Multitarget Molecular Hybrids of Cinnamic Acids

Directory of Open Access Journals (Sweden)

Aikaterini Peperidou

2014-12-01

Full Text Available In an attempt to synthesize potential new multitarget agents, 11 novel hybrids incorporating cinnamic acids and paracetamol, 4-/7-hydroxycoumarin, benzocaine, p-aminophenol and m-aminophenol were synthesized. Three hybrids—2e, 2a, 2g—and 3b were found to be multifunctional agents. The hybrid 2e derived from the phenoxyphenyl cinnamic acid and m-acetamidophenol showed the highest lipoxygenase (LOX inhibition and analgesic activity (IC50 = 0.34 μΜ and 98.1%, whereas the hybrid 3b of bromobenzyloxycinnamic acid and hymechromone exhibited simultaneously good LOX inhibitory activity (IC50 = 50 μΜ and the highest anti-proteolytic activity (IC50= 5 μΜ. The hybrid 2a of phenyloxyphenyl acid with paracetamol showed a high analgesic activity (91% and appears to be a promising agent for treating peripheral nerve injuries. Hybrid 2g which has an ester and an amide bond presents an interesting combination of anti-LOX and anti-proteolytic activity. The esters were found very potent and especially those derived from paracetamol and m-acetamidophenol. The amides follow. Based on 2D-structure–activity relationships it was observed that both steric and electronic parameters play major roles in the activity of these compounds. Molecular docking studies point to the fact that allosteric interactions might govern the LOX-inhibitor binding.

Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes.

Science.gov (United States)

Cao, Jing; Feng, Chao; Liu, Yan; Wang, Shouyu; Liu, Fei

2014-07-15

Since many diseases are caused by pathogenic bacterial infections, accurate and rapid detection of pathogenic bacteria is in urgent need to timely apply appropriate treatments and to reduce economic costs. To end this, we designed molecular beacon-Au nanoparticle hybrid nanoprobes to improve the bacterial detection efficiency and sensitivity. Here, we show that the designed molecular beacon modified Au nanoparticles could specifically recognize synthetic DNAs targets and can readily detect targets in clinical samples. Moreover, the hybrid nanoprobes can recognize Escherichia coli within an hour at a concentration of 10(2) cfu/ml, which is 1000-folds sensitive than using molecular beacon directly. Our results show that the molecular beacon-Au nanoparticle hybrid nanoprobes have great potential in medical and biological applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Hybrid Materials Based on Magnetic Layered Double Hydroxides: A Molecular Perspective.

Science.gov (United States)

Abellán, Gonzalo; Martí-Gastaldo, Carlos; Ribera, Antonio; Coronado, Eugenio

2015-06-16

Design of functional hybrids lies at the very core of synthetic chemistry as it has enabled the development of an unlimited number of solids displaying unprecedented or even improved properties built upon the association at the molecular level of quite disparate components by chemical design. Multifunctional hybrids are a particularly appealing case among hybrid organic/inorganic materials. Here, chemical knowledge is used to deploy molecular components bearing different functionalities within a single solid so that these properties can coexist or event interact leading to unprecedented phenomena. From a molecular perspective, this can be done either by controlled assembly of organic/inorganic molecular tectons into an extended architecture of hybrid nature or by intercalation of organic moieties within the empty channels or interlamellar space offered by inorganic solids with three-dimensional (MOFs, zeolites, and mesoporous hosts) or layered structures (phosphates, silicates, metal dichalcogenides, or anionic clays). This Account specifically illustrates the use of layered double hydroxides (LDHs) in the preparation of magnetic hybrids, in line with the development of soft inorganic chemistry processes (also called "Chimie Douce"), which has significantly contributed to boost the preparation hybrid materials based on solid-state hosts and subsequent development of applications. Several features sustain the importance of LDHs in this context. Their magnetism can be manipulated at a molecular level by adequate choice of constituting metals and interlayer separation for tuning the nature and extent of magnetic interactions across and between planes. They display unparalleled versatility in accommodating a broad range of anionic species in their interlamellar space that encompasses not only simple anions but chemical systems of increasing dimensionality and functionalities. Their swelling characteristics allow for their exfoliation in organic solvents with high

Hybrid2 - The hybrid power system simulation model

Energy Technology Data Exchange (ETDEWEB)

Baring-Gould, E.I.; Green, H.J.; Dijk, V.A.P. van [National Renewable Energy Lab., Golden, CO (United States); Manwell, J.F. [Univ. of Massachusetts, Amherst, MA (United States)

1996-12-31

There is a large-scale need and desire for energy in remote communities, especially in the developing world; however the lack of a user friendly, flexible performance prediction model for hybrid power systems incorporating renewables hindered the analysis of hybrids as options to conventional solutions. A user friendly model was needed with the versatility to simulate the many system locations, widely varying hardware configurations, and differing control options for potential hybrid power systems. To meet these ends, researchers from the National Renewable Energy Laboratory (NREL) and the University of Massachusetts (UMass) developed the Hybrid2 software. This paper provides an overview of the capabilities, features, and functionality of the Hybrid2 code, discusses its validation and future plans. Model availability and technical support provided to Hybrid2 users are also discussed. 12 refs., 3 figs., 4 tabs.

FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography.

Science.gov (United States)

Ale, Angelique; Ermolayev, Vladimir; Herzog, Eva; Cohrs, Christian; de Angelis, Martin Hrabé; Ntziachristos, Vasilis

2012-06-01

The development of hybrid optical tomography methods to improve imaging performance has been suggested over a decade ago and has been experimentally demonstrated in animals and humans. Here we examined in vivo performance of a camera-based hybrid fluorescence molecular tomography (FMT) system for 360° imaging combined with X-ray computed tomography (XCT). Offering an accurately co-registered, information-rich hybrid data set, FMT-XCT has new imaging possibilities compared to stand-alone FMT and XCT. We applied FMT-XCT to a subcutaneous 4T1 tumor mouse model, an Aga2 osteogenesis imperfecta model and a Kras lung cancer mouse model, using XCT information during FMT inversion. We validated in vivo imaging results against post-mortem planar fluorescence images of cryoslices and histology data. Besides offering concurrent anatomical and functional information, FMT-XCT resulted in the most accurate FMT performance to date. These findings indicate that addition of FMT optics into the XCT gantry may be a potent upgrade for small-animal XCT systems.

Hybrid incompatibility arises in a sequence-based bioenergetic model of transcription factor binding.

Science.gov (United States)

Tulchinsky, Alexander Y; Johnson, Norman A; Watt, Ward B; Porter, Adam H

2014-11-01

Postzygotic isolation between incipient species results from the accumulation of incompatibilities that arise as a consequence of genetic divergence. When phenotypes are determined by regulatory interactions, hybrid incompatibility can evolve even as a consequence of parallel adaptation in parental populations because interacting genes can produce the same phenotype through incompatible allelic combinations. We explore the evolutionary conditions that promote and constrain hybrid incompatibility in regulatory networks using a bioenergetic model (combining thermodynamics and kinetics) of transcriptional regulation, considering the bioenergetic basis of molecular interactions between transcription factors (TFs) and their binding sites. The bioenergetic parameters consider the free energy of formation of the bond between the TF and its binding site and the availability of TFs in the intracellular environment. Together these determine fractional occupancy of the TF on the promoter site, the degree of subsequent gene expression and in diploids, and the degree of dominance among allelic interactions. This results in a sigmoid genotype-phenotype map and fitness landscape, with the details of the shape determining the degree of bioenergetic evolutionary constraint on hybrid incompatibility. Using individual-based simulations, we subjected two allopatric populations to parallel directional or stabilizing selection. Misregulation of hybrid gene expression occurred under either type of selection, although it evolved faster under directional selection. Under directional selection, the extent of hybrid incompatibility increased with the slope of the genotype-phenotype map near the derived parental expression level. Under stabilizing selection, hybrid incompatibility arose from compensatory mutations and was greater when the bioenergetic properties of the interaction caused the space of nearly neutral genotypes around the stable expression level to be wide. F2's showed higher

Multi-level molecular modelling for plasma medicine

International Nuclear Information System (INIS)

Bogaerts, Annemie; Khosravian, Narjes; Van der Paal, Jonas; Verlackt, Christof C W; Yusupov, Maksudbek; Kamaraj, Balu; Neyts, Erik C

2016-01-01

Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions. (paper)

Fabrication of hybrid molecular devices using multi-layer graphene break junctions

Science.gov (United States)

Island, J. O.; Holovchenko, A.; Koole, M.; Alkemade, P. F. A.; Menelaou, M.; Aliaga-Alcalde, N.; Burzurí, E.; van der Zant, H. S. J.

2014-11-01

We report on the fabrication of hybrid molecular devices employing multi-layer graphene (MLG) flakes which are patterned with a constriction using a helium ion microscope or an oxygen plasma etch. The patterning step allows for the localization of a few-nanometer gap, created by electroburning, that can host single molecules or molecular ensembles. By controlling the width of the sculpted constriction, we regulate the critical power at which the electroburning process begins. We estimate the flake temperature given the critical power and find that at low powers it is possible to electroburn MLG with superconducting contacts in close proximity. Finally, we demonstrate the fabrication of hybrid devices with superconducting contacts and anthracene-functionalized copper curcuminoid molecules. This method is extendable to spintronic devices with ferromagnetic contacts and a first step towards molecular integrated circuits.

[Use of ITS and ISSR markers in the molecular characterisation of Pleurotus djamor hybrid strains].

Science.gov (United States)

Aguilar Doroteo, Leticia; Zárate Segura, Paola Berenice; Villanueva Arce, Ramón; Yáñez Fernández, Jorge; Garín Aguilar, María Eugenia; Guadarrama Mendoza, Paula Cecilia; Valencia Del Toro, Gustavo

Molecular characterisation of wild type Pleurotus species is important for germplasm conservation and its further use for genetic improvement. No molecular studies have been performed with monokaryons used for producing hybrid strains, either with the reconstituted strains obtained by pairing those monokaryons. The molecular characterisation of parental dikaryons, hybrid, and reconstituted strains as well as monokaryotic strains, is therefore of utmost importance. To carry out the molecular identification of Pleurotus djamor strains, i.e. dikaryotic wild type strains, hybrid strains, and the monokaryotic strains used for the hybrid formation. Five wild type strains of P. djamor from different states in Mexico were collected and molecularly identified by sequencing the ITS1-5.8-ITS2 region using ITS1 and ITS4 universal oligonucleotides. Four hybrid strains were obtained by pairing neohaplonts of two wild type strains selected. Six ISSR markers were used for the molecular characterisation of monokaryotic and dikaryotic strains. Using the ITS markers, an amplified product of 700bp was obtained in five wild type strains, with a 99-100% similarity with P. djamor. A total of 95 fragments were obtained using the ISSR markers, with 99% of polymorphism. Wild type strains were identified as P. djamor, and were clearly grouped with Mexican strains from other states of Mexico. ISSR markers allowed the generation of polymorphic bands in monokaryotic and dikaryotic strains, splitting both types of strains. The high degree of polymorphism indicates the genetic diversity of P. djamor, an advantage in mushroom production and in the improving of the species. Copyright © 2017 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

Biocompatible magnetic and molecular dual-targeting polyelectrolyte hybrid hollow microspheres for controlled drug release.

Science.gov (United States)

Du, Pengcheng; Zeng, Jin; Mu, Bin; Liu, Peng

2013-05-06

Well-defined biocompatible magnetic and molecular dual-targeting polyelectrolyte hybrid hollow microspheres have been accomplished via the layer-by-layer (LbL) self-assembly technique. The hybrid shell was fabricated by the electrostatic interaction between the polyelectrolyte cation, chitosan (CS), and the hybrid anion, citrate modified ferroferric oxide nanoparticles (Fe3O4-CA), onto the uniform polystyrene sulfonate microsphere templates. Then the magnetic hybrid core/shell composite particles were modified with a linear, functional poly(ethylene glycol) (PEG) monoterminated with a biotargeting molecule (folic acid (FA)). Afterward the dual targeting hybrid hollow microspheres were obtained after etching the templates by dialysis. The dual targeting hybrid hollow microspheres exhibit exciting pH response and stability in high salt-concentration media. Their pH-dependent controlled release of the drug molecule (anticancer drug, doxorubicin (DOX)) was also investigated in different human body fluids. As expected, the cell viability of the HepG2 cells which decreased more rapidly was treated by the FA modified hybrid hollow microspheres rather than the unmodified one in the in vitro study. The dual-targeting hybrid hollow microspheres demonstrate selective killing of the tumor cells. The precise magnetic and molecular targeting properties and pH-dependent controlled release offers promise for cancer treatment.

Hybridization improved bacteria resistance in abalone: Evidence from physiological and molecular responses.

Science.gov (United States)

Liang, Shuang; Luo, Xuan; You, Weiwei; Ke, Caihuan

2018-01-01

Hybridization is an effective way of improving germplasm in abalone, as it often generates benign traits in the hybrids. The hybrids of Haliotis discus hannai and H. gigantea have shown heterosis in terms of disease resistance than one or both parental species. In the present study, to elucidate the physiological and molecular mechanism of this heterosis, we analyzed the dynamic changes of several immune indexes including survival rate, total circulating haemocyte count (THC), phagocytic activity, reactive oxygen species level (ROS) and phenoloxidase activity (PO) in two parental species, H. discus hannai (DD) and H. gigantea (GG), and their reciprocal hybrids H. discus hannai ♀ × H. gigantea ♂ (DG), H. gigantea ♀ × H. discus hannai ♂ (GD) challenged with a mixture of Vibrio harveyi, V. alginolyticus and V. parahaemolyticus (which have been demonstrated to be pathogenic to abalone). Besides, we cloned and analyzed three important immune genes: heat shock protein 70 (hsp70), ferritin and cold shock domain protein (csdp) in H. discus hannai and H. gigantea, then further investigated their mRNA level changes in the four abalone genotypes after bacterial challenge. Results showed that these physiological and molecular parameters were significantly induced by bacterial exposure, and their changing patterns were obviously different between the four genotypes: (1) Survival rates of the two hybrids were higher than both parental species after bacterial exposure; (2) DG had higher THC than the other three genotypes; (3) Phagocytosis responded slower in the hybrids than in the parental species; (4) DD's ROS level was lower than the other three genotypes at 48 h post infection; (5) Phenoloxidase activity was lower in DD during the infection compared to the other genotypes; (6) mRNA levels of hsp70 and csdp, were always lower in at least one parental species (DD) than in the hybrids after the bacterial exposure. Results from this study indicate that the hybrids

Compositional Modelling of Stochastic Hybrid Systems

NARCIS (Netherlands)

Strubbe, S.N.

2005-01-01

In this thesis we present a modelling framework for compositional modelling of stochastic hybrid systems. Hybrid systems consist of a combination of continuous and discrete dynamics. The state space of a hybrid system is hybrid in the sense that it consists of a continuous component and a discrete

Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species

Science.gov (United States)

Burgess, Treena I.

2015-01-01

Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones. PMID:26248187

A Hybrid Imperative and Functional Molecular Mechanics Application

Directory of Open Access Journals (Sweden)

Thomas Deboni

1996-01-01

Full Text Available Molecular mechanics applications model the interactions among large ensembles of discrete particles. They are used where probabilistic methods are inadequate, such as drug chemistry. This methodology is difficult to parallelize with good performance, due to its poor locality, uneven partitions, and dynamic behavior. Imperative programs have been written that attempt this on shared and distributed memory machines. Given such a program, the computational kernel can be rewritten in Sisal, a functional programming language, and integrated with the rest of the imperative program under the Sisal Foreign Language Interface. This allows minimal effort and maximal return from parallelization work, and leaves the work appropriate to imperative implementation in its original form. We describe such an effort, focusing on the parts of the application that are appropriate for Sisal implementation, the specifics of mixed-language programming, and the complex performance behavior of the resulting hybrid code.

Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

Science.gov (United States)

Ghobadi, Ahmadreza F; Jayaraman, Arthi

2016-02-28

In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

Travelling Waves in Hybrid Chemotaxis Models

KAUST Repository

Franz, Benjamin

2013-12-18

Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are investigated. Bacteria are modelled using an agent-based (individual-based) approach with internal dynamics describing signal transduction. In addition to the chemotactic behaviour of the bacteria, the individual-based model also includes cell proliferation and death. Cells consume the extracellular nutrient field (chemoattractant), which is modelled using a partial differential equation. Mesoscopic and macroscopic equations representing the behaviour of the hybrid model are derived and the existence of travelling wave solutions for these models is established. It is shown that cell proliferation is necessary for the existence of non-transient (stationary) travelling waves in hybrid models. Additionally, a numerical comparison between the wave speeds of the continuum models and the hybrid models shows good agreement in the case of weak chemotaxis and qualitative agreement for the strong chemotaxis case. In the case of slow cell adaptation, we detect oscillating behaviour of the wave, which cannot be explained by mean-field approximations. © 2013 Society for Mathematical Biology.

A hybrid mammalian cell cycle model

Directory of Open Access Journals (Sweden)

Vincent Noël

2013-08-01

Full Text Available Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle, leading to cell division and proliferation, combines slow growth, spatio-temporal re-organisation of the cell, and rapid changes of regulatory proteins concentrations induced by post-translational modifications. The advancement through the cell cycle comprises a well defined sequence of stages, separated by checkpoint transitions. The combination of continuous and discrete changes justifies hybrid modelling approaches to cell cycle dynamics. We present a piecewise-smooth version of a mammalian cell cycle model, obtained by hybridization from a smooth biochemical model. The approximate hybridization scheme, leading to simplified reaction rates and binary event location functions, is based on learning from a training set of trajectories of the smooth model. We discuss several learning strategies for the parameters of the hybrid model.

Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

Directory of Open Access Journals (Sweden)

Jiyoung Kang

2012-01-01

Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

Comments On Clock Models In Hybrid Automata And Hybrid Control Systems

Directory of Open Access Journals (Sweden)

Virginia Ecaterina OLTEAN

2001-12-01

Full Text Available Hybrid systems have received a lot of attention in the past decade and a number of different models have been proposed in order to establish mathematical framework that is able to handle both continuous and discrete aspects. This contribution is focused on two models: hybrid automata and hybrid control systems with continuous-discrete interface and the importance of clock models is emphasized. Simple and relevant examples, some taken from the literature, accompany the presentation.

Caged molecular beacons: controlling nucleic acid hybridization with light.

Science.gov (United States)

Wang, Chunming; Zhu, Zhi; Song, Yanling; Lin, Hui; Yang, Chaoyong James; Tan, Weihong

2011-05-28

We have constructed a novel class of light-activatable caged molecular beacons (cMBs) that are caged by locking two stems with a photo-labile biomolecular interaction or covalent bond. With the cMBs, the nucleic acid hybridization process can be easily controlled with light, which offers the possibility for a high spatiotemporal resolution study of intracellular mRNAs. © The Royal Society of Chemistry 2011

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism

DEFF Research Database (Denmark)

Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik

2016-01-01

)-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers......The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R...... indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site...

Mechanical Properties of Graphene Nanoplatelet/Carbon Fiber/Epoxy Hybrid Composites: Multiscale Modeling and Experiments

Science.gov (United States)

Hadden, C. M.; Klimek-McDonald, D. R.; Pineda, E. J.; King, J. A.; Reichanadter, A. M.; Miskioglu, I.; Gowtham, S.; Odegard, G. M.

2015-01-01

Because of the relatively high specific mechanical properties of carbon fiber/epoxy composite materials, they are often used as structural components in aerospace applications. Graphene nanoplatelets (GNPs) can be added to the epoxy matrix to improve the overall mechanical properties of the composite. The resulting GNP/carbon fiber/epoxy hybrid composites have been studied using multiscale modeling to determine the influence of GNP volume fraction, epoxy crosslink density, and GNP dispersion on the mechanical performance. The hierarchical multiscale modeling approach developed herein includes Molecular Dynamics (MD) and micromechanical modeling, and it is validated with experimental testing of the same hybrid composite material system. The results indicate that the multiscale modeling approach is accurate and provides physical insight into the composite mechanical behavior. Also, the results quantify the substantial impact of GNP volume fraction and dispersion on the transverse mechanical properties of the hybrid composite, while the effect on the axial properties is shown to be insignificant.

Mechanical Properties of Graphene Nanoplatelet Carbon Fiber Epoxy Hybrid Composites: Multiscale Modeling and Experiments

Science.gov (United States)

Hadden, Cameron M.; Klimek-McDonald, Danielle R.; Pineda, Evan J.; King, Julie A.; Reichanadter, Alex M.; Miskioglu, Ibrahim; Gowtham, S.; Odegard, Gregory M.

2015-01-01

Because of the relatively high specific mechanical properties of carbon fiber/epoxy composite materials, they are often used as structural components in aerospace applications. Graphene nanoplatelets (GNPs) can be added to the epoxy matrix to improve the overall mechanical properties of the composite. The resulting GNP/carbon fiber/epoxy hybrid composites have been studied using multiscale modeling to determine the influence of GNP volume fraction, epoxy crosslink density, and GNP dispersion on the mechanical performance. The hierarchical multiscale modeling approach developed herein includes Molecular Dynamics (MD) and micromechanical modeling, and it is validated with experimental testing of the same hybrid composite material system. The results indicate that the multiscale modeling approach is accurate and provides physical insight into the composite mechanical behavior. Also, the results quantify the substantial impact of GNP volume fraction and dispersion on the transverse mechanical properties of the hybrid composite, while the effect on the axial properties is shown to be insignificant.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach

Science.gov (United States)

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-07-01

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach.

Science.gov (United States)

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-07-07

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

Directory of Open Access Journals (Sweden)

Manoj Kumar Mishra

2011-06-01

Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.

Gas-Transport-Property Performance of Hybrid Carbon Molecular Sieve−Polymer Materials

KAUST Repository

Das, Mita

2010-10-06

High-performance hybrid materials using carbon molecular sieve materials and 6FDA-6FpDA were produced. A detailed analysis of the effects of casting processes and the annealing temperature is reported. Two existing major obstacles, sieve agglomeration and residual stress, were addressed in this work, and subsequently a new membrane formation technique was developed to produce high-performing membranes. The successfully improved interfacial region of the hybrid membranes allows the sieves to increase the selectivity of the membranes above the neat polymer properties. Furthermore, an additional performance enhancement was seen with increased sieve loading in the hybrid membranes, leading to an actual performance above the upper bound for pure polymer membranes. The membranes were also tested under a mixed-gas environment, which further demonstrated promising results. © 2010 American Chemical Society.

Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

Science.gov (United States)

Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

2016-05-13

Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content.

Parametric Linear Hybrid Automata for Complex Environmental Systems Modeling

Directory of Open Access Journals (Sweden)

Samar Hayat Khan Tareen

2015-07-01

Full Text Available Environmental systems, whether they be weather patterns or predator-prey relationships, are dependent on a number of different variables, each directly or indirectly affecting the system at large. Since not all of these factors are known, these systems take on non-linear dynamics, making it difficult to accurately predict meaningful behavioral trends far into the future. However, such dynamics do not warrant complete ignorance of different efforts to understand and model close approximations of these systems. Towards this end, we have applied a logical modeling approach to model and analyze the behavioral trends and systematic trajectories that these systems exhibit without delving into their quantification. This approach, formalized by René Thomas for discrete logical modeling of Biological Regulatory Networks (BRNs and further extended in our previous studies as parametric biological linear hybrid automata (Bio-LHA, has been previously employed for the analyses of different molecular regulatory interactions occurring across various cells and microbial species. As relationships between different interacting components of a system can be simplified as positive or negative influences, we can employ the Bio-LHA framework to represent different components of the environmental system as positive or negative feedbacks. In the present study, we highlight the benefits of hybrid (discrete/continuous modeling which lead to refinements among the fore-casted behaviors in order to find out which ones are actually possible. We have taken two case studies: an interaction of three microbial species in a freshwater pond, and a more complex atmospheric system, to show the applications of the Bio-LHA methodology for the timed hybrid modeling of environmental systems. Results show that the approach using the Bio-LHA is a viable method for behavioral modeling of complex environmental systems by finding timing constraints while keeping the complexity of the model

Hybrid organic-inorganic rotaxanes and molecular shuttles.

Science.gov (United States)

Lee, Chin-Fa; Leigh, David A; Pritchard, Robin G; Schultz, David; Teat, Simon J; Timco, Grigore A; Winpenny, Richard E P

2009-03-19

The tetravalency of carbon and its ability to form covalent bonds with itself and other elements enables large organic molecules with complex structures, functions and dynamics to be constructed. The varied electronic configurations and bonding patterns of inorganic elements, on the other hand, can impart diverse electronic, magnetic, catalytic and other useful properties to molecular-level structures. Some hybrid organic-inorganic materials that combine features of both chemistries have been developed, most notably metal-organic frameworks, dense and extended organic-inorganic frameworks and coordination polymers. Metal ions have also been incorporated into molecules that contain interlocked subunits, such as rotaxanes and catenanes, and structures in which many inorganic clusters encircle polymer chains have been described. Here we report the synthesis of a series of discrete rotaxane molecules in which inorganic and organic structural units are linked together mechanically at the molecular level. Structural units (dialkyammonium groups) in dumb-bell-shaped organic molecules template the assembly of essentially inorganic 'rings' about 'axles' to form rotaxanes consisting of various numbers of rings and axles. One of the rotaxanes behaves as a 'molecular shuttle': the ring moves between two binding sites on the axle in a large-amplitude motion typical of some synthetic molecular machine systems. The architecture of the rotaxanes ensures that the electronic, magnetic and paramagnetic characteristics of the inorganic rings-properties that could make them suitable as qubits for quantum computers-can influence, and potentially be influenced by, the organic portion of the molecule.

Deriving simulators for hybrid Chi models

NARCIS (Netherlands)

Beek, van D.A.; Man, K.L.; Reniers, M.A.; Rooda, J.E.; Schiffelers, R.R.H.

2006-01-01

The hybrid Chi language is formalism for modeling, simulation and verification of hybrid systems. The formal semantics of hybrid Chi allows the definition of provably correct implementations for simulation, verification and realtime control. This paper discusses the principles of deriving an

Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

Science.gov (United States)

Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

2015-04-14

We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein–Zernike self-consistent field approach

International Nuclear Information System (INIS)

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-01-01

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein–Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple S N 2 reaction (Cl − + CH 3 Cl → ClCH 3 + Cl − ) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF

Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles

Science.gov (United States)

Petrini, Paula A.; Silva, Ricardo M. L.; de Oliveira, Rafael F.; Merces, Leandro; Bof Bufon, Carlos C.

2018-06-01

Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscopy. The incorporation of molecular materials in devices is not a trivial task as the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (k CuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensembles have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (k CuPc = 4.5 ± 0.5). These values suggest a mild contribution of the molecular orientation on the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology.

Hybrid rocket engine, theoretical model and experiment

Science.gov (United States)

Chelaru, Teodor-Viorel; Mingireanu, Florin

2011-06-01

The purpose of this paper is to build a theoretical model for the hybrid rocket engine/motor and to validate it using experimental results. The work approaches the main problems of the hybrid motor: the scalability, the stability/controllability of the operating parameters and the increasing of the solid fuel regression rate. At first, we focus on theoretical models for hybrid rocket motor and compare the results with already available experimental data from various research groups. A primary computation model is presented together with results from a numerical algorithm based on a computational model. We present theoretical predictions for several commercial hybrid rocket motors, having different scales and compare them with experimental measurements of those hybrid rocket motors. Next the paper focuses on tribrid rocket motor concept, which by supplementary liquid fuel injection can improve the thrust controllability. A complementary computation model is also presented to estimate regression rate increase of solid fuel doped with oxidizer. Finally, the stability of the hybrid rocket motor is investigated using Liapunov theory. Stability coefficients obtained are dependent on burning parameters while the stability and command matrixes are identified. The paper presents thoroughly the input data of the model, which ensures the reproducibility of the numerical results by independent researchers.

Hybrid simulation models of production networks

CERN Document Server

Kouikoglou, Vassilis S

2001-01-01

This book is concerned with a most important area of industrial production, that of analysis and optimization of production lines and networks using discrete-event models and simulation. The book introduces a novel approach that combines analytic models and discrete-event simulation. Unlike conventional piece-by-piece simulation, this method observes a reduced number of events between which the evolution of the system is tracked analytically. Using this hybrid approach, several models are developed for the analysis of production lines and networks. The hybrid approach combines speed and accuracy for exceptional analysis of most practical situations. A number of optimization problems, involving buffer design, workforce planning, and production control, are solved through the use of hybrid models.

Analysis of chromosome aberration data by hybrid-scale models

International Nuclear Information System (INIS)

Indrawati, Iwiq; Kumazawa, Shigeru

2000-02-01

This paper presents a new methodology for analyzing data of chromosome aberrations, which is useful to understand the characteristics of dose-response relationships and to construct the calibration curves for the biological dosimetry. The hybrid scale of linear and logarithmic scales brings a particular plotting paper, where the normal section paper, two types of semi-log papers and the log-log paper are continuously connected. The hybrid-hybrid plotting paper may contain nine kinds of linear relationships, and these are conveniently called hybrid scale models. One can systematically select the best-fit model among the nine models by among the conditions for a straight line of data points. A biological interpretation is possible with some hybrid-scale models. In this report, the hybrid scale models were applied to separately reported data on chromosome aberrations in human lymphocytes as well as on chromosome breaks in Tradescantia. The results proved that the proposed models fit the data better than the linear-quadratic model, despite the demerit of the increased number of model parameters. We showed that the hybrid-hybrid model (both variables of dose and response using the hybrid scale) provides the best-fit straight lines to be used as the reliable and readable calibration curves of chromosome aberrations. (author)

Self-regulated growth of LaVO3 thin films by hybrid molecular beam epitaxy

International Nuclear Information System (INIS)

Zhang, Hai-Tian; Engel-Herbert, Roman; Dedon, Liv R.; Martin, Lane W.

2015-01-01

LaVO 3 thin films were grown on SrTiO 3 (001) by hybrid molecular beam epitaxy. A volatile metalorganic precursor, vanadium oxytriisopropoxide (VTIP), and elemental La were co-supplied in the presence of a molecular oxygen flux. By keeping the La flux fixed and varying the VTIP flux, stoichiometric LaVO 3 films were obtained for a range of cation flux ratios, indicating the presence of a self-regulated growth window. Films grown under stoichiometric conditions were found to have the largest lattice parameter, which decreased monotonically with increasing amounts of excess La or V. Energy dispersive X-ray spectroscopy and Rutherford backscattering measurements were carried out to confirm film compositions. Stoichiometric growth of complex vanadate thin films independent of cation flux ratios expands upon the previously reported self-regulated growth of perovskite titanates using hybrid molecular beam epitaxy, thus demonstrating the general applicability of this growth approach to other complex oxide materials, where a precise control over film stoichiometry is demanded by the application

Numerical Study on Couette Flow in Nanostructured Channel using Molecular-continuum Hybrid Method

Energy Technology Data Exchange (ETDEWEB)

Kim, Youngjin; Jeong, Myunggeun; Ha, Man Yeong [Pusan Nat’l Univ., Busan (Korea, Republic of)

2017-06-15

A molecular-continuum hybrid method was developed to simulate microscale and nanoscale fluids where continuum fluidic cannot be used to predict Couette flow. Molecular dynamics simulation is used near the solid surface where the flow cannot be predicted by continuum fluidic, and Navier-Stokes equations are used in the other regions. Numerical simulation of Couette flow was performed using the hybrid method to investigate the effect of solid-liquid interaction and surface roughness in a nanochannel. It was found that the solid-liquid interaction and surface roughness influence the boundary condition. When the surface energy is low, slippage occurs near the solid surface, and the magnitude of slippage decreases with increase in surface energy. When the surface energy is high, a locking boundary condition is formed. The roughness disturbs slippage near the solid surface and promotes the locking boundary condition.

Molecular confirmation of hybridization between Dascyllus reticulatus × Dascyllus aruanus from the Great Barrier Reef

KAUST Repository

He, Song; Johansen, Jacob L.; Hoey, Andrew S.; Pappas, Melissa; Berumen, Michael L.

2017-01-01

To date, more than 81 species of tropical coral reef fish have been reported to hybridize in nature, spanning multiple families, including the Chaetodontidae, Pomacanthidae, and Labridae. Hybridization, however, is seemingly rare among benthic nesting species that engage in pair spawning, such as the Pomacentridae. Here, we present evidence for the first molecularly confirmed record of hybridization within the genus Dascyllus; D. aruanus and D. reticulatus. Interestingly, although many hybridization events are attributed to peripheral range effects or areas of limited overlap among otherwise allopatric species, this hybrid individual was collected from the northern Great Barrier Reef, centrally located within the distribution ranges of both species. The hybrid exhibited coloration and meristic counts intermediate between D. aruanus and D. reticulatus. Diagnostic genetic markers and subsequent microsatellites analysis confirmed that this individual was a hybrid offspring of D. aruanus and D. reticulatus, with the latter providing the maternal contribution. The occurrence of the D. aruanus × D. reticulatus hybrid on the Great Barrier Reef represents an exception to the otherwise species-specific haplotypes. The nuclear diagnostic marker which was identified during this study could serve as a hybrid indicator and benefit future hybrid investigations for hybridization between these two species.

Molecular confirmation of hybridization between Dascyllus reticulatus × Dascyllus aruanus from the Great Barrier Reef

KAUST Repository

He, Song

2017-11-17

To date, more than 81 species of tropical coral reef fish have been reported to hybridize in nature, spanning multiple families, including the Chaetodontidae, Pomacanthidae, and Labridae. Hybridization, however, is seemingly rare among benthic nesting species that engage in pair spawning, such as the Pomacentridae. Here, we present evidence for the first molecularly confirmed record of hybridization within the genus Dascyllus; D. aruanus and D. reticulatus. Interestingly, although many hybridization events are attributed to peripheral range effects or areas of limited overlap among otherwise allopatric species, this hybrid individual was collected from the northern Great Barrier Reef, centrally located within the distribution ranges of both species. The hybrid exhibited coloration and meristic counts intermediate between D. aruanus and D. reticulatus. Diagnostic genetic markers and subsequent microsatellites analysis confirmed that this individual was a hybrid offspring of D. aruanus and D. reticulatus, with the latter providing the maternal contribution. The occurrence of the D. aruanus × D. reticulatus hybrid on the Great Barrier Reef represents an exception to the otherwise species-specific haplotypes. The nuclear diagnostic marker which was identified during this study could serve as a hybrid indicator and benefit future hybrid investigations for hybridization between these two species.

Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles.

Science.gov (United States)

Petrini, Paula Andreia; Lopes da Silva, Ricardo Magno; de Oliveira, Rafael Furlan; Merces, Leandro; Bufon, Carlos César Bof

2018-04-06

Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscope (STM). The incorporation of molecular materials in devices is not a trivial task since the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (kCuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensemble have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (< 30 nm). From the electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (kCuPc = 4.5 ± 0.5). These values suggest a mild contribution of molecular orientation in the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology. © 2018 IOP Publishing Ltd.

Hybrid molecularly imprinted poly(methacrylic acid-TRIM)-silica chemically modified with (3-glycidyloxypropyl)trimethoxysilane for the extraction of folic acid in aqueous medium

Energy Technology Data Exchange (ETDEWEB)

Midori de Oliveira, Fernanda; Gava Segatelli, Mariana [Departamento de Química, Universidade Estadual de Londrina, Rod. Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, PR CEP 86051-990 (Brazil); Tarley, César Ricardo Teixeira, E-mail: ctarleyquim@yahoo.com.br [Departamento de Química, Universidade Estadual de Londrina, Rod. Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, PR CEP 86051-990 (Brazil); Instituto Nacional de Ciência e Tecnologia (INCT) de Bioanalítica, Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Departamento de Química Analítica, Cidade Universitária Zeferino Vaz s/n, CEP 13083-970 Campinas, SP (Brazil)

2016-02-01

In the present study a hybrid molecularly imprinted poly(methacrylic acid-trimethylolpropane trimethacrylate)-silica (MIP) was synthesized and modified with (3-glycidyloxypropyl)trimethoxysilane (GPTMS) with posterior opening of epoxy ring to provide hydrophilic properties of material in the extraction of folic acid from aqueous medium. The chemical and structural aggregates of hybrid material were characterized by means of Fourier Transform Infrared (FT-IR), Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Thermogravimetric analysis (TGA) and textural data. Selectivity data of MIP were compared to non-imprinted polymer (NIP) through competitive sorption studies in the presence of caffeine, paracetamol or 4-aminobenzamide yielding relative selectivity coefficients (k′) higher than one unit, thus confirming the selective character of MIP even in the presence of structurally smaller compounds than the folic acid. The lower hydrophobic sorption by bovine serum albumin (BSA) in the MIP as compared to unmodified MIP proves the hydrophilicity of polymer surface by using GPTMS with opening ring. Under acid medium (pH 1.5) the sorption of folic acid onto MIP from batch experiments was higher than the one achieved for NIP. Equilibrium sorption of folic acid was reached at 120 min for MIP, NIP and MIP without GPTMS and kinetic sorption data were well described by pseudo-second-order, Elovich and intraparticle diffusion models. Thus, these results indicate the existence of different binding energy sites in the polymers and a complex mechanism consisting of both surface sorption and intraparticle transport of folic acid within the pores of polymers. - Highlights: • The molecularly imprinted hybrid polymer showed high adsorption capacity for folic acid. • The molecularly imprinted hybrid polymer showed high selectivity for folic acid. • The molecularly imprinted hybrid polymer modified with GPTMS excludes higher amount of BSA.

Hybrid Modelling of Individual Movement and Collective Behaviour

KAUST Repository

Franz, Benjamin

2013-01-01

Mathematical models of dispersal in biological systems are often written in terms of partial differential equations (PDEs) which describe the time evolution of population-level variables (concentrations, densities). A more detailed modelling approach is given by individual-based (agent-based) models which describe the behaviour of each organism. In recent years, an intermediate modelling methodology - hybrid modelling - has been applied to a number of biological systems. These hybrid models couple an individual-based description of cells/animals with a PDE-model of their environment. In this chapter, we overview hybrid models in the literature with the focus on the mathematical challenges of this modelling approach. The detailed analysis is presented using the example of chemotaxis, where cells move according to extracellular chemicals that can be altered by the cells themselves. In this case, individual-based models of cells are coupled with PDEs for extracellular chemical signals. Travelling waves in these hybrid models are investigated. In particular, we show that in contrary to the PDEs, hybrid chemotaxis models only develop a transient travelling wave. © 2013 Springer-Verlag Berlin Heidelberg.

Effect of Molecular Weight on the Properties of Liquid Epoxidized Natural Rubber Acrylate (LENRA)/ Silica Hybrid Composites

International Nuclear Information System (INIS)

Eda Yuhana Ariffin; Azizan Ahmad; Dahlan Mohd; Mahathir Mohamed

2011-01-01

This paper reports on the effect of molecular weight on the morphological and mechanical properties of liquid epoxidized natural rubber acrylate (LENRA)/ silica hybrid composites prepared by sol-gel technique. The sol-gel reaction was conducted at different concentration of tetraethyl orthosilicate (TEOS), used as a precursor of silica. TEOS were introduced in 10, 20, 30, 40 and 50 parts per hundred rubber (phr) in the composites. Two different molecular weights of ENR were used to study the effect of molecular weight on the mechanical and morphological properties of the compounds. These compounds were cured by ultraviolet (UV) irradiation. The mechanical properties were studied through pendulum hardness and scratch tests. Higher molecular weight of ENR showed better mechanical properties than lower molecular weight. Transmission electron microscope was used to determine the silica size and to study the distribution and dispersion of the silica particles. High molecular weight showed greater distribution and dispersion of silica particles with diameter of 13 - 256 nm. Morphological and mechanical properties of LENRA/ silica hybrid composites were improved by using high molecular weight of ENR. (author)

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

Science.gov (United States)

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Bayesian estimation of realized stochastic volatility model by Hybrid Monte Carlo algorithm

International Nuclear Information System (INIS)

Takaishi, Tetsuya

2014-01-01

The hybrid Monte Carlo algorithm (HMCA) is applied for Bayesian parameter estimation of the realized stochastic volatility (RSV) model. Using the 2nd order minimum norm integrator (2MNI) for the molecular dynamics (MD) simulation in the HMCA, we find that the 2MNI is more efficient than the conventional leapfrog integrator. We also find that the autocorrelation time of the volatility variables sampled by the HMCA is very short. Thus it is concluded that the HMCA with the 2MNI is an efficient algorithm for parameter estimations of the RSV model

Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.

Directory of Open Access Journals (Sweden)

Kecheng Yang

Full Text Available Sampling enrichment toward a target state, an analogue of the improvement of sampling efficiency (SE, is critical in both the refinement of protein structures and the generation of near-native structure ensembles for the exploration of structure-function relationships. We developed a hybrid molecular dynamics (MD-Monte Carlo (MC approach to enrich the sampling toward the target structures. In this approach, the higher SE is achieved by perturbing the conventional MD simulations with a MC structure-acceptance judgment, which is based on the coincidence degree of small angle x-ray scattering (SAXS intensity profiles between the simulation structures and the target structure. We found that the hybrid simulations could significantly improve SE by making the top-ranked models much closer to the target structures both in the secondary and tertiary structures. Specifically, for the 20 mono-residue peptides, when the initial structures had the root-mean-squared deviation (RMSD from the target structure smaller than 7 Å, the hybrid MD-MC simulations afforded, on average, 0.83 Å and 1.73 Å in RMSD closer to the target than the parallel MD simulations at 310K and 370K, respectively. Meanwhile, the average SE values are also increased by 13.2% and 15.7%. The enrichment of sampling becomes more significant when the target states are gradually detectable in the MD-MC simulations in comparison with the parallel MD simulations, and provide >200% improvement in SE. We also performed a test of the hybrid MD-MC approach in the real protein system, the results showed that the SE for 3 out of 5 real proteins are improved. Overall, this work presents an efficient way of utilizing solution SAXS to improve protein structure prediction and refinement, as well as the generation of near native structures for function annotation.

Fabrication of reproducible, integration-compatible hybrid molecular/si electronics.

Science.gov (United States)

Yu, Xi; Lovrinčić, Robert; Kraynis, Olga; Man, Gabriel; Ely, Tal; Zohar, Arava; Toledano, Tal; Cahen, David; Vilan, Ayelet

2014-12-29

Reproducible molecular junctions can be integrated within standard CMOS technology. Metal-molecule-semiconductor junctions are fabricated by direct Si-C binding of hexadecane or methyl-styrene onto oxide-free H-Si(111) surfaces, with the lateral size of the junctions defined by an etched SiO2 well and with evaporated Pb as the top contact. The current density, J, is highly reproducible with a standard deviation in log(J) of 0.2 over a junction diameter change from 3 to 100 μm. Reproducibility over such a large range indicates that transport is truly across the molecules and does not result from artifacts like edge effects or defects in the molecular monolayer. Device fabrication is tested for two n-Si doping levels. With highly doped Si, transport is dominated by tunneling and reveals sharp conductance onsets at room temperature. Using the temperature dependence of current across medium-doped n-Si, the molecular tunneling barrier can be separated from the Si-Schottky one, which is a 0.47 eV, in agreement with the molecular-modified surface dipole and quite different from the bare Si-H junction. This indicates that Pb evaporation does not cause significant chemical changes to the molecules. The ability to manufacture reliable devices constitutes important progress toward possible future hybrid Si-based molecular electronics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploratory Topology Modelling of Form-Active Hybrid Structures

DEFF Research Database (Denmark)

Holden Deleuran, Anders; Pauly, Mark; Tamke, Martin

2016-01-01

The development of novel form-active hybrid structures (FAHS) is impeded by a lack of modelling tools that allow for exploratory topology modelling of shaped assemblies. We present a flexible and real-time computational design modelling pipeline developed for the exploratory modelling of FAHS...... that enables designers and engineers to iteratively construct and manipulate form-active hybrid assembly topology on the fly. The pipeline implements Kangaroo2's projection-based methods for modelling hybrid structures consisting of slender beams and cable networks. A selection of design modelling sketches...

