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Sample records for voltage-sensing domain model

  1. In search of a consensus model of the resting state of a voltage-sensing domain.

    Science.gov (United States)

    Vargas, Ernesto; Bezanilla, Francisco; Roux, Benoît

    2011-12-08

    Voltage-sensing domains (VSDs) undergo conformational changes in response to the membrane potential and are the critical structural modules responsible for the activation of voltage-gated channels. Structural information about the key conformational states underlying voltage activation is currently incomplete. Through the use of experimentally determined residue-residue interactions as structural constraints, we determine and refine a model of the Kv channel VSD in the resting conformation. The resulting structural model is in broad agreement with results that originate from various labs using different techniques, indicating the emergence of a consensus for the structural basis of voltage sensing. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Atomistic Modeling of Ion Conduction through the Voltage-Sensing Domain of the Shaker K+ Ion Channel.

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    Wood, Mona L; Freites, J Alfredo; Tombola, Francesco; Tobias, Douglas J

    2017-04-20

    Voltage-sensing domains (VSDs) sense changes in the membrane electrostatic potential and, through conformational changes, regulate a specific function. The VSDs of wild-type voltage-dependent K + , Na + , and Ca 2+ channels do not conduct ions, but they can become ion-permeable through pathological mutations in the VSD. Relatively little is known about the underlying mechanisms of conduction through VSDs. The most detailed studies have been performed on Shaker K + channel variants in which ion conduction through the VSD is manifested in electrophysiology experiments as a voltage-dependent inward current, the so-called omega current, which appears when the VSDs are in their resting state conformation. Only monovalent cations appear to permeate the Shaker VSD via a pathway that is believed to be, at least in part, the same as that followed by the S4 basic side chains during voltage-dependent activation. We performed μs-time scale atomistic molecular dynamics simulations of a cation-conducting variant of the Shaker VSD under applied electric fields in an experimentally validated resting-state conformation, embedded in a lipid bilayer surrounded by solutions containing guanidinium chloride or potassium chloride. Our simulations provide insights into the Shaker VSD permeation pathway, the protein-ion interactions that control permeation kinetics, and the mechanism of voltage-dependent activation of voltage-gated ion channels.

  3. Domain-to-domain coupling in voltage-sensing phosphatase.

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    Sakata, Souhei; Matsuda, Makoto; Kawanabe, Akira; Okamura, Yasushi

    2017-01-01

    Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain.

  4. Functional diversity of potassium channel voltage-sensing domains.

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    Islas, León D

    2016-01-01

    Voltage-gated potassium channels or Kv's are membrane proteins with fundamental physiological roles. They are composed of 2 main functional protein domains, the pore domain, which regulates ion permeation, and the voltage-sensing domain, which is in charge of sensing voltage and undergoing a conformational change that is later transduced into pore opening. The voltage-sensing domain or VSD is a highly conserved structural motif found in all voltage-gated ion channels and can also exist as an independent feature, giving rise to voltage sensitive enzymes and also sustaining proton fluxes in proton-permeable channels. In spite of the structural conservation of VSDs in potassium channels, there are several differences in the details of VSD function found across variants of Kvs. These differences are mainly reflected in variations in the electrostatic energy needed to open different potassium channels. In turn, the differences in detailed VSD functioning among voltage-gated potassium channels might have physiological consequences that have not been explored and which might reflect evolutionary adaptations to the different roles played by Kv channels in cell physiology.

  5. Voltage-sensing phosphatase modulation by a C2 domain

    Directory of Open Access Journals (Sweden)

    Paul M. Castle

    2015-04-01

    Full Text Available The voltage-sensing phosphatase (VSP is the first example of an enzyme controlled by changes in membrane potential. VSP has four distinct regions: the transmembrane voltage-sensing domain (VSD, the inter-domain linker, the cytosolic catalytic domain and the C2 domain. The VSD transmits the changes in membrane potential through the inter-domain linker activating the catalytic domain which then dephosphorylates phosphatidylinositol phosphate lipids. The role of the C2, however, has not been established. In this study, we explore two possible roles for the C2: catalysis and membrane-binding. The Ci-VSP crystal structures show that the C2 residue Y522 lines the active site suggesting a contribution to catalysis. When we mutated Y522 to phenylalanine, we found a shift in the voltage dependence of activity. This suggests hydrogen bonding as a mechanism of action. Going one step further, when we deleted the entire C2 domain, we found voltage-dependent enzyme activity was no longer detectable. This result clearly indicates the entire C2 is necessary for catalysis as well as for modulating activity. As C2s are known membrane-binding domains, we tested whether the VSP C2 interacts with the membrane. We probed a cluster of four positively charged residues lining the top of the C2 and suggested by previous studies to interact with phosphatidylinositol 4,5-bisphosphate (PI(4,5P2 (Kalli et al., 2014. Neutralizing those positive charges significantly shifted the voltage dependence of activity to higher voltages. We tested membrane binding by depleting PI(4,5P2 from the membrane using the 5HT2C receptor and found that the VSD motions as measured by voltage clamp fluorometry were not changed. These results suggest that if the C2 domain interacts with the membrane to influence VSP function it may not occur exclusively through PI(4,5P2. Together, this data advances our understanding of the VSP C2 by demonstrating a necessary and critical role for the C2 domain in

  6. Voltage-sensing phosphatase modulation by a C2 domain.

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    Castle, Paul M; Zolman, Kevin D; Kohout, Susy C

    2015-01-01

    The voltage-sensing phosphatase (VSP) is the first example of an enzyme controlled by changes in membrane potential. VSP has four distinct regions: the transmembrane voltage-sensing domain (VSD), the inter-domain linker, the cytosolic catalytic domain, and the C2 domain. The VSD transmits the changes in membrane potential through the inter-domain linker activating the catalytic domain which then dephosphorylates phosphatidylinositol phosphate (PIP) lipids. The role of the C2, however, has not been established. In this study, we explore two possible roles for the C2: catalysis and membrane-binding. The Ci-VSP crystal structures show that the C2 residue Y522 lines the active site suggesting a contribution to catalysis. When we mutated Y522 to phenylalanine, we found a shift in the voltage dependence of activity. This suggests hydrogen bonding as a mechanism of action. Going one step further, when we deleted the entire C2 domain, we found voltage-dependent enzyme activity was no longer detectable. This result clearly indicates the entire C2 is necessary for catalysis as well as for modulating activity. As C2s are known membrane-binding domains, we tested whether the VSP C2 interacts with the membrane. We probed a cluster of four positively charged residues lining the top of the C2 and suggested by previous studies to interact with phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] (Kalli et al., 2014). Neutralizing those positive charges significantly shifted the voltage dependence of activity to higher voltages. We tested membrane binding by depleting PI(4,5)P2 from the membrane using the 5HT2C receptor and found that the VSD motions as measured by voltage clamp fluorometry (VCF) were not changed. These results suggest that if the C2 domain interacts with the membrane to influence VSP function it may not occur exclusively through PI(4,5)P2. Together, this data advances our understanding of the VSP C2 by demonstrating a necessary and critical role for the C2 domain in

  7. The orientation and molecular movement of a k(+) channel voltage-sensing domain.

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    Gandhi, Chris S; Clark, Eliana; Loots, Eli; Pralle, Arnd; Isacoff, Ehud Y

    2003-10-30

    Voltage-gated channels operate through the action of a voltage-sensing domain (membrane segments S1-S4) that controls the conformation of gates located in the pore domain (membrane segments S5-S6). Recent structural studies on the bacterial K(v)AP potassium channel have led to a new model of voltage sensing in which S4 lies in the lipid at the channel periphery and moves through the membrane as a unit with a portion of S3. Here we describe accessibility probing and disulfide scanning experiments aimed at determining how well the K(v)AP model describes the Drosophila Shaker potassium channel. We find that the S1-S3 helices have one end that is externally exposed, S3 does not undergo a transmembrane motion, and S4 lies in close apposition to the pore domain in the resting and activated state.

  8. A common pathway for charge transport through voltage-sensing domains.

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    Chanda, Baron; Bezanilla, Francisco

    2008-02-07

    Voltage-gated ion channels derive their voltage sensitivity from the movement of specific charged residues in response to a change in transmembrane potential. Several studies on mechanisms of voltage sensing in ion channels support the idea that these gating charges move through a well-defined permeation pathway. This gating pathway in a voltage-gated ion channel can also be mutated to transport free cations, including protons. The recent discovery of proton channels with sequence homology to the voltage-sensing domains suggests that evolution has perhaps exploited the same gating pathway to generate a bona fide voltage-dependent proton transporter. Here we will discuss implications of these findings on the mechanisms underlying charge (and ion) transport by voltage-sensing domains.

  9. The twisted ion-permeation pathway of a resting voltage-sensing domain.

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    Tombola, Francesco; Pathak, Medha M; Gorostiza, Pau; Isacoff, Ehud Y

    2007-02-01

    Proteins containing voltage-sensing domains (VSDs) translate changes in membrane potential into changes in ion permeability or enzymatic activity. In channels, voltage change triggers a switch in conformation of the VSD, which drives gating in a separate pore domain, or, in channels lacking a pore domain, directly gates an ion pathway within the VSD. Neither mechanism is well understood. In the Shaker potassium channel, mutation of the first arginine residue of the S4 helix to a smaller uncharged residue makes the VSD permeable to ions ('omega current') in the resting conformation ('S4 down'). Here we perform a structure-guided perturbation analysis of the omega conductance to map its VSD permeation pathway. We find that there are four omega pores per channel, which is consistent with one conduction path per VSD. Permeating ions from the extracellular medium enter the VSD at its peripheral junction with the pore domain, and then plunge into the core of the VSD in a curved conduction pathway. Our results provide a model of the resting conformation of the VSD.

  10. Domain cooperativity in the β1a subunit is essential for dihydropyridine receptor voltage sensing in skeletal muscle.

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    Dayal, Anamika; Bhat, Vinayakumar; Franzini-Armstrong, Clara; Grabner, Manfred

    2013-04-30

    The dihydropyridine receptor (DHPR) β1a subunit is crucial for enhancement of DHPR triad expression, assembly of DHPRs in tetrads, and elicitation of DHPRα1S charge movement--the three prerequisites of skeletal muscle excitation-contraction coupling. Despite the ability to fully target α1S into triadic junctions and tetradic arrays, the neuronal isoform β3 was unable to restore considerable charge movement (measure of α1S voltage sensing) upon expression in β1-null zebrafish relaxed myotubes, unlike the other three vertebrate β-isoforms (β1a, β2a, and β4). Thus, we used β3 for chimerization with β1a to investigate whether any of the five distinct molecular regions of β1a is dominantly involved in inducing the voltage-sensing function of α1S. Surprisingly, systematic domain swapping between β1a and β3 revealed a pivotal role of the src homology 3 (SH3) domain and C terminus of β1a in charge movement restoration. More interestingly, β1a SH3 domain and C terminus, when simultaneously engineered into β3 sequence background, were able to fully restore charge movement together with proper intracellular Ca(2+) release, suggesting cooperativity of these two domains in induction of the α1S voltage-sensing function in skeletal muscle excitation-contraction coupling. Furthermore, substitution of a proline by alanine in the putative SH3-binding polyproline motif in the proximal C terminus of β1a (also of β2a and β4) fully obstructed α1S charge movement. Consequently, we postulate a model according to which β subunits, probably via the SH3-C-terminal polyproline interaction, adapt a discrete conformation required to modify the α1S conformation apt for voltage sensing in skeletal muscle.

  11. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.

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    Li, Qufei; Wanderling, Sherry; Paduch, Marcin; Medovoy, David; Singharoy, Abhishek; McGreevy, Ryan; Villalba-Galea, Carlos A; Hulse, Raymond E; Roux, Benoît; Schulten, Klaus; Kossiakoff, Anthony; Perozo, Eduardo

    2014-03-01

    The transduction of transmembrane electric fields into protein motion has an essential role in the generation and propagation of cellular signals. Voltage-sensing domains (VSDs) carry out these functions through reorientations of positive charges in the S4 helix. Here, we determined crystal structures of the Ciona intestinalis VSD (Ci-VSD) in putatively active and resting conformations. S4 undergoes an ~5-Å displacement along its main axis, accompanied by an ~60° rotation. This movement is stabilized by an exchange in countercharge partners in helices S1 and S3 that generates an estimated net charge transfer of ~1 eo. Gating charges move relative to a ''hydrophobic gasket' that electrically divides intra- and extracellular compartments. EPR spectroscopy confirms the limited nature of S4 movement in a membrane environment. These results provide an explicit mechanism for voltage sensing and set the basis for electromechanical coupling in voltage-dependent enzymes and ion channels.

  12. Structural interactions between lipids, water and S1-S4 voltage-sensing domains.

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    Krepkiy, Dmitriy; Gawrisch, Klaus; Swartz, Kenton J

    2012-11-02

    Membrane proteins serve crucial signaling and transport functions, yet relatively little is known about their structures in membrane environments or how lipids interact with these proteins. For voltage-activated ion channels, X-ray structures suggest that the mobile voltage-sensing S4 helix would be exposed to the membrane, and functional studies reveal that lipid modification can profoundly alter channel activity. Here, we use solid-state NMR to investigate structural interactions of lipids and water with S1-S4 voltage-sensing domains and to explore whether lipids influence the structure of the protein. Our results demonstrate that S1-S4 domains exhibit extensive interactions with lipids and that these domains are heavily hydrated when embedded in a membrane. We also find evidence for preferential interactions of anionic lipids with S1-S4 domains and that these interactions have lifetimes on the timescale of ≤ 10(-3)s. Arg residues within S1-S4 domains are well hydrated and are positioned in close proximity to lipids, exhibiting local interactions with both lipid headgroups and acyl chains. Comparative studies with a positively charged lipid lacking a phosphodiester group reveal that this lipid modification has only modest effects on the structure and hydration of S1-S4 domains. Taken together, our results demonstrate that Arg residues in S1-S4 voltage-sensing domains reside in close proximity to the hydrophobic interior of the membrane yet are well hydrated, a requirement for carrying charge and driving protein motions in response to changes in membrane voltage. Published by Elsevier Ltd.

  13. A localized interaction surface for voltage-sensing domains on the pore domain of a K+ channel.

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    Li-Smerin, Y; Hackos, D H; Swartz, K J

    2000-02-01

    Voltage-gated K+ channels contain a central pore domain and four surrounding voltage-sensing domains. How and where changes in the structure of the voltage-sensing domains couple to the pore domain so as to gate ion conduction is not understood. The crystal structure of KcsA, a bacterial K+ channel homologous to the pore domain of voltage-gated K+ channels, provides a starting point for addressing this question. Guided by this structure, we used tryptophan-scanning mutagenesis on the transmembrane shell of the pore domain in the Shaker voltage-gated K+ channel to localize potential protein-protein and protein-lipid interfaces. Some mutants cause only minor changes in gating and when mapped onto the KcsA structure cluster away from the interface between pore domain subunits. In contrast, mutants producing large changes in gating tend to cluster near this interface. These results imply that voltage-sensing domains interact with localized regions near the interface between adjacent pore domain subunits.

  14. alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.

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    Li-Smerin, Y; Hackos, D H; Swartz, K J

    2000-01-01

    Voltage-gated K(+) channels are tetramers with each subunit containing six (S1-S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5-S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1-S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K(+) channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of alpha-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure. In addition, both the S1-S2 and S3-S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

  15. α-Helical Structural Elements within the Voltage-Sensing Domains of a K+ Channel

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    Li-Smerin, Yingying; Hackos, David H.; Swartz, Kenton J.

    2000-01-01

    Voltage-gated K+ channels are tetramers with each subunit containing six (S1–S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5–S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1–S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K+ channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of α-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting α-helical secondary structure. In addition, both the S1–S2 and S3–S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain. PMID:10613917

  16. Regulation of Na+ channel inactivation by the DIII and DIV voltage-sensing domains.

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    Hsu, Eric J; Zhu, Wandi; Schubert, Angela R; Voelker, Taylor; Varga, Zoltan; Silva, Jonathan R

    2017-03-06

    Functional eukaryotic voltage-gated Na + (Na V ) channels comprise four domains (DI-DIV), each containing six membrane-spanning segments (S1-S6). Voltage sensing is accomplished by the first four membrane-spanning segments (S1-S4), which together form a voltage-sensing domain (VSD). A critical Na V channel gating process, inactivation, has previously been linked to activation of the VSDs in DIII and DIV. Here, we probe this interaction by using voltage-clamp fluorometry to observe VSD kinetics in the presence of mutations at locations that have been shown to impair Na V channel inactivation. These locations include the DIII-DIV linker, the DIII S4-S5 linker, and the DIV S4-S5 linker. Our results show that, within the 10-ms timeframe of fast inactivation, the DIV-VSD is the primary regulator of inactivation. However, after longer 100-ms pulses, the DIII-DIV linker slows DIII-VSD deactivation, and the rate of DIII deactivation correlates strongly with the rate of recovery from inactivation. Our results imply that, over the course of an action potential, DIV-VSDs regulate the onset of fast inactivation while DIII-VSDs determine its recovery. © 2017 Hsu et al.

  17. Structure and hydration of membranes embedded with voltage-sensing domains.

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    Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J Alfredo; Schow, Eric V; Worcester, David L; Gawrisch, Klaus; Tobias, Douglas J; White, Stephen H; Swartz, Kenton J

    2009-11-26

    Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly charged S1-S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated ion channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations and cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings indicate that voltage sensors have evolved to interact with the lipid membrane while keeping energetic and structural perturbations to a minimum, and that water penetrates the membrane, to hydrate charged residues and shape the transmembrane electric field.

  18. The voltage-sensing domain of a phosphatase gates the pore of a potassium channel.

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    Arrigoni, Cristina; Schroeder, Indra; Romani, Giulia; Van Etten, James L; Thiel, Gerhard; Moroni, Anna

    2013-03-01

    The modular architecture of voltage-gated K(+) (Kv) channels suggests that they resulted from the fusion of a voltage-sensing domain (VSD) to a pore module. Here, we show that the VSD of Ciona intestinalis phosphatase (Ci-VSP) fused to the viral channel Kcv creates Kv(Synth1), a functional voltage-gated, outwardly rectifying K(+) channel. Kv(Synth1) displays the summed features of its individual components: pore properties of Kcv (selectivity and filter gating) and voltage dependence of Ci-VSP (V(1/2) = +56 mV; z of ~1), including the depolarization-induced mode shift. The degree of outward rectification of the channel is critically dependent on the length of the linker more than on its amino acid composition. This highlights a mechanistic role of the linker in transmitting the movement of the sensor to the pore and shows that electromechanical coupling can occur without coevolution of the two domains.

  19. MOLECULAR PATHOPHYSIOLOGY AND PHARMACOLOGY OF THE VOLTAGE-SENSING DOMAIN OF NEURONAL ION CHANNELS

    Directory of Open Access Journals (Sweden)

    Francesco eMiceli

    2015-07-01

    Full Text Available Voltage-gated ion channels (VGIC are membrane proteins that switch from a closed to open state in response to changes in membrane potential, thus enabling ion fluxes across the cell membranes. The mechanism that regulate the structural rearrangements occurring in VGIC in response to changes in membrane potential still remains one of the most challenging topic of modern biophysics. Na+, Ca2+ and K+ voltage-gated channels are structurally formed by the assembly of four similar domains, each comprising six transmembrane segments. Each domain can be divided in two main regions: the Pore Module (PM and the Voltage-Sensing Module (VSM. The PM (helices S5 and S6 and intervening linker is responsible for gate opening and ion selectivity; by contrast, the VSM, comprising the first four transmembrane helices (S1-S4, undergoes the first conformational changes in response to membrane voltage. In particular, the S4 segment of each domain, which contains several positively charged residues interspersed with hydrophobic amino acids, is located within the membrane electric field and plays an essential role in voltage sensing. In neurons, specific gating properties of each channel subtype underlie a variety of biological events, ranging from the generation and propagation of electrical impulses, to the secretion of neurotransmitters, to the regulation of gene expression. Given the important functional role played by the VSM in neuronal VGICs, it is not surprising that various VSM mutations affecting the gating process of these channels are responsible for human diseases, and that compounds acting on the VSM have emerged as important investigational tools with great therapeutic potential. In the present review we will briefly describe the most recent discoveries concerning how the VSM exerts its function, how genetically inherited diseases caused by mutations occurring in the VSM affects gating in VGICs, and how several classes of drugs and toxins selectively

  20. Expression, purification, and reconstitution of the voltage-sensing domain from Ci-VSP.

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    Li, Qufei; Jogini, Vishwanath; Wanderling, Sherry; Cortes, D Marien; Perozo, Eduardo

    2012-10-16

    The voltage-sensing domain (VSD) is the common scaffold responsible for the functional behavior of voltage-gated ion channels, voltage sensitive enzymes, and proton channels. Because of the position of the voltage dependence of the available VSD structures, at present, they all represent the activated state of the sensor. Yet in the absence of a consensus resting state structure, the mechanistic details of voltage sensing remain controversial. The voltage dependence of the VSD from Ci-VSP (Ci-VSD) is dramatically right shifted, so that at 0 mV it presumably populates the putative resting state. Appropriate biochemical methods are an essential prerequisite for generating sufficient amounts of Ci-VSD protein for high-resolution structural studies. Here, we present a simple and robust protocol for the expression of eukaryotic Ci-VSD in Escherichia coli at milligram levels. The protein is pure, homogeneous, monodisperse, and well-folded after solubilization in Anzergent 3-14 at the analyzed concentration (~0.3 mg/mL). Ci-VSD can be reconstituted into liposomes of various compositions, and initial site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopic measurements indicate its first transmembrane segment folds into an α-helix, in agreement with the homologous region of other VSDs. On the basis of our results and enhanced relaxation EPR spectroscopy measurement, Ci-VSD reconstitutes essentially randomly in proteoliposomes, precluding straightforward application of transmembrane voltages in combination with spectroscopic methods. Nevertheless, these results represent an initial step that makes the resting state of a VSD accessible to a variety of biophysical and structural approaches, including X-ray crystallography, spectroscopic methods, and electrophysiology in lipid bilayers.

