire arrays on plastic substrates for ultrasensitive flexible chemical sensors
McAlpine, Michael C.; Ahmad, Habib; Wang, Dunwei; Heath, James R.
2007-05-01
The development of a robust method for integrating high-performance semiconductors on flexible plastics could enable exciting avenues in fundamental research and novel applications. One area of vital relevance is chemical and biological sensing, which if implemented on biocompatible substrates, could yield breakthroughs in implantable or wearable monitoring systems. Semiconducting nanowires (and nanotubes) are particularly sensitive chemical sensors because of their high surface-to-volume ratios. Here, we present a scalable and parallel process for transferring hundreds of pre-aligned silicon nanowires onto plastic to yield highly ordered films for low-power sensor chips. The nanowires are excellent field-effect transistors, and, as sensors, exhibit parts-per-billion sensitivity to NO2, a hazardous pollutant. We also use SiO2 surface chemistries to construct a `nano-electronic nose' library, which can distinguish acetone and hexane vapours via distributed responses. The excellent sensing performance coupled with bendable plastic could open up opportunities in portable, wearable or even implantable sensors.
MULTIPOLE GRAVITATIONAL LENSING AND HIGH-ORDER PERTURBATIONS ON THE QUADRUPOLE LENS
Energy Technology Data Exchange (ETDEWEB)
Chu, Z.; Lin, W. P. [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, 80 Nandan Road, Shanghai 200030 (China); Li, G. L. [Purple Mountain Observatory, 2 West Beijing Road, Nanjing 210008 (China); Kang, X., E-mail: chuzhe@shao.ac.cn, E-mail: linwp@shao.ac.cn [Partner Group of MPI for Astronomy, Purple Mountain Observatory, 2 West Beijing Road, Nanjing 210008 (China)
2013-03-10
An arbitrary surface mass density of the gravitational lens can be decomposed into multipole components. We simulate the ray tracing for the multipolar mass distribution of the generalized Singular Isothermal Sphere model based on deflection angles, which are analytically calculated. The magnification patterns in the source plane are then derived from an inverse shooting technique. As has been found, the caustics of odd mode lenses are composed of two overlapping layers for some lens models. When a point source traverses this kind of overlapping caustics, the image numbers change by {+-}4, rather than {+-}2. There are two kinds of caustic images. One is the critical curve and the other is the transition locus. It is found that the image number of the fold is exactly the average value of image numbers on two sides of the fold, while the image number of the cusp is equal to the smaller one. We also focus on the magnification patterns of the quadrupole (m = 2) lenses under the perturbations of m = 3, 4, and 5 mode components and found that one, two, and three butterfly or swallowtail singularities can be produced, respectively. With the increasing intensity of the high-order perturbations, the singularities grow up to bring sixfold image regions. If these perturbations are large enough to let two or three of the butterflies or swallowtails make contact, then eightfold or tenfold image regions can be produced as well. The possible astronomical applications are discussed.
Rectangular optical filter based on high-order silicon microring resonators
Bao, Jia-qi; Yu, Kan; Wang, Li-jun; Yin, Juan-juan
2017-07-01
The rectangular optical filter is one of the most important optical switching components in the dense wavelength division multiplexing (DWDM) fiber-optic communication system and the intelligent optical network. The integrated highorder silicon microring resonator (MRR) is one of the best candidates to achieve rectangular filtering spectrum response. In general, the spectrum response rectangular degree of the single MRR is very low, so it cannot be used in the DWDM system. Using the high-order MRRs, the bandwidth of flat-top pass band, the out-of-band rejection degree and the roll-off coefficient of the edge will be improved obviously. In this paper, a rectangular optical filter based on highorder MRRs with uniform couplers is presented and demonstrated. Using 15 coupled race-track MRRs with 10 μm in radius, the 3 dB flat-top pass band of 2 nm, the out-of-band rejection ratio of 30 dB and the rising and falling edges of 48 dB/nm can be realized successfully.
Yan, Bing-Nan; Liu, Chong-Xin; Ni, Jun-Kang; Zhao, Liang
2016-10-01
In order to grasp the downhole situation immediately, logging while drilling (LWD) technology is adopted. One of the LWD technologies, called acoustic telemetry, can be successfully applied to modern drilling. It is critical for acoustic telemetry technology that the signal is successfully transmitted to the ground. In this paper, binary phase shift keying (BPSK) is used to modulate carrier waves for the transmission and a new BPSK demodulation scheme based on Duffing chaos is investigated. Firstly, a high-order system is given in order to enhance the signal detection capability and it is realized through building a virtual circuit using an electronic workbench (EWB). Secondly, a new BPSK demodulation scheme is proposed based on the intermittent chaos phenomena of the new Duffing system. Finally, a system variable crossing zero-point equidistance method is proposed to obtain the phase difference between the system and the BPSK signal. Then it is determined that the digital signal transmitted from the bottom of the well is ‘0’ or ‘1’. The simulation results show that the demodulation method is feasible. Project supported by the National Natural Science Foundation of China (Grant No. 51177117) and the National Key Science & Technology Special Projects, China (Grant No. 2011ZX05021-005).
A High Order Theory for Linear Thermoelastic Shells: Comparison with Classical Theories
Directory of Open Access Journals (Sweden)
V. V. Zozulya
2013-01-01
Full Text Available A high order theory for linear thermoelasticity and heat conductivity of shells has been developed. The proposed theory is based on expansion of the 3-D equations of theory of thermoelasticity and heat conductivity into Fourier series in terms of Legendre polynomials. The first physical quantities that describe thermodynamic state have been expanded into Fourier series in terms of Legendre polynomials with respect to a thickness coordinate. Thereby all equations of elasticity and heat conductivity including generalized Hooke's and Fourier's laws have been transformed to the corresponding equations for coefficients of the polynomial expansion. Then in the same way as in the 3D theories system of differential equations in terms of displacements and boundary conditions for Fourier coefficients has been obtained. First approximation theory is considered in more detail. The obtained equations for the first approximation theory are compared with the corresponding equations for Timoshenko's and Kirchhoff-Love's theories. Special case of plates and cylindrical shell is also considered, and corresponding equations in displacements are presented.
Micropolar curved rods. 2-D, high order, Timoshenko’s and Euler-Bernoulli models
Directory of Open Access Journals (Sweden)
Zozulya V.V.
2017-01-01
Full Text Available New models for micropolar plane curved rods have been developed. 2-D theory is developed from general 2-D equations of linear micropolar elasticity using a special curvilinear system of coordinates related to the middle line of the rod and special hypothesis based on assumptions that take into account the fact that the rod is thin.High order theory is based on the expansion of the equations of the theory of elasticity into Fourier series in terms of Legendre polynomials. First stress and strain tensors,vectors of displacements and rotation and body force shave been expanded into Fourier series in terms of Legendre polynomials with respect to a thickness coordinate.Thereby all equations of elasticity including Hooke’s law have been transformed to the corresponding equations for Fourier coefficients. Then in the same way as in the theory of elasticity, system of differential equations in term of displacements and boundary conditions for Fourier coefficients have been obtained. The Timoshenko’s and Euler-Bernoulli theories are based on the classical hypothesis and 2-D equations of linear micropolar elasticity in a special curvilinear system. The obtained equations can be used to calculate stress-strain and to model thin walled structures in macro, micro and nano scale when taking in to account micropolar couple stress and rotation effects.
High-Order Hyperbolic Residual-Distribution Schemes on Arbitrary Triangular Grids
Mazaheri, Alireza; Nishikawa, Hiroaki
2015-01-01
In this paper, we construct high-order hyperbolic residual-distribution schemes for general advection-diffusion problems on arbitrary triangular grids. We demonstrate that the second-order accuracy of the hyperbolic schemes can be greatly improved by requiring the scheme to preserve exact quadratic solutions. We also show that the improved second-order scheme can be easily extended to third-order by further requiring the exactness for cubic solutions. We construct these schemes based on the LDA and the SUPG methodology formulated in the framework of the residual-distribution method. For both second- and third-order-schemes, we construct a fully implicit solver by the exact residual Jacobian of the second-order scheme, and demonstrate rapid convergence of 10-15 iterations to reduce the residuals by 10 orders of magnitude. We demonstrate also that these schemes can be constructed based on a separate treatment of the advective and diffusive terms, which paves the way for the construction of hyperbolic residual-distribution schemes for the compressible Navier-Stokes equations. Numerical results show that these schemes produce exceptionally accurate and smooth solution gradients on highly skewed and anisotropic triangular grids, including curved boundary problems, using linear elements. We also present Fourier analysis performed on the constructed linear system and show that an under-relaxation parameter is needed for stabilization of Gauss-Seidel relaxation.
Application of a sensitivity analysis technique to high-order digital flight control systems
Paduano, James D.; Downing, David R.
1987-01-01
A sensitivity analysis technique for multiloop flight control systems is studied. This technique uses the scaled singular values of the return difference matrix as a measure of the relative stability of a control system. It then uses the gradients of these singular values with respect to system and controller parameters to judge sensitivity. The sensitivity analysis technique is first reviewed; then it is extended to include digital systems, through the derivation of singular-value gradient equations. Gradients with respect to parameters which do not appear explicitly as control-system matrix elements are also derived, so that high-order systems can be studied. A complete review of the integrated technique is given by way of a simple example: the inverted pendulum problem. The technique is then demonstrated on the X-29 control laws. Results show linear models of real systems can be analyzed by this sensitivity technique, if it is applied with care. A computer program called SVA was written to accomplish the singular-value sensitivity analysis techniques. Thus computational methods and considerations form an integral part of many of the discussions. A user's guide to the program is included. The SVA is a fully public domain program, running on the NASA/Dryden Elxsi computer.
High-resolution nanosphere lithography (NSL) to fabricate highly-ordered ZnO nanorod arrays.
Zhang, Xiaoxian; Zhang, Lihuan; Gao, Min; Zhou, Weiya; Xie, Sishen
2010-11-01
Here we report our successful development of a high-resolution, low-cost, simple and convenient technique based on nanosphere lithography (NSL) to fabricate large-scale periodic gold nanoparticle pattern, which is the most common catalyst material in the synthesis of nanostructure and also a feature material for surface plasmon resonation (SPR) research. In order to improve lithography resolution by PS nanosphere self-assembling monolayer (SAM), we adapted the following steps in our fabrication strategy. The original continuous etching by oxygen plasma was replaced by multiple short treatments to avoid heating effect. In addition, direct oxidation was utilized to remove the nanospheres instead of the supersonic process. Using the obtained Au nanoparticle pattern, ZnO nanorod arrays with an average diameter of 50 nm were easily obtained by 600 nm PS nanospheres SAM, which was even smaller than the minimum size by utilizing 400 nm nanospheres SAM in the previous work. Thus, we succeeded in the fabrication of highly-ordered ZnO nanorod arrays with largely tunable diameter by this higher-resolution nanosphere lithography. We also present X-ray diffraction (XRD), transmission electron microscopy (TEM), photoluminescence (PL) and Raman results of our as-grown samples, indicating great crystallization quality and optical property.
High order vector mode coupling mechanism based on mode matching method
Zhang, Zhishen; Gan, Jiulin; Heng, Xiaobo; Li, Muqiao; Li, Jiong; Xu, Shanhui; Yang, Zhongmin
2017-06-01
The high order vector mode (HOVM) coupling mechanism is investigated based on the mode matching method (MMM). In the case of strong HOVM coupling where the weakly guiding approximation fails, conventional coupling analysis methods become invalid due to the asynchronous coupling feature of the horizontal and vertical polarization components of HOVM. The MMM, which uses the interference of the local eigenmodes instead of the assumptive modes to simulate the light propagation, is adopted as a more efficient analysis method for investigating HOVM coupling processes, especially for strong coupling situations. The rules of the optimal coupling length, coupling efficiency, and mode purity in microfiber directional coupler are firstly quantitatively analyzed and summarized. Different from the specific input modes, some special new modes would be excited at the output through the strong HOVM coupling process. The analysis of HOVM coupling mechanism based on MMM could provide precise and accurate design guidance for HOVM directional coupler and mode converter, which are believed to be fundamental devices for multi-mode communication applications.
Role of high-order aberrations in senescent changes in spatial vision
Elliott, Sarah L.; Choi, Stacey S.; Doble, Nathan; Hardy, Joseph L.; Evans, Julia W.; Werner, John S.
2009-01-01
The contributions of optical and neural factors to age-related losses in spatial vision are not fully understood. We used closed-loop adaptive optics to test the visual benefit of correcting monochromatic high-order aberrations (HOAs) on spatial vision for observers ranging in age from 18 to 81 years. Contrast sensitivity was measured monocularly using a two-alternative forced-choice (2AFC) procedure for sinusoidal gratings over 6 mm and 3 mm pupil diameters. Visual acuity was measured using a spatial 4AFC procedure. Over a 6 mm pupil, young observers showed a large benefit of AO at high spatial frequencies, whereas older observers exhibited the greatest benefit at middle spatial frequencies, plus a significantly larger increase in visual acuity. When age-related miosis is controlled, young and old observers exhibited a similar benefit of AO for spatial vision. An increase in HOAs cannot account for the complete senescent decline in spatial vision. These results may indicate a larger role of additional optical factors when the impact of HOAs is removed, but also lend support for the importance of neural factors in age-related changes in spatial vision. PMID:19271934
High order local absorbing boundary conditions for acoustic waves in terms of farfield expansions
Villamizar, Vianey; Acosta, Sebastian; Dastrup, Blake
2017-03-01
We devise a new high order local absorbing boundary condition (ABC) for radiating problems and scattering of time-harmonic acoustic waves from obstacles of arbitrary shape. By introducing an artificial boundary S enclosing the scatterer, the original unbounded domain Ω is decomposed into a bounded computational domain Ω- and an exterior unbounded domain Ω+. Then, we define interface conditions at the artificial boundary S, from truncated versions of the well-known Wilcox and Karp farfield expansion representations of the exact solution in the exterior region Ω+. As a result, we obtain a new local absorbing boundary condition (ABC) for a bounded problem on Ω-, which effectively accounts for the outgoing behavior of the scattered field. Contrary to the low order absorbing conditions previously defined, the error at the artificial boundary induced by this novel ABC can be easily reduced to reach any accuracy within the limits of the computational resources. We accomplish this by simply adding as many terms as needed to the truncated farfield expansions of Wilcox or Karp. The convergence of these expansions guarantees that the order of approximation of the new ABC can be increased arbitrarily without having to enlarge the radius of the artificial boundary. We include numerical results in two and three dimensions which demonstrate the improved accuracy and simplicity of this new formulation when compared to other absorbing boundary conditions.