Molecular level in silico studies for oncology. Direct models review

Science.gov (United States)

Psakhie, S. G.; Tsukanov, A. A.

2017-09-01

The combination of therapy and diagnostics in one process "theranostics" is a trend in a modern medicine, especially in oncology. Such an approach requires development and usage of multifunctional hybrid nanoparticles with a hierarchical structure. Numerical methods and mathematical models play a significant role in the design of the hierarchical nanoparticles and allow looking inside the nanoscale mechanisms of agent-cell interactions. The current position of in silico approach in biomedicine and oncology is discussed. The review of the molecular level in silico studies in oncology, which are using the direct models, is presented.

Hierarchical coassembly of DNA–triptycene hybrid molecular building blocks and zinc protoporphyrin IX

Directory of Open Access Journals (Sweden)

Rina Kumari

2016-05-01

Full Text Available Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA–DNA building blocks and zinc protoporphyrin IX (Zn PpIX. DNA–organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5′-C12-amine-terminated modified single strand DNA (ssDNA and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE, reverse-phase high-performance liquid chromatography (RP-HPLC and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF. The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA–TPA molecular building blocks as well as a model guest molecule within the DNA–TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD and atomic force microscopy (AFM have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA–TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA–DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA–TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT applications as well as photocatalytic reactions.

Hybrid discrete choice models: Gained insights versus increasing effort

Energy Technology Data Exchange (ETDEWEB)

Mariel, Petr, E-mail: petr.mariel@ehu.es [UPV/EHU, Economía Aplicada III, Avda. Lehendakari Aguire, 83, 48015 Bilbao (Spain); Meyerhoff, Jürgen [Institute for Landscape Architecture and Environmental Planning, Technical University of Berlin, D-10623 Berlin, Germany and The Kiel Institute for the World Economy, Duesternbrooker Weg 120, 24105 Kiel (Germany)

2016-10-15

Hybrid choice models expand the standard models in discrete choice modelling by incorporating psychological factors as latent variables. They could therefore provide further insights into choice processes and underlying taste heterogeneity but the costs of estimating these models often significantly increase. This paper aims at comparing the results from a hybrid choice model and a classical random parameter logit. Point of departure for this analysis is whether researchers and practitioners should add hybrid choice models to their suite of models routinely estimated. Our comparison reveals, in line with the few prior studies, that hybrid models gain in efficiency by the inclusion of additional information. The use of one of the two proposed approaches, however, depends on the objective of the analysis. If disentangling preference heterogeneity is most important, hybrid model seems to be preferable. If the focus is on predictive power, a standard random parameter logit model might be the better choice. Finally, we give recommendations for an adequate use of hybrid choice models based on known principles of elementary scientific inference. - Highlights: • The paper compares performance of a Hybrid Choice Model (HCM) and a classical Random Parameter Logit (RPL) model. • The HCM indeed provides insights regarding preference heterogeneity not gained from the RPL. • The RPL has similar predictive power as the HCM in our data. • The costs of estimating HCM seem to be justified when learning more on taste heterogeneity is a major study objective.

Hybrid discrete choice models: Gained insights versus increasing effort

International Nuclear Information System (INIS)

Mariel, Petr; Meyerhoff, Jürgen

2016-01-01

Hybrid choice models expand the standard models in discrete choice modelling by incorporating psychological factors as latent variables. They could therefore provide further insights into choice processes and underlying taste heterogeneity but the costs of estimating these models often significantly increase. This paper aims at comparing the results from a hybrid choice model and a classical random parameter logit. Point of departure for this analysis is whether researchers and practitioners should add hybrid choice models to their suite of models routinely estimated. Our comparison reveals, in line with the few prior studies, that hybrid models gain in efficiency by the inclusion of additional information. The use of one of the two proposed approaches, however, depends on the objective of the analysis. If disentangling preference heterogeneity is most important, hybrid model seems to be preferable. If the focus is on predictive power, a standard random parameter logit model might be the better choice. Finally, we give recommendations for an adequate use of hybrid choice models based on known principles of elementary scientific inference. - Highlights: • The paper compares performance of a Hybrid Choice Model (HCM) and a classical Random Parameter Logit (RPL) model. • The HCM indeed provides insights regarding preference heterogeneity not gained from the RPL. • The RPL has similar predictive power as the HCM in our data. • The costs of estimating HCM seem to be justified when learning more on taste heterogeneity is a major study objective.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

Science.gov (United States)

Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

2018-01-01

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield

Hybrid Models of Alternative Current Filter for Hvdc

Directory of Open Access Journals (Sweden)

Ufa Ruslan A.

2017-01-01

Full Text Available Based on a hybrid simulation concept of HVDC, the developed hybrid AC filter models, providing the sufficiently full and adequate modeling of all single continuous spectrum of quasi-steady-state and transient processes in the filter, are presented. The obtained results suggest that usage of the hybrid simulation approach is carried out a methodically accurate with guaranteed instrumental error solution of differential equation systems of mathematical models of HVDC.

A hybrid algorithm for parallel molecular dynamics simulations

Science.gov (United States)

Mangiardi, Chris M.; Meyer, R.

2017-10-01

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

Some hybrid models applicable to dose-response relationships

International Nuclear Information System (INIS)

Kumazawa, Shigeru

1992-01-01

A new type of models of dose-response relationships has been studied as an initial stage to explore a reliable extrapolation of the relationships decided by high dose data to the range of low dose covered by radiation protection. The approach is to use a 'hybrid scale' of linear and logarithmic scales; the first model is that the normalized surviving fraction (ρ S > 0) in a hybrid scale decreases linearly with dose in a linear scale, and the second is that the induction in a log scale increases linearly with the normalized dose (τ D > 0) in a hybrid scale. The hybrid scale may reflect an overall effectiveness of a complex system against adverse events caused by various agents. Some data of leukemia in the atomic bomb survivors and of rodent experiments were used to show the applicability of hybrid scale models. The results proved that proposed models fit these data not less than the popular linear-quadratic models, providing the possible interpretation of shapes of dose-response curves, e.g. shouldered survival curves varied by recovery time. (author)

Molecular Evidence for the Hybrid Origin of Ilex dabieshanensis (Aquifoliaceae.

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Lin Shi

Full Text Available Ilex, the largest genus of dioecious woody plants, is a good study system to assess the role of hybridization in speciation and evolution. Ilex dabieshanensis, a tree endemic to Dabieshan Mountains region, was initially described as a new species. Based on morphological intermediacy and sympatric distribution with its putative parental species, I. cornuta and I. latifolia, we proposed it as a natural hybrid between them. In this study, we sequenced one chloroplast intergenic spacer (trnH-psbA and two nuclear genes (gapC and nepGS in I. dabieshanensis and its putative parental species to test the hybrid origin hypothesis. Our results showed that there were one to two differentially fixed sequence differences between I. cornuta and I. latifolia at the two nuclear genes. Twelve of the 14 individuals of I. dabieshanensis exhibited additivity in chromatograms on these differentially fixed sites at both nuclear genes, and the remaining two exhibited additivity in chromatograms on the fixed site at only the nepGS gene. Except one haplotype of I. cornuta at the nepGS gene, all of the haplotypes of I. cornuta at the two nuclear genes were well separated from those of I. latifolia, and most haplotypes of I. dabieshanensis were shared with those of I. cornuta and I. latifolia. Phylogenetic analysis of these haplotypes was largely consistent with haplotype network analysis. I. cornuta and I. latifolia differed by two nucleotide substitutions in the chloroplast intergenic spacer, and 12 individuals of I. dabieshanensis had the same sequences as I. latifolia, while the remaining two were identical with I. cornuta. The molecular data provide convincing evidence for the hybrid origin of I. dabieshanensis and asymmetrical direction of hybridization. One haplotype of I. cornuta at the nepGS gene was nested with those of I. latifolia, indicating introgression to I. cornuta.

Modelling the solar wind interaction with Mercury by a quasi-neutral hybrid model

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E. Kallio

2003-11-01

Full Text Available Quasi-neutral hybrid model is a self-consistent modelling approach that includes positively charged particles and an electron fluid. The approach has received an increasing interest in space plasma physics research because it makes it possible to study several plasma physical processes that are difficult or impossible to model by self-consistent fluid models, such as the effects associated with the ions’ finite gyroradius, the velocity difference between different ion species, or the non-Maxwellian velocity distribution function. By now quasi-neutral hybrid models have been used to study the solar wind interaction with the non-magnetised Solar System bodies of Mars, Venus, Titan and comets. Localized, two-dimensional hybrid model runs have also been made to study terrestrial dayside magnetosheath. However, the Hermean plasma environment has not yet been analysed by a global quasi-neutral hybrid model. In this paper we present a new quasi-neutral hybrid model developed to study various processes associated with the Mercury-solar wind interaction. Emphasis is placed on addressing advantages and disadvantages of the approach to study different plasma physical processes near the planet. The basic assumptions of the approach and the algorithms used in the new model are thoroughly presented. Finally, some of the first three-dimensional hybrid model runs made for Mercury are presented. The resulting macroscopic plasma parameters and the morphology of the magnetic field demonstrate the applicability of the new approach to study the Mercury-solar wind interaction globally. In addition, the real advantage of the kinetic hybrid model approach is to study the property of individual ions, and the study clearly demonstrates the large potential of the approach to address these more detailed issues by a quasi-neutral hybrid model in the future.Key words. Magnetospheric physics (planetary magnetospheres; solar wind-magnetosphere interactions – Space plasma

Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

International Nuclear Information System (INIS)

Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

2014-01-01

Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

Hybrid computer modelling in plasma physics

International Nuclear Information System (INIS)

Hromadka, J; Ibehej, T; Hrach, R

2016-01-01

Our contribution is devoted to development of hybrid modelling techniques. We investigate sheath structures in the vicinity of solids immersed in low temperature argon plasma of different pressures by means of particle and fluid computer models. We discuss the differences in results obtained by these methods and try to propose a way to improve the results of fluid models in the low pressure area. There is a possibility to employ Chapman-Enskog method to find appropriate closure relations of fluid equations in a case when particle distribution function is not Maxwellian. We try to follow this way to enhance fluid model and to use it in hybrid plasma model further. (paper)

Modeling of Hybrid Growth Wastewater Bio-reactor

International Nuclear Information System (INIS)

EI Nashaei, S.; Garhyan, P.; Prasad, P.; Abdel Halim, H.S.; Ibrahim, G.

2004-01-01

The attached/suspended growth mixed reactors are considered one of the recently tried approaches to improve the performance of the biological treatment by increasing the volume of the accumulated biomass in terms of attached growth as well as suspended growth. Moreover, the domestic WW can be easily mixed with a high strength non-hazardous industrial wastewater and treated together in these bio-reactors if the need arises. Modeling of Hybrid hybrid growth wastewater reactor addresses the need of understanding the rational of such system in order to achieve better design and operation parameters. This paper aims at developing a heterogeneous mathematical model for hybrid growth system considering the effect of diffusion, external mass transfer, and power input to the system in a rational manner. The model will be based on distinguishing between liquid/solid phase (bio-film and bio-floc). This model would be a step ahead to the fine tuning the design of hybrid systems based on the experimental data of a pilot plant to be implemented in near future

Self-organizing bioinspired oligothiophene–oligopeptide hybrids

Directory of Open Access Journals (Sweden)

Alexey K. Shaytan

2011-09-01

Full Text Available In this minireview, we survey recent advances in the synthesis, characterization, and modeling of new oligothiophene–oligopeptide hybrids capable of forming nanostructured fibrillar aggregates in solution and on solid substrates. Compounds of this class are promising for applications because their self-assembly and stimuli-responsive properties, provided by the peptide moieties combined with the semiconducting properties of the thiophene blocks, can result in novel opportunities for the design of advanced smart materials. These bio-inspired molecular hybrids are experimentally shown to form stable fibrils as visualized by AFM and TEM. While the experimental evidence alone is not sufficient to reveal the exact molecular organization of the fibrils, theoretical approaches based on quantum chemistry calculations and large-scale atomistic molecular dynamics simulations are attempted in an effort to reveal the structure of the fibrils at the nanoscale. Based on the combined theoretical and experimental analysis, the most likely models of fibril formation and aggregation are suggested.

Modelling the solar wind interaction with Mercury by a quasi-neutral hybrid model

Directory of Open Access Journals (Sweden)

E. Kallio

Full Text Available Quasi-neutral hybrid model is a self-consistent modelling approach that includes positively charged particles and an electron fluid. The approach has received an increasing interest in space plasma physics research because it makes it possible to study several plasma physical processes that are difficult or impossible to model by self-consistent fluid models, such as the effects associated with the ions’ finite gyroradius, the velocity difference between different ion species, or the non-Maxwellian velocity distribution function. By now quasi-neutral hybrid models have been used to study the solar wind interaction with the non-magnetised Solar System bodies of Mars, Venus, Titan and comets. Localized, two-dimensional hybrid model runs have also been made to study terrestrial dayside magnetosheath. However, the Hermean plasma environment has not yet been analysed by a global quasi-neutral hybrid model.

In this paper we present a new quasi-neutral hybrid model developed to study various processes associated with the Mercury-solar wind interaction. Emphasis is placed on addressing advantages and disadvantages of the approach to study different plasma physical processes near the planet. The basic assumptions of the approach and the algorithms used in the new model are thoroughly presented. Finally, some of the first three-dimensional hybrid model runs made for Mercury are presented.

The resulting macroscopic plasma parameters and the morphology of the magnetic field demonstrate the applicability of the new approach to study the Mercury-solar wind interaction globally. In addition, the real advantage of the kinetic hybrid model approach is to study the property of individual ions, and the study clearly demonstrates the large potential of the approach to address these more detailed issues by a quasi-neutral hybrid model in the future.

Key words. Magnetospheric physics

Optimized molecular reconstruction procedure combining hybrid reverse Monte Carlo and molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Bousige, Colin; Boţan, Alexandru; Coasne, Benoît, E-mail: coasne@mit.edu [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Ulm, Franz-Josef [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Pellenq, Roland J.-M. [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); CINaM, CNRS/Aix Marseille Université, Campus de Luminy, 13288 Marseille Cedex 09 (France)

2015-03-21

We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight ω of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.

Fabrication of molecular hybrid films of gold nanoparticle and polythiophene by covalent assembly

Energy Technology Data Exchange (ETDEWEB)

Sundaramurthy, Jayaraman, E-mail: jsu2@np.edu.sg [Department of Chemical & Biomolecular Engineering, National University of Singapore, Block E5, 4 Engineering Drive 4, 117576 (Singapore); Environmental & Water Technology Centre of Innovation, Ngee Ann Polytechnic, 599489 (Singapore); Dharmarajan, Rajarathnam [CERAR, University of South Australia, Mawson Lakes, SA 5095 (Australia); Srinivasan, M.P., E-mail: chesmp@nus.edu.sg [Department of Chemical & Biomolecular Engineering, National University of Singapore, Block E5, 4 Engineering Drive 4, 117576 (Singapore)

2015-08-31

This work demonstrates the fabrication of molecular hybrid films comprising gold nanoparticles (AuNPs) incorporated in covalently assembled, substituted polythiophene (poly(3-(2-bromoethoxy)ethoxymethylthiophene-2,5-diyl (PBrEEMT))) films by different surface chemistry routes. AuNPs are incorporated in the immobilized polythiophene matrix due to its affinity for amine and sulfur. The amount of AuNPs present depends on the nature of the incorporation, the extent of film coverage and interaction of thiophene and amine groups. PBrEEMT films functionalized with amine rich polyallylamine immobilize greater numbers of AuNPs due to more extensive gold–amine interactions. Covalent binding between AuNP and PBrEEMT films was accomplished by using pre-functionalised AuNPs (4-aminothiophenol functionalized AuNPs). Atomic force microscopy, field emission scanning electron microscopy and X-ray photoelectron spectroscopy were used to study the morphology and chemical constituents of assembled films. These approaches will pave the way for developing facile methods for nanoparticle incorporation and will also facilitate direct interaction of nanoparticles with the conducting polymer matrix and enhance the electrical properties of the films. - Highlights: • Covalent molecular assembly enabled the fabrication of molecular hybrid films. • Monomeric and polymeric species were employed as intermediate linkers. • Adopted approaches facilitated the direct interaction of gold nanoparticle in films. • The amount of nanoparticle incorporation depended on the extent of film coverage.

A hybrid absorbing boundary condition for frequency-domain finite-difference modelling

International Nuclear Information System (INIS)

Ren, Zhiming; Liu, Yang

2013-01-01

Liu and Sen (2010 Geophysics 75 A1–6; 2012 Geophys. Prospect. 60 1114–32) proposed an efficient hybrid scheme to significantly absorb boundary reflections for acoustic and elastic wave modelling in the time domain. In this paper, we extend the hybrid absorbing boundary condition (ABC) into the frequency domain and develop specific strategies for regular-grid and staggered-grid modelling, respectively. Numerical modelling tests of acoustic, visco-acoustic, elastic and vertically transversely isotropic (VTI) equations show significant absorptions for frequency-domain modelling. The modelling results of the Marmousi model and the salt model also demonstrate the effectiveness of the hybrid ABC. For elastic modelling, the hybrid Higdon ABC and the hybrid Clayton and Engquist (CE) ABC are implemented, respectively. Numerical simulations show that the hybrid Higdon ABC gets better absorption than the hybrid CE ABC, especially for S-waves. We further compare the hybrid ABC with the classical perfectly matched layer (PML). Results show that the two ABCs cost the same computation time and memory space for the same absorption width. However, the hybrid ABC is more effective than the PML for the same small absorption width and the absorption effects of the two ABCs gradually become similar when the absorption width is increased. (paper)

Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts.

Science.gov (United States)

Wen, Fuyu; Li, Can

2013-11-19

Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

Model Reduction of Hybrid Systems

DEFF Research Database (Denmark)

Shaker, Hamid Reza

gramians. Generalized gramians are the solutions to the observability and controllability Lyapunov inequalities. In the first framework the projection matrices are found based on the common generalized gramians. This framework preserves the stability of the original switched system for all switching...... is guaranteed to be preserved for arbitrary switching signal. To compute the common generalized gramians linear matrix inequalities (LMI’s) need to be solved. These LMI’s are not always feasible. In order to solve the problem of conservatism, the second framework is presented. In this method the projection......High-Technological solutions of today are characterized by complex dynamical models. A lot of these models have inherent hybrid/switching structure. Hybrid/switched systems are powerful models for distributed embedded systems design where discrete controls are applied to continuous processes...

Mathematical Modeling of Hybrid Electrical Engineering Systems

Directory of Open Access Journals (Sweden)

A. A. Lobaty

2016-01-01

Full Text Available A large class of systems that have found application in various industries and households, electrified transportation facilities and energy sector has been classified as electrical engineering systems. Their characteristic feature is a combination of continuous and discontinuous modes of operation, which is reflected in the appearance of a relatively new term “hybrid systems”. A wide class of hybrid systems is pulsed DC converters operating in a pulse width modulation, which are non-linear systems with variable structure. Using various methods for linearization it is possible to obtain linear mathematical models that rather accurately simulate behavior of such systems. However, the presence in the mathematical models of exponential nonlinearities creates considerable difficulties in the implementation of digital hardware. The solution can be found while using an approximation of exponential functions by polynomials of the first order, that, however, violates the rigor accordance of the analytical model with characteristics of a real object. There are two practical approaches to synthesize algorithms for control of hybrid systems. The first approach is based on the representation of the whole system by a discrete model which is described by difference equations that makes it possible to synthesize discrete algorithms. The second approach is based on description of the system by differential equations. The equations describe synthesis of continuous algorithms and their further implementation in a digital computer included in the control loop system. The paper considers modeling of a hybrid electrical engineering system using differential equations. Neglecting the pulse duration, it has been proposed to describe behavior of vector components in phase coordinates of the hybrid system by stochastic differential equations containing generally non-linear differentiable random functions. A stochastic vector-matrix equation describing dynamics of the

Cross-link guided molecular modeling with ROSETTA.

Directory of Open Access Journals (Sweden)

Abdullah Kahraman

Full Text Available Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.

Probabilistic modelling and analysis of stand-alone hybrid power systems

International Nuclear Information System (INIS)

Lujano-Rojas, Juan M.; Dufo-López, Rodolfo; Bernal-Agustín, José L.

2013-01-01

As a part of the Hybrid Intelligent Algorithm, a model based on an ANN (artificial neural network) has been proposed in this paper to represent hybrid system behaviour considering the uncertainty related to wind speed and solar radiation, battery bank lifetime, and fuel prices. The Hybrid Intelligent Algorithm suggests a combination of probabilistic analysis based on a Monte Carlo simulation approach and artificial neural network training embedded in a genetic algorithm optimisation model. The installation of a typical hybrid system was analysed. Probabilistic analysis was used to generate an input–output dataset of 519 samples that was later used to train the ANNs to reduce the computational effort required. The generalisation ability of the ANNs was measured in terms of RMSE (Root Mean Square Error), MBE (Mean Bias Error), MAE (Mean Absolute Error), and R-squared estimators using another data group of 200 samples. The results obtained from the estimation of the expected energy not supplied, the probability of a determined reliability level, and the estimation of expected value of net present cost show that the presented model is able to represent the main characteristics of a typical hybrid power system under uncertain operating conditions. - Highlights: • This paper presents a probabilistic model for stand-alone hybrid power system. • The model considers the main sources of uncertainty related to renewable resources. • The Hybrid Intelligent Algorithm has been applied to represent hybrid system behaviour. • The installation of a typical hybrid system was analysed. • The results obtained from the study case validate the presented model

Ionocovalency and Applications 1. Ionocovalency Model and Orbital Hybrid Scales

Directory of Open Access Journals (Sweden)

Yonghe Zhang

2010-11-01

Full Text Available Ionocovalency (IC, a quantitative dual nature of the atom, is defined and correlated with quantum-mechanical potential to describe quantitatively the dual properties of the bond. Orbiotal hybrid IC model scale, IC, and IC electronegativity scale, XIC, are proposed, wherein the ionicity and the covalent radius are determined by spectroscopy. Being composed of the ionic function I and the covalent function C, the model describes quantitatively the dual properties of bond strengths, charge density and ionic potential. Based on the atomic electron configuration and the various quantum-mechanical built-up dual parameters, the model formed a Dual Method of the multiple-functional prediction, which has much more versatile and exceptional applications than traditional electronegativity scales and molecular properties. Hydrogen has unconventional values of IC and XIC, lower than that of boron. The IC model can agree fairly well with the data of bond properties and satisfactorily explain chemical observations of elements throughout the Periodic Table.

Using Whole Mount in situ Hybridization to Link Molecular and Organismal Biology

OpenAIRE

Jacobs, Nicole L.; Albertson, R. Craig; Wiles, Jason R.

2011-01-01

Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the ...

Modelling dependable systems using hybrid Bayesian networks

International Nuclear Information System (INIS)

Neil, Martin; Tailor, Manesh; Marquez, David; Fenton, Norman; Hearty, Peter

2008-01-01

A hybrid Bayesian network (BN) is one that incorporates both discrete and continuous nodes. In our extensive applications of BNs for system dependability assessment, the models are invariably hybrid and the need for efficient and accurate computation is paramount. We apply a new iterative algorithm that efficiently combines dynamic discretisation with robust propagation algorithms on junction tree structures to perform inference in hybrid BNs. We illustrate its use in the field of dependability with two example of reliability estimation. Firstly we estimate the reliability of a simple single system and next we implement a hierarchical Bayesian model. In the hierarchical model we compute the reliability of two unknown subsystems from data collected on historically similar subsystems and then input the result into a reliability block model to compute system level reliability. We conclude that dynamic discretisation can be used as an alternative to analytical or Monte Carlo methods with high precision and can be applied to a wide range of dependability problems

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Science.gov (United States)

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

Hybrid photovoltaic–thermal solar collectors dynamic modeling

International Nuclear Information System (INIS)

Amrizal, N.; Chemisana, D.; Rosell, J.I.

2013-01-01

Highlights: ► A hybrid photovoltaic/thermal dynamic model is presented. ► The model, once calibrated, can predict the power output for any set of climate data. ► The physical electrical model includes explicitly thermal and irradiance dependences. ► The results agree with those obtained through steady-state characterization. ► The model approaches the junction cell temperature through the system energy balance. -- Abstract: A hybrid photovoltaic/thermal transient model has been developed and validated experimentally. The methodology extends the quasi-dynamic thermal model stated in the EN 12975 in order to involve the electrical performance and consider the dynamic behavior minimizing constraints when characterizing the collector. A backward moving average filtering procedure has been applied to improve the model response for variable working conditions. Concerning the electrical part, the model includes the thermal and radiation dependences in its variables. The results revealed that the characteristic parameters included in the model agree reasonably well with the experimental values obtained from the standard steady-state and IV characteristic curve measurements. After a calibration process, the model is a suitable tool to predict the thermal and electrical performance of a hybrid solar collector, for a specific weather data set.

Synthesis, spectroscopic investigations, DFT studies, molecular docking and antimicrobial potential of certain new indole-isatin molecular hybrids: Experimental and theoretical approaches

Science.gov (United States)

Almutairi, Maha S.; Zakaria, Azza S.; Ignasius, P. Primsa; Al-Wabli, Reem I.; Joe, Isaac Hubert; Attia, Mohamed I.

2018-02-01

Indole-isatin molecular hybrids 5a-i have been synthesized and characterized by different spectroscopic methods to be evaluated as new antimicrobial agents against a panel of Gram positive bacteria, Gram negative bacteria, and moulds. Compound 5h was selected as a representative example of the prepared compounds 5a-i to perform computational investigations. Its vibrational properties have been studied using FT-IR and FT-Raman with the aid of density functional theory approach. The natural bond orbital analysis as well as HOMO and LUMO molecular orbitals investigations of compound 5h were carried out to explore its possible intermolecular delocalization or hyperconjugation and its possible interactions with the target protein. Molecular docking of compound 5h predicted its binding mode with the fungal target protein.

Evaporator modeling - A hybrid approach

International Nuclear Information System (INIS)

Ding Xudong; Cai Wenjian; Jia Lei; Wen Changyun

2009-01-01

In this paper, a hybrid modeling approach is proposed to model two-phase flow evaporators. The main procedures for hybrid modeling includes: (1) Based on the energy and material balance, and thermodynamic principles to formulate the process fundamental governing equations; (2) Select input/output (I/O) variables responsible to the system performance which can be measured and controlled; (3) Represent those variables existing in the original equations but are not measurable as simple functions of selected I/Os or constants; (4) Obtaining a single equation which can correlate system inputs and outputs; and (5) Identify unknown parameters by linear or nonlinear least-squares methods. The method takes advantages of both physical and empirical modeling approaches and can accurately predict performance in wide operating range and in real-time, which can significantly reduce the computational burden and increase the prediction accuracy. The model is verified with the experimental data taken from a testing system. The testing results show that the proposed model can predict accurately the performance of the real-time operating evaporator with the maximum error of ±8%. The developed models will have wide applications in operational optimization, performance assessment, fault detection and diagnosis

Comparative molecular modeling study of Arabidopsis NADPH-dependent thioredoxin reductase and its hybrid protein.

Directory of Open Access Journals (Sweden)

Yuno Lee

Full Text Available 2-Cys peroxiredoxins (Prxs play important roles in the protection of chloroplast proteins from oxidative damage. Arabidopsis NADPH-dependent thioredoxin reductase isotype C (AtNTRC was identified as efficient electron donor for chloroplastic 2-Cys Prx-A. There are three isotypes (A, B, and C of thioredoxin reductase (TrxR in Arabidopsis. AtNTRA contains only TrxR domain, but AtNTRC consists of N-terminal TrxR and C-terminal thioredoxin (Trx domains. AtNTRC has various oligomer structures, and Trx domain is important for chaperone activity. Our previous experimental study has reported that the hybrid protein (AtNTRA-(Trx-D, which was a fusion of AtNTRA and Trx domain from AtNTRC, has formed variety of structures and shown strong chaperone activity. But, electron transfer mechanism was not detected at all. To find out the reason of this problem with structural basis, we performed two different molecular dynamics (MD simulations on AtNTRC and AtNTRA-(Trx-D proteins with same cofactors such as NADPH and flavin adenine dinucleotide (FAD for 50 ns. Structural difference has found from superimposition of two structures that were taken relatively close to average structure. The main reason that AtNTRA-(Trx-D cannot transfer the electron from TrxR domain to Trx domain is due to the difference of key catalytic residues in active site. The long distance between TrxR C153 and disulfide bond of Trx C387-C390 has been observed in AtNTRA-(Trx-D because of following reasons: i unstable and unfavorable interaction of the linker region, ii shifted Trx domain, and iii different or weak interface interaction of Trx domains. This study is one of the good examples for understanding the relationship between structure formation and reaction activity in hybrid protein. In addition, this study would be helpful for further study on the mechanism of electron transfer reaction in NADPH-dependent thioredoxin reductase proteins.

A Structural Model Decomposition Framework for Hybrid Systems Diagnosis

Science.gov (United States)

Daigle, Matthew; Bregon, Anibal; Roychoudhury, Indranil

2015-01-01

Nowadays, a large number of practical systems in aerospace and industrial environments are best represented as hybrid systems that consist of discrete modes of behavior, each defined by a set of continuous dynamics. These hybrid dynamics make the on-line fault diagnosis task very challenging. In this work, we present a new modeling and diagnosis framework for hybrid systems. Models are composed from sets of user-defined components using a compositional modeling approach. Submodels for residual generation are then generated for a given mode, and reconfigured efficiently when the mode changes. Efficient reconfiguration is established by exploiting causality information within the hybrid system models. The submodels can then be used for fault diagnosis based on residual generation and analysis. We demonstrate the efficient causality reassignment, submodel reconfiguration, and residual generation for fault diagnosis using an electrical circuit case study.

Creating Ruddlesden-Popper phases by hybrid molecular beam epitaxy

International Nuclear Information System (INIS)

Haislmaier, Ryan C.; Stone, Greg; Alem, Nasim; Engel-Herbert, Roman

2016-01-01

The synthesis of a 50 unit cell thick n = 4 Sr_n_+_1Ti_nO_3_n_+_1 (Sr_5Ti_4O_1_3) Ruddlesden-Popper (RP) phase film is demonstrated by sequentially depositing SrO and TiO_2 layers in an alternating fashion using hybrid molecular beam epitaxy (MBE), where Ti was supplied using titanium tetraisopropoxide (TTIP). A detailed calibration procedure is outlined for determining the shuttering times to deposit SrO and TiO_2 layers with precise monolayer doses using in-situ reflection high energy electron diffraction (RHEED) as feedback. Using optimized Sr and TTIP shuttering times, a fully automated growth of the n = 4 RP phase was carried out over a period of >4.5 h. Very stable RHEED intensity oscillations were observed over the entire growth period. The structural characterization by X-ray diffraction and high resolution transmission electron microscopy revealed that a constant periodicity of four SrTiO_3 perovskite unit cell blocks separating the double SrO rocksalt layer was maintained throughout the entire film thickness with a very little amount of planar faults oriented perpendicular to the growth front direction. These results illustrate that hybrid MBE is capable of layer-by-layer growth with atomic level precision and excellent flux stability.

A Novel Hybrid Similarity Calculation Model

Directory of Open Access Journals (Sweden)

Xiaoping Fan

2017-01-01

Full Text Available This paper addresses the problems of similarity calculation in the traditional recommendation algorithms of nearest neighbor collaborative filtering, especially the failure in describing dynamic user preference. Proceeding from the perspective of solving the problem of user interest drift, a new hybrid similarity calculation model is proposed in this paper. This model consists of two parts, on the one hand the model uses the function fitting to describe users’ rating behaviors and their rating preferences, and on the other hand it employs the Random Forest algorithm to take user attribute features into account. Furthermore, the paper combines the two parts to build a new hybrid similarity calculation model for user recommendation. Experimental results show that, for data sets of different size, the model’s prediction precision is higher than the traditional recommendation algorithms.

Hybrid attacks on model-based social recommender systems

Science.gov (United States)

Yu, Junliang; Gao, Min; Rong, Wenge; Li, Wentao; Xiong, Qingyu; Wen, Junhao

2017-10-01

With the growing popularity of the online social platform, the social network based approaches to recommendation emerged. However, because of the open nature of rating systems and social networks, the social recommender systems are susceptible to malicious attacks. In this paper, we present a certain novel attack, which inherits characteristics of the rating attack and the relation attack, and term it hybrid attack. Furtherly, we explore the impact of the hybrid attack on model-based social recommender systems in multiple aspects. The experimental results show that, the hybrid attack is more destructive than the rating attack in most cases. In addition, users and items with fewer ratings will be influenced more when attacked. Last but not the least, the findings suggest that spammers do not depend on the feedback links from normal users to become more powerful, the unilateral links can make the hybrid attack effective enough. Since unilateral links are much cheaper, the hybrid attack will be a great threat to model-based social recommender systems.

Bond graph model-based fault diagnosis of hybrid systems

CERN Document Server

Borutzky, Wolfgang

2015-01-01

This book presents a bond graph model-based approach to fault diagnosis in mechatronic systems appropriately represented by a hybrid model. The book begins by giving a survey of the fundamentals of fault diagnosis and failure prognosis, then recalls state-of-art developments referring to latest publications, and goes on to discuss various bond graph representations of hybrid system models, equations formulation for switched systems, and simulation of their dynamic behavior. The structured text: • focuses on bond graph model-based fault detection and isolation in hybrid systems; • addresses isolation of multiple parametric faults in hybrid systems; • considers system mode identification; • provides a number of elaborated case studies that consider fault scenarios for switched power electronic systems commonly used in a variety of applications; and • indicates that bond graph modelling can also be used for failure prognosis. In order to facilitate the understanding of fault diagnosis and the presented...

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory

Science.gov (United States)

Langenbach, K.; Heilig, M.; Horsch, M.; Hasse, H.

2018-03-01

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO2). The molecular model of CO2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory.

Science.gov (United States)

Langenbach, K; Heilig, M; Horsch, M; Hasse, H

2018-03-28

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO 2 ). The molecular model of CO 2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

Modelling and control of a light-duty hybrid electric truck

OpenAIRE

Park, Jong-Kyu

2006-01-01

This study is concentrated on modelling and developing the controller for the light-duty hybrid electric truck. The hybrid electric vehicle has advantages in fuel economy. However, there have been relatively few studies on commercial HEVs, whilst a considerable number of studies on the hybrid electric system have been conducted in the field of passenger cars. So the current status and the methodologies to develop the LD hybrid electric truck model have been studied through the ...

An Efficient Hybrid DSMC/MD Algorithm for Accurate Modeling of Micro Gas Flows

KAUST Repository

Liang, Tengfei

2013-01-01

Aiming at simulating micro gas flows with accurate boundary conditions, an efficient hybrid algorithmis developed by combining themolecular dynamics (MD) method with the direct simulationMonte Carlo (DSMC)method. The efficiency comes from the fact that theMD method is applied only within the gas-wall interaction layer, characterized by the cut-off distance of the gas-solid interaction potential, to resolve accurately the gas-wall interaction process, while the DSMC method is employed in the remaining portion of the flow field to efficiently simulate rarefied gas transport outside the gas-wall interaction layer. A unique feature about the present scheme is that the coupling between the two methods is realized by matching the molecular velocity distribution function at the DSMC/MD interface, hence there is no need for one-toone mapping between a MD gas molecule and a DSMC simulation particle. Further improvement in efficiency is achieved by taking advantage of gas rarefaction inside the gas-wall interaction layer and by employing the "smart-wall model" proposed by Barisik et al. The developed hybrid algorithm is validated on two classical benchmarks namely 1-D Fourier thermal problem and Couette shear flow problem. Both the accuracy and efficiency of the hybrid algorithm are discussed. As an application, the hybrid algorithm is employed to simulate thermal transpiration coefficient in the free-molecule regime for a system with atomically smooth surface. Result is utilized to validate the coefficients calculated from the pure DSMC simulation with Maxwell and Cercignani-Lampis gas-wall interaction models. ©c 2014 Global-Science Press.

Weather forecasting based on hybrid neural model

Science.gov (United States)

Saba, Tanzila; Rehman, Amjad; AlGhamdi, Jarallah S.

2017-11-01

Making deductions and expectations about climate has been a challenge all through mankind's history. Challenges with exact meteorological directions assist to foresee and handle problems well in time. Different strategies have been investigated using various machine learning techniques in reported forecasting systems. Current research investigates climate as a major challenge for machine information mining and deduction. Accordingly, this paper presents a hybrid neural model (MLP and RBF) to enhance the accuracy of weather forecasting. Proposed hybrid model ensure precise forecasting due to the specialty of climate anticipating frameworks. The study concentrates on the data representing Saudi Arabia weather forecasting. The main input features employed to train individual and hybrid neural networks that include average dew point, minimum temperature, maximum temperature, mean temperature, average relative moistness, precipitation, normal wind speed, high wind speed and average cloudiness. The output layer composed of two neurons to represent rainy and dry weathers. Moreover, trial and error approach is adopted to select an appropriate number of inputs to the hybrid neural network. Correlation coefficient, RMSE and scatter index are the standard yard sticks adopted for forecast accuracy measurement. On individual standing MLP forecasting results are better than RBF, however, the proposed simplified hybrid neural model comes out with better forecasting accuracy as compared to both individual networks. Additionally, results are better than reported in the state of art, using a simple neural structure that reduces training time and complexity.

Application of soft computing based hybrid models in hydrological variables modeling: a comprehensive review

Science.gov (United States)

Fahimi, Farzad; Yaseen, Zaher Mundher; El-shafie, Ahmed

2017-05-01

Since the middle of the twentieth century, artificial intelligence (AI) models have been used widely in engineering and science problems. Water resource variable modeling and prediction are the most challenging issues in water engineering. Artificial neural network (ANN) is a common approach used to tackle this problem by using viable and efficient models. Numerous ANN models have been successfully developed to achieve more accurate results. In the current review, different ANN models in water resource applications and hydrological variable predictions are reviewed and outlined. In addition, recent hybrid models and their structures, input preprocessing, and optimization techniques are discussed and the results are compared with similar previous studies. Moreover, to achieve a comprehensive view of the literature, many articles that applied ANN models together with other techniques are included. Consequently, coupling procedure, model evaluation, and performance comparison of hybrid models with conventional ANN models are assessed, as well as, taxonomy and hybrid ANN models structures. Finally, current challenges and recommendations for future researches are indicated and new hybrid approaches are proposed.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.

Science.gov (United States)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

Science.gov (United States)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Molecular Breeding of Rice Restorer Lines and Hybrids for Brown Planthopper (BPH) Resistance Using the Bph14 and Bph15 Genes.

Science.gov (United States)

Wang, Hongbo; Ye, Shengtuo; Mou, Tongmin

2016-12-01

The development of hybrid rice is a practical approach for increasing rice production. However, the brown planthopper (BPH), Nilaparvata lugens Stål, causes severe yield loss of rice (Oryza sativa L.) and can threaten food security. Therefore, breeding hybrid rice resistant to BPH is the most effective and economical strategy to maintain high and stable production. Fortunately, numerous BPH resistance genes have been identified, and abundant linkage markers are available for molecular marker-assisted selection (MAS) in breeding programs. Hence, we pyramided two BPH resistance genes, Bph14 and Bph15, into a susceptive CMS restorer line Huahui938 and its derived hybrids using MAS to improve the BPH resistance of hybrid rice. Three near-isogenic lines (NILs) with pyramided Bph14 and Bph15 were obtained by molecular marker-assisted backcross (MAB) and phenotypic selection. The genomic components of these NILs were detected using the whole-genome SNP (Single nucleotide polymorphism) array, RICE6K, suggesting that the recurrent parent genome (RPG) recovery of the NILs was 87.88, 87.70 and 86.62 %, respectively. BPH bioassays showed that the improved NILs and their derived hybrids carrying homozygous Bph14 and Bph15 were resistant to BPH. However, the hybrids with heterozygous Bph14 and Bph15 remained susceptible to BPH. The developed NILs showed no significant differences in major agronomic traits and rice qualities compared with the recurrent parent. Moreover, the improved hybrids derived from the NILs exhibited better agronomic performance and rice quality compared with the controls under natural field conditions. This study demonstrates that it is essential to stack Bph14 and Bph15 into both the maternal and paternal parents for developing BPH-resistant hybrid rice varieties. The SNP array with abundant DNA markers is an efficient tool for analyzing the RPG recovery of progenies and can be used to monitor the donor segments in NILs, thus being extremely important

A Hybrid 3D Indoor Space Model

Directory of Open Access Journals (Sweden)

A. Jamali

2016-10-01

Full Text Available GIS integrates spatial information and spatial analysis. An important example of such integration is for emergency response which requires route planning inside and outside of a building. Route planning requires detailed information related to indoor and outdoor environment. Indoor navigation network models including Geometric Network Model (GNM, Navigable Space Model, sub-division model and regular-grid model lack indoor data sources and abstraction methods. In this paper, a hybrid indoor space model is proposed. In the proposed method, 3D modeling of indoor navigation network is based on surveying control points and it is less dependent on the 3D geometrical building model. This research proposes a method of indoor space modeling for the buildings which do not have proper 2D/3D geometrical models or they lack semantic or topological information. The proposed hybrid model consists of topological, geometrical and semantical space.

Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization

Science.gov (United States)

Ullrich, Thomas; Ermantraut, Eugen; Schulz, Torsten; Steinmetzer, Katrin

2012-01-01

Background State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. Methodology and Principal Findings The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. Conclusions and Significance The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a

Competitive reporter monitored amplification (CMA--quantification of molecular targets by real time monitoring of competitive reporter hybridization.

Directory of Open Access Journals (Sweden)

Thomas Ullrich

Full Text Available BACKGROUND: State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. METHODOLOGY AND PRINCIPAL FINDINGS: The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. CONCLUSIONS AND SIGNIFICANCE: The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2, we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls

Creating Ruddlesden-Popper phases by hybrid molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Haislmaier, Ryan C.; Stone, Greg; Alem, Nasim; Engel-Herbert, Roman, E-mail: rue2@psu.edu [Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

2016-07-25

The synthesis of a 50 unit cell thick n = 4 Sr{sub n+1}Ti{sub n}O{sub 3n+1} (Sr{sub 5}Ti{sub 4}O{sub 13}) Ruddlesden-Popper (RP) phase film is demonstrated by sequentially depositing SrO and TiO{sub 2} layers in an alternating fashion using hybrid molecular beam epitaxy (MBE), where Ti was supplied using titanium tetraisopropoxide (TTIP). A detailed calibration procedure is outlined for determining the shuttering times to deposit SrO and TiO{sub 2} layers with precise monolayer doses using in-situ reflection high energy electron diffraction (RHEED) as feedback. Using optimized Sr and TTIP shuttering times, a fully automated growth of the n = 4 RP phase was carried out over a period of >4.5 h. Very stable RHEED intensity oscillations were observed over the entire growth period. The structural characterization by X-ray diffraction and high resolution transmission electron microscopy revealed that a constant periodicity of four SrTiO{sub 3} perovskite unit cell blocks separating the double SrO rocksalt layer was maintained throughout the entire film thickness with a very little amount of planar faults oriented perpendicular to the growth front direction. These results illustrate that hybrid MBE is capable of layer-by-layer growth with atomic level precision and excellent flux stability.