  1. Expression, Purification and Reconstitution of the Voltage Sensing Domain from Ci-VSP

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    Li, Qufei; Jogini, Vishwanath; Wanderling, Sherry; Cortes, D. Marien; Perozo, Eduardo

    2013-01-01

    The voltage-sensing domain (VSD) is the common scaffold responsible for the functional behavior of voltage gated ion channels, voltage sensitive enzymes and proton channels. Because of the position of the voltage dependence of the available VSD structures, at present, they all represent the activated state of the sensor. Yet, in the absence of a consensus resting state structure, the mechanistic details of voltage sensing remain controversial. The voltage dependence of the VSD from Ci-VSP (Ci-VSD) is dramatically right shifted, so that at 0 mV It presumably populates the putative resting state. Appropriate biochemical methods are an essential prerequisite to generate sufficient amounts of Ci-VSD protein for high-resolution structural studies. Here, we present a simple and robust protocol for the Escherichia coli expression of eukaryotic Ci-VSD at milligram levels. The protein is pure, homogeneous, mono-disperse and well folded after solubilization in Anzergent 3-14 at the analyzed concentration (~ 0.3 mg/mL). Ci-VSD can be reconstituted into liposomes of various compositions and initial site-directed spin labeling and EPR spectroscopic measurements indicate its first transmembrane segment folds into an α-helix, in agreement to the homologous region of other VSDs. Based on current results and enhanced relaxation EPR spectroscopy measurement, Ci-VSD reconstitutes essentially randomly in proteo-liposomes, precluding straightforward application of transmembrane voltages in combination with spectroscopic methods. Nevertheless, the present results represent an initial step that makes the resting state of a VSD accessible to a variety of biophysical and structural approaches, including X-ray crystallography, spectroscopic methods and electrophysiology in lipid bilayers. PMID:22989304

  2. Gating of the two-pore cation channel AtTPC1 in the plant vacuole is based on a single voltage-sensing domain.

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    Jaślan, D; Mueller, T D; Becker, D; Schultz, J; Cuin, T A; Marten, I; Dreyer, I; Schönknecht, G; Hedrich, R

    2016-09-01

    The two-pore cation channel TPC1 operates as a dimeric channel in animal and plant endomembranes. Each subunit consists of two homologous Shaker-like halves, with 12 transmembrane domains in total (S1-S6, S7-S12). In plants, TPC1 channels reside in the vacuolar membrane, and upon voltage stimulation, give rise to the well-known slow-activating SV currents. Here, we combined bioinformatics, structure modelling, site-directed mutagenesis, and in planta patch clamp studies to elucidate the molecular mechanisms of voltage-dependent channel gating in TPC1 in its native plant background. Structure-function analysis of the Arabidopsis TPC1 channel in planta confirmed that helix S10 operates as the major voltage-sensing site, with Glu450 and Glu478 identified as possible ion-pair partners for voltage-sensing Arg537. The contribution of helix S4 to voltage sensing was found to be negligible. Several conserved negative residues on the luminal site contribute to calcium binding, stabilizing the closed channel. During evolution of plant TPC1s from two separate Shaker-like domains, the voltage-sensing function in the N-terminal Shaker-unit (S1-S4) vanished. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

  3. Coupling between the voltage-sensing and pore domains in a voltage-gated potassium channel.

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    Schow, Eric V; Freites, J Alfredo; Nizkorodov, Alex; White, Stephen H; Tobias, Douglas J

    2012-07-01

    Voltage-dependent potassium (Kv), sodium (Nav), and calcium channels open and close in response to changes in transmembrane (TM) potential, thus regulating cell excitability by controlling ion flow across the membrane. An outstanding question concerning voltage gating is how voltage-induced conformational changes of the channel voltage-sensing domains (VSDs) are coupled through the S4-S5 interfacial linking helices to the opening and closing of the pore domain (PD). To investigate the coupling between the VSDs and the PD, we generated a closed Kv channel configuration from Aeropyrum pernix (KvAP) using atomistic simulations with experiment-based restraints on the VSDs. Full closure of the channel required, in addition to the experimentally determined TM displacement, that the VSDs be displaced both inwardly and laterally around the PD. This twisting motion generates a tight hydrophobic interface between the S4-S5 linkers and the C-terminal ends of the pore domain S6 helices in agreement with available experimental evidence.

  4. KCNQ1 channel modulation by KCNE proteins via the voltage-sensing domain.

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    Nakajo, Koichi; Kubo, Yoshihiro

    2015-06-15

    The gating of the KCNQ1 potassium channel is drastically regulated by auxiliary subunit KCNE proteins. KCNE1, for example, slows the activation kinetics of KCNQ1 by two orders of magnitude. Like other voltage-gated ion channels, the opening of KCNQ1 is regulated by the voltage-sensing domain (VSD; S1-S4 segments). Although it has been known that KCNE proteins interact with KCNQ1 via the pore domain, some recent reports suggest that the VSD movement may be altered by KCNE. The altered VSD movement of KCNQ1 by KCNE proteins has been examined by site-directed mutagenesis, the scanning cysteine accessibility method (SCAM), voltage clamp fluorometry (VCF) and gating charge measurements. These accumulated data support the idea that KCNE proteins interact with the VSDs of KCNQ1 and modulate the gating of the KCNQ1 channel. In this review, we will summarize recent findings and current views of the KCNQ1 modulation by KCNE via the VSD. In this context, we discuss our recent findings that KCNE1 may alter physical interactions between the S4 segment (VSD) and the S5 segment (pore domain) of KCNQ1. Based on these findings from ourselves and others, we propose a hypothetical mechanism for how KCNE1 binding alters the VSD movement and the gating of the channel. © 2015 The Authors. The Journal of Physiology © 2015 The Physiological Society.

  5. Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain.

    Science.gov (United States)

    Li, Qufei; Wanderling, Sherry; Sompornpisut, Pornthep; Perozo, Eduardo

    2014-02-01

    Voltage-gated ion channels respond to transmembrane electric fields through reorientations of the positively charged S4 helix within the voltage-sensing domain (VSD). Despite a wealth of structural and functional data, the details of this conformational change remain controversial. Recent electrophysiological evidence showed that equilibrium between the resting ('down') and activated ('up') conformations of the KvAP VSD from Aeropyrum pernix can be biased through reconstitution in lipids with or without phosphate groups. We investigated the structural transition between these functional states, using site-directed spin-labeling and EPR spectroscopic methods. Solvent accessibility and interhelical distance determinations suggest that KvAP gates through S4 movements involving an ∼3-Å upward tilt and simultaneous ∼2-Å axial shift. This motion leads to large accessibly changes in the intracellular water-filled crevice and supports a new model of gating that combines structural rearrangements and electric-field remodeling.

  6. Coupling between the voltage-sensing and phosphatase domains of Ci-VSP.

    Science.gov (United States)

    Villalba-Galea, Carlos A; Miceli, Francesco; Taglialatela, Maurizio; Bezanilla, Francisco

    2009-07-01

    The Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP) shares high homology with the phosphatidylinositol phosphatase enzyme known as PTEN (phosphatase and tensin homologue deleted on chromosome 10). We have taken advantage of the similarity between these proteins to inquire about the coupling between the voltage sensing and the phosphatase domains in Ci-VSP. Recently, it was shown that four basic residues (R11, K13, R14, and R15) in PTEN are critical for its binding onto the membrane, required for its catalytic activity. Ci-VSP has three of the basic residues of PTEN. Here, we show that when R253 and R254 (which are the homologues of R14 and R15 in PTEN) are mutated to alanines in Ci-VSP, phosphatase activity is disrupted, as revealed by a lack of effect on the ionic currents of KCNQ2/3, where current decrease is a measure of phosphatase activity. The enzymatic activity was not rescued by the introduction of lysines, indicating that the binding is an arginine-specific interaction between the phosphatase binding domain and the membrane, presumably through the phosphate groups of the phospholipids. We also found that the kinetics and steady-state voltage dependence of the S4 segment movement are affected when the arginines are not present, indicating that the interaction of R253 and R254 with the membrane, required for the catalytic action of the phosphatase, restricts the movement of the voltage sensor.

  7. Exploration of genetically encoded voltage indicators based on a chimeric voltage sensing domain

    Directory of Open Access Journals (Sweden)

    Yukiko eMishina

    2014-09-01

    Full Text Available Deciphering how the brain generates cognitive function from patterns of electrical signals is one of the ultimate challenges in neuroscience. To this end, it would be highly desirable to monitor the activities of very large numbers of neurons while an animal engages in complex behaviours. Optical imaging of electrical activity using genetically encoded voltage indicators (GEVIs has the potential to meet this challenge. Currently prevalent GEVIs are based on the voltage-sensitive fluorescent protein (VSFP prototypical design or on the voltage dependent state transitions of microbial opsins.We recently introduced a new VSFP design in which the voltage-sensing domain (VSD is sandwiched between a FRET pair of fluorescent proteins (termed VSFP-Butterflies and also demonstrated a series of chimeric VSD in which portions of the VSD of Ciona intestinalis voltage-sensitive phosphatase (Ci-VSP are substituted by homologous portions of a voltage-gated potassium channel subunit. These chimeric VSD had faster sensing kinetics than that of the native Ci-VSD. Here, we describe a new set of VSFPs that combine chimeric VSD with the Butterfly structure. We show that these chimeric VSFP-Butterflies can report membrane voltage oscillations of up to 200 Hz in cultured cells and report sensory evoked cortical population responses in living mice. This class of GEVIs may be suitable for imaging of brain rhythms in behaving mammalians.

  8. Exploration of genetically encoded voltage indicators based on a chimeric voltage sensing domain.

    Science.gov (United States)

    Mishina, Yukiko; Mutoh, Hiroki; Song, Chenchen; Knöpfel, Thomas

    2014-01-01

    Deciphering how the brain generates cognitive function from patterns of electrical signals is one of the ultimate challenges in neuroscience. To this end, it would be highly desirable to monitor the activities of very large numbers of neurons while an animal engages in complex behaviors. Optical imaging of electrical activity using genetically encoded voltage indicators (GEVIs) has the potential to meet this challenge. Currently prevalent GEVIs are based on the voltage-sensitive fluorescent protein (VSFP) prototypical design or on the voltage-dependent state transitions of microbial opsins. We recently introduced a new VSFP design in which the voltage-sensing domain (VSD) is sandwiched between a fluorescence resonance energy transfer pair of fluorescent proteins (termed VSFP-Butterflies) and also demonstrated a series of chimeric VSD in which portions of the VSD of Ciona intestinalis voltage-sensitive phosphatase are substituted by homologous portions of a voltage-gated potassium channel subunit. These chimeric VSD had faster sensing kinetics than that of the native Ci-VSD. Here, we describe a new set of VSFPs that combine chimeric VSD with the Butterfly structure. We show that these chimeric VSFP-Butterflies can report membrane voltage oscillations of up to 200 Hz in cultured cells and report sensory evoked cortical population responses in living mice. This class of GEVIs may be suitable for imaging of brain rhythms in behaving mammalians.

  9. Voltage-dependent gating of KCNH potassium channels lacking a covalent link between voltage-sensing and pore domains

    Science.gov (United States)

    Lörinczi, Éva; Gómez-Posada, Juan Camilo; de La Peña, Pilar; Tomczak, Adam P.; Fernández-Trillo, Jorge; Leipscher, Ulrike; Stühmer, Walter; Barros, Francisco; Pardo, Luis A.

    2015-03-01

    Voltage-gated channels open paths for ion permeation upon changes in membrane potential, but how voltage changes are coupled to gating is not entirely understood. Two modules can be recognized in voltage-gated potassium channels, one responsible for voltage sensing (transmembrane segments S1 to S4), the other for permeation (S5 and S6). It is generally assumed that the conversion of a conformational change in the voltage sensor into channel gating occurs through the intracellular S4-S5 linker that provides physical continuity between the two regions. Using the pathophysiologically relevant KCNH family, we show that truncated proteins interrupted at, or lacking the S4-S5 linker produce voltage-gated channels in a heterologous model that recapitulate both the voltage-sensing and permeation properties of the complete protein. These observations indicate that voltage sensing by the S4 segment is transduced to the channel gate in the absence of physical continuity between the modules.

  10. Genetically encoded fluorescent voltage sensors using the voltage-sensing domain of Nematostella and Danio phosphatases exhibit fast kinetics.

    Science.gov (United States)

    Baker, Bradley J; Jin, Lei; Han, Zhou; Cohen, Lawrence B; Popovic, Marko; Platisa, Jelena; Pieribone, Vincent

    2012-07-15

    A substantial increase in the speed of the optical response of genetically encoded fluorescent protein voltage sensors (FP voltage sensors) was achieved by using the voltage-sensing phosphatase genes of Nematostella vectensis and Danio rerio. A potential N. vectensis voltage-sensing phosphatase was identified in silico. The voltage-sensing domain (S1-S4) of the N. vectensis homolog was used to create an FP voltage sensor called Nema. By replacing the phosphatase with a cerulean/citrine FRET pair, a new FP voltage sensor was synthesized with fast off kinetics (Tau(off)voltage-sensing phosphatase homolog, designated Zahra and Zahra 2, exhibited fast on and off kinetics within 2ms of the time constants observed with the organic voltage-sensitive dye, di4-ANEPPS. Mutagenesis of the S4 region of the Danio FP voltage sensor shifted the voltage dependence to more negative potentials but did not noticeably affect the kinetics of the optical signal. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Genetically-encoded fluorescent voltage sensors using the voltage-sensing domain of Nematostella and Danio phosphatases exhibit fast kinetics

    Science.gov (United States)

    Baker, Bradley J.; Jin, Lei; Han, Zhou; Cohen, Lawrence B.; Popovic, Marko; Platisa, Jelena; Pieribone, Vincent

    2012-01-01

    A substantial increase in the speed of the optical response of genetically-encoded Fluorescent Protein voltage sensors (FP voltage sensors) was achieved by using the voltage-sensing phosphatase genes of Nematostella vectensis and Danio rerio. A potential N. vectensis voltage-sensing phosphatase was identified in silico. The voltage-sensing domain (S1–S4) of the N. vectensis homolog was used to create an FP voltage sensor called Nema. By replacing the phosphatase with a cerulean/citrine FRET pair, a new FP voltage sensor was synthesized with fast off kinetics (Tauoff voltage-sensing phosphatase homolog, designated Zahra and Zahra 2, exhibited fast on and off kinetics within 2 msec of the time constants observed with the organic voltage-sensitive dye, di4-ANEPPS. Mutagenesis of the S4 region of the Danio FP voltage sensor shifted the voltage dependence to more negative potentials but did not noticeably affect the kinetics of the optical signal. PMID:22634212

  12. Biophysical characterization of the fluorescent protein voltage probe VSFP2.3 based on the voltage-sensing domain of Ci-VSP

    DEFF Research Database (Denmark)

    Lundby, Alicia; Akemann, Walther; Knöpfel, Thomas

    2010-01-01

    A voltage sensitive phosphatase was discovered in the ascidian Ciona intestinalis. The phosphatase, Ci-VSP, contains a voltage-sensing domain homologous to those known from voltage-gated ion channels, but unlike ion channels, the voltage-sensing domain of Ci-VSP can reside in the cell membrane...... as a monomer. We fused the voltage-sensing domain of Ci-VSP to a pair of fluorescent reporter proteins to generate a genetically encodable voltage-sensing fluorescent probe, VSFP2.3. VSFP2.3 is a fluorescent voltage probe that reports changes in membrane potential as a FRET (fluorescence resonance energy....... Neutralization of an arginine in S4, previously suggested to be a sensing charge, and measuring associated sensing currents indicate that this charge is likely to reside at the membrane-aqueous interface rather than within the membrane electric field. The data presented give us insights into the voltage-sensing...

  13. Mapping the membrane-aqueous border for the voltage-sensing domain of a potassium channel.

    Science.gov (United States)

    Neale, Edward J; Rong, Honglin; Cockcroft, Christopher J; Sivaprasadarao, Asipu

    2007-12-28

    Voltage-sensing domains (VSDs) play diverse roles in biology. As integral components, they can detect changes in the membrane potential of a cell and couple these changes to activity of ion channels and enzymes. As independent proteins, homologues of the VSD can function as voltage-dependent proton channels. To sense voltage changes, the positively charged fourth transmembrane segment, S4, must move across the energetically unfavorable hydrophobic core of the bilayer, which presents a barrier to movement of both charged species and protons. To reduce the barrier to S4 movement, it has been suggested that aqueous crevices may penetrate the protein, reducing the extent of total movement. To investigate this hypothesis in a system containing fully functional channels in a native environment with an intact membrane potential, we have determined the contour of the membrane-aqueous border of the VSD of KvAP in Escherichia coli by examining the chemical accessibility of introduced cysteines. The results revealed the contour of the membrane-aqueous border of the VSD in its activated conformation. The water-inaccessible regions of S1 and S2 correspond to the standard width of the membrane bilayer (~28 A), but those of S3 and S4 are considerably shorter (> or = 40%), consistent with aqueous crevices pervading both the extracellular and intracellular ends. One face of S3b and the entire S3a were water-accessible, reducing the water-inaccessible region of S3 to just 10 residues, significantly shorter than for S4. The results suggest a key role for S3 in reducing the distance S4 needs to move to elicit gating.

  14. Interactions between charged residues in the transmembrane segments of the voltage-sensing domain in the hERG channel.

    Science.gov (United States)

    Zhang, M; Liu, J; Jiang, M; Wu, D-M; Sonawane, K; Guy, H R; Tseng, G-N

    2005-10-01

    Studies on voltage-gated K channels such as Shaker have shown that positive charges in the voltage-sensor (S4) can form salt bridges with negative charges in the surrounding transmembrane segments in a state-dependent manner, and different charge pairings can stabilize the channels in closed or open states. The goal of this study is to identify such charge interactions in the hERG channel. This knowledge can provide constraints on the spatial relationship among transmembrane segments in the channel's voltage-sensing domain, which are necessary for modeling its structure. We first study the effects of reversing S4's positive charges on channel activation. Reversing positive charges at the outer (K525D) and inner (K538D) ends of S4 markedly accelerates hERG activation, whereas reversing the 4 positive charges in between either has no effect or slows activation. We then use the 'mutant cycle analysis' to test whether D456 (outer end of S2) and D411 (inner end of S1) can pair with K525 and K538, respectively. Other positive charges predicted to be able, or unable, to interact with D456 or D411 are also included in the analysis. The results are consistent with predictions based on the distribution of these charged residues, and confirm that there is functional coupling between D456 and K525 and between D411 and K538.

  15. Voltage-sensing domain of voltage-gated proton channel Hv1 shares mechanism of block with pore domains.

    Science.gov (United States)

    Hong, Liang; Pathak, Medha M; Kim, Iris H; Ta, Dennis; Tombola, Francesco

    2013-01-23

    Voltage-gated sodium, potassium, and calcium channels are made of a pore domain (PD) controlled by four voltage-sensing domains (VSDs). The PD contains the ion permeation pathway and the activation gate located on the intracellular side of the membrane. A large number of small molecules are known to inhibit the PD by acting as open channel blockers. The voltage-gated proton channel Hv1 is made of two VSDs and lacks the PD. The location of the activation gate in the VSD is unknown and open channel blockers for VSDs have not yet been identified. Here, we describe a class of small molecules which act as open channel blockers on the Hv1 VSD and find that a highly conserved phenylalanine in the charge transfer center of the VSD plays a key role in blocker binding. We then use one of the blockers to show that Hv1 contains two intracellular and allosterically coupled gates. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Combinatorial mutagenesis of the voltage-sensing domain enables the optical resolution of action potentials firing at 60 Hz by a genetically encoded fluorescent sensor of membrane potential.

    Science.gov (United States)

    Piao, Hong Hua; Rajakumar, Dhanarajan; Kang, Bok Eum; Kim, Eun Ha; Baker, Bradley J

    2015-01-07

    ArcLight is a genetically encoded fluorescent voltage sensor using the voltage-sensing domain of the voltage-sensing phosphatase from Ciona intestinalis that gives a large but slow-responding optical signal in response to changes in membrane potential (Jin et al., 2012). Fluorescent voltage sensors using the voltage-sensing domain from other species give faster yet weaker optical signals (Baker et al., 2012; Han et al., 2013). Sequence alignment of voltage-sensing phosphatases from different species revealed conserved polar and charged residues at 7 aa intervals in the S1-S3 transmembrane segments of the voltage-sensing domain, suggesting potential coil-coil interactions. The contribution of these residues to the voltage-induced optical signal was tested using a cassette mutagenesis screen by flanking each transmembrane segment with unique restriction sites to allow for the testing of individual mutations in each transmembrane segment, as well as combinations in all four transmembrane segments. Addition of a counter charge in S2 improved the kinetics of the optical response. A double mutation in the S4 domain dramatically reduced the slow component of the optical signal seen in ArcLight. Combining that double S4 mutant with the mutation in the S2 domain yielded a probe with kinetics voltage-sensing domain could potentially lead to fluorescent sensors capable of optically resolving neuronal inhibition and subthreshold synaptic activity. Copyright © 2015 the authors 0270-6474/15/350372-15$15.00/0.