The high order dispersion analysis based on first-passage-time probability in financial markets
Liu, Chenggong; Shang, Pengjian; Feng, Guochen
2017-04-01
The study of first-passage-time (FPT) event about financial time series has gained broad research recently, which can provide reference for risk management and investment. In this paper, a new measurement-high order dispersion (HOD)-is developed based on FPT probability to explore financial time series. The tick-by-tick data of three Chinese stock markets and three American stock markets are investigated. We classify the financial markets successfully through analyzing the scaling properties of FPT probabilities of six stock markets and employing HOD method to compare the differences of FPT decay curves. It can be concluded that long-range correlation, fat-tailed broad probability density function and its coupling with nonlinearity mainly lead to the multifractality of financial time series by applying HOD method. Furthermore, we take the fluctuation function of multifractal detrended fluctuation analysis (MF-DFA) to distinguish markets and get consistent results with HOD method, whereas the HOD method is capable of fractionizing the stock markets effectively in the same region. We convince that such explorations are relevant for a better understanding of the financial market mechanisms.
Au coated PS nanopillars as a highly ordered and reproducible SERS substrate
Kim, Yong-Tae; Schilling, Joerg; Schweizer, Stefan L.; Sauer, Guido; Wehrspohn, Ralf B.
2017-07-01
Noble metal nanostructures with nanometer gap size provide strong surface-enhanced Raman scattering (SERS) which can be used to detect trace amounts of chemical and biological molecules. Although several approaches were reported to obtain active SERS substrates, it still remains a challenge to fabricate SERS substrates with high sensitivity and reproducibility using low-cost techniques. In this article, we report on the fabrication of Au sputtered PS nanopillars based on a template synthetic method as highly ordered and reproducible SERS substrates. The SERS substrates are fabricated by anodic aluminum oxide (AAO) template-assisted infiltration of polystyrene (PS) resulting in hemispherical structures, and a following Au sputtering process. The optimum gap size between adjacent PS nanopillars and thickness of the Au layers for high SERS sensitivity are investigated. Using the Au sputtered PS nanopillars as an active SERS substrate, the Raman signal of 4-methylbenzenethiol (4-MBT) with a concentration down to 10-9 M is identified with good signal reproducibility, showing great potential as promising tool for SERS-based detection.
Directory of Open Access Journals (Sweden)
Germán A. Ramos-Fuentes
2016-01-01
Full Text Available Controlled rectifiers are electronic power devices aimed at reducing the harmonic pollution in electrical networks caused by the power conversion process. The main goal is to obtain a sinusoidal shape current in phase with the voltage network. Although Proportional Integral controllers are widely used for the current control loop, they do not provide high performance results. On the contrary, Resonant and Repetitive Control are techniques with remarkable results on this area. However, their main drawback is the lost of performance due to frequency changes in the exogenous signal. In this work, the implementation of an Odd Harmonic High Order Repetitive Controller is proposed for the rectifier current loop. The odd harmonic characteristic of this compensator makes possible to obtain a computational burden that is very similar to the one obtained by conventional repetitive controllers with the advantage of increase the robustness against frequency variations. Experimental results show the high performance obtained even when the network frequency does not match the designed nominal frequency
Methods for compressible fluid simulation on GPUs using high-order finite differences
Pekkilä, Johannes; Väisälä, Miikka S.; Käpylä, Maarit J.; Käpylä, Petri J.; Anjum, Omer
2017-08-01
We focus on implementing and optimizing a sixth-order finite-difference solver for simulating compressible fluids on a GPU using third-order Runge-Kutta integration. Since graphics processing units perform well in data-parallel tasks, this makes them an attractive platform for fluid simulation. However, high-order stencil computation is memory-intensive with respect to both main memory and the caches of the GPU. We present two approaches for simulating compressible fluids using 55-point and 19-point stencils. We seek to reduce the requirements for memory bandwidth and cache size in our methods by using cache blocking and decomposing a latency-bound kernel into several bandwidth-bound kernels. Our fastest implementation is bandwidth-bound and integrates 343 million grid points per second on a Tesla K40t GPU, achieving a 3 . 6 × speedup over a comparable hydrodynamics solver benchmarked on two Intel Xeon E5-2690v3 processors. Our alternative GPU implementation is latency-bound and achieves the rate of 168 million updates per second.
High-order Large Eddy Simulations of Confined Rotor-Stator Flows
Viazzo, Stéphane; Serre, Eric; Randriamampianina, Anthony; Bontoux, Patrick; 10.1007/s10494-011-9345-0
2013-01-01
In many engineering and industrial applications, the investigation of rotating turbulent flow is of great interest. In rotor-stator cavities, the centrifugal and Coriolis forces have a strong influence on the turbulence by producing a secondary flow in the meridian plane composed of two thin boundary layers along the disks separated by a non-viscous geostrophic core. Most numerical simulations have been performed using RANS and URANS modelling, and very few investigations have been performed using LES. This paper reports on quantitative comparisons of two high-order LES methods to predict a turbulent rotor-stator flow at the rotational Reynolds number Re=400000. The classical dynamic Smagorinsky model for the subgrid-scale stress (Germano et al., Phys Fluids A 3(7):1760-1765, 1991) is compared to a spectral vanishing viscosity technique (S\\'everac & Serre, J Comp Phys 226(2):1234-1255, 2007). Numerical results include both instantaneous data and postprocessed statistics. The results show that both LES met...
Optimization of multi-color laser waveform for high-order harmonic generation
Jin, Cheng; Lin, C. D.
2016-09-01
With the development of laser technologies, multi-color light-field synthesis with complete amplitude and phase control would make it possible to generate arbitrary optical waveforms. A practical optimization algorithm is needed to generate such a waveform in order to control strong-field processes. We review some recent theoretical works of the optimization of amplitudes and phases of multi-color lasers to modify the single-atom high-order harmonic generation based on genetic algorithm. By choosing different fitness criteria, we demonstrate that: (i) harmonic yields can be enhanced by 10 to 100 times, (ii) harmonic cutoff energy can be substantially extended, (iii) specific harmonic orders can be selectively enhanced, and (iv) single attosecond pulses can be efficiently generated. The possibility of optimizing macroscopic conditions for the improved phase matching and low divergence of high harmonics is also discussed. The waveform control and optimization are expected to be new drivers for the next wave of breakthrough in the strong-field physics in the coming years. Project supported by the Fundamental Research Funds for the Central Universities of China (Grant No. 30916011207), Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. Department of Energy (Grant No. DE-FG02-86ER13491), and Air Force Office of Scientific Research, USA (Grant No. FA9550-14-1-0255).
High-Order Fully General-Relativistic Hydrodynamics: new Approaches and Tests
Radice, David; Galeazzi, Filippo
2013-01-01
We present a new approach for achieving high-order convergence in fully general-relativistic hydrodynamic simulations. The approach is implemented in WhiskyTHC, a new code that makes use of state-of-the-art numerical schemes and was key in achieving, for the first time, higher than second-order convergence in the calculation of the gravitational radiation from inspiraling binary neutron stars Radice et al. (2013). Here, we give a detailed description of the algorithms employed and present results obtained for a series of classical tests involving isolated neutron stars. In addition, using the gravitational-wave emission from the late inspiral and merger of binary neutron stars, we make a detailed comparison between the results obtained with the new code and those obtained when using standard second-order schemes commonly employed for matter simulations in numerical relativity. We find that even at moderate resolutions and for binaries with large compactness, the phase accuracy is improved by a factor 50 or mo...
Bayesian Modeling of ChIP-chip Data Through a High-Order Ising Model
Mo, Qianxing
2010-01-29
ChIP-chip experiments are procedures that combine chromatin immunoprecipitation (ChIP) and DNA microarray (chip) technology to study a variety of biological problems, including protein-DNA interaction, histone modification, and DNA methylation. The most important feature of ChIP-chip data is that the intensity measurements of probes are spatially correlated because the DNA fragments are hybridized to neighboring probes in the experiments. We propose a simple, but powerful Bayesian hierarchical approach to ChIP-chip data through an Ising model with high-order interactions. The proposed method naturally takes into account the intrinsic spatial structure of the data and can be used to analyze data from multiple platforms with different genomic resolutions. The model parameters are estimated using the Gibbs sampler. The proposed method is illustrated using two publicly available data sets from Affymetrix and Agilent platforms, and compared with three alternative Bayesian methods, namely, Bayesian hierarchical model, hierarchical gamma mixture model, and Tilemap hidden Markov model. The numerical results indicate that the proposed method performs as well as the other three methods for the data from Affymetrix tiling arrays, but significantly outperforms the other three methods for the data from Agilent promoter arrays. In addition, we find that the proposed method has better operating characteristics in terms of sensitivities and false discovery rates under various scenarios. © 2010, The International Biometric Society.
Borsche, Raul; Kall, Jochen
2016-12-01
In this paper we construct high order finite volume schemes on networks of hyperbolic conservation laws with coupling conditions involving ODEs. We consider two generalized Riemann solvers at the junction, one of Toro-Castro type and a solver of Harten, Enquist, Osher, Chakravarthy type. The ODE is treated with a Taylor method or an explicit Runge-Kutta scheme, respectively. Both resulting high order methods conserve quantities exactly if the conservation is part of the coupling conditions. Furthermore we present a technique to incorporate lumped parameter models, which arise from simplifying parts of a network. The high order convergence and the robust capturing of shocks are investigated numerically in several test cases.
Parsani, Matteo
2011-09-01
The main goal of this paper is to develop an efficient numerical algorithm to compute the radiated far field noise provided by an unsteady flow field from bodies in arbitrary motion. The method computes a turbulent flow field in the near fields using a high-order spectral difference method coupled with large-eddy simulation approach. The unsteady equations are solved by advancing in time using a second-order backward difference formulae scheme. The nonlinear algebraic system arising from the time discretization is solved with the nonlinear lowerupper symmetric GaussSeidel algorithm. In the second step, the method calculates the far field sound pressure based on the acoustic source information provided by the first step simulation. The method is based on the Ffowcs WilliamsHawkings approach, which provides noise contributions for monopole, dipole and quadrupole acoustic sources. This paper will focus on the validation and assessment of this hybrid approach using different test cases. The test cases used are: a laminar flow over a two-dimensional (2D) open cavity at Re = 1.5 × 10 3 and M = 0.15 and a laminar flow past a 2D square cylinder at Re = 200 and M = 0.5. In order to show the application of the numerical method in industrial cases and to assess its capability for sound field simulation, a three-dimensional turbulent flow in a muffler at Re = 4.665 × 10 4 and M = 0.05 has been chosen as a third test case. The flow results show good agreement with numerical and experimental reference solutions. Comparison of the computed noise results with those of reference solutions also shows that the numerical approach predicts noise accurately. © 2011 IMACS.
Geometrically nonlinear analysis of hyperelastic solids by high-order tetrahedral finite elements
Pascon, João P.; Coda, Humberto B.
2010-06-01
The purpose of this study is to develop a computer code for accurate prediction of the mechanical behavior of hyperelastic solids under large deformation and finite strains. It is used, in the present work, the Lagrangian positional version of the Finite Element Method, in which the degrees of freedom are current positions instead of displacements. The main mechanical variables are the Green-Lagrange strain and the second Piola-Kirchhoff stress tensors. Isoparametric tetrahedral solid finite element of any approximation degree is employed with full integration in order to obtain accuracy. In order to be general, it is developed a numerical strategy to determine the shape functions coefficients of any order, following tetrahedral basis. The solid equilibrium is achieved at the current position by means of the Minimal Potential Energy Principle regarding positions and is solved by the Newton-Raphson iterative scheme. It is important to mention that the adopted constitutive laws are nonlinear, isotropic and homogeneous hyperelastic, normally used in mechanical analysis of elastomers, with the near compressibility assumption. It is applied the Flory decomposition, i.e., the multiplicative split of the deformation gradient into a volumetric and an isochoric part. A parallel processing strategy is used to increase the simulation speed and memory capacity, justifying the use of high order elements for solid analysis. Results confirm that the developed computer code is capable of predicting the static behavior of complex problems, such as Cook's membrane and partially loaded block. The shape functions generator code exhibits simplicity and, thus, it may be easily implemented in other finite elements. The increase in the order of approximation and the mesh refinement improve accuracy and, therefore, the proposed methodology together with parallel computing indicate a safe way for further developments in plasticity and damage mechanics for large strain and deformations.
Trajectory analysis of high-order-harmonic generation from periodic crystals
Ikemachi, Takuya; Shinohara, Yasushi; Sato, Takeshi; Yumoto, Junji; Kuwata-Gonokami, Makoto; Ishikawa, Kenichi L.
2017-04-01
We theoretically study high-order-harmonic generation (HHG) from solids driven by intense laser pulses using a one-dimensional model periodic crystal. By numerically solving the time-dependent Schrödinger equation directly on a real-space grid, we successfully reproduce experimentally observed unique features of solid-state HHG such as the linear cutoff-energy scaling and the sudden transition from a single- to multiple-plateau structure. Based on the simulation results, we propose a simple model that incorporates vector-potential-induced intraband displacement, interband tunneling, and recombination with the valence-band hole. One key parameter is the peak-to-valley amplitude of the pulse vector potential, which determines the crystal momentum displacement during the half cycle. When the maximum peak-to-valley amplitude Apeak reaches the half width π/a of the Brillouin zone with a being the lattice constant, the HHG spectrum exhibits a transition from a single- to multiple-plateau structure, and even further plateaus appear at Apeak=2/π a ,3/π a ,⋯ . The multiple cutoff positions are given as functions of Apeak and the second maximum Apeak', in terms of the energy difference between different bands. Using our recipe, one can draw electron trajectories in the momentum space, from which one can deduce, for example, the time-frequency structure of HHG without elaborate quantum-mechanical calculations. Finally, we reveal that the cutoff positions depend on not only the intensity and wavelength of the pulse, but also its duration, in marked contrast to the gas-phase case. Our model can be viewed as a solid-state and momentum-space counterpart of the familiar three-step model, highly successful for gas-phase HHG, and provide a unified basis to understand HHG from solid-state materials and gaseous media.