HyLTL: a temporal logic for model checking hybrid systems

Directory of Open Access Journals (Sweden)

Davide Bresolin

2013-08-01

Full Text Available The model-checking problem for hybrid systems is a well known challenge in the scientific community. Most of the existing approaches and tools are limited to safety properties only, or operates by transforming the hybrid system to be verified into a discrete one, thus loosing information on the continuous dynamics of the system. In this paper we present a logic for specifying complex properties of hybrid systems called HyLTL, and we show how it is possible to solve the model checking problem by translating the formula into an equivalent hybrid automaton. In this way the problem is reduced to a reachability problem on hybrid automata that can be solved by using existing tools.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

Science.gov (United States)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Molecular Modeling

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:

The effect of empirical potential functions on modeling of amorphous carbon using molecular dynamics method

International Nuclear Information System (INIS)

Li, Longqiu; Xu, Ming; Song, Wenping; Ovcharenko, Andrey; Zhang, Guangyu; Jia, Ding

2013-01-01

Empirical potentials have a strong effect on the hybridization and structure of amorphous carbon and are of great importance in molecular dynamics (MD) simulations. In this work, amorphous carbon at densities ranging from 2.0 to 3.2 g/cm 3 was modeled by a liquid quenching method using Tersoff, 2nd REBO, and ReaxFF empirical potentials. The hybridization, structure and radial distribution function G(r) of carbon atoms were analyzed as a function of the three potentials mentioned above. The ReaxFF potential is capable to model the change of the structure of amorphous carbon and MD results are in a good agreement with experimental results and density function theory (DFT) at low density of 2.6 g/cm 3 and below. The 2nd REBO potential can be used when amorphous carbon has a very low density of 2.4 g/cm 3 and below. Considering the computational efficiency, the Tersoff potential is recommended to model amorphous carbon at a high density of 2.6 g/cm 3 and above. In addition, the influence of the quenching time on the hybridization content obtained with the three potentials is discussed.

Hybrid dynamics for currency modeling

OpenAIRE

Theodosopoulos, Ted; Trifunovic, Alex

2006-01-01

We present a simple hybrid dynamical model as a tool to investigate behavioral strategies based on trend following. The multiplicative symbolic dynamics are generated using a lognormal diffusion model for the at-the-money implied volatility term structure. Thus, are model exploits information from derivative markets to obtain qualititative properties of the return distribution for the underlier. We apply our model to the JPY-USD exchange rate and the corresponding 1mo., 3mo., 6mo. and 1yr. im...

Evolution and molecular control of hybrid incompatibility in plants

Directory of Open Access Journals (Sweden)

Chen Chen

2016-08-01

Full Text Available Postzygotic reproductive isolation (RI plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with parasitic selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities.

Ring-Opening Polymerization of N-Carboxyanhydrides for Preparation of Polypeptides and Polypeptide-Based Hybrid Materials with Various Molecular Architectures

KAUST Repository

Pahovnik, David; Hadjichristidis, Nikolaos

2015-01-01

Different synthetic approaches utilizing ring-opening polymerization of N-carboxyanhydrides for preparation of polypeptide and polypeptide-based hybrid materials with various molecular architectures are described. An overview of polymerization

Optimization of hybrid model on hajj travel

Science.gov (United States)

Cahyandari, R.; Ariany, R. L.; Sukono

2018-03-01

Hajj travel insurance is an insurance product offered by the insurance company in preparing funds to perform the pilgrimage. This insurance product helps would-be pilgrims to set aside a fund of saving hajj with regularly, but also provides funds of profit sharing (mudharabah) and insurance protection. Scheme of insurance product fund management is largely using the hybrid model, which is the fund from would-be pilgrims will be divided into three account management, that is personal account, tabarru’, and ujrah. Scheme of hybrid model on hajj travel insurance was already discussed at the earlier paper with titled “The Hybrid Model Algorithm on Sharia Insurance”, taking the example case of Mitra Mabrur Plus product from Bumiputera company. On these advanced paper, will be made the previous optimization model design, with partition of benefit the tabarru’ account. Benefits such as compensation for 40 critical illness which initially only for participants of insurance only, on optimization is intended for participants of the insurance and his heir, also to benefit the hospital bills. Meanwhile, the benefits of death benefit is given if the participant is fixed die.

A New Sythetic Hybrid (A1D5 between Gossypium herbaceum and G. raimondii and Its Morphological, Cytogenetic, Molecular Characterization.

Directory of Open Access Journals (Sweden)

Yuxiang Wu

Full Text Available The diploid species G. herbaceum (A1 and G. raimondii (D5 are the progenitors of allotetraploid cotton, respectively. However, hybrids between G. herbaceum and G. raimondii haven't been reported. In the present study, hybridization between G. herbaceum and G. raimondii was explored. Morphological, cytogenetic and molecular analyses were used to assess the hybridity. The interspecific hybrid plants were successfully obtained. Most of the morphological characteristics of the hybrids were intermediate between G. herbaceum and G. raimondii. However, the color of glands, anther cases, pollen and corolla, and the state of bracteoles in hybrids were associated with the G. herbaceum. The color of staminal columns and filaments in hybrids were associated with G. raimondii. Cytogenetic analysis confirmed abnormal meiotic behavior existed in hybrids. The hybrids couldn't produce boll-set. Simple sequence repeat results found that besides the fragments inherited from the two parents, some novel bands were amplified in hybrids, indicating that potential mutations and chromosomal recombination occurred between parental genomes during hybridization. These results may provide some novel insights in speciation, genome interaction, and evolution of the tetraploid cotton species.

Superconductivity in the periodic Anderson model with anisotropic hybridization

International Nuclear Information System (INIS)

Sarasua, L.G.; Continentino, Mucio A.

2003-01-01

In this work we study superconductivity in the periodic Anderson model with both on-site and intersite hybridization, including the interband Coulomb repulsion. We show that the presence of the intersite hybridization together with the on-site hybridization significantly affects the superconducting properties of the system. The symmetry of the hybridization has a strong influence in the symmetry of the superconducting order parameter of the ground state. The interband Coulomb repulsion may increase or decrease the superconducting critical temperature at small values of this interaction, while is detrimental to superconductivity for strong values. We show that the present model can give rise to positive or negative values of dT c /dP, depending on the values of the system parameters

The existence of fertile hybrids of closely related model earthworm species, Eisenia andrei and E. fetida.

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Barbara Plytycz

Full Text Available Lumbricid earthworms Eisenia andrei (Ea and E. fetida (Ef are simultaneous hermaphrodites with reciprocal insemination capable of self-fertilization while the existence of hybridization of these two species was still debatable. During the present investigation fertile hybrids of Ea and Ef were detected. Virgin specimens of Ea and Ef were laboratory crossed (Ea+Ef and their progeny was doubly identified. 1 -identified by species-specific maternally derived haploid mitochondrial DNA sequences of the COI gene being either 'a' for worms hatched from Ea ova or 'f' for worms hatched from Ef ova. 2 -identified by the diploid maternal/paternal nuclear DNA sequences of 28s rRNA gene being either 'AA' for Ea, 'FF' for Ef, or AF/FA for their hybrids derived either from the 'aA' or 'fF' ova, respectively. Among offspring of Ea+Ef pairs in F1 generation there were mainly aAA and fFF earthworms resulted from the facilitated self-fertilization and some aAF hybrids from aA ova but none fFA hybrids from fF ova. In F2 generation resulting from aAF hybrids mated with aAA a new generations of aAA and aAF hybrids were noticed, while aAF hybrids mated with fFF gave fFF and both aAF and fFA hybrids. Hybrids intercrossed together produced plenty of cocoons but no hatchlings independently whether aAF+aAF or aAF+fFA were mated. These results indicated that Ea and Ef species, easy to maintain in laboratory and commonly used as convenient models in biomedicine and ecotoxicology, may also serve in studies on molecular basis of interspecific barriers and mechanisms of introgression and speciation. Hypothetically, their asymmetrical hybridization can be modified by some external factors.

Daily air quality index forecasting with hybrid models: A case in China

International Nuclear Information System (INIS)

Zhu, Suling; Lian, Xiuyuan; Liu, Haixia; Hu, Jianming; Wang, Yuanyuan; Che, Jinxing

2017-01-01

Air quality is closely related to quality of life. Air pollution forecasting plays a vital role in air pollution warnings and controlling. However, it is difficult to attain accurate forecasts for air pollution indexes because the original data are non-stationary and chaotic. The existing forecasting methods, such as multiple linear models, autoregressive integrated moving average (ARIMA) and support vector regression (SVR), cannot fully capture the information from series of pollution indexes. Therefore, new effective techniques need to be proposed to forecast air pollution indexes. The main purpose of this research is to develop effective forecasting models for regional air quality indexes (AQI) to address the problems above and enhance forecasting accuracy. Therefore, two hybrid models (EMD-SVR-Hybrid and EMD-IMFs-Hybrid) are proposed to forecast AQI data. The main steps of the EMD-SVR-Hybrid model are as follows: the data preprocessing technique EMD (empirical mode decomposition) is utilized to sift the original AQI data to obtain one group of smoother IMFs (intrinsic mode functions) and a noise series, where the IMFs contain the important information (level, fluctuations and others) from the original AQI series. LS-SVR is applied to forecast the sum of the IMFs, and then, S-ARIMA (seasonal ARIMA) is employed to forecast the residual sequence of LS-SVR. In addition, EMD-IMFs-Hybrid first separately forecasts the IMFs via statistical models and sums the forecasting results of the IMFs as EMD-IMFs. Then, S-ARIMA is employed to forecast the residuals of EMD-IMFs. To certify the proposed hybrid model, AQI data from June 2014 to August 2015 collected from Xingtai in China are utilized as a test case to investigate the empirical research. In terms of some of the forecasting assessment measures, the AQI forecasting results of Xingtai show that the two proposed hybrid models are superior to ARIMA, SVR, GRNN, EMD-GRNN, Wavelet-GRNN and Wavelet-SVR. Therefore, the

Hybrid model for simulation of plasma jet injection in tokamak

Science.gov (United States)

Galkin, Sergei A.; Bogatu, I. N.

2016-10-01

Hybrid kinetic model of plasma treats the ions as kinetic particles and the electrons as charge neutralizing massless fluid. The model is essentially applicable when most of the energy is concentrated in the ions rather than in the electrons, i.e. it is well suited for the high-density hyper-velocity C60 plasma jet. The hybrid model separates the slower ion time scale from the faster electron time scale, which becomes disregardable. That is why hybrid codes consistently outperform the traditional PIC codes in computational efficiency, still resolving kinetic ions effects. We discuss 2D hybrid model and code with exact energy conservation numerical algorithm and present some results of its application to simulation of C60 plasma jet penetration through tokamak-like magnetic barrier. We also examine the 3D model/code extension and its possible applications to tokamak and ionospheric plasmas. The work is supported in part by US DOE DE-SC0015776 Grant.

Gonad morphogenesis defects drive hybrid male sterility in asymmetric hybrid breakdown of Caenorhabditis nematodes.

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Dey, Alivia; Jin, Qi; Chen, Yen-Chu; Cutter, Asher D

2014-01-01

Determining the causes and evolution of reproductive barriers to gene flow between populations, speciation, is the key to understanding the origin of diversity in nature. Many species manifest hybrid breakdown when they intercross, characterized by increasingly exacerbated problems in later generations of hybrids. Recently, Caenorhabditis nematodes have emerged as a genetic model for studying speciation, and here we investigate the nature and causes of hybrid breakdown between Caenorhabditis remanei and C. latens. We quantify partial F1 hybrid inviability and extensive F2 hybrid inviability; the ~75% F2 embryonic arrest occurs primarily during gastrulation or embryonic elongation. Moreover, F1 hybrid males exhibit Haldane's rule asymmetrically for both sterility and inviability, being strongest when C. remanei serves as maternal parent. We show that the mechanism by which sterile hybrid males are incapable of transferring sperm or a copulatory plug involves defective gonad morphogenesis, which we hypothesize results from linker cell defects in migration and/or cell death during development. This first documented case of partial hybrid male sterility in Caenorhabditis follows expectations of Darwin's corollary to Haldane's rule for asymmetric male fitness, providing a powerful foundation for molecular dissection of intrinsic reproductive barriers and divergence of genetic pathways controlling organ morphogenesis. © 2014 Wiley Periodicals, Inc.

Photoconductivity enhancement and charge transport properties in ruthenium-containing block copolymer/carbon nanotube hybrids.

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Lo, Kin Cheung; Hau, King In; Chan, Wai Kin

2018-04-05

Functional polymer/carbon nanotube (CNT) hybrid materials can serve as a good model for light harvesting systems based on CNTs. This paper presents the synthesis of block copolymer/CNT hybrids and the characterization of their photocurrent responses by both experimental and computational approaches. A series of functional diblock copolymers was synthesized by reversible addition-fragmentation chain transfer polymerizations for the dispersion and functionalization of CNTs. The block copolymers contain photosensitizing ruthenium complexes and modified pyrene-based anchoring units. The photocurrent responses of the polymer/CNT hybrids were measured by photoconductive atomic force microscopy (PCAFM), from which the experimental data were analyzed by vigorous statistical models. The difference in photocurrent response among different hybrids was correlated to the conformations of the hybrids, which were elucidated by molecular dynamics simulations, and the electronic properties of polymers. The photoresponse of the block copolymer/CNT hybrids can be enhanced by introducing an electron-accepting block between the photosensitizing block and the CNT. We have demonstrated that the application of a rigorous statistical methodology can unravel the charge transport properties of these hybrid materials and provide general guidelines for the design of molecular light harvesting systems.

Novel flavonolignan hybrid antioxidants: From enzymatic preparation to molecular rationalization.

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Vavříková, Eva; Křen, Vladimír; Jezova-Kalachova, Lubica; Biler, Michal; Chantemargue, Benjamin; Pyszková, Michaela; Riva, Sergio; Kuzma, Marek; Valentová, Kateřina; Ulrichová, Jitka; Vrba, Jiří; Trouillas, Patrick; Vacek, Jan

2017-02-15

A series of antioxidants was designed and synthesized based on conjugation of the hepatoprotective flavonolignan silybin with l-ascorbic acid, trolox alcohol or tyrosol via a C 12 aliphatic linker. These hybrid molecules were prepared from 12-vinyl dodecanedioate-23-O-silybin using the enzymatic regioselective acylation procedure with Novozym 435 (lipase B) or with lipase PS. Voltammetric analyses showed that the silybin-ascorbic acid conjugate exhibited excellent electron donating ability, in comparison to the other conjugates. Free radical scavenging, antioxidant activities and cytoprotective action were evaluated. The silybin-ascorbic acid hybrid exhibited the best activities (IC 50  = 30.2 μM) in terms of lipid peroxidation inhibition. The promising protective action of the conjugate against lipid peroxidation can be attributed to modulated electron transfer abilities of both the silybin and ascorbate moieties, but also to the hydrophobic C 12 linker facilitating membrane insertion. This was supported experimentally and theoretically by density functional theory (DFT) and molecular dynamics (MD) calculations. The results presented here can be used in the further development of novel multipotent antioxidants and cytoprotective agents, in particular for substances acting at an aqueous/lipid interface. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Assessment of Molecular Modeling & Simulation

Energy Technology Data Exchange (ETDEWEB)

None

2002-01-03

This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.

Hybrid Imaging Labels: Providing the Link Between Mass Spectrometry-Based Molecular Pathology and Theranostics

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Buckle, Tessa; van der Wal, Steffen; van Malderen, Stijn J.M.; Müller, Larissa; Kuil, Joeri; van Unen, Vincent; Peters, Ruud J.B.; van Bemmel, Margaretha E.M.; McDonnell, Liam A.; Velders, Aldrik H.; Koning, Frits; Vanhaeke, Frank; van Leeuwen, Fijs W. B.

2017-01-01

Background: Development of theranostic concepts that include inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS (LA-ICP-MS) imaging can be hindered by the lack of a direct comparison to more standardly used methods for in vitro and in vivo evaluation; e.g. fluorescence or nuclear medicine. In this study a bimodal (or rather, hybrid) tracer that contains both a fluorescent dye and a chelate was used to evaluate the existence of a direct link between mass spectrometry (MS) and in vitro and in vivo molecular imaging findings using fluorescence and radioisotopes. At the same time, the hybrid label was used to determine whether the use of a single isotope label would allow for MS-based diagnostics. Methods: A hybrid label that contained both a DTPA chelate (that was coordinated with either 165Ho or 111In) and a Cy5 fluorescent dye was coupled to the chemokine receptor 4 (CXCR4) targeting peptide Ac-TZ14011 (hybrid-Cy5-Ac-TZ4011). This receptor targeting tracer was used to 1) validate the efficacy of (165Ho-based) mass-cytometry in determining the receptor affinity via comparison with fluorescence-based flow cytometry (Cy5), 2) evaluate the microscopic binding pattern of the tracer in tumor cells using both fluorescence confocal imaging (Cy5) and LA-ICP-MS-imaging (165Ho), 3) compare in vivo biodistribution patterns obtained with ICP-MS (165Ho) and radiodetection (111In) after intravenous administration of hybrid-Cy5-Ac-TZ4011 in tumor-bearing mice. Finally, LA-ICP-MS-imaging (165Ho) was linked to fluorescence-based analysis of excised tissue samples (Cy5). Results: Analysis with both mass-cytometry and flow cytometry revealed a similar receptor affinity, respectively 352 ± 141 nM and 245 ± 65 nM (p = 0.08), but with a much lower detection sensitivity for the first modality. In vitro LA-ICP-MS imaging (165Ho) enabled clear discrimination between CXCR4 positive and negative cells, but fluorescence microscopy was required to determine the

Workable male sterility systems for hybrid rice: Genetics, biochemistry, molecular biology, and utilization.

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Huang, Jian-Zhong; E, Zhi-Guo; Zhang, Hua-Li; Shu, Qing-Yao

2014-12-01

The exploitation of male sterility systems has enabled the commercialization of heterosis in rice, with greatly increased yield and total production of this major staple food crop. Hybrid rice, which was adopted in the 1970s, now covers nearly 13.6 million hectares each year in China alone. Various types of cytoplasmic male sterility (CMS) and environment-conditioned genic male sterility (EGMS) systems have been applied in hybrid rice production. In this paper, recent advances in genetics, biochemistry, and molecular biology are reviewed with an emphasis on major male sterility systems in rice: five CMS systems, i.e., BT-, HL-, WA-, LD- and CW- CMS, and two EGMS systems, i.e., photoperiod- and temperature-sensitive genic male sterility (P/TGMS). The interaction of chimeric mitochondrial genes with nuclear genes causes CMS, which may be restored by restorer of fertility (Rf) genes. The PGMS, on the other hand, is conditioned by a non-coding RNA gene. A survey of the various CMS and EGMS lines used in hybrid rice production over the past three decades shows that the two-line system utilizing EGMS lines is playing a steadily larger role and TGMS lines predominate the current two-line system for hybrid rice production. The findings and experience gained during development and application of, and research on male sterility in rice not only advanced our understanding but also shed light on applications to other crops.

Hybrid Energy System Modeling in Modelica

Energy Technology Data Exchange (ETDEWEB)

William R. Binder; Christiaan J. J. Paredis; Humberto E. Garcia

2014-03-01

In this paper, a Hybrid Energy System (HES) configuration is modeled in Modelica. Hybrid Energy Systems (HES) have as their defining characteristic the use of one or more energy inputs, combined with the potential for multiple energy outputs. Compared to traditional energy systems, HES provide additional operational flexibility so that high variability in both energy production and consumption levels can be absorbed more effectively. This is particularly important when including renewable energy sources, whose output levels are inherently variable, determined by nature. The specific HES configuration modeled in this paper include two energy inputs: a nuclear plant, and a series of wind turbines. In addition, the system produces two energy outputs: electricity and synthetic fuel. The models are verified through simulations of the individual components, and the system as a whole. The simulations are performed for a range of component sizes, operating conditions, and control schemes.

Reactor systems modeling for ICF hybrids

International Nuclear Information System (INIS)

Berwald, D.H.; Meier, W.R.

1980-10-01

The computational models of ICF reactor subsystems developed by LLNL and TRW are described and a computer program was incorporated for use in the EPRI-sponsored Feasibility Assessment of Fusion-Fission Hybrids. Representative parametric variations have been examined. Many of the ICF subsystem models are very preliminary and more quantitative models need to be developed and included in the code

An Evaluation of Molecular Dynamics Performance on the Hybrid Cray XK6 Supercomputer

International Nuclear Information System (INIS)

Brown, W. Michael; Nguyen, Trung D.; Fuentes-Cabrera, Miguel A.; Fowlkes, Jason Davidson; Rack, Philip D.; Berger, Mark

2012-01-01

For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little modification to existing codes. Engineering and electrical power constraints have disrupted this trend, requiring more drastic changes to both hardware and software solutions. Here, we present details of the Cray XK6 architecture that achieves increased performance with the use of GPU accelerators. We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers. We present benchmark results for solid-state, biological, and mesoscopic systems and discuss some challenges for utilizing hybrid systems. We present some early work in improving application performance on the XK6 and performance results for the simulation of liquid copper nanostructures with the embedded atom method.

Model-based design of RNA hybridization networks implemented in living cells.

Science.gov (United States)

Rodrigo, Guillermo; Prakash, Satya; Shen, Shensi; Majer, Eszter; Daròs, José-Antonio; Jaramillo, Alfonso

2017-09-19

Synthetic gene circuits allow the behavior of living cells to be reprogrammed, and non-coding small RNAs (sRNAs) are increasingly being used as programmable regulators of gene expression. However, sRNAs (natural or synthetic) are generally used to regulate single target genes, while complex dynamic behaviors would require networks of sRNAs regulating each other. Here, we report a strategy for implementing such networks that exploits hybridization reactions carried out exclusively by multifaceted sRNAs that are both targets of and triggers for other sRNAs. These networks are ultimately coupled to the control of gene expression. We relied on a thermodynamic model of the different stable conformational states underlying this system at the nucleotide level. To test our model, we designed five different RNA hybridization networks with a linear architecture, and we implemented them in Escherichia coli. We validated the network architecture at the molecular level by native polyacrylamide gel electrophoresis, as well as the network function at the bacterial population and single-cell levels with a fluorescent reporter. Our results suggest that it is possible to engineer complex cellular programs based on RNA from first principles. Because these networks are mainly based on physical interactions, our designs could be expanded to other organisms as portable regulatory resources or to implement biological computations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dual-Channel, Molecular-Sieving Core/Shell ZIF@MOF Architectures as Engineered Fillers in Hybrid Membranes for Highly Selective CO2 Separation.

Science.gov (United States)

Song, Zhuonan; Qiu, Fen; Zaia, Edmond W; Wang, Zhongying; Kunz, Martin; Guo, Jinghua; Brady, Michael; Mi, Baoxia; Urban, Jeffrey J

2017-11-08

A novel core/shell porous crystalline structure was prepared using a large pore metal organic framework (MOF, UiO-66-NH 2 , pore size, ∼ 0.6 nm) as core surrounded by a small pore zeolitic imidazolate framework (ZIF, ZIF-8, pore size, ∼ 0.4 nm) through a layer-by-layer deposition method and subsequently used as an engineered filler to construct hybrid polysulfone (PSF) membranes for CO 2 capture. Compared to traditional fillers utilizing only one type of porous material with rigid channels (either large or small), our custom designed core/shell fillers possess clear advantages via pore engineering: the large internal channels of the UiO-66-NH 2 MOFs create molecular highways to accelerate molecular transport through the membrane, while the thin shells with small pores (ZIF-8) or even smaller pores generated at the interface by the imperfect registry between the overlapping pores of ZIF and MOF enhance molecular sieving thus serving to distinguish slightly larger N 2 molecules (kinetic diameter, 0.364 nm) from smaller CO 2 molecules (kinetic diameter, 0.33 nm). The resultant core/shell ZIF@MOF and as-prepared hybrid PSF membranes were characterized by transmission electron microscopy, X-ray diffraction, wide-angle X-ray scattering, scanning electron microscopy, Fourier transform infrared, thermogravimetric analysis, differential scanning calorimetry, and contact angle tests. The dependence of the separation performance of the membranes on the MOF/ZIF ratio was also studied by varying the number of layers of ZIF coatings. The integrated PSF-ZIF@MOF hybrid membrane (40 wt % loading) with optimized ZIF coating cycles showed improved hydrophobicity and excellent CO 2 separation performance by simultaneously increasing CO 2 permeability (CO 2 permeability of 45.2 barrer, 710% higher than PSF membrane) and CO 2 /N 2 selectivity (CO 2 /N 2 selectivity of 39, 50% higher than PSF membrane), which is superior to most reported hybrid PSF membranes. The strategy of using

Stochastic linear hybrid systems: Modeling, estimation, and application

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Seah, Chze Eng

Hybrid systems are dynamical systems which have interacting continuous state and discrete state (or mode). Accurate modeling and state estimation of hybrid systems are important in many applications. We propose a hybrid system model, known as the Stochastic Linear Hybrid System (SLHS), to describe hybrid systems with stochastic linear system dynamics in each mode and stochastic continuous-state-dependent mode transitions. We then develop a hybrid estimation algorithm, called the State-Dependent-Transition Hybrid Estimation (SDTHE) algorithm, to estimate the continuous state and discrete state of the SLHS from noisy measurements. It is shown that the SDTHE algorithm is more accurate or more computationally efficient than existing hybrid estimation algorithms. Next, we develop a performance analysis algorithm to evaluate the performance of the SDTHE algorithm in a given operating scenario. We also investigate sufficient conditions for the stability of the SDTHE algorithm. The proposed SLHS model and SDTHE algorithm are illustrated to be useful in several applications. In Air Traffic Control (ATC), to facilitate implementations of new efficient operational concepts, accurate modeling and estimation of aircraft trajectories are needed. In ATC, an aircraft's trajectory can be divided into a number of flight modes. Furthermore, as the aircraft is required to follow a given flight plan or clearance, its flight mode transitions are dependent of its continuous state. However, the flight mode transitions are also stochastic due to navigation uncertainties or unknown pilot intents. Thus, we develop an aircraft dynamics model in ATC based on the SLHS. The SDTHE algorithm is then used in aircraft tracking applications to estimate the positions/velocities of aircraft and their flight modes accurately. Next, we develop an aircraft conformance monitoring algorithm to detect any deviations of aircraft trajectories in ATC that might compromise safety. In this application, the SLHS

Molecular data highlight hybridization in squirrel monkeys (Saimiri, Cebidae

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Jeferson Carneiro

Full Text Available Abstract Hybridization has been reported increasingly frequently in recent years, fueling the debate on its role in the evolutionary history of species. Some studies have shown that hybridization is very common in captive New World primates, and hybrid offspring have phenotypes and physiological responses distinct from those of the "pure" parents, due to gene introgression. Here we used the TA15 Alu insertion to investigate hybridization in the genus Saimiri. Our results indicate the hybridization of Saimiri boliviensis peruviensis with S. sciureus macrodon, and S. b. boliviensis with S. ustus. Unexpectedly, some hybrids of both S. boliviensis peruviensis and S. b. boliviensis were homozygous for the absence of the insertion, which indicates that the hybrids were fertile.

A conservative and a hybrid early rejection schemes for accelerating Monte Carlo molecular simulation

KAUST Repository

Kadoura, Ahmad Salim

2014-03-17

Molecular simulation could provide detailed description of fluid systems when compared to experimental techniques. They can also replace equations of state; however, molecular simulation usually costs considerable computational efforts. Several techniques have been developed to overcome such high computational costs. In this paper, two early rejection schemes, a conservative and a hybrid one, are introduced. In these two methods, undesired configurations generated by the Monte Carlo trials are rejected earlier than it would when using conventional algorithms. The methods are tested for structureless single-component Lennard-Jones particles in both canonical and NVT-Gibbs ensembles. The computational time reduction for both ensembles is observed at a wide range of thermodynamic conditions. Results show that computational time savings are directly proportional to the rejection rate of Monte Carlo trials. The proposed conservative scheme has shown to be successful in saving up to 40% of the computational time in the canonical ensemble and up to 30% in the NVT-Gibbs ensemble when compared to standard algorithms. In addition, it preserves the exact Markov chains produced by the Metropolis scheme. Further enhancement for NVT-Gibbs ensemble is achieved by combining this technique with the bond formation early rejection one. The hybrid method achieves more than 50% saving of the central processing unit (CPU) time.

Fluid Petri Nets and hybrid model-checking: a comparative case study

International Nuclear Information System (INIS)

Gribaudo, M.; Horvath, A.; Bobbio, A.; Tronci, E.; Ciancamerla, E.; Minichino, M.

2003-01-01

The modeling and analysis of hybrid systems is a recent and challenging research area which is actually dominated by two main lines: a functional analysis based on the description of the system in terms of discrete state (hybrid) automata (whose goal is to ascertain conformity and reachability properties), and a stochastic analysis (whose aim is to provide performance and dependability measures). This paper investigates a unifying view between formal methods and stochastic methods by proposing an analysis methodology of hybrid systems based on Fluid Petri Nets (FPNs). FPNs can be analyzed directly using appropriate tools. Our paper shows that the same FPN model can be fed to different functional analyzers for model checking. In order to extensively explore the capability of the technique, we have converted the original FPN into languages for discrete as well as hybrid as well as stochastic model checkers. In this way, a first comparison among the modeling power of well known tools can be carried out. Our approach is illustrated by means of a 'real world' hybrid system: the temperature control system of a co-generative plant

Model Predictive Control for Connected Hybrid Electric Vehicles

Directory of Open Access Journals (Sweden)

Kaijiang Yu

2015-01-01

Full Text Available This paper presents a new model predictive control system for connected hybrid electric vehicles to improve fuel economy. The new features of this study are as follows. First, the battery charge and discharge profile and the driving velocity profile are simultaneously optimized. One is energy management for HEV for Pbatt; the other is for the energy consumption minimizing problem of acc control of two vehicles. Second, a system for connected hybrid electric vehicles has been developed considering varying drag coefficients and the road gradients. Third, the fuel model of a typical hybrid electric vehicle is developed using the maps of the engine efficiency characteristics. Fourth, simulations and analysis (under different parameters, i.e., road conditions, vehicle state of charge, etc. are conducted to verify the effectiveness of the method to achieve higher fuel efficiency. The model predictive control problem is solved using numerical computation method: continuation and generalized minimum residual method. Computer simulation results reveal improvements in fuel economy using the proposed control method.

Kalman Filtered Bio Heat Transfer Model Based Self-adaptive Hybrid Magnetic Resonance Thermometry.

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Zhang, Yuxin; Chen, Shuo; Deng, Kexin; Chen, Bingyao; Wei, Xing; Yang, Jiafei; Wang, Shi; Ying, Kui

2017-01-01

To develop a self-adaptive and fast thermometry method by combining the original hybrid magnetic resonance thermometry method and the bio heat transfer equation (BHTE) model. The proposed Kalman filtered Bio Heat Transfer Model Based Self-adaptive Hybrid Magnetic Resonance Thermometry, abbreviated as KalBHT hybrid method, introduced the BHTE model to synthesize a window on the regularization term of the hybrid algorithm, which leads to a self-adaptive regularization both spatially and temporally with change of temperature. Further, to decrease the sensitivity to accuracy of the BHTE model, Kalman filter is utilized to update the window at each iteration time. To investigate the effect of the proposed model, computer heating simulation, phantom microwave heating experiment and dynamic in-vivo model validation of liver and thoracic tumor were conducted in this study. The heating simulation indicates that the KalBHT hybrid algorithm achieves more accurate results without adjusting λ to a proper value in comparison to the hybrid algorithm. The results of the phantom heating experiment illustrate that the proposed model is able to follow temperature changes in the presence of motion and the temperature estimated also shows less noise in the background and surrounding the hot spot. The dynamic in-vivo model validation with heating simulation demonstrates that the proposed model has a higher convergence rate, more robustness to susceptibility problem surrounding the hot spot and more accuracy of temperature estimation. In the healthy liver experiment with heating simulation, the RMSE of the hot spot of the proposed model is reduced to about 50% compared to the RMSE of the original hybrid model and the convergence time becomes only about one fifth of the hybrid model. The proposed model is able to improve the accuracy of the original hybrid algorithm and accelerate the convergence rate of MR temperature estimation.

Molecular modeling

Directory of Open Access Journals (Sweden)

Aarti Sharma

2009-01-01

Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.

HYbrid Coordinate Ocean Model (HYCOM): Global

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Global HYbrid Coordinate Ocean Model (HYCOM) and U.S. Navy Coupled Ocean Data Assimilation (NCODA) 3-day, daily forecast at approximately 9-km (1/12-degree)...

A Hybrid Wind-Farm Parametrization for Mesoscale and Climate Models

Science.gov (United States)

Pan, Yang; Archer, Cristina L.

2018-04-01

To better understand the potential impact of wind farms on weather and climate at the regional to global scales, a new hybrid wind-farm parametrization is proposed for mesoscale and climate models. The proposed parametrization is a hybrid model because it is not based on physical processes or conservation laws, but on the multiple linear regression of the results of large-eddy simulations (LES) with the geometric properties of the wind-farm layout (e.g., the blockage ratio and blockage distance). The innovative aspect is that each wind turbine is treated individually based on its position in the farm and on the wind direction by predicting the velocity upstream of each turbine. The turbine-induced forces and added turbulence kinetic energy (TKE) are first derived analytically and then implemented in the Weather Research and Forecasting model. Idealized simulations of the offshore Lillgrund wind farm are conducted. The wind-speed deficit and TKE predicted with the hybrid model are in excellent agreement with those from the LES results, while the wind-power production estimated with the hybrid model is within 10% of that observed. Three additional wind farms with larger inter-turbine spacing than at Lillgrund are also considered, and a similar agreement with LES results is found, proving that the hybrid parametrization works well with any wind farm regardless of the spacing between turbines. These results indicate the wind-turbine position, wind direction, and added TKE are essential in accounting for the wind-farm effects on the surroundings, for which the hybrid wind-farm parametrization is a promising tool.

Rapidity distributions of hadrons in the HydHSD hybrid model

Energy Technology Data Exchange (ETDEWEB)

Khvorostukhin, A. S., E-mail: hvorost@theor.jinr.ru; Toneev, V. D. [Joint Institute for Nuclear Research (Russian Federation)

2017-03-15

A multistage hybrid model intended for describing heavy-ion interactions in the energy region of the NICA collider under construction in Dubna is proposed. The model combines the initial, fast, interaction stage described by the model of hadron string dynamics (HSD) and the subsequent evolution that the expanding system formed at the first stage experiences at the second stage and which one treats on the basis of ideal hydrodynamics; after the completion of the second stage, the particles involved may still undergo rescattering (third interaction stage). The model admits three freeze-out scenarios: isochronous, isothermal, and isoenergetic. Generally, the HydHSD hybrid model developed in the present study provides fairly good agreement with available experimental data on proton rapidity spectra. It is shown that, within this hybrid model, the two-humped structure of proton rapidity distributions can be obtained either by increasing the freeze-out temperature and energy density or by more lately going over to the hydrodynamic stage. Although the proposed hybrid model reproduces rapidity spectra of protons, it is unable to describe rapidity distributions of pions, systematically underestimating their yield. It is necessary to refine the model by including viscosity effects at the hydrodynamic stage of evolution of the system and by considering in more detail the third interaction stage.

Design, analysis and modeling of a novel hybrid powertrain system based on hybridized automated manual transmission

Science.gov (United States)

Wu, Guang; Dong, Zuomin

2017-09-01

Hybrid electric vehicles are widely accepted as a promising short to mid-term technical solution due to noticeably improved efficiency and lower emissions at competitive costs. In recent years, various hybrid powertrain systems were proposed and implemented based on different types of conventional transmission. Power-split system, including Toyota Hybrid System and Ford Hybrid System, are well-known examples. However, their relatively low torque capacity, and the drive of alternative and more advanced designs encouraged other innovative hybrid system designs. In this work, a new type of hybrid powertrain system based hybridized automated manual transmission (HAMT) is proposed. By using the concept of torque gap filler (TGF), this new hybrid powertrain type has the potential to overcome issue of torque gap during gearshift. The HAMT design (patent pending) is described in details, from gear layout and design of gear ratios (EV mode and HEV mode) to torque paths at different gears. As an analytical tool, mutli-body model of vehicle equipped with this HAMT was built to analyze powertrain dynamics at various steady and transient modes. A gearshift was decomposed and analyzed based basic modes. Furthermore, a Simulink-SimDriveline hybrid vehicle model was built for the new transmission, driveline and vehicle modular. Control strategy has also been built to harmonically coordinate different powertrain components to realize TGF function. A vehicle launch simulation test has been completed under 30% of accelerator pedal position to reveal details during gearshift. Simulation results showed that this HAMT can eliminate most torque gap that has been persistent issue of traditional AMT, improving both drivability and performance. This work demonstrated a new type of transmission that features high torque capacity, high efficiency and improved drivability.

Enzymatic Amplification of DNA/RNA Hybrid Molecular Beacon Signaling in Nucleic Acid Detection

OpenAIRE

Jacroux, Thomas; Rieck, Daniel C.; Cui, Rong; Ouyang, Yexin; Dong, Wen-Ji

2012-01-01

A rapid assay operable under isothermal or non-isothermal conditions is described wherein the sensitivity of a typical molecular beacon (MB) system is improved by utilizing thermostable RNase H to enzymatically cleave an MB comprised of a DNA stem and RNA loop (R/D-MB). Upon hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7x above background) due to an opening of the probe and concomitant reduction in the Förster resonance energy transfer e...

A four-stage hybrid model for hydrological time series forecasting.

Science.gov (United States)

Di, Chongli; Yang, Xiaohua; Wang, Xiaochao

2014-01-01

Hydrological time series forecasting remains a difficult task due to its complicated nonlinear, non-stationary and multi-scale characteristics. To solve this difficulty and improve the prediction accuracy, a novel four-stage hybrid model is proposed for hydrological time series forecasting based on the principle of 'denoising, decomposition and ensemble'. The proposed model has four stages, i.e., denoising, decomposition, components prediction and ensemble. In the denoising stage, the empirical mode decomposition (EMD) method is utilized to reduce the noises in the hydrological time series. Then, an improved method of EMD, the ensemble empirical mode decomposition (EEMD), is applied to decompose the denoised series into a number of intrinsic mode function (IMF) components and one residual component. Next, the radial basis function neural network (RBFNN) is adopted to predict the trend of all of the components obtained in the decomposition stage. In the final ensemble prediction stage, the forecasting results of all of the IMF and residual components obtained in the third stage are combined to generate the final prediction results, using a linear neural network (LNN) model. For illustration and verification, six hydrological cases with different characteristics are used to test the effectiveness of the proposed model. The proposed hybrid model performs better than conventional single models, the hybrid models without denoising or decomposition and the hybrid models based on other methods, such as the wavelet analysis (WA)-based hybrid models. In addition, the denoising and decomposition strategies decrease the complexity of the series and reduce the difficulties of the forecasting. With its effective denoising and accurate decomposition ability, high prediction precision and wide applicability, the new model is very promising for complex time series forecasting. This new forecast model is an extension of nonlinear prediction models.

A Four-Stage Hybrid Model for Hydrological Time Series Forecasting

Science.gov (United States)

Di, Chongli; Yang, Xiaohua; Wang, Xiaochao

2014-01-01

Hydrological time series forecasting remains a difficult task due to its complicated nonlinear, non-stationary and multi-scale characteristics. To solve this difficulty and improve the prediction accuracy, a novel four-stage hybrid model is proposed for hydrological time series forecasting based on the principle of ‘denoising, decomposition and ensemble’. The proposed model has four stages, i.e., denoising, decomposition, components prediction and ensemble. In the denoising stage, the empirical mode decomposition (EMD) method is utilized to reduce the noises in the hydrological time series. Then, an improved method of EMD, the ensemble empirical mode decomposition (EEMD), is applied to decompose the denoised series into a number of intrinsic mode function (IMF) components and one residual component. Next, the radial basis function neural network (RBFNN) is adopted to predict the trend of all of the components obtained in the decomposition stage. In the final ensemble prediction stage, the forecasting results of all of the IMF and residual components obtained in the third stage are combined to generate the final prediction results, using a linear neural network (LNN) model. For illustration and verification, six hydrological cases with different characteristics are used to test the effectiveness of the proposed model. The proposed hybrid model performs better than conventional single models, the hybrid models without denoising or decomposition and the hybrid models based on other methods, such as the wavelet analysis (WA)-based hybrid models. In addition, the denoising and decomposition strategies decrease the complexity of the series and reduce the difficulties of the forecasting. With its effective denoising and accurate decomposition ability, high prediction precision and wide applicability, the new model is very promising for complex time series forecasting. This new forecast model is an extension of nonlinear prediction models. PMID:25111782

Hybrid modelling framework by using mathematics-based and information-based methods

International Nuclear Information System (INIS)

Ghaboussi, J; Kim, J; Elnashai, A

2010-01-01

Mathematics-based computational mechanics involves idealization in going from the observed behaviour of a system into mathematical equations representing the underlying mechanics of that behaviour. Idealization may lead mathematical models that exclude certain aspects of the complex behaviour that may be significant. An alternative approach is data-centric modelling that constitutes a fundamental shift from mathematical equations to data that contain the required information about the underlying mechanics. However, purely data-centric methods often fail for infrequent events and large state changes. In this article, a new hybrid modelling framework is proposed to improve accuracy in simulation of real-world systems. In the hybrid framework, a mathematical model is complemented by information-based components. The role of informational components is to model aspects which the mathematical model leaves out. The missing aspects are extracted and identified through Autoprogressive Algorithms. The proposed hybrid modelling framework has a wide range of potential applications for natural and engineered systems. The potential of the hybrid methodology is illustrated through modelling highly pinched hysteretic behaviour of beam-to-column connections in steel frames.

Ring-Opening Polymerization of N-Carboxyanhydrides for Preparation of Polypeptides and Polypeptide-Based Hybrid Materials with Various Molecular Architectures

KAUST Repository

Pahovnik, David

2015-09-01

Different synthetic approaches utilizing ring-opening polymerization of N-carboxyanhydrides for preparation of polypeptide and polypeptide-based hybrid materials with various molecular architectures are described. An overview of polymerization mechanisms using conventional (various amines) as well as some recently developed initiators (hexamethyldisilazane, N-heterocyclic persistent carbenes, etc.) is presented, and their benefits and drawbacks for preparation of polypeptides with well-defined chain lengths and chain-end functionality are discussed. Recent examples from literature are used to illustrate different possibilities for synthesis of pure polypeptide materials with different molecular architectures bearing various functional groups, which are introduced either by modification of amino acids, before they are transformed into corresponding Ncarboxyanhydrides, or by post-polymerization modifications using protective groups and/or orthogonal functional groups. Different approaches for preparation of polypeptide-based hybrid materials are discussed as well using examples from recent literature. Syntheses of simple block copolymers or copolymers with more complex molecular architectures (graft and star copolymers) as well as modifications of nanoparticles and other surfaces with polypeptides are described.