  17. Blue Light-excited Light-Oxygen-Voltage-sensing Domain 2 (LOV2) Triggers a Rearrangement of the Kinase Domain to Induce Phosphorylation Activity in Arabidopsis Phototropin1.

    Science.gov (United States)

    Oide, Mao; Okajima, Koji; Kashojiya, Sachiko; Takayama, Yuki; Oroguchi, Tomotaka; Hikima, Takaaki; Yamamoto, Masaki; Nakasako, Masayoshi

    2016-09-16

    Phototropin1 is a blue light (BL) receptor in plants and shows BL-dependent kinase activation. The BL-excited light-oxygen-voltage-sensing domain 2 (LOV2) is primarily responsible for the activation of the kinase domain; however, the molecular mechanism by which conformational changes in LOV2 are transmitted to the kinase domain remains unclear. Here, we investigated BL-induced structural changes of a minimum functional fragment of Arabidopsis phototropin1 composed of LOV2, the kinase domain, and a linker connecting the two domains using small-angle x-ray scattering (SAXS). The fragment existed as a dimer and displayed photoreversible SAXS changes reflected in the radii of gyration of 42.9 Å in the dark and 48.8 Å under BL irradiation. In the dark, the molecular shape reconstructed from the SAXS profiles appeared as two bean-shaped lobes in a twisted arrangement that was 170 Å long, 80 Å wide, and 50 Å thick. The molecular shape under BL became slightly elongated from that in the dark. By fitting the crystal structure of the LOV2 dimer and a homology model of the kinase domain to their inferred shapes, the BL-dependent change could be interpreted as the positional shift in the kinase domain relative to that of the LOV2 dimer. In addition, we found that lysine 475, a functionally important residue, in the N-terminal region of LOV2 plays a critical role in transmitting the structural changes in LOV2 to the kinase domain. The interface between the domains is critical for signaling, suitably changing the structure to activate the kinase in response to conformational changes in the adjoining LOV2. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Functional interactions at the interface between voltage-sensing and pore domains in the Shaker K(v) channel.

    Science.gov (United States)

    Soler-Llavina, Gilberto J; Chang, Tsg-Hui; Swartz, Kenton J

    2006-11-22

    Voltage-activated potassium (K(v)) channels contain a central pore domain that is partially surrounded by four voltage-sensing domains. Recent X-ray structures suggest that the two domains lack extensive protein-protein contacts within presumed transmembrane regions, but whether this is the case for functional channels embedded in lipid membranes remains to be tested. We investigated domain interactions in the Shaker K(v) channel by systematically mutating the pore domain and assessing tolerance by examining channel maturation, S4 gating charge movement, and channel opening. When mapped onto the X-ray structure of the K(v)1.2 channel the large number of permissive mutations support the notion of relatively independent domains, consistent with crystallographic studies. Inspection of the maps also identifies portions of the interface where residues are sensitive to mutation, an external cluster where mutations hinder voltage sensor activation, and an internal cluster where domain interactions between S4 and S5 helices from adjacent subunits appear crucial for the concerted opening transition.

  19. Biophysical characterization of the fluorescent protein voltage probe VSFP2.3 based on the voltage-sensing domain of Ci-VSP.

    Science.gov (United States)

    Lundby, Alicia; Akemann, Walther; Knöpfel, Thomas

    2010-11-01

    A voltage sensitive phosphatase was discovered in the ascidian Ciona intestinalis. The phosphatase, Ci-VSP, contains a voltage-sensing domain homologous to those known from voltage-gated ion channels, but unlike ion channels, the voltage-sensing domain of Ci-VSP can reside in the cell membrane as a monomer. We fused the voltage-sensing domain of Ci-VSP to a pair of fluorescent reporter proteins to generate a genetically encodable voltage-sensing fluorescent probe, VSFP2.3. VSFP2.3 is a fluorescent voltage probe that reports changes in membrane potential as a FRET (fluorescence resonance energy transfer) signal. Here we report sensing current measurements from VSFP2.3, and show that VSFP2.3 carries 1.2 e sensing charges, which are displaced within 1.5 ms. The sensing currents become faster at higher temperatures, and the voltage dependence of the decay time constants is temperature dependent. Neutralization of an arginine in S4, previously suggested to be a sensing charge, and measuring associated sensing currents indicate that this charge is likely to reside at the membrane-aqueous interface rather than within the membrane electric field. The data presented give us insights into the voltage-sensing mechanism of Ci-VSP, which will allow us to further improve the sensitivity and kinetics of the family of VSFP proteins.

  20. Functional characterization of Kv11.1 (hERG) potassium channels split in the voltage-sensing domain.

    Science.gov (United States)

    de la Peña, Pilar; Domínguez, Pedro; Barros, Francisco

    2018-03-23

    Voltage-dependent KCNH family potassium channel functionality can be reconstructed using non-covalently linked voltage-sensing domain (VSD) and pore modules (split channels). However, the necessity of a covalent continuity for channel function has not been evaluated at other points within the two functionally independent channel modules. We find here that by cutting Kv11.1 (hERG, KCNH2) channels at the different loops linking the transmembrane spans of the channel core, not only channels split at the S4-S5 linker level, but also those split at the intracellular S2-S3 and the extracellular S3-S4 loops, yield fully functional channel proteins. Our data indicate that albeit less markedly, channels split after residue 482 in the S2-S3 linker resemble the uncoupled gating phenotype of those split at the C-terminal end of the VSD S4 transmembrane segment. Channels split after residues 514 and 518 in the S3-S4 linker show gating characteristics similar to those of the continuous wild-type channel. However, breaking the covalent link at this level strongly accelerates the voltage-dependent accessibility of a membrane impermeable methanethiosulfonate reagent to an engineered cysteine at the N-terminal region of the S4 transmembrane helix. Thus, besides that of the S4-S5 linker, structural integrity of the intracellular S2-S3 linker seems to constitute an important factor for proper transduction of VSD rearrangements to opening and closing the cytoplasmic gate. Furthermore, our data suggest that the short and probably rigid characteristics of the extracellular S3-S4 linker are not an essential component of the Kv11.1 voltage sensing machinery.

  1. Enzyme domain affects the movement of the voltage sensor in ascidian and zebrafish voltage-sensing phosphatases.

    Science.gov (United States)

    Hossain, Md Israil; Iwasaki, Hirohide; Okochi, Yoshifumi; Chahine, Mohamed; Higashijima, Shinichi; Nagayama, Kuniaki; Okamura, Yasushi

    2008-06-27

    The ascidian voltage-sensing phosphatase (Ci-VSP) consists of the voltage sensor domain (VSD) and a cytoplasmic phosphatase region that has significant homology to the phosphatase and tensin homolog deleted on chromosome TEN (PTEN). The phosphatase activity of Ci-VSP is modified by the conformational change of the VSD. In many proteins, two protein modules are bidirectionally coupled, but it is unknown whether the phosphatase domain could affect the movement of the VSD in VSP. We addressed this issue by whole-cell patch recording of gating currents from a teleost VSP (Dr-VSP) cloned from Danio rerio expressed in tsA201 cells. Replacement of a critical cysteine residue, in the phosphatase active center of Dr-VSP, by serine sharpened both ON- and OFF-gating currents. Similar changes were produced by treatment with phosphatase inhibitors, pervanadate and orthovanadate, that constitutively bind to cysteine in the active catalytic center of phosphatases. The distinct kinetics of gating currents dependent on enzyme activity were not because of altered phosphatidylinositol 4,5-bisphosphate levels, because the kinetics of gating current did not change by depletion of phosphatidylinositol 4,5-bisphosphate, as reported by coexpressed KCNQ2/3 channels. These results indicate that the movement of the VSD is influenced by the enzymatic state of the cytoplasmic domain, providing an important clue for understanding mechanisms of coupling between the VSD and its effector.

  2. Mutations in the voltage-sensing domain affect the alternative ion permeation pathway in the TRPM3 channel.

    Science.gov (United States)

    Held, Katharina; Gruss, Fabian; Aloi, Vincenzo Davide; Janssens, Annelies; Ulens, Chris; Voets, Thomas; Vriens, Joris

    2018-03-31

    Mutagenesis at positively charged amino acids (arginines and lysines) (R1-R4) in the voltage-sensor domain (transmembrane segment (S) 4) of voltage-gated Na + , K + and Ca 2+ channels can lead to an alternative ion permeation pathway distinct from the central pore. Recently, a non-canonical ion permeation pathway was described in TRPM3, a member of the transient receptor potential (TRP) superfamily. The non-canonical pore exists in the native TRPM3 channel and can be activated by co-stimulation of the endogenous agonist pregnenolone sulphate and the antifungal drug clotrimazole or by stimulation of the synthetic agonist CIM0216. Alignment of the voltage sensor of Shaker K + channels with the entire TRPM3 sequence revealed the highest degree of similarity in the putative S4 region of TRPM3, and suggested that only one single gating charge arginine (R2) in the putative S4 region is conserved. Mutagenesis studies in the voltage-sensing domain of TRPM3 revealed several residues in the voltage sensor (S4) as well as in S1 and S3 that are crucial for the occurrence of the non-canonical inward currents. In conclusion, this study provides evidence for the involvement of the voltage-sensing domain of TRPM3 in the formation of an alternative ion permeation pathway. Transient receptor potential (TRP) channels are cationic channels involved in a broad array of functions, including homeostasis, motility and sensory functions. TRP channel subunits consist of six transmembrane segments (S1-S6), and form tetrameric channels with a central pore formed by the region encompassing S5 and S6. Recently, evidence was provided for the existence of an alternative ion permeation pathway in TRPM3, which allows large inward currents upon hyperpolarization independently of the central pore. However, very little knowledge is available concerning the localization of this alternative pathway in the native TRPM3 channel protein. Guided by sequence homology with Shaker K + channels, in which

  3. Localization and Molecular Determinants of the Hanatoxin Receptors on the Voltage-Sensing Domains of a K+ Channel

    Science.gov (United States)

    Li-Smerin, Yingying; Swartz, Kenton J.

    2000-01-01

    Hanatoxin inhibits voltage-gated K+ channels by modifying the energetics of activation. We studied the molecular determinants and physical location of the Hanatoxin receptors on the drk1 voltage-gated K+ channel. First, we made multiple substitutions at three previously identified positions in the COOH terminus of S3 to examine whether these residues interact intimately with the toxin. We also examined a region encompassing S1–S3 using alanine-scanning mutagenesis to identify additional determinants of the toxin receptors. Finally, guided by the structure of the KcsA K+ channel, we explored whether the toxin interacts with the peripheral extracellular surface of the pore domain in the drk1 K+ channel. Our results argue for an intimate interaction between the toxin and the COOH terminus of S3 and suggest that the Hanatoxin receptors are confined within the voltage-sensing domains of the channel, at least 20–25 Å away from the central pore axis. PMID:10828242

  4. NMR investigation of the isolated second voltage-sensing domain of human Nav1.4 channel.

    Science.gov (United States)

    Paramonov, A S; Lyukmanova, E N; Myshkin, M Yu; Shulepko, M A; Kulbatskii, D S; Petrosian, N S; Chugunov, A O; Dolgikh, D A; Kirpichnikov, M P; Arseniev, A S; Shenkarev, Z O

    2017-03-01

    Voltage-gated Na + channels are essential for the functioning of cardiovascular, muscular, and nervous systems. The α-subunit of eukaryotic Na + channel consists of ~2000 amino acid residues and encloses 24 transmembrane (TM) helices, which form five membrane domains: four voltage-sensing (VSD) and one pore domain. The structural complexity significantly impedes recombinant production and structural studies of full-sized Na + channels. Modular organization of voltage-gated channels gives an idea for studying of the isolated second VSD of human skeletal muscle Nav1.4 channel (VSD-II). Several variants of VSD-II (~150a.a., four TM helices) with different N- and C-termini were produced by cell-free expression. Screening of membrane mimetics revealed low stability of VSD-II samples in media containing phospholipids (bicelles, nanodiscs) associated with the aggregation of electrically neutral domain molecules. The almost complete resonance assignment of 13 C, 15 N-labeled VSD-II was obtained in LPPG micelles. The secondary structure of VSD-II showed similarity with the structures of bacterial Na + channels. The fragment of S4 TM helix between the first and second conserved Arg residues probably adopts 3 10 -helical conformation. Water accessibility of S3 helix, observed by the Mn 2+ titration, pointed to the formation of water-filled crevices in the micelle embedded VSD-II. 15 N relaxation data revealed characteristic pattern of μs-ms time scale motions in the VSD-II regions sharing expected interhelical contacts. VSD-II demonstrated enhanced mobility at ps-ns time scale as compared to isolated VSDs of K + channels. These results validate structural studies of isolated VSDs of Na + channels and show possible pitfalls in application of this 'divide and conquer' approach. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. The Voltage-Sensing Domain of Kv7.2 Channels as a Molecular Target for Epilepsy-Causing Mutations and Anticonvulsants

    Science.gov (United States)

    Miceli, Francesco; Soldovieri, Maria Virginia; Iannotti, Fabio Arturo; Barrese, Vincenzo; Ambrosino, Paolo; Martire, Maria; Cilio, Maria Roberta; Taglialatela, Maurizio

    2010-01-01

    Understanding the molecular mechanisms underlying voltage-dependent gating in voltage-gated ion channels (VGICs) has been a major effort over the last decades. In recent years, changes in the gating process have emerged as common denominators for several genetically determined channelopathies affecting heart rhythm (arrhythmias), neuronal excitability (epilepsy, pain), or skeletal muscle contraction (periodic paralysis). Moreover, gating changes appear as the main molecular mechanism by which several natural toxins from a variety of species affect ion channel function. In this work, we describe the pathophysiological and pharmacological relevance of the gating process in voltage-gated K+ channels encoded by the Kv7 gene family. After reviewing the current knowledge on the molecular mechanisms and on the structural models of voltage-dependent gating in VGICs, we describe the physiological relevance of these channels, with particular emphasis on those formed by Kv7.2–Kv7.5 subunits having a well-established role in controlling neuronal excitability in humans. In fact, genetically determined alterations in Kv7.2 and Kv7.3 genes are responsible for benign familial neonatal convulsions, a rare seizure disorder affecting newborns, and the pharmacological activation of Kv7.2/3 channels can exert antiepileptic activity in humans. Both mutation-triggered channel dysfunction and drug-induced channel activation can occur by impeding or facilitating, respectively, channel sensitivity to membrane voltage and can affect overlapping molecular sites within the voltage-sensing domain of these channels. Thus, understanding the molecular steps involved in voltage-sensing in Kv7 channels will allow to better define the pathogenesis of rare human epilepsy, and to design innovative pharmacological strategies for the treatment of epilepsies and, possibly, other human diseases characterized by neuronal hyperexcitability. PMID:21687499

  6. The voltage-sensing domain of kv7.2 channels as a molecular target for epilepsy-causing mutations and anticonvulsants

    Directory of Open Access Journals (Sweden)

    Francesco eMiceli

    2011-02-01

    Full Text Available Understanding the molecular mechanisms underlying voltage-dependent gating in voltage-gated ion channels (VGICs has been a major effort over the last decades. In recent years, changes in the gating process have emerged as common denominators for several genetically-determined channelopathies affecting heart rhythm (arrhythmias, neuronal excitability (epilepsy, pain or skeletal muscle contraction (periodic paralysis. Moreover, gating changes appear as the main molecular mechanism by which several natural toxins from a variety of species affect ion channel function.In this work, we describe the pathophysiological and pharmacological relevance of the gating process in voltage-gated K+ channels encoded by the Kv7 gene family. After reviewing the current knowledge on the molecular mechanisms and on the structural models of voltage-dependent gating in VGICs, we describe the physiological relevance of these channels, with particular emphasis on those formed by Kv7.2-5 subunits having a well-established role in controlling neuronal excitability in humans. In fact, genetically-determined alterations in Kv7.2 and Kv7.3 genes are responsible for benign familial neonatal convulsions, a rare seizure disorder affecting newborns, and the pharmacological activation of Kv7.2/3 channels can exert antiepileptic activity in humans. Both mutation-triggered channel dysfunction and drug-induced channel activation can occur by impeding or facilitating, respectively, channel sensitivity to membrane voltage and can affect overlapping molecular sites within the voltage-sensing domain of these channels. Thus, understanding the molecular steps involved in voltage-sensing in Kv7 channels will allow to better define the pathogenesis of rare human epilepsy, and to design innovative pharmacological strategies for the treatment of epilepsies and, possibly, other human diseases characterized by neuronal hyperexcitability.

  7. The Voltage-Sensing Domain of K(v)7.2 Channels as a Molecular Target for Epilepsy-Causing Mutations and Anticonvulsants.

    Science.gov (United States)

    Miceli, Francesco; Soldovieri, Maria Virginia; Iannotti, Fabio Arturo; Barrese, Vincenzo; Ambrosino, Paolo; Martire, Maria; Cilio, Maria Roberta; Taglialatela, Maurizio

    2011-01-01

    Understanding the molecular mechanisms underlying voltage-dependent gating in voltage-gated ion channels (VGICs) has been a major effort over the last decades. In recent years, changes in the gating process have emerged as common denominators for several genetically determined channelopathies affecting heart rhythm (arrhythmias), neuronal excitability (epilepsy, pain), or skeletal muscle contraction (periodic paralysis). Moreover, gating changes appear as the main molecular mechanism by which several natural toxins from a variety of species affect ion channel function. In this work, we describe the pathophysiological and pharmacological relevance of the gating process in voltage-gated K(+) channels encoded by the K(v)7 gene family. After reviewing the current knowledge on the molecular mechanisms and on the structural models of voltage-dependent gating in VGICs, we describe the physiological relevance of these channels, with particular emphasis on those formed by K(v)7.2-K(v)7.5 subunits having a well-established role in controlling neuronal excitability in humans. In fact, genetically determined alterations in K(v)7.2 and K(v)7.3 genes are responsible for benign familial neonatal convulsions, a rare seizure disorder affecting newborns, and the pharmacological activation of K(v)7.2/3 channels can exert antiepileptic activity in humans. Both mutation-triggered channel dysfunction and drug-induced channel activation can occur by impeding or facilitating, respectively, channel sensitivity to membrane voltage and can affect overlapping molecular sites within the voltage-sensing domain of these channels. Thus, understanding the molecular steps involved in voltage-sensing in K(v)7 channels will allow to better define the pathogenesis of rare human epilepsy, and to design innovative pharmacological strategies for the treatment of epilepsies and, possibly, other human diseases characterized by neuronal hyperexcitability.

  8. Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.

    Science.gov (United States)

    Subbotina, Julia; Yarov-Yarovoy, Vladimir; Lees-Miller, James; Durdagi, Serdar; Guo, Jiqing; Duff, Henry J; Noskov, Sergei Yu

    2010-11-01

    The hERG1 gene (Kv11.1) encodes a voltage-gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template-driven de-novo design with ROSETTA-membrane modeling using side-chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2-Kv2.1 chimera channels, the missing parts are modeled de-novo. The impact of several alignments on the structure of the S4 helix in the voltage-sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage-sensor domain; and the topology of the extracellular S5-pore linker compared with that established by toxin foot-printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed. © 2010 Wiley-Liss, Inc.

  9. Inter-subunit interactions across the upper voltage sensing-pore domain interface contribute to the concerted pore opening transition of Kv channels.

    Directory of Open Access Journals (Sweden)

    Tzilhav Shem-Ad

    Full Text Available The tight electro-mechanical coupling between the voltage-sensing and pore domains of Kv channels lies at the heart of their fundamental roles in electrical signaling. Structural data have identified two voltage sensor pore inter-domain interaction surfaces, thus providing a framework to explain the molecular basis for the tight coupling of these domains. While the contribution of the intra-subunit lower domain interface to the electro-mechanical coupling that underlies channel opening is relatively well understood, the contribution of the inter-subunit upper interface to channel gating is not yet clear. Relying on energy perturbation and thermodynamic coupling analyses of tandem-dimeric Shaker Kv channels, we show that mutation of upper interface residues from both sides of the voltage sensor-pore domain interface stabilizes the closed channel state. These mutations, however, do not affect slow inactivation gating. We, moreover, find that upper interface residues form a network of state-dependent interactions that stabilize the open channel state. Finally, we note that the observed residue interaction network does not change during slow inactivation gating. The upper voltage sensing-pore interaction surface thus only undergoes conformational rearrangements during channel activation gating. We suggest that inter-subunit interactions across the upper domain interface mediate allosteric communication between channel subunits that contributes to the concerted nature of the late pore opening transition of Kv channels.

  10. Inter-subunit interactions across the upper voltage sensing-pore domain interface contribute to the concerted pore opening transition of Kv channels.