Mat Teridi, Mohd Asri; Sookhakian, Mehran; Basirun, Wan Jefrey; Zakaria, R.; Schneider, Fabio Kurt; da Silva, Wilson Jose; Kim, Jaeyeon; Lee, Seung Joo; Kim, Hyeong Pil; Mohd Yusoff, Abd. Rashid Bin; Jang, Jin
2015-04-01
High performance organic devices including polymer solar cells (PSCs) and light emitting diodes (PLEDs) were successfully demonstrated with the presence of highly ordered nanoimprinted Au nanodisks (Au NDs) in their solution-processed active/emissive layers, respectively. PSCs and PLEDs were fabricated using a low bandgap polymer and acceptor, nitrogen doped multiwalled carbon nanotubes poly[4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b']dithiophene-2,6-diyl][3-fluoro-2-[(2-ethylhexyl)carbonyl] thieno[3,4-b]-thiophenediyl] (n-MWCNTs:PTB7), and [6,6]-phenyl C71 butyric acid methyl ester (PC71BM) and (4,4-N,N-dicarbazole) biphenyl (CBP) doped with tris(2-phenylpyridine) iridium(iii) (Ir(ppy)3) as active/emissive layers, respectively. We synthesized nitrogen doped graphene and used it as anodic buffer layer in both devices. The localized surface plasmon resonance (LSPR) effect from Au NDs clearly contributed to the increase in light absorption/emission in the active layers from electromagnetic field enhancement, which originated from the excited LSPR in PSCs and PLEDs. In addition to the high density of LSPR and strong exciton-SP coupling, the electroluminescent (EL) enhancement is ascribed to enhanced spontaneous emission rates. This is due to the plasmonic near-field effect induced by Au NDs. The PSCs and PLEDs exhibited 14.98% (8.08% to 9.29%) under one sun of simulated air mass 1.5 global (AM1.5G) illumination (100 mW cm-2) and 19.18% (8.24 to 9.82 lm W-1) enhancement in the power conversion efficiencies (PCEs) compared to the control devices without Au NDs.
Energy Technology Data Exchange (ETDEWEB)
Azmy, Yousry [North Carolina State Univ., Raleigh, NC (United States); Wang, Yaqi [North Carolina State Univ., Raleigh, NC (United States)
2013-12-20
The research team has developed a practical, high-order, discrete-ordinates, short characteristics neutron transport code for three-dimensional configurations represented on unstructured tetrahedral grids that can be used for realistic reactor physics applications at both the assembly and core levels. This project will perform a comprehensive verification and validation of this new computational tool against both a continuous-energy Monte Carlo simulation (e.g. MCNP) and experimentally measured data, an essential prerequisite for its deployment in reactor core modeling. Verification is divided into three phases. The team will first conduct spatial mesh and expansion order refinement studies to monitor convergence of the numerical solution to reference solutions. This is quantified by convergence rates that are based on integral error norms computed from the cell-by-cell difference between the code’s numerical solution and its reference counterpart. The latter is either analytic or very fine- mesh numerical solutions from independent computational tools. For the second phase, the team will create a suite of code-independent benchmark configurations to enable testing the theoretical order of accuracy of any particular discretization of the discrete ordinates approximation of the transport equation. For each tested case (i.e. mesh and spatial approximation order), researchers will execute the code and compare the resulting numerical solution to the exact solution on a per cell basis to determine the distribution of the numerical error. The final activity comprises a comparison to continuous-energy Monte Carlo solutions for zero-power critical configuration measurements at Idaho National Laboratory’s Advanced Test Reactor (ATR). Results of this comparison will allow the investigators to distinguish between modeling errors and the above-listed discretization errors introduced by the deterministic method, and to separate the sources of uncertainty.
Risk factors for blood transfusion in patients undergoing high-order Cesarean delivery.
Spiegelman, Jessica; Mourad, Mirella; Melka, Stephanie; Gupta, Simi; Lam-Rachlin, Jennifer; Rebarber, Andrei; Saltzman, Daniel H; Fox, Nathan S
2017-11-01
The objective was to identify risk factors associated with blood transfusion in patients undergoing high-order Cesarean delivery (CD). This was a retrospective cohort study of patients undergoing third or more CD by a single maternal-fetal medicine practice between 2005 and 2016. We compared risk factors between women who did and did not receive a red blood cell transfusion during the operation or before discharge. Repeat analysis was performed after excluding women with placenta previa. A total of 514 patients were included, 18 of whom (3.5%; 95% confidence interval [CI], 2.2%-5.5%) received a blood transfusion. Placenta previa was the most significant risk factor for transfusion (61.1% of patients who received a transfusion vs. 1% of patients who did not; p blood transfusion. After women who had placenta previa were excluded, the incidence of blood transfusion was seven of 498 (1.4%; 95% CI, 0.7%-2.9%). Risk factors significantly associated with blood transfusion in the absence of previa were prophylactic anticoagulation during pregnancy and having labored. The incidence of transfusion in patients with no placenta previa, no anticoagulation, and no labor was 0.7% (95% CI, 0.3%-2.1%). Placenta previa was the most predictive risk factor for transfusion with a positive predictive value of 68.8% and a negative predictive value of 98.4%. In patients undergoing a third or more CD, only placenta previa, prophylactic anticoagulation during pregnancy, and having labored are independently associated with requiring a blood transfusion. These data can be used to guide physician ordering of prepared blood products preoperatively. © 2017 AABB.
SFG synthesis of general high-order all-pass and all-pole current transfer functions using CFTAs
National Research Council Canada - National Science Library
Tangsrirat, Worapong
2014-01-01
An approach of using the signal flow graph (SFG) technique to synthesize general high-order all-pass and all-pole current transfer functions with current follower transconductance amplifiers (CFTAs...
National Research Council Canada - National Science Library
Xue, Rui; Sun, Yanbo; Wei, Qiang
2016-01-01
This paper mainly studies the association between non-binary low-density parity-check codes and high-order partial response continuous phase modulation, which prevents information loss in the mutual...
El-Safty, Sherif A
2008-03-15
Design of nanocatalysts for efficient heterogeneous catalytic systems is needed to high ingredients for environmental cleanup of organic pollutant species. Here, well-defined order NiO-silica monolithic catalysts with hexagonal P6mm and cubic Pm3n mesostructures were successfully fabricated by using an instant direct-templating method of lyotropic and microemulsion phases of Brij 76 (C18H37(OCH2CH2)10 OH, C18EO 10). Ordered hexagonal P6mm NiO/HOM-2 monoliths could be fabricated in lyotropic system of Brij 76 at phase composition domains of TMOS/Brij 76 (50 wt%). However, periodically ordered cubic Pm3n NiO-supported monoliths were synthesized in microemulsion system formed by addition of C12-alkane to the hexagonal phase domains. This synthetic strategy also revealed that the NiO particles were well-dispersed into the silicate pore surface matrices of mesostructures. Monolithic NiO-silica composites with 2D hexagonal and 3D cubic geometries and with large particle morphologies show promise to act as catalysts. The current study revealed evidence of the advantages of nanoscale pore geometry and shape, and particle morphology of the supported silica monoliths in the design of nanocatalysts that can efficiently enhance the catalytic functionality in terms of stability, reversibility and reactivity. Furthermore, a key finding in our study was that 2D hexagonal and 3D cubic mesostructured NiO-silica catalysts retained the specific activity towards the oxidation reaction even after several regeneration/reuse cycles. Significant study of the mechanistic cyclization of the organic reactant using the density functional (DFT) calculations provided evidence of the key components of conformations of the functional model during the formation of the oxidation product.
Stein, David B.; Guy, Robert D; Thomases, Becca
2015-01-01
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet it only achieves first-order spatial accuracy near embedded boundaries. In this paper, we introduce a new high-order numerical method which we call the Immersed Boundary Smooth Extension (IBSE) method. The IBSE method achieves high-order accuracy by smoothly extending the unknown solution of the PDE from a given sm...
Lunt, Richard Royal, III
Organic semiconductors have gained tremendous attention recently as their use in field effect transistors, sensors, solar cells, lasers, and organic light emitting diodes have been demonstrated, offering the potential for low-cost alternatives. Since renewable energy remains one the greatest challenges of the 21st century, the possibility for low-cost and flexible organic photovoltaics is particularly exciting. In the first part of this thesis, we demonstrate a route to the controlled growth of oriented crystalline films through organic vapor-phase deposition (OVPD), in conjunction with organic-inorganic, and organic-organic quasi-epitaxy. This method for producing highly ordered crystalline thin-film heterostructures combines the control of film growth with the electronic properties expected to approach that of organic single crystals, making them potentially useful for high efficiency organic thin-film devices and solar cells. We further demonstrate OVPD as a method for the deposition of large-scale organic electronics with low material waste, a key ability in fulfilling the promise of low-cost organic devices. The second part of this thesis is focused on understanding factors that govern energy (i.e. exciton) transport. The two single most important and fundamental properties of organic semiconductors are the transport of charge and energy. While charge mobility has been extensively studied and convincingly linked to the degree of crystalline order and orientation, the principles governing energy transport, i.e. exciton migration, in this class of materials and the subsequent connection to crystalline properties still remain ambiguous. Therefore, we aim to understand key aspects governing exciton motion in organic materials to better engineer materials, film morphologies, and film architectures for organic electronics with improved performance. To this end, we have developed a new method for measuring exciton diffusion and characterize a range of archetypal
Finite volume schemes of very high order of accuracy for stiff hyperbolic balance laws
Dumbser, Michael; Enaux, Cedric; Toro, Eleuterio F.
2008-04-01
In this article, we propose a new class of finite volume schemes of arbitrary accuracy in space and time for systems of hyperbolic balance laws with stiff source terms. The new class of schemes is based on a three stage procedure. First a high-order WENO reconstruction procedure is applied to the cell averages at the current time level. Second, the temporal evolution of the reconstruction polynomials is computed locally inside each cell using the governing equations. In the original ENO scheme of Harten et al. and in the ADER schemes of Titarev and Toro, this time evolution is achieved via a Taylor series expansion where the time derivatives are computed by repeated differentiation of the governing PDE with respect to space and time, i.e. by applying the so-called Cauchy-Kovalewski procedure. However, this approach is not able to handle stiff source terms. Therefore, we present a new strategy that only replaces the Cauchy-Kovalewski procedure compared to the previously mentioned schemes. For the time-evolution part of the algorithm, we introduce a local space-time discontinuous Galerkin (DG) finite element scheme that is able to handle also stiff source terms. This step is the only part of the algorithm which is locally implicit. The third and last step of the proposed ADER finite volume schemes consists of the standard explicit space-time integration over each control volume, using the local space-time DG solutions at the Gaussian integration points for the intercell fluxes and for the space-time integral over the source term. We will show numerical convergence studies for nonlinear systems in one space dimension with both non-stiff and with very stiff source terms up to sixth order of accuracy in space and time. The application of the new method to a large set of different test cases is shown, in particular the stiff scalar model problem of LeVeque and Yee [R.J. LeVeque, H.C. Yee, A study of numerical methods for hyperbolic conservation laws with stiff source
Improving near vision in presbyopic eyes by selective treatment of high-order aberrations
Directory of Open Access Journals (Sweden)
Khalifa MA
2011-10-01
Full Text Available Mounir A Khalifa1,2, Waleed A Allam1,2, Ahmed M Khalifa21Tanta University Eye Hospital, Tanta, Egypt; 2Horus Vision Correction Center, Alexandria, EgyptPurpose: Evaluation of improving near vision in presbyopic patients with low to moderate myopia with selective treatment of high-order aberrations (HOAs using the ORK-CAM software aberrometer and a SCHWIND ESIRIS excimer laser. In this study, all HOAs except vertical coma were treated and the effect on near visual function was evaluated.Setting: Horus Vision Correction Center, Alexandria, Egypt.Methods: Twenty-six presbyopic patients (52 eyes with low to moderate myopia were divided into two groups, A and B. The ORK-CAM software aberrometer was used in both groups to measure HOAs and design wavefront-guided treatment. All included eyes had total coma >0.2 µm. The Moria M2 mechanical microkeratome was used for flap making in both groups. Wavefront-guided laser-assisted in situ keratomileusis using ESIRIS laser was done for all eyes. In Group A (30 eyes all HOAs were treated. In Group B (22 eyes vertical coma was left untreated. Postoperative uncorrected distance visual acuity (UCVA, best corrected distance visual acuity (BCVA, uncorrected near acuity (UCNA, distance corrected near acuity (DCNA, best corrected near acuity with addition for near vision (BCNA, manifest refractive spherical equivalent (MRSE, HOAs, and contrast sensitivity for both groups were done preoperatively and at 3 months postoperatively.Results: Mean age was 47.46 and 45.2 years for groups A and B, respectively. Mean preoperative MRSE was -2.37 and -2.87 D and mean preoperative total HOAs was 0.35 and 0.38 µm in groups A and B, respectively. There was no significant difference between groups regarding age, sex, preoperative MRSE, and preoperative total HOAs. After 3 months, there was no significant difference between groups in terms of UCVA, BCVA, MRSE, and contrast sensitivity. Analysis of postoperative HOAs showed
Kirkpatrick, John P; Li, Ping; Carlomagno, Teresa
2009-04-17
Confident interpretation of biochemical experiments performed with mutated proteins relies on verification of the integrity of the mutant structures. We present a simple and rapid refinement protocol for comparing the structures of mutated and wild-type proteins. Our approach involves measurement of residual dipolar couplings, and only requires assignment of the backbone resonances of the mutant species. We demonstrate application of the protocol to a mutant of the 15.5K protein, a core component of the U4 spliceosomal ribonucleoprotein (RNP) complex. Confirmation of the unperturbed structure of the mutated protein prompted re-examination of a previous mutagenesis study and indicated that the interpretation of mutant binding affinities in terms of direct interfacial contacts should be applied with caution.
Scaling high-order harmonic generation from laser-solid interactions to ultrahigh intensity.
Dollar, F; Cummings, P; Chvykov, V; Willingale, L; Vargas, M; Yanovsky, V; Zulick, C; Maksimchuk, A; Thomas, A G R; Krushelnick, K
2013-04-26
Coherent x-ray beams with a subfemtosecond (scale length, which can strongly influence the harmonic generation mechanism. It is shown that for intensities in excess of 10(21) W cm(-2) an optimum density ramp scale length exists that balances an increase in efficiency with a growth of parametric plasma wave instabilities. We show that for these higher intensities the optimal scale length is c/ω0, for which a variety of HOHG properties are optimized, including total conversion efficiency, HOHG divergence, and their power law scaling. Particle-in-cell simulations show striking evidence of the HOHG loss mechanism through parametric instabilities and relativistic self-phase modulation, which affect the produced spectra and conversion efficiency.
High-Order Unsteady Heat Transfer with the Harmonic Balance Method
Knapke, Robert David
accurately and efficiently simulating the unsteady heat transfer in turbomachinery flows. The HB and CHT methods are developed within a framework that uses a high-order Discontinuous Galerkin (DG) spatial discretization and a versatile Chimera overset scheme. The implemented HB method is fully linearized, allowing the use of an efficient Quasi-Newton solver. The HB equations are coupled within a linear system that includes the linearized HB pseudo-spectral operator. Phase lag and relative motion interfaces are included, hence the computational domain of multistage turbomachinery simulations is reduced to one passage per blade row. Modeling turbulent flows is achieved with the Spalart-Allmaras turbulence model. A strongly coupled CHT method is introduced. The solid and fluid domains are both discretized with the DG method. The fluid to solid interface enforces a consistent wall temperature and heat flux. The Harmonic Balance method, the Conjugate Heat Transfer method, and the Spalart-Allmaras turbulence model are independently verified using a series of test cases. In addition, CHT on curved 3D geometries is performed for the first time. Lastly, unsteady heat transfer is simulated using the combination of the HB and CHT methods. These test cases demonstrate the fast convergence and accurate modeling of the implemented methods. This work provides the basis for the accurate and efficient simulation of turbomachinery flows.