Hybrid Model of Content Extraction

DEFF Research Database (Denmark)

Qureshi, Pir Abdul Rasool; Memon, Nasrullah

2012-01-01

We present a hybrid model for content extraction from HTML documents. The model operates on Document Object Model (DOM) tree of the corresponding HTML document. It evaluates each tree node and associated statistical features like link density and text distribution across the node to predict...... significance of the node towards overall content provided by the document. Once significance of the nodes is determined, the formatting characteristics like fonts, styles and the position of the nodes are evaluated to identify the nodes with similar formatting as compared to the significant nodes. The proposed...

Model predictive control of hybrid systems : stability and robustness

NARCIS (Netherlands)

Lazar, M.

2006-01-01

This thesis considers the stabilization and the robust stabilization of certain classes of hybrid systems using model predictive control. Hybrid systems represent a broad class of dynamical systems in which discrete behavior (usually described by a finite state machine) and continuous behavior

Nuclear Hybrid Energy System Modeling: RELAP5 Dynamic Coupling Capabilities

Energy Technology Data Exchange (ETDEWEB)

Piyush Sabharwall; Nolan Anderson; Haihua Zhao; Shannon Bragg-Sitton; George Mesina

2012-09-01

The nuclear hybrid energy systems (NHES) research team is currently developing a dynamic simulation of an integrated hybrid energy system. A detailed simulation of proposed NHES architectures will allow initial computational demonstration of a tightly coupled NHES to identify key reactor subsystem requirements, identify candidate reactor technologies for a hybrid system, and identify key challenges to operation of the coupled system. This work will provide a baseline for later coupling of design-specific reactor models through industry collaboration. The modeling capability addressed in this report focuses on the reactor subsystem simulation.

A global hybrid coupled model based on atmosphere-SST feedbacks

Energy Technology Data Exchange (ETDEWEB)

Cimatoribus, Andrea A.; Drijfhout, Sybren S. [Royal Netherlands Meteorological Institute, De Bilt (Netherlands); Dijkstra, Henk A. [Utrecht University, Institute for Marine and Atmospheric Research Utrecht, Utrecht (Netherlands)

2012-02-15

A global hybrid coupled model is developed, with the aim of studying the effects of ocean-atmosphere feedbacks on the stability of the Atlantic meridional overturning circulation. The model includes a global ocean general circulation model and a statistical atmosphere model. The statistical atmosphere model is based on linear regressions of data from a fully coupled climate model on sea surface temperature both locally and hemispherically averaged, being the footprint of Atlantic meridional overturning variability. It provides dynamic boundary conditions to the ocean model for heat, freshwater and wind-stress. A basic but consistent representation of ocean-atmosphere feedbacks is captured in the hybrid coupled model and it is more than 10 times faster than the fully coupled climate model. The hybrid coupled model reaches a steady state with a climate close to the one of the fully coupled climate model, and the two models also have a similar response (collapse) of the Atlantic meridional overturning circulation to a freshwater hosing applied in the northern North Atlantic. (orig.)

Molecular Modelling

Directory of Open Access Journals (Sweden)

Aarti Sharma

2009-12-01

Full Text Available

Hybrid model for forecasting time series with trend, seasonal and salendar variation patterns

Science.gov (United States)

Suhartono; Rahayu, S. P.; Prastyo, D. D.; Wijayanti, D. G. P.; Juliyanto

2017-09-01

Most of the monthly time series data in economics and business in Indonesia and other Moslem countries not only contain trend and seasonal, but also affected by two types of calendar variation effects, i.e. the effect of the number of working days or trading and holiday effects. The purpose of this research is to develop a hybrid model or a combination of several forecasting models to predict time series that contain trend, seasonal and calendar variation patterns. This hybrid model is a combination of classical models (namely time series regression and ARIMA model) and/or modern methods (artificial intelligence method, i.e. Artificial Neural Networks). A simulation study was used to show that the proposed procedure for building the hybrid model could work well for forecasting time series with trend, seasonal and calendar variation patterns. Furthermore, the proposed hybrid model is applied for forecasting real data, i.e. monthly data about inflow and outflow of currency at Bank Indonesia. The results show that the hybrid model tend to provide more accurate forecasts than individual forecasting models. Moreover, this result is also in line with the third results of the M3 competition, i.e. the hybrid model on average provides a more accurate forecast than the individual model.

Preparation of Low Molecular Weight Gelatin Using Microwave Discharge Electrodeless Lamp/TiO2 Photocatalyst Hybrid System.

Science.gov (United States)

Lee, Do-Jin; Kim, Hangun; Park, Young-Kwon; Kim, Byung Hoon; Lee, Heon; Jungf, Sana-Chul

2016-02-01

In this study, an MDEL/TiO2 photocatalyst hybrid system was applied to the production of low molecular weight gelatin. The molecular weight of produed gelatin decreased with increasing microwave intensity and increasing treatment time. The abscission of the chemical bonds between the con- stituents of gelatin by photocatalytic reaction did not alter the characteristics of gelatin. Formation of any by-products due to side reaction was not observed. It is suggested that gelatin was depolymerized by hydroxyl radicals produced during the MDEL/TiO2 photochemical reaction.

Molecular evidence for natural hybridization in the mangrove genus avicennia

International Nuclear Information System (INIS)

Huang, L.; Huang Y; Shi, S.; Zhou, R

2014-01-01

Hybridization has been observed in several multi-species genera of mangroves; however, there has been no report on hybridization in Avicennia in the Indo-West Pacific region. In this study, we sequenced 5 low-copy nuclear genes of Avicennia marina, A. rumphiana and 2 individuals of their putative hybrid in the Southeast Asia region to test the hypothesis of natural hybridization between these 2 species. We demonstrated that both putative hybrid individuals possessed two types of sequences at each of the 5 genes, perfectly corresponding to those of A. marina and A. rumphiana, confirming the hybridization between these 2 Avicennia species, and the 2 hybrid individuals are most likely F1 hybrids. Sequencing of the chloroplast trnH-psbA regions indicated that A. marina was the maternal parent of the two hybrid individuals. (author)

Craniomandibular form and body size variation of first generation mouse hybrids: A model for hominin hybridization.

Science.gov (United States)

Warren, Kerryn A; Ritzman, Terrence B; Humphreys, Robyn A; Percival, Christopher J; Hallgrímsson, Benedikt; Ackermann, Rebecca Rogers

2018-03-01

Hybridization occurs in a number of mammalian lineages, including among primate taxa. Analyses of ancient genomes have shown that hybridization between our lineage and other archaic hominins in Eurasia occurred numerous times in the past. However, we still have limited empirical data on what a hybrid skeleton looks like, or how to spot patterns of hybridization among fossils for which there are no genetic data. Here we use experimental mouse models to supplement previous studies of primates. We characterize size and shape variation in the cranium and mandible of three wild-derived inbred mouse strains and their first generation (F 1 ) hybrids. The three parent taxa in our analysis represent lineages that diverged over approximately the same period as the human/Neanderthal/Denisovan lineages and their hybrids are variably successful in the wild. Comparisons of body size, as quantified by long bone measurements, are also presented to determine whether the identified phenotypic effects of hybridization are localized to the cranium or represent overall body size changes. The results indicate that hybrid cranial and mandibular sizes, as well as limb length, exceed that of the parent taxa in all cases. All three F 1 hybrid crosses display similar patterns of size and form variation. These results are generally consistent with earlier studies on primates and other mammals, suggesting that the effects of hybridization may be similar across very different scenarios of hybridization, including different levels of hybrid fitness. This paper serves to supplement previous studies aimed at identifying F 1 hybrids in the fossil record and to introduce further research that will explore hybrid morphologies using mice as a proxy for better understanding hybridization in the hominin fossil record. Copyright © 2017 Elsevier Ltd. All rights reserved.

A model for particle acceleration in lower hybrid collapse

International Nuclear Information System (INIS)

Retterer, J.M.

1997-01-01

A model for particle acceleration during the nonlinear collapse of lower hybrid waves is described. Using the Musher-Sturman wave equation to describe the effects of nonlinear processes and a velocity diffusion equation for the particle velocity distribution, the model self-consistently describes the exchange of energy between the fields and the particles in the local plasma. Two-dimensional solutions are presented for the modulational instability of a plane wave and the collapse of a cylindrical wave packet. These calculations were motivated by sounding rocket observations in the vicinity of auroral arcs in the Earth close-quote s ionosphere, which have revealed the existence of large-amplitude lower-hybrid wave packets associated with ions accelerated to energies of 100 eV. The scaling of the sizes of these wave packets is consistent with the theory of lower-hybrid collapse and the observed lower-hybrid field amplitudes are adequate to accelerate the ionospheric ions to the observed energies

Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.

Science.gov (United States)

Nina, Mafalda; Fonné-Pfister, Raymonde; Beaudegnies, Renaud; Chekatt, Habiba; Jung, Pierre M J; Murphy-Kessabi, Fiona; De Mesmaeker, Alain; Wendeborn, Sebastian

2005-04-27

Thermodynamic and structural properties of a chemically modified DNA-RNA hybrid in which a phosphodiester linkage is replaced by a neutral amide-3 linkage (3'-CH(2)-CONH-5') were investigated using UV melting experiments, molecular dynamics simulations in explicit water, and continuum solvent models. van't Hoff analysis of the experimental UV melting curves suggests that the significant increase of the thermodynamic stability of a 15-mer DNA-RNA with seven alternated amide-3 modifications (+11 degrees C) is mainly due to an increased binding enthalpy. To further evaluate the origin in the observed affinities differences, the electrostatic contribution to the binding free energy was calculated by solving the Poisson-Boltzmann equation numerically. The nonelectrostatic contribution was estimated as the product of a hydrophobic surface tension coefficient and the surface area that is buried upon double strand formation. Structures were taken from 10 ns molecular dynamics simulations computed in a consistent fashion using explicit solvent, counterions, and the particle-mesh Ewald procedure. The present preliminary thermodynamic study suggests that the favorable binding free energy of the amide-3 DNA single strand to the complementary RNA is equally driven by electrostatic and nonpolar contributions to the binding compared to their natural analogues. In addition, molecular dynamics simulations in explicit water were performed on an amide-3 DNA single strand and the corresponding natural DNA. Results from the conformations cluster analysis of the simulated amide-3 DNA single strand ensembles suggest that the 25% of the population sampled within 10 ns has a pre-organized conformation where the sugar C3' endo pucker is favored at the 3'-flanking nucleotides. These structural and thermodynamic features contribute to the understanding of the observed increased affinities of the amide-3 DNA-RNA hybrids at the microscopic level.

Hybrid Modeling and Optimization of Yogurt Starter Culture Continuous Fermentation

Directory of Open Access Journals (Sweden)

Silviya Popova

2009-10-01

Full Text Available The present paper presents a hybrid model of yogurt starter mixed culture fermentation. The main nonlinearities within a classical structure of continuous process model are replaced by neural networks. The new hybrid model accounts for the dependence of the two microorganisms' kinetics from the on-line measured characteristics of the culture medium - pH. Then the model was used further for calculation of the optimal time profile of pH. The obtained results are with agreement with the experimental once.

An Investigation of a Hybrid Mixing Timescale Model for PDF Simulations of Turbulent Premixed Flames

Science.gov (United States)

Zhou, Hua; Kuron, Mike; Ren, Zhuyin; Lu, Tianfeng; Chen, Jacqueline H.

2016-11-01

Transported probability density function (TPDF) method features the generality for all combustion regimes, which is attractive for turbulent combustion simulations. However, the modeling of micromixing due to molecular diffusion is still considered to be a primary challenge for TPDF method, especially in turbulent premixed flames. Recently, a hybrid mixing rate model for TPDF simulations of turbulent premixed flames has been proposed, which recovers the correct mixing rates in the limits of flamelet regime and broken reaction zone regime while at the same time aims to properly account for the transition in between. In this work, this model is employed in TPDF simulations of turbulent premixed methane-air slot burner flames. The model performance is assessed by comparing the results from both direct numerical simulation (DNS) and conventional constant mechanical-to-scalar mixing rate model. This work is Granted by NSFC 51476087 and 91441202.

Transient Model of Hybrid Concentrated Photovoltaic with Thermoelectric Generator

DEFF Research Database (Denmark)

Mahmoudi Nezhad, Sajjad; Qing, Shaowei; Rezaniakolaei, Alireza

2017-01-01

Transient performance of a concentrated photovoltaic thermoelectric (CPV-TEG) hybrid system is modeled and investigated. A heat sink with water, as the working fluid has been implemented as the cold reservoir of the hybrid system to harvest the heat loss from CPV cell and to increase the efficiency...

Bounded Model Checking and Inductive Verification of Hybrid Discrete-Continuous Systems

DEFF Research Database (Denmark)

Becker, Bernd; Behle, Markus; Eisenbrand, Fritz

2004-01-01

We present a concept to signicantly advance the state of the art for bounded model checking (BMC) and inductive verication (IV) of hybrid discrete-continuous systems. Our approach combines the expertise of partners coming from dierent domains, like hybrid systems modeling and digital circuit veri...

Hybridization of tensor-optimized and high-momentum antisymmetrized molecular dynamics for light nuclei with bare interaction

Science.gov (United States)

Lyu, Mengjiao; Isaka, Masahiro; Myo, Takayuki; Toki, Hiroshi; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro; Yamada, Taiichi

2018-01-01

Many-body correlations play an essential role in the ab initio description of nuclei with nuclear bare interactions. We propose a new framework to describe light nuclei by the hybridization of the tensor-optimized antisymmetrized molecular dynamics (TOAMD) and the high-momentum AMD (HM-AMD), which we call "HM-TOAMD." In this framework, we describe the many-body correlations in terms of not only the correlation functions in TOAMD, but also the high-momentum pairs in the AMD wave function. With the bare nucleon-nucleon interaction AV8^', we sufficiently reproduce the energy and radius of the {^3}H nucleus in HM-TOAMD. The effects of tensor force and short-range repulsion in the bare interaction are nicely described in this new framework. We also discuss the convergence in calculation and flexibility of the model space for this new method.

Dynamical coupling of plasmons and molecular excitations by hybrid quantum/classical calculations: time-domain approach

International Nuclear Information System (INIS)

Sakko, Arto; Rossi, Tuomas P; Nieminen, Risto M

2014-01-01

The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na 2 molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics. The nanoparticle dimer has a plasmon resonance in the visible part of the electromagnetic spectrum, and the Na 2 molecule has an electron-hole excitation in the same energy range. Due to the dynamical interaction of the two subsystems the plasmon and the molecular excitations couple, creating a hybridized molecular-plasmon excited state. This state has unique properties that yield e.g. enhanced photoabsorption compared to the freestanding Na 2 molecule. The computational approach used enables decoupling of the mutual plasmon-molecule interaction, and our analysis verifies that it is not legitimate to neglect the backcoupling effect when describing the dynamical interaction between plasmonic material and nearby molecules. Time-resolved analysis shows nearly instantaneous formation of the coupled state, and provides an intuitive picture of the underlying physics. (paper)

Modeling of hybrid vehicle fuel economy and fuel engine efficiency

Science.gov (United States)

Wu, Wei

"Near-CV" (i.e., near-conventional vehicle) hybrid vehicles, with an internal combustion engine, and a supplementary storage with low-weight, low-energy but high-power capacity, are analyzed. This design avoids the shortcoming of the "near-EV" and the "dual-mode" hybrid vehicles that need a large energy storage system (in terms of energy capacity and weight). The small storage is used to optimize engine energy management and can provide power when needed. The energy advantage of the "near-CV" design is to reduce reliance on the engine at low power, to enable regenerative braking, and to provide good performance with a small engine. The fuel consumption of internal combustion engines, which might be applied to hybrid vehicles, is analyzed by building simple analytical models that reflect the engines' energy loss characteristics. Both diesel and gasoline engines are modeled. The simple analytical models describe engine fuel consumption at any speed and load point by describing the engine's indicated efficiency and friction. The engine's indicated efficiency and heat loss are described in terms of several easy-to-obtain engine parameters, e.g., compression ratio, displacement, bore and stroke. Engine friction is described in terms of parameters obtained by fitting available fuel measurements on several diesel and spark-ignition engines. The engine models developed are shown to conform closely to experimental fuel consumption and motored friction data. A model of the energy use of "near-CV" hybrid vehicles with different storage mechanism is created, based on simple algebraic description of the components. With powertrain downsizing and hybridization, a "near-CV" hybrid vehicle can obtain a factor of approximately two in overall fuel efficiency (mpg) improvement, without considering reductions in the vehicle load.

Modeling and optimization of batteryless hybrid PV (photovoltaic)/Diesel systems for off-grid applications

International Nuclear Information System (INIS)

Tsuanyo, David; Azoumah, Yao; Aussel, Didier; Neveu, Pierre

2015-01-01

This paper presents a new model and optimization procedure for off-grid hybrid PV (photovoltaic)/Diesel systems operating without battery storage. The proposed technico-economic model takes into account the variability of both the solar irradiation and the electrical loads. It allows optimizing the design and the operation of the hybrid systems by searching their lowest LCOE (Levelized Cost of Electricity). Two cases have been investigated: identical Diesel generators and Diesel generators with different sizes, and both are compared to conventional standalone Diesel generator systems. For the same load profile, the optimization results show that the LCOE of the optimized batteryless hybrid solar PV/Diesel (0.289 €/kWh for the hybrid system with identical Diesel generators and 0.284 €/kWh for the hybrid system with different sizes of Diesel generators) is lower than the LCOE obtained with standalone Diesel generators (0.32 €/kWh for the both cases). The obtained results are then confirmed by HOMER (Hybrid Optimization Model for Electric Renewables) software. - Highlights: • A technico-economic model for optimal design and operation management of batteryless hybrid systems is developed. • The model allows optimizing design and operation of hybrid systems by ensuring their lowest LCOE. • The model was validated by HOMER. • Batteryless hybrid system are suitable for off-grid applications

Comparison of a hybrid model to a global model of atmospheric pressure radio-frequency capacitive discharges

International Nuclear Information System (INIS)

Lazzaroni, C; Lieberman, M A; Lichtenberg, A J; Chabert, P

2012-01-01

A one-dimensional hybrid analytical-numerical global model of atmospheric pressure radio-frequency (rf) driven capacitive discharges, previously developed, is compared with a basic global model. A helium feed gas with small admixtures of oxygen is studied. For the hybrid model, the electrical characteristics are calculated analytically as a current-driven homogeneous discharge. The electron power balance is solved analytically to determine a time-varying Maxwellian electron temperature, which oscillates on the rf timescale. Averaging over the rf period yields effective rate coefficients for gas phase activated processes. For the basic global model, the electron temperature is constant in time and the sheath physics is neglected. For both models, the particle balance relations for all species are integrated numerically to determine the equilibrium discharge parameters. Variations of discharge parameters with composition and rf power are determined and compared. The rate coefficients for electron-activated processes are strongly temperature dependent, leading to significantly larger neutral and charged particle densities for the hybrid model. For small devices, finite sheath widths limit the operating regimes to low O 2 fractions. This is captured by the hybrid model but cannot be predicted from the basic global model.

Ultra-Short-Term Wind Power Prediction Using a Hybrid Model

Science.gov (United States)

Mohammed, E.; Wang, S.; Yu, J.

2017-05-01

This paper aims to develop and apply a hybrid model of two data analytical methods, multiple linear regressions and least square (MLR&LS), for ultra-short-term wind power prediction (WPP), for example taking, Northeast China electricity demand. The data was obtained from the historical records of wind power from an offshore region, and from a wind farm of the wind power plant in the areas. The WPP achieved in two stages: first, the ratios of wind power were forecasted using the proposed hybrid method, and then the transformation of these ratios of wind power to obtain forecasted values. The hybrid model combines the persistence methods, MLR and LS. The proposed method included two prediction types, multi-point prediction and single-point prediction. WPP is tested by applying different models such as autoregressive moving average (ARMA), autoregressive integrated moving average (ARIMA) and artificial neural network (ANN). By comparing results of the above models, the validity of the proposed hybrid model is confirmed in terms of error and correlation coefficient. Comparison of results confirmed that the proposed method works effectively. Additional, forecasting errors were also computed and compared, to improve understanding of how to depict highly variable WPP and the correlations between actual and predicted wind power.

A hybrid agent-based approach for modeling microbiological systems.

Science.gov (United States)

Guo, Zaiyi; Sloot, Peter M A; Tay, Joc Cing

2008-11-21

Models for systems biology commonly adopt Differential Equations or Agent-Based modeling approaches for simulating the processes as a whole. Models based on differential equations presuppose phenomenological intracellular behavioral mechanisms, while models based on Multi-Agent approach often use directly translated, and quantitatively less precise if-then logical rule constructs. We propose an extendible systems model based on a hybrid agent-based approach where biological cells are modeled as individuals (agents) while molecules are represented by quantities. This hybridization in entity representation entails a combined modeling strategy with agent-based behavioral rules and differential equations, thereby balancing the requirements of extendible model granularity with computational tractability. We demonstrate the efficacy of this approach with models of chemotaxis involving an assay of 10(3) cells and 1.2x10(6) molecules. The model produces cell migration patterns that are comparable to laboratory observations.

Control-relevant modeling and simulation of a SOFC-GT hybrid system

OpenAIRE

Rambabu Kandepu; Lars Imsland; Christoph Stiller; Bjarne A. Foss; Vinay Kariwala

2006-01-01

In this paper, control-relevant models of the most important components in a SOFC-GT hybrid system are described. Dynamic simulations are performed on the overall hybrid system. The model is used to develop a simple control structure, but the simulations show that more elaborate control is needed.

Modelling and Verifying Communication Failure of Hybrid Systems in HCSP

DEFF Research Database (Denmark)

Wang, Shuling; Nielson, Flemming; Nielson, Hanne Riis

2016-01-01

Hybrid systems are dynamic systems with interacting discrete computation and continuous physical processes. They have become ubiquitous in our daily life, e.g. automotive, aerospace and medical systems, and in particular, many of them are safety-critical. For a safety-critical hybrid system......, in the presence of communication failure, the expected control from the controller will get lost and as a consequence the physical process cannot behave as expected. In this paper, we mainly consider the communication failure caused by the non-engagement of one party in communication action, i.......e. the communication itself fails to occur. To address this issue, this paper proposes a formal framework by extending HCSP, a formal modeling language for hybrid systems, for modeling and verifying hybrid systems in the absence of receiving messages due to communication failure. We present two inference systems...

Magnetohydrodynamic Models of Molecular Tornadoes

Science.gov (United States)

Au, Kelvin; Fiege, Jason D.

2017-07-01

Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

Magnetohydrodynamic Models of Molecular Tornadoes

Energy Technology Data Exchange (ETDEWEB)

Au, Kelvin; Fiege, Jason D., E-mail: fiege@physics.umanitoba.ca [Department of Physics and Astronomy, University of Manitoba Winnipeg, MB R3T 2N2 (Canada)

2017-07-10

Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

A hybrid modeling with data assimilation to evaluate human exposure level

Science.gov (United States)

Koo, Y. S.; Cheong, H. K.; Choi, D.; Kim, A. L.; Yun, H. Y.

2015-12-01

Exposure models are designed to better represent human contact with PM (Particulate Matter) and other air pollutants such as CO, SO2, O3, and NO2. The exposure concentrations of the air pollutants to human are determined by global and regional long range transport of global and regional scales from Europe and China as well as local emissions from urban and road vehicle sources. To assess the exposure level in detail, the multiple scale influence from background to local sources should be considered. A hybrid air quality modeling methodology combing a grid-based chemical transport model with a local plume dispersion model was used to provide spatially and temporally resolved air quality concentration for human exposure levels in Korea. In the hybrid modeling approach, concentrations from a grid-based chemical transport model and a local plume dispersion model are added to provide contributions from photochemical interactions, long-range (regional) transport and local-scale dispersion. The CAMx (Comprehensive Air quality Model with Extensions was used for the background concentrations from anthropogenic and natural emissions in East Asia including Korea while the road dispersion by vehicle emission was calculated by CALPUFF model. The total exposure level of the pollutants was finally assessed by summing the background and road contributions. In the hybrid modeling, the data assimilation method based on the optimal interpolation was applied to overcome the discrepancies between the model predicted concentrations and observations. The air quality data from the air quality monitoring stations in Korea. The spatial resolution of the hybrid model was 50m for the Seoul Metropolitan Ares. This example clearly demonstrates that the exposure level could be estimated to the fine scale for the exposure assessment by using the hybrid modeling approach with data assimilation.

Multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer’s disease: design, synthesis, biochemical evaluation, ADMET, molecular modeling, and QSAR analysis of novel donepezil-pyridyl hybrids

Directory of Open Access Journals (Sweden)

Bautista-Aguilera OM

2014-10-01

BuChE. Concerning human monoamine oxidase (hMAO A inhibition, only DPH9 and 5 proved active, compound DPH9 being the most potent (IC50 [MAO A] =5,700±2,100 nM. For hMAO B, only DPHs 13 and 14 were moderate inhibitors, and compound DPH14 was the most potent (IC50 [MAO B] =3,950±940 nM. Molecular modeling of inhibitor DPH14 within EeAChE showed a binding mode with an extended conformation, interacting simultaneously with both catalytic and peripheral sites of EeAChE thanks to a linker of appropriate length. Absortion, distribution, metabolism, excretion and toxicity analysis showed that structures lacking phenyl-substituent show better druglikeness profiles; in particular, DPHs13–15 showed the most suitable absortion, distribution, metabolism, excretion and toxicity properties. Novel donepezil-pyridyl hybrid DPH14 is a potent, moderately selective hAChE and selective irreversible hMAO B inhibitor which might be considered as a promising compound for further development for the treatment of AD. Keywords: donepezil-pyridyl hybrids, ChE, MAO, 3D-QSAR, molecular modeling, ADMET

Scalability of Sustainable Business Models in Hybrid Organizations

Directory of Open Access Journals (Sweden)

Adam Jabłoński

2016-02-01

Full Text Available The dynamics of change in modern business create new mechanisms for company management to determine their pursuit and the achievement of their high performance. This performance maintained over a long period of time becomes a source of ensuring business continuity by companies. An ontological being enabling the adoption of such assumptions is such a business model that has the ability to generate results in every possible market situation and, moreover, it has the features of permanent adaptability. A feature that describes the adaptability of the business model is its scalability. Being a factor ensuring more work and more efficient work with an increasing number of components, scalability can be applied to the concept of business models as the company’s ability to maintain similar or higher performance through it. Ensuring the company’s performance in the long term helps to build the so-called sustainable business model that often balances the objectives of stakeholders and shareholders, and that is created by the implemented principles of value-based management and corporate social responsibility. This perception of business paves the way for building hybrid organizations that integrate business activities with pro-social ones. The combination of an approach typical of hybrid organizations in designing and implementing sustainable business models pursuant to the scalability criterion seems interesting from the cognitive point of view. Today, hybrid organizations are great spaces for building effective and efficient mechanisms for dialogue between business and society. This requires the appropriate business model. The purpose of the paper is to present the conceptualization and operationalization of scalability of sustainable business models that determine the performance of a hybrid organization in the network environment. The paper presents the original concept of applying scalability in sustainable business models with detailed

Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

Science.gov (United States)

Chen, Yunjie; Roux, Benoît

2014-09-21

Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

Science.gov (United States)

Chen, Yunjie; Roux, Benoît

2014-09-01

Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study.

Science.gov (United States)

Suresh, Gorle; Priyakumar, U Deva

2015-09-01

Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes. Copyright © 2015 Elsevier Inc. All rights reserved.

A hybrid parallel framework for the cellular Potts model simulations

Energy Technology Data Exchange (ETDEWEB)

Jiang, Yi [Los Alamos National Laboratory; He, Kejing [SOUTH CHINA UNIV; Dong, Shoubin [SOUTH CHINA UNIV

2009-01-01

The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).

Control-relevant modeling and simulation of a SOFC-GT hybrid system

Directory of Open Access Journals (Sweden)

Rambabu Kandepu

2006-07-01

Full Text Available In this paper, control-relevant models of the most important components in a SOFC-GT hybrid system are described. Dynamic simulations are performed on the overall hybrid system. The model is used to develop a simple control structure, but the simulations show that more elaborate control is needed.

A new adaptive hybrid electromagnetic damper: modelling, optimization, and experiment

International Nuclear Information System (INIS)

Asadi, Ehsan; Ribeiro, Roberto; Behrad Khamesee, Mir; Khajepour, Amir

2015-01-01

This paper presents the development of a new electromagnetic hybrid damper which provides regenerative adaptive damping force for various applications. Recently, the introduction of electromagnetic technologies to the damping systems has provided researchers with new opportunities for the realization of adaptive semi-active damping systems with the added benefit of energy recovery. In this research, a hybrid electromagnetic damper is proposed. The hybrid damper is configured to operate with viscous and electromagnetic subsystems. The viscous medium provides a bias and fail-safe damping force while the electromagnetic component adds adaptability and the capacity for regeneration to the hybrid design. The electromagnetic component is modeled and analyzed using analytical (lumped equivalent magnetic circuit) and electromagnetic finite element method (FEM) (COMSOL ® software package) approaches. By implementing both modeling approaches, an optimization for the geometric aspects of the electromagnetic subsystem is obtained. Based on the proposed electromagnetic hybrid damping concept and the preliminary optimization solution, a prototype is designed and fabricated. A good agreement is observed between the experimental and FEM results for the magnetic field distribution and electromagnetic damping forces. These results validate the accuracy of the modeling approach and the preliminary optimization solution. An analytical model is also presented for viscous damping force, and is compared with experimental results The results show that the damper is able to produce damping coefficients of 1300 and 0–238 N s m −1 through the viscous and electromagnetic components, respectively. (paper)

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.

Science.gov (United States)

Nayar, Divya; Chakravarty, Charusita

2015-08-27

Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.

Three hybridization models based on local search scheme for job shop scheduling problem

Science.gov (United States)

Balbi Fraga, Tatiana

2015-05-01

This work presents three different hybridization models based on the general schema of Local Search Heuristics, named Hybrid Successive Application, Hybrid Neighborhood, and Hybrid Improved Neighborhood. Despite similar approaches might have already been presented in the literature in other contexts, in this work these models are applied to analyzes the solution of the job shop scheduling problem, with the heuristics Taboo Search and Particle Swarm Optimization. Besides, we investigate some aspects that must be considered in order to achieve better solutions than those obtained by the original heuristics. The results demonstrate that the algorithms derived from these three hybrid models are more robust than the original algorithms and able to get better results than those found by the single Taboo Search.

Dynamic Model of Islamic Hybrid Securities: Empirical Evidence From Malaysia Islamic Capital Market

Directory of Open Access Journals (Sweden)

Jaafar Pyeman

2016-12-01

Full Text Available Capital structure selection is fundamentally important in corporate financial management as it influence on mutually return and risk to stakeholders. Despite of Malaysia’s position as one of the major players of Islamic Financial Market, there are still lack of studies has been conducted on the capital structure of shariah compliant firms especially related to hybrid securities. The objective of this study is to determine the hybrid securities issuance model among the shariah compliant firms in Malaysia. As such, this study is to expand the literature review by providing comprehensive analysis on the hybrid capital structure and to develop dynamic Islamic hybrid securities model for shariah compliant firms. We use panel data of 50 companies that have been issuing the hybrid securities from the year of 2004- 2012. The outcomes of the studies are based on the dynamic model GMM estimation for the determinants of hybrid securities. Based on our model, risk and growth are considered as the most determinant factors for issuing convertible bond and loan stock. These results suggest that, the firms that have high risk but having good growth prospect will choose hybrid securities of convertible bond. The model also support the backdoor equity listing hypothesis by Stein (1992 where the hybrid securities enable the profitable firms to venture into positive NPV project by issuing convertible bond as it offer lower coupon rate as compare to the normal debt rate

[Hybrids of human and monkey adenoviruses (adeno-adeno hybrids) that can reproduce in monkey cells: biological and molecular genetic peculiarities].

Science.gov (United States)

Grinenko, N F; Savitskaia, N V; Pashvykina, G V; Al'tshteĭn, A D

2003-06-01

A highly oncogenic monkey adenovirus SA7(C8) facilitates the reproduction of human adenovirus type 2 (Ad2) in monkey cells. Upon mixed infection of monkey cells with both viruses, these viruses recombine producing defective adeno-adeno hybrids Ad2C8 serologically identical to Ad2 and capable of assisting Ad2 to reproduce in monkey cells. Ad2C8 and Ad2 form an intercomplementary pair inseparable in monkey cells. Unlike oncogenic SA7(C8), Ad2C8 is a nononcogenic virus for hamsters but is able to induce tumor antigens of this virus (T and TSTA). Molecular genetic analysis of 68 clones of adeno-adeno hybrids revealed that the left part of their genome consists of Ad2 DNA, and the right part contains no less than 40% of the viral SA7(C8) genome where E2A, E3, and E4 genes are located. Apparently, the products of these genes contribute to the composition of adenoviral tumor antigens, while the E4 gene is involved in complementation of monkey and human adenoviruses and makes a contribution to host range determination of these viruses.

Modelling of hybrid energy system - Part I: Problem formulation and model development

Energy Technology Data Exchange (ETDEWEB)

Gupta, Ajai; Saini, R.P.; Sharma, M.P. [Alternate Hydro Energy Centre, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 (India)

2011-02-15

A well designed hybrid energy system can be cost effective, has a high reliability and can improve the quality of life in remote rural areas. The economic constraints can be met, if these systems are fundamentally well designed, use appropriate technology and make use effective dispatch control techniques. The first paper of this tri-series paper, presents the analysis and design of a mixed integer linear mathematical programming model (time series) to determine the optimal operation and cost optimization for a hybrid energy generation system consisting of a photovoltaic array, biomass (fuelwood), biogas, small/micro-hydro, a battery bank and a fossil fuel generator. The optimization is aimed at minimizing the cost function based on demand and potential constraints. Further, mathematical models of all other components of hybrid energy system are also developed. This is the generation mix of the remote rural of India; it may be applied to other rural areas also. (author)

Establishment of a new human pleomorphic malignant fibrous histiocytoma cell line, FU-MFH-2: molecular cytogenetic characterization by multicolor fluorescence in situ hybridization and comparative genomic hybridization

Directory of Open Access Journals (Sweden)

Isayama Teruto

2010-11-01

Full Text Available Abstract Background Pleomorphic malignant fibrous histiocytoma (MFH is one of the most frequent malignant soft tissue tumors in adults. Despite the considerable amount of research on MFH cell lines, their characterization at a molecular cytogenetic level has not been extensively analyzed. Methods and results We established a new permanent human cell line, FU-MFH-2, from a metastatic pleomorphic MFH of a 72-year-old Japanese man, and applied multicolor fluorescence in situ hybridization (M-FISH, Urovysion™ FISH, and comparative genomic hybridization (CGH for the characterization of chromosomal aberrations. FU-MFH-2 cells were spindle or polygonal in shape with oval nuclei, and were successfully maintained in vitro for over 80 passages. The histological features of heterotransplanted tumors in severe combined immunodeficiency mice were essentially the same as those of the original tumor. Cytogenetic and M-FISH analyses displayed a hypotriploid karyotype with numerous structural aberrations. Urovysion™ FISH revealed a homozygous deletion of the p16INK4A locus on chromosome band 9p21. CGH analysis showed a high-level amplification of 9q31-q34, gains of 1p12-p34.3, 2p21, 2q11.2-q21, 3p, 4p, 6q22-qter, 8p11.2, 8q11.2-q21.1, 9q21-qter, 11q13, 12q24, 15q21-qter, 16p13, 17, 20, and X, and losses of 1q43-qter, 4q32-qter, 5q14-q23, 7q32-qter, 8p21-pter, 8q23, 9p21-pter, 10p11.2-p13, and 10q11.2-q22. Conclusion The FU-MFH-2 cell line will be a particularly useful model for studying molecular pathogenesis of human pleomorphic MFH.

Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

KAUST Repository

Kadoura, Ahmad

2016-09-01

This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method to replace correlations and equations of state in subsurface flow simulators. In order to accelerate MC simulations, a set of early rejection schemes (conservative, hybrid, and non-conservative) in addition to extrapolation methods through reweighting and reconstruction of pre-generated MC Markov chains were developed. Furthermore, an extensive study was conducted to investigate sorption and transport processes of methane, carbon dioxide, water, and their mixtures in the inorganic part of shale using both MC and MD simulations. These simulations covered a wide range of thermodynamic conditions, pore sizes, and fluid compositions shedding light on several interesting findings. For example, the possibility to have more carbon dioxide adsorbed with more preadsorbed water concentrations at relatively large basal spaces. The dissertation is divided into four chapters. The first chapter corresponds to the introductory part where a brief background about molecular simulation and motivations are given. The second chapter is devoted to discuss the theoretical aspects and methodology of the proposed MC speeding up techniques in addition to the corresponding results leading to the successful multi-scale simulation of the compressible single-phase flow scenario. In chapter 3, the results regarding our extensive study on shale gas at laboratory conditions are reported. At the fourth and last chapter, we end the dissertation with few concluding remarks highlighting the key findings and summarizing the future directions.

Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach

Science.gov (United States)

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.

A new hybrid model optimized by an intelligent optimization algorithm for wind speed forecasting

International Nuclear Information System (INIS)

Su, Zhongyue; Wang, Jianzhou; Lu, Haiyan; Zhao, Ge

2014-01-01

Highlights: • A new hybrid model is developed for wind speed forecasting. • The model is based on the Kalman filter and the ARIMA. • An intelligent optimization method is employed in the hybrid model. • The new hybrid model has good performance in western China. - Abstract: Forecasting the wind speed is indispensable in wind-related engineering studies and is important in the management of wind farms. As a technique essential for the future of clean energy systems, reducing the forecasting errors related to wind speed has always been an important research subject. In this paper, an optimized hybrid method based on the Autoregressive Integrated Moving Average (ARIMA) and Kalman filter is proposed to forecast the daily mean wind speed in western China. This approach employs Particle Swarm Optimization (PSO) as an intelligent optimization algorithm to optimize the parameters of the ARIMA model, which develops a hybrid model that is best adapted to the data set, increasing the fitting accuracy and avoiding over-fitting. The proposed method is subsequently examined on the wind farms of western China, where the proposed hybrid model is shown to perform effectively and steadily

Molecular Modeling of Aerospace Polymer Matrices Including Carbon Nanotube-Enhanced Epoxy

Science.gov (United States)

Radue, Matthew S.

-functionalresins) are simulated with embedded CNT to understand how the affinity to nanoparticles affects the mechanical response. Multiscale modeling techniques are then employed to translate the molecular phenomena observed to predict the behavior of realistic composites. The effective stiffness of hybrid composites are predicted for CNT/epoxy composites with randomly oriented CNTs, for CF/CNT/epoxy systems with aligned CFs and randomly oriented CNTs, and for woven CF/CNT/epoxy fabric with randomly oriented CNTs. The results indicate that in the CNT/epoxy systems the epoxy type has a significant influence on the elastic properties. For the CF/CNT/epoxy hybrid composites, the axial modulus is highly influenced by CF concentration, while the transverse modulus is primarily affected by the CNT weight fraction.

Hybrid functional pseudopotentials

Science.gov (United States)

Yang, Jing; Tan, Liang Z.; Rappe, Andrew M.

2018-02-01

The consistency between the exchange-correlation functional used in pseudopotential construction and in the actual density functional theory calculation is essential for the accurate prediction of fundamental properties of materials. However, routine hybrid density functional calculations at present still rely on generalized gradient approximation pseudopotentials due to the lack of hybrid functional pseudopotentials. Here, we present a scheme for generating hybrid functional pseudopotentials, and we analyze the importance of pseudopotential density functional consistency for hybrid functionals. For the PBE0 hybrid functional, we benchmark our pseudopotentials for structural parameters and fundamental electronic gaps of the Gaussian-2 (G2) molecular dataset and some simple solids. Our results show that using our PBE0 pseudopotentials in PBE0 calculations improves agreement with respect to all-electron calculations.

Hybrid stochastic simplifications for multiscale gene networks

Directory of Open Access Journals (Sweden)

Debussche Arnaud

2009-09-01

Full Text Available Abstract Background Stochastic simulation of gene networks by Markov processes has important applications in molecular biology. The complexity of exact simulation algorithms scales with the number of discrete jumps to be performed. Approximate schemes reduce the computational time by reducing the number of simulated discrete events. Also, answering important questions about the relation between network topology and intrinsic noise generation and propagation should be based on general mathematical results. These general results are difficult to obtain for exact models. Results We propose a unified framework for hybrid simplifications of Markov models of multiscale stochastic gene networks dynamics. We discuss several possible hybrid simplifications, and provide algorithms to obtain them from pure jump processes. In hybrid simplifications, some components are discrete and evolve by jumps, while other components are continuous. Hybrid simplifications are obtained by partial Kramers-Moyal expansion 123 which is equivalent to the application of the central limit theorem to a sub-model. By averaging and variable aggregation we drastically reduce simulation time and eliminate non-critical reactions. Hybrid and averaged simplifications can be used for more effective simulation algorithms and for obtaining general design principles relating noise to topology and time scales. The simplified models reproduce with good accuracy the stochastic properties of the gene networks, including waiting times in intermittence phenomena, fluctuation amplitudes and stationary distributions. The methods are illustrated on several gene network examples. Conclusion Hybrid simplifications can be used for onion-like (multi-layered approaches to multi-scale biochemical systems, in which various descriptions are used at various scales. Sets of discrete and continuous variables are treated with different methods and are coupled together in a physically justified approach.

DNA Immobilization and Hybridization Detection by the Intrinsic Molecular Charge Using Capacitive Field-Effect Sensors Modified with a Charged Weak Polyelectrolyte Layer.

Science.gov (United States)

Bronder, Thomas S; Poghossian, Arshak; Scheja, Sabrina; Wu, Chunsheng; Keusgen, Michael; Mewes, Dieter; Schöning, Michael J

2015-09-16

Miniaturized setup, compatibility with advanced micro- and nanotechnologies, and ability to detect biomolecules by their intrinsic molecular charge favor the semiconductor field-effect platform as one of the most attractive approaches for the development of label-free DNA chips. In this work, a capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensor covered with a layer-by-layer prepared, positively charged weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was used for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization. The negatively charged probe single-stranded DNA (ssDNA) molecules were electrostatically adsorbed onto the positively charged PAH layer, resulting in a preferentially flat orientation of the ssDNA molecules within the Debye length, thus yielding a reduced charge-screening effect and a higher sensor signal. Each sensor-surface modification step (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), reducing an unspecific adsorption by a blocking agent, incubation with noncomplementary DNA (ncDNA) solution) was monitored by means of capacitance-voltage and constant-capacitance measurements. In addition, the surface morphology of the PAH layer was studied by atomic force microscopy and contact-angle measurements. High hybridization signals of 34 and 43 mV were recorded in low-ionic strength solutions of 10 and 1 mM, respectively. In contrast, a small signal of 4 mV was recorded in the case of unspecific adsorption of fully mismatched ncDNA. The density of probe ssDNA and dsDNA molecules as well as the hybridization efficiency was estimated using the experimentally measured DNA immobilization and hybridization signals and a simplified double-layer capacitor model. The results of field-effect experiments were supported by fluorescence measurements, verifying the DNA-immobilization and hybridization event.