    Science.gov (United States)

    Shem-Ad, Tzilhav; Irit, Orr; Yifrach, Ofer

    2013-01-01

    The tight electro-mechanical coupling between the voltage-sensing and pore domains of Kv channels lies at the heart of their fundamental roles in electrical signaling. Structural data have identified two voltage sensor pore inter-domain interaction surfaces, thus providing a framework to explain the molecular basis for the tight coupling of these domains. While the contribution of the intra-subunit lower domain interface to the electro-mechanical coupling that underlies channel opening is relatively well understood, the contribution of the inter-subunit upper interface to channel gating is not yet clear. Relying on energy perturbation and thermodynamic coupling analyses of tandem-dimeric Shaker Kv channels, we show that mutation of upper interface residues from both sides of the voltage sensor-pore domain interface stabilizes the closed channel state. These mutations, however, do not affect slow inactivation gating. We, moreover, find that upper interface residues form a network of state-dependent interactions that stabilize the open channel state. Finally, we note that the observed residue interaction network does not change during slow inactivation gating. The upper voltage sensing-pore interaction surface thus only undergoes conformational rearrangements during channel activation gating. We suggest that inter-subunit interactions across the upper domain interface mediate allosteric communication between channel subunits that contributes to the concerted nature of the late pore opening transition of Kv channels.

  11. Substitutions in the domain III voltage-sensing module enhance the sensitivity of an insect sodium channel to a scorpion beta-toxin.

    Science.gov (United States)

    Song, Weizhong; Du, Yuzhe; Liu, Zhiqi; Luo, Ningguang; Turkov, Michael; Gordon, Dalia; Gurevitz, Michael; Goldin, Alan L; Dong, Ke

    2011-05-06

    Scorpion β-toxins bind to the extracellular regions of the voltage-sensing module of domain II and to the pore module of domain III in voltage-gated sodium channels and enhance channel activation by trapping and stabilizing the voltage sensor of domain II in its activated state. We investigated the interaction of a highly potent insect-selective scorpion depressant β-toxin, Lqh-dprIT(3), from Leiurus quinquestriatus hebraeus with insect sodium channels from Blattella germanica (BgNa(v)). Like other scorpion β-toxins, Lqh-dprIT(3) shifts the voltage dependence of activation of BgNa(v) channels expressed in Xenopus oocytes to more negative membrane potentials but only after strong depolarizing prepulses. Notably, among 10 BgNa(v) splice variants tested for their sensitivity to the toxin, only BgNa(v)1-1 was hypersensitive due to an L1285P substitution in IIIS1 resulting from a U-to-C RNA-editing event. Furthermore, charge reversal of a negatively charged residue (E1290K) at the extracellular end of IIIS1 and the two innermost positively charged residues (R4E and R5E) in IIIS4 also increased the channel sensitivity to Lqh-dprIT(3). Besides enhancement of toxin sensitivity, the R4E substitution caused an additional 20-mV negative shift in the voltage dependence of activation of toxin-modified channels, inducing a unique toxin-modified state. Our findings provide the first direct evidence for the involvement of the domain III voltage-sensing module in the action of scorpion β-toxins. This hypersensitivity most likely reflects an increase in IIS4 trapping via allosteric mechanisms, suggesting coupling between the voltage sensors in neighboring domains during channel activation.

  12. C-terminal modulatory domain controls coupling of voltage-sensing to pore opening in Cav1.3 L-type Ca(2+) channels.

    Science.gov (United States)

    Lieb, Andreas; Ortner, Nadine; Striessnig, Jörg

    2014-04-01

    Activity of voltage-gated Cav1.3 L-type Ca(2+) channels is required for proper hearing as well as sinoatrial node and brain function. This critically depends on their negative activation voltage range, which is further fine-tuned by alternative splicing. Shorter variants miss a C-terminal regulatory domain (CTM), which allows them to activate at even more negative potentials than C-terminally long-splice variants. It is at present unclear whether this is due to an increased voltage sensitivity of the Cav1.3 voltage-sensing domain, or an enhanced coupling of voltage-sensor conformational changes to the subsequent opening of the activation gate. We studied the voltage-dependence of voltage-sensor charge movement (QON-V) and of current activation (ICa-V) of the long (Cav1.3L) and a short Cav1.3 splice variant (Cav1.342A) expressed in tsA-201 cells using whole cell patch-clamp. Charge movement (QON) of Cav1.3L displayed a much steeper voltage-dependence and a more negative half-maximal activation voltage than Cav1.2 and Cav3.1. However, a significantly higher fraction of the total charge had to move for activation of Cav1.3 half-maximal conductance (Cav1.3: 68%; Cav1.2: 52%; Cav3.1: 22%). This indicated a weaker coupling of Cav1.3 voltage-sensor charge movement to pore opening. However, the coupling efficiency was strengthened in the absence of the CTM in Cav1.342A, thereby shifting ICa-V by 7.2 mV to potentials that were more negative without changing QON-V. We independently show that the presence of intracellular organic cations (such as n-methyl-D-glucamine) induces a pronounced negative shift of QON-V and a more negative activation of ICa-V of all three channels. These findings illustrate that the voltage sensors of Cav1.3 channels respond more sensitively to depolarization than those of Cav1.2 or Cav3.1. Weak coupling of voltage sensing to pore opening is enhanced in the absence of the CTM, allowing short Cav1.342A splice variants to activate at lower voltages

  13. Kv7.1 ion channels require a lipid to couple voltage sensing to pore opening.

    Science.gov (United States)

    Zaydman, Mark A; Silva, Jonathan R; Delaloye, Kelli; Li, Yang; Liang, Hongwu; Larsson, H Peter; Shi, Jingyi; Cui, Jianmin

    2013-08-06

    Voltage-gated ion channels generate dynamic ionic currents that are vital to the physiological functions of many tissues. These proteins contain separate voltage-sensing domains, which detect changes in transmembrane voltage, and pore domains, which conduct ions. Coupling of voltage sensing and pore opening is critical to the channel function and has been modeled as a protein-protein interaction between the two domains. Here, we show that coupling in Kv7.1 channels requires the lipid phosphatidylinositol 4,5-bisphosphate (PIP2). We found that voltage-sensing domain activation failed to open the pore in the absence of PIP2. This result is due to loss of coupling because PIP2 was also required for pore opening to affect voltage-sensing domain activation. We identified a critical site for PIP2-dependent coupling at the interface between the voltage-sensing domain and the pore domain. This site is actually a conserved lipid-binding site among different K(+) channels, suggesting that lipids play an important role in coupling in many ion channels.

  14. NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating.

    Science.gov (United States)

    Shenkarev, Zakhar O; Paramonov, Alexander S; Lyukmanova, Ekaterina N; Shingarova, Lyudmila N; Yakimov, Sergei A; Dubinnyi, Maxim A; Chupin, Vladimir V; Kirpichnikov, Mikhail P; Blommers, Marcel J J; Arseniev, Alexander S

    2010-04-28

    The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein domain solubilized in DPC/LDAO (2:1) mixed micelles. Secondary and tertiary structures of the VSD were characterized using secondary chemical shifts and NOE contacts. These data indicate that the spatial structure of the VSD solubilized in micelles corresponds to the structure of the domain in an open state of the channel. NOE contacts and secondary chemical shifts of amide protons indicate the presence of tightly bound water molecule as well as hydrogen bond formation involving an interhelical salt bridge (Asp62-R133) that stabilizes the overall structure of the domain. The backbone dynamics of the VSD was studied using (15)N relaxation measurements. The loop regions S1-S2 and S2-S3 were found mobile, while the S3-S4 loop (voltage-sensor paddle) was found stable at the ps-ns time scale. The moieties of S1, S2, S3, and S4 helices sharing interhelical contacts (at the level of the Asp62-R133 salt bridge) were observed in conformational exchange on the micros-ms time scale. Similar exchange-induced broadening of characteristic resonances was observed for the VSD solubilized in the membrane of lipid-protein nanodiscs composed of DMPC, DMPG, and POPC/DOPG lipids. Apparently, the observed interhelical motions represent an inherent property of the VSD of the KvAP channel and can play an important role in the voltage gating.

  15. Caution Is Required in Interpretation of Mutations in the Voltage Sensing Domain of Voltage Gated Channels as Evidence for Gating Mechanisms

    Directory of Open Access Journals (Sweden)

    Alisher M. Kariev

    2015-01-01

    Full Text Available The gating mechanism of voltage sensitive ion channels is generally considered to be the motion of the S4 transmembrane segment of the voltage sensing domains (VSD. The primary supporting evidence came from R→C mutations on the S4 transmembrane segment of the VSD, followed by reaction with a methanethiosulfonate (MTS reagent. The cys side chain is –SH (reactive form –S−; the arginine side chain is much larger, leaving space big enough to accommodate the MTS sulfonate head group. The cavity created by the mutation has space for up to seven more water molecules than were present in wild type, which could be displaced irreversibly by the MTS reagent. Our quantum calculations show there is major reorientation of three aromatic residues that face into the cavity in response to proton displacement within the VSD. Two phenylalanines reorient sufficiently to shield/unshield the cysteine from the intracellular and extracellular ends, depending on the proton positions, and a tyrosine forms a hydrogen bond to the cysteine sulfur with its side chain –OH. These could produce the results of the experiments that have been interpreted as evidence for physical motion of the S4 segment, without physical motion of the S4 backbone. The computations strongly suggest that the interpretation of cysteine substitution reaction experiments be re-examined in the light of these considerations.

  16. Voltage-sensing domain mode shift is coupled to the activation gate by the N-terminal tail of hERG channels.

    Science.gov (United States)

    Tan, Peter S; Perry, Matthew D; Ng, Chai Ann; Vandenberg, Jamie I; Hill, Adam P

    2012-09-01

    Human ether-a-go-go-related gene (hERG) potassium channels exhibit unique gating kinetics characterized by unusually slow activation and deactivation. The N terminus of the channel, which contains an amphipathic helix and an unstructured tail, has been shown to be involved in regulation of this slow deactivation. However, the mechanism of how this occurs and the connection between voltage-sensing domain (VSD) return and closing of the gate are unclear. To examine this relationship, we have used voltage-clamp fluorometry to simultaneously measure VSD motion and gate closure in N-terminally truncated constructs. We report that mode shifting of the hERG VSD results in a corresponding shift in the voltage-dependent equilibrium of channel closing and that at negative potentials, coupling of the mode-shifted VSD to the gate defines the rate of channel closure. Deletion of the first 25 aa from the N terminus of hERG does not alter mode shifting of the VSD but uncouples the shift from closure of the cytoplasmic gate. Based on these observations, we propose the N-terminal tail as an adaptor that couples voltage sensor return to gate closure to define slow deactivation gating in hERG channels. Furthermore, because the mode shift occurs on a time scale relevant to the cardiac action potential, we suggest a physiological role for this phenomenon in maximizing current flow through hERG channels during repolarization.

  17. Niflumic acid alters gating of HCN2 pacemaker channels by interaction with the outer region of S4 voltage sensing domains.

    Science.gov (United States)

    Cheng, Lan; Sanguinetti, Michael C

    2009-05-01

    Niflumic acid, 2-[[3-(trifluoromethyl)phenyl]amino]pyridine-3-carboxylic acid (NFA), is a nonsteroidal anti-inflammatory drug that also blocks or modifies the gating of many ion channels. Here, we investigated the effects of NFA on hyperpolarization-activated cyclic nucleotide-gated cation (HCN) pacemaker channels expressed in X. laevis oocytes using site-directed mutagenesis and the two-electrode voltage-clamp technique. Extracellular NFA acted rapidly and caused a slowing of activation and deactivation and a hyperpolarizing shift in the voltage dependence of HCN2 channel activation (-24.5 +/- 1.2 mV at 1 mM). Slowed channel gating and reduction of current magnitude was marked in oocytes treated with NFA, while clamped at 0 mV but minimal in oocytes clamped at -100 mV, indicating the drug preferentially interacts with channels in the closed state. NFA at 0.1 to 3 mM shifted the half-point for channel activation in a concentration-dependent manner, with an EC(50) of 0.54 +/- 0.068 mM and a predicted maximum shift of -38 mV. NFA at 1 mM also reduced maximum HCN2 conductance by approximately 20%, presumably by direct block of the pore. The rapid onset and state-dependence of NFA-induced changes in channel gating suggests an interaction with the extracellular region of the S4 transmembrane helix, the primary voltage-sensing domain of HCN2. Neutralization (by mutation to Gln) of any three of the outer four basic charged residues in S4, but not single mutations, abrogated the NFA-induced shift in channel activation. We conclude that NFA alters HCN2 gating by interacting with the extracellular end of the S4 voltage sensor domains.

  18. Two distinct voltage-sensing domains control voltage sensitivity and kinetics of current activation in CaV1.1 calcium channels.

    Science.gov (United States)

    Tuluc, Petronel; Benedetti, Bruno; Coste de Bagneaux, Pierre; Grabner, Manfred; Flucher, Bernhard E

    2016-06-01

    Alternative splicing of the skeletal muscle CaV1.1 voltage-gated calcium channel gives rise to two channel variants with very different gating properties. The currents of both channels activate slowly; however, insertion of exon 29 in the adult splice variant CaV1.1a causes an ∼30-mV right shift in the voltage dependence of activation. Existing evidence suggests that the S3-S4 linker in repeat IV (containing exon 29) regulates voltage sensitivity in this voltage-sensing domain (VSD) by modulating interactions between the adjacent transmembrane segments IVS3 and IVS4. However, activation kinetics are thought to be determined by corresponding structures in repeat I. Here, we use patch-clamp analysis of dysgenic (CaV1.1 null) myotubes reconstituted with CaV1.1 mutants and chimeras to identify the specific roles of these regions in regulating channel gating properties. Using site-directed mutagenesis, we demonstrate that the structure and/or hydrophobicity of the IVS3-S4 linker is critical for regulating voltage sensitivity in the IV VSD, but by itself cannot modulate voltage sensitivity in the I VSD. Swapping sequence domains between the I and the IV VSDs reveals that IVS4 plus the IVS3-S4 linker is sufficient to confer CaV1.1a-like voltage dependence to the I VSD and that the IS3-S4 linker plus IS4 is sufficient to transfer CaV1.1e-like voltage dependence to the IV VSD. Any mismatch of transmembrane helices S3 and S4 from the I and IV VSDs causes a right shift of voltage sensitivity, indicating that regulation of voltage sensitivity by the IVS3-S4 linker requires specific interaction of IVS4 with its corresponding IVS3 segment. In contrast, slow current kinetics are perturbed by any heterologous sequences inserted into the I VSD and cannot be transferred by moving VSD I sequences to VSD IV. Thus, CaV1.1 calcium channels are organized in a modular manner, and control of voltage sensitivity and activation kinetics is accomplished by specific molecular mechanisms

  19. Dimerization of the voltage-sensing phosphatase controls its voltage-sensing and catalytic activity.

    Science.gov (United States)

    Rayaprolu, Vamseedhar; Royal, Perrine; Stengel, Karen; Sandoz, Guillaume; Kohout, Susy C

    2018-05-07

    Multimerization is a key characteristic of most voltage-sensing proteins. The main exception was thought to be the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP). In this study, we show that multimerization is also critical for Ci-VSP function. Using coimmunoprecipitation and single-molecule pull-down, we find that Ci-VSP stoichiometry is flexible. It exists as both monomers and dimers, with dimers favored at higher concentrations. We show strong dimerization via the voltage-sensing domain (VSD) and weak dimerization via the phosphatase domain. Using voltage-clamp fluorometry, we also find that VSDs cooperate to lower the voltage dependence of activation, thus favoring the activation of Ci-VSP. Finally, using activity assays, we find that dimerization alters Ci-VSP substrate specificity such that only dimeric Ci-VSP is able to dephosphorylate the 3-phosphate from PI(3,4,5)P 3 or PI(3,4)P 2 Our results indicate that dimerization plays a significant role in Ci-VSP function. © 2018 Rayaprolu et al.

  20. Identification of an evolutionarily conserved extracellular threonine residue critical for surface expression and its potential coupling of adjacent voltage-sensing and gating domains in voltage-gated potassium channels.

    Science.gov (United States)

    Mckeown, Lynn; Burnham, Matthew P; Hodson, Charlotte; Jones, Owen T

    2008-10-31

    The dynamic expression of voltage-gated potassium channels (Kvs) at the cell surface is a fundamental factor controlling membrane excitability. In exploring possible mechanisms controlling Kv surface expression, we identified a region in the extracellular linker between the first and second of the six (S1-S6) transmembrane-spanning domains of the Kv1.4 channel, which we hypothesized to be critical for its biogenesis. Using immunofluorescence microscopy, flow cytometry, patch clamp electrophysiology, and mutagenesis, we identified a single threonine residue at position 330 within the Kv1.4 S1-S2 linker that is absolutely required for cell surface expression. Mutation of Thr-330 to an alanine, aspartate, or lysine prevented surface expression. However, surface expression occurred upon co-expression of mutant and wild type Kv1.4 subunits or mutation of Thr-330 to a serine. Mutation of the corresponding residue (Thr-211) in Kv3.1 to alanine also caused intracellular retention, suggesting that the conserved threonine plays a generalized role in surface expression. In support of this idea, sequence comparisons showed conservation of the critical threonine in all Kv families and in organisms across the evolutionary spectrum. Based upon the Kv1.2 crystal structure, further mutagenesis, and the partial restoration of surface expression in an electrostatic T330K bridging mutant, we suggest that Thr-330 hydrogen bonds to equally conserved outer pore residues, which may include a glutamate at position 502 that is also critical for surface expression. We propose that Thr-330 serves to interlock the voltage-sensing and gating domains of adjacent monomers, thereby yielding a structure competent for the surface expression of functional tetramers.

  1. Allosteric substrate switching in a voltage-sensing lipid phosphatase.

    Science.gov (United States)

    Grimm, Sasha S; Isacoff, Ehud Y

    2016-04-01

    Allostery provides a critical control over enzyme activity, biasing the catalytic site between inactive and active states. We found that the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP), which modifies phosphoinositide signaling lipids (PIPs), has not one but two sequential active states with distinct substrate specificities, whose occupancy is allosterically controlled by sequential conformations of the voltage-sensing domain (VSD). Using fast fluorescence resonance energy transfer (FRET) reporters of PIPs to monitor enzyme activity and voltage-clamp fluorometry to monitor conformational changes in the VSD, we found that Ci-VSP switches from inactive to a PIP3-preferring active state when the VSD undergoes an initial voltage-sensing motion and then into a second PIP2-preferring active state when the VSD activates fully. This two-step allosteric control over a dual-specificity enzyme enables voltage to shape PIP concentrations in time, and provides a mechanism for the complex modulation of PIP-regulated ion channels, transporters, cell motility, endocytosis and exocytosis.

  2. Allosteric substrate switching in a voltage sensing lipid phosphatase

    Science.gov (United States)

    Grimm, Sasha S.; Isacoff, Ehud Y.

    2016-01-01

    Allostery provides a critical control over enzyme activity, biasing the catalytic site between inactive and active states. We find the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP), which modifies phosphoinositide signaling lipids (PIPs), to have not one but two sequential active states with distinct substrate specificities, whose occupancy is allosterically controlled by sequential conformations of the voltage sensing domain (VSD). Using fast FRET reporters of PIPs to monitor enzyme activity and voltage clamp fluorometry to monitor conformational changes in the VSD, we find that Ci-VSP switches from inactive to a PIP3-preferring active state when the VSD undergoes an initial voltage sensing motion and then into a second PIP2-preferring active state when the VSD activates fully. This novel 2-step allosteric control over a dual specificity enzyme enables voltage to shape PIP concentrations in time, and provides a mechanism for the complex modulation of PIP-regulated ion channels, transporters, cell motility and endo/exocytosis. PMID:26878552

  3. Voltage-sensing phosphatase: its molecular relationship with PTEN.

    Science.gov (United States)

    Okamura, Yasushi; Dixon, Jack E

    2011-02-01

    Voltage-sensing phosphoinositide phosphatase (VSP) contains voltage sensor and cytoplasmic phosphatase domains. A unique feature of this protein is that depolarization-induced motions of the voltage sensor activate PtdIns(3,4,5)P(3) and PtdIns(4,5)P(2) phosphatase activities. VSP exhibits remarkable structural similarities with PTEN, the phosphatase and tensin homolog deleted on chromosome 10. These similarities include the cytoplasmic phosphatase region, the phosphoinositide binding region, and the putative membrane interacting C2 domain.

  4. Engineering of a genetically encodable fluorescent voltage sensor exploiting fast Ci-VSP voltage-sensing movements

    DEFF Research Database (Denmark)

    Lundby, Alicia; Mutoh, Hiroki; Dimitrov, Dimitar

    2008-01-01

    Ci-VSP contains a voltage-sensing domain (VSD) homologous to that of voltage-gated potassium channels. Using charge displacement ('gating' current) measurements we show that voltage-sensing movements of this VSD can occur within 1 ms in mammalian membranes. Our analysis lead to development...

  5. Light-induced conformational changes of LOV1 (light oxygen voltage-sensing domain 1) and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin.