Wei, Bing; Li, Linqian; Yang, Qian; Ge, Debiao
Based on high order hierarchical basis function and the ideal of shift operator, shift operator discontinuous Galerkin time domain (SO-DGTD) technique for dealing with weakly ionized dusty plasma electromagnetic problems is proposed. Lagrange interpolation is used to transform the metallic blunt cone aircraft with weakly ionized dusty plasma sheath from geometric model built by COMSOL to electromagnetic computational model. In the case of two-dimensional transverse magnetic (TM) wave, the electromagnetic wave propagation in weakly ionized dusty plasma sheath is calculated by SO-DGTD technique. And then, the influence of dust particle concentration and dust radius on the radio wave transmission is analyzed, and the radio wave propagation characteristics pass through the sheath is compared with the flight speed and height change.
Directory of Open Access Journals (Sweden)
Hao Guo
2017-12-01
Full Text Available Functional magnetic resonance imaging (fMRI is one of the most useful methods to generate functional connectivity networks of the brain. However, conventional network generation methods ignore dynamic changes of functional connectivity between brain regions. Previous studies proposed constructing high-order functional connectivity networks that consider the time-varying characteristics of functional connectivity, and a clustering method was performed to decrease computational cost. However, random selection of the initial clustering centers and the number of clusters negatively affected classification accuracy, and the network lost neurological interpretability. Here we propose a novel method that introduces the minimum spanning tree method to high-order functional connectivity networks. As an unbiased method, the minimum spanning tree simplifies high-order network structure while preserving its core framework. The dynamic characteristics of time series are not lost with this approach, and the neurological interpretation of the network is guaranteed. Simultaneously, we propose a multi-parameter optimization framework that involves extracting discriminative features from the minimum spanning tree high-order functional connectivity networks. Compared with the conventional methods, our resting-state fMRI classification method based on minimum spanning tree high-order functional connectivity networks greatly improved the diagnostic accuracy for Alzheimer's disease.
High-order time-splitting Hermite and Fourier spectral methods
Thalhammer, Mechthild; Caliari, Marco; Neuhauser, Christof
2009-02-01
In this paper, we are concerned with the numerical solution of the time-dependent Gross-Pitaevskii Equation (GPE) involving a quasi-harmonic potential. Primarily, we consider discretisations that are based on spectral methods in space and higher-order exponential operator splitting methods in time. The resulting methods are favourable in view of accuracy and efficiency; moreover, geometric properties of the equation such as particle number and energy conservation are well captured. Regarding the spatial discretisation of the GPE, we consider two approaches. In the unbounded domain, we employ a spectral decomposition of the solution into Hermite basis functions; on the other hand, restricting the equation to a sufficiently large bounded domain, Fourier techniques are applicable. For the time integration of the GPE, we study various exponential operator splitting methods of convergence orders two, four, and six. Our main objective is to provide accuracy and efficiency comparisons of exponential operator splitting Fourier and Hermite pseudospectral methods for the time evolution of the GPE. Furthermore, we illustrate the effectiveness of higher-order time-splitting methods compared to standard integrators in a long-term integration.
High-order Fuchsian equations for the square lattice Ising model: {chi}{sup (6)}
Energy Technology Data Exchange (ETDEWEB)
Boukraa, S [LPTHIRM and Departement d' Aeronautique, Universite de Blida (Algeria); Hassani, S; Zenine, N [Centre de Recherche Nucleaire d' Alger, 2 Bd. Frantz Fanon, BP 399, 16000 Alger (Algeria); Jensen, I [ARC Centre of Excellence for Mathematics and Statistics of Complex Systems, Department of Mathematics and Statistics, University of Melbourne, Victoria 3010 (Australia); Maillard, J-M [LPTMC, Universite de Paris 6, Tour 24, 4eme etage, case 121, 4 Place Jussieu, 75252 Paris Cedex 05 (France)], E-mail: boukraa@mail.univ-blida.dz, E-mail: I.Jensen@ms.unimelb.edu.au, E-mail: maillard@lptmc.jussieu.fr, E-mail: njzenine@yahoo.com
2010-03-19
This paper deals with {chi}-tilde{sup (6)}, the six-particle contribution to the magnetic susceptibility of the square lattice Ising model. We have generated, modulo a prime, series coefficients for {chi}-tilde{sup (6)}. The length of the series is sufficient to produce the corresponding Fuchsian linear differential equation (modulo a prime). We obtain the Fuchsian linear differential equation that annihilates the 'depleted' series {phi}{sup (6)}={chi}-tilde{sup (6)} - 2/3 {chi}-tilde{sup (4)} + 2/45 {chi}-tilde{sup (2)}. The factorization of the corresponding differential operator is performed using a method of factorization modulo a prime, introduced in a previous paper. The 'depleted' differential operator is shown to have a structure similar to the corresponding operator for {chi}-tilde{sup (5)}. It splits into factors of smaller orders, with the left-most factor of order 6 being equivalent to the symmetric fifth power of the linear differential operator corresponding to the elliptic integral E. The right-most factor has a direct sum structure, and using series calculated modulo several primes, all the factors in the direct sum have been reconstructed in exact arithmetics.
Fonseca, Emanuella Maria Barreto; Scorsato, Valéria; Dos Santos, Marcelo Leite; Júnior, Atilio Tomazini; Tada, Susely Ferraz Siqueira; Dos Santos, Clelton Aparecido; de Toledo, Marcelo Augusto Szymanski; de Souza, Anete Pereira; Polikarpov, Igor; Aparicio, Ricardo
2017-04-01
Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity.
Lai, XuanYang; Wang, ChuanLiang; Chen, YongJu; Hu, ZiLong; Quan, Wei; Liu, XiaoJun; Chen, Jing; Cheng, Ya; Xu, ZhiZhan; Becker, Wilhelm
2013-01-25
We demonstrate the significant role of long quantum orbits in strong-field atomic processes by investigating experimentally and theoretically the above-threshold ionization spectra of noble gases in intense elliptically polarized laser pulses. With increasing laser ellipticity, the yields of different energy regions of the measured electron spectrum in high-order above-threshold ionization drop at different rates. The experimental features can be reproduced by a theoretical simulation based on quantum-orbit theory, revealing that increasing ellipticity favors the contributions of the long quantum orbits in the high-order above-threshold ionization process.
Wen, Liaoyong; Shao, Zhengzheng; Fang, Yaoguo; Wong, Kin Mun; Lei, Yong; Bian, Lifeng; Wilde, Gerhard
2010-08-01
A well controlled and cost effective method of fabricating highly ordered arrays of vertical zinc oxide (ZnO) nanowires or nanopores is demonstrated where an ultrathin alumina membrane (UTAM) itself is utilized as a substrate for the selective growth of the ordered arrays. A thin film of gold was thermally evaporated on the UTAM followed by the growth of highly regular ZnO nanowires using chemical vapor deposition (CVD). Alternatively, highly ordered ZnO nanopores arrays were also grown by CVD on the bare UTAM. Additionally, piezoelectric currents were generated from the ZnO nanowires during the conductive atomic force microscopy probe tip scan across the array.
Analysis and Design of a High-Order Discrete-Time Passive IIR Low-Pass Filter
Tohidian, M.; Madadi, I.; Staszewski, R.B.
2014-01-01
In this paper, we propose a discrete-time IIR low-pass filter that achieves a high-order of filtering through a charge-sharing rotation. Its sampling rate is then multiplied through pipelining. The first stage of the filter can operate in either a voltage-sampling or charge-sampling mode. It uses
DEFF Research Database (Denmark)
Laitinen, Tommi; Pivnenko, Sergey; Breinbjerg, Olav
2006-01-01
An iterative probe-correction technique for spherical near-field antenna measurements is examined. This technique has previously been shown to be well-suited for non-ideal first-order probes. In this paper, its performance in the case of a high-order probe (a dual-ridged horn) is examined....
Directory of Open Access Journals (Sweden)
François-Xavier Gillet
2017-04-01
Full Text Available Genetically modified (GM crops producing double-stranded RNAs (dsRNAs are being investigated largely as an RNA interference (RNAi-based resistance strategy against crop insect pests. However, limitations of this strategy include the sensitivity of dsRNA to insect gut nucleases and its poor insect cell membrane penetration. Working with the insect pest cotton boll weevil (Anthonomus grandis, we showed that the chimeric protein PTD-DRBD (peptide transduction domain—dsRNA binding domain combined with dsRNA forms a ribonucleoprotein particle (RNP that improves the effectiveness of the RNAi mechanism in the insect. The RNP slows down nuclease activity, probably by masking the dsRNA. Furthermore, PTD-mediated internalization in insect gut cells is achieved within minutes after plasma membrane contact, limiting the exposure time of the RNPs to gut nucleases. Therefore, the RNP provides an approximately 2-fold increase in the efficiency of insect gene silencing upon oral delivery when compared to naked dsRNA. Taken together, these data demonstrate the role of engineered RNPs in improving dsRNA stability and cellular entry, representing a path toward the design of enhanced RNAi strategies in GM plants against crop insect pests.
Qu, Xiangping; Lykke-Andersen, Søren; Nasser, Tommy; Saguez, Cyril; Bertrand, Edouard; Jensen, Torben Heick; Moore, Claire
2009-10-01
Before polyadenylated mRNA is exported from the nucleus, the 3'-end processing complex is removed by a poorly described mechanism. In this study, we asked whether factors involved in mRNP maturation and export are also required for disassembly of the cleavage and polyadenylation complex. An RNA immunoprecipitation assay monitoring the amount of the cleavage factor (CF) IA component Rna15p associated with poly(A)(+) RNA reveals defective removal of Rna15p in mutants of the nuclear export receptor Mex67p as well as other factors important for assembly of an export-competent mRNP. In contrast, Rna15p is not retained in mutants of export factors that function primarily on the cytoplasmic side of the nuclear pore. Consistent with a functional interaction between Mex67p and the 3'-end processing complex, a mex67 mutant accumulates unprocessed SSA4 transcripts and exhibits a severe growth defect when this mutation is combined with mutation of Rna15p or another CF IA subunit, Rna14p. RNAs that become processed in a mex67 mutant have longer poly(A) tails both in vivo and in vitro. This influence of Mex67p on 3'-end processing is conserved, as depletion of its human homolog, TAP/NXF1, triggers mRNA hyperadenylation. Our results indicate a function for nuclear mRNP assembly factors in releasing the 3'-end processing complex once polyadenylation is complete.
... Your Health Particle Pollution Public Health Issues Particle Pollution Recommend on Facebook Tweet Share Compartir Particle pollution — ... see them in the air. Where does particle pollution come from? Particle pollution can come from two ...
A high-order CESE scheme with a new divergence-free method for MHD numerical simulation
Yang, Yun; Feng, Xue-Shang; Jiang, Chao-Wei
2017-11-01
In this paper, we give a high-order space-time conservation element and solution element (CESE) method with a most compact stencil for magneto-hydrodynamics (MHD) equations. This is the first study to extend the second-order CESE scheme to a high order for MHD equations. In the CESE method, the conservative variables and their spatial derivatives are regarded as the independent marching quantities, making the CESE method significantly different from the finite difference method (FDM) and finite volume method (FVM). To utilize the characteristics of the CESE method to the maximum extent possible, our proposed method based on the least-squares method fundamentally keeps the magnetic field divergence-free. The results of some test examples indicate that this new method is very efficient.
Zhang, Lanqiang; Guo, Youming; Rao, Changhui
2017-02-20
Multi-conjugate adaptive optics (MCAO) is the most promising technique currently developed to enlarge the corrected field of view of adaptive optics for astronomy. In this paper, we propose a new configuration of solar MCAO based on high order ground layer adaptive optics and low order high altitude correction, which result in a homogeneous correction effect in the whole field of view. An individual high order multiple direction Shack-Hartmann wavefront sensor is employed in the configuration to detect the ground layer turbulence for low altitude correction. Furthermore, the other low order multiple direction Shack-Hartmann wavefront sensor supplies the wavefront information caused by high layers' turbulence through atmospheric tomography for high altitude correction. Simulation results based on the system design at the 1-meter New Vacuum Solar Telescope show that the correction uniform of the new scheme is obviously improved compared to conventional solar MCAO configuration.
Engwirda, Darren; Marshall, John
2016-01-01
The development of a set of high-order accurate finite-volume formulations for evaluation of the pressure gradient force in layered ocean models is described. A pair of new schemes are presented, both based on an integration of the contact pressure force about the perimeter of an associated momentum control-volume. The two proposed methods differ in their choice of control-volume geometries. High-order accurate numerical integration techniques are employed in both schemes to account for non-linearities in the underlying equation-of-state definitions and thermodynamic profiles, and details of an associated vertical interpolation and quadrature scheme are discussed in detail. Numerical experiments are used to confirm the consistency of the two formulations, and it is demonstrated that the new methods maintain hydrostatic and thermobaric equilibrium in the presence of strongly-sloping layer-wise geometry, non-linear equation-of-state definitions and non-uniform vertical stratification profiles. Additionally, one...
DEFF Research Database (Denmark)
Ashabani, Mahdi; Gooi, Hoay Beng; Guerrero, Josep M.
2018-01-01
This paper deals with development of a versatile and compact control strategy for voltage source converters in grid-connected and islanded microgrids using synchronous current converters technology. The key feature is its new integrated high-order controller/synchronizer with applicability to both...... operational modes without strategy rearrangement. Using high-order controllers, on the other hand, results in rather complex analysis and design process, therefore this paper aims at providing a general and simple theme for the design and parameter selection. The controller also provides adaptive...... and automated current-based grid synchronization. Moreover, the controller realizes a power-source current-controlled microgrid with minimum control loops, as compared to widely adopted voltage controlled microgrids in the literature, with advantages such as fault-ride-through and inherent droop-less power...
Supurwoko; Cari; Sarwanto; Sukarmin; Fauzi, Ahmad; Faradilla, Lisa; Summa Dewi, Tiarasita
2017-11-01
The process of learning and teaching in Physics is often confronted with abstract concepts. It makes difficulty for students to understand and teachers to teach the concept. One of the materials that has an abstract concept is Compton Effect. The purpose of this research is to evaluate computer simulation model on Compton Effect material which is used to improve high thinking ability of Physics teacher candidate students. This research is a case study. The subject is students at physics educations who have attended Modern Physics lectures. Data were obtained through essay test for measuring students’ high-order thinking skills and quisioners for measuring students’ responses. The results obtained indicate that computer simulation model can be used to improve students’ high order thinking skill and can be used to improve students’ responses. With this result it is suggested that the audiences use the simulation media in learning
Zhang, Ancai; Qiu, Jianlong; She, Jinhua
2014-02-01
This paper concerns the existence and exponential stability of periodic solution for the high-order discrete-time bidirectional associative memory (BAM) neural networks with time-varying delays. First, we present the criteria for the existence of periodic solution based on the continuation theorem of coincidence degree theory and the Young's inequality, and then we give the criteria for the global exponential stability of periodic solution by using a non-Lyapunov method. After that, we give a numerical example that demonstrates the effectiveness of the theoretical results. The criteria presented in this paper are easy to verify. In addition, the proposed analysis method is easy to extend to other high-order neural networks. Copyright © 2013 Elsevier Ltd. All rights reserved.