A modeling method for hybrid energy behaviors in flexible machining systems

International Nuclear Information System (INIS)

Li, Yufeng; He, Yan; Wang, Yan; Wang, Yulin; Yan, Ping; Lin, Shenlong

2015-01-01

Increasingly environmental and economic pressures have led to great concerns regarding the energy consumption of machining systems. Understanding energy behaviors of flexible machining systems is a prerequisite for improving energy efficiency of these systems. This paper proposes a modeling method to predict energy behaviors in flexible machining systems. The hybrid energy behaviors not only depend on the technical specification related of machine tools and workpieces, but are significantly affected by individual production scenarios. In the method, hybrid energy behaviors are decomposed into Structure-related energy behaviors, State-related energy behaviors, Process-related energy behaviors and Assignment-related energy behaviors. The modeling method for the hybrid energy behaviors is proposed based on Colored Timed Object-oriented Petri Net (CTOPN). The former two types of energy behaviors are modeled by constructing the structure of CTOPN, whist the latter two types of behaviors are simulated by applying colored tokens and associated attributes. Machining on two workpieces in the experimental workshop were undertaken to verify the proposed modeling method. The results showed that the method can provide multi-perspective transparency on energy consumption related to machine tools, workpieces as well as production management, and is particularly suitable for flexible manufacturing system when frequent changes in machining systems are often encountered. - Highlights: • Energy behaviors in flexible machining systems are modeled in this paper. • Hybrid characteristics of energy behaviors are examined from multiple viewpoints. • Flexible modeling method CTOPN is used to predict the hybrid energy behaviors. • This work offers a multi-perspective transparency on energy consumption

Hybrid quantum teleportation: A theoretical model

Energy Technology Data Exchange (ETDEWEB)

Takeda, Shuntaro; Mizuta, Takahiro; Fuwa, Maria; Yoshikawa, Jun-ichi; Yonezawa, Hidehiro; Furusawa, Akira [Department of Applied Physics, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)

2014-12-04

Hybrid quantum teleportation – continuous-variable teleportation of qubits – is a promising approach for deterministically teleporting photonic qubits. We propose how to implement it with current technology. Our theoretical model shows that faithful qubit transfer can be achieved for this teleportation by choosing an optimal gain for the teleporter’s classical channel.

Hybrid model of steam boiler

International Nuclear Information System (INIS)

Rusinowski, Henryk; Stanek, Wojciech

2010-01-01

In the case of big energy boilers energy efficiency is usually determined with the application of the indirect method. Flue gas losses and unburnt combustible losses have a significant influence on the boiler's efficiency. To estimate these losses the knowledge of the operating parameters influence on the flue gases temperature and the content of combustible particles in the solid combustion products is necessary. A hybrid model of a boiler developed with the application of both analytical modelling and artificial intelligence is described. The analytical part of the model includes the balance equations. The empirical models express the dependence of the flue gas temperature and the mass fraction of the unburnt combustibles in solid combustion products on the operating parameters of a boiler. The empirical models have been worked out by means of neural and regression modelling.

Compression of Born ratio for fluorescence molecular tomography/x-ray computed tomography hybrid imaging: methodology and in vivo validation.

Science.gov (United States)

Mohajerani, Pouyan; Ntziachristos, Vasilis

2013-07-01

The 360° rotation geometry of the hybrid fluorescence molecular tomography/x-ray computed tomography modality allows for acquisition of very large datasets, which pose numerical limitations on the reconstruction. We propose a compression method that takes advantage of the correlation of the Born-normalized signal among sources in spatially formed clusters to reduce the size of system model. The proposed method has been validated using an ex vivo study and an in vivo study of a nude mouse with a subcutaneous 4T1 tumor, with and without inclusion of a priori anatomical information. Compression rates of up to two orders of magnitude with minimum distortion of reconstruction have been demonstrated, resulting in large reduction in weight matrix size and reconstruction time.

A Hybrid Acoustic and Pronunciation Model Adaptation Approach for Non-native Speech Recognition

Science.gov (United States)

Oh, Yoo Rhee; Kim, Hong Kook

In this paper, we propose a hybrid model adaptation approach in which pronunciation and acoustic models are adapted by incorporating the pronunciation and acoustic variabilities of non-native speech in order to improve the performance of non-native automatic speech recognition (ASR). Specifically, the proposed hybrid model adaptation can be performed at either the state-tying or triphone-modeling level, depending at which acoustic model adaptation is performed. In both methods, we first analyze the pronunciation variant rules of non-native speakers and then classify each rule as either a pronunciation variant or an acoustic variant. The state-tying level hybrid method then adapts pronunciation models and acoustic models by accommodating the pronunciation variants in the pronunciation dictionary and by clustering the states of triphone acoustic models using the acoustic variants, respectively. On the other hand, the triphone-modeling level hybrid method initially adapts pronunciation models in the same way as in the state-tying level hybrid method; however, for the acoustic model adaptation, the triphone acoustic models are then re-estimated based on the adapted pronunciation models and the states of the re-estimated triphone acoustic models are clustered using the acoustic variants. From the Korean-spoken English speech recognition experiments, it is shown that ASR systems employing the state-tying and triphone-modeling level adaptation methods can relatively reduce the average word error rates (WERs) by 17.1% and 22.1% for non-native speech, respectively, when compared to a baseline ASR system.

Hybrid Analytical and Data-Driven Modeling for Feed-Forward Robot Control.

Science.gov (United States)

Reinhart, René Felix; Shareef, Zeeshan; Steil, Jochen Jakob

2017-02-08

Feed-forward model-based control relies on models of the controlled plant, e.g., in robotics on accurate knowledge of manipulator kinematics or dynamics. However, mechanical and analytical models do not capture all aspects of a plant's intrinsic properties and there remain unmodeled dynamics due to varying parameters, unmodeled friction or soft materials. In this context, machine learning is an alternative suitable technique to extract non-linear plant models from data. However, fully data-based models suffer from inaccuracies as well and are inefficient if they include learning of well known analytical models. This paper thus argues that feed-forward control based on hybrid models comprising an analytical model and a learned error model can significantly improve modeling accuracy. Hybrid modeling here serves the purpose to combine the best of the two modeling worlds. The hybrid modeling methodology is described and the approach is demonstrated for two typical problems in robotics, i.e., inverse kinematics control and computed torque control. The former is performed for a redundant soft robot and the latter for a rigid industrial robot with redundant degrees of freedom, where a complete analytical model is not available for any of the platforms.

Performance dependence of hybrid x-ray computed tomography/fluorescence molecular tomography on the optical forward problem.

Science.gov (United States)

Hyde, Damon; Schulz, Ralf; Brooks, Dana; Miller, Eric; Ntziachristos, Vasilis

2009-04-01

Hybrid imaging systems combining x-ray computed tomography (CT) and fluorescence tomography can improve fluorescence imaging performance by incorporating anatomical x-ray CT information into the optical inversion problem. While the use of image priors has been investigated in the past, little is known about the optimal use of forward photon propagation models in hybrid optical systems. In this paper, we explore the impact on reconstruction accuracy of the use of propagation models of varying complexity, specifically in the context of these hybrid imaging systems where significant structural information is known a priori. Our results demonstrate that the use of generically known parameters provides near optimal performance, even when parameter mismatch remains.

Modeling and Simulation of Renewable Hybrid Power System using Matlab Simulink Environment

Directory of Open Access Journals (Sweden)

Cristian Dragoş Dumitru

2010-12-01

Full Text Available The paper presents the modeling of a solar-wind-hydroelectric hybrid system in Matlab/Simulink environment. The application is useful for analysis and simulation of a real hybrid solar-wind-hydroelectric system connected to a public grid. Application is built on modular architecture to facilitate easy study of each component module influence. Blocks like wind model, solar model, hydroelectric model, energy conversion and load are implemented and the results of simulation are also presented. As an example, one of the most important studies is the behavior of hybrid system which allows employing renewable and variable in time energy sources while providing a continuous supply. Application represents a useful tool in research activity and also in teaching

Hybrid programming model for implicit PDE simulations on multicore architectures

KAUST Repository

Kaushik, Dinesh; Keyes, David E.; Balay, Satish; Smith, Barry F.

2011-01-01

The complexity of programming modern multicore processor based clusters is rapidly rising, with GPUs adding further demand for fine-grained parallelism. This paper analyzes the performance of the hybrid (MPI+OpenMP) programming model in the context of an implicit unstructured mesh CFD code. At the implementation level, the effects of cache locality, update management, work division, and synchronization frequency are studied. The hybrid model presents interesting algorithmic opportunities as well: the convergence of linear system solver is quicker than the pure MPI case since the parallel preconditioner stays stronger when hybrid model is used. This implies significant savings in the cost of communication and synchronization (explicit and implicit). Even though OpenMP based parallelism is easier to implement (with in a subdomain assigned to one MPI process for simplicity), getting good performance needs attention to data partitioning issues similar to those in the message-passing case. © 2011 Springer-Verlag.

Strategy and gaps for modeling, simulation, and control of hybrid systems

Energy Technology Data Exchange (ETDEWEB)

Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Garcia, Humberto E. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hovsapian, Rob [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kinoshita, Robert [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mesina, George L. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Bragg-Sitton, Shannon M. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Boardman, Richard D. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2015-04-01

The purpose of this report is to establish a strategy for modeling and simulation of candidate hybrid energy systems. Modeling and simulation is necessary to design, evaluate, and optimize the system technical and economic performance. Accordingly, this report first establishes the simulation requirements to analysis candidate hybrid systems. Simulation fidelity levels are established based on the temporal scale, real and synthetic data availability or needs, solution accuracy, and output parameters needed to evaluate case-specific figures of merit. Accordingly, the associated computational and co-simulation resources needed are established; including physical models when needed, code assembly and integrated solutions platforms, mathematical solvers, and data processing. This report first attempts to describe the figures of merit, systems requirements, and constraints that are necessary and sufficient to characterize the grid and hybrid systems behavior and market interactions. Loss of Load Probability (LOLP) and effective cost of Effective Cost of Energy (ECE), as opposed to the standard Levelized Cost of Electricty (LCOE), are introduced as technical and economical indices for integrated energy system evaluations. Financial assessment methods are subsequently introduced for evaluation of non-traditional, hybrid energy systems. Algorithms for coupled and iterative evaluation of the technical and economic performance are subsequently discussed. This report further defines modeling objectives, computational tools, solution approaches, and real-time data collection and processing (in some cases using real test units) that will be required to model, co-simulate, and optimize; (a) an energy system components (e.g., power generation unit, chemical process, electricity management unit), (b) system domains (e.g., thermal, electrical or chemical energy generation, conversion, and transport), and (c) systems control modules. Co-simulation of complex, tightly coupled

Molecular hybridization conceded exceptionally potent quinolinyl-oxadiazole hybrids through phenyl linked thiosemicarbazide antileishmanial scaffolds: In silico validation and SAR studies.

Science.gov (United States)

Taha, Muhammad; Ismail, Nor Hadiani; Ali, Muhammad; Rashid, Umer; Imran, Syahrul; Uddin, Nizam; Khan, Khalid Mohammed

2017-04-01

The high potential of quinoline containing natural products and their derivatives in medicinal chemistry led us to discover a novel series of compounds 6-23 based on the concept of molecular hybridization. Most of the synthesized analogues exhibited potent leishmanicidal potential. The most potent compound (23, IC 50 =0.10±0.001μM) among the series was found ∼70 times more lethal than the standard drug. The current series 6-23 conceded in the development of fourteen (14) extraordinarily active compounds against leishmaniasis. In silico analysis were also performed to probe the mode of action while all the compounds structure were established by NMR and Mass spectral analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach

Directory of Open Access Journals (Sweden)

Oliveira Rui

2010-09-01

Full Text Available Abstract Background This paper presents a method for modelling dynamical biochemical networks with intrinsic time delays. Since the fundamental mechanisms leading to such delays are many times unknown, non conventional modelling approaches become necessary. Herein, a hybrid semi-parametric identification methodology is proposed in which discrete time series are incorporated into fundamental material balance models. This integration results in hybrid delay differential equations which can be applied to identify unknown cellular dynamics. Results The proposed hybrid modelling methodology was evaluated using two case studies. The first of these deals with dynamic modelling of transcriptional factor A in mammalian cells. The protein transport from the cytosol to the nucleus introduced a delay that was accounted for by discrete time series formulation. The second case study focused on a simple network with distributed time delays that demonstrated that the discrete time delay formalism has broad applicability to both discrete and distributed delay problems. Conclusions Significantly better prediction qualities of the novel hybrid model were obtained when compared to dynamical structures without time delays, being the more distinctive the more significant the underlying system delay is. The identification of the system delays by studies of different discrete modelling delays was enabled by the proposed structure. Further, it was shown that the hybrid discrete delay methodology is not limited to discrete delay systems. The proposed method is a powerful tool to identify time delays in ill-defined biochemical networks.

Synthesis and characterization of curcumin-sulfonamide hybrids: Biological evaluation and molecular docking studies

Science.gov (United States)

Banuppriya, Govindharasu; Sribalan, Rajendran; Padmini, Vediappen

2018-03-01

Curcumin-sulfonamide hybrids (4a-e) were synthesized and their in vitro antioxidant, anti-inflammatory and anticancer activities were studied. The synthesized compounds showed a very good potent activity towards antioxidant and anti-inflammatory studies rather than its parent as well as standard. These compounds have exhibited an excellent toxicity effect to the cancer cell lines such as A549 and AGS. The compounds 4a and 4c have showed good anticancer activity than curcumin. The molecular docking studies were also performed against various Epidermal Growth Factor Receptor (EGFR) enzymes. The DFT calculations were also done in order to support the docking results.

Hybrid modelling of soil-structure interaction for embedded structures

International Nuclear Information System (INIS)

Gupta, S.; Penzien, J.

1981-01-01

The basic methods currently being used for the analysis of soil-structure interaction fail to properly model three-dimensional embedded structures with flexible foundations. A hybrid model for the analysis of soil-structure interaction is developed in this investigation which takes advantage of the desirable features of both the finite element and substructure methods and which minimizes their undesirable features. The hybrid model is obtained by partitioning the total soil-structure system into a nearfield and a far-field with a smooth hemispherical interface. The near-field consists of the structure and a finite region of soil immediately surrounding its base. The entire near-field may be modelled in three-dimensional form using the finite element method; thus, taking advantage of its ability to model irregular geometries, and the non-linear soil behavior in the immediate vicinity of the structure. (orig./WL)

Open source molecular modeling.

Science.gov (United States)

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-09-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

A hybrid model of primary radiation damage in crystals

International Nuclear Information System (INIS)

Samarin, S.I.; Dremov, V.V.

2009-01-01

The paper offers a hybrid model which combines molecular dynamics and Monte Carlo (MD+MC) methods to describe primary radiation damage in crystals, caused by particles whose energies are no higher than several tens of keV. The particles are tracked in accord with equations of motion with account for pair interaction. The model also considers particle interaction with the mean-field potential (MFP) of the crystal. Only particles involved in cascading are tracked. Equations of motion for these particles include dissipative forces which describe energy exchange between cascade particles and electrons. New particles - the atoms of the crystal in the cascade region - have stochastic parameters (phase coordinates); they are sampled by the Monte Carlo method from the distribution that describes the classic canonical ensemble of non-interacting particles subjected to the external MFP. The introduction of particle interaction with the MFP helps avoid difficulties related to crystal stability and the choice of an adequate interparticle interaction potential in the traditional MD methods. Our technique is many times as fast as the traditional MD methods because we consider only particles which are involved in cascading and apply special methods to speedup the calculation of forces by accounting for the short-range pair potential used

Torsional properties of hexagonal boron nitride nanotubes, carbon nanotubes and their hybrid structures: A molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Xiong, Qi-lin, E-mail: xiongql@hust.edu.cn [Department of Mechanics, Huazhong University of Science & Technology, 1037 Luoyu Road, Wuhan 430074 (China); Hubei Key Laboratory of Engineering Structural Analysis and Safety Assessment, Luoyu Road 1037, Wuhan 430074 (China); Tian, Xiao Geng [State Key Laboratory for Mechanical Structure Strength and Vibration, Xi’an Jiaotong University, Xi’an 710049 (China)

2015-10-15

The torsional mechanical properties of hexagonal single-walled boron nitride nanotubes (SWBNNTs), single-walled carbon nanotubes (SWCNTs), and their hybrid structures (SWBN-CNTs) are investigated using molecular dynamics (MD) simulation. Two approaches - force approach and energy approach, are adopted to calculate the shear moduli of SWBNNTs and SWCNTs, the discrepancy between two approaches is analyzed. The results show that the shear moduli of single-walled nanotubes (SWNTs), including SWBNNTs and SWCNTs are dependent on the diameter, especially for armchair SWNTs. The armchair SWNTs show the better ability of resistance the twisting comparable to the zigzag SWNTs. The effects of diameter and length on the critical values of torque of SWNTs are obtained by comparing the torsional behaviors of SWNTs with different diameters and different lengths. It is observed that the MD results of the effect of diameter and length on the critical values of torque agrees well with the prediction of continuum shell model. The shear modulus of SWBN-CNT has a significant dependence on the percentages of SWCNT and the hybrid style has also an influence on shear modulus. The critical values of torque of SWBN-CNTs increase with the increase of the percentages of SWCNT. This phenomenon can be interpreted by the function relationship between the torque of different bonds (B-N-X, C-C-X, C-B-X, C-N-X) and the angles of bonds.

Modeling hydraulic regenerative hybrid vehicles using AMESim and Matlab/Simulink

Science.gov (United States)

Lynn, Alfred; Smid, Edzko; Eshraghi, Moji; Caldwell, Niall; Woody, Dan

2005-05-01

This paper presents the overview of the simulation modeling of a hydraulic system with regenerative braking used to improve vehicle emissions and fuel economy. Two simulation software packages were used together to enhance the simulation capability for fuel economy results and development of vehicle and hybrid control strategy. AMESim, a hydraulic simulation software package modeled the complex hydraulic circuit and component hardware and was interlinked with a Matlab/Simulink model of the vehicle, engine and the control strategy required to operate the vehicle and the hydraulic hybrid system through various North American and European drive cycles.

Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.

Science.gov (United States)

Chen, Yunjie; Kale, Seyit; Weare, Jonathan; Dinner, Aaron R; Roux, Benoît

2016-04-12

A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method.

Solving Problem of Graph Isomorphism by Membrane-Quantum Hybrid Model

Directory of Open Access Journals (Sweden)

Artiom Alhazov

2015-10-01

Full Text Available This work presents the application of new parallelization methods based on membrane-quantum hybrid computing to graph isomorphism problem solving. Applied membrane-quantum hybrid computational model was developed by authors. Massive parallelism of unconventional computing is used to implement classic brute force algorithm efficiently. This approach does not suppose any restrictions of considered graphs types. The estimated performance of the model is less then quadratic that makes a very good result for the problem of \\textbf{NP} complexity.

Photoclickable dendritic molecular glue: noncovalent-to-covalent photochemical transformation of protein hybrids.

Science.gov (United States)

Uchida, Noriyuki; Okuro, Kou; Niitani, Yamato; Ling, Xiao; Ariga, Takayuki; Tomishige, Michio; Aida, Takuzo

2013-03-27

A water-soluble dendron with a fluorescein isothiocyanate (FITC) fluorescent label and bearing nine pendant guanidinium ion (Gu(+))/benzophenone (BP) pairs at its periphery (Glue(BP)-FITC) serves as a "photoclickable molecular glue". By multivalent salt-bridge formation between Gu(+) ions and oxyanions, Glue(BP)-FITC temporarily adheres to a kinesin/microtubule hybrid. Upon subsequent exposure to UV light, this noncovalent binding is made permanent via a cross-linking reaction mediated by carbon radicals derived from the photoexcited BP units. This temporal-to-permanent transformation by light occurs quickly and efficiently in this preorganized state, allowing the movements of microtubules on a kinesin-coated glass plate to be photochemically controlled. A fundamental difference between such temporal and permanent bindings was visualized by the use of "optical tweezers".

Modelling and analysis of real-time and hybrid systems

Energy Technology Data Exchange (ETDEWEB)

Olivero, A

1994-09-29

This work deals with the modelling and analysis of real-time and hybrid systems. We first present the timed-graphs as model for the real-time systems and we recall the basic notions of the analysis of real-time systems. We describe the temporal properties on the timed-graphs using TCTL formulas. We consider two methods for property verification: in one hand we study the symbolic model-checking (based on backward analysis) and in the other hand we propose a verification method derived of the construction of the simulation graph (based on forward analysis). Both methods have been implemented within the KRONOS verification tool. Their application for the automatic verification on several real-time systems confirms the practical interest of our approach. In a second part we study the hybrid systems, systems combining discrete components with continuous ones. As in the general case the analysis of this king of systems is not decidable, we identify two sub-classes of hybrid systems and we give a construction based method for the generation of a timed-graph from an element into the sub-classes. We prove that in one case the timed-graph obtained is bi-similar with the considered system and that there exists a simulation in the other case. These relationships allow the application of the described technics on the hybrid systems into the defined sub-classes. (authors). 60 refs., 43 figs., 8 tabs., 2 annexes.

Activity Recognition Using Hybrid Generative/Discriminative Models on Home Environments Using Binary Sensors

Directory of Open Access Journals (Sweden)

Araceli Sanchis

2013-04-01

Full Text Available Activities of daily living are good indicators of elderly health status, and activity recognition in smart environments is a well-known problem that has been previously addressed by several studies. In this paper, we describe the use of two powerful machine learning schemes, ANN (Artificial Neural Network and SVM (Support Vector Machines, within the framework of HMM (Hidden Markov Model in order to tackle the task of activity recognition in a home setting. The output scores of the discriminative models, after processing, are used as observation probabilities of the hybrid approach. We evaluate our approach by comparing these hybrid models with other classical activity recognition methods using five real datasets. We show how the hybrid models achieve significantly better recognition performance, with significance level p < 0:05, proving that the hybrid approach is better suited for the addressed domain.

Innovative molecular approach to the identification of Colossoma macropomum and its hybrids

Directory of Open Access Journals (Sweden)

Fátima Gomes

2012-06-01

Full Text Available Tambaqui (Colossoma macropomum is the fish species most commonly raised in the Brazilian fish farms. The species is highly adaptable to captive conditions, and is both fast-growing and relatively fecund. In recent years, artificial breeding has produced hybrids with Characiform species, known as "Tambacu" and "Tambatinga". Identifying hybrids is a difficult process, given their morphological similarities with the parent species. This study presents an innovative molecular approach to the identification of hybrids based primarily on Multiplex PCR of a nuclear gene (α-Tropomyosin, which was tested on 93 specimens obtained from fish farms in northern Brazil. The sequencing of a 505-bp fragment of the Control Region (CR permitted the identification of the maternal lineage of the specimen, all of which corresponded to C. macropomum. Unexpectedly, only two CR haplotype were found in 93 samples, a very low genetic diversity for the pisciculture of Tambaqui. Multiplex PCR identified 42 hybrids, in contrast with 23 identified by the supplier on the basis of external morphology. This innovative tool has considerable potential for the development of the Brazilian aquaculture, given the possibility of the systematic identification of the genetic traits of both fry-producing stocks, and the fry and juveniles raised in farms.O Tambaqui (Colossoma macropomum é a espécie de peixe mais comumente cultivada em pisciculturas no Brasil. A espécie é altamente adaptada às condições de cativeiro, apresentando rápido crescimento e alta fecundidade. Nos últimos anos tem ocorrido o cruzamento artificial entre espécies de Characiformes, produzindo os híbridos "Tambacu" e "Tambatinga". A identificação de híbridos é uma tarefa difícil, em virtude da grande similaridade morfológica entre as espécies parentais. O presente estudo apresenta uma abordagem molecular inovadora para identificação de híbridos com base em PCR Multiplex de um gene nuclear (�

Synthesis of a hybrid model of the VSC FACTS devices and HVDC technologies

Science.gov (United States)

Borovikov, Yu S.; Gusev, A. S.; Sulaymanov, A. O.; Ufa, R. A.

2014-10-01

The motivation of the presented research is based on the need for development of new methods and tools for adequate simulation of FACTS devices and HVDC systems as part of real electric power systems (EPS). The Research object: An alternative hybrid approach for synthesizing VSC-FACTS and -HVDC hybrid model is proposed. The results: the VSC- FACTS and -HVDC hybrid model is designed in accordance with the presented concepts of hybrid simulation. The developed model allows us to carry out adequate simulation in real time of all the processes in HVDC, FACTS devices and EPS as a whole without any decomposition and limitation on their duration, and also use the developed tool for effective solution of a design, operational and research tasks of EPS containing such devices.

Synthesis of a hybrid model of the VSC FACTS devices and HVDC technologies

International Nuclear Information System (INIS)

Borovikov, Yu S; Gusev, A S; Sulaymanov, A O; Ufa, R A

2014-01-01

The motivation of the presented research is based on the need for development of new methods and tools for adequate simulation of FACTS devices and HVDC systems as part of real electric power systems (EPS). The Research object: An alternative hybrid approach for synthesizing VSC-FACTS and -HVDC hybrid model is proposed. The results: the VSC- FACTS and -HVDC hybrid model is designed in accordance with the presented concepts of hybrid simulation. The developed model allows us to carry out adequate simulation in real time of all the processes in HVDC, FACTS devices and EPS as a whole without any decomposition and limitation on their duration, and also use the developed tool for effective solution of a design, operational and research tasks of EPS containing such devices

Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

International Nuclear Information System (INIS)

Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

2014-01-01

In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW 12 O 40 3− , as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

Competition Between Two Large-Amplitude Motion Models: New Hybrid Hamiltonian Versus Old Pure-Tunneling Hamiltonian

Science.gov (United States)

Kleiner, Isabelle; Hougen, Jon T.

2017-06-01

In this talk we report on our progress in trying to make the hybrid Hamiltonian competitive with the pure-tunneling Hamiltonian for treating large-amplitude motions in methylamine. A treatment using the pure-tunneling model has the advantages of: (i) requiring relatively little computer time, (ii) working with relatively uncorrelated fitting parameters, and (iii) yielding in the vast majority of cases fits to experimental measurement accuracy. These advantages are all illustrated in the work published this past year on a gigantic v_{t} = 1 data set for the torsional fundamental band in methyl amine. A treatment using the hybrid model has the advantages of: (i) being able to carry out a global fit involving both v_{t} = 0 and v_{t} = 1 energy levels and (ii) working with fitting parameters that have a clearer physical interpretation. Unfortunately, a treatment using the hybrid model has the great disadvantage of requiring a highly correlated set of fitting parameters to achieve reasonable fitting accuracy, which complicates the search for a good set of molecular fitting parameters and a fit to experimental accuracy. At the time of writing this abstract, we have been able to carry out a fit with J up to 15 that includes all available infrared data in the v_{t} = 1-0 torsional fundamental band, all ground-state microwave data with K up to 10 and J up to 15, and about a hundred microwave lines within the v_{t} = 1 torsional state, achieving weighted root-mean-square (rms) deviations of about 1.4, 2.8, and 4.2 for these three categories of data. We will give an update of this situation at the meeting. I. Gulaczyk, M. Kreglewski, V.-M. Horneman, J. Mol. Spectrosc., in Press (2017).

Model predictive control of an air suspension system with damping multi-mode switching damper based on hybrid model

Science.gov (United States)

Sun, Xiaoqiang; Yuan, Chaochun; Cai, Yingfeng; Wang, Shaohua; Chen, Long

2017-09-01

This paper presents the hybrid modeling and the model predictive control of an air suspension system with damping multi-mode switching damper. Unlike traditional damper with continuously adjustable damping, in this study, a new damper with four discrete damping modes is applied to vehicle semi-active air suspension. The new damper can achieve different damping modes by just controlling the on-off statuses of two solenoid valves, which makes its damping adjustment more efficient and more reliable. However, since the damping mode switching induces different modes of operation, the air suspension system with the new damper poses challenging hybrid control problem. To model both the continuous/discrete dynamics and the switching between different damping modes, the framework of mixed logical dynamical (MLD) systems is used to establish the system hybrid model. Based on the resulting hybrid dynamical model, the system control problem is recast as a model predictive control (MPC) problem, which allows us to optimize the switching sequences of the damping modes by taking into account the suspension performance requirements. Numerical simulations results demonstrate the efficacy of the proposed control method finally.

Modelling Chemical Preservation of Plantain Hybrid Fruits

Directory of Open Access Journals (Sweden)

Ogueri Nwaiwu

2017-08-01

Full Text Available New plantain hybrids plants have been developed but not much has been done on the post-harvest keeping quality of the fruits and how they are affected by microbial colonization. Hence fruits from a tetraploid hybrid PITA 2 (TMPx 548-9 obtained by crossing plantain varieties Obino l’Ewai and Calcutta 4 (AA and two local triploid (AAB plantain landraces Agbagba and Obino l’Ewai were subjected to various concentrations of acetic, sorbic and propionic acid to determine the impact of chemical concentration, chemical type and plantain variety on ripening and weight loss of plantain fruits. Analysis of titratable acidity, moisture content and total soluble solids showed that there were no significant differences between fruits of hybrid and local varieties. The longest time to ripening from harvest (24 days was achieved with fruits of Agbagba treated with 3% propionic acid. However, fruits of PITA 2 hybrid treated with propionic and sorbic acid at 3% showed the longest green life which indicated that the chemicals may work better at higher concentrations. The Obino l’Ewai cultivar had the highest weight loss for all chemical types used. Modelling data obtained showed that plantain variety had the most significant effect on ripening and indicates that ripening of the fruits may depend on the plantain variety. It appears that weight loss of fruits from the plantain hybrid and local cultivars was not affected by the plantain variety, chemical type. The chemicals at higher concentrations may have an effect on ripening of the fruits and will need further investigation.

A hybrid hydrostatic and non-hydrostatic numerical model for shallow flow simulations

Science.gov (United States)

Zhang, Jingxin; Liang, Dongfang; Liu, Hua

2018-05-01

Hydrodynamics of geophysical flows in oceanic shelves, estuaries, and rivers, are often studied by solving shallow water model equations. Although hydrostatic models are accurate and cost efficient for many natural flows, there are situations where the hydrostatic assumption is invalid, whereby a fully hydrodynamic model is necessary to increase simulation accuracy. There is a growing concern about the decrease of the computational cost of non-hydrostatic pressure models to improve the range of their applications in large-scale flows with complex geometries. This study describes a hybrid hydrostatic and non-hydrostatic model to increase the efficiency of simulating shallow water flows. The basic numerical model is a three-dimensional hydrostatic model solved by the finite volume method (FVM) applied to unstructured grids. Herein, a second-order total variation diminishing (TVD) scheme is adopted. Using a predictor-corrector method to calculate the non-hydrostatic pressure, we extended the hydrostatic model to a fully hydrodynamic model. By localising the computational domain in the corrector step for non-hydrostatic pressure calculations, a hybrid model was developed. There was no prior special treatment on mode switching, and the developed numerical codes were highly efficient and robust. The hybrid model is applicable to the simulation of shallow flows when non-hydrostatic pressure is predominant only in the local domain. Beyond the non-hydrostatic domain, the hydrostatic model is still accurate. The applicability of the hybrid method was validated using several study cases.

A hybrid society model for simulating residential electricity consumption

International Nuclear Information System (INIS)

Xu, Minjie; Hu, Zhaoguang; Wu, Junyong; Zhou, Yuhui

2008-01-01

In this paper, a hybrid social model of econometric model and social influence model is proposed for evaluating the influence of pricing policy and public education policy on residential habit of electricity using in power resources management. And, a hybrid society simulation platform based on the proposed model, called residential electricity consumption multi-agent systems (RECMAS), is designed for simulating residential electricity consumption by multi-agent system. RECMAS is composed of consumer agent, power supplier agent, and policy maker agent. It provides the policy makers with a useful tool to evaluate power price policies and public education campaigns in different scenarios. According to an influenced diffusion mechanism, RECMAS can simulate the residential electricity demand-supply chain and analyze impacts of the factors on residential electricity consumption. Finally, the proposed method is used to simulate urban residential electricity consumption in China. (author)

A hybrid society model for simulating residential electricity consumption

Energy Technology Data Exchange (ETDEWEB)

Xu, Minjie [School of Electrical Engineering, Beijing Jiaotong University, Beijing (China); State Power Economic Research Institute, Beijing (China); Hu, Zhaoguang [State Power Economic Research Institute, Beijing (China); Wu, Junyong; Zhou, Yuhui [School of Electrical Engineering, Beijing Jiaotong University, Beijing (China)

2008-12-15

In this paper, a hybrid social model of econometric model and social influence model is proposed for evaluating the influence of pricing policy and public education policy on residential habit of electricity using in power resources management. And, a hybrid society simulation platform based on the proposed model, called residential electricity consumption multi-agent systems (RECMAS), is designed for simulating residential electricity consumption by multi-agent system. RECMAS is composed of consumer agent, power supplier agent, and policy maker agent. It provides the policy makers with a useful tool to evaluate power price policies and public education campaigns in different scenarios. According to an influenced diffusion mechanism, RECMAS can simulate the residential electricity demand-supply chain and analyze impacts of the factors on residential electricity consumption. Finally, the proposed method is used to simulate urban residential electricity consumption in China. (author)

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

Science.gov (United States)

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-07-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

Stabilization process in Saccharomyces intra and interspecific hybrids in fermentative conditions.

Science.gov (United States)

Pérez-Través, Laura; Lopes, Christian A; Barrio, Eladio; Querol, Amparo

2014-12-01

We evaluated the genetic stabilization of artificial intra- (Saccharomyces cerevisiae) and interspecific (S. cerevisiae × S. kudriavzevii) hybrids under wine fermentative conditions. Large-scale transitions in genome size and genome reorganizations were observed during this process. Interspecific hybrids seem to need fewer generations to reach genetic stability than intraspecific hybrids. The largest number of molecular patterns recovered among the derived clones was observed for intraspecific hybrids, particularly for those obtained by rare-mating. Molecular marker analyses revealed that unstable clones could change during the industrial process to obtain active dry yeast. When no changes in molecular markers and ploidy were observed after this process, no changes in genetic composition were confirmed by comparative genome hybridization, considering the clone as a stable hybrid. According to our results, under these conditions, fermentation steps 3 and 5 (30-50 generations) would suffice to obtain genetically stable interspecific and intraspecific hybrids, respectively. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Design, synthesis, conformational and molecular docking study of some novel acyl hydrazone based molecular hybrids as antimalarial and antimicrobial agents.

Science.gov (United States)

Kumar, Parvin; Kadyan, Kulbir; Duhan, Meenakshi; Sindhu, Jayant; Singh, Vineeta; Saharan, Baljeet Singh

2017-11-14

Acyl hydrazones are an important class of heterocyclic compounds promising pharmacological characteristics. Malaria is a life-threatening mosquito-borne blood disease caused by a plasmodium parasite. In some places, malaria can be treated and controlled with early diagnosis. However, some countries lack the resources to do this effectively. The present work involves the design and synthesis of some novel acyl hydrazone based molecular hybrids of 1,4-dihydropyridine and pyrazole (5a-g). These molecular hybrids were synthesised by condensation of 1,4-dihydropyridin-4-yl-phenoxyacetohydrazides with differently substituted pyrazole carbaldehyde. The final compound (5) showed two conformations (the major, E, s-cis and the minor, E, s-trans) as revealed by NMR spectral data and further supported by the energy calculations (MOPAC2016 using PM7 method). All the synthesised compounds were screened for their in vitro antimalarial activities against chloroquine-sensitive malaria parasite Plasmodium falciparum (3D7) and antimicrobial activity against Gram positive bacteria i.e. Bacillus cereus, Gram negative bacteria i.e. Escherichia coli and antifungal activity against one yeast i.e. Aspergillus niger. All these compounds were found more potent than chloroquine and clotrimazole, the standard drugs. In vitro antiplasmodial IC 50 value of the most potent compound 5d was found to be 4.40 nM which is even less than all the three reference drugs chloroquine (18.7 nM), pyrimethamine (11 nM) and artimisinin (6 nM). In silico binding study of compound 5d with plasmodial cysteine protease falcipain-2 indicated the inhibition of falcipain-2 as the probable reason for the antimalarial potency of compound 5d. All the compounds had shown good to excellent antimicrobial and antifungal activities.

Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

DEFF Research Database (Denmark)

Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...

Simulation of Mercury's magnetosheath with a combined hybrid-paraboloid model

Science.gov (United States)

Parunakian, David; Dyadechkin, Sergey; Alexeev, Igor; Belenkaya, Elena; Khodachenko, Maxim; Kallio, Esa; Alho, Markku

2017-08-01

In this paper we introduce a novel approach for modeling planetary magnetospheres that involves a combination of the hybrid model and the paraboloid magnetosphere model (PMM); we further refer to it as the combined hybrid model. While both of these individual models have been successfully applied in the past, their combination enables us both to overcome the traditional difficulties of hybrid models to develop a self-consistent magnetic field and to compensate the lack of plasma simulation in the PMM. We then use this combined model to simulate Mercury's magnetosphere and investigate the geometry and configuration of Mercury's magnetosheath controlled by various conditions in the interplanetary medium. The developed approach provides a unique comprehensive view of Mercury's magnetospheric environment for the first time. Using this setup, we compare the locations of the bow shock and the magnetopause as determined by simulations with the locations predicted by stand-alone PMM runs and also verify the magnetic and dynamic pressure balance at the magnetopause. We also compare the results produced by these simulations with observational data obtained by the magnetometer on board the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft along a dusk-dawn orbit and discuss the signatures of the magnetospheric features that appear in these simulations. Overall, our analysis suggests that combining the semiempirical PMM with a self-consistent global kinetic model creates new modeling possibilities which individual models cannot provide on their own.

Fluorescence background subtraction technique for hybrid fluorescence molecular tomography/x-ray computed tomography imaging of a mouse model of early stage lung cancer.

Science.gov (United States)

Ale, Angelique; Ermolayev, Vladimir; Deliolanis, Nikolaos C; Ntziachristos, Vasilis

2013-05-01

The ability to visualize early stage lung cancer is important in the study of biomarkers and targeting agents that could lead to earlier diagnosis. The recent development of hybrid free-space 360-deg fluorescence molecular tomography (FMT) and x-ray computed tomography (XCT) imaging yields a superior optical imaging modality for three-dimensional small animal fluorescence imaging over stand-alone optical systems. Imaging accuracy was improved by using XCT information in the fluorescence reconstruction method. Despite this progress, the detection sensitivity of targeted fluorescence agents remains limited by nonspecific background accumulation of the fluorochrome employed, which complicates early detection of murine cancers. Therefore we examine whether x-ray CT information and bulk fluorescence detection can be combined to increase detection sensitivity. Correspondingly, we research the performance of a data-driven fluorescence background estimator employed for subtraction of background fluorescence from acquisition data. Using mice containing known fluorochromes ex vivo, we demonstrate the reduction of background signals from reconstructed images and sensitivity improvements. Finally, by applying the method to in vivo data from K-ras transgenic mice developing lung cancer, we find small tumors at an early stage compared with reconstructions performed using raw data. We conclude with the benefits of employing fluorescence subtraction in hybrid FMT-XCT for early detection studies.

Synthesis, antimalarial activity, heme binding and docking studies of N-substituted 4-aminoquinoline-pyrimidine molecular hybrids.

Science.gov (United States)

Maurya, Shiv Shyam; Khan, Shabana I; Bahuguna, Aparna; Kumar, Deepak; Rawat, Diwan S

2017-03-31

A series of novel N-substituted 4-aminoquinoline-pyrimidine hybrids have been synthesized via simple and economic route and evaluated for their antimalarial activity. Most compounds showed potent antimalarial activity against both CQ-sensitive and CQ-resistant strains with high selectivity index. All the compounds were found to be non-toxic to the mammalian cell lines. The most active compound 7b was analysed for heme binding activity using UV-spectrophotometer. Compound was found to interact with heme and a complex formation between compound and heme in a 1:1 stoichiometry ratio was determined using job plots. The interaction of these hybrids was also investigated by the molecular docking studies in the binding site of wild type Pf-DHFR-TS and quadruple mutant Pf-DHFR-TS. The pharmacokinetic property analysis of best active compounds was also studied by ADMET prediction. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Hybrid continuum–molecular modelling of multiscale internal gas flows

International Nuclear Information System (INIS)

Patronis, Alexander; Lockerby, Duncan A.; Borg, Matthew K.; Reese, Jason M.

2013-01-01

We develop and apply an efficient multiscale method for simulating a large class of low-speed internal rarefied gas flows. The method is an extension of the hybrid atomistic–continuum approach proposed by Borg et al. (2013) [28] for the simulation of micro/nano flows of high-aspect ratio. The major new extensions are: (1) incorporation of fluid compressibility; (2) implementation using the direct simulation Monte Carlo (DSMC) method for dilute rarefied gas flows, and (3) application to a broader range of geometries, including periodic, non-periodic, pressure-driven, gravity-driven and shear-driven internal flows. The multiscale method is applied to micro-scale gas flows through a periodic converging–diverging channel (driven by an external acceleration) and a non-periodic channel with a bend (driven by a pressure difference), as well as the flow between two eccentric cylinders (with the inner rotating relative to the outer). In all these cases there exists a wide variation of Knudsen number within the geometries, as well as substantial compressibility despite the Mach number being very low. For validation purposes, our multiscale simulation results are compared to those obtained from full-scale DSMC simulations: very close agreement is obtained in all cases for all flow variables considered. Our multiscale simulation is an order of magnitude more computationally efficient than the full-scale DSMC for the first and second test cases, and two orders of magnitude more efficient for the third case

Hybrid Electric Vehicle Experimental Model with CAN Network Real Time Control

Directory of Open Access Journals (Sweden)

RATOI, M.

2010-05-01

Full Text Available In this paper an experimental model with a distributed control system of a hybrid electrical vehicle is presented. A communication CAN network of high speed (1 Mbps assures a distributed control of the all components. The modeling and the control of different operating regimes are realized on an experimental test-bench of a hybrid electrical vehicle. The experimental results concerning the variations of the mains variables (currents, torques, speeds are presented.

Hybrid neural network bushing model for vehicle dynamics simulation

International Nuclear Information System (INIS)

Sohn, Jeong Hyun; Lee, Seung Kyu; Yoo, Wan Suk

2008-01-01

Although the linear model was widely used for the bushing model in vehicle suspension systems, it could not express the nonlinear characteristics of bushing in terms of the amplitude and the frequency. An artificial neural network model was suggested to consider the hysteretic responses of bushings. This model, however, often diverges due to the uncertainties of the neural network under the unexpected excitation inputs. In this paper, a hybrid neural network bushing model combining linear and neural network is suggested. A linear model was employed to represent linear stiffness and damping effects, and the artificial neural network algorithm was adopted to take into account the hysteretic responses. A rubber test was performed to capture bushing characteristics, where sine excitation with different frequencies and amplitudes is applied. Random test results were used to update the weighting factors of the neural network model. It is proven that the proposed model has more robust characteristics than a simple neural network model under step excitation input. A full car simulation was carried out to verify the proposed bushing models. It was shown that the hybrid model results are almost identical to the linear model under several maneuvers

Bias-dependent hybrid PKI empirical-neural model of microwave FETs

Science.gov (United States)

Marinković, Zlatica; Pronić-Rančić, Olivera; Marković, Vera

2011-10-01

Empirical models of microwave transistors based on an equivalent circuit are valid for only one bias point. Bias-dependent analysis requires repeated extractions of the model parameters for each bias point. In order to make model bias-dependent, a new hybrid empirical-neural model of microwave field-effect transistors is proposed in this article. The model is a combination of an equivalent circuit model including noise developed for one bias point and two prior knowledge input artificial neural networks (PKI ANNs) aimed at introducing bias dependency of scattering (S) and noise parameters, respectively. The prior knowledge of the proposed ANNs involves the values of the S- and noise parameters obtained by the empirical model. The proposed hybrid model is valid in the whole range of bias conditions. Moreover, the proposed model provides better accuracy than the empirical model, which is illustrated by an appropriate modelling example of a pseudomorphic high-electron mobility transistor device.