    Science.gov (United States)

    Okajima, Koji; Aihara, Yusuke; Takayama, Yuki; Nakajima, Mihoko; Kashojiya, Sachiko; Hikima, Takaaki; Oroguchi, Tomotaka; Kobayashi, Amane; Sekiguchi, Yuki; Yamamoto, Masaki; Suzuki, Tomomi; Nagatani, Akira; Nakasako, Masayoshi; Tokutomi, Satoru

    2014-01-03

    Phototropin (phot), a blue light (BL) receptor in plants, has two photoreceptive domains named LOV1 and LOV2 as well as a Ser/Thr kinase domain (KD) and acts as a BL-regulated protein kinase. A LOV domain harbors a flavin mononucleotide that undergoes a cyclic photoreaction upon BL excitation via a signaling state in which the inhibition of the kinase activity by LOV2 is negated. To understand the molecular mechanism underlying the BL-dependent activation of the kinase, the photochemistry, kinase activity, and molecular structure were studied with the phot of Chlamydomonas reinhardtii. Full-length and LOV2-KD samples of C. reinhardtii phot showed cyclic photoreaction characteristics with the activation of LOV- and BL-dependent kinase. Truncation of LOV1 decreased the photosensitivity of the kinase activation, which was well explained by the fact that the signaling state lasted for a shorter period of time compared with that of the phot. Small angle x-ray scattering revealed monomeric forms of the proteins in solution and detected BL-dependent conformational changes, suggesting an extension of the global molecular shapes of both samples. Constructed molecular model of full-length phot based on the small angle x-ray scattering data proved the arrangement of LOV1, LOV2, and KD for the first time that showed a tandem arrangement both in the dark and under BL irradiation. The models suggest that LOV1 alters its position relative to LOV2-KD under BL irradiation. This finding demonstrates that LOV1 may interact with LOV2 and modify the photosensitivity of the kinase activation through alteration of the duration of the signaling state in LOV2.

  6. Sensing charges of the Ciona intestinalis voltage-sensing phosphatase.

    Science.gov (United States)

    Villalba-Galea, Carlos A; Frezza, Ludivine; Sandtner, Walter; Bezanilla, Francisco

    2013-11-01

    Voltage control over enzymatic activity in voltage-sensitive phosphatases (VSPs) is conferred by a voltage-sensing domain (VSD) located in the N terminus. These VSDs are constituted by four putative transmembrane segments (S1 to S4) resembling those found in voltage-gated ion channels. The putative fourth segment (S4) of the VSD contains positive residues that likely function as voltage-sensing elements. To study in detail how these residues sense the plasma membrane potential, we have focused on five arginines in the S4 segment of the Ciona intestinalis VSP (Ci-VSP). After implementing a histidine scan, here we show that four arginine-to-histidine mutants, namely R223H to R232H, mediate voltage-dependent proton translocation across the membrane, indicating that these residues transit through the hydrophobic core of Ci-VSP as a function of the membrane potential. These observations indicate that the charges carried by these residues are sensing charges. Furthermore, our results also show that the electrical field in VSPs is focused in a narrow hydrophobic region that separates the extracellular and intracellular space and constitutes the energy barrier for charge crossing.

  7. Voltage Sensing in Membranes: From Macroscopic Currents to Molecular Motions.

    Science.gov (United States)

    Freites, J Alfredo; Tobias, Douglas J

    2015-06-01

    Voltage-sensing domains (VSDs) are integral membrane protein units that sense changes in membrane electric potential, and through the resulting conformational changes, regulate a specific function. VSDs confer voltage-sensitivity to a large superfamily of membrane proteins that includes voltage-gated Na[Formula: see text], K[Formula: see text], Ca[Formula: see text] ,and H[Formula: see text] selective channels, hyperpolarization-activated cyclic nucleotide-gated channels, and voltage-sensing phosphatases. VSDs consist of four transmembrane segments (termed S1 through S4). Their most salient structural feature is the highly conserved positions for charged residues in their sequences. S4 exhibits at least three conserved triplet repeats composed of one basic residue (mostly arginine) followed by two hydrophobic residues. These S4 basic side chains participate in a state-dependent internal salt-bridge network with at least four acidic residues in S1-S3. The signature of voltage-dependent activation in electrophysiology experiments is a transient current (termed gating or sensing current) upon a change in applied membrane potential as the basic side chains in S4 move across the membrane electric field. Thus, the unique structural features of the VSD architecture allow for competing requirements: maintaining a series of stable transmembrane conformations, while allowing charge motion, as briefly reviewed here.

  8. Engineering of a genetically encodable fluorescent voltage sensor exploiting fast Ci-VSP voltage-sensing movements.

    Science.gov (United States)

    Lundby, Alicia; Mutoh, Hiroki; Dimitrov, Dimitar; Akemann, Walther; Knöpfel, Thomas

    2008-06-25

    Ci-VSP contains a voltage-sensing domain (VSD) homologous to that of voltage-gated potassium channels. Using charge displacement ('gating' current) measurements we show that voltage-sensing movements of this VSD can occur within 1 ms in mammalian membranes. Our analysis lead to development of a genetically encodable fluorescent protein voltage sensor (VSFP) in which the fast, voltage-dependent conformational changes of the Ci-VSP voltage sensor are transduced to similarly fast fluorescence read-outs.

  9. Independent and cooperative motions of the Kv1.2 channel: voltage sensing and gating.

    Science.gov (United States)

    Yeheskel, Adva; Haliloglu, Turkan; Ben-Tal, Nir

    2010-05-19

    Voltage-gated potassium (Kv) channels, such as Kv1.2, are involved in the generation and propagation of action potentials. The Kv channel is a homotetramer, and each monomer is composed of a voltage-sensing domain (VSD) and a pore domain (PD). We analyzed the fluctuations of a model structure of Kv1.2 using elastic network models. The analysis suggested a network of coupled fluctuations of eight rigid structural units and seven hinges that may control the transition between the active and inactive states of the channel. For the most part, the network is composed of amino acids that are known to affect channel activity. The results suggested allosteric interactions and cooperativity between the subunits in the coupling between the motion of the VSD and the selectivity filter of the PD, in accordance with recent empirical data. There are no direct contacts between the VSDs of the four subunits, and the contacts between these and the PDs are loose, suggesting that the VSDs are capable of functioning independently. Indeed, they manifest many inherent fluctuations that are decoupled from the rest of the structure. In general, the analysis suggests that the two domains contribute to the channel function both individually and cooperatively. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. Engineering of a genetically encodable fluorescent voltage sensor exploiting fast Ci-VSP voltage-sensing movements.

    Directory of Open Access Journals (Sweden)

    Alicia Lundby

    2008-06-01

    Full Text Available Ci-VSP contains a voltage-sensing domain (VSD homologous to that of voltage-gated potassium channels. Using charge displacement ('gating' current measurements we show that voltage-sensing movements of this VSD can occur within 1 ms in mammalian membranes. Our analysis lead to development of a genetically encodable fluorescent protein voltage sensor (VSFP in which the fast, voltage-dependent conformational changes of the Ci-VSP voltage sensor are transduced to similarly fast fluorescence read-outs.

  11. Local anesthetics disrupt energetic coupling between the voltage-sensing segments of a sodium channel.

    Science.gov (United States)

    Muroi, Yukiko; Chanda, Baron

    2009-01-01

    Local anesthetics block sodium channels in a state-dependent fashion, binding with higher affinity to open and/or inactivated states. Gating current measurements show that local anesthetics immobilize a fraction of the gating charge, suggesting that the movement of voltage sensors is modified when a local anesthetic binds to the pore of the sodium channel. Here, using voltage clamp fluorescence measurements, we provide a quantitative description of the effect of local anesthetics on the steady-state behavior of the voltage-sensing segments of a sodium channel. Lidocaine and QX-314 shifted the midpoints of the fluorescence-voltage (F-V) curves of S4 domain III in the hyperpolarizing direction by 57 and 65 mV, respectively. A single mutation in the S6 of domain IV (F1579A), a site critical for local anesthetic block, abolished the effect of QX-314 on the voltage sensor of domain III. Both local anesthetics modestly shifted the F-V relationships of S4 domain IV toward hyperpolarized potentials. In contrast, the F-V curve of the S4 domain I was shifted by 11 mV in the depolarizing direction upon QX-314 binding. These antagonistic effects of the local anesthetic indicate that the drug modifies the coupling between the voltage-sensing domains of the sodium channel. Our findings suggest a novel role of local anesthetics in modulating the gating apparatus of the sodium channel.

  12. Disulfide mapping the voltage-sensing mechanism of a voltage-dependent potassium channel.

    Science.gov (United States)

    Nozaki, Tomohiro; Ozawa, Shin-Ichiro; Harada, Hitomi; Kimura, Tomomi; Osawa, Masanori; Shimada, Ichio

    2016-11-17

    Voltage-dependent potassium (Kv) channels allow for the selective permeability of potassium ions in a membrane potential dependent manner, playing crucial roles in neurotransmission and muscle contraction. Kv channel is a tetramer, in which each subunit possesses a voltage-sensing domain (VSD) and a pore domain (PD). Although several lines of evidence indicated that membrane depolarization is sensed as the movement of helix S4 of the VSD, the detailed voltage-sensing mechanism remained elusive, due to the difficulty of structural analyses at resting potential. In this study, we conducted a comprehensive disulfide locking analysis of the VSD using 36 double Cys mutants, in order to identify the proximal residue pairs of the VSD in the presence or absence of a membrane potential. An intramolecular SS-bond was formed between 6 Cys pairs under both polarized and depolarized environment, and one pair only under depolarized environment. The multiple conformations captured by the SS-bond can be divided by two states, up and down, where S4 lies on the extracellular and intracellular sides of the membrane, respectively, with axial rotation of 180°. The transition between these two states is caused by the S4 translocation of 12 Å, enabling allosteric regulation of the gating at the PD.

  13. TENCompetence Domain Model

    NARCIS (Netherlands)

    2006-01-01

    This is the version 1.1 of the TENCompetence Domain Model (version 1.0 released at 19-6-2006; version 1.1 at 9-11-2008). It contains several files: a) a pdf with the model description, b) three jpg files with class models (also in the pdf), c) a MagicDraw zip file with the model itself, d) a release

  14. Molecular pathophysiology and pharmacology of the voltage-sensing module of neuronal ion channels.

    Science.gov (United States)

    Miceli, Francesco; Soldovieri, Maria Virginia; Ambrosino, Paolo; De Maria, Michela; Manocchio, Laura; Medoro, Alessandro; Taglialatela, Maurizio

    2015-01-01

    Voltage-gated ion channels (VGICs) are membrane proteins that switch from a closed to open state in response to changes in membrane potential, thus enabling ion fluxes across the cell membranes. The mechanism that regulate the structural rearrangements occurring in VGICs in response to changes in membrane potential still remains one of the most challenging topic of modern biophysics. Na(+), Ca(2+) and K(+) voltage-gated channels are structurally formed by the assembly of four similar domains, each comprising six transmembrane segments. Each domain can be divided into two main regions: the Pore Module (PM) and the Voltage-Sensing Module (VSM). The PM (helices S5 and S6 and intervening linker) is responsible for gate opening and ion selectivity; by contrast, the VSM, comprising the first four transmembrane helices (S1-S4), undergoes the first conformational changes in response to membrane voltage variations. In particular, the S4 segment of each domain, which contains several positively charged residues interspersed with hydrophobic amino acids, is located within the membrane electric field and plays an essential role in voltage sensing. In neurons, specific gating properties of each channel subtype underlie a variety of biological events, ranging from the generation and propagation of electrical impulses, to the secretion of neurotransmitters and to the regulation of gene expression. Given the important functional role played by the VSM in neuronal VGICs, it is not surprising that various VSM mutations affecting the gating process of these channels are responsible for human diseases, and that compounds acting on the VSM have emerged as important investigational tools with great therapeutic potential. In the present review we will briefly describe the most recent discoveries concerning how the VSM exerts its function, how genetically inherited diseases caused by mutations occurring in the VSM affects gating in VGICs, and how several classes of drugs and toxins

  15. A complicated complex: Ion channels, voltage sensing, cell membranes and peptide inhibitors.

    Science.gov (United States)

    Zhang, Alan H; Sharma, Gagan; Undheim, Eivind A B; Jia, Xinying; Mobli, Mehdi

    2018-04-21

    Voltage-gated ion channels (VGICs) are specialised ion channels that have a voltage dependent mode of action, where ion conduction, or gating, is controlled by a voltage-sensing mechanism. VGICs are critical for electrical signalling and are therefore important pharmacological targets. Among these, voltage-gated sodium channels (Na V s) have attracted particular attention as potential analgesic targets. Na V s, however, comprise several structurally similar subtypes with unique localisations and distinct functions, ranging from amplification of action potentials in nociception (e.g. Na V 1.7) to controlling electrical signalling in cardiac function (Na V 1.5). Understanding the structural basis of Na V function is therefore of great significance, both to our knowledge of electrical signalling and in development of subtype and state selective drugs. An important tool in this pursuit has been the use of peptides from animal venoms as selective Na V modulators. In this review, we look at peptides, particularly from spider venoms, that inhibit Na V s by binding to the voltage sensing domain (VSD) of this channel, known as gating modifier toxins (GMT). In the first part of the review, we look at the structural determinants of voltage sensing in VGICs, the gating cycle and the conformational changes that accompany VSD movement. Next, the modulation of the analgesic target Na V 1.7 by GMTs is reviewed to develop bioinformatic tools that, based on sequence information alone, can identify toxins that are likely to inhibit this channel. The same approach is also used to define VSD sequences, other than that from Na V 1.7, which are likely to be sensitive to this class of toxins. The final section of the review focuses on the important role of the cellular membrane in channel modulation and also how the lipid composition affects measurements of peptide-channel interactions both in binding kinetics measurements in solution and in cell-based functional assays. Copyright © 2018

  16. A Photostable Silicon Rhodamine Platform for Optical Voltage Sensing

    Science.gov (United States)

    Huang, Yi-Lin; Walker, Alison S.; Miller, Evan W.

    2015-01-01

    This paper describes the design and synthesis of a photostable, far-red to near-infrared (NIR) platform for optical voltage sensing. We developed a new, sulfonated silicon rhodamine fluorophore and integrated it with a phenylenevinylene molecular wire to create a Berkeley Red Sensor of Transmembrane potential, or BeRST 1 (“burst”). BeRST 1 is the first member of a class of farred to NIR voltage sensitive dyes that make use of a photoinduced electron transfer (PeT) trigger for optical interrogation of membrane voltage. We show that BeRST 1 displays bright, membrane-localized fluorescence in living cells, high photostability, and excellent voltage sensitivity in neurons. Depolarization of the plasma membrane results in rapid fluorescence increases (24% ΔF/F per 100 mV). BeRST 1 can be used in conjunction with fluorescent stains for organelles, Ca2+ indicators, and voltage-sensitive fluorescent proteins. In addition, the red-shifted spectral profile of BeRST 1, relative to commonly employed optogenetic actuators like ChannelRhodopsin2 (ChR2), which require blue light, enables optical electrophysiology in neurons. The high speed, sensitivity, photostability and long-wavelength fluorescence profiles of BeRST 1 make it a useful platform for the non-invasive, optical dissection of neuronal activity. PMID:26237573

  17. A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K(+) Channels.

    Science.gov (United States)

    Schewe, Marcus; Nematian-Ardestani, Ehsan; Sun, Han; Musinszki, Marianne; Cordeiro, Sönke; Bucci, Giovanna; de Groot, Bert L; Tucker, Stephen J; Rapedius, Markus; Baukrowitz, Thomas

    2016-02-25

    Two-pore domain (K2P) K(+) channels are major regulators of excitability that endow cells with an outwardly rectifying background "leak" conductance. In some K2P channels, strong voltage-dependent activation has been observed, but the mechanism remains unresolved because they lack a canonical voltage-sensing domain. Here, we show voltage-dependent gating is common to most K2P channels and that this voltage sensitivity originates from the movement of three to four ions into the high electric field of an inactive selectivity filter. Overall, this ion-flux gating mechanism generates a one-way "check valve" within the filter because outward movement of K(+) induces filter opening, whereas inward movement promotes inactivation. Furthermore, many physiological stimuli switch off this flux gating mode to convert K2P channels into a leak conductance. These findings provide insight into the functional plasticity of a K(+)-selective filter and also refine our understanding of K2P channels and the mechanisms by which ion channels can sense voltage. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Functional diversity of voltage-sensing phosphatases in two urodele amphibians.

    Science.gov (United States)

    Mutua, Joshua; Jinno, Yuka; Sakata, Souhei; Okochi, Yoshifumi; Ueno, Shuichi; Tsutsui, Hidekazu; Kawai, Takafumi; Iwao, Yasuhiro; Okamura, Yasushi

    2014-07-16

    Voltage-sensing phosphatases (VSPs) share the molecular architecture of the voltage sensor domain (VSD) with voltage-gated ion channels and the phosphoinositide phosphatase region with the phosphatase and tensin homolog (PTEN), respectively. VSPs enzymatic activities are regulated by the motions of VSD upon depolarization. The physiological role of these proteins has remained elusive, and insights may be gained by investigating biological variations in different animal species. Urodele amphibians are vertebrates with potent activities of regeneration and also show diverse mechanisms of polyspermy prevention. We cloned cDNAs of VSPs from the testes of two urodeles; Hynobius nebulosus and Cynops pyrrhogaster, and compared their expression and voltage-dependent activation. Their molecular architecture is highly conserved in both Hynobius VSP (Hn-VSP) and Cynops VSP (Cp-VSP), including the positively-charged arginine residues in the S4 segment of the VSD and the enzymatic active site for substrate binding, yet the C-terminal C2 domain of Hn-VSP is significantly shorter than that of Cp-VSP and other VSP orthologs. RT-PCR analysis showed that gene expression pattern was distinct between two VSPs. The voltage sensor motions and voltage-dependent phosphatase activities were investigated electrophysiologically by expression in Xenopus oocytes. Both VSPs showed "sensing" currents, indicating that their voltage sensor domains are functional. The phosphatase activity of Cp-VSP was found to be voltage dependent, as shown by its ability to regulate the conductance of coexpressed GIRK2 channels, but Hn-VSP lacked such phosphatase activity due to the truncation of its C2 domain. © 2014 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

  19. Improved detection of electrical activity with a voltage probe based on a voltage-sensing phosphatase.

    Science.gov (United States)

    Tsutsui, Hidekazu; Jinno, Yuka; Tomita, Akiko; Niino, Yusuke; Yamada, Yoshiyuki; Mikoshiba, Katsuhiko; Miyawaki, Atsushi; Okamura, Yasushi

    2013-09-15

      One of the most awaited techniques in modern physiology is the sensitive detection of spatiotemporal electrical activity in a complex network of excitable cells. The use of genetically encoded voltage probes has been expected to enable such analysis. However, in spite of recent progress, existing probes still suffer from low signal amplitude and/or kinetics too slow to detect fast electrical activity. Here, we have developed an improved voltage probe named Mermaid2, which is based on the voltage-sensor domain of the voltage-sensing phosphatase from Ciona intestinalis and Förster energy transfer between a pair of fluorescent proteins. In mammalian cells, Mermaid2 permits ratiometric readouts of fractional changes of more than 50% over a physiologically relevant voltage range with fast kinetics, and it was used to follow a train of action potentials at frequencies of up to 150 Hz. Mermaid2 was also able to detect single action potentials and subthreshold voltage responses in hippocampal neurons in vitro, in addition to cortical electrical activity evoked by sound stimuli in single trials in living mice.

  20. Impedance models in time domain

    NARCIS (Netherlands)

    Rienstra, S.W.

    2005-01-01

    Necessary conditions for an impedance function are derived. Methods available in the literature are discussed. A format with recipe is proposed for an exact impedance condition in time domain on a time grid, based on the Helmholtz resonator model. An explicit solution is given of a pulse reflecting

  1. High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers.

    Science.gov (United States)

    Doherty, Tim; Su, Yongchao; Hong, Mei

    2010-08-27

    The opening and closing of voltage-gated potassium (Kv) channels are controlled by several conserved Arg residues in the S4 helix of the voltage-sensing domain. The interaction of these positively charged Arg residues with the lipid membrane has been of intense interest for understanding how membrane proteins fold to allow charged residues to insert into lipid bilayers against free-energy barriers. Using solid-state NMR, we have now determined the orientation and insertion depth of the S4 peptide of the KvAP channel in lipid bilayers. Two-dimensional (15)N correlation experiments of macroscopically oriented S4 peptide in phospholipid bilayers revealed a tilt angle of 40 degrees and two possible rotation angles differing by 180 degrees around the helix axis. Remarkably, the tilt angle and one of the two rotation angles are identical to those of the S4 helix in the intact voltage-sensing domain, suggesting that interactions between the S4 segment and other helices of the voltage-sensing domain are not essential for the membrane topology of the S4 helix. (13)C-(31)P distances between the S4 backbone and the lipid (31)P indicate a approximately 9 A local thinning and 2 A average thinning of the DMPC (1,2-dimyristoyl-sn-glycero-3-phosphochloline)/DMPG (1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol) bilayer, consistent with neutron diffraction data. Moreover, a short distance of 4.6 A from the guanidinium C(zeta) of the second Arg to (31)P indicates the existence of guanidinium phosphate hydrogen bonding and salt bridges. These data suggest that the structure of the Kv gating helix is mainly determined by protein-lipid interactions instead of interhelical protein-protein interactions, and the S4 amino acid sequence encodes sufficient information for the membrane topology of this crucial gating helix. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  2. Expression of the voltage-sensing phosphatase gene in the chick embryonic tissues and in the adult cerebellum.