Phosphorylation of SAF-A/hnRNP-U Serine 59 by Polo-Like Kinase 1 Is Required for Mitosis.
Douglas, Pauline; Ye, Ruiqiong; Morrice, Nicholas; Britton, Sébastien; Trinkle-Mulcahy, Laura; Lees-Miller, Susan P
2015-08-01
Scaffold attachment factor A (SAF-A), also called heterogenous nuclear ribonuclear protein U (hnRNP-U), is phosphorylated on serine 59 by the DNA-dependent protein kinase (DNA-PK) in response to DNA damage. Since SAF-A, DNA-PK catalytic subunit (DNA-PKcs), and protein phosphatase 6 (PP6), which interacts with DNA-PKcs, have all been shown to have roles in mitosis, we asked whether DNA-PKcs phosphorylates SAF-A in mitosis. We show that SAF-A is phosphorylated on serine 59 in mitosis, that phosphorylation requires polo-like kinase 1 (PLK1) rather than DNA-PKcs, that SAF-A interacts with PLK1 in nocodazole-treated cells, and that serine 59 is dephosphorylated by protein phosphatase 2A (PP2A) in mitosis. Moreover, cells expressing SAF-A in which serine 59 is mutated to alanine have multiple characteristics of aberrant mitoses, including misaligned chromosomes, lagging chromosomes, polylobed nuclei, and delayed passage through mitosis. Our findings identify serine 59 of SAF-A as a new target of both PLK1 and PP2A in mitosis and reveal that both phosphorylation and dephosphorylation of SAF-A serine 59 by PLK1 and PP2A, respectively, are required for accurate and timely exit from mitosis. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
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Jansen Ralf-Peter
2004-10-01
Full Text Available Abstract Background The completion of several genome-sequencing projects has increased our need to assign functions to newly identified genes. The presence of a specific protein domain has been used as the determinant for suggesting a function for these new genes. In the case of proteins that are predicted to interact with mRNA, most RNAs bound by these proteins are still unknown. In yeast, several protocols for the identification of protein-protein interactions in high-throughput analyses have been developed during the last years leading to an increased understanding of cellular proteomics. If any of these protocols or similar approaches shall be used for the identification of mRNA-protein complexes, the integrity of mRNA is a critical factor. Results We compared the effect of different lysis protocols on RNA integrity. We report dramatic differences in RNA stability depending on the method used for yeast cell lysis. Glass bead milling and French Press lead to degraded mRNAs even in the presence of RNase inhibitors. Thus, they are not suitable to purify intact mRNP complexes or to identify specific mRNAs bound to proteins. Conclusion We suggest a novel protocol, grinding deep-frozen cells, for the preparation of protein extracts that contain intact RNAs, as lysis method for the purification of mRNA-protein complexes from yeast cells.
Gill, E. N.
1986-01-01
The requirements are identified for a very high order natural language to be used by crew members on board the Space Station. The hardware facilities, databases, realtime processes, and software support are discussed. The operations and capabilities that will be required in both normal (routine) and abnormal (nonroutine) situations are evaluated. A structure and syntax for an interface (front-end) language to satisfy the above requirements are recommended.
DEFF Research Database (Denmark)
Flindt, Christian; Novotny, Tomás; Braggio, Alessandro
2010-01-01
Recent experimental progress has made it possible to detect in real-time single electrons tunneling through Coulomb blockade nanostructures, thereby allowing for precise measurements of the statistical distribution of the number of transferred charges, the so-called full counting statistics......-Condon blockade, and transport through coherently coupled quantum dots embedded in a dissipative environment. We discuss properties of high-order cumulants as well as possible subtleties associated with non-Markovian dynamics....
2013-09-01
boundaries and 3-D pathway of titanium dioxide (TiO2) nanoparticles . In this work, highly ordered, densely packed, hexagonal TiO2 nanotubes were...synthesized in a single-step anodization of Ti foil using a constant dc potential of 60 V. The synthesized titania nanotubes exhibit a bamboo-like structure...INTENTIONALLY LEFT BLANK. 1 1. Introduction and Background Ordered titanium dioxide (TiO2) nanostructures, especially nanotubes and nanoparticles , have
Stein, David B.; Guy, Robert D.; Thomases, Becca
2016-01-01
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet it only achieves first-order spatial accuracy near embedded boundaries. In this paper, we introduce a new high-order numerical method which we call the Immersed Boundary Smooth Extension (IBSE) method. The IBSE method achieves high-order accuracy by smoothly extending the unknown solution of the PDE from a given smooth domain to a larger computational domain, enabling the use of simple Cartesian-grid discretizations (e.g. Fourier spectral methods). The method preserves much of the flexibility and robustness of the original IB method. In particular, it requires minimal geometric information to describe the boundary and relies only on convolution with regularized delta-functions to communicate information between the computational grid and the boundary. We present a fast algorithm for solving elliptic equations, which forms the basis for simple, high-order implicit-time methods for parabolic PDE and implicit-explicit methods for related nonlinear PDE. We apply the IBSE method to solve the Poisson, heat, Burgers', and Fitzhugh-Nagumo equations, and demonstrate fourth-order pointwise convergence for Dirichlet problems and third-order pointwise convergence for Neumann problems.
Hejlesen, M. M.; Rasmussen, J. T.; Chatelain, P.; Walther, J. H.
2012-11-01
This work improves upon Hockney and Eastwood's Fourier-based algorithm for the unbounded Poisson equation to formally achieve an arbitrary high order of convergence. The high order convergence is achieved by constructing regularized Green's functions through a filtering procedure. High order filters and regularized kernels are obtained by canceling the corresponding moments, a task which we show can be performed through a recursive application of extrapolation. We assess the methodology on the kinematic relations between the velocity and vorticity fields. In fluid mechanics the velocity is determined from the curl of the stream function which in turn is related to vorticity through the Poisson equation. The curl operator can be computed analytically, as a multi-component convolution kernel or, alternatively, computed directly in Fourier space through a spectral differentiation of the convolution product. The latter solution allows to reduce the computational cost and memory footprint of the algorithm while conserving its convergence order. Also at: Computational Science and Engineering Laboratory, ETH Zurich, Universitatsstrasse 6, CH-8092, Zurich, Switzerland.
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Bassi, F. [Universita degli Studi di Ancona (Italy); Rebay, S. [Universita degli Studi di Brescia (Italy)
1997-03-01
This paper deals with a high-order accurate discontinuous finite element method for the numerical solution of the compressible Navier-Stokes equations. We extend a discontinuous finite element discretization originally considered for hyperbolic systems such as the Euler equations to the case of the Navier-Stokes equations by treating the viscous terms with a mixed formulation. The method combines two key ideas which are at the basis of the finite volume and of the finite element method, the physics of wave propagation being accounted for by means of Riemann problems and accuracy being obtained by means of high-order polynomial approximations within elements. As a consequence the method is ideally suited to compute high-order accurate solution of the Navier-Stokes equations on unstructured grids. The performance of the proposed method is illustrated by computing the compressible viscous flow on a flat plate and around a NACA0012 airfoil for several flow regimes using constant, linear, quadratic, and cubic elements. 23 refs., 24 figs., 3 tabs.
Feng, Xiao; Ding, Xuesong; Chen, Long; Wu, Yang; Liu, Lili; Addicoat, Matthew; Irle, Stephan; Dong, Yuping; Jiang, Donglin
2016-09-01
Highly ordered discrete assemblies of chlorophylls that are found in natural light-harvesting antennae are key to photosynthesis, which converts light energy to chemical energy and is the principal producer of organic matter on Earth. Porphyrins and phthalocyanines, which are analogues of chlorophylls, exhibit a strong absorbance of visible and near-infrared light, respectively. A highly ordered porphyrin-co-phthalocyanine antennae would harvest photons over the entire solar spectrum for chemical transformation. However, such a robust antennae has not yet been synthesised. Herein, we report a strategy that merges covalent bonds and noncovalent forces to produce highly ordered two-dimensional porphyrin-co-phthalocyanine antennae. This methodology enables control over the stoichiometry and order of the porphyrin and phthalocyanine units; more importantly, this approach is compatible with various metalloporphyrin and metallophthalocyanine derivatives and thus may lead to the generation of a broad structural diversity of two-dimensional artificial antennae. These ordered porphyrin-co-phthalocyanine two-dimensional antennae exhibit unique optical properties and catalytic functions that are not available with single-component or non-structured materials. These 2D artificial antennae exhibit exceptional light-harvesting capacity over the entire solar spectrum as a result of a synergistic light-absorption effect. In addition, they exhibit outstanding photosensitising activities in using both visible and near-infrared photons for producing singlet oxygen.
Pelties, Christian
2012-02-18
Accurate and efficient numerical methods to simulate dynamic earthquake rupture and wave propagation in complex media and complex fault geometries are needed to address fundamental questions in earthquake dynamics, to integrate seismic and geodetic data into emerging approaches for dynamic source inversion, and to generate realistic physics-based earthquake scenarios for hazard assessment. Modeling of spontaneous earthquake rupture and seismic wave propagation by a high-order discontinuous Galerkin (DG) method combined with an arbitrarily high-order derivatives (ADER) time integration method was introduced in two dimensions by de la Puente et al. (2009). The ADER-DG method enables high accuracy in space and time and discretization by unstructured meshes. Here we extend this method to three-dimensional dynamic rupture problems. The high geometrical flexibility provided by the usage of tetrahedral elements and the lack of spurious mesh reflections in the ADER-DG method allows the refinement of the mesh close to the fault to model the rupture dynamics adequately while concentrating computational resources only where needed. Moreover, ADER-DG does not generate spurious high-frequency perturbations on the fault and hence does not require artificial Kelvin-Voigt damping. We verify our three-dimensional implementation by comparing results of the SCEC TPV3 test problem with two well-established numerical methods, finite differences, and spectral boundary integral. Furthermore, a convergence study is presented to demonstrate the systematic consistency of the method. To illustrate the capabilities of the high-order accurate ADER-DG scheme on unstructured meshes, we simulate an earthquake scenario, inspired by the 1992 Landers earthquake, that includes curved faults, fault branches, and surface topography. Copyright 2012 by the American Geophysical Union.
Zhang, Changkun; Yu, Hongmei; Li, Yongkun; Gao, Yuan; Zhao, Yun; Song, Wei; Shao, Zhigang; Yi, Baolian
2013-04-01
Hydrogen-treated TiO2 nanotube (H-TNT) arrays serve as highly ordered nanostructured electrode supports, which are able to significantly improve the electrochemical performance and durability of fuel cells. The electrical conductivity of H-TNTs increases by approximately one order of magnitude in comparison to air-treated TNTs. The increase in the number of oxygen vacancies and hydroxyl groups on the H-TNTs help to anchor a greater number of Pt atoms during Pt electrodeposition. The H-TNTs are pretreated by using a successive ion adsorption and reaction (SIAR) method that enhances the loading and dispersion of Pt catalysts when electrodeposited. In the SIAR method a Pd activator can be used to provide uniform nucleation sites for Pt and leads to increased Pt loading on the H-TNTs. Furthermore, fabricated Pt nanoparticles with a diameter of 3.4 nm are located uniformly around the pretreated H-TNT support. The as-prepared and highly ordered electrodes exhibit excellent stability during accelerated durability tests, particularly for the H-TNT-loaded Pt catalysts that have been annealed in ultrahigh purity H2 for a second time. There is minimal decrease in the electrochemical surface area of the as-prepared electrode after 1000 cycles compared to a 68 % decrease for the commercial JM 20 % Pt/C electrode after 800 cycles. X-ray photoelectron spectroscopy shows that after the H-TNT-loaded Pt catalysts are annealed in H2 for the second time, the strong metal-support interaction between the H-TNTs and the Pt catalysts enhances the electrochemical stability of the electrodes. Fuel-cell testing shows that the power density reaches a maximum of 500 mWcm(-2) when this highly ordered electrode is used as the anode. When used as the cathode in a fuel cell with extra-low Pt loading, the new electrode generates a specific power density of 2.68 kWg(Pt) (-1) . It is indicated that H-TNT arrays, which have highly ordered nanostructures, could be used as ordered electrode supports
Leader–follower fixed-time consensus of multi-agent systems with high-order integrator dynamics
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Tian, Bailing; Zuo, Zongyu; Wang, Hong
2016-07-27
The leader-follower fixed-time consensus of high-order multi-agent systems with external disturbances is investigated in this paper. A novel sliding manifold is designed to ensure that the tracking errors converge to zero in a fixed-time during the sliding motion. Then, a distributed control law is designed based on Lyapunov technique to drive the system states to the sliding manifold in finite-time independent of initial conditions. Finally, the efficiency of the proposed method is illustrated by numerical simulations.
Directory of Open Access Journals (Sweden)
Weiguo Rui
2014-01-01
Full Text Available By using the integral bifurcation method together with factoring technique, we study a water wave model, a high-order nonlinear wave equation of KdV type under some newly solvable conditions. Based on our previous research works, some exact traveling wave solutions such as broken-soliton solutions, periodic wave solutions of blow-up type, smooth solitary wave solutions, and nonsmooth peakon solutions within more extensive parameter ranges are obtained. In particular, a series of smooth solitary wave solutions and nonsmooth peakon solutions are obtained. In order to show the properties of these exact solutions visually, we plot the graphs of some representative traveling wave solutions.
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Wang, Yang; Song, Hai-Ying; Liu, H.Y.; Liu, Shi-Bing, E-mail: sbliu@bjut.edu.cn
2017-07-12
Highlights: • Proposed a valid mechanism of high harmonic generation by laser grating target interaction: oscillation of equivalent electric dipole (OEED). • Found that there also exist harmonic emission at large emission angle but not just near-surface direction as the former researches had pointed out. • Show the process of the formation and motion of electron bunches at the grating-target surface irradiating with femtosecond laser pulse. - Abstract: We theoretically study high-order harmonic generation (HHG) from relativistically driven overdense plasma targets with rectangularly grating-structured surfaces by femtosecond laser pulses. Our particle-in-cell (PIC) simulations show that, under the conditions of low laser intensity and plasma density, the harmonics emit principally along small angles deviating from the target surface. Further investigation of the surface electron dynamics reveals that the electron bunches are formed by the interaction between the laser field and the target surface, giving rise to the oscillation of equivalent electric-dipole (OEED), which enhances specific harmonic orders. Our work helps understand the mechanism of harmonic emissions from grating targets and the distinction from the planar harmonic scheme.