Origin and cross-century dynamics of an avian hybrid zone.

Science.gov (United States)

Morales-Rozo, Andrea; Tenorio, Elkin A; Carling, Matthew D; Cadena, Carlos Daniel

2017-12-15

Characterizations of the dynamics of hybrid zones in space and time can give insights about traits and processes important in population divergence and speciation. We characterized a hybrid zone between tanagers in the genus Ramphocelus (Aves, Thraupidae) located in southwestern Colombia. We evaluated whether this hybrid zone originated as a result of secondary contact or of primary differentiation, and described its dynamics across time using spatial analyses of molecular, morphological, and coloration data in combination with paleodistribution modeling. Models of potential historical distributions based on climatic data and genetic signatures of demographic expansion suggested that the hybrid zone likely originated following secondary contact between populations that expanded their ranges out of isolated areas in the Quaternary. Concordant patterns of variation in phenotypic characters across the hybrid zone and its narrow extent are suggestive of a tension zone, maintained by a balance between dispersal and selection against hybrids. Estimates of phenotypic cline parameters obtained using specimens collected over nearly a century revealed that, in recent decades, the zone appears to have moved to the east and to higher elevations, and may have become narrower. Genetic variation was not clearly structured along the hybrid zone, but comparisons between historical and contemporary specimens suggested that temporal changes in its genetic makeup may also have occurred. Our data suggest that the hybrid zone likey resulted from secondary contact between populations. The observed changes in the hybrid zone may be a result of sexual selection, asymmetric gene flow, or environmental change.

Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2016-01-06

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2015-01-07

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2014-01-06

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

Hybrid Analytical and Data-Driven Modeling for Feed-Forward Robot Control †

Directory of Open Access Journals (Sweden)

René Felix Reinhart

2017-02-01

Full Text Available Feed-forward model-based control relies on models of the controlled plant, e.g., in robotics on accurate knowledge of manipulator kinematics or dynamics. However, mechanical and analytical models do not capture all aspects of a plant’s intrinsic properties and there remain unmodeled dynamics due to varying parameters, unmodeled friction or soft materials. In this context, machine learning is an alternative suitable technique to extract non-linear plant models from data. However, fully data-based models suffer from inaccuracies as well and are inefficient if they include learning of well known analytical models. This paper thus argues that feed-forward control based on hybrid models comprising an analytical model and a learned error model can significantly improve modeling accuracy. Hybrid modeling here serves the purpose to combine the best of the two modeling worlds. The hybrid modeling methodology is described and the approach is demonstrated for two typical problems in robotics, i.e., inverse kinematics control and computed torque control. The former is performed for a redundant soft robot and the latter for a rigid industrial robot with redundant degrees of freedom, where a complete analytical model is not available for any of the platforms.

Hybrid Analytical and Data-Driven Modeling for Feed-Forward Robot Control †

Science.gov (United States)

Reinhart, René Felix; Shareef, Zeeshan; Steil, Jochen Jakob

2017-01-01

Feed-forward model-based control relies on models of the controlled plant, e.g., in robotics on accurate knowledge of manipulator kinematics or dynamics. However, mechanical and analytical models do not capture all aspects of a plant’s intrinsic properties and there remain unmodeled dynamics due to varying parameters, unmodeled friction or soft materials. In this context, machine learning is an alternative suitable technique to extract non-linear plant models from data. However, fully data-based models suffer from inaccuracies as well and are inefficient if they include learning of well known analytical models. This paper thus argues that feed-forward control based on hybrid models comprising an analytical model and a learned error model can significantly improve modeling accuracy. Hybrid modeling here serves the purpose to combine the best of the two modeling worlds. The hybrid modeling methodology is described and the approach is demonstrated for two typical problems in robotics, i.e., inverse kinematics control and computed torque control. The former is performed for a redundant soft robot and the latter for a rigid industrial robot with redundant degrees of freedom, where a complete analytical model is not available for any of the platforms. PMID:28208697

Hybrid nested sampling algorithm for Bayesian model selection applied to inverse subsurface flow problems

KAUST Repository

Elsheikh, Ahmed H.; Wheeler, Mary Fanett; Hoteit, Ibrahim

2014-01-01

A Hybrid Nested Sampling (HNS) algorithm is proposed for efficient Bayesian model calibration and prior model selection. The proposed algorithm combines, Nested Sampling (NS) algorithm, Hybrid Monte Carlo (HMC) sampling and gradient estimation using

Modeling a calixarene-crown-6 and its alkali complexes by means of a hybrid quantum mechanical/molecular mechanical method

International Nuclear Information System (INIS)

Lamare, V.; Golebiowski, J.; Ruiz-Lopez, M.F.; Martins-Costa, M.; Millot, C.

2000-01-01

Calixarene-crown-6s in 1,3-alternate conformation are compounds currently investigated for their ability to selectively extract traces of cesium from acidic or strong salinity aqueous solutions. Studies based on molecular modeling were undertaken on these systems to understand their behavior regarding cesium and other alkali cations, in particular sodium. In this work, a recently developed molecular modeling approach was used to investigate calixarene BC6 and its alkali complexes. The whole calixarene ligand is treated by the semiempirical AM1 quantum method (QM) whereas the cation and solvent are treated by a conventional force field (MM). The total energy of the system is the sum of the QM and MM sub-system contributions plus the QM/MM interaction energy. The latter includes the electrostatic interaction between QM charges (nuclei + electrons) and MM sites, and the non-electrostatic QM/MM van der Weals term, usually expressed by a Lennard-Jones potential. In the QM/MM method, van der Waals interactions between the QM and MM sub-systems are described by empirical Lennard-Jones parameters which must be adapted to the hybrid potential considered. Parameters on oxygen atoms were optimized. For the cations, two sets of Parameters were tested: Aqvist empirical parameters, derived to represent cation/water interactions in classical dynamics (set 2), and a new set of parameters which we calculated from dispersion coefficients available in the literature (set 1). The latter gave better results for the interactions with the crown. In the sodium complex, the cation interacts with only four oxygen atoms of the crown, whereas in the complex with cesium, the interaction involves six oxygen atoms. Distortion of the BC6 is therefore less with sodium and favors the corresponding complex by 4 kcal/mol. The cation/BC6 van der Waals energy is very weak for the two complexes. Hence the interaction between the cation and BC6 is primarily electrostatic. The BC6 polarization energy due

Photoanodic Hybrid Semiconductor–Molecular Heterojunction for Solar Water Oxidation

KAUST Repository

Joya, Khurram Saleem

2015-06-29

Inorganic photo-responsive semiconducting materials have been employed in photoelectrochemical(PEC) water oxidation devicesin pursuit of solar to fuel conversion.[1]The reaction kinetics in semiconductors is limited by poor contact at the interfaces, and charge transfer is impeded by surface defects and the grain boundaries.[2]It has shown that successful surface functionalization of the photo-responsive semiconducting materials with co-catalysts can maximize the charge separation, hole delivery and its effective consumption, and enhances the efficiency and performane of the PEC based water oxidation assembly.[3]We present here unique modification of photoanodic hematite (α-Fe2O3) and bismuth vanadate (BiVO4) with molecular co-catalysts for enhanced photoelectrochemical water oxidation (Figure 1). These hybrid inorganic–organometallic heterojunctions manifest impressive cathodic shifts in the onset potentials, and the photocurrent densities have been enhanced by > 90% at all potentials relative to uncatalyzed α-Fe2O3 or BiVO4, and other catalyst-semiconductor based heterojunctions.This is a novel development in the solar to fuel conversion field, and is crucially important for designing a tandem device where light interfere very little with the catalyst layer on top of semiconducting light absorber.

Fluid and hybrid models for streamers

Science.gov (United States)

Bonaventura, Zdeněk

2016-09-01

Streamers are contracted ionizing waves with self-generated field enhancement that propagate into a low-ionized medium exposed to high electric field leaving filamentary trails of plasma behind. The widely used model to study streamer dynamics is based on drift-diffusion equations for electrons and ions, assuming local field approximation, coupled with Poisson's equation. For problems where presence of energetic electrons become important a fluid approach needs to be extended by a particle model, accompanied also with Monte Carlo Collision technique, that takes care of motion of these electrons. A combined fluid-particle approach is used to study an influence of surface emission processes on a fast-pulsed dielectric barrier discharge in air at atmospheric pressure. It is found that fluid-only model predicts substantially faster reignition dynamics compared to coupled fluid-particle model. Furthermore, a hybrid model can be created in which the population of electrons is divided in the energy space into two distinct groups: (1) low energy `bulk' electrons that are treated with fluid model, and (2) high energy `beam' electrons, followed as particles. The hybrid model is then capable not only to deal with streamer discharges in laboratory conditions, but also allows us to study electron acceleration in streamer zone of lighting leaders. There, the production of fast electrons from streamers is investigated, since these (runaway) electrons act as seeds for the relativistic runaway electron avalanche (RREA) mechanism, important for high-energy atmospheric physics phenomena. Results suggest that high energy electrons effect the streamer propagation, namely the velocity, the peak electric field, and thus also the production rate of runaway electrons. This work has been supported by the Czech Science Foundation research project 15-04023S.

Gravitational waves in hybrid quintessential inflationary models

International Nuclear Information System (INIS)

Sa, Paulo M; Henriques, Alfredo B

2011-01-01

The generation of primordial gravitational waves is investigated within the hybrid quintessential inflationary model. Using the method of continuous Bogoliubov coefficients, we calculate the full gravitational-wave energy spectrum. The post-inflationary kination period, characteristic of quintessential inflationary models, leaves a clear signature on the spectrum, namely, a sharp rise of the gravitational-wave spectral energy density Ω GW at high frequencies. For appropriate values of the parameters of the model, Ω GW can be as high as 10 -12 in the MHz-GHz range of frequencies.

Two-field axion-monodromy hybrid inflation model: Dante's Waterfall

Science.gov (United States)

Carone, Christopher D.; Erlich, Joshua; Sensharma, Anuraag; Wang, Zhen

2015-02-01

We describe a hybrid axion-monodromy inflation model motivated by the Dante's Inferno scenario. In Dante's Inferno, a two-field potential features a stable trench along which a linear combination of the two fields slowly rolls, rendering the dynamics essentially identical to that of single-field chaotic inflation. A shift symmetry allows for the Lyth bound to be effectively evaded as in other axion-monodromy models. In our proposal, the potential is concave downward near the origin and the inflaton trajectory is a gradual downward spiral, ending at a point where the trench becomes unstable. There, the fields begin falling rapidly towards the minimum of the potential and inflation terminates as in a hybrid model. We find parameter choices that reproduce observed features of the cosmic microwave background, and discuss our model in light of recent results from the BICEP2 and Planck experiments.

Numerical modeling of hybrid fiber-reinforced concrete (hyfrc)

International Nuclear Information System (INIS)

Hameed, R.; Turatsinze, A.

2015-01-01

A model for numerical simulation of mechanical response of concrete reinforced with slipping and non slipping metallic fibers in hybrid form is presented in this paper. Constitutive law used to model plain concrete behaviour is based on plasticity and damage theories, and is capable to determine localized crack opening in three dimensional (3-D) systems. Behaviour law used for slipping metallic fibers is formulated based on effective stress carried by these fibers after when concrete matrix is cracked. A continuous approach is proposed to model the effect of addition of non-slipping metallic fibers in plain concrete. This approach considers the constitutive law of concrete matrix with increased fracture energy in tension obtained experimentally in direct tension tests on Fiber Reinforced Concrete (FRC). To simulate the mechanical behaviour of hybrid fiber-reinforced concrete (HyFRC), proposed approaches to model non-slipping metallic fibers and constitutive law of plain concrete and slipping fibers are used simultaneously without any additive equation. All the parameters used by the proposed model have physical meanings and are determined through experiments or drawn from literature. The model was implemented in Finite Element (FE) Code CASTEM and tested on FRC prismatic notched specimens in flexure. Model prediction showed good agreement with experimental results. (author)

Quantum mechanical/molecular mechanical and docking study of the novel analogues based on hybridization of common pharmacophores as potential anti-breast cancer agents.

Science.gov (United States)

Asadi, Parvin; Khodarahmi, Ghadamali; Farrokhpour, Hossein; Hassanzadeh, Farshid; Saghaei, Lotfollah

2017-06-01

In an attempt to identify some new potential leads as anti-breast cancer agents, novel hybrid compounds were designed by molecular hybridization approach. These derivatives were structurally derived from hybrid benzofuran-imidazole and quinazolinone derivatives, which had shown good cytotoxicity against the breast cancer cell line (MCF-7). Since aromatase enzyme (CYP19) is highly expressed in the MCF-7 cell line, the binding of these novel hybrid compounds to aromatase was investigated using the docking method. In this study, due to the positive charge on the imidazole ring of the designed ligands and also, the presence of heme iron in the active site of the enzyme, it was decided to optimize the ligand inside the protein to obtain more realistic atomic charges for it. Quantum mechanical/molecular mechanical (QM/MM) method was used to obtain more accurate atomic charges of ligand for docking calculations by considering the polarization effects of CYP19 on ligands. It was observed that the refitted charge improved the binding energy of the docked compounds. Also, the results showed that these novel hybrid compounds were adopted properly within the aromatase binding site, thereby suggesting that they could be potential inhibitors of aromatase. The main binding modes in these complexes were through hydrophobic and H bond interactions showing agreement with the basic physicochemical features of known anti aromatase compounds. Finally, the complex structures obtained from the docking study were used for single point QM/MM calculations to obtain more accurate electronic interaction energy, considering the electronic polarization of the ligand by its protein environment.

Design and fabrication of a hybrid maglev model employing PML and SML

Science.gov (United States)

Sun, R. X.; Zheng, J.; Zhan, L. J.; Huang, S. Y.; Li, H. T.; Deng, Z. G.

2017-10-01

A hybrid maglev model combining permanent magnet levitation (PML) and superconducting magnetic levitation (SML) was designed and fabricated to explore a heavy-load levitation system advancing in passive stability and simple structure. In this system, the PML was designed to levitate the load, and the SML was introduced to guarantee the stability. In order to realize different working gaps of the two maglev components, linear bearings were applied to connect the PML layer (for load) and the SML layer (for stability) of the hybrid maglev model. Experimental results indicate that the hybrid maglev model possesses excellent advantages of heavy-load ability and passive stability at the same time. This work presents a possible way to realize a heavy-load passive maglev concept.

Molecular structure of hybrid imino-chalcone in the solid state: X-ray diffraction, spectroscopy study and third-order nonlinear optical properties

Science.gov (United States)

Custodio, J. M. F.; Santos, F. G.; Vaz, W. F.; Cunha, C. E. P.; Silveira, R. G.; Anjos, M. M.; Campos, C. E. M.; Oliveira, G. R.; Martins, F. T.; da Silva, C. C.; Valverde, C.; Baseia, B.; Napolitano, H. B.

2018-04-01

A comprehensive structural study of the compound (2E)-1-((E)-4-(4-methoxybenzylideneamino)phenyl)-3-(4-methoxyphenyl)prop-2-en-1-one was carried out in this work. Single crystal X-ray diffraction (SCXRD), X-ray powder diffraction (XRPD), NMR, Raman and Infrared spectroscopies, and DFT calculations were performed for characterization of this iminochalcone hybrid. Intermolecular interactions were described by Hirshfeld surface analysis derived from crystal structure. Reactivity and intramolecular charge transfer were investigated using the frontier molecular orbitals and molecular electrostatic potential. In addition, we have calculated the Nonlinear Optical Properties at the CAM-B3LYP/6-311+g(d) level of theory in the presence of different solvents (gas-phase, acetone, chloroform, dichloromethane, dimethyl sulfoxide, ethanol, methanol, and water), being found meaningful NLO parameters for our compound. At last, there is a good agreement between calculated and experimental IR spectrum, allowing the assignment of some of normal vibrational modes of the iminochalcone hybrid.

Dynamic Modeling and Simulation on a Hybrid Power System for Electric Vehicle Applications

Directory of Open Access Journals (Sweden)

Hong-Wen He

2010-11-01

Full Text Available Hybrid power systems, formed by combining high-energy-density batteries and high-power-density ultracapacitors in appropriate ways, provide high-performance and high-efficiency power systems for electric vehicle applications. This paper first establishes dynamic models for the ultracapacitor, the battery and a passive hybrid power system, and then based on the dynamic models a comparative simulation between a battery only power system and the proposed hybrid power system was done under the UDDS (Urban Dynamometer Driving Schedule. The simulation results showed that the hybrid power system could greatly optimize and improve the efficiency of the batteries and their dynamic current was also decreased due to the participation of the ultracapacitors, which would have a good influence on batteries’ cycle life. Finally, the parameter matching for the passive hybrid power system was studied by simulation and comparisons.

Dynamic Modeling and Simulation of a Switched Reluctance Motor in a Series Hybrid Electric Vehicle

OpenAIRE

Siavash Sadeghi; Mojtaba Mirsalim; Arash Hassanpour Isfahani

2010-01-01

Dynamic behavior analysis of electric motors is required in order to accuratelyevaluate the performance, energy consumption and pollution level of hybrid electricvehicles. Simulation tools for hybrid electric vehicles are divided into steady state anddynamic models. Tools with steady-state models are useful for system-level analysiswhereas tools that utilize dynamic models give in-depth information about the behavior ofsublevel components. For the accurate prediction of hybrid electric vehicl...

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

Science.gov (United States)

Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

2017-09-30

GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Structural hybrid reliability index and its convergent solving method based on random–fuzzy–interval reliability model

Directory of Open Access Journals (Sweden)

Hai An

2016-08-01

Full Text Available Aiming to resolve the problems of a variety of uncertainty variables that coexist in the engineering structure reliability analysis, a new hybrid reliability index to evaluate structural hybrid reliability, based on the random–fuzzy–interval model, is proposed in this article. The convergent solving method is also presented. First, the truncated probability reliability model, the fuzzy random reliability model, and the non-probabilistic interval reliability model are introduced. Then, the new hybrid reliability index definition is presented based on the random–fuzzy–interval model. Furthermore, the calculation flowchart of the hybrid reliability index is presented and it is solved using the modified limit-step length iterative algorithm, which ensures convergence. And the validity of convergent algorithm for the hybrid reliability model is verified through the calculation examples in literature. In the end, a numerical example is demonstrated to show that the hybrid reliability index is applicable for the wear reliability assessment of mechanisms, where truncated random variables, fuzzy random variables, and interval variables coexist. The demonstration also shows the good convergence of the iterative algorithm proposed in this article.

Model-on-Demand Predictive Control for Nonlinear Hybrid Systems With Application to Adaptive Behavioral Interventions

Science.gov (United States)

Nandola, Naresh N.; Rivera, Daniel E.

2011-01-01

This paper presents a data-centric modeling and predictive control approach for nonlinear hybrid systems. System identification of hybrid systems represents a challenging problem because model parameters depend on the mode or operating point of the system. The proposed algorithm applies Model-on-Demand (MoD) estimation to generate a local linear approximation of the nonlinear hybrid system at each time step, using a small subset of data selected by an adaptive bandwidth selector. The appeal of the MoD approach lies in the fact that model parameters are estimated based on a current operating point; hence estimation of locations or modes governed by autonomous discrete events is achieved automatically. The local MoD model is then converted into a mixed logical dynamical (MLD) system representation which can be used directly in a model predictive control (MPC) law for hybrid systems using multiple-degree-of-freedom tuning. The effectiveness of the proposed MoD predictive control algorithm for nonlinear hybrid systems is demonstrated on a hypothetical adaptive behavioral intervention problem inspired by Fast Track, a real-life preventive intervention for improving parental function and reducing conduct disorder in at-risk children. Simulation results demonstrate that the proposed algorithm can be useful for adaptive intervention problems exhibiting both nonlinear and hybrid character. PMID:21874087

Performance modeling of hybrid MPI/OpenMP scientific applications on large-scale multicore supercomputers

KAUST Repository

Wu, Xingfu; Taylor, Valerie

2013-01-01

In this paper, we present a performance modeling framework based on memory bandwidth contention time and a parameterized communication model to predict the performance of OpenMP, MPI and hybrid applications with weak scaling on three large-scale multicore supercomputers: IBM POWER4, POWER5+ and BlueGene/P, and analyze the performance of these MPI, OpenMP and hybrid applications. We use STREAM memory benchmarks and Intel's MPI benchmarks to provide initial performance analysis and model validation of MPI and OpenMP applications on these multicore supercomputers because the measured sustained memory bandwidth can provide insight into the memory bandwidth that a system should sustain on scientific applications with the same amount of workload per core. In addition to using these benchmarks, we also use a weak-scaling hybrid MPI/OpenMP large-scale scientific application: Gyrokinetic Toroidal Code (GTC) in magnetic fusion to validate our performance model of the hybrid application on these multicore supercomputers. The validation results for our performance modeling method show less than 7.77% error rate in predicting the performance of hybrid MPI/OpenMP GTC on up to 512 cores on these multicore supercomputers. © 2013 Elsevier Inc.

Performance modeling of hybrid MPI/OpenMP scientific applications on large-scale multicore supercomputers

KAUST Repository

Wu, Xingfu

2013-12-01

In this paper, we present a performance modeling framework based on memory bandwidth contention time and a parameterized communication model to predict the performance of OpenMP, MPI and hybrid applications with weak scaling on three large-scale multicore supercomputers: IBM POWER4, POWER5+ and BlueGene/P, and analyze the performance of these MPI, OpenMP and hybrid applications. We use STREAM memory benchmarks and Intel\\'s MPI benchmarks to provide initial performance analysis and model validation of MPI and OpenMP applications on these multicore supercomputers because the measured sustained memory bandwidth can provide insight into the memory bandwidth that a system should sustain on scientific applications with the same amount of workload per core. In addition to using these benchmarks, we also use a weak-scaling hybrid MPI/OpenMP large-scale scientific application: Gyrokinetic Toroidal Code (GTC) in magnetic fusion to validate our performance model of the hybrid application on these multicore supercomputers. The validation results for our performance modeling method show less than 7.77% error rate in predicting the performance of hybrid MPI/OpenMP GTC on up to 512 cores on these multicore supercomputers. © 2013 Elsevier Inc.

AMITIS: A 3D GPU-Based Hybrid-PIC Model for Space and Plasma Physics

Science.gov (United States)

Fatemi, Shahab; Poppe, Andrew R.; Delory, Gregory T.; Farrell, William M.

2017-05-01

We have developed, for the first time, an advanced modeling infrastructure in space simulations (AMITIS) with an embedded three-dimensional self-consistent grid-based hybrid model of plasma (kinetic ions and fluid electrons) that runs entirely on graphics processing units (GPUs). The model uses NVIDIA GPUs and their associated parallel computing platform, CUDA, developed for general purpose processing on GPUs. The model uses a single CPU-GPU pair, where the CPU transfers data between the system and GPU memory, executes CUDA kernels, and writes simulation outputs on the disk. All computations, including moving particles, calculating macroscopic properties of particles on a grid, and solving hybrid model equations are processed on a single GPU. We explain various computing kernels within AMITIS and compare their performance with an already existing well-tested hybrid model of plasma that runs in parallel using multi-CPU platforms. We show that AMITIS runs ∼10 times faster than the parallel CPU-based hybrid model. We also introduce an implicit solver for computation of Faraday’s Equation, resulting in an explicit-implicit scheme for the hybrid model equation. We show that the proposed scheme is stable and accurate. We examine the AMITIS energy conservation and show that the energy is conserved with an error < 0.2% after 500,000 timesteps, even when a very low number of particles per cell is used.

Gravitational waves in hybrid quintessential inflationary models

Energy Technology Data Exchange (ETDEWEB)

Sa, Paulo M [Departamento de Fisica, Faculdade de Ciencias e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Henriques, Alfredo B, E-mail: pmsa@ualg.pt, E-mail: alfredo.henriques@ist.utl.pt [Centro Multidisciplinar de Astrofisica - CENTRA and Departamento de Fisica, Instituto Superior Tecnico, UTL, Av. Rovisco Pais, 1049-001 Lisboa (Portugal)

2011-09-22

The generation of primordial gravitational waves is investigated within the hybrid quintessential inflationary model. Using the method of continuous Bogoliubov coefficients, we calculate the full gravitational-wave energy spectrum. The post-inflationary kination period, characteristic of quintessential inflationary models, leaves a clear signature on the spectrum, namely, a sharp rise of the gravitational-wave spectral energy density {Omega}{sub GW} at high frequencies. For appropriate values of the parameters of the model, {Omega}{sub GW} can be as high as 10{sup -12} in the MHz-GHz range of frequencies.

Molecular marker systems for Oenothera genetics.

Science.gov (United States)

Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

2008-11-01

The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

Application of a New Hybrid RANS/LES Modeling Paradigm to Compressible Flow

Science.gov (United States)

Oliver, Todd; Pederson, Clark; Haering, Sigfried; Moser, Robert

2017-11-01

It is well-known that traditional hybrid RANS/LES modeling approaches suffer from a number of deficiencies. These deficiencies often stem from overly simplistic blending strategies based on scalar measures of turbulence length scale and grid resolution and from use of isotropic subgrid models in LES regions. A recently developed hybrid modeling approach has shown promise in overcoming these deficiencies in incompressible flows [Haering, 2015]. In the approach, RANS/LES blending is accomplished using a hybridization parameter that is governed by an additional model transport equation and is driven to achieve equilibrium between the resolved and unresolved turbulence for the given grid. Further, the model uses an tensor eddy viscosity that is formulated to represent the effects of anisotropic grid resolution on subgrid quantities. In this work, this modeling approach is extended to compressible flows and implemented in the compressible flow solver SU2 (http://su2.stanford.edu/). We discuss both modeling and implementation challenges and show preliminary results for compressible flow test cases with smooth wall separation.

Adaptive control using a hybrid-neural model: application to a polymerisation reactor

Directory of Open Access Journals (Sweden)

Cubillos F.

2001-01-01

Full Text Available This work presents the use of a hybrid-neural model for predictive control of a plug flow polymerisation reactor. The hybrid-neural model (HNM is based on fundamental conservation laws associated with a neural network (NN used to model the uncertain parameters. By simulations, the performance of this approach was studied for a peroxide-initiated styrene tubular reactor. The HNM was synthesised for a CSTR reactor with a radial basis function neural net (RBFN used to estimate the reaction rates recursively. The adaptive HNM was incorporated in two model predictive control strategies, a direct synthesis scheme and an optimum steady state scheme. Tests for servo and regulator control showed excellent behaviour following different setpoint variations, and rejecting perturbations. The good generalisation and training capacities of hybrid models, associated with the simplicity and robustness characteristics of the MPC formulations, make an attractive combination for the control of a polymerisation reactor.

Status and modeling improvements of hybrid wind/PV/diesel power systems for Brazilian applications

Energy Technology Data Exchange (ETDEWEB)

McGowan, J.G.; Manwell, J.F.; Avelar, C. [Univ. of Massachusetts, Amherst, MA (United States); Taylor, R. [National Renewable Energy Lab., Golden, CO (United States)

1997-12-31

This paper present a summary of the ongoing work on the modeling and system design of hybrid wind/PV/diesel systems for two different sites in the Amazonia region of Brazil. The work incorporates the latest resource data and is based on the use of the Hybrid2 simulation code developed by the University of Massachusetts and NREL. Details of the baseline operating hybrid systems are reviewed, and the results of the latest detailed hybrid system evaluation for each site are summarized. Based on the system modeling results, separate recommendations for system modification and improvements are made.

On the Likely Utility of Hybrid Weights Optimized for Variances in Hybrid Error Covariance Models

Science.gov (United States)

Satterfield, E.; Hodyss, D.; Kuhl, D.; Bishop, C. H.

2017-12-01

Because of imperfections in ensemble data assimilation schemes, one cannot assume that the ensemble covariance is equal to the true error covariance of a forecast. Previous work demonstrated how information about the distribution of true error variances given an ensemble sample variance can be revealed from an archive of (observation-minus-forecast, ensemble-variance) data pairs. Here, we derive a simple and intuitively compelling formula to obtain the mean of this distribution of true error variances given an ensemble sample variance from (observation-minus-forecast, ensemble-variance) data pairs produced by a single run of a data assimilation system. This formula takes the form of a Hybrid weighted average of the climatological forecast error variance and the ensemble sample variance. Here, we test the extent to which these readily obtainable weights can be used to rapidly optimize the covariance weights used in Hybrid data assimilation systems that employ weighted averages of static covariance models and flow-dependent ensemble based covariance models. Univariate data assimilation and multi-variate cycling ensemble data assimilation are considered. In both cases, it is found that our computationally efficient formula gives Hybrid weights that closely approximate the optimal weights found through the simple but computationally expensive process of testing every plausible combination of weights.

Obtaining interspecific hybrids, and molecular analysis by microsatellite markers in grapevine

OpenAIRE

Mariane Ruzza Schuck; Luiz Antonio Biasi; Ada Michele Mariano; Bernardo Lipski; Summaira Riaz; Michael Andrew Walker

2011-01-01

The objective of this work was to assess the potential of interspecific hybridization of Vitis labruscana and Muscadinia rotundifolia by using artificial cross-pollinations. Microsatellite markers were used to confirm interspecific hybridizations and the identity of the parental genotypes. In crosses in which M. rotundifolia was used as the female parent, no true hybrids were obtained. In the reciprocal crosses, 114 seedlings were identified as true V. labruscana x M. rotundifolia hybrids. Se...

Using the hybrid fuzzy goal programming model and hybrid genetic algorithm to solve a multi-objective location routing problem for infectious waste disposaL

Energy Technology Data Exchange (ETDEWEB)

Wichapa, Narong; Khokhajaikiat, Porntep

2017-07-01

Disposal of infectious waste remains one of the most serious problems in the social and environmental domains of almost every nation. Selection of new suitable locations and finding the optimal set of transport routes to transport infectious waste, namely location routing problem for infectious waste disposal, is one of the major problems in hazardous waste management. Design/methodology/approach: Due to the complexity of this problem, location routing problem for a case study, forty hospitals and three candidate municipalities in sub-Northeastern Thailand, was divided into two phases. The first phase is to choose suitable municipalities using hybrid fuzzy goal programming model which hybridizes the fuzzy analytic hierarchy process and fuzzy goal programming. The second phase is to find the optimal routes for each selected municipality using hybrid genetic algorithm which hybridizes the genetic algorithm and local searches including 2-Opt-move, Insertion-move and ?-interchange-move. Findings: The results indicate that the hybrid fuzzy goal programming model can guide the selection of new suitable municipalities, and the hybrid genetic algorithm can provide the optimal routes for a fleet of vehicles effectively. Originality/value: The novelty of the proposed methodologies, hybrid fuzzy goal programming model, is the simultaneous combination of both intangible and tangible factors in order to choose new suitable locations, and the hybrid genetic algorithm can be used to determine the optimal routes which provide a minimum number of vehicles and minimum transportation cost under the actual situation, efficiently.

Using the hybrid fuzzy goal programming model and hybrid genetic algorithm to solve a multi-objective location routing problem for infectious waste disposaL

International Nuclear Information System (INIS)

Wichapa, Narong; Khokhajaikiat, Porntep

2017-01-01

Disposal of infectious waste remains one of the most serious problems in the social and environmental domains of almost every nation. Selection of new suitable locations and finding the optimal set of transport routes to transport infectious waste, namely location routing problem for infectious waste disposal, is one of the major problems in hazardous waste management. Design/methodology/approach: Due to the complexity of this problem, location routing problem for a case study, forty hospitals and three candidate municipalities in sub-Northeastern Thailand, was divided into two phases. The first phase is to choose suitable municipalities using hybrid fuzzy goal programming model which hybridizes the fuzzy analytic hierarchy process and fuzzy goal programming. The second phase is to find the optimal routes for each selected municipality using hybrid genetic algorithm which hybridizes the genetic algorithm and local searches including 2-Opt-move, Insertion-move and ?-interchange-move. Findings: The results indicate that the hybrid fuzzy goal programming model can guide the selection of new suitable municipalities, and the hybrid genetic algorithm can provide the optimal routes for a fleet of vehicles effectively. Originality/value: The novelty of the proposed methodologies, hybrid fuzzy goal programming model, is the simultaneous combination of both intangible and tangible factors in order to choose new suitable locations, and the hybrid genetic algorithm can be used to determine the optimal routes which provide a minimum number of vehicles and minimum transportation cost under the actual situation, efficiently.

3D Printing of Molecular Models

Science.gov (United States)

Gardner, Adam; Olson, Arthur

2016-01-01

Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…

Hybrid Spatial Data Model for Indoor Space: Combined Topology and Grid

Directory of Open Access Journals (Sweden)

Zhiyong Lin

2017-11-01

Full Text Available The construction and application of an indoor spatial data model is an important prerequisite to meet the requirements of diversified indoor spatial location services. The traditional indoor spatial topology model focuses on the construction of topology information. It has high path analysis and query efficiency, but ignores the spatial location information. The grid model retains the plane position information by grid, but increases the data volume and complexity of the model and reduces the efficiency of the model analysis. This paper presents a hybrid model for interior space based on topology and grid. Based on the spatial meshing and spatial division of the interior space, the model retains the position information and topological connectivity information of the interior space by establishing the connection or affiliation between the grid subspace and the topological subspace. The model improves the speed of interior spatial analysis and solves the problem of the topology information and location information updates not being synchronized. In this study, the A* shortest path query efficiency of typical daily indoor activities under the grid model and the hybrid model were compared for the indoor plane of an apartment and a shopping mall. The results obtained show that the hybrid model is 43% higher than the A* algorithm of the grid model as a result of the existence of topology communication information. This paper provides a useful idea for the establishment of a highly efficient and highly available interior spatial data model.

Quantifying and Visualizing Uncertainties in Molecular Models

OpenAIRE

Rasheed, Muhibur; Clement, Nathan; Bhowmick, Abhishek; Bajaj, Chandrajit

2015-01-01

Computational molecular modeling and visualization has seen significant progress in recent years with sev- eral molecular modeling and visualization software systems in use today. Nevertheless the molecular biology community lacks techniques and tools for the rigorous analysis, quantification and visualization of the associated errors in molecular structure and its associated properties. This paper attempts at filling this vacuum with the introduction of a systematic statistical framework whe...

Fuzzy logic-based analogue forecasting and hybrid modelling of horizontal visibility

Science.gov (United States)

Tuba, Zoltán; Bottyán, Zsolt

2018-04-01

Forecasting visibility is one of the greatest challenges in aviation meteorology. At the same time, high accuracy visibility forecasts can significantly reduce or make avoidable weather-related risk in aviation as well. To improve forecasting visibility, this research links fuzzy logic-based analogue forecasting and post-processed numerical weather prediction model outputs in hybrid forecast. Performance of analogue forecasting model was improved by the application of Analytic Hierarchy Process. Then, linear combination of the mentioned outputs was applied to create ultra-short term hybrid visibility prediction which gradually shifts the focus from statistical to numerical products taking their advantages during the forecast period. It gives the opportunity to bring closer the numerical visibility forecast to the observations even it is wrong initially. Complete verification of categorical forecasts was carried out; results are available for persistence and terminal aerodrome forecasts (TAF) as well in order to compare. The average value of Heidke Skill Score (HSS) of examined airports of analogue and hybrid forecasts shows very similar results even at the end of forecast period where the rate of analogue prediction in the final hybrid output is 0.1-0.2 only. However, in case of poor visibility (1000-2500 m), hybrid (0.65) and analogue forecasts (0.64) have similar average of HSS in the first 6 h of forecast period, and have better performance than persistence (0.60) or TAF (0.56). Important achievement that hybrid model takes into consideration physics and dynamics of the atmosphere due to the increasing part of the numerical weather prediction. In spite of this, its performance is similar to the most effective visibility forecasting methods and does not follow the poor verification results of clearly numerical outputs.

Evaluation of vertical coordinate and vertical mixing algorithms in the HYbrid-Coordinate Ocean Model (HYCOM)

Science.gov (United States)

Halliwell, George R.

Vertical coordinate and vertical mixing algorithms included in the HYbrid Coordinate Ocean Model (HYCOM) are evaluated in low-resolution climatological simulations of the Atlantic Ocean. The hybrid vertical coordinates are isopycnic in the deep ocean interior, but smoothly transition to level (pressure) coordinates near the ocean surface, to sigma coordinates in shallow water regions, and back again to level coordinates in very shallow water. By comparing simulations to climatology, the best model performance is realized using hybrid coordinates in conjunction with one of the three available differential vertical mixing models: the nonlocal K-Profile Parameterization, the NASA GISS level 2 turbulence closure, and the Mellor-Yamada level 2.5 turbulence closure. Good performance is also achieved using the quasi-slab Price-Weller-Pinkel dynamical instability model. Differences among these simulations are too small relative to other errors and biases to identify the "best" vertical mixing model for low-resolution climate simulations. Model performance deteriorates slightly when the Kraus-Turner slab mixed layer model is used with hybrid coordinates. This deterioration is smallest when solar radiation penetrates beneath the mixed layer and when shear instability mixing is included. A simulation performed using isopycnic coordinates to emulate the Miami Isopycnic Coordinate Ocean Model (MICOM), which uses Kraus-Turner mixing without penetrating shortwave radiation and shear instability mixing, demonstrates that the advantages of switching from isopycnic to hybrid coordinates and including more sophisticated turbulence closures outweigh the negative numerical effects of maintaining hybrid vertical coordinates.

Pedagogy and Process: A Case Study of Writing in a Hybrid Learning Model

Science.gov (United States)

Keiner, Jason F.

2017-01-01

This qualitative case study explored the perceived experiences and outcomes of writing in a hybrid model of instruction in a large suburban high school. In particular, the impact of a hybrid model on the writing process and on future writing performance were examined. In addition, teacher expectation and teacher attitude and their impact upon…

Modelling and Optimising the Value of a Hybrid Solar-Wind System

Science.gov (United States)

Nair, Arjun; Murali, Kartik; Anbuudayasankar, S. P.; Arjunan, C. V.

2017-05-01

In this paper, a net present value (NPV) approach for a solar hybrid system has been presented. The system, in question aims at supporting an investor by assessing an investment in solar-wind hybrid system in a given area. The approach follow a combined process of modelling the system, with optimization of major investment-related variables to maximize the financial yield of the investment. The consideration of solar wind hybrid supply presents significant potential for cost reduction. The investment variables concern the location of solar wind plant, and its sizing. The system demand driven, meaning that its primary aim is to fully satisfy the energy demand of the customers. Therefore, the model is a practical tool in the hands of investor to assess and optimize in financial terms an investment aiming at covering real energy demand. Optimization is performed by taking various technical, logical constraints. The relation between the maximum power obtained between individual system and the hybrid system as a whole in par with the net present value of the system has been highlighted.

Hybrid breeding in wheat: technologies to improve hybrid wheat seed production.

Science.gov (United States)

Whitford, Ryan; Fleury, Delphine; Reif, Jochen C; Garcia, Melissa; Okada, Takashi; Korzun, Viktor; Langridge, Peter

2013-12-01

Global food security demands the development and delivery of new technologies to increase and secure cereal production on finite arable land without increasing water and fertilizer use. There are several options for boosting wheat yields, but most offer only small yield increases. Wheat is an inbred plant, and hybrids hold the potential to deliver a major lift in yield and will open a wide range of new breeding opportunities. A series of technological advances are needed as a base for hybrid wheat programmes. These start with major changes in floral development and architecture to separate the sexes and force outcrossing. Male sterility provides the best method to block self-fertilization, and modifying the flower structure will enhance pollen access. The recent explosion in genomic resources and technologies provides new opportunities to overcome these limitations. This review outlines the problems with existing hybrid wheat breeding systems and explores molecular-based technologies that could improve the hybrid production system to reduce hybrid seed production costs, a prerequisite for a commercial hybrid wheat system.

Fluid Survival Tool: A Model Checker for Hybrid Petri Nets

NARCIS (Netherlands)

Postema, Björn Frits; Remke, Anne Katharina Ingrid; Haverkort, Boudewijn R.H.M.; Ghasemieh, Hamed

2014-01-01

Recently, algorithms for model checking Stochastic Time Logic (STL) on Hybrid Petri nets with a single general one-shot transition (HPNG) have been introduced. This paper presents a tool for model checking HPNG models against STL formulas. A graphical user interface (GUI) not only helps to

Photocatalytic oxidation of organic compounds in a hybrid system composed of a molecular catalyst and visible light-absorbing semiconductor.

Science.gov (United States)

Zhou, Xu; Li, Fei; Li, Xiaona; Li, Hua; Wang, Yong; Sun, Licheng

2015-01-14

Photocatalytic oxidation of organic compounds proceeded efficiently in a hybrid system with ruthenium aqua complexes as catalysts, BiVO4 as a light absorber, [Co(NH3)5Cl](2+) as a sacrificial electron acceptor and water as an oxygen source. The photogenerated holes in the semiconductor are used to oxidize molecular catalysts into the high-valent Ru(IV)=O intermediates for 2e(-) oxidation.

Saccharomyces interspecies hybrids as model organisms for studying yeast adaptation to stressful environments.

Science.gov (United States)

Lopandic, Ksenija

2018-01-01

The strong development of molecular biology techniques and next-generation sequencing technologies in the last two decades has significantly improved our understanding of the evolutionary history of Saccharomyces yeasts. It has been shown that many strains isolated from man-made environments are not pure genetic lines, but contain genetic materials from different species that substantially increase their genome complexity. A number of strains have been described as interspecies hybrids, implying different yeast species that under specific circumstances exchange and recombine their genomes. Such fusing usually results in a wide variety of alterations at the genetic and chromosomal levels. The observed changes have suggested a high genome plasticity and a significant role of interspecies hybridization in the adaptation of yeasts to environmental stresses and industrial processes. There is a high probability that harsh wine and beer fermentation environments, from which the majority of interspecies hybrids have been isolated so far, influence their selection and stabilization as well as their genomic and phenotypic heterogeneity. The lessons we have learned about geno- and phenotype plasticity and the diversity of natural and commercial yeast hybrids have already had a strong impact on the development of artificial hybrids that can be successfully used in the fermentation-based food and beverage industry. The creation of artificial hybrids through the crossing of strains with desired attributes is a possibility to obtain a vast variety of new, but not genetically modified yeasts with a range of improved and beneficial traits. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Hybrid Adaptive Flight Control with Model Inversion Adaptation

Science.gov (United States)

Nguyen, Nhan

2011-01-01

This study investigates a hybrid adaptive flight control method as a design possibility for a flight control system that can enable an effective adaptation strategy to deal with off-nominal flight conditions. The hybrid adaptive control blends both direct and indirect adaptive control in a model inversion flight control architecture. The blending of both direct and indirect adaptive control provides a much more flexible and effective adaptive flight control architecture than that with either direct or indirect adaptive control alone. The indirect adaptive control is used to update the model inversion controller by an on-line parameter estimation of uncertain plant dynamics based on two methods. The first parameter estimation method is an indirect adaptive law based on the Lyapunov theory, and the second method is a recursive least-squares indirect adaptive law. The model inversion controller is therefore made to adapt to changes in the plant dynamics due to uncertainty. As a result, the modeling error is reduced that directly leads to a decrease in the tracking error. In conjunction with the indirect adaptive control that updates the model inversion controller, a direct adaptive control is implemented as an augmented command to further reduce any residual tracking error that is not entirely eliminated by the indirect adaptive control.