    Science.gov (United States)

    Yamaguchi, Shinji; Aoki, Naoya; Kitajima, Takaaki; Okamura, Yasushi; Homma, Koichi J

    2014-10-01

    Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor domain (VSD) and the cytoplasmic domain with phosphoinositide-phosphatase activities. It operates as the voltage sensor and directly translates membrane potential into phosphoinositide turnover by coupling VSD to the cytoplasmic domain. VSPs are evolutionarily conserved from marine invertebrate up to humans. Recently, we demonstrated that ectopic expression of the chick ortholog of VSP, Gg-VSP, in a fibroblast cell line caused characteristic cell process outgrowths. Co-expression of chick PTEN suppressed such morphological change, suggesting that VSP regulates cell shape by increasing PI(3,4)P2. However, the in vivo function of Gg-VSP remains unclear. Here, we showed that in chick embryos Gg-VSP is expressed in the stomach, mesonephros, pharyngeal arch, limb bud, somites, floor plate of neural tube, and notochord. In addition, both Gg-VSP transcripts and the protein were found in the cerebellar Purkinje neurons. These findings provide an insight into the physiological functions of VSP.

  3. Generic domain models in software engineering

    Science.gov (United States)

    Maiden, Neil

    1992-01-01

    This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

  4. Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid.

    Science.gov (United States)

    Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

    2016-07-05

    The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane.

  5. Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid

    Science.gov (United States)

    Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

    2016-01-01

    The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane. PMID:27330112

  6. A micromagnetic study of domain structure modeling

    International Nuclear Information System (INIS)

    Matsuo, Tetsuji; Mimuro, Naoki; Shimasaki, Masaaki

    2008-01-01

    To develop a mesoscopic model for magnetic-domain behavior, a domain structure model (DSM) was examined and compared with a micromagnetic simulation. The domain structure of this model is given by several domains with uniform magnetization vectors and domain walls. The directions of magnetization vectors and the locations of domain walls are determined so as to minimize the magnetic total energy of the magnetic material. The DSM was modified to improve its representation capability for domain behavior. The domain wall energy is multiplied by a vanishing factor to represent the disappearance of magnetic domain. The sequential quadratic programming procedure is divided into two steps to improve an energy minimization process. A comparison with micromagnetic simulation shows that the modified DSM improves the representation accuracy of the magnetization process

  7. Latent domain models for statistical machine translation

    NARCIS (Netherlands)

    Hoàng, C.

    2017-01-01

    A data-driven approach to model translation suffers from the data mismatch problem and demands domain adaptation techniques. Given parallel training data originating from a specific domain, training an MT system on the data would result in a rather suboptimal translation for other domains. But does

  8. Domain-Specific Modelling Languages in Bigraphs

    DEFF Research Database (Denmark)

    Perrone, Gian David

    " of models, in order to improve the utility of the models we build, and to ease the process of model construction by moving the languages we use to express such models closer to their respective domains. This thesis is concerned with the study of bigraphical reactive systems as a host for domain...... for deciding reaction rule causation. Finally, we provide a mechanism for the modular construction of domain-specic modelling languages as bigraphical reactive systems, exploring the relationship between vertical renement and language specialisation in this setting. The thesis is composed of several...

  9. Time versus frequency domain measurements: layered model ...

    African Journals Online (AJOL)

    ... their high frequency content while among TEM data sets with low frequency content, the averaging times for the FEM ellipticity were shorter than the TEM quality. Keywords: ellipticity, frequency domain, frequency electromagnetic method, model parameter, orientation error, time domain, transient electromagnetic method

  10. Depression of voltage-activated Ca2+ release in skeletal muscle by activation of a voltage-sensing phosphatase.

    Science.gov (United States)

    Berthier, Christine; Kutchukian, Candice; Bouvard, Clément; Okamura, Yasushi; Jacquemond, Vincent

    2015-04-01

    Phosphoinositides act as signaling molecules in numerous cellular transduction processes, and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) regulates the function of several types of plasma membrane ion channels. We investigated the potential role of PtdIns(4,5)P2 in Ca(2+) homeostasis and excitation-contraction (E-C) coupling of mouse muscle fibers using in vivo expression of the voltage-sensing phosphatases (VSPs) Ciona intestinalis VSP (Ci-VSP) or Danio rerio VSP (Dr-VSP). Confocal images of enhanced green fluorescent protein-tagged Dr-VSP revealed a banded pattern consistent with VSP localization within the transverse tubule membrane. Rhod-2 Ca(2+) transients generated by 0.5-s-long voltage-clamp depolarizing pulses sufficient to elicit Ca(2+) release from the sarcoplasmic reticulum (SR) but below the range at which VSPs are activated were unaffected by the presence of the VSPs. However, in Ci-VSP-expressing fibers challenged by 5-s-long depolarizing pulses, the Ca(2+) level late in the pulse (3 s after initiation) was significantly lower at 120 mV than at 20 mV. Furthermore, Ci-VSP-expressing fibers showed a reversible depression of Ca(2+) release during trains, with the peak Ca(2+) transient being reduced by ∼30% after the application of 10 200-ms-long pulses to 100 mV. A similar depression was observed in Dr-VSP-expressing fibers. Cav1.1 Ca(2+) channel-mediated current was unaffected by Ci-VSP activation. In fibers expressing Ci-VSP and a pleckstrin homology domain fused with monomeric red fluorescent protein (PLCδ1PH-mRFP), depolarizing pulses elicited transient changes in mRFP fluorescence consistent with release of transverse tubule-bound PLCδ1PH domain into the cytosol; the voltage sensitivity of these changes was consistent with that of Ci-VSP activation, and recovery occurred with a time constant in the 10-s range. Our results indicate that the PtdIns(4,5)P2 level is tightly maintained in the transverse tubule membrane of the muscle fibers

  11. Work domain constraints for modelling surgical performance.

    Science.gov (United States)

    Morineau, Thierry; Riffaud, Laurent; Morandi, Xavier; Villain, Jonathan; Jannin, Pierre

    2015-10-01

    Three main approaches can be identified for modelling surgical performance: a competency-based approach, a task-based approach, both largely explored in the literature, and a less known work domain-based approach. The work domain-based approach first describes the work domain properties that constrain the agent's actions and shape the performance. This paper presents a work domain-based approach for modelling performance during cervical spine surgery, based on the idea that anatomical structures delineate the surgical performance. This model was evaluated through an analysis of junior and senior surgeons' actions. Twenty-four cervical spine surgeries performed by two junior and two senior surgeons were recorded in real time by an expert surgeon. According to a work domain-based model describing an optimal progression through anatomical structures, the degree of adjustment of each surgical procedure to a statistical polynomial function was assessed. Each surgical procedure showed a significant suitability with the model and regression coefficient values around 0.9. However, the surgeries performed by senior surgeons fitted this model significantly better than those performed by junior surgeons. Analysis of the relative frequencies of actions on anatomical structures showed that some specific anatomical structures discriminate senior from junior performances. The work domain-based modelling approach can provide an overall statistical indicator of surgical performance, but in particular, it can highlight specific points of interest among anatomical structures that the surgeons dwelled on according to their level of expertise.

  12. A low-voltage sense amplifier with two-stage operational amplifier clamping for flash memory

    Science.gov (United States)

    Guo, Jiarong

    2017-04-01

    A low-voltage sense amplifier with reference current generator utilizing two-stage operational amplifier clamp structure for flash memory is presented in this paper, capable of operating with minimum supply voltage at 1 V. A new reference current generation circuit composed of a reference cell and a two-stage operational amplifier clamping the drain pole of the reference cell is used to generate the reference current, which avoids the threshold limitation caused by current mirror transistor in the traditional sense amplifier. A novel reference voltage generation circuit using dummy bit-line structure without pull-down current is also adopted, which not only improves the sense window enhancing read precision but also saves power consumption. The sense amplifier was implemented in a flash realized in 90 nm flash technology. Experimental results show the access time is 14.7 ns with power supply of 1.2 V and slow corner at 125 °C. Project supported by the National Natural Science Fundation of China (No. 61376028).

  13. Domain specific modeling and analysis

    NARCIS (Netherlands)

    Jacob, Joost Ferdinand

    2008-01-01

    It is desirable to model software systems in such a way that analysis of the systems, and tool development for such analysis, is readily possible and feasible in the context of large scientific research projects. This thesis emphasizes the methodology that serves as a basis for such developments.

  14. Structuring very large domain models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2010-01-01

    View/Viewpoint approaches like IEEE 1471-2000, or Kruchten's 4+1-view model are used to structure software architectures at a high level of granularity. While research has focused on architectural languages and with consistency between multiple views, practical questions such as the structuring a...

  15. Multi-Domain Modeling Based on Modelica

    Directory of Open Access Journals (Sweden)

    Liu Jun

    2016-01-01

    Full Text Available With the application of simulation technology in large-scale and multi-field problems, multi-domain unified modeling become an effective way to solve these problems. This paper introduces several basic methods and advantages of the multidisciplinary model, and focuses on the simulation based on Modelica language. The Modelica/Mworks is a newly developed simulation software with features of an object-oriented and non-casual language for modeling of the large, multi-domain system, which makes the model easier to grasp, develop and maintain.It This article shows the single degree of freedom mechanical vibration system based on Modelica language special connection mechanism in Mworks. This method that multi-domain modeling has simple and feasible, high reusability. it closer to the physical system, and many other advantages.

  16. Modeling Network Traffic in Wavelet Domain

    Directory of Open Access Journals (Sweden)

    Sheng Ma

    2004-12-01

    Full Text Available This work discovers that although network traffic has the complicated short- and long-range temporal dependence, the corresponding wavelet coefficients are no longer long-range dependent. Therefore, a "short-range" dependent process can be used to model network traffic in the wavelet domain. Both independent and Markov models are investigated. Theoretical analysis shows that the independent wavelet model is sufficiently accurate in terms of the buffer overflow probability for Fractional Gaussian Noise traffic. Any model, which captures additional correlations in the wavelet domain, only improves the performance marginally. The independent wavelet model is then used as a unified approach to model network traffic including VBR MPEG video and Ethernet data. The computational complexity is O(N for developing such wavelet models and generating synthesized traffic of length N, which is among the lowest attained.

  17. Regional climate model sensitivity to domain size

    Energy Technology Data Exchange (ETDEWEB)

    Leduc, Martin [Universite du Quebec a Montreal, Canadian Regional Climate Modelling and Diagnostics (CRCMD) Network, ESCER Centre, Montreal (Canada); UQAM/Ouranos, Montreal, QC (Canada); Laprise, Rene [Universite du Quebec a Montreal, Canadian Regional Climate Modelling and Diagnostics (CRCMD) Network, ESCER Centre, Montreal (Canada)

    2009-05-15

    Regional climate models are increasingly used to add small-scale features that are not present in their lateral boundary conditions (LBC). It is well known that the limited area over which a model is integrated must be large enough to allow the full development of small-scale features. On the other hand, integrations on very large domains have shown important departures from the driving data, unless large scale nudging is applied. The issue of domain size is studied here by using the ''perfect model'' approach. This method consists first of generating a high-resolution climatic simulation, nicknamed big brother (BB), over a large domain of integration. The next step is to degrade this dataset with a low-pass filter emulating the usual coarse-resolution LBC. The filtered nesting data (FBB) are hence used to drive a set of four simulations (LBs for Little Brothers), with the same model, but on progressively smaller domain sizes. The LB statistics for a climate sample of four winter months are compared with BB over a common region. The time average (stationary) and transient-eddy standard deviation patterns of the LB atmospheric fields generally improve in terms of spatial correlation with the reference (BB) when domain gets smaller. The extraction of the small-scale features by using a spectral filter allows detecting important underestimations of the transient-eddy variability in the vicinity of the inflow boundary, which can penalize the use of small domains (less than 100 x 100 grid points). The permanent ''spatial spin-up'' corresponds to the characteristic distance that the large-scale flow needs to travel before developing small-scale features. The spin-up distance tends to grow in size at higher levels in the atmosphere. (orig.)

  18. Regional climate model sensitivity to domain size

    Science.gov (United States)

    Leduc, Martin; Laprise, René

    2009-05-01

    Regional climate models are increasingly used to add small-scale features that are not present in their lateral boundary conditions (LBC). It is well known that the limited area over which a model is integrated must be large enough to allow the full development of small-scale features. On the other hand, integrations on very large domains have shown important departures from the driving data, unless large scale nudging is applied. The issue of domain size is studied here by using the “perfect model” approach. This method consists first of generating a high-resolution climatic simulation, nicknamed big brother (BB), over a large domain of integration. The next step is to degrade this dataset with a low-pass filter emulating the usual coarse-resolution LBC. The filtered nesting data (FBB) are hence used to drive a set of four simulations (LBs for Little Brothers), with the same model, but on progressively smaller domain sizes. The LB statistics for a climate sample of four winter months are compared with BB over a common region. The time average (stationary) and transient-eddy standard deviation patterns of the LB atmospheric fields generally improve in terms of spatial correlation with the reference (BB) when domain gets smaller. The extraction of the small-scale features by using a spectral filter allows detecting important underestimations of the transient-eddy variability in the vicinity of the inflow boundary, which can penalize the use of small domains (less than 100 × 100 grid points). The permanent “spatial spin-up” corresponds to the characteristic distance that the large-scale flow needs to travel before developing small-scale features. The spin-up distance tends to grow in size at higher levels in the atmosphere.

  19. Developing a Domain Model for Relay Circuits

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth

    2009-01-01

    In this paper we stepwise develop a domain model for relay circuits as used in railway control systems. First we provide an abstract, property-oriented model of networks consisting of components that can be glued together with connectors. This model is strongly inspired by a network model...... for railways madeby Bjørner et.al., however our model is more general: the components can be of any kind and can later be refined to e.g. railway components or circuit components. Then we show how the abstract network model can be refined into an explicit model for relay circuits. The circuit model describes...... the statics as well as the dynamics of relay circuits, i.e. how a relay circuit can be composed legally from electrical components as well as how the components may change state over time. Finally the circuit model is transformed into an executable model, and we show how a concrete circuit can be defined...

  20. 3' Phosphatase activity toward phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] by voltage-sensing phosphatase (VSP).

    Science.gov (United States)

    Kurokawa, Tatsuki; Takasuga, Shunsuke; Sakata, Souhei; Yamaguchi, Shinji; Horie, Shigeo; Homma, Koichi J; Sasaki, Takehiko; Okamura, Yasushi

    2012-06-19

    Voltage-sensing phosphatases (VSPs) consist of a voltage-sensor domain and a cytoplasmic region with remarkable sequence similarity to phosphatase and tensin homolog deleted on chromosome 10 (PTEN), a tumor suppressor phosphatase. VSPs dephosphorylate the 5' position of the inositol ring of both phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P(3)] and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P(2)] upon voltage depolarization. However, it is unclear whether VSPs also have 3' phosphatase activity. To gain insights into this question, we performed in vitro assays of phosphatase activities of Ciona intestinalis VSP (Ci-VSP) and transmembrane phosphatase with tensin homology (TPTE) and PTEN homologous inositol lipid phosphatase (TPIP; one human ortholog of VSP) with radiolabeled PI(3,4,5)P(3). TLC assay showed that the 3' phosphate of PI(3,4,5)P(3) was not dephosphorylated, whereas that of phosphatidylinositol 3,4-bisphosphate [PI(3,4)P(2)] was removed by VSPs. Monitoring of PI(3,4)P(2) levels with the pleckstrin homology (PH) domain from tandem PH domain-containing protein (TAPP1) fused with GFP (PH(TAPP1)-GFP) by confocal microscopy in amphibian oocytes showed an increase of fluorescence intensity during depolarization to 0 mV, consistent with 5' phosphatase activity of VSP toward PI(3,4,5)P(3). However, depolarization to 60 mV showed a transient increase of GFP fluorescence followed by a decrease, indicating that, after PI(3,4,5)P(3) is dephosphorylated at the 5' position, PI(3,4)P(2) is then dephosphorylated at the 3' position. These results suggest that substrate specificity of the VSP changes with membrane potential.

  1. Potential role of voltage-sensing phosphatases in regulation of cell structure through the production of PI(3,4)P2.

    Science.gov (United States)

    Yamaguchi, Shinji; Kurokawa, Tatsuki; Taira, Ikuko; Aoki, Naoya; Sakata, Souhei; Okamura, Yasushi; Homma, Koichi J

    2014-04-01

    Voltage-sensing phosphatase, VSP, consists of the transmembrane domain, operating as the voltage sensor, and the cytoplasmic domain with phosphoinositide-phosphatase activities. The voltage sensor tightly couples with the cytoplasmic phosphatase and membrane depolarization induces dephosphorylation of several species of phosphoinositides. VSP gene is conserved from urochordate to human. There are some diversities among VSP ortholog proteins; range of voltage of voltage sensor motions as well as substrate selectivity. In contrast with recent understandings of biophysical mechanisms of VSPs, little is known about its physiological roles. Here we report that chick ortholog of VSP (designated as Gg-VSP) induces morphological feature of cell process outgrowths with round cell body in DF-1 fibroblasts upon its forced expression. Expression of the voltage sensor mutant, Gg-VSPR153Q with shifted voltage dependence to a lower voltage led to more frequent changes of cell morphology than the wild-type protein. Coexpression of PTEN that dephosphorylates PI(3,4)P2 suppressed this effect by Gg-VSP, indicating that the increase of PI(3,4)P2 leads to changes of cell shape. In addition, visualization of PI(3,4)P2 with the fluorescent protein fused with the TAPP1-derived pleckstrin homology (PH) domain suggested that Gg-VSP influenced the distribution of PI(3,4)P2 . These findings raise a possibility that one of the VSP's functions could be to regulate cell morphology through voltage-sensitive tuning of phosphoinositide profile. © 2013 Wiley Periodicals, Inc.

  2. Time-domain modeling of electromagnetic diffusion with a frequency-domain code

    NARCIS (Netherlands)

    Mulder, W.A.; Wirianto, M.; Slob, E.C.

    2007-01-01

    We modeled time-domain EM measurements of induction currents for marine and land applications with a frequency-domain code. An analysis of the computational complexity of a number of numerical methods shows that frequency-domain modeling followed by a Fourier transform is an attractive choice if a

  3. A systemic domain model for ambient pervasive persuasive games

    OpenAIRE

    Eglin, Roger; Eyles, Mark; Dansey, Neil

    2008-01-01

    By the development of the system domain model it is hoped that a greater conceptual and theoretical clarity may be brought to understanding the complex and multifaceted nature of pervasive and ambient computer games. This paper presents a conceptual model, the system domain model, to illustrate domain areas that exist in a console, pervasive or ambient game. It is implicit that the regions that the systemic domain model describes are contextually dependent. By developing this model it is poss...

  4. Domain Endurants: An Analysis and Description Process Model

    DEFF Research Database (Denmark)

    Bjørner, Dines

    2014-01-01

    We present a summary, Sect. 2, of a structure of domain analysis and description concepts: techniques and tools. And we link, in Sect. 3, these concepts, embodied in domain analysis prompts and domain description prompts, in a model of how a diligent domain analyser cum describer would use them. We...

  5. Domain Adaptation of Translation Models for Multilingual Applications

    Science.gov (United States)

    2009-04-01

    employed. In the past two years, domain adaptation for NLP tasks has become an active research area [3, 38, 25, 23]. New domain adaptation tasks have...and unlabeled data in the target domain and learn a mixture model to adapt from the source domain. Other NLP tasks where domain adaptation has been...evaluation forum, http://www.clef-campaign.org. [13] K. Darwish and D. Oard, CLIR experiments at maryland for TREC-2002: Evidence combination for arabic

  6. A Review of Domain Modelling and Domain Imaging Techniques in Ferroelectric Crystals

    Directory of Open Access Journals (Sweden)

    John E. Huber

    2011-02-01

    Full Text Available The present paper reviews models of domain structure in ferroelectric crystals, thin films and bulk materials. Common crystal structures in ferroelectric materials are described and the theory of compatible domain patterns is introduced. Applications to multi-rank laminates are presented. Alternative models employing phase-field and related techniques are reviewed. The paper then presents methods of observing ferroelectric domain structure, including optical, polarized light, scanning electron microscopy, X-ray and neutron diffraction, atomic force microscopy and piezo-force microscopy. Use of more than one technique for unambiguous identification of the domain structure is also described.

  7. Domain Theory, Its Models and Concepts

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup; Howard, Thomas J.; Bruun, Hans Peter Lomholt

    2014-01-01

    Domain Theory is a systems approach for the analysis and synthesis of products. Its basic idea is to view a product as systems of activities, organs and parts and to define structure, elements, behaviour and function in these domains. The theory is a basis for a long line of research contribution...