DEFF Research Database (Denmark)
Stock, Andreas; Neudorfer, Jonathan; Riedlinger, Marc
2012-01-01
Fast design codes for the simulation of the particle–field interaction in the interior of gyrotron resonators are available. They procure their rapidity by making strong physical simplifications and approximations, which are not known to be valid for many variations of the geometry and the operat...
Koren, E; Koscec, M; Wolfson-Reichlin, M; Ebling, F M; Tsao, B; Hahn, B H; Reichlin, M
1995-05-01
Murine monoclonal and human affinity-purified Abs to native DNA (anti-nDNA) that cross-react with the A and D SnRNP polypeptides were analyzed for direct injurious effects against cultured pig kidney (PK15) cells under ordinary cell-culture conditions. Of the two murine nephritogenic Abs derived from NZB/NZW F1 mice (BWds1 and BWds3), BWds1 initially bound to the cell surface and subsequently penetrated into cells localizing in nuclei and cytoplasm. BWds3 was consistently and abundantly associated with the surface of live cells without penetration. In the presence of rabbit C, BWds3 caused massive cell lysis (85% dead cells) whereas BWds1 had only a modest lytic effect (24% dead cells). One of the nonpathogenic murine anti-nDNA Abs (5GD5) that did not cross-react with the A and D polypeptides showed no interaction with PK-15 cells and had no injurious effects. Affinity-purified autoantibodies to nDNA isolated from two SLE patients with high anti-nDNA titers and clinically active lupus nephritis showed properties similar to the murine mAbs. They both strongly cross-reacted with the A and D SnRNP polypeptides and interacted with live PK-15 cells. One of them (Cr) penetrated into live cells and localized within cytoplasm and nuclei whereas the other (Pe) bound mostly to the cell surface and caused significant cell lysis in the presence of C. Results of this study suggest that the nephritogenic murine anti-nDNA as well as subpopulations of human anti-nDNA Abs could exert their injurious influence through direct interactions with kidney cells using two different pathogenic mechanisms (i.e., C-mediated cytotoxicity and potential cell cycle dysfunctions. Interestingly, cross-reactivity of anti-nDNA Abs with the A and D SnRNP polypeptides appears to be a prerequisite for their direct pathogenicity.
Directory of Open Access Journals (Sweden)
Travis J Loya
Full Text Available Many RNA-binding proteins possess domains with a biased amino acid content. A common property of these low complexity domains (LCDs is that they assemble into an ordered amyloid form, juxtaposing RNA recognition motifs in a subcellular compartment in which RNA metabolism is focused. Yeast Nab3 is one such protein that contains RNA-binding domains and a low complexity, glutamine/proline-rich, prion-like domain that can self-assemble. Nab3 also contains a region of structural homology to human hnRNP-C that resembles a leucine zipper which can oligomerize. Here we show that the LCD and the human hnRNP-C homology domains of Nab3 were experimentally separable, as cells were viable with either segment, but not when both were missing. In exploiting the lethality of deleting these regions of Nab3, we were able to test if heterologous prion-like domains known to assemble into amyloid, could substitute for the native sequence. Those from the hnRNP-like protein Hrp1, the canonical prion Sup35, or the epsin-related protein Ent2, could rescue viability and enable the new Nab3 chimeric protein to support transcription termination. Other low complexity domains from RNA-binding, termination-related proteins or a yeast prion, could not. As well, an unbiased genetic selection revealed a new protein sequence that could rescue the loss of Nab3's essential domain via multimerization. This new sequence and Sup35's prion domain could also rescue the lethal loss of Hrp1's prion-like domain when substituted for it. This suggests there are different cross-functional classes of amyloid-forming LCDs and that appending merely any assembly-competent LCD to Nab3 does not restore function or rescue viability. The analysis has revealed the functional complexity of LCDs and provides a means by which the differing classes of LCD can be dissected and understood.
Woodward, Cora L; Cheng, Sarah N; Jensen, Grant J
2015-01-15
To better characterize the assembly of the HIV-1 core, we have used electron cryotomography (ECT) to image infected cells and the viral particles cryopreserved next to them. We observed progressive stages of virus assembly and egress, including flower-like flat Gag lattice assemblies, hemispherical budding profiles, and virus buds linked to the plasma membrane via a thin membrane neck. The population of budded viral particles contains immature, maturation-intermediate, and mature core morphologies. Structural characteristics of the maturation intermediates suggest that the core assembly pathway involves the formation of a CA sheet that associates with the condensed ribonucleoprotein (RNP) complex. Our analysis also reveals a correlation between RNP localization within the viral particle and the formation of conical cores, suggesting that the RNP helps drive conical core assembly. Our findings support an assembly pathway for the HIV-1 core that begins with a small CA sheet that associates with the RNP to form the core base, followed by polymerization of the CA sheet along one side of the conical core toward the tip, and then closure around the body of the cone. During HIV-1 assembly and release, the Gag polyprotein is organized into a signature hexagonal lattice, termed the immature lattice. To become infectious, the newly budded virus must disassemble the immature lattice by proteolyzing Gag and then reassemble the key proteolytic product, the structural protein p24 (CA), into a distinct, mature hexagonal lattice during a process termed maturation. The mature HIV-1 virus contains a conical capsid that encloses the condensed viral genome at its wide base. Mutations or small molecules that interfere with viral maturation also disrupt viral infectivity. Little is known about the assembly pathway that results in the conical core and genome encapsidation. Here, we have used electron cryotomography to structurally characterize HIV-1 particles that are actively maturing
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Minghua Zhou
2012-01-01
Full Text Available Highly ordered sodium-free titanate nanotube films were one-step prepared on F-doped SnO2-coated (FTO glass via an electrophoretic deposition method by using sodium titanate nanotubes as the precursor. It was found that the self-assembled formation of highly ordered sodium titanate nanotube films was accompanied with the effective removal of sodium ions in the nanotubes during the electrophoretic deposition process, resulting in the final formation of protonated titanate nanotube film. With increasing calcination temperature, the amorphous TiO2 phase is formed by a dehydration process of the protonated titanate nanotubes at 300°C and further transforms into anatase TiO2 when the calcination temperature is higher than 400°C. Compared with the as-prepared titanate nanotube film, the calcined titanate nanotube film (300–600°C exhibits attractive photoinduced superhydrophilicity under UV-light irradiation. In particular, 500°C-calcined films show the best photoinduced superhydrophilicity, probably due to synergetic effects of enhanced crystallization, surface roughness, and ordered structures of the films.
Ketcheson, David I.
2014-06-13
We compare the three main types of high-order one-step initial value solvers: extrapolation, spectral deferred correction, and embedded Runge–Kutta pairs. We consider orders four through twelve, including both serial and parallel implementations. We cast extrapolation and deferred correction methods as fixed-order Runge–Kutta methods, providing a natural framework for the comparison. The stability and accuracy properties of the methods are analyzed by theoretical measures, and these are compared with the results of numerical tests. In serial, the eighth-order pair of Prince and Dormand (DOP8) is most efficient. But other high-order methods can be more efficient than DOP8 when implemented in parallel. This is demonstrated by comparing a parallelized version of the wellknown ODEX code with the (serial) DOP853 code. For an N-body problem with N = 400, the experimental extrapolation code is as fast as the tuned Runge–Kutta pair at loose tolerances, and is up to two times as fast at tight tolerances.
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Jan Hesthaven
2012-02-06
Final report for DOE Contract DE-FG02-98ER25346 entitled Parallel High Order Accuracy Methods Applied to Non-Linear Hyperbolic Equations and to Problems in Materials Sciences. Principal Investigator Jan S. Hesthaven Division of Applied Mathematics Brown University, Box F Providence, RI 02912 Jan.Hesthaven@Brown.edu February 6, 2012 Note: This grant was originally awarded to Professor David Gottlieb and the majority of the work envisioned reflects his original ideas. However, when Prof Gottlieb passed away in December 2008, Professor Hesthaven took over as PI to ensure proper mentoring of students and postdoctoral researchers already involved in the project. This unusual circumstance has naturally impacted the project and its timeline. However, as the report reflects, the planned work has been accomplished and some activities beyond the original scope have been pursued with success. Project overview and main results The effort in this project focuses on the development of high order accurate computational methods for the solution of hyperbolic equations with application to problems with strong shocks. While the methods are general, emphasis is on applications to gas dynamics with strong shocks.
Mitri, F G
2010-05-01
The aim of this short communication is to report that Gegenbauer's (partial-wave) expansion, that may be used (under some specific conditions) to represent the incident field of an acoustical (or optical) high-order Bessel beam (HOBB) in spherical coordinates, anticipates earlier expressions for undistorted waves. The incident wave-field is written in terms of the spherical Bessel function of the first kind, the gamma function as well as the Gegenbauer or ultraspherical functions given in terms of the associated Legendre functions when the order m of the HOBB is an integer number. Expressions for high-order and zero-order Bessel beams as well as for plane progressive waves reported in prior works can be deduced from Gegenbauer's partial-wave expansion by appropriate choice of the beams' parameters. Hence the value of this note becomes historical. In addition, Gegenbauer's expansion in spherical coordinates may be used to advantage to model the wave-field of a fractional HOBB at the origin (i.e. z=0). Copyright 2010 Elsevier B.V. All rights reserved.
Ruberti, M; Averbukh, V; Decleva, P
2014-10-28
We present the first implementation of the ab initio many-body Green's function method, algebraic diagrammatic construction (ADC), in the B-spline single-electron basis. B-spline versions of the first order [ADC(1)] and second order [ADC(2)] schemes for the polarization propagator are developed and applied to the ab initio calculation of static (photoionization cross-sections) and dynamic (high-order harmonic generation spectra) quantities. We show that the cross-section features that pose a challenge for the Gaussian basis calculations, such as Cooper minima and high-energy tails, are found to be reproduced by the B-spline ADC in a very good agreement with the experiment. We also present the first dynamic B-spline ADC results, showing that the effect of the Cooper minimum on the high-order harmonic generation spectrum of Ar is correctly predicted by the time-dependent ADC calculation in the B-spline basis. The present development paves the way for the application of the B-spline ADC to both energy- and time-resolved theoretical studies of many-electron phenomena in atoms, molecules, and clusters.
Angel, Jordan B.; Banks, Jeffrey W.; Henshaw, William D.
2018-01-01
High-order accurate upwind approximations for the wave equation in second-order form on overlapping grids are developed. Although upwind schemes are well established for first-order hyperbolic systems, it was only recently shown by Banks and Henshaw [1] how upwinding could be incorporated into the second-order form of the wave equation. This new upwind approach is extended here to solve the time-domain Maxwell's equations in second-order form; schemes of arbitrary order of accuracy are formulated for general curvilinear grids. Taylor time-stepping is used to develop single-step space-time schemes, and the upwind dissipation is incorporated by embedding the exact solution of a local Riemann problem into the discretization. Second-order and fourth-order accurate schemes are implemented for problems in two and three space dimensions, and overlapping grids are used to treat complex geometry and problems with multiple materials. Stability analysis of the upwind-scheme on overlapping grids is performed using normal mode theory. The stability analysis and computations confirm that the upwind scheme remains stable on overlapping grids, including the difficult case of thin boundary grids when the traditional non-dissipative scheme becomes unstable. The accuracy properties of the scheme are carefully evaluated on a series of classical scattering problems for both perfect conductors and dielectric materials in two and three space dimensions. The upwind scheme is shown to be robust and provide high-order accuracy.
Medenbach, J.; Schreiner, S.; Liu, S.; Luehrmann, R.; Bindereif, A
2004-01-01
After each spliceosome cycle, the U4 and U6 snRNAs are released separately and are recycled to the functional U4/U6 snRNP, requiring in the mammalian system the U6-specific RNA binding protein p110 (SART3). Its domain structure is made up of an extensive N-terminal domain with at least seven tetratricopeptide repeat (TPR) motifs, followed by two RNA recognition motifs (RRMs) and a highly conserved C-terminal sequence of 10 amino acids. Here we demonstrate under in vitro recycling conditions t...
Directory of Open Access Journals (Sweden)
Boukakis Georgios
2010-08-01
Full Text Available Abstract Background Heterogeneous nuclear ribonucleoproteins (hnRNPs of the A/B type (hnRNP A1, A2/B1, A3 are highly related multifunctional proteins participating in alternative splicing by antagonising other splicing factors, notably ASF/SF2. The altered expression pattern of hnRNP A2/B1 and/or splicing variant B1 alone in human lung cancer and their potential to serve as molecular markers for early diagnosis remain issues of intense investigation. The main objective of the present study was to use paired tumour/non-tumour biopsies from patients with non-small cell lung cancer (NSCLC to investigate the expression profiles of hnRNP A1, A2/B1 and A3 in conjunction with ASF/SF2. Methods We combined western blotting of tissue homogenates with immunohistochemical examination of fixed tissue sections and quantification of mRNA expression levels in tumour versus adjacent normal-looking areas of the lung in the same patient. Results Our study, in addition to clear evidence of mostly uncoupled deregulation of hnRNPs A/B, has revealed hnRNP A1 to be the most deregulated protein with a high frequency of over-expression (76%, followed by A3 (52% and A2/B1 (43%. Moreover, direct comparison of protein/mRNA levels showed a lack of correlation in the case of hnRNP A1 (as well as of ASF/SF2, but not of A2/B1, suggesting that different mechanisms underlie their deregulation. Conclusion Our results provide strong evidence for the up-regulation of hnRNP A/B in NSCLC, and they support the existence of distinct mechanisms responsible for their deregulated expression.
Guo, Rong; Li, Yong; Ning, Jinying; Sun, Dan; Lin, Lianjun; Liu, Xinmin
2013-01-01
Heterogeneous nuclear ribonucleoparticule A1/A2 (hnRNP A1/A2) and splicing factor 2/alternative splicing factor (SF2/ASF) are pivotal for precursor messenger RNA (pre-mRNA) splicing. Interferon regulatory factor-3 (IRF-3) plays critical roles in host defense against viral and microbial infection. Truncated IRF-3 proteins resulting from alternative splicing have been identified and characterized as functional antagonists to full-length IRF-3. In this study, we examined the molecular mechanism for splicing regulation of IRF-3 pre-mRNA and first reported the regulatory effect of hnRNP A1/A2 and SF2/ASF on IRF-3 splicing and activation. RNA interference-mediated depletion of hnRNP A1/A2 or SF2/ASF in human non-small cell lung cancer (NSCLC) cells increased exclusion of exons 2 and 3 of IRF-3 gene and reduced expression levels of IRF-3 protein and IRF-3 downstream effector molecules interferon-beta and CXCL10/IP-10. In addition, direct binding of hnRNP A1 and SF2/ASF to specific binding motifs in IRF-3 intron 1 was confirmed by RNA electrophoretic mobility shift assay. Subsequent minigene splicing assay showed that IRF-3 minigenes with mutated hnRNPA 1/A2 or SF2/ASF binding motifs increased exclusion of exons 2 and 3. Moreover, knockdown of hnRNP A1/A2 or SF2/ASF in NSCLC cells reinforced phytohemagglutinin-induced tumor necrosis factor-alpha release by peripheral blood mononuclear cells (PBMC) but suppressed that of interleukin-10 in NSCLC/PBMC co-cultures. Taken together, our results suggest that specific knockdown for hnRNP A1/A2 or SF2/ASF increase exclusion of exons 2 and 3 of IRF-3 pre-mRNA and influence immunomodulatory functions of human NSCLC cells.