Hybrid ATDL-gamma distribution model for predicting area source acid gas concentrations

Energy Technology Data Exchange (ETDEWEB)

Jakeman, A J; Taylor, J A

1985-01-01

An air quality model is developed to predict the distribution of concentrations of acid gas in an urban airshed. The model is hybrid in character, combining reliable features of a deterministic ATDL-based model with statistical distributional approaches. The gamma distribution was identified from a range of distributional models as the best model. The paper shows that the assumptions of a previous hybrid model may be relaxed and presents a methodology for characterizing the uncertainty associated with model predictions. Results are demonstrated for the 98-percentile predictions of 24-h average data over annual periods at six monitoring sites. This percentile relates to the World Health Organization goal for acid gas concentrations.

A computational model for lower hybrid current drive

International Nuclear Information System (INIS)

Englade, R.C.; Bonoli, P.T.; Porkolab, M.

1983-01-01

A detailed simulation model for lower hybrid (LH) current drive in toroidal devices is discussed. This model accounts reasonably well for the magnitude of radio frequency (RF) current observed in the PLT and Alcator C devices. It also reproduces the experimental dependencies of RF current generation on toroidal magnetic field and has provided insights about mechanisms which may underlie the observed density limit of current drive. (author)

Hierarchical models and iterative optimization of hybrid systems

Energy Technology Data Exchange (ETDEWEB)

Rasina, Irina V. [Ailamazyan Program Systems Institute, Russian Academy of Sciences, Peter One str. 4a, Pereslavl-Zalessky, 152021 (Russian Federation); Baturina, Olga V. [Trapeznikov Control Sciences Institute, Russian Academy of Sciences, Profsoyuznaya str. 65, 117997, Moscow (Russian Federation); Nasatueva, Soelma N. [Buryat State University, Smolina str.24a, Ulan-Ude, 670000 (Russian Federation)

2016-06-08

A class of hybrid control systems on the base of two-level discrete-continuous model is considered. The concept of this model was proposed and developed in preceding works as a concretization of the general multi-step system with related optimality conditions. A new iterative optimization procedure for such systems is developed on the base of localization of the global optimality conditions via contraction the control set.

Leptospira borgpetersenii hybrid leucine-rich repeat protein: Cloning and expression, immunogenic identification and molecular docking evaluation.

Science.gov (United States)

Sritrakul, Tepyuda; Nitipan, Supachai; Wajjwalku, Worawidh; La-Ard, Anchalee; Suphatpahirapol, Chattip; Petkarnjanapong, Wimol; Ongphiphadhanakul, Boonsong; Prapong, Siriwan

2017-11-01

Leptospirosis is an important zoonotic disease, and the major outbreak of this disease in Thailand in 1999 was due largely to the Leptospira borgpetersenii serovar Sejroe. Identification of the leucine-rich repeat (LRR) LBJ_2271 protein containing immunogenic epitopes and the discovery of the LBJ_2271 ortholog in Leptospira serovar Sejroe, KU_Sej_R21_2271, led to further studies of the antigenic immune properties of KU_Sej_LRR_2271. The recombinant hybrid (rh) protein was created and expressed from a hybrid PCR fragment of KU_Sej_R21_2271 fused with DNA encoding the LBJ_2271 signal sequence for targeting protein as a membrane-anchoring protein. The fusion DNA was cloned into pET160/GW/D-TOPO® to form the pET160_hKU_R21_2271 plasmid. The plasmid was used to express the rhKU_Sej_LRR_2271 protein in Escherichia coli BL21 Star™ (DE3). The expressed protein was immunologically detected by Western blotting and immunoreactivity detection with hyperimmune sera, T cell epitope prediction by HLA allele and epitope peptide binding affinity, and potential T cell reactivity analysis. The immunogenic epitopes of the protein were evaluated and verified by HLA allele and epitope peptide complex structure molecular docking. Among fourteen best allele epitopes of this protein, binding affinity values of 12 allele epitopes remained unchanged compared to LBJ_2271. Two epitopes for alleles HLA-A0202 and -A0301 had higher IC 50 values, while T cell reactivity values of these peptides were better than values from LBJ_2271 epitopes. Eight of twelve epitope peptides had positive T-cell reactivity scores. Although the molecular docking of two epitopes, 3FPLLKEFLV11/47FPLLKEFLV55 and 50KLSTVPEGV58, into an HLA-A0202 model revealed a good fit in the docked structures, 50KLSTVPEGV58 and 94KLSTVPEEV102 are still considered as the proteins' best epitopes for allele HLA-A0202. The results of this study showed that rhKU_Sej_LRR_2271 protein contained natural immunological properties that should

Deep Generative Models for Molecular Science

DEFF Research Database (Denmark)

Jørgensen, Peter Bjørn; Schmidt, Mikkel Nørgaard; Winther, Ole

2018-01-01

Generative deep machine learning models now rival traditional quantum-mechanical computations in predicting properties of new structures, and they come with a significantly lower computational cost, opening new avenues in computational molecular science. In the last few years, a variety of deep...... generative models have been proposed for modeling molecules, which differ in both their model structure and choice of input features. We review these recent advances within deep generative models for predicting molecular properties, with particular focus on models based on the probabilistic autoencoder (or...

Energy level alignment at hybridized organic-metal interfaces from a GW projection approach

Science.gov (United States)

Chen, Yifeng; Tamblyn, Isaac; Quek, Su Ying

Energy level alignments at organic-metal interfaces are of profound importance in numerous (opto)electronic applications. Standard density functional theory (DFT) calculations generally give incorrect energy level alignments and missing long-range polarization effects. Previous efforts to address this problem using the many-electron GW method have focused on physisorbed systems where hybridization effects are insignificant. Here, we use state-of-the-art GW methods to predict the level alignment at the amine-Au interface, where molecular levels do hybridize with metallic states. This non-trivial hybridization implies that DFT result is a poor approximation to the quasiparticle states. However, we find that the self-energy operator is approximately diagonal in the molecular basis, allowing us to use a projection approach to predict the level alignments. Our results indicate that the metallic substrate reduces the HOMO-LUMO gap by 3.5 4.0 eV, depending on the molecular coverage/presence of Au adatoms. Our GW results are further compared with those of a simple image charge model that describes the level alignment in physisorbed systems. Syq and YC acknowledge Grant NRF-NRFF2013-07 and the medium-sized centre program from the National Research Foundation, Singapore.

The Cheshire Cat principle for hybrid bag models

International Nuclear Information System (INIS)

Nielsen, H.B.

1987-05-01

The Cheshire Cat point of view where the bag in the chiral bag model has no physical significance, but only a notational one is argued for. It is explained how a fermion - in, say, a 1+1 dimensional exact Cheshire Cat model - escapes the bag by means of an anomaly. The possibility to construct sophisticated hybrid bag models is suggested which use the lack of physical significance of the bag to fix the many parameters so as to anyway give hope of a phenomenologically sensible model. (orig.)

A control-oriented cycle-life model for hybrid electric vehicle lithium-ion batteries

International Nuclear Information System (INIS)

Suri, Girish; Onori, Simona

2016-01-01

In this paper, a semi-empirical Lithium-iron phosphate-graphite battery aging model is identified over data mimicking actual cycling conditions that a hybrid electric vehicle battery encounters under real driving scenarios. The aging model is then used to construct the severity factor map, used to characterize relative aging of the battery under different operating conditions. This is used as a battery degradation criterion within a multi-objective optimization problem where battery aging minimization is to be achieved along with fuel consumption minimization. The method proposed is general and can be applied to other battery chemistry as well as different vehicular applications. Finally, simulations conducted using a hybrid electric vehicle simulator show how the two modeling tools developed in this paper, i.e., the severity factor map and the aging model, can be effectively used in a multi-objective optimization problem to predict and control battery degradation. - Highlights: • Battery aging model for hybrid electric vehicles using real driving conditions data. • Development of a modeling tool to assess battery degradation for real time optimization. • "3"1P NMR analysis of an enzyme-treated extract showed expected hydrolysis of P forms. • Development of an energy management strategy to minimize battery degradation. • Simulation results from hybrid electric vehicle simulator.

Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets

Directory of Open Access Journals (Sweden)

Mostafa eHerajy

2015-07-01

Full Text Available Predicting and studying the dynamics and properties of environmental systems necessitates the construction and simulation of mathematical models entailing different levels of complexities. Such type of computational experiments often require the combination of discrete and continuous variables as well as processes operating at different time scales. Furthermore, the iterative steps of constructing and analyzing environmental models might involve researchers with different background. Hybrid Petri nets may contribute in overcoming such challenges as they facilitate the implementation of systems integrating discrete and continuous dynamics. Additionally, the visual depiction of model components will inevitably help to bridge the gap between scientists with distinct expertise working on the same problem. Thus, modeling environmental systems with hybrid Petri nets enables the construction of complex processes while keeping the models comprehensible for researchers working on the same project with significantly divergent education path. In this paper we propose the utilization of a special class of hybrid Petri nets, Generalized Hybrid Petri Nets (GHPN, to model and simulate environmental systems exposing processes interacting at different time-scales. GHPN integrate stochastic and deterministic semantics as well as other types of special basic events. Moreover, a case study is presented to illustrate the use of GHPN in constructing and simulating multi-timescale environmental scenarios.

Static stiffness modeling of a novel hybrid redundant robot machine

International Nuclear Information System (INIS)

Li Ming; Wu Huapeng; Handroos, Heikki

2011-01-01

This paper presents a modeling method to study the stiffness of a hybrid serial-parallel robot IWR (Intersector Welding Robot) for the assembly of ITER vacuum vessel. The stiffness matrix of the basic element in the robot is evaluated using matrix structural analysis (MSA); the stiffness of the parallel mechanism is investigated by taking account of the deformations of both hydraulic limbs and joints; the stiffness of the whole integrated robot is evaluated by employing the virtual joint method and the principle of virtual work. The obtained stiffness model of the hybrid robot is analytical and the deformation results of the robot workspace under certain external load are presented.

Evaluation of models generated via hybrid evolutionary algorithms ...

African Journals Online (AJOL)

2016-04-02

Apr 2, 2016 ... Evaluation of models generated via hybrid evolutionary algorithms for the prediction of Microcystis ... evolutionary algorithms (HEA) proved to be highly applica- ble to the hypertrophic reservoirs of South Africa. .... discovered and optimised using a large-scale parallel computational device and relevant soft-.

Nuclear Hybrid Energy Systems FY16 Modeling Efforts at ORNL

Energy Technology Data Exchange (ETDEWEB)

Cetiner, Sacit M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Greenwood, Michael Scott [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Harrison, Thomas J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Qualls, A. L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Guler Yigitoglu, Askin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Fugate, David W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2016-09-01

A nuclear hybrid system uses a nuclear reactor as the basic power generation unit. The power generated by the nuclear reactor is utilized by one or more power customers as either thermal power, electrical power, or both. In general, a nuclear hybrid system will couple the nuclear reactor to at least one thermal power user in addition to the power conversion system. The definition and architecture of a particular nuclear hybrid system is flexible depending on local markets needs and opportunities. For example, locations in need of potable water may be best served by coupling a desalination plant to the nuclear system. Similarly, an area near oil refineries may have a need for emission-free hydrogen production. A nuclear hybrid system expands the nuclear power plant from its more familiar central power station role by diversifying its immediately and directly connected customer base. The definition, design, analysis, and optimization work currently performed with respect to the nuclear hybrid systems represents the work of three national laboratories. Idaho National Laboratory (INL) is the lead lab working with Argonne National Laboratory (ANL) and Oak Ridge National Laboratory. Each laboratory is providing modeling and simulation expertise for the integration of the hybrid system.

Complete modeling and software implementation of a virtual solar hydrogen hybrid system

International Nuclear Information System (INIS)

Pedrazzi, S.; Zini, G.; Tartarini, P.

2010-01-01

A complete mathematical model and software implementation of a solar hydrogen hybrid system has been developed and applied to real data. The mathematical model has been derived from sub-models taken from literature with appropriate modifications and improvements. The model has been implemented as a stand-alone virtual energy system in a model-based, multi-domain software environment. A test run has then been performed on typical residential user data-sets over a year-long period. Results show that the virtual hybrid system can bring about complete grid independence; in particular, hydrogen production balance is positive (+1.25 kg) after a year's operation with a system efficiency of 7%.

Deep Belief Network Based Hybrid Model for Building Energy Consumption Prediction

Directory of Open Access Journals (Sweden)

Chengdong Li

2018-01-01

Full Text Available To enhance the prediction performance for building energy consumption, this paper presents a modified deep belief network (DBN based hybrid model. The proposed hybrid model combines the outputs from the DBN model with the energy-consuming pattern to yield the final prediction results. The energy-consuming pattern in this study represents the periodicity property of building energy consumption and can be extracted from the observed historical energy consumption data. The residual data generated by removing the energy-consuming pattern from the original data are utilized to train the modified DBN model. The training of the modified DBN includes two steps, the first one of which adopts the contrastive divergence (CD algorithm to optimize the hidden parameters in a pre-train way, while the second one determines the output weighting vector by the least squares method. The proposed hybrid model is applied to two kinds of building energy consumption data sets that have different energy-consuming patterns (daily-periodicity and weekly-periodicity. In order to examine the advantages of the proposed model, four popular artificial intelligence methods—the backward propagation neural network (BPNN, the generalized radial basis function neural network (GRBFNN, the extreme learning machine (ELM, and the support vector regressor (SVR are chosen as the comparative approaches. Experimental results demonstrate that the proposed DBN based hybrid model has the best performance compared with the comparative techniques. Another thing to be mentioned is that all the predictors constructed by utilizing the energy-consuming patterns perform better than those designed only by the original data. This verifies the usefulness of the incorporation of the energy-consuming patterns. The proposed approach can also be extended and applied to some other similar prediction problems that have periodicity patterns, e.g., the traffic flow forecasting and the electricity consumption

Imaging performance of a hybrid x-ray computed tomography-fluorescence molecular tomography system using priors.

Science.gov (United States)

Ale, Angelique; Schulz, Ralf B; Sarantopoulos, Athanasios; Ntziachristos, Vasilis

2010-05-01

The performance is studied of two newly introduced and previously suggested methods that incorporate priors into inversion schemes associated with data from a recently developed hybrid x-ray computed tomography and fluorescence molecular tomography system, the latter based on CCD camera photon detection. The unique data set studied attains accurately registered data of high spatially sampled photon fields propagating through tissue along 360 degrees projections. Approaches that incorporate structural prior information were included in the inverse problem by adding a penalty term to the minimization function utilized for image reconstructions. Results were compared as to their performance with simulated and experimental data from a lung inflammation animal model and against the inversions achieved when not using priors. The importance of using priors over stand-alone inversions is also showcased with high spatial sampling simulated and experimental data. The approach of optimal performance in resolving fluorescent biodistribution in small animals is also discussed. Inclusion of prior information from x-ray CT data in the reconstruction of the fluorescence biodistribution leads to improved agreement between the reconstruction and validation images for both simulated and experimental data.

Simulation-optimization framework for multi-site multi-season hybrid stochastic streamflow modeling

Science.gov (United States)

Srivastav, Roshan; Srinivasan, K.; Sudheer, K. P.

2016-11-01

A simulation-optimization (S-O) framework is developed for the hybrid stochastic modeling of multi-site multi-season streamflows. The multi-objective optimization model formulated is the driver and the multi-site, multi-season hybrid matched block bootstrap model (MHMABB) is the simulation engine within this framework. The multi-site multi-season simulation model is the extension of the existing single-site multi-season simulation model. A robust and efficient evolutionary search based technique, namely, non-dominated sorting based genetic algorithm (NSGA - II) is employed as the solution technique for the multi-objective optimization within the S-O framework. The objective functions employed are related to the preservation of the multi-site critical deficit run sum and the constraints introduced are concerned with the hybrid model parameter space, and the preservation of certain statistics (such as inter-annual dependence and/or skewness of aggregated annual flows). The efficacy of the proposed S-O framework is brought out through a case example from the Colorado River basin. The proposed multi-site multi-season model AMHMABB (whose parameters are obtained from the proposed S-O framework) preserves the temporal as well as the spatial statistics of the historical flows. Also, the other multi-site deficit run characteristics namely, the number of runs, the maximum run length, the mean run sum and the mean run length are well preserved by the AMHMABB model. Overall, the proposed AMHMABB model is able to show better streamflow modeling performance when compared with the simulation based SMHMABB model, plausibly due to the significant role played by: (i) the objective functions related to the preservation of multi-site critical deficit run sum; (ii) the huge hybrid model parameter space available for the evolutionary search and (iii) the constraint on the preservation of the inter-annual dependence. Split-sample validation results indicate that the AMHMABB model is

Molecular Evidence for Natural Hybridization between Cotoneaster dielsianus and C. glaucophyllus

Directory of Open Access Journals (Sweden)

Mingwan Li

2017-05-01

Full Text Available Hybridization accompanied by polyploidization and apomixis has been demonstrated as a driving force in the evolution and speciation of many plants. A good example to study the evolutionary process of hybridization associated with polyploidy and apomixis is the genus Cotoneaster (Rosaceae, which includes approximately 150 species, most of which are polyploid apomicts. In this study, we investigated all Cotoneaster taxa distributed in a small region of Malipo, Yunnan, China. Based on the morphological characteristics, four Cotoneaster taxa were identified and sampled: C. dielsianus, C. glaucophyllus, C. franchetii, and a putative hybrid. Flow cytometry analyses showed that C. glaucophyllus was diploid, while the other three taxa were tetraploid. A total of five low-copy nuclear genes and six chloroplast regions were sequenced to validate the status of the putative hybrid. Sequence analyses showed that C. dielsianus and C. glaucophyllus are distantly related and they could be well separated using totally 50 fixed nucleotide substitutions and four fixed indels at the 11 investigated genes. All individuals of the putative hybrid harbored identical sequences: they showed chromatogram additivity for all fixed differences between C. dielsianus and C. glaucophyllus at the five nuclear genes, and were identical with C. glaucophyllus at the six chloroplast regions. Haplotype analysis revealed that C. dielsianus possessed nine haplotypes for the 11 genes, while C. glaucophyllus had ten, and there were no shared haplotypes between the two species. The putative hybrid harbored two haplotypes for each nuclear gene: one shared with C. dielsianus and the other with C. glaucophyllus. They possessed the same chloroplast haplotype with C. glaucophyllus. Our study provided convincing evidence for natural hybridization between C. dielsianus and C. glaucophyllus, and revealed that all hybrid individuals were derivatives of one initial F1 via apomixes. C. glaucophyllus

HYBRIDIZATION AND MOLECULAR GEOMETRY: A NUMBER GAME

African Journals Online (AJOL)

Temechegn

This article is not emphasizing the theory behind the hybridization, but only on how to ... The new orbitals have the same total electron capacity .... the quantum mechanics and from a theory of paramagnetic susceptibility to the structure.

Multilevel Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2016-01-06

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks, among many others. In this work [6] we present a novel multilevel algorithm for the Chernoff-based hybrid tauleap algorithm. This variance reduction technique allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

Multilevel Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2015-01-07

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks, among many others. In this work [6] we present a novel multilevel algorithm for the Chernoff-based hybrid tauleap algorithm. This variance reduction technique allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

Multilevel Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2014-01-06

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks, among many others. In this work [6] we present a novel multilevel algorithm for the Chernoff-based hybrid tauleap algorithm. This variance reduction technique allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models

DEFF Research Database (Denmark)

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob

2018-01-01

embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdWTS) scheme aimed......Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable...... at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdWTSexpression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We...

Hybrid time/frequency domain modeling of nonlinear components

DEFF Research Database (Denmark)

Wiechowski, Wojciech Tomasz; Lykkegaard, Jan; Bak, Claus Leth

2007-01-01

This paper presents a novel, three-phase hybrid time/frequency methodology for modelling of nonlinear components. The algorithm has been implemented in the DIgSILENT PowerFactory software using the DIgSILENT Programming Language (DPL), as a part of the work described in [1]. Modified HVDC benchmark...

Non-Poisson counting statistics of a hybrid G-M counter dead time model

International Nuclear Information System (INIS)

Lee, Sang Hoon; Jae, Moosung; Gardner, Robin P.

2007-01-01

The counting statistics of a G-M counter with a considerable dead time event rate deviates from Poisson statistics. Important characteristics such as observed counting rates as a function true counting rates, variances and interval distributions were analyzed for three dead time models, non-paralyzable, paralyzable and hybrid, with the help of GMSIM, a Monte Carlo dead time effect simulator. The simulation results showed good agreements with the models in observed counting rates and variances. It was found through GMSIM simulations that the interval distribution for the hybrid model showed three distinctive regions, a complete cutoff region for the duration of the total dead time, a degraded exponential and an enhanced exponential regions. By measuring the cutoff and the duration of degraded exponential from the pulse interval distribution, it is possible to evaluate the two dead times in the hybrid model

Coupled thermal model of photovoltaic-thermoelectric hybrid panel for sample cities in Europe

DEFF Research Database (Denmark)

Rezaniakolaei, Alireza; Sera, Dezso; Rosendahl, Lasse Aistrup

2016-01-01

of the hybrid system under different weather conditions. The model takes into account solar irradiation, wind speed and ambient temperature as well as convective and radiated heat losses from the front and rear surfaces of the panel. The model is developed for three sample cities in Europe with different......In general, modeling of photovoltaic-thermoelectric (PV/TEG) hybrid panels have been mostly simplified and disconnected from the actual ambient conditions and thermal losses from the panel. In this study, a thermally coupled model of PV/TEG panel is established to precisely predict performance...... weather conditions. The results show that radiated heat loss from the front surface and the convective heat loss due to the wind speed are the most critical parameters on performance of the hybrid panel performance. The results also indicate that, with existing thermoelectric materials, the power...

Obtaining interspecific hybrids, and molecular analysis by microsatellite markers in grapevine

Directory of Open Access Journals (Sweden)

Mariane Ruzza Schuck

2011-11-01

Full Text Available The objective of this work was to assess the potential of interspecific hybridization of Vitis labruscana and Muscadinia rotundifolia by using artificial cross-pollinations. Microsatellite markers were used to confirm interspecific hybridizations and the identity of the parental genotypes. In crosses in which M. rotundifolia was used as the female parent, no true hybrids were obtained. In the reciprocal crosses, 114 seedlings were identified as true V. labruscana x M. rotundifolia hybrids. Self pollination occurred in direct and in reciprocal crosses. The crossings between 'Bordo' x 'Carlos', 'Magnolia', 'Regale' and' Roanoke', and between' Isabel' x 'Bountiful', 'Carlos', 'Magnolia', 'Regale' and 'Roanoke' were confirmed. The 15 markers evaluated showed that two M. rotundifolia parental genotypes had the same fingerprint profile, indicating a like lyplanting error. The success of hybridization depends mainly on the species and on the cultivar used as the female parent. Microsatellite markers are efficient to confirm the paternity of interspecific F1 hybrids and to determine the correct identity of M. rotundifolia cultivars.

Bayesian inference for hybrid discrete-continuous stochastic kinetic models

International Nuclear Information System (INIS)

Sherlock, Chris; Golightly, Andrew; Gillespie, Colin S

2014-01-01

We consider the problem of efficiently performing simulation and inference for stochastic kinetic models. Whilst it is possible to work directly with the resulting Markov jump process (MJP), computational cost can be prohibitive for networks of realistic size and complexity. In this paper, we consider an inference scheme based on a novel hybrid simulator that classifies reactions as either ‘fast’ or ‘slow’ with fast reactions evolving as a continuous Markov process whilst the remaining slow reaction occurrences are modelled through a MJP with time-dependent hazards. A linear noise approximation (LNA) of fast reaction dynamics is employed and slow reaction events are captured by exploiting the ability to solve the stochastic differential equation driving the LNA. This simulation procedure is used as a proposal mechanism inside a particle MCMC scheme, thus allowing Bayesian inference for the model parameters. We apply the scheme to a simple application and compare the output with an existing hybrid approach and also a scheme for performing inference for the underlying discrete stochastic model. (paper)

Performance Modeling of Hybrid MPI/OpenMP Scientific Applications on Large-scale Multicore Cluster Systems

KAUST Repository

Wu, Xingfu; Taylor, Valerie

2011-01-01

In this paper, we present a performance modeling framework based on memory bandwidth contention time and a parameterized communication model to predict the performance of OpenMP, MPI and hybrid applications with weak scaling on three large-scale multicore clusters: IBM POWER4, POWER5+ and Blue Gene/P, and analyze the performance of these MPI, OpenMP and hybrid applications. We use STREAM memory benchmarks to provide initial performance analysis and model validation of MPI and OpenMP applications on these multicore clusters because the measured sustained memory bandwidth can provide insight into the memory bandwidth that a system should sustain on scientific applications with the same amount of workload per core. In addition to using these benchmarks, we also use a weak-scaling hybrid MPI/OpenMP large-scale scientific application: Gyro kinetic Toroidal Code in magnetic fusion to validate our performance model of the hybrid application on these multicore clusters. The validation results for our performance modeling method show less than 7.77% error rate in predicting the performance of hybrid MPI/OpenMP GTC on up to 512 cores on these multicore clusters. © 2011 IEEE.

Performance Modeling of Hybrid MPI/OpenMP Scientific Applications on Large-scale Multicore Cluster Systems

KAUST Repository

Wu, Xingfu

2011-08-01

In this paper, we present a performance modeling framework based on memory bandwidth contention time and a parameterized communication model to predict the performance of OpenMP, MPI and hybrid applications with weak scaling on three large-scale multicore clusters: IBM POWER4, POWER5+ and Blue Gene/P, and analyze the performance of these MPI, OpenMP and hybrid applications. We use STREAM memory benchmarks to provide initial performance analysis and model validation of MPI and OpenMP applications on these multicore clusters because the measured sustained memory bandwidth can provide insight into the memory bandwidth that a system should sustain on scientific applications with the same amount of workload per core. In addition to using these benchmarks, we also use a weak-scaling hybrid MPI/OpenMP large-scale scientific application: Gyro kinetic Toroidal Code in magnetic fusion to validate our performance model of the hybrid application on these multicore clusters. The validation results for our performance modeling method show less than 7.77% error rate in predicting the performance of hybrid MPI/OpenMP GTC on up to 512 cores on these multicore clusters. © 2011 IEEE.

Investigation of multi-state charge-storage properties of redox-active organic molecules in silicon-molecular hybrid devices for DRAM and Flash applications

Science.gov (United States)

Gowda, Srivardhan Shivappa

Molecular electronics has recently spawned a considerable amount of interest with several molecules possessing charge-conduction and charge-storage properties proposed for use in electronic devices. Hybrid silicon-molecular technology has the promise of augmenting the current silicon technology and provide for a transitional path to future molecule-only technology. The focus of this dissertation work has been on developing a class of hybrid silicon-molecular electronic devices for DRAM and Flash memory applications utilizing redox-active molecules. This work exploits the ability of molecules to store charges with single-electron precision at room temperature. The hybrid devices are fabricated by forming self-assembled monolayers of redox-active molecules on Si and oxide (SiO2 and HfO2) surfaces via formation of covalent linkages. The molecules possess discrete quantum states from which electrons can tunnel to the Si substrate at discrete applied voltages (oxidation process, cell write), leaving behind a positively charged layer of molecules. The reduction (erase) process, which is the process of electrons tunneling back from Si to the molecules, neutralizes the positively charged molecular monolayer. Hybrid silicon-molecular capacitor test structures were electrically characterized with an electrolyte gate using cyclic voltammetry (CyV) and impedance spectroscopy (CV) techniques. The redox voltages, kinetics (write/erase speeds) and charge-retention characteristics were found to be strongly dependent on the Si doping type and densities, and ambient light. It was also determined that the redox energy states in the molecules communicate with the valence band of the Si substrate. This allows tuning of write and read states by modulating minority carriers in n- and p-Si substrates. Ultra-thin dielectric tunnel barriers (SiO2, HfO2) were placed between the molecules and the Si substrate to augment charge-retention for Flash memory applications. The redox response was

HYBRID WAYS OF DOING: A MODEL FOR TEACHING PUBLIC SPACE

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Gabrielle Bendiner-Viani

2010-07-01

Full Text Available This paper addresses an exploratory practice undertaken by the authors in a co-taught class to hybridize theory, research and practice. This experiment in critical transdisciplinary design education took the form of a “critical studio + practice-based seminar on public space”, two interlinked classes co-taught by landscape architect Elliott Maltby and environmental psychologist Gabrielle Bendiner-Viani at the Parsons, The New School for Design. This design process was grounded in the political and social context of the contested East River waterfront of New York City and valued both intensive study (using a range of social science and design methods and a partnership with a local community organization, engaging with the politics, issues and human needs of a complex site. The paper considers how we encouraged interdisciplinary collaboration and dialogue between teachers as well as between liberal arts and design students and developed strategies to overcome preconceived notions of traditional “studio” and “seminar” work. By exploring the challenges and adjustments made during the semester and the process of teaching this class, this paper addresses how we moved from a model of intertwining theory, research and practice, to a hybrid model of multiple ways of doing, a model particularly apt for teaching public space. Through examples developed for and during our course, the paper suggests practical ways of supporting this transdisciplinary hybrid model.

Hybrid Modeling Improves Health and Performance Monitoring

Science.gov (United States)

2007-01-01

Scientific Monitoring Inc. was awarded a Phase I Small Business Innovation Research (SBIR) project by NASA's Dryden Flight Research Center to create a new, simplified health-monitoring approach for flight vehicles and flight equipment. The project developed a hybrid physical model concept that provided a structured approach to simplifying complex design models for use in health monitoring, allowing the output or performance of the equipment to be compared to what the design models predicted, so that deterioration or impending failure could be detected before there would be an impact on the equipment's operational capability. Based on the original modeling technology, Scientific Monitoring released I-Trend, a commercial health- and performance-monitoring software product named for its intelligent trending, diagnostics, and prognostics capabilities, as part of the company's complete ICEMS (Intelligent Condition-based Equipment Management System) suite of monitoring and advanced alerting software. I-Trend uses the hybrid physical model to better characterize the nature of health or performance alarms that result in "no fault found" false alarms. Additionally, the use of physical principles helps I-Trend identify problems sooner. I-Trend technology is currently in use in several commercial aviation programs, and the U.S. Air Force recently tapped Scientific Monitoring to develop next-generation engine health-management software for monitoring its fleet of jet engines. Scientific Monitoring has continued the original NASA work, this time under a Phase III SBIR contract with a joint NASA-Pratt & Whitney aviation security program on propulsion-controlled aircraft under missile-damaged aircraft conditions.

The influence of nonlocal hybridization on ground-state properties of the Falicov-Kimball model

International Nuclear Information System (INIS)

Farkasovsky, Pavol

2005-01-01

The density matrix renormalization group is used to examine effects of nonlocal hybridization on ground-state properties of the Falicov-Kimball model (FKM) in one dimension. Special attention is devoted to the problem of hybridization-induced insulator-metal transition. It is shown that the picture of insulator-metal transitions found for the FKM with nonlocal hybridization strongly differs from one found for the FKM without hybridization (as well as with local hybridization). The effect of nonlocal hybridization is so strong that it can induce the insulator-metal transition, even in the half-filled band case where the ground states of the FKM without hybridization are insulating for all finite Coulomb interactions. Outside the half-filled band case the metal-insulator transition driven by pressure is found for finite values of nonlocal hybridization

Electrochemical sensor for catechol and dopamine based on a catalytic molecularly imprinted polymer-conducting polymer hybrid recognition element.

Science.gov (United States)

Lakshmi, Dhana; Bossi, Alessandra; Whitcombe, Michael J; Chianella, Iva; Fowler, Steven A; Subrahmanyam, Sreenath; Piletska, Elena V; Piletsky, Sergey A

2009-05-01

One of the difficulties with using molecularly imprinted polymers (MIPs) and other electrically insulating materials as the recognition element in electrochemical sensors is the lack of a direct path for the conduction of electrons from the active sites to the electrode. We have sought to address this problem through the preparation and characterization of novel hybrid materials combining a catalytic MIP, capable of oxidizing the template, catechol, with an electrically conducting polymer. In this way a network of "molecular wires" assists in the conduction of electrons from the active sites within the MIP to the electrode surface. This was made possible by the design of a new monomer that combines orthogonal polymerizable functionality; comprising an aniline group and a methacrylamide. Conducting films were prepared on the surface of electrodes (Au on glass) by electropolymerization of the aniline moiety. A layer of MIP was photochemically grafted over the polyaniline, via N,N'-diethyldithiocarbamic acid benzyl ester (iniferter) activation of the methacrylamide groups. Detection of catechol by the hybrid-MIP sensor was found to be specific, and catechol oxidation was detected by cyclic voltammetry at the optimized operating conditions: potential range -0.6 V to +0.8 V (vs Ag/AgCl), scan rate 50 mV/s, PBS pH 7.4. The calibration curve for catechol was found to be linear to 144 microM, with a limit of detection of 228 nM. Catechol and dopamine were detected by the sensor, whereas analogues and potentially interfering compounds, including phenol, resorcinol, hydroquinone, serotonin, and ascorbic acid, had minimal effect (< or = 3%) on the detection of either analyte. Non-imprinted hybrid electrodes and bare gold electrodes failed to give any response to catechol at concentrations below 0.5 mM. Finally, the catalytic properties of the sensor were characterized by chronoamperometry and were found to be consistent with Michaelis-Menten kinetics.

An Advanced Environment for Hybrid Modeling of Biological Systems Based on Modelica

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Proß Sabrina

2011-03-01

Full Text Available Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. Hybrid Petri Nets, consisting of time-discrete Petri Net elements as well as continuous ones, have proven to be ideal for this task. Therefore, a new Petri Net library was implemented based on the object-oriented modeling language Modelica which allows the modeling of discrete, stochastic and continuous Petri Net elements by differential, algebraic and discrete equations. An appropriate Modelica-tool performs the hybrid simulation with discrete events and the solution of continuous differential equations. A special sub-library contains so-called wrappers for specific reactions to simplify the modeling process.

Using whole mount in situ hybridization to link molecular and organismal biology.

Science.gov (United States)

Jacobs, Nicole L; Albertson, R Craig; Wiles, Jason R

2011-03-31

Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the embryology and gross anatomy of several organisms representing various chordate taxa primarily via traditional dissections and the use of models. The final portion of the course involved an innovative approach to teaching anatomy through observation of vertebrate development employing molecular techniques in which WISH was performed on zebrafish embryos. A heterozygous fibroblast growth factor 8 a (fgf8a) mutant line, ace, was used. Due to Mendelian inheritance, ace intercrosses produced wild type, heterozygous, and homozygous ace/fgf8a mutants in a 1:2:1 ratio. RNA probes with known expression patterns in the midline and in developing anatomical structures such as the heart, somites, tailbud, myotome, and brain were used. WISH was performed using zebrafish at the 13 somite and prim-6 stages, with students performing the staining reaction in class. The study of zebrafish embryos at different stages of development gave students the ability to observe how these anatomical structures changed over ontogeny. In addition, some ace/fgf8a mutants displayed improper heart looping, and defects in somite and brain development. The students in this lab observed the normal development of various organ systems using both external anatomy as well as gene expression patterns. They also identified and described embryos displaying improper anatomical development and gene expression (i.e., putative mutants). For instructors at institutions that do not already own the necessary equipment or where

Thermal modeling of a hydraulic hybrid vehicle transmission based on thermodynamic analysis

International Nuclear Information System (INIS)

Kwon, Hyukjoon; Sprengel, Michael; Ivantysynova, Monika

2016-01-01

Hybrid vehicles have become a popular alternative to conventional powertrain architectures by offering improved fuel efficiency along with a range of environmental benefits. Hydraulic Hybrid Vehicles (HHV) offer one approach to hybridization with many benefits over competing technologies. Among these benefits are lower component costs, more environmentally friendly construction materials, and the ability to recover a greater quantity of energy during regenerative braking which make HHVs partially well suited to urban environments. In order to further the knowledge base regarding HHVs, this paper explores the thermodynamic characteristics of such a system. A system model is detailed for both the hydraulic and thermal components of a closed circuit hydraulic hybrid transmission following the FTP-72 driving cycle. Among the new techniques proposed in this paper is a novel method for capturing rapid thermal transients. This paper concludes by comparing the results of this model with experimental data gathered on a Hardware-in-the-Loop (HIL) transmission dynamometer possessing the same architecture, components, and driving cycle used within the simulation model. This approach can be used for several applications such as thermal stability analysis of HHVs, optimal thermal management, and analysis of the system's thermodynamic efficiency. - Highlights: • Thermal modeling for HHVs is introduced. • A model for the hydraulic and thermal system is developed for HHVs. • A novel method for capturing rapid thermal transients is proposed. • The thermodynamic system diagram of a series HHV is predicted.

Hybrid Scheme for Modeling Local Field Potentials from Point-Neuron Networks.

Science.gov (United States)

Hagen, Espen; Dahmen, David; Stavrinou, Maria L; Lindén, Henrik; Tetzlaff, Tom; van Albada, Sacha J; Grün, Sonja; Diesmann, Markus; Einevoll, Gaute T

2016-12-01

With rapidly advancing multi-electrode recording technology, the local field potential (LFP) has again become a popular measure of neuronal activity in both research and clinical applications. Proper understanding of the LFP requires detailed mathematical modeling incorporating the anatomical and electrophysiological features of neurons near the recording electrode, as well as synaptic inputs from the entire network. Here we propose a hybrid modeling scheme combining efficient point-neuron network models with biophysical principles underlying LFP generation by real neurons. The LFP predictions rely on populations of network-equivalent multicompartment neuron models with layer-specific synaptic connectivity, can be used with an arbitrary number of point-neuron network populations, and allows for a full separation of simulated network dynamics and LFPs. We apply the scheme to a full-scale cortical network model for a ∼1 mm 2 patch of primary visual cortex, predict laminar LFPs for different network states, assess the relative LFP contribution from different laminar populations, and investigate effects of input correlations and neuron density on the LFP. The generic nature of the hybrid scheme and its public implementation in hybridLFPy form the basis for LFP predictions from other and larger point-neuron network models, as well as extensions of the current application with additional biological detail. © The Author 2016. Published by Oxford University Press.

Model-based design approaches for plug-in hybrid vehicle design

Energy Technology Data Exchange (ETDEWEB)

Mendes, C.J. [CrossChasm Technologies, Cambridge, ON (Canada); Stevens, M.B.; Fowler, M.W. [Waterloo Univ., ON (Canada). Dept. of Chemical Engineering; Fraser, R.A. [Waterloo Univ., ON (Canada). Dept. of Mechanical Engineering; Wilhelm, E.J. [Paul Scherrer Inst., Villigen (Switzerland). Energy Systems Analysis

2007-07-01

A model-based design process for plug-in hybrid vehicles (PHEVs) was presented. The paper discussed steps between the initial design concept and a working vehicle prototype, and focused on an investigation of the software-in-the-loop (SIL), hardware-in-the-loop (HIL), and component-in-the-loop (CIL) design phases. The role and benefits of using simulation were also reviewed. A method for mapping and identifying components was provided along with a hybrid control strategy and component-level control optimization process. The role of simulation in component evaluation, architecture design, and de-bugging procedures was discussed, as well as the role simulation networks can play in speeding deployment times. The simulations focused on work performed on a 2005 Chevrolet Equinox converted to a fuel cell hybrid electric vehicle (FCHEV). Components were aggregated to create a complete virtual vehicle. A simplified vehicle model was implemented onto the on-board vehicle control hardware. Optimization metrics were estimated at 10 alpha values during each control loop iteration. The simulation was then used to tune the control system under a variety of drive cycles and conditions. A CIL technique was used to place a physical hybrid electric vehicle (HEV) component under the control of a real time HEV/PHEV simulation. It was concluded that controllers should have a standardized component description that supports integration into advanced testing procedures. 4 refs., 9 figs.

A photoactivated artificial muscle model unit: reversible, photoinduced sliding of nanosheets.

Science.gov (United States)

Nabetani, Yu; Takamura, Hazuki; Hayasaka, Yuika; Shimada, Tetsuya; Takagi, Shinsuke; Tachibana, Hiroshi; Masui, Dai; Tong, Zhiwei; Inoue, Haruo

2011-11-02

A novel photoactivated artificial muscle model unit is reported. Here we show that organic/inorganic hybrid nanosheets reversibly slide horizontally on a giant scale and the interlayer spaces in the layered hybrid structure shrink and expand vertically by photoirradiation. The sliding movement of the system on a giant scale is the first example of an artificial muscle model unit having much similarity with that in natural muscle fibrils. In particular, our layered hybrid molecular system exhibits a macroscopic morphological change on a giant scale (~1500 nm) relative to the molecular size of ~1 nm by means of a reversible sliding mechanism.

Improving Hybrid III injury assessment in steering wheel rim to chest impacts using responses from finite element Hybrid III and human body model.

Science.gov (United States)

Holmqvist, Kristian; Davidsson, Johan; Mendoza-Vazquez, Manuel; Rundberget, Peter; Svensson, Mats Y; Thorn, Stefan; Törnvall, Fredrik

2014-01-01

The main aim of this study was to improve the quality of injury risk assessments in steering wheel rim to chest impacts when using the Hybrid III crash test dummy in frontal heavy goods vehicle (HGV) collision tests. Correction factors for chest injury criteria were calculated as the model chest injury parameter ratios between finite element (FE) Hybrid III, evaluated in relevant load cases, and the Total Human Model for Safety (THUMS). This is proposed to be used to compensate Hybrid III measurements in crash tests where steering wheel rim to chest impacts occur. The study was conducted in an FE environment using an FE-Hybrid III model and the THUMS. Two impactor shapes were used, a circular hub and a long, thin horizontal bar. Chest impacts at velocities ranging from 3.0 to 6.0 m/s were simulated at 3 impact height levels. A ratio between FE-Hybrid III and THUMS chest injury parameters, maximum chest compression C max, and maximum viscous criterion VC max, were calculated for the different chest impact conditions to form a set of correction factors. The definition of the correction factor is based on the assumption that the response from a circular hub impact to the middle of the chest is well characterized and that injury risk measures are independent of impact height. The current limits for these chest injury criteria were used as a basis to develop correction factors that compensate for the limitations in biofidelity of the Hybrid III in steering wheel rim to chest impacts. The hub and bar impactors produced considerably higher C max and VC max responses in the THUMS compared to the FE-Hybrid III. The correction factor for the responses of the FE-Hybrid III showed that the criteria responses for the bar impactor were consistently overestimated. Ratios based on Hybrid III and THUMS responses provided correction factors for the Hybrid III responses ranging from 0.84 to 0.93. These factors can be used to estimate C max and VC max values when the Hybrid III is

Hybrid Neuro-Fuzzy Classifier Based On Nefclass Model

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Bogdan Gliwa

2011-01-01

Full Text Available The paper presents hybrid neuro-fuzzy classifier, based on NEFCLASS model, which wasmodified. The presented classifier was compared to popular classifiers – neural networks andk-nearest neighbours. Efficiency of modifications in classifier was compared with methodsused in original model NEFCLASS (learning methods. Accuracy of classifier was testedusing 3 datasets from UCI Machine Learning Repository: iris, wine and breast cancer wisconsin.Moreover, influence of ensemble classification methods on classification accuracy waspresented.

Modeling of renewable hybrid energy sources

Directory of Open Access Journals (Sweden)

Dumitru Cristian Dragos

2009-12-01

Full Text Available Recent developments and trends in the electric power consumption indicate an increasing use of renewable energy. Renewable energy technologies offer the promise of clean, abundant energy gathered from self-renewing resources such as the sun, wind, earth and plants. Virtually all regions of the world have renewable resources of one type or another. By this point of view studies on renewable energies focuses more and more attention. The present paper intends to present different mathematical models related to different types of renewable energy sources such as: solar energy and wind energy. It is also presented the validation and adaptation of such models to hybrid systems working in geographical and meteorological conditions specific to central part of Transylvania region. The conclusions based on validation of such models are also shown.