  8. Predicting detection performance with model observers: Fourier domain or spatial domain?

    Science.gov (United States)

    Chen, Baiyu; Yu, Lifeng; Leng, Shuai; Kofler, James; Favazza, Christopher; Vrieze, Thomas; McCollough, Cynthia

    2016-02-27

    The use of Fourier domain model observer is challenged by iterative reconstruction (IR), because IR algorithms are nonlinear and IR images have noise texture different from that of FBP. A modified Fourier domain model observer, which incorporates nonlinear noise and resolution properties, has been proposed for IR and needs to be validated with human detection performance. On the other hand, the spatial domain model observer is theoretically applicable to IR, but more computationally intensive than the Fourier domain method. The purpose of this study is to compare the modified Fourier domain model observer to the spatial domain model observer with both FBP and IR images, using human detection performance as the gold standard. A phantom with inserts of various low contrast levels and sizes was repeatedly scanned 100 times on a third-generation, dual-source CT scanner at 5 dose levels and reconstructed using FBP and IR algorithms. The human detection performance of the inserts was measured via a 2-alternative-forced-choice (2AFC) test. In addition, two model observer performances were calculated, including a Fourier domain non-prewhitening model observer and a spatial domain channelized Hotelling observer. The performance of these two mode observers was compared in terms of how well they correlated with human observer performance. Our results demonstrated that the spatial domain model observer correlated well with human observers across various dose levels, object contrast levels, and object sizes. The Fourier domain observer correlated well with human observers using FBP images, but overestimated the detection performance using IR images.

  9. Contributions of counter-charge in a potassium channel voltage-sensor domain

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Galpin, Jason D; Niciforovic, Ana P

    2011-01-01

    Voltage-sensor domains couple membrane potential to conformational changes in voltage-gated ion channels and phosphatases. Highly coevolved acidic and aromatic side chains assist the transfer of cationic side chains across the transmembrane electric field during voltage sensing. We investigated...... the functional contribution of negative electrostatic potentials from these residues to channel gating and voltage sensing with unnatural amino acid mutagenesis, electrophysiology, voltage-clamp fluorometry and ab initio calculations. The data show that neutralization of two conserved acidic side chains...

  10. The SHOCT domain: a widespread domain under-represented in model organisms.

    Directory of Open Access Journals (Sweden)

    Ruth Y Eberhardt

    Full Text Available We have identified a new protein domain, which we have named the SHOCT domain (Short C-terminal domain. This domain is widespread in bacteria with over a thousand examples. But we found it is missing from the most commonly studied model organisms, despite being present in closely related species. It's predominantly C-terminal location, co-occurrence with numerous other domains and short size is reminiscent of the Gram-positive anchor motif, however it is present in a much wider range of species. We suggest several hypotheses about the function of SHOCT, including oligomerisation and nucleic acid binding. Our initial experiments do not support its role as an oligomerisation domain.

  11. Molecular mechanism of voltage sensing in voltage-gated proton channels

    Science.gov (United States)

    Rebolledo, Santiago; Perez, Marta E.

    2013-01-01

    Voltage-gated proton (Hv) channels play an essential role in phagocytic cells by generating a hyperpolarizing proton current that electrically compensates for the depolarizing current generated by the NADPH oxidase during the respiratory burst, thereby ensuring a sustained production of reactive oxygen species by the NADPH oxidase in phagocytes to neutralize engulfed bacteria. Despite the importance of the voltage-dependent Hv current, it is at present unclear which residues in Hv channels are responsible for the voltage activation. Here we show that individual neutralizations of three charged residues in the fourth transmembrane domain, S4, all reduce the voltage dependence of activation. In addition, we show that the middle S4 charged residue moves from a position accessible from the cytosolic solution to a position accessible from the extracellular solution, suggesting that this residue moves across most of the membrane electric field during voltage activation of Hv channels. Our results show for the first time that the charge movement of these three S4 charges accounts for almost all of the measured gating charge in Hv channels. PMID:23401575

  12. Probing α-3(10) transitions in a voltage-sensing S4 helix.

    Science.gov (United States)

    Kubota, Tomoya; Lacroix, Jérôme J; Bezanilla, Francisco; Correa, Ana M

    2014-09-02

    The S4 helix of voltage sensor domains (VSDs) transfers its gating charges across the membrane electrical field in response to changes of the membrane potential. Recent studies suggest that this process may occur via the helical conversion of the entire S4 between α and 310 conformations. Here, using LRET and FRET, we tested this hypothesis by measuring dynamic changes in the transmembrane length of S4 from engineered VSDs expressed in Xenopus oocytes. Our results suggest that the native S4 from the Ciona intestinalis voltage-sensitive phosphatase (Ci-VSP) does not exhibit extended and long-lived 310 conformations and remains mostly α-helical. Although the S4 of NavAb displays a fully extended 310 conformation in x-ray structures, its transplantation in the Ci-VSP VSD scaffold yielded similar results as the native Ci-VSP S4. Taken together, our study does not support the presence of long-lived extended α-to-310 helical conversions of the S4 in Ci-VSP associated with voltage activation. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  13. Interoperable domain models : The ISO land administration domain model LADM and its external classes

    NARCIS (Netherlands)

    Lemmen, C.H.J.; Van Oosterom, P.J.M.; Uitermark, H.T.; Zevenbergen, J.A.; Cooper, A.K.

    2011-01-01

    This paper provides a brief overview of one of the first spatial domain standards: a standard for the domain of Land Administration (LA). This standard is in the draft stage of development now (May 2011). The development of domain standards is a logical follow up after domain-independent standards,

  14. Crystal structure of the cytoplasmic phosphatase and tensin homolog (PTEN)-like region of Ciona intestinalis voltage-sensing phosphatase provides insight into substrate specificity and redox regulation of the phosphoinositide phosphatase activity.

    Science.gov (United States)

    Matsuda, Makoto; Takeshita, Kohei; Kurokawa, Tatsuki; Sakata, Souhei; Suzuki, Mamoru; Yamashita, Eiki; Okamura, Yasushi; Nakagawa, Atsushi

    2011-07-01

    Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) has a transmembrane voltage sensor domain and a cytoplasmic region sharing similarity to the phosphatase and tensin homolog (PTEN). It dephosphorylates phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate upon membrane depolarization. The cytoplasmic region is composed of a phosphatase domain and a putative membrane interaction domain, C2. Here we determined the crystal structures of the Ci-VSP cytoplasmic region in three distinct constructs, wild-type (248-576), wild-type (236-576), and G365A mutant (248-576). The crystal structure of WT-236 and G365A-248 had the disulfide bond between the catalytic residue Cys-363 and the adjacent residue Cys-310. On the other hand, the disulfide bond was not present in the crystal structure of WT-248. These suggest the possibility that Ci-VSP is regulated by reactive oxygen species as found in PTEN. These structures also revealed that the conformation of the TI loop in the active site of the Ci-VSP cytoplasmic region was distinct from the corresponding region of PTEN; Ci-VSP has glutamic acid (Glu-411) in the TI loop, orienting toward the center of active site pocket. Mutation of Glu-411 led to acquirement of increased activity toward phosphatidylinositol 3,5-bisphosphate, suggesting that this site is required for determining substrate specificity. Our results provide the basic information of the enzymatic mechanism of Ci-VSP.

  15. Interoperable domain models: the ISO land administration domain model LADM and its external classes

    CSIR Research Space (South Africa)

    Lemmen, CHJ

    2011-09-01

    Full Text Available This paper provides a brief overview of one of the first spatial domain standards: a standard for the domain of Land Administration (LA). This standard is in the draft stage of development now (May 2011). The development of domain standards is a...

  16. On Automatic Modeling and Use of Domain-specific Ontologies

    DEFF Research Database (Denmark)

    Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

    2005-01-01

    In this paper, we firstly introduce an approach to the modeling of a domain-specific ontology for use in connection with a given document collection. Secondly, we present a methodology for deriving conceptual similarity from the domain-specific ontology. Adopted for ontology representation is a s...

  17. Towards Clone Detection in UML Domain Models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2013-01-01

    Code clones (i.e., duplicate fragments of code) have been studied for long, and there is strong evidence that they are a major source of software faults. Anecdotal evidence suggests that this phenomenon occurs similarly in models, suggesting that model clones are as detrimental to model quality...... as they are to code quality. However, programming language code and visual models have significant differences that make it difficult to directly transfer notions and algorithms developed in the code clone arena to model clones. In this article, we develop and propose a definition of the notion of “model clone” based...... we believe that our approach advances the state of the art significantly, it is restricted to UML models, its results leave room for improvements, and there is no validation by field studies....

  18. Stochastic lattice model of synaptic membrane protein domains.

    Science.gov (United States)

    Li, Yiwei; Kahraman, Osman; Haselwandter, Christoph A

    2017-05-01

    Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments. We show that our stochastic lattice model yields quantitative agreement with mean-field models of nonlinear diffusion in crowded membranes. Through a combination of analytic and numerical solutions of the master equation governing the reaction dynamics at synaptic domains, together with kinetic Monte Carlo simulations, we find substantial discrepancies between mean-field and stochastic models for the reaction dynamics at synaptic domains. Based on the reaction and diffusion properties of synaptic receptors and scaffolds suggested by previous experiments and mean-field calculations, we show that the stochastic reaction-diffusion dynamics of synaptic receptors and scaffolds provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the observed single-molecule trajectories, and spatial heterogeneity in the effective rates at which receptors and scaffolds are recycled at the cell membrane. Our work sheds light on the physical mechanisms and principles linking the collective properties of membrane protein domains to the stochastic dynamics that rule their molecular components.

  19. Models for randomly distributed nanoscopic domains on spherical vesicles

    Science.gov (United States)

    Anghel, Vinicius N. P.; Bolmatov, Dima; Katsaras, John

    2018-06-01

    The existence of lipid domains in the plasma membrane of biological systems has proven controversial, primarily due to their nanoscopic size—a length scale difficult to interrogate with most commonly used experimental techniques. Scattering techniques have recently proven capable of studying nanoscopic lipid domains populating spherical vesicles. However, the development of analytical methods able of predicting and analyzing domain pair correlations from such experiments has not kept pace. Here, we developed models for the random distribution of monodisperse, circular nanoscopic domains averaged on the surface of a spherical vesicle. Specifically, the models take into account (i) intradomain correlations corresponding to form factors and interdomain correlations corresponding to pair distribution functions, and (ii) the analytical computation of interdomain correlations for cases of two and three domains on a spherical vesicle. In the case of more than three domains, these correlations are treated either by Monte Carlo simulations or by spherical analogs of the Ornstein-Zernike and Percus-Yevick (PY) equations. Importantly, the spherical analog of the PY equation works best in the case of nanoscopic size domains, a length scale that is mostly inaccessible by experimental approaches such as, for example, fluorescent techniques and optical microscopies. The analytical form factors and structure factors of nanoscopic domains populating a spherical vesicle provide a new and important framework for the quantitative analysis of experimental data from commonly studied phase-separated vesicles used in a wide range of biophysical studies.

  20. Topic modelling in the information warfare domain

    CSIR Research Space (South Africa)

    De Waal, A

    2013-11-01

    Full Text Available for interesting and relevant topics. The objectives of this paper is to describe topic modelling, put it in context as a useful IW technique and illustrate its use with two examples. They discuss several applications of topic modelling in the safety and security...

  1. Domain Specific Language for Modeling Waste Management Systems

    DEFF Research Database (Denmark)

    Zarrin, Bahram

    environmental technologies i.e. solid waste management systems. Flow-based programming is used to support concurrent execution of the processes, and provides a model-integration language for composing processes from homogeneous or heterogeneous domains. And a domain-specific language is used to define atomic......In order to develop sustainable waste management systems with considering life cycle perspective, scientists and domain experts in environmental science require readily applicable tools for modeling and evaluating the life cycle impacts of the waste management systems. Practice has proved...... a domain specific language for modeling of waste-management systems on the basis of our framework. We evaluate the language by providing a set of case studies. The contributions of this thesis are; addressing separation of concerns in Flow-based programming and providing the formal specification of its...

  2. Domain walls in the extensions of the Standard Model

    Science.gov (United States)

    Krajewski, Tomasz; Lalak, Zygmunt; Lewicki, Marek; Olszewski, Paweł

    2018-05-01

    Our main interest is the evolution of domain walls of the Higgs field in the early Universe. The aim of this paper is to understand how dynamics of Higgs domain walls could be influenced by yet unknown interactions from beyond the Standard Model. We assume that the Standard Model is valid up to certain, high, energy scale Λ and use the framework of the effective field theory to describe physics below that scale. Performing numerical simulations with different values of the scale Λ we are able to extend our previous analysis [1]. Our recent numerical simulations show that evolution of Higgs domain walls is rather insensitive to interactions beyond the Standard Model as long as masses of new particles are grater than 1012 GeV. For lower values of Λ the RG improved effective potential is strongly modified at field strengths crucial to the evolution of domain walls. However, we find that even for low values of Λ, Higgs domain walls decayed shortly after their formation for generic initial conditions. On the other hand, in simulations with specifically chosen initial conditions Higgs domain walls can live longer and enter the scaling regime. We also determine the energy spectrum of gravitational waves produced by decaying domain walls of the Higgs field. For generic initial field configurations the amplitude of the signal is too small to be observed in planned detectors.

  3. Towards Clone Detection in UML Domain Models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2010-01-01

    Code clones - that is, duplicate fragments of code - have been studied for a long time. There is strong evidence that code clones are a major source of software faults. Anecdotal evidence suggests that this phenomenon is not restricted to code, but occurs in models in a very similar way. So it is...

  4. Mechanisms for integration of information models across related domains

    Science.gov (United States)

    Atkinson, Rob

    2010-05-01

    It is well recognised that there are opportunities and challenges in cross-disciplinary data integration. A significant barrier, however, is creating a conceptual model of the combined domains and the area of integration. For example, a groundwater domain application may require information from several related domains: geology, hydrology, water policy, etc. Each domain may have its own data holdings and conceptual models, but these will share various common concepts (eg. The concept of an aquifer). These areas of semantic overlap present significant challenges, firstly to choose a single representation (model) of a concept that appears in multiple disparate models,, then to harmonise these other models with the single representation. In addition, models may exist at different levels of abstraction depending on how closely aligned they are with a particular implementation. This makes it hard for modellers in one domain to introduce elements from another domain without either introducing a specific style of implementation, or conversely dealing with a set of abstract patterns that are hard to integrate with existing implementations. Models are easier to integrate if they are broken down into small units, with common concepts implemented using common models from well-known, and predictably managed shared libraries. This vision however requires development of a set of mechanisms (tools and procedures) for implementing and exploiting libraries of model components. These mechanisms need to handle publication, discovery, subscription, versioning and implementation of models in different forms. In this presentation a coherent suite of such mechanisms is proposed, using a scenario based on re-use of geosciences models. This approach forms the basis of a comprehensive strategy to empower domain modellers to create more interoperable systems. The strategy address a range of concerns and practice, and includes methodologies, an accessible toolkit, improvements to available

  5. A Probabilistic Graphical Model to Detect Chromosomal Domains

    Science.gov (United States)

    Heermann, Dieter; Hofmann, Andreas; Weber, Eva

    To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These experiments yield topological information, consistently showing a hierarchical subdivision of the genome into self-interacting domains across many organisms. Current methods for detecting these domains using the Hi-C contact matrix, i.e. a doubly-stochastic matrix, are mostly based on the assumption that the domains are distinct, thus non-overlapping. For overcoming this simplification and for being able to unravel a possible nested domain structure, we developed a probabilistic graphical model that makes no a priori assumptions on the domain structure. Within this approach, the Hi-C contact matrix is analyzed using an Ising like probabilistic graphical model whose coupling constant is proportional to each lattice point (entry in the contact matrix). The results show clear boundaries between identified domains and the background. These domain boundaries are dependent on the coupling constant, so that one matrix yields several clusters of different sizes, which show the self-interaction of the genome on different scales. This work was supported by a Grant from the International Human Frontier Science Program Organization (RGP0014/2014).

  6. Vertically Integrated Models for Carbon Storage Modeling in Heterogeneous Domains

    Science.gov (United States)

    Bandilla, K.; Celia, M. A.

    2017-12-01

    Numerical modeling is an essential tool for studying the impacts of geologic carbon storage (GCS). Injection of carbon dioxide (CO2) into deep saline aquifers leads to multi-phase flow (injected CO2 and resident brine), which can be described by a set of three-dimensional governing equations, including mass-balance equation, volumetric flux equations (modified Darcy), and constitutive equations. This is the modeling approach on which commonly used reservoir simulators such as TOUGH2 are based. Due to the large density difference between CO2 and brine, GCS models can often be simplified by assuming buoyant segregation and integrating the three-dimensional governing equations in the vertical direction. The integration leads to a set of two-dimensional equations coupled with reconstruction operators for vertical profiles of saturation and pressure. Vertically-integrated approaches have been shown to give results of comparable quality as three-dimensional reservoir simulators when applied to realistic CO2 injection sites such as the upper sand wedge at the Sleipner site. However, vertically-integrated approaches usually rely on homogeneous properties over the thickness of a geologic layer. Here, we investigate the impact of general (vertical and horizontal) heterogeneity in intrinsic permeability, relative permeability functions, and capillary pressure functions. We consider formations involving complex fluvial deposition environments and compare the performance of vertically-integrated models to full three-dimensional models for a set of hypothetical test cases consisting of high permeability channels (streams) embedded in a low permeability background (floodplains). The domains are randomly generated assuming that stream channels can be represented by sinusoidal waves in the plan-view and by parabolas for the streams' cross-sections. Stream parameters such as width, thickness and wavelength are based on values found at the Ketzin site in Germany. Results from the

  7. Translation of overlay models of student knowledge for relative domains based on domain ontology mapping

    DEFF Research Database (Denmark)

    Sosnovsky, Sergey; Dolog, Peter; Henze, Nicola

    2007-01-01

    The effectiveness of an adaptive educational system in many respects depends on the precision of modeling assumptions it makes about a student. One of the well-known challenges in student modeling is to adequately assess the initial level of student's knowledge when s/he starts working...... with a system. Sometimes potentially handful data are available as a part of user model from a system used by the student before. The usage of external user modeling information is troublesome because of differences in system architecture, knowledge representation, modeling constraints, etc. In this paper, we...... argue that the implementation of underlying knowledge models in a sharable format, as domain ontologies - along with application of automatic ontology mapping techniques for model alignment - can help to overcome the "new-user" problem and will greatly widen opportunities for student model translation...

  8. Domain walls and fermion scattering in grand unified models

    International Nuclear Information System (INIS)

    Steer, D.A.; Vachaspati, T.

    2006-01-01

    Motivated by grand unification, we study the properties of domain walls formed in a model with SU(5)xZ 2 symmetry which is spontaneously broken to SU(3)xSU(2)xU(1)/Z 6 , and subsequently to SU(3)xU(1)/Z 3 . Even after the first stage of symmetry breaking, the SU(3) symmetry is broken to SU(2)xU(1)/Z 2 on the domain wall. In a certain range of parameters, flux tubes carrying color- and hyper-charge live on the domain wall and appear as 'boojums' when viewed from one side of the domain wall. Magnetic monopoles are also formed in the symmetry breaking and those carrying color and hyper-charge can be repelled from the wall due to the Meissner effect, or else their magnetic flux can penetrate the domain wall in quantized units. After the second stage of symmetry breaking, fermions can transmute when they scatter with the domain wall, providing a simpler version of fermion-monopole scattering: for example, neutrinos can scatter into d-quarks, leaving behind electric charge and color which is carried by gauge field excitations living on the domain wall

  9. Finite difference time domain modelling of particle accelerators

    International Nuclear Information System (INIS)

    Jurgens, T.G.; Harfoush, F.A.

    1989-03-01

    Finite Difference Time Domain (FDTD) modelling has been successfully applied to a wide variety of electromagnetic scattering and interaction problems for many years. Here the method is extended to incorporate the modelling of wake fields in particle accelerators. Algorithmic comparisons are made to existing wake field codes, such as MAFIA T3. 9 refs., 7 figs

  10. Three-dimensional transient electromagnetic modeling in the Laplace Domain

    International Nuclear Information System (INIS)

    Mizunaga, H.; Lee, Ki Ha; Kim, H.J.

    1998-01-01

    In modeling electromagnetic responses, Maxwell's equations in the frequency domain are popular and have been widely used (Nabighian, 1994; Newman and Alumbaugh, 1995; Smith, 1996, to list a few). Recently, electromagnetic modeling in the time domain using the finite difference (FDTD) method (Wang and Hohmann, 1993) has also been used to study transient electromagnetic interactions in the conductive medium. This paper presents a new technique to compute the electromagnetic response of three-dimensional (3-D) structures. The proposed new method is based on transforming Maxwell's equations to the Laplace domain. For each discrete Laplace variable, Maxwell's equations are discretized in 3-D using the staggered grid and the finite difference method (FDM). The resulting system of equations is then solved for the fields using the incomplete Cholesky conjugate gradient (ICCG) method. The new method is particularly effective in saving computer memory since all the operations are carried out in real numbers. For the same reason, the computing speed is faster than frequency domain modeling. The proposed approach can be an extremely useful tool in developing an inversion algorithm using the time domain data

  11. From scenarios to domain models: processes and representations

    Science.gov (United States)

    Haddock, Gail; Harbison, Karan

    1994-03-01

    The domain specific software architectures (DSSA) community has defined a philosophy for the development of complex systems. This philosophy improves productivity and efficiency by increasing the user's role in the definition of requirements, increasing the systems engineer's role in the reuse of components, and decreasing the software engineer's role to the development of new components and component modifications only. The scenario-based engineering process (SEP), the first instantiation of the DSSA philosophy, has been adopted by the next generation controller project. It is also the chosen methodology of the trauma care information management system project, and the surrogate semi-autonomous vehicle project. SEP uses scenarios from the user to create domain models and define the system's requirements. Domain knowledge is obtained from a variety of sources including experts, documents, and videos. This knowledge is analyzed using three techniques: scenario analysis, task analysis, and object-oriented analysis. Scenario analysis results in formal representations of selected scenarios. Task analysis of the scenario representations results in descriptions of tasks necessary for object-oriented analysis and also subtasks necessary for functional system analysis. Object-oriented analysis of task descriptions produces domain models and system requirements. This paper examines the representations that support the DSSA philosophy, including reference requirements, reference architectures, and domain models. The processes used to create and use the representations are explained through use of the scenario-based engineering process. Selected examples are taken from the next generation controller project.