Hejranfar, Kazem; Ezzatneshan, Eslam
2014-06-01
In this work, the implementation of a high-order compact finite-difference lattice Boltzmann method (CFDLBM) is performed in the generalized curvilinear coordinates to improve the computational efficiency of the solution algorithm to handle curved geometries with non-uniform grids. The incompressible form of the discrete Boltzmann equation with the Bhatnagar-Gross-Krook (BGK) approximation with the pressure as the independent dynamic variable is transformed into the generalized curvilinear coordinates. Herein, the spatial derivatives in the resulting lattice Boltzmann (LB) equation in the computational plane are discretized by using the fourth-order compact finite-difference scheme and the temporal term is discretized with the fourth-order Runge-Kutta scheme to provide an accurate and efficient incompressible flow solver. A high-order spectral-type low-pass compact filter is used to regularize the numerical solution and remove spurious waves generated by boundary conditions, flow non-linearities and grid non-uniformity. All boundary conditions are implemented based on the solution of governing equations in the generalized curvilinear coordinates. The accuracy and efficiency of the solution methodology presented are demonstrated by computing different benchmark steady and unsteady incompressible flow problems. A sensitivity study is also conducted to evaluate the effects of grid size and filtering on the accuracy and convergence rate of the solution. Four test cases considered herein for validating the present computations and demonstrating the accuracy and robustness of the solution algorithm are: unsteady Couette flow and steady flow in a 2-D cavity with non-uniform grid and steady and unsteady flows over a circular cylinder and the NACA0012 hydrofoil at different flow conditions. Results obtained for the above test cases are in good agreement with the existing numerical and experimental results. The study shows the present solution methodology based on the
Sharan, Nek; Pantano, Carlos; Bodony, Daniel
2015-11-01
Overset grids provide an efficient and flexible framework to implement high-order finite difference methods for simulations of compressible viscous flows over complex geometries. However, prior overset methods were not provably stable and were applied with artificial dissipation in the interface regions. We will discuss new, provably time-stable methods for solving hyperbolic problems on overlapping grids. The proposed methods use the summation-by-parts (SBP) derivative approximations coupled with the simultaneous-approximation-term (SAT) methodology for applying boundary conditions and interface treatments. The performance of the methods will be assessed against the commonly-used approach of injecting the interpolated data onto each grid. Numerical results will be presented to confirm the stability and the accuracy of the methods for solving the Euler equations. The extension of these methods to solve the Navier-Stokes equations on overset grids in a time-stable manner will be briefly discussed.
Electronic structure and properties of highly ordered C60 nano arrays on Au (111): STM & DFT study
Win, Zaw-Myo; HUANG, Chao; ZHANG, Rui-Qin
2017-06-01
Template assisted assembly of molecular nano arrays is one of the key steps towards molecular electronics and fullerene is one of the potential structural building blocks in fabrication of identical molecular nano arrays for miniature devices such as photovoltaic devices and single-molecule transistors. In this report, the reconstructed Au (111) with defect areas (steps) has been used as a template to assemble the highly ordered C60 nano array at low coverage studied with scanning tunnelling microscopy (STM) in conjunction with density functional theory (DFT). The interaction between the substrate and C60 nano arrays is strong enough to change the geometrical shape of C60. As a result of strong interaction, the C60 molecule appears to be deformed into ellipsoidal shape which causes the reduction of C60 nano arrays on step sites of Au (111).
Chabot, S.; Glinsky, N.; Mercerat, E. D.; Bonilla Hidalgo, L. F.
2018-02-01
We propose a nodal high-order discontinuous Galerkin method for 1D wave propagation in nonlinear media. We solve the elastodynamic equations written in the velocity-strain formulation and apply an upwind flux adapted to heterogeneous media with nonlinear constitutive behavior coupling stress and strain. Accuracy, convergence and stability of the method are studied through several numerical applications. Hysteresis loops distinguishing loading and unloading-reloading paths are also taken into account. We investigate several effects of nonlinearity in wave propagation, such as the generation of high frequencies and the frequency shift of resonant peaks to lower frequencies. Finally, we compare the results for both nonlinear models, with and without hysteresis, and highlight the effects of the former on the stabilization of the numerical scheme.
Energy Technology Data Exchange (ETDEWEB)
Hack, Szabolcs [ELI-ALPS, ELI-HU Non-Profit Ltd., Dugonics tér 13, H-6720 Szeged (Hungary); Department of Theoretical Physics, University of Szeged, Tisza L. krt. 84-86, H-6720 Szeged (Hungary); Varró, Sándor [ELI-ALPS, ELI-HU Non-Profit Ltd., Dugonics tér 13, H-6720 Szeged (Hungary); Wigner Research Center for Physics, SZFI, PO Box 49, H-1525 Budapest (Hungary); Czirják, Attila [ELI-ALPS, ELI-HU Non-Profit Ltd., Dugonics tér 13, H-6720 Szeged (Hungary); Department of Theoretical Physics, University of Szeged, Tisza L. krt. 84-86, H-6720 Szeged (Hungary)
2016-02-15
We investigate nonlinear Thomson scattering as a source of high-order harmonic radiation with the potential to enable attosecond light pulse generation. We present a new analytic solution of the electron’s relativistic equations of motion in the case of a short laser pulse with a sine-squared envelope. Based on the single electron emission, we compute and analyze the radiated amplitude and phase spectrum for a realistic electron bunch, with special attention to the correct initial values. These results show that the radiation spectrum of an electron bunch in head-on collision with a sufficiently strong laser pulse of sine-squared envelope has a smooth frequency dependence to allow for the synthesis of attosecond light pulses.
Xu, Xiaobin; Gao, Fuyu; Song, Ningfang; Jin, Jing
2016-05-16
Air-core photonic bandgap fiber (PBF) is a good choice for fiber-optic gyroscopes (FOGs) owing to the fact that it can be adapted to a wide variety of environments. However, its multimode properties are disadvantageous for the application to FOGs. An interference-based method is proposed to precisely determine the secondary waves caused by the high-order modes and their coupling. Based on the method, two groups of secondary waves have been found, having optical path differences (OPDs) of ~1.859 m and ~0.85 m, respectively, relative to the primary waves in a PBFOG that consists of a 7-cell PBF coil, approximately 180 m in length. Multi-turn bends of the PBF at both ends of the PBF coil after the fusion splicing points are shown to suppress the intensity of these secondary waves by approximately 10 dB.
Seber, Gonca; Rudnev, Alexander V; Droghetti, Andrea; Rungger, Ivan; Veciana, Jaume; Mas-Torrent, Marta; Rovira, Concepció; Crivillers, Núria
2017-01-26
A novel, persistent, electrochemically active perchlorinated triphenylmethyl (PTM) radical with a diazonium functionality has been covalently attached to highly ordered pyrolytic graphite (HOPG) by electrografting in a single-step process. Electrochemical scanning tunneling microscopy (EC-STM) and Raman spectroscopy measurements revealed that PTM molecules had a higher tendency to covalently react at the HOPG step edges. The cross-section profiles from EC-STM images showed that there was current enhancement at the functionalized areas, which could be explained by redox-mediated electron tunneling through surface-confined redox-active molecules. Cyclic voltammetry clearly demonstrated that the intrinsic properties of the organic radical were preserved upon grafting and DFT calculations also revealed that the magnetic character of the PTM radical was preserved. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Gui, Tao; Lu, Chao; Lau, Alan Pak Tao; Wai, P K A
2017-08-21
In this paper, we experimentally investigate high-order modulation over a single discrete eigenvalue under the nonlinear Fourier transform (NFT) framework and exploit all degrees of freedom for encoding information. For a fixed eigenvalue, we compare different 4 bit/symbol modulation formats on the spectral amplitude and show that a 2-ring 16-APSK constellation achieves optimal performance. We then study joint spectral phase, spectral magnitude and eigenvalue modulation and found that while modulation on the real part of the eigenvalue induces pulse timing drift and leads to neighboring pulse interactions and nonlinear inter-symbol interference (ISI), it is more bandwidth efficient than modulation on the imaginary part of the eigenvalue in practical settings. We propose a spectral amplitude scaling method to mitigate such nonlinear ISI and demonstrate a record 4 GBaud 16-APSK on the spectral amplitude plus 2-bit eigenvalue modulation (total 6 bit/symbol at 24 Gb/s) transmission over 1000 km.
Janssen, Bärbel
2011-01-01
A multilevel method on adaptive meshes with hanging nodes is presented, and the additional matrices appearing in the implementation are derived. Smoothers of overlapping Schwarz type are discussed; smoothing is restricted to the interior of the subdomains refined to the current level; thus it has optimal computational complexity. When applied to conforming finite element discretizations of elliptic problems and Maxwell equations, the method\\'s convergence rates are very close to those for the nonadaptive version. Furthermore, the smoothers remain efficient for high order finite elements. We discuss the implementation in a general finite element code using the example of the deal.II library. © 2011 Societ y for Industrial and Applied Mathematics.
Zhao, Xiang; Bai, Gang; Zheng, Ye; Chen, Xiaolong; Yang, Yifeng; Qi, Yunfeng; He, Bing; Zhou, Jun
2017-10-01
To suppress high order modes and improve the beam quality, an active self-imaging mode filter based on multimode interference and self-imaging effect is proposed in large mode area (LMA) fiber amplifier. With this filter structure, transverse mode competition and individual transverse mode power distributions in strongly pumped fiber amplifiers are theoretically demonstrated. Employing this mode selection technique in 30/400 LMA strongly pumped fiber amplifier, the percentage of the fundamental mode rises from 27.8% (without filter) to 96.3%. By the modal power decomposition, the M2 parameter of beam quality decrease dramatically from 2.24 to 1.11 (0 relative phase) and from 3.01 to 1.24 (π/2 relative phase). This study provides a new method to achieve single mode in LMA fiber amplifier and this filter would be extended to larger mode area fiber amplifier to improve the beam quality.
Liu, Yilong; Fischer, Achim; Eberhard, Peter; Wu, Baohai
2015-06-01
A high-order full-discretization method (FDM) using Hermite interpolation (HFDM) is proposed and implemented for periodic systems with time delay. Both Lagrange interpolation and Hermite interpolation are used to approximate state values and delayed state values in each discretization step. The transition matrix over a single period is determined and used for stability analysis. The proposed method increases the approximation order of the semidiscretization method and the FDM without increasing the computational time. The convergence, precision, and efficiency of the proposed method are investigated using several Mathieu equations and a complex turning model as examples. Comparison shows that the proposed HFDM converges faster and uses less computational time than existing methods.
Energy Technology Data Exchange (ETDEWEB)
Li, Mao; Qiu, Zihua; Liang, Chunlei; Sprague, Michael; Xu, Min
2017-01-13
In the present study, a new spectral difference (SD) method is developed for viscous flows on meshes with a mixture of triangular and quadrilateral elements. The standard SD method for triangular elements, which employs Lagrangian interpolating functions for fluxes, is not stable when the designed accuracy of spatial discretization is third-order or higher. Unlike the standard SD method, the method examined here uses vector interpolating functions in the Raviart-Thomas (RT) spaces to construct continuous flux functions on reference elements. Studies have been performed for 2D wave equation and Euler equa- tions. Our present results demonstrated that the SDRT method is stable and high-order accurate for a number of test problems by using triangular-, quadrilateral-, and mixed- element meshes.
Larsen, E. W.; Carlström, S.; Lorek, E.; Heyl, C. M.; Paleček, D.; Schafer, K. J.; L’Huillier, A.; Zigmantas, D.; Mauritsson, J.
2016-01-01
The sub-cycle dynamics of electrons driven by strong laser fields is central to the emerging field of attosecond science. We demonstrate how the dynamics can be probed through high-order harmonic generation, where different trajectories leading to the same harmonic order are initiated at different times, thereby probing different field strengths. We find large differences between the trajectories with respect to both their sensitivity to driving field ellipticity and resonant enhancement. To accurately describe the ellipticity dependence of the long trajectory harmonics we must include a sub-cycle change of the initial velocity distribution of the electron and its excursion time. The resonant enhancement is observed only for the long trajectory contribution of a particular harmonic when a window resonance in argon, which is off-resonant in the field-free case, is shifted into resonance due to a large dynamic Stark shift. PMID:27991521
Liu, Xiuhua; Gao, Xianwen; Han, Jian
2016-03-01
This paper is devoted to fault detection (FD) for high-order multi-agent systems with disturbances. In order to detect the fault occurred in one agent, the unknown input observer (UIO) is constructed in its neighbor. Two cases are considered, if the perfect UI decoupling condition is satisfied, the UI does not affect the residual; if the condition is not satisfied, this paper proposes a method of partitioning the UI into two parts, such that a subset of the UI does not appear in residual dynamics, and the influence of the other UI is constrained. Simulations are given to demonstrate the effectiveness of the proposed method. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.
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S.C. Jardin; J.A. Breslau
2004-12-17
Here we describe a technique for solving the four-field extended-magnetohydrodynamic (MHD) equations in two dimensions. The introduction of triangular high-order finite elements with continuous first derivatives (C{sup 1} continuity) leads to a compact representation compatible with direct inversion of the associated sparse matrices. The split semi-implicit method is introduced and used to integrate the equations in time, yielding unconditional stability for arbitrary time step. The method is applied to the cylindrical tilt mode problem with the result that a non-zero value of the collisionless ion skin depth will increase the growth rate of that mode. The effect of this parameter on the reconnection rate and geometry of a Harris equilibrium and on the Taylor reconnection problem is also demonstrated. This method forms the basis for a generalization to a full extended-MHD description of the plasma with six, eight, or more scalar fields.