A hybrid model for the computationally-efficient simulation of the cerebellar granular layer

Directory of Open Access Journals (Sweden)

Anna eCattani

2016-04-01

Full Text Available The aim of the present paper is to efficiently describe the membrane potential dynamics of neural populations formed by species having a high density difference in specific brain areas. We propose a hybrid model whose main ingredients are a conductance-based model (ODE system and its continuous counterpart (PDE system obtained through a limit process in which the number of neurons confined in a bounded region of the brain tissue is sent to infinity. Specifically, in the discrete model, each cell is described by a set of time-dependent variables, whereas in the continuum model, cells are grouped into populations that are described by a set of continuous variables.Communications between populations, which translate into interactions among the discrete and the continuous models, are the essence of the hybrid model we present here. The cerebellum and cerebellum-like structures show in their granular layer a large difference in the relative density of neuronal species making them a natural testing ground for our hybrid model. By reconstructing the ensemble activity of the cerebellar granular layer network and by comparing our results to a more realistic computational network, we demonstrate that our description of the network activity, even though it is not biophysically detailed, is still capable of reproducing salient features of neural network dynamics. Our modeling approach yields a significant computational cost reduction by increasing the simulation speed at least $270$ times. The hybrid model reproduces interesting dynamics such as local microcircuit synchronization, traveling waves, center-surround and time-windowing.

Hybrid Computational Model for High-Altitude Aeroassist Vehicles, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — A hybrid continuum/noncontinuum computational model will be developed for analyzing the aerodynamics and heating on aeroassist vehicles. Unique features of this...

A Hybrid Model for Forecasting Sales in Turkish Paint Industry

Directory of Open Access Journals (Sweden)

Alp Ustundag

2009-12-01

Full Text Available Sales forecasting is important for facilitating effective and efficient allocation of scarce resources. However, how to best model and forecast sales has been a long-standing issue. There is no best forecasting method that is applicable in all circumstances. Therefore, confidence in the accuracy of sales forecasts is achieved by corroborating the results using two or more methods. This paper proposes a hybrid forecasting model that uses an artificial intelligence method (AI with multiple linear regression (MLR to predict product sales for the largest Turkish paint producer. In the hybrid model, three different AI methods, fuzzy rule-based system (FRBS, artificial neural network (ANN and adaptive neuro fuzzy network (ANFIS, are used and compared to each other. The results indicate that FRBS yields better forecasting accuracy in terms of root mean squared error (RMSE and mean absolute percentage error (MAPE.

Optimization of ultrasonic array inspections using an efficient hybrid model and real crack shapes

Energy Technology Data Exchange (ETDEWEB)

Felice, Maria V., E-mail: maria.felice@bristol.ac.uk [Department of Mechanical Engineering, University of Bristol, Bristol, U.K. and NDE Laboratory, Rolls-Royce plc., Bristol (United Kingdom); Velichko, Alexander, E-mail: p.wilcox@bristol.ac.uk; Wilcox, Paul D., E-mail: p.wilcox@bristol.ac.uk [Department of Mechanical Engineering, University of Bristol, Bristol (United Kingdom); Barden, Tim; Dunhill, Tony [NDE Laboratory, Rolls-Royce plc., Bristol (United Kingdom)

2015-03-31

Models which simulate the interaction of ultrasound with cracks can be used to optimize ultrasonic array inspections, but this approach can be time-consuming. To overcome this issue an efficient hybrid model is implemented which includes a finite element method that requires only a single layer of elements around the crack shape. Scattering Matrices are used to capture the scattering behavior of the individual cracks and a discussion on the angular degrees of freedom of elastodynamic scatterers is included. Real crack shapes are obtained from X-ray Computed Tomography images of cracked parts and these shapes are inputted into the hybrid model. The effect of using real crack shapes instead of straight notch shapes is demonstrated. An array optimization methodology which incorporates the hybrid model, an approximate single-scattering relative noise model and the real crack shapes is then described.

[Molecular classification of breast cancer patients obtained through the technique of chromogenic in situ hybridization (CISH)].

Science.gov (United States)

Fernández, Angel; Reigosa, Aldo

2013-12-01

Breast cancer is a heterogeneous disease composed of a growing number of biological subtypes, with substantial variability of the disease progression within each category. The aim of this research was to classify the samples object of study according to the molecular classes of breast cancer: luminal A, luminal B, HER2 and triple negative, as a result of the state of HER2 amplification obtained by the technique of chromogenic in situ hybridization (CISH). The sample consisted of 200 biopsies fixed in 10% formalin, processed by standard techniques up to paraffin embedding, corresponding to patients diagnosed with invasive ductal carcinoma of the breast. These biopsies were obtained from patients from private practice and the Institute of Oncology "Dr. Miguel Pérez Carreño", for immunohistochemistry (IHC) of hormone receptors and HER2 made in the Hospital Metropolitano del Norte, Valencia, Venezuela. The molecular classification of the patient's tumors considering the expression of estrogen and progesterone receptors by IHC and HER2 amplification by CISH, allowed those cases originally classified as unknown, since they had an indeterminate (2+) outcome for HER2 expression by IHC, to be grouped into the different molecular classes. Also, this classification permitted that some cases, initially considered as belonging to a molecular class, were assigned to another class, after the revaluation of the HER2 status by CISH.

Model for optimum design of standalone hybrid renewable energy ...

African Journals Online (AJOL)

An optimization model for the design of a hybrid renewable energy microgrid ... and increasing the rated power of the wind energy conversion system (WECS) or solar ... a 70% reduction in gas emissions and an 80% reduction in energy costs.

Modeling and performance analysis of a concentrated photovoltaic–thermoelectric hybrid power generation system

International Nuclear Information System (INIS)

Lamba, Ravita; Kaushik, S.C.

2016-01-01

Highlights: • Thermodynamic model of concentrated photovoltaic–thermoelectric system is analysed. • Thomson effect reduces the power output of PV, TE and hybrid PV–TEG system. • Effect of thermocouple number, irradiance, PV and TE current have been studied. • The optimum concentration ratio for maximum power output has been found out. • The overall efficiency and power output of hybrid PV–TEG system has been improved. - Abstract: In this study, a thermodynamic model for analysing the performance of a concentrated photovoltaic–thermoelectric generator (CPV–TEG) hybrid system including Thomson effect in conjunction with Seebeck, Joule and Fourier heat conduction effects has been developed and simulated in MATALB environment. The expressions for calculating the temperature of photovoltaic (PV) module, hot and cold sides of thermoelectric (TE) module are derived analytically as well. The effect of concentration ratio, number of thermocouples in TE module, solar irradiance, PV module current and TE module current on power output and efficiency of the PV, TEG and hybrid PV–TEG system have been studied. The optimum concentration ratio corresponding to maximum power output of the hybrid system has been found out. It has been observed that by considering Thomson effect in TEG module, the power output of the PV, TE and hybrid PV–TEG systems decreases and at C = 1 and 5, it reduces the power output of hybrid system by 0.7% and 4.78% respectively. The results of this study may provide basis for performance optimization of a practical irreversible CPV–TEG hybrid system.

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

Science.gov (United States)

Munir, Ahsan; Waseem, Hassan; Williams, Maggie R.; Stedtfeld, Robert D.; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A.

2017-01-01

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131). PMID:28555058

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

Directory of Open Access Journals (Sweden)

Ahsan Munir

2017-05-01

Full Text Available Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs. Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131.

Driving-behavior-aware stochastic model predictive control for plug-in hybrid electric buses

International Nuclear Information System (INIS)

Li, Liang; You, Sixiong; Yang, Chao; Yan, Bingjie; Song, Jian; Chen, Zheng

2016-01-01

Highlights: • The novel approximated global optimal energy management strategy has been proposed for hybrid powertrains. • Eight typical driving behaviors have been classified with K-means to deal with the multiplicative traffic conditions. • The stochastic driver models of different driving behaviors were established based on the Markov chains. • ECMS was used to modify the SMPC-based energy management strategy to improve its fuel economy. • The approximated global optimal energy management strategy for plug-in hybrid electric buses has been verified and analyzed. - Abstract: Driving cycles of a city bus is statistically characterized by some repetitive features, which makes the predictive energy management strategy very desirable to obtain approximate optimal fuel economy of a plug-in hybrid electric bus. But dealing with the complicated traffic conditions and finding an approximated global optimal strategy which is applicable to the plug-in hybrid electric bus still remains a challenging technique. To solve this problem, a novel driving-behavior-aware modified stochastic model predictive control method is proposed for the plug-in hybrid electric bus. Firstly, the K-means is employed to classify driving behaviors, and the driver models based on Markov chains is obtained under different kinds of driving behaviors. While the obtained driver behaviors are regarded as stochastic disturbance inputs, the local minimum fuel consumption might be obtained with a traditional stochastic model predictive control at each step, taking tracking the reference battery state of charge trajectory into consideration in the finite predictive horizons. However, this technique is still accompanied by some working points with reduced/worsened fuel economy. Thus, the stochastic model predictive control is modified with the equivalent consumption minimization strategy to eliminate these undesirable working points. The results in real-world city bus routines show that the

Hybrid artificial bee colony algorithm for parameter optimization of five-parameter bidirectional reflectance distribution function model.

Science.gov (United States)

Wang, Qianqian; Zhao, Jing; Gong, Yong; Hao, Qun; Peng, Zhong

2017-11-20

A hybrid artificial bee colony (ABC) algorithm inspired by the best-so-far solution and bacterial chemotaxis was introduced to optimize the parameters of the five-parameter bidirectional reflectance distribution function (BRDF) model. To verify the performance of the hybrid ABC algorithm, we measured BRDF of three kinds of samples and simulated the undetermined parameters of the five-parameter BRDF model using the hybrid ABC algorithm and the genetic algorithm, respectively. The experimental results demonstrate that the hybrid ABC algorithm outperforms the genetic algorithm in convergence speed, accuracy, and time efficiency under the same conditions.

Viscoelastic and fractal characteristics of a supramolecular hydrogel hybridized with clay nanoparticles.

Science.gov (United States)

Song, Fei; Zhang, Li-Ming; Shi, Jun-Feng; Li, Nan-Nan

2010-12-01

The supramolecular hydrogels derived from low-molecular-mass gelators represent a unique class of soft matters and have important potential applications in biomedical fields, separation technology and cosmetic science. However, they suffer usually from weak mechanical and viscoelastic properties. In this work, we carry out the in situ hybridization of clay nanoparticles (Laponite RD) into the supramolecular hydrogel formed from a low-molecular-mass hydrogelator, 2,6-di[N-(carboxyethyl carbonyl)amino]pyridine (DAP), and investigate the viscoelastic and structural characteristics of resultant hybrid hydrogel. It was found that a small concentration of Laponite RD could lead to a significant increase in the storage modulus, loss modulus or complex viscosity. Compared with neat DAP hydrogel, the hybrid hydrogel has a greater hydrogel strength and a lower relaxation exponent. In particular, the enhancement of the clay nanoparticles to the viscoelastic properties of the DAP hydrogel is more effective in the case of higher DAP concentration. By relating its macroscopic elastic properties to a scaling fractal model, such a hybrid hydrogel was confirmed to be in the strong-link regime and to have a more complex network structure with a higher fractal dimension when compared with neat DAP hydrogel. Copyright © 2010 Elsevier B.V. All rights reserved.

Report: Optimization study of the preparation factors for argan oil microcapsule based on hybrid-level orthogonal array design via SPSS modeling.

Science.gov (United States)

Zhao, Xi; Wu, Xiaoli; Zhou, Hui; Jiang, Tao; Chen, Chun; Liu, Mingshi; Jin, Yuanbao; Yang, Dongsheng

2014-11-01

To optimize the preparation factors for argan oil microcapsule using complex coacervation of chitosan cross-linked with gelatin based on hybrid-level orthogonal array design via SPSS modeling. Eight relatively significant factors were firstly investigated and selected as calculative factors for the orthogonal array design from the total of ten factors effecting the preparation of argan oil microcapsule by utilizing the single factor variable method. The modeling of hybrid-level orthogonal array design was built in these eight factors with the relevant levels (9, 9, 9, 9, 7, 6, 2 and 2 respectively). The preparation factors for argan oil microcapsule were investigated and optimized according to the results of hybrid-level orthogonal array design. The priorities order and relevant optimum levels of preparation factors standard to base on the percentage of microcapsule with the diameter of 30~40 μm via SPSS. Experimental data showed that the optimum factors were controlling the chitosan/gelatin ratio, the systemic concentration and the core/shell ratio at 1:2, 1.5% and 1:7 respectively, presetting complex coacervation pH at 6.4, setting cross-linking time and complex coacervation at 75 min and 30 min, using the glucose-delta lactone as the type of cross-linking agent, and selecting chitosan with the molecular weight of 2000～3000.

A hybrid discrete-continuum mathematical model of pattern prediction in the developing retinal vasculature.

Science.gov (United States)

McDougall, S R; Watson, M G; Devlin, A H; Mitchell, C A; Chaplain, M A J

2012-10-01

Pathological angiogenesis has been extensively explored by the mathematical modelling community over the past few decades, specifically in the contexts of tumour-induced vascularisation and wound healing. However, there have been relatively few attempts to model angiogenesis associated with normal development, despite the availability of animal models with experimentally accessible and highly ordered vascular topologies: for example, growth and development of the vascular plexus layers in the murine retina. The current study aims to address this issue through the development of a hybrid discrete-continuum mathematical model of the developing retinal vasculature in neonatal mice that is closely coupled with an ongoing experimental programme. The model of the functional vasculature is informed by a range of morphological and molecular data obtained over a period of several days, from 6 days prior to birth to approximately 8 days after birth. The spatio-temporal formation of the superficial retinal vascular plexus (RVP) in wild-type mice occurs in a well-defined sequence. Prior to birth, astrocytes migrate from the optic nerve over the surface of the inner retina in response to a chemotactic gradient of PDGF-A, formed at an earlier stage by migrating retinal ganglion cells (RGCs). Astrocytes express a variety of chemotactic and haptotactic proteins, including VEGF and fibronectin (respectively), which subsequently induce endothelial cell sprouting and modulate growth of the RVP. The developing RVP is not an inert structure; however, the vascular bed adapts and remodels in response to a wide variety of metabolic and biomolecular stimuli. The main focus of this investigation is to understand how these interacting cellular, molecular, and metabolic cues regulate RVP growth and formation. In an earlier one-dimensional continuum model of astrocyte and endothelial migration, we showed that the measured frontal velocities of the two cell types could be accurately reproduced

Breeding of lilies and tulips—Interspecific hybridization and genetic background—

Science.gov (United States)

Marasek-Ciolakowska, Agnieszka; Nishikawa, Tomotaro; Shea, Daniel J.; Okazaki, Keiichi

2018-01-01

Lilies and tulips (Liliaceae family) are economically very important ornamental bulbous plants. Here, we summarize major breeding goals, the role of an integrated method of cut-style pollination and fertilization followed by embryo rescue and mitotic and meiotic polyploidization involved in new assortment development. Both crops have been subjected to extensive interspecific hybridization followed by selection. Additionally, spontaneous polyploidization has played a role in their evolution. In lilies, there is a tendency to replace diploids with polyploid cultivars, whereas in tulip a majority of the cultivars that exist today are still diploid except for triploid Darwin hybrid tulips. The introduction of molecular cytogenetic techniques such as genomic in situ hybridization (GISH) permitted the detailed studies of genome composition in lily and tulip interspecific hybrids and to follow the chromosome inheritance in interspecific crosses. In addition, this review presents the latest information on phylogenetic relationship in lily and tulip and recent developments in molecular mapping using different DNA molecular techniques. PMID:29681746

From hybrid swarms to swarms of hybrids

Science.gov (United States)

Stohlgren, Thomas J.; Szalanski, Allen L; Gaskin, John F.; Young, Nicholas E.; West, Amanda; Jarnevich, Catherine S.; Tripodi, Amber

2014-01-01

Science has shown that the introgression or hybridization of modern humans (Homo sapiens) with Neanderthals up to 40,000 YBP may have led to the swarm of modern humans on earth. However, there is little doubt that modern trade and transportation in support of the humans has continued to introduce additional species, genotypes, and hybrids to every country on the globe. We assessed the utility of species distributions modeling of genotypes to assess the risk of current and future invaders. We evaluated 93 locations of the genus Tamarix for which genetic data were available. Maxent models of habitat suitability showed that the hybrid, T. ramosissima x T. chinensis, was slightly greater than the parent taxa (AUCs > 0.83). General linear models of Africanized honey bees, a hybrid cross of Tanzanian Apis mellifera scutellata and a variety of European honey bee including A. m. ligustica, showed that the Africanized bees (AUC = 0.81) may be displacing European honey bees (AUC > 0.76) over large areas of the southwestern U.S. More important, Maxent modeling of sub-populations (A1 and A26 mitotypes based on mDNA) could be accurately modeled (AUC > 0.9), and they responded differently to environmental drivers. This suggests that rapid evolutionary change may be underway in the Africanized bees, allowing the bees to spread into new areas and extending their total range. Protecting native species and ecosystems may benefit from risk maps of harmful invasive species, hybrids, and genotypes.

Hybrid modeling approach to improve the forecasting capability for the gaseous radionuclide in a nuclear site

International Nuclear Information System (INIS)

Jeong, Hyojoon; Hwang, Wontae; Kim, Eunhan; Han, Moonhee

2012-01-01

Highlights: ► This study is to improve the reliability of air dispersion modeling. ► Tracer experiments assumed gaseous radionuclides were conducted at a nuclear site. ► The performance of a hybrid modeling combined ISC with ANFIS was investigated.. ► Hybrid modeling approach shows better performance rather than a single ISC model. - Abstract: Predicted air concentrations of radioactive materials are important for an environmental impact assessment for the public health. In this study, the performance of a hybrid modeling combined with the industrial source complex (ISC) model and an adaptive neuro-fuzzy inference system (ANFIS) for predicting tracer concentrations was investigated. Tracer dispersion experiments were performed to produce the field data assuming the accidental release of radioactive material. ANFIS was trained in order that the outputs of the ISC model are similar to the measured data. Judging from the higher correlation coefficients between the measured and the calculated ones, the hybrid modeling approach could be an appropriate technique for an improvement of the modeling capability to predict the air concentrations for radioactive materials.

A Novel Hybrid Model for Drawing Trace Reconstruction from Multichannel Surface Electromyographic Activity.

Science.gov (United States)

Chen, Yumiao; Yang, Zhongliang

2017-01-01

Recently, several researchers have considered the problem of reconstruction of handwriting and other meaningful arm and hand movements from surface electromyography (sEMG). Although much progress has been made, several practical limitations may still affect the clinical applicability of sEMG-based techniques. In this paper, a novel three-step hybrid model of coordinate state transition, sEMG feature extraction and gene expression programming (GEP) prediction is proposed for reconstructing drawing traces of 12 basic one-stroke shapes from multichannel surface electromyography. Using a specially designed coordinate data acquisition system, we recorded the coordinate data of drawing traces collected in accordance with the time series while 7-channel EMG signals were recorded. As a widely-used time domain feature, Root Mean Square (RMS) was extracted with the analysis window. The preliminary reconstruction models can be established by GEP. Then, the original drawing traces can be approximated by a constructed prediction model. Applying the three-step hybrid model, we were able to convert seven channels of EMG activity recorded from the arm muscles into smooth reconstructions of drawing traces. The hybrid model can yield a mean accuracy of 74% in within-group design (one set of prediction models for all shapes) and 86% in between-group design (one separate set of prediction models for each shape), averaged for the reconstructed x and y coordinates. It can be concluded that it is feasible for the proposed three-step hybrid model to improve the reconstruction ability of drawing traces from sEMG.

Molecular Dynamics Simulations of Silica Nanoparticles Grafted with Poly(ethylene oxide) Oligomer Chains

KAUST Repository

Hong, Bingbing; Panagiotopoulos, Athanassios Z.

2012-01-01

A molecular model of silica nanoparticles grafted with poly(ethylene oxide) oligomers has been developed for predicting the transport properties of nanoparticle organic-hybrid materials (NOHMs). Ungrafted silica nanoparticles in a medium of poly(ethylene

A Generalized Hybrid Multiscale Modeling Approach for Flow and Reactive Transport in Porous Media

Science.gov (United States)

Yang, X.; Meng, X.; Tang, Y. H.; Guo, Z.; Karniadakis, G. E.

2017-12-01

Using emerging understanding of biological and environmental processes at fundamental scales to advance predictions of the larger system behavior requires the development of multiscale approaches, and there is strong interest in coupling models at different scales together in a hybrid multiscale simulation framework. A limited number of hybrid multiscale simulation methods have been developed for subsurface applications, mostly using application-specific approaches for model coupling. The proposed generalized hybrid multiscale approach is designed with minimal intrusiveness to the at-scale simulators (pre-selected) and provides a set of lightweight C++ scripts to manage a complex multiscale workflow utilizing a concurrent coupling approach. The workflow includes at-scale simulators (using the lattice-Boltzmann method, LBM, at the pore and Darcy scale, respectively), scripts for boundary treatment (coupling and kriging), and a multiscale universal interface (MUI) for data exchange. The current study aims to apply the generalized hybrid multiscale modeling approach to couple pore- and Darcy-scale models for flow and mixing-controlled reaction with precipitation/dissolution in heterogeneous porous media. The model domain is packed heterogeneously that the mixing front geometry is more complex and not known a priori. To address those challenges, the generalized hybrid multiscale modeling approach is further developed to 1) adaptively define the locations of pore-scale subdomains, 2) provide a suite of physical boundary coupling schemes and 3) consider the dynamic change of the pore structures due to mineral precipitation/dissolution. The results are validated and evaluated by comparing with single-scale simulations in terms of velocities, reactive concentrations and computing cost.

The cognitive life of mechanical molecular models.

Science.gov (United States)

Charbonneau, Mathieu

2013-12-01

The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler's cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models' materiality contributing to the solving of the molecule's structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Energy Efficiency Comparison between Hydraulic Hybrid and Hybrid Electric Vehicles

Directory of Open Access Journals (Sweden)

Jia-Shiun Chen

2015-05-01

Full Text Available Conventional vehicles tend to consume considerable amounts of fuel, which generates exhaust gases and environmental pollution during intermittent driving cycles. Therefore, prospective vehicle designs favor improved exhaust emissions and energy consumption without compromising vehicle performance. Although pure electric vehicles feature high performance and low pollution characteristics, their limitations are their short driving range and high battery costs. Hybrid electric vehicles (HEVs are comparatively environmentally friendly and energy efficient, but cost substantially more compared with conventional vehicles. Hydraulic hybrid vehicles (HHVs are mainly operated using engines, or using alternate combinations of engine and hydraulic power sources while vehicles accelerate. When the hydraulic system accumulator is depleted, the conventional engine reengages; concurrently, brake-regenerated power is recycled and reused by employing hydraulic motor–pump modules in circulation patterns to conserve fuel and recycle brake energy. This study adopted MATLAB Simulink to construct complete HHV and HEV models for backward simulations. New European Driving Cycles were used to determine the changes in fuel economy. The output of power components and the state-of-charge of energy could be retrieved. Varying power component models, energy storage component models, and series or parallel configurations were combined into seven different vehicle configurations: the conventional manual transmission vehicle, series hybrid electric vehicle, series hydraulic hybrid vehicle, parallel hybrid electric vehicle, parallel hydraulic hybrid vehicle, purely electric vehicle, and hydraulic-electric hybrid vehicle. The simulation results show that fuel consumption was 21.80% lower in the series hydraulic hybrid vehicle compared to the series hybrid electric vehicle; additionally, fuel consumption was 3.80% lower in the parallel hybrid electric vehicle compared to the

A general model of distant hybridization reveals the conditions for extinction in Atlantic salmon and brown trout.

Science.gov (United States)

Quilodrán, Claudio S; Currat, Mathias; Montoya-Burgos, Juan I

2014-01-01

Interspecific hybridization is common in nature but can be increased in frequency or even originated by human actions, such as species introduction or habitat modification, which may threaten species persistence. When hybridization occurs between distantly related species, referred to as "distant hybridization," the resulting hybrids are generally infertile or fertile but do not undergo chromosomal recombination during gametogenesis. Here, we present a model describing this frequent but poorly studied interspecific hybridization to assess its consequences on parental species and to anticipate the conditions under which they can reach extinction. Our general model fully incorporates three important processes: density-dependent competition, dominance/recessivity inheritance of traits and assortative mating. We demonstrate its use and flexibility by assessing population extinction risk between Atlantic salmon and brown trout in Norway, whose interbreeding has recently increased due to farmed fish releases into the wild. We identified the set of conditions under which hybridization may threaten salmonid species. Thanks to the flexibility of our model, we evaluated the effect of an additional risk factor, a parasitic disease, and showed that the cumulative effects dramatically increase the extinction risk. The consequences of distant hybridization are not genetically, but demographically mediated. Our general model is useful to better comprehend the evolution of such hybrid systems and we demonstrated its importance in the field of conservation biology to set up management recommendations when this increasingly frequent type of hybridization is in action.

A General Model of Distant Hybridization Reveals the Conditions for Extinction in Atlantic Salmon and Brown Trout

Science.gov (United States)

Quilodrán, Claudio S.; Currat, Mathias; Montoya-Burgos, Juan I.

2014-01-01

Interspecific hybridization is common in nature but can be increased in frequency or even originated by human actions, such as species introduction or habitat modification, which may threaten species persistence. When hybridization occurs between distantly related species, referred to as “distant hybridization,” the resulting hybrids are generally infertile or fertile but do not undergo chromosomal recombination during gametogenesis. Here, we present a model describing this frequent but poorly studied interspecific hybridization to assess its consequences on parental species and to anticipate the conditions under which they can reach extinction. Our general model fully incorporates three important processes: density-dependent competition, dominance/recessivity inheritance of traits and assortative mating. We demonstrate its use and flexibility by assessing population extinction risk between Atlantic salmon and brown trout in Norway, whose interbreeding has recently increased due to farmed fish releases into the wild. We identified the set of conditions under which hybridization may threaten salmonid species. Thanks to the flexibility of our model, we evaluated the effect of an additional risk factor, a parasitic disease, and showed that the cumulative effects dramatically increase the extinction risk. The consequences of distant hybridization are not genetically, but demographically mediated. Our general model is useful to better comprehend the evolution of such hybrid systems and we demonstrated its importance in the field of conservation biology to set up management recommendations when this increasingly frequent type of hybridization is in action. PMID:25003336

A general model of distant hybridization reveals the conditions for extinction in Atlantic salmon and brown trout.

Directory of Open Access Journals (Sweden)

Claudio S Quilodrán

Full Text Available Interspecific hybridization is common in nature but can be increased in frequency or even originated by human actions, such as species introduction or habitat modification, which may threaten species persistence. When hybridization occurs between distantly related species, referred to as "distant hybridization," the resulting hybrids are generally infertile or fertile but do not undergo chromosomal recombination during gametogenesis. Here, we present a model describing this frequent but poorly studied interspecific hybridization to assess its consequences on parental species and to anticipate the conditions under which they can reach extinction. Our general model fully incorporates three important processes: density-dependent competition, dominance/recessivity inheritance of traits and assortative mating. We demonstrate its use and flexibility by assessing population extinction risk between Atlantic salmon and brown trout in Norway, whose interbreeding has recently increased due to farmed fish releases into the wild. We identified the set of conditions under which hybridization may threaten salmonid species. Thanks to the flexibility of our model, we evaluated the effect of an additional risk factor, a parasitic disease, and showed that the cumulative effects dramatically increase the extinction risk. The consequences of distant hybridization are not genetically, but demographically mediated. Our general model is useful to better comprehend the evolution of such hybrid systems and we demonstrated its importance in the field of conservation biology to set up management recommendations when this increasingly frequent type of hybridization is in action.

Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations.

Science.gov (United States)

Bayse, Craig A; Merz, Kenneth M

2014-08-05

Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.

Hybrid sediment transport model for the “linguado” channel, state of Santa Catarina, Brazil

Directory of Open Access Journals (Sweden)

Edison Conde Perez dos Santos

2017-12-01

Full Text Available This study involves an assessment of various artificial intelligence-related techniques which aim to produce a more robust system for sediment transport modeling. The intelligent systems developed in this research are directly applicable to academic knowledge and use data from a report on "water circulation assessment in the “Linguado” Channel and Babitonga Bay ,”Santa Catarina”, Brazil, developed by  Military Engineering Institute (IME. The solution employed for sediment transport was built using an intelligent system from the conception of two hybrid models. The first was a Neuro-Fuzzy (ANFIS hybrid model for the study of hydrodynamic behavior, aiming to determine flow rate in the channel. The second was a fuzzy genetic model, able to assess sediment transport in the “Linguado” Channel. The study's conclusion compares the different effects involved in the dredging equilibrium in the “Linguado” Channel according to this hybrid model with the results obtained using a finite element model in the MIKE21® software.

Model Predictive Control of the Hybrid Ventilation for Livestock

DEFF Research Database (Denmark)

Wu, Zhuang; Stoustrup, Jakob; Trangbæk, Klaus

2006-01-01

In this paper, design and simulation results of Model Predictive Control (MPC) strategy for livestock hybrid ventilation systems and associated indoor climate through variable valve openings and exhaust fans are presented. The design is based on thermal comfort parameters for poultry in barns...

Hybrid quantum-classical modeling of quantum dot devices

Science.gov (United States)

Kantner, Markus; Mittnenzweig, Markus; Koprucki, Thomas

2017-11-01

The design of electrically driven quantum dot devices for quantum optical applications asks for modeling approaches combining classical device physics with quantum mechanics. We connect the well-established fields of semiclassical semiconductor transport theory and the theory of open quantum systems to meet this requirement. By coupling the van Roosbroeck system with a quantum master equation in Lindblad form, we introduce a new hybrid quantum-classical modeling approach, which provides a comprehensive description of quantum dot devices on multiple scales: it enables the calculation of quantum optical figures of merit and the spatially resolved simulation of the current flow in realistic semiconductor device geometries in a unified way. We construct the interface between both theories in such a way, that the resulting hybrid system obeys the fundamental axioms of (non)equilibrium thermodynamics. We show that our approach guarantees the conservation of charge, consistency with the thermodynamic equilibrium and the second law of thermodynamics. The feasibility of the approach is demonstrated by numerical simulations of an electrically driven single-photon source based on a single quantum dot in the stationary and transient operation regime.

Axelrod Model of Social Influence with Cultural Hybridization

Science.gov (United States)

Radillo-Díaz, Alejandro; Pérez, Luis A.; Del Castillo-Mussot, Marcelo

2012-10-01

Since cultural interactions between a pair of social agents involve changes in both individuals, we present simulations of a new model based on Axelrod's homogenization mechanism that includes hybridization or mixture of the agents' features. In this new hybridization model, once a cultural feature of a pair of agents has been chosen for the interaction, the average of the values for this feature is reassigned as the new value for both agents after interaction. Moreover, a parameter representing social tolerance is implemented in order to quantify whether agents are similar enough to engage in interaction, as well as to determine whether they belong to the same cluster of similar agents after the system has reached the frozen state. The transitions from a homogeneous state to a fragmented one decrease in abruptness as tolerance is increased. Additionally, the entropy associated to the system presents a maximum within the transition, the width of which increases as tolerance does. Moreover, a plateau was found inside the transition for a low-tolerance system of agents with only two cultural features.

Non-linear hybrid control oriented modelling of a digital displacement machine

DEFF Research Database (Denmark)

Pedersen, Niels Henrik; Johansen, Per; Andersen, Torben O.

2017-01-01

Proper feedback control of digital fluid power machines (Pressure, flow, torque or speed control) requires a control oriented model, from where the system dynamics can be analyzed, stability can be proven and design criteria can be specified. The development of control oriented models for hydraulic...... Digital Displacement Machines (DDM) is complicated due to non-smooth machine behavior, where the dynamics comprises both analog, digital and non-linear elements. For a full stroke operated DDM the power throughput is altered in discrete levels based on the ratio of activated pressure chambers....... In this paper, a control oriented hybrid model is established, which combines the continuous non-linear pressure chamber dynamics and the discrete shaft position dependent activation of the pressure chambers. The hybrid machine model is further extended to describe the dynamics of a Digital Fluid Power...

Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential

International Nuclear Information System (INIS)

Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V; Carloni, Paolo

2006-01-01

Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases

Modeling and Optimal Control of a Class of Warfare Hybrid Dynamic Systems Based on Lanchester (n,1 Attrition Model

Directory of Open Access Journals (Sweden)

Xiangyong Chen

2014-01-01

hybrid dynamic systems is established based on Lanchester equation in a (n,1 battle, where a heterogeneous force of n different troop types faces a homogeneous force. This model can be characterized by the interaction of continuous-time models (governed by Lanchester equation, and discrete event systems (described by variable tactics. Furthermore, an expository discussion is presented on an optimal variable tactics control problem for warfare hybrid dynamic system. The optimal control strategies are designed based on dynamic programming and differential game theory. As an example of the consequences of this optimal control problem, we take the (2, 1 case and solve the optimal strategies in a (2, 1 case. Simulation results show the feasibility of warfare hybrid system model and the effectiveness of the optimal control strategies designed.

Medulloblastoma: Molecular Genetics and Animal Models

Directory of Open Access Journals (Sweden)

Corey Raffel

2004-07-01

Full Text Available Medulloblastoma is a primary brain tumor found in the cerebellum of children. The tumor occurs in association with two inherited cancer syndromes: Turcot syndrome and Gorlin syndrome. Insights into the molecular biology of the tumor have come from looking at alterations in the genes altered in these syndromes, PTC and APC, respectively. Murine models of medulloblastoma have been constructed based on these alterations. Additional murine models that, while mimicking the appearance of the human tumor, seem unrelated to the human tumor's molecular alterations have been made. In this review, the clinical picture, origin, molecular biology, murine models of medulloblastoma are discussed. Although a great deal has been discovered about this tumor, the genetic alterations responsible for tumor development in a majority of patients have yet to be described.

A n-vector model for charge transport in molecular semiconductors.

Science.gov (United States)

Jackson, Nicholas E; Kohlstedt, Kevin L; Chen, Lin X; Ratner, Mark A

2016-11-28

We develop a lattice model utilizing coarse-grained molecular sites to study charge transport in molecular semiconducting materials. The model bridges atomistic descriptions and structureless lattice models by mapping molecular structure onto sets of spatial vectors isomorphic with spin vectors in a classical n-vector Heisenberg model. Specifically, this model incorporates molecular topology-dependent orientational and intermolecular coupling preferences, including the direct inclusion of spatially correlated transfer integrals and site energy disorder. This model contains the essential physics required to explicitly simulate the interplay of molecular topology and correlated structural disorder, and their effect on charge transport. As a demonstration of its utility, we apply this model to analyze the effects of long-range orientational correlations, molecular topology, and intermolecular interaction strength on charge motion in bulk molecular semiconductors.

A hybrid classical-quantum approach for ultra-scaled confined nanostructures : modeling and simulation*

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Pietra Paola

2012-04-01

Full Text Available We propose a hybrid classical-quantum model to study the motion of electrons in ultra-scaled confined nanostructures. The transport of charged particles, considered as one dimensional, is described by a quantum effective mass model in the active zone coupled directly to a drift-diffusion problem in the rest of the device. We explain how this hybrid model takes into account the peculiarities due to the strong confinement and we present numerical simulations for a simplified carbon nanotube. Nous proposons un modèle hybride classique-quantique pour décrire le mouvement des électrons dans des nanostructures très fortement confinées. Le transport des particules, consideré unidimensionel, est décrit par un modèle quantique avec masse effective dans la zone active couplé à un problème de dérive-diffusion dans le reste du domaine. Nous expliquons comment ce modèle hybride prend en compte les spécificités de ce très fort confinement et nous présentons des résultats numériques pour un nanotube de carbone simplifié.

Hybrid quantum computation

International Nuclear Information System (INIS)

Sehrawat, Arun; Englert, Berthold-Georg; Zemann, Daniel

2011-01-01

We present a hybrid model of the unitary-evolution-based quantum computation model and the measurement-based quantum computation model. In the hybrid model, part of a quantum circuit is simulated by unitary evolution and the rest by measurements on star graph states, thereby combining the advantages of the two standard quantum computation models. In the hybrid model, a complicated unitary gate under simulation is decomposed in terms of a sequence of single-qubit operations, the controlled-z gates, and multiqubit rotations around the z axis. Every single-qubit and the controlled-z gate are realized by a respective unitary evolution, and every multiqubit rotation is executed by a single measurement on a required star graph state. The classical information processing in our model requires only an information flow vector and propagation matrices. We provide the implementation of multicontrol gates in the hybrid model. They are very useful for implementing Grover's search algorithm, which is studied as an illustrative example.

A New Model for Baryogenesis through Hybrid Inflation

International Nuclear Information System (INIS)

Delepine, D.; Prieto, C. Martinez; Lopez, L. A. Urena

2009-01-01

We propose a hybrid inflation model with a complex waterfall field which contains an interaction term that breaks the U(1) global symmetry associated to the waterfall field charge. The asymmetric evolution of the real and imaginary parts of the complex field during the phase transition at the end of inflation translates into a charge asymmetry.

A hybrid fuzzy multi-criteria decision making model for green ...

African Journals Online (AJOL)

A hybrid fuzzy multi-criteria decision making model for green supplier selection. ... Hence,supplier selection is significant factor in supply chain success. ... reduce purchasing cost, lead time and improve quality and environmental issue.

Systems theoretic analysis of the central dogma of molecular biology: some recent results.

Science.gov (United States)

Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

2010-03-01

This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

MODEL APLIKASI FIKIH MUAMALAH PADA FORMULASI HYBRID CONTRACT

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Ali Murtadho

2013-10-01

Full Text Available Modern literatures of fiqh mu’āmalah talk alot about various contract formulation with capability of maximizing profit in shariah finance industry. This new contract modification is the synthesis among existing contracts which is formulated in such a way to be an integrated contract. This formulation is known as a hybrid contract or multicontract (al-'uqūd al-murakkabah. Some of them are, bay' bi thaman 'ājil, Ijārah muntahiyah bi ’l-tamlīk dan mushārakah mutanāqiṣah. This study intends to further describe models of hybrid contract, and explore the shari'ah principles in modern financial institutions. This study found a potential shift from the ideal values of the spirit of shari'ah into the spirit of competition based shari'ah formally.

Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems

Science.gov (United States)

Winkelmann, Stefanie; Schütte, Christof

2017-09-01

Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations.

Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems.

Science.gov (United States)

Winkelmann, Stefanie; Schütte, Christof

2017-09-21

Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations.

Software development infrastructure for the HYBRID modeling and simulation project

International Nuclear Information System (INIS)

Epiney, Aaron S.; Kinoshita, Robert A.; Kim, Jong Suk; Rabiti, Cristian; Greenwood, M. Scott

2016-01-01

One of the goals of the HYBRID modeling and simulation project is to assess the economic viability of hybrid systems in a market that contains renewable energy sources like wind. The idea is that it is possible for the nuclear plant to sell non-electric energy cushions, which absorb (at least partially) the volatility introduced by the renewable energy sources. This system is currently modeled in the Modelica programming language. To assess the economics of the system, an optimization procedure is trying to find the minimal cost of electricity production. The RAVEN code is used as a driver for the whole problem. It is assumed that at this stage, the HYBRID modeling and simulation framework can be classified as non-safety “research and development” software. The associated quality level is Quality Level 3 software. This imposes low requirements on quality control, testing and documentation. The quality level could change as the application development continues.Despite the low quality requirement level, a workflow for the HYBRID developers has been defined that include a coding standard and some documentation and testing requirements. The repository performs automated unit testing of contributed models. The automated testing is achieved via an open-source python script called BuildingsP from Lawrence Berkeley National Lab. BuildingsPy runs Modelica simulation tests using Dymola in an automated manner and generates and runs unit tests from Modelica scripts written by developers. In order to assure effective communication between the different national laboratories a biweekly videoconference has been set-up, where developers can report their progress and issues. In addition, periodic face-face meetings are organized intended to discuss high-level strategy decisions with management. A second means of communication is the developer email list. This is a list to which everybody can send emails that will be received by the collective of the developers and managers

Software development infrastructure for the HYBRID modeling and simulation project

Energy Technology Data Exchange (ETDEWEB)

Epiney, Aaron S. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kinoshita, Robert A. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kim, Jong Suk [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Greenwood, M. Scott [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2016-09-01

One of the goals of the HYBRID modeling and simulation project is to assess the economic viability of hybrid systems in a market that contains renewable energy sources like wind. The idea is that it is possible for the nuclear plant to sell non-electric energy cushions, which absorb (at least partially) the volatility introduced by the renewable energy sources. This system is currently modeled in the Modelica programming language. To assess the economics of the system, an optimization procedure is trying to find the minimal cost of electricity production. The RAVEN code is used as a driver for the whole problem. It is assumed that at this stage, the HYBRID modeling and simulation framework can be classified as non-safety “research and development” software. The associated quality level is Quality Level 3 software. This imposes low requirements on quality control, testing and documentation. The quality level could change as the application development continues.Despite the low quality requirement level, a workflow for the HYBRID developers has been defined that include a coding standard and some documentation and testing requirements. The repository performs automated unit testing of contributed models. The automated testing is achieved via an open-source python script called BuildingsP from Lawrence Berkeley National Lab. BuildingsPy runs Modelica simulation tests using Dymola in an automated manner and generates and runs unit tests from Modelica scripts written by developers. In order to assure effective communication between the different national laboratories a biweekly videoconference has been set-up, where developers can report their progress and issues. In addition, periodic face-face meetings are organized intended to discuss high-level strategy decisions with management. A second means of communication is the developer email list. This is a list to which everybody can send emails that will be received by the collective of the developers and managers

Two molecular markers based on mitochondrial genomes for varieties identification of the northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids.

Science.gov (United States)

Xincheng, Zhang; Kunci, Chen; Xinping, Zhu; Jian, Zhao; Qing, Luo; Xiaoyou, Hong; Wei, Li; Fengfang, Xiao

2015-08-01

The northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids have played important roles in the Chinese freshwater aquaculture industry, with an annual production in China exceeding 400 thousand tons. While these are popular aquaculture breeds in China, it is not easy to identify northern snakehead, blotched snakehead, and their hybrids. Thus, a method should be developed to identify these varieties. To distinguish between the reciprocal hybrids (C. argus ♀ × C. maculata ♂ and C. maculata ♀ × C. argus ♂), the mitochondrial genome sequences of northern snakehead and blotched snakehead and their reciprocal hybrids were compared. Following the alignment and analysis of mtDNA sequences of northern snakehead, blotched snakehead and their hybrids, two pairs of specific primers were designed based on identified differences ranging from 12S rRNA to 16S rRNA gene. The BY1 primers amplified the same bands in the blotched snakehead and the hybrid (C. maculata ♀ × C. argus ♂), while producing no products in northern snakehead and the hybrid (C. argus ♀ × C. maculata ♂). Amplification with WY1 yielded the opposite results. Then, 30 individuals per fish were randomized to verify the primers, and the results showed that the primers were specific for breeds, as intended. The specific primers can not only simply distinguish between two kinds of hybrids, but also rapidly identify the two parents. This study provides a method of molecular marker identification to identify reciprocal hybrids.

Dynamical analysis of Parkinsonian state emulated by hybrid Izhikevich neuron models

Science.gov (United States)