High-Order Dimension Synthesis of Planar/Spatial Mechanisms with One-DoF by CAD Variational Geometry
Directory of Open Access Journals (Sweden)
Yi Lu
2012-01-01
Full Text Available This paper proposes a (computer aided design CAD variational geometry approach for the high-order dimension synthesis of one-DoF mechanisms based on the given velocity/acceleration of a moving platform along a prescribed trajectory. The objective of this approach is to determine the reasonable dimensions of the mechanisms when given the velocity or/and the acceleration of the moving platform along a prescribed trajectory. First, some concepts and mathematical foundations are explained for constructing the velocity/acceleration simulation mechanism of a general mechanism. Second, the inverse velocity/acceleration simulation mechanisms of the planar/spatial four-bar mechanisms with one-DoF are constructed by the CAD variational geometry. Third, when given the position and the velocity/acceleration of the coupler along a prescribed trajectory, all the reasonable dimensions of the planar/spatial four-bar mechanisms are solved from their simulation mechanisms.
Ambruş, Victor Eugen; Sofonea, Victor
2012-07-01
We use the spherical coordinate system in the momentum space and an appropriate discretization procedure to derive a hierarchy of lattice Boltzmann (LB) models with variable temperature. The separation of the integrals in the momentum space into angular and radial parts allows us to compute the moments of the equilibrium distribution function by means of Gauss-Legendre and Gauss-Laguerre quadratures, as well as to find the elements of the discrete momentum set for each LB model in the hierarchy. The capability of the high-order models in this hierarchy to capture specific effects in microfluidics is investigated through a computer simulation of Couette flow by using the Shakhov collision term to get the right value of the Prandtl number.
Highly ordered nanotubular film formation on Ti–25Nb–xZr and Ti–25Ta–xHf
Energy Technology Data Exchange (ETDEWEB)
Kim, Jeong-Jae; Byeon, In-Seop [Department of Dental Materials, Research Center of Nano-Interface Activation for Biomaterials, & Research Center for Oral Disease Regulation of the Aged, College of Dentistry, Chosun University, Gwangju (Korea, Republic of); Brantley, William A. [Division of Restorative Sciences and Prosthodontics, College of Dentistry, The Ohio State University, Columbus, OH (United States); Choe, Han-Cheol, E-mail: hcchoe@chosun.ac.kr [Department of Dental Materials, Research Center of Nano-Interface Activation for Biomaterials, & Research Center for Oral Disease Regulation of the Aged, College of Dentistry, Chosun University, Gwangju (Korea, Republic of)
2015-12-01
The purpose of this study was to investigate the highly ordered nanotubular film formation on Ti–25Nb–xZr and Ti–25Ta–xHf, examining the roles of niobium, zirconium, tantalum and hafnium alloying elements. The Ti–25Nb–xZr and Ti–25Ta–xHf ternary alloys contained 0, 7 and 15 wt.% of these alloying elements and were manufactured using a vacuum arc-melting furnace. Cast ingots of the alloys were homogenized in Ar atmosphere at 1050 °C for 2 h, followed by quenching into ice water. Formation of nanotubular films was achieved by an electrochemical method in 1 M H{sub 3}PO{sub 4} + 0.8 wt.% NaF at 30 V and 1 h for the Ti–25Nb–xZr alloys and 2 h for the Ti–25Ta–xHf alloys. Microstructures of the Ti–25Ta–xHf alloys transformed from α″ phase to β phase, changing from a needle-like structure to an equiaxed structure as the Hf content increased. In a similar manner, the needle-like structure of the Ti–25Nb–xZr alloys transformed to an equiaxed structure as the Zr content increased. Highly ordered nanotubes formed on the Ti–25Ta–15Hf and Ti–25Nb–15Zr alloys compared to the other alloys, and the nanotube layer thickness on Ti–25Ta–15Hf and Ti–25Nb–15Zr was greater than for the other alloys. Nanotubes formed on Ti–25Ta–15Hf and Ti–25Nb–15Zr showed two sizes of highly ordered structures. The diameters of the large nanotubes decreased and the diameters of the small nanotubes increased as Zr and Hf contents increased. It was found that the layer thickness, diameter, surface density and growth rate of nanotubes on the Ti–25Ta–xHf and Ti–25Nb–xZr alloys can be controlled by varying the Hf and Zr contents. X-ray diffraction analyses revealed only weak peaks for crystalline anatase or rutile TiO{sub 2} phases from the nanotubes on the Ti–25Nb–xZr and Ti–25Ta–xHf alloys, indicating a largely amorphous condition. - Highlights: • Nanotubular film formation on anodized Ti-25Nb-xZr and Ti-25Ta-xHf (x = 0, 7 and
In-line production of a bi-circular field for generation of helically polarized high-order harmonics
Energy Technology Data Exchange (ETDEWEB)
Kfir, Ofer, E-mail: ofertx@technion.ac.il, E-mail: oren@si.technion.ac.il; Bordo, Eliyahu; Ilan Haham, Gil; Lahav, Oren; Cohen, Oren, E-mail: ofertx@technion.ac.il, E-mail: oren@si.technion.ac.il [Solid State Institute and Physics Department, Technion, Haifa 32000 (Israel); Fleischer, Avner [Solid State Institute and Physics Department, Technion, Haifa 32000 (Israel); Department of Physics and Optical Engineering, Ort Braude College, Karmiel 21982 (Israel)
2016-05-23
The recent demonstration of bright circularly polarized high-order harmonics of a bi-circular pump field gave rise to new opportunities in ultrafast chiral science. In previous works, the required nontrivial bi-circular pump field was produced using a relatively complicated and sensitive Mach-Zehnder-like interferometer. We propose a compact and stable in-line apparatus for converting a quasi-monochromatic linearly polarized ultrashort driving laser field into a bi-circular field and employ it for generation of helically polarized high-harmonics. Furthermore, utilizing the apparatus for a spectroscopic spin-mixing measurement, we identify the photon spins of the bi-circular weak component field that are annihilated during the high harmonics process.
Plaja, L; Pérez-Hernández, J A
2007-04-02
We present a S-matrix description of the process of high order harmonic generation during the interaction of atoms with strong electromagnetic fields. In contrast with the state-of-the-art approaches, our model does not employ the stationary phase approximation and accounts as well for the continuum-continuum transitions. Therefore we are able to reproduce quantitatively the higher frequency part of the spectrum for arbitrary pulse shapes, and for intensities corresponding to multiphoton, tunnel and soft over-the barrier ionization regimes. In addition this model can be implemented very efficiently in a Personal Computer to calculate the harmonic generation for the atom interacting with an eight-cycle pulse at lambda =800 nm in, roughly, ten minutes (a reduction of two orders of magnitude from the typical time requirements of the exact integration).
Energy Technology Data Exchange (ETDEWEB)
Dobosz, S.; Stabile, H.; Tortora, A.; Monot, P.; Reau, F.; Bougeard, M.; Merdji, H.; Carre, B.; Martin, Ph. [CEA, IRAMIS, Service des Photons Atomes et Molecules, F-91191 Gif- sur-Yvette (France); Joyeux, D.; Phalippou, D.; Delmotte, F.; Gautier, J.; Mercier, R. [Laboratoire Charles Fabry de l' Institut d' Optique, CNRS et Universite Paris Sud, Campus Polytechnique, RD 128, F-91127 Palaiseau cedex (France)
2009-11-15
We report on an innovative two-dimensional imaging extreme ultraviolet (XUV) interferometer operating at 32 nm based on the mutual coherence of two laser high order harmonics (HOH) sources, separately generated in gas. We give the first evidence that the two mutually coherent HOH sources can be produced in two independent spatially separated gas jets, allowing for probing centimeter-sized objects. A magnification factor of 10 leads to a micron resolution associated with a subpicosecond temporal resolution. Single shot interferograms with a fringe visibility better than 30% are routinely produced. As a test of the XUV interferometer, we measure a maximum electronic density of 3x10{sup 20} cm{sup -3} 1.1 ns after the creation of a plasma on aluminum target.
Modave, A.; Atle, A.; Chan, J.; Warburton, T.
2017-12-01
Discontinuous Galerkin finite element schemes exhibit attractive features for accurate large-scale wave-propagation simulations on modern parallel architectures. For many applications, these schemes must be coupled with non-reflective boundary treatments to limit the size of the computational domain without losing accuracy or computational efficiency, which remains a challenging task. In this paper, we present a combination of a nodal discontinuous Galerkin method with high-order absorbing boundary conditions (HABCs) for cuboidal computational domains. Compatibility conditions are derived for HABCs intersecting at the edges and the corners of a cuboidal domain. We propose a GPU implementation of the computational procedure, which results in a multidimensional solver with equations to be solved on 0D, 1D, 2D and 3D spatial regions. Numerical results demonstrate both the accuracy and the computational efficiency of our approach.
Modave, Axel; Chan, Jesse; Warburton, Tim
2016-01-01
Discontinuous Galerkin finite element schemes exhibit attractive features for accurate large-scale wave-propagation simulations on modern parallel architectures. For many applications, these schemes must be coupled with non-reflective boundary treatments to limit the size of the computational domain without losing accuracy or computational efficiency, which remains a challenging task. In this paper, we present a combination of high-order absorbing boundary conditions (HABCs) with a nodal discontinuous Galerkin method for cuboidal computational domains. Compatibility conditions are derived for HABCs intersecting at the edges and the corners of a cuboidal domain. We propose a GPU implementation of the computational procedure, which results in a multidimensional solver with equations to be solved on 0D, 1D, 2D and 3D spatial regions. Numerical results demonstrate both the accuracy and the computational efficiency of our approach. We have considered academic benchmarks, as well as a realistic benchmark based on t...
Das, T
2016-01-01
We analyze the imprint of nodal planes in high-order harmonic spectra from aligned diatomic molecules in intense laser fields whose components exhibit orthogonal polarizations. We show that the typical suppression in the spectra associated to nodal planes is distorted, and that this distortion can be employed to map the electron's angle of return to its parent ion. This investigation is performed semi-analytically at the single-molecule response and single-active orbital level, using the strong-field approximation and the steepest descent method. We show that the velocity form of the dipole operator is superior to the length form in providing information about this distortion. However, both forms introduce artifacts that are absent in the actual momentum-space wavefunction. Furthermore, elliptically polarized fields lead to larger distortions in comparison to two-color orthogonally polarized fields. These features are investigated in detail for $\\mathrm{O}_2$, whose highest occupied molecular orbital provides...
An efficient implementation of a high-order filter for a cubed-sphere spectral element model
Kang, Hyun-Gyu; Cheong, Hyeong-Bin
2017-03-01
A parallel-scalable, isotropic, scale-selective spatial filter was developed for the cubed-sphere spectral element model on the sphere. The filter equation is a high-order elliptic (Helmholtz) equation based on the spherical Laplacian operator, which is transformed into cubed-sphere local coordinates. The Laplacian operator is discretized on the computational domain, i.e., on each cell, by the spectral element method with Gauss-Lobatto Lagrange interpolating polynomials (GLLIPs) as the orthogonal basis functions. On the global domain, the discrete filter equation yielded a linear system represented by a highly sparse matrix. The density of this matrix increases quadratically (linearly) with the order of GLLIP (order of the filter), and the linear system is solved in only O (Ng) operations, where Ng is the total number of grid points. The solution, obtained by a row reduction method, demonstrated the typical accuracy and convergence rate of the cubed-sphere spectral element method. To achieve computational efficiency on parallel computers, the linear system was treated by an inverse matrix method (a sparse matrix-vector multiplication). The density of the inverse matrix was lowered to only a few times of the original sparse matrix without degrading the accuracy of the solution. For better computational efficiency, a local-domain high-order filter was introduced: The filter equation is applied to multiple cells, and then the central cell was only used to reconstruct the filtered field. The parallel efficiency of applying the inverse matrix method to the global- and local-domain filter was evaluated by the scalability on a distributed-memory parallel computer. The scale-selective performance of the filter was demonstrated on Earth topography. The usefulness of the filter as a hyper-viscosity for the vorticity equation was also demonstrated.
Photo-electro-catalytic performance of highly ordered nitrogen doped TiO2 nanotubes array photoanode
Aritonang, Anthoni B.; Surahman, Hedi; Krisnandi, Yuni K.; Gunlazuardi, Jarnuzi
2017-02-01
Highly ordered nitrogen doped TiO2 nanotube arrays (N-TNTAs) were synthesized via a one step anodization method at 40 V for 1 hour, in the electrolyte containing ammonium fluoride (NH4F), water and triethylamine solution, followed calcination under N2 atmosphere at 450oC for 3 h. The obtained samples were characterized by means of FE-SEM image showed that the N-TNTs are in a highly ordered array, having inner diameters, wall thickness, tube length of 65 nm, 30 nm and 900 nm, respectively. The X-ray diffraction (XRD) patterns of N-TNTAs and undoped TiO2 nanotubes arrays (TNTAs) are identical consists of anatase phase, which suggests that the doping of N does not affect the crystalline structure. X-ray photoelectron spectroscopy (XPS), revealed that N atom was incorporated into the lattice of a TiO2 nanotube array film. The infrared spectra, showed a new peak at 1240 cm-1 may indicate the incorporation of N into the lattice of TiO2 through substituting O atoms, in the form of ∼N-Ti-O∼. A red shift of the absorption edge toward the visible region of N-TNTAs are observed by diffuse reflectance spectroscopy (DRS), which is corresponding to a band gap of 2.8 eV. The photo-electro-catalytic (PEC) degradation efficiency toward methylene blue solution under visible light illumination of the N-TNTAs electrode was 89%, in which the rate constant of N-TNTAs electrode was 8 times better compared to that the undoped TNTAs photo-electrode.
Plis, Sergey M; Sui, Jing; Lane, Terran; Roy, Sushmita; Clark, Vincent P; Potluru, Vamsi K; Huster, Rene J; Michael, Andrew; Sponheim, Scott R; Weisend, Michael P; Calhoun, Vince D
2014-11-15
Identifying the complex activity relationships present in rich, modern neuroimaging data sets remains a key challenge for neuroscience. The problem is hard because (a) the underlying spatial and temporal networks may be nonlinear and multivariate and (b) the observed data may be driven by numerous latent factors. Further, modern experiments often produce data sets containing multiple stimulus contexts or tasks processed by the same subjects. Fusing such multi-session data sets may reveal additional structure, but raises further statistical challenges. We present a novel analysis method for extracting complex activity networks from such multifaceted imaging data sets. Compared to previous methods, we choose a new point in the trade-off space, sacrificing detailed generative probability models and explicit latent variable inference in order to achieve robust estimation of multivariate, nonlinear group factors ("network clusters"). We apply our method to identify relationships of task-specific intrinsic networks in schizophrenia patients and control subjects from a large fMRI study. After identifying network-clusters characterized by within- and between-task interactions, we find significant differences between patient and control groups in interaction strength among networks. Our results are consistent with known findings of brain regions exhibiting deviations in schizophrenic patients. However, we also find high-order, nonlinear interactions that discriminate groups but that are not detected by linear, pairwise methods. We additionally identify high-order relationships that provide new insights into schizophrenia but that have not been found by traditional univariate or second-order methods. Overall, our approach can identify key relationships that are missed by existing analysis methods, without losing the ability to find relationships that are known to be important. © 2013.