  12. Frequency-domain thermal modelling of power semiconductor devices

    DEFF Research Database (Denmark)

    Ma, Ke; Blaabjerg, Frede; Andresen, Markus

    2015-01-01

    to correctly predict the device temperatures, especially when considering the thermal grease and heat sink attached to the power semiconductor devices. In this paper, the frequency-domain approach is applied to the modelling of thermal dynamics for power devices. The limits of the existing RC lump...

  13. Towards an ontological model defining the social engineering domain

    CSIR Research Space (South Africa)

    Mouton, F

    2014-08-01

    Full Text Available -1 ICT and Society IFIP Advances in Information and Communication Technology Volume 431, 2014, pp 266- 279 Towards an Ontological Model Defining the Social Engineering Domain Francois Mouton 1 , Louise Leenen 1 , Mercia M. Malan 2 , and H...

  14. An Integrated Framework to Specify Domain-Specific Modeling Languages

    DEFF Research Database (Denmark)

    Zarrin, Bahram; Baumeister, Hubert

    2018-01-01

    , a logic-based specification language. The drawback of MS DSL Tools is it does not provide a formal and rigorous approach for semantics specifications. In this framework, we use Microsoft DSL Tools to define the metamodel and graphical notations of DSLs, and an extended version of ForSpec as a formal......In this paper, we propose an integrated framework that can be used by DSL designers to implement their desired graphical domain-specific languages. This framework relies on Microsoft DSL Tools, a meta-modeling framework to build graphical domain-specific languages, and an extension of ForSpec...... language to define their semantics. Integrating these technologies under the umbrella of Microsoft Visual Studio IDE allows DSL designers to utilize a single development environment for developing their desired domain-specific languages....

  15. The critical domain size of stochastic population models.

    Science.gov (United States)

    Reimer, Jody R; Bonsall, Michael B; Maini, Philip K

    2017-02-01

    Identifying the critical domain size necessary for a population to persist is an important question in ecology. Both demographic and environmental stochasticity impact a population's ability to persist. Here we explore ways of including this variability. We study populations with distinct dispersal and sedentary stages, which have traditionally been modelled using a deterministic integrodifference equation (IDE) framework. Individual-based models (IBMs) are the most intuitive stochastic analogues to IDEs but yield few analytic insights. We explore two alternate approaches; one is a scaling up to the population level using the Central Limit Theorem, and the other a variation on both Galton-Watson branching processes and branching processes in random environments. These branching process models closely approximate the IBM and yield insight into the factors determining the critical domain size for a given population subject to stochasticity.

  16. Modelling of Context: Designing Mobile Systems from Domain-Dependent Models

    DEFF Research Database (Denmark)

    Nielsen, Peter Axel; Stage, Jan

    2009-01-01

    Modelling of domain-dependent aspects is a key prerequisite for the design of software for mobile systems. Most mobile systems include a more or less advanced model of selected aspects of the domain in which they are used. This paper discusses the creation of such a model and its relevance for te...

  17. Synthetic Domain Theory and Models of Linear Abadi & Plotkin Logic

    DEFF Research Database (Denmark)

    Møgelberg, Rasmus Ejlers; Birkedal, Lars; Rosolini, Guiseppe

    2008-01-01

    Plotkin suggested using a polymorphic dual intuitionistic/linear type theory (PILLY) as a metalanguage for parametric polymorphism and recursion. In recent work the first two authors and R.L. Petersen have defined a notion of parametric LAPL-structure, which are models of PILLY, in which one can...... reason using parametricity and, for example, solve a large class of domain equations, as suggested by Plotkin.In this paper, we show how an interpretation of a strict version of Bierman, Pitts and Russo's language Lily into synthetic domain theory presented by Simpson and Rosolini gives rise...... to a parametric LAPL-structure. This adds to the evidence that the notion of LAPL-structure is a general notion, suitable for treating many different parametric models, and it provides formal proofs of consequences of parametricity expected to hold for the interpretation. Finally, we show how these results...

  18. Time domain series system definition and gear set reliability modeling

    International Nuclear Information System (INIS)

    Xie, Liyang; Wu, Ningxiang; Qian, Wenxue

    2016-01-01

    Time-dependent multi-configuration is a typical feature for mechanical systems such as gear trains and chain drives. As a series system, a gear train is distinct from a traditional series system, such as a chain, in load transmission path, system-component relationship, system functioning manner, as well as time-dependent system configuration. Firstly, the present paper defines time-domain series system to which the traditional series system reliability model is not adequate. Then, system specific reliability modeling technique is proposed for gear sets, including component (tooth) and subsystem (tooth-pair) load history description, material priori/posterior strength expression, time-dependent and system specific load-strength interference analysis, as well as statistically dependent failure events treatment. Consequently, several system reliability models are developed for gear sets with different tooth numbers in the scenario of tooth root material ultimate tensile strength failure. The application of the models is discussed in the last part, and the differences between the system specific reliability model and the traditional series system reliability model are illustrated by virtue of several numerical examples. - Highlights: • A new type of series system, i.e. time-domain multi-configuration series system is defined, that is of great significance to reliability modeling. • Multi-level statistical analysis based reliability modeling method is presented for gear transmission system. • Several system specific reliability models are established for gear set reliability estimation. • The differences between the traditional series system reliability model and the new model are illustrated.

  19. Finite difference time domain modeling of spiral antennas

    Science.gov (United States)

    Penney, Christopher W.; Beggs, John H.; Luebbers, Raymond J.

    1992-01-01

    The objectives outlined in the original proposal for this project were to create a well-documented computer analysis model based on the finite-difference, time-domain (FDTD) method that would be capable of computing antenna impedance, far-zone radiation patterns, and radar cross-section (RCS). The ability to model a variety of penetrable materials in addition to conductors is also desired. The spiral antennas under study by this project meet these requirements since they are constructed of slots cut into conducting surfaces which are backed by dielectric materials.

  20. A domain-independent descriptive design model and its application to structured reflection on design processes

    NARCIS (Netherlands)

    Reymen, Isabelle; Hammer, D.K.; Kroes, P.A.; van Aken, Joan Ernst; van Aken, J.E.; Dorst, C.H.; Bax, M.F.T.; Basten, T

    2006-01-01

    Domain-independent models of the design process are an important means for facilitating interdisciplinary communication and for supporting multidisciplinary design. Many so-called domain-independent models are, however, not really domain independent. We state that to be domain independent, the

  1. Modelling DNA origami self-assembly at the domain level

    Energy Technology Data Exchange (ETDEWEB)

    Dannenberg, Frits; Kwiatkowska, Marta [Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD (United Kingdom); Dunn, Katherine E. [Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU (United Kingdom); Department of Electronics, University of York, York YO10 5DD (United Kingdom); Bath, Jonathan; Turberfield, Andrew J. [Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU (United Kingdom); Ouldridge, Thomas E. [Department of Physics, University of Oxford, Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ (United Kingdom)

    2015-10-28

    We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

  2. Modelling DNA origami self-assembly at the domain level

    International Nuclear Information System (INIS)

    Dannenberg, Frits; Kwiatkowska, Marta; Dunn, Katherine E.; Bath, Jonathan; Turberfield, Andrew J.; Ouldridge, Thomas E.

    2015-01-01

    We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami

  3. Modelling DNA origami self-assembly at the domain level

    Science.gov (United States)

    Dannenberg, Frits; Dunn, Katherine E.; Bath, Jonathan; Kwiatkowska, Marta; Turberfield, Andrew J.; Ouldridge, Thomas E.

    2015-10-01

    We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

  4. Towards the maturity model for feature oriented domain analysis

    Directory of Open Access Journals (Sweden)

    Muhammad Javed

    2014-09-01

    Full Text Available Assessing the quality of a model has always been a challenge for researchers in academia and industry. The quality of a feature model is a prime factor because it is used in the development of products. A degraded feature model leads the development of low quality products. Few efforts have been made on improving the quality of feature models. This paper is an effort to present our ongoing work i.e. development of FODA (Feature Oriented Domain Analysis maturity model which will help to evaluate the quality of a given feature model. In this paper, we provide the quality levels along with their descriptions. The proposed model consists of four levels starting from level 0 to level 3. Design of each level is based on the severity of errors, whereas severity of errors decreases from level 0 to level 3. We elaborate each level with the help of examples. We borrowed all examples from the material published by the research community of Software Product Lines (SPL for the application of our framework.

  5. Domain-specific modeling enabling full code generation

    CERN Document Server

    Kelly, Steven

    2007-01-01

    Domain-Specific Modeling (DSM) is the latest approach tosoftware development, promising to greatly increase the speed andease of software creation. Early adopters of DSM have been enjoyingproductivity increases of 500–1000% in production for over adecade. This book introduces DSM and offers examples from variousfields to illustrate to experienced developers how DSM can improvesoftware development in their teams. Two authorities in the field explain what DSM is, why it works,and how to successfully create and use a DSM solution to improveproductivity and quality. Divided into four parts, the book covers:background and motivation; fundamentals; in-depth examples; andcreating DSM solutions. There is an emphasis throughout the book onpractical guidelines for implementing DSM, including how toidentify the nece sary language constructs, how to generate fullcode from models, and how to provide tool support for a new DSMlanguage. The example cases described in the book are available thebook's Website, www.dsmbook....

  6. Analysis and modelling of engineering structures in frequency domain

    International Nuclear Information System (INIS)

    Ishtev, K.; Bonev, Z.; Petrov, P.; Philipov, P.

    1987-01-01

    This paper deals with some possible applications for modelling and analysis of engineering structures, basing on technique, mentioned above. The governing system of equations is written by using frequency domain approach since elemination technique has computational significance in this field. Modelling is made basing on the well known relationship Y(jw) = W(jw) * X(jw). Here X(jw) is a complex Fourier spectra associated with the imput signals being defined as earthquake, wind, hydrodynamic, control or other type of action. W(jw) is a matrix complex transfer function which reveals the correlation between input X und output Y spectra. Y (ja) represents a complex Fourier spectra of output signals. Input and output signals are both associated with master degrees of freedom, thus matrix transfer function is composed of elements in such a manner that solve unknown parameters are implemented implicitly. It is available an integration algorithm of 'condensed' system of equations. (orig./GL)

  7. A global reference model of the domain name system

    NARCIS (Netherlands)

    Koc, Y.; Jamakovic, A.; Gijsen, B.M.M.

    2012-01-01

    The domain name system (DNS) is a crucial component of the Internet. At this time, the DNS is facing major changes such as the introduction of DNSSEC and Internationalized Domain Name extensions (IDNs), the adoption of IPv6 and the upcoming extension of new generic top-level domains. These changes

  8. Constitutive Modelling of Resins in the Stiffness Domain

    Science.gov (United States)

    Klasztorny, M.

    2004-09-01

    An analytic method for inverting the constitutive compliance equations of viscoelasticity for resins is developed. These equations describe the HWKK/H rheological model, which makes it possible to simulate, with a good accuracy, short-, medium- and long-term viscoelastic processes in epoxy and polyester resins. These processes are of first-rank reversible isothermal type. The time histories of deviatoric stresses are simulated with three independent strain history functions of fractional and normal exponential types. The stiffness equations are described by two elastic and six viscoelastic constants having a clear physic meaning (three long-term relaxation coefficients and three relaxation times). The time histories of axiatoric stresses are simulated as perfectly elastic. The inversion method utilizes approximate constitutive stiffness equations of viscoelasticity for the HWKK/H model. The constitutive compliance equations for the model are a basis for determining the exact complex shear stiffness, whereas the approximate constitutive stiffness equations are used for determining the approximate complex shear stiffness. The viscoelastic constants in the stiffness domain are derived by equating the exact and approximate complex shear stiffnesses. The viscoelastic constants are obtained for Epidian 53 epoxy and Polimal 109 polyester resins. The accuracy of the approximate constitutive stiffness equations are assessed by comparing the approximate and exact complex shear stiffnesses. The constitutive stiffness equations for the HWKK/H model are presented in uncoupled (shear/bulk) and coupled forms. Formulae for converting the constants of shear viscoelasticity into the constants of coupled viscoelasticity are given as well.

  9. Comparative study of 0° X-cut and Y + 36°-cut lithium niobate high-voltage sensing

    Science.gov (United States)

    Patel, N.; Branch, D. W.; Schamiloglu, E.; Cular, S.

    2015-08-01

    A comparison study between Y + 36° and 0° X-cut lithium niobate (LiNbO3) was performed to evaluate the influence of crystal cut on the acoustic propagation to realize a piezoelectric high-voltage sensor. The acoustic time-of-flight for each crystal cut was measured when applying direct current (DC), alternating current (AC), and pulsed voltages. Results show that the voltage-induced shift in the acoustic wave propagation time scaled quadratically with voltage for DC and AC voltages applied to X-cut crystals. For the Y + 36° crystal, the voltage-induced shift scales linearly with DC voltages and quadratically with AC voltages. When applying 5 μs voltage pulses to both crystals, the voltage-induced shift scaled linearly with voltage. For the Y + 36° cut, the voltage-induced shift from applying DC voltages ranged from 10 to 54 ps and 35 to 778 ps for AC voltages at 640 V over the frequency range of 100 Hz-100 kHz. Using the same conditions as the Y + 36° cut, the 0° X-cut crystal sensed a shift of 10-273 ps for DC voltages and 189-813 ps for AC voltage application. For 5 μs voltage pulses, the 0° X-cut crystal sensed a voltage induced shift of 0.250-2 ns and the Y + 36°-cut crystal sensed a time shift of 0.115-1.6 ns. This suggests a frequency sensitive response to voltage where the influence of the crystal cut was not a significant contributor under DC, AC, or pulsed voltage conditions. The measured DC data were compared to a 1-D impedance matrix model where the predicted incremental length changed as a function of voltage. When the voltage source error was eliminated through physical modeling from the uncertainty budget, the combined uncertainty of the sensor (within a 95% confidence interval) decreased to 0.0033% using a Y + 36°-cut crystal and 0.0032% using an X-cut crystal for all the voltage conditions used in this experiment.

  10. Comparative study of 0° X-cut and Y + 36°-cut lithium niobate high-voltage sensing

    International Nuclear Information System (INIS)

    Patel, N.; Branch, D. W.; Cular, S.; Schamiloglu, E.

    2015-01-01

    A comparison study between Y + 36° and 0° X-cut lithium niobate (LiNbO 3 ) was performed to evaluate the influence of crystal cut on the acoustic propagation to realize a piezoelectric high-voltage sensor. The acoustic time-of-flight for each crystal cut was measured when applying direct current (DC), alternating current (AC), and pulsed voltages. Results show that the voltage-induced shift in the acoustic wave propagation time scaled quadratically with voltage for DC and AC voltages applied to X-cut crystals. For the Y + 36° crystal, the voltage-induced shift scales linearly with DC voltages and quadratically with AC voltages. When applying 5 μs voltage pulses to both crystals, the voltage-induced shift scaled linearly with voltage. For the Y + 36° cut, the voltage-induced shift from applying DC voltages ranged from 10 to 54 ps and 35 to 778 ps for AC voltages at 640 V over the frequency range of 100 Hz–100 kHz. Using the same conditions as the Y + 36° cut, the 0° X-cut crystal sensed a shift of 10–273 ps for DC voltages and 189–813 ps for AC voltage application. For 5 μs voltage pulses, the 0° X-cut crystal sensed a voltage induced shift of 0.250–2 ns and the Y + 36°-cut crystal sensed a time shift of 0.115–1.6 ns. This suggests a frequency sensitive response to voltage where the influence of the crystal cut was not a significant contributor under DC, AC, or pulsed voltage conditions. The measured DC data were compared to a 1-D impedance matrix model where the predicted incremental length changed as a function of voltage. When the voltage source error was eliminated through physical modeling from the uncertainty budget, the combined uncertainty of the sensor (within a 95% confidence interval) decreased to 0.0033% using a Y + 36°-cut crystal and 0.0032% using an X-cut crystal for all the voltage conditions used in this experiment

  11. Is the isolated ligand binding domain a good model of the domain in the native receptor?

    Science.gov (United States)

    Deming, Dustin; Cheng, Qing; Jayaraman, Vasanthi

    2003-05-16

    Numerous studies have used the atomic level structure of the isolated ligand binding domain of the glutamate receptor to elucidate the agonist-induced activation and desensitization processes in this group of proteins. However, no study has demonstrated the structural equivalence of the isolated ligand binding fragments and the protein in the native receptor. In this report, using visible absorption spectroscopy we show that the electronic environment of the antagonist 6-cyano-7-nitro-2,3-dihydroxyquinoxaline is identical for the isolated protein and the native glutamate receptors expressed in cells. Our results hence establish that the local structure of the ligand binding site is the same in the two proteins and validate the detailed structure-function relationships that have been developed based on a comparison of the structure of the isolated ligand binding domain and electrophysiological consequences in the native receptor.

  12. Domain engineering product lines, languages, and conceptual models

    CERN Document Server

    Reinhartz-Berger, Iris; Clark, Tony

    2013-01-01

    Domain engineering is a set of activities intended to develop, maintain, and manage the creation and evolution of an area of knowledge suitable for processing by a range of software systems.  It is of considerable practical significance, as it provides methods and techniques that help reduce time-to-market, development costs, and project risks on one hand, and helps improve system quality and performance on a consistent basis on the other. In this book, the editors present a collection of invited chapters from various fields related to domain engineering. The individual chapters pres

  13. Conceptual model of the globalization for domain-specific languages

    NARCIS (Netherlands)

    Clark, T.; van den Brand, M.; Combemale, B.; Rumpe, B.; Combemale, B.

    2015-01-01

    Domain Specific Languages (DSL) have received some prominence recently. Designing a DSL and all their tools is still cumbersome and lots of work. Engineering of DSLs is still at infancy, not even the terms have been coined and agreed on. In particular globalization and all its consequences need to

  14. Atomic force microscopy on domains in biological model membranes

    NARCIS (Netherlands)

    Rinia, H.A.

    2001-01-01

    This thesis describes the preparation and imaging of supported lipid bilayers, which can be regarded as biological modelmembranes, in the light of the formation of domains. The bilayers were prepared with either the Langmuir-Blodgett method, or with vesicle fusion. They were imaged with Atomic Force

  15. Using the Domain Identification Model to Study Major and Career Decision-Making Processes

    Science.gov (United States)

    Tendhar, Chosang; Singh, Kusum; Jones, Brett D.

    2018-01-01

    The purpose of this study was to examine the extent to which (1) a domain identification model could be used to predict students' engineering major and career intentions and (2) the MUSIC Model of Motivation components could be used to predict domain identification. The data for this study were collected from first-year engineering students. We…

  16. Plane symmetric cosmological model with thick domain walls in Brans-Dicke theory of gravitation

    International Nuclear Information System (INIS)

    Pawar, D.; Bayaskar, S.; Patil, V.

    2009-01-01

    We have investigated plane symmetric cosmological model in presence of thick domain walls in Brans-Dicke theory of gravitation, some geometrical and physical behavior of the model are discussed. (authors)

  17. Hydrogeological characterisation and modelling of deformation zones and fracture domains, Forsmark modelling stage 2.2

    Energy Technology Data Exchange (ETDEWEB)

    Follin, Sven (SF GeoLogic AB, Taeby (SE)); Leven, Jakob (Swedish Nuclear Fuel and Waste Management Co., Stockholm (SE)); Hartley, Lee; Jackson, Peter; Joyce, Steve; Roberts, David; Swift, Ben (Serco Assurance, Harwell (GB))

    2007-09-15

    The work reported here collates the structural-hydraulic information gathered in 21 cored boreholes and 32 percussion-drilled boreholes belonging to Forsmark site description, modelling stage 2.2. The analyses carried out provide the hydrogeological input descriptions of the bedrock in Forsmark needed by the end users Repository Engineering, Safety Assessment and Environmental Impact Assessment; that is, hydraulic properties of deformation zones and fracture domains. The same information is also needed for constructing 3D groundwater flow models of the Forsmark site and surrounding area. The analyses carried out render the following conceptual model regarding the observed heterogeneity in deformation zone transmissivity: We find the geological division of the deterministically modelled deformation zones into eight categories (sets) useful from a hydrogeological point of view. Seven of the eight categories are steeply dipping, WNW, NW, NNW, NNE, NE, ENE and EW, and on is gently dipping, G. All deformation zones, regardless of orientation (strike and dip), are subjected to a substantial decrease in transmissivity with depth. The data gathered suggest a contrast of c. 20,000 times for the uppermost one kilometre of bedrock, i.e. more than four orders of magnitude. The hydraulic properties below this depth are not investigated. The lateral heterogeneity is also substantial but more irregular in its appearance. For instance, for a given elevation and deformation zone category (orientation), the spatial variability in transmissivity within a particular deformation zone appears to be as large as the variability between all deformation zones. This suggests that the lateral correlation length is shorter than the shortest distance between two adjacent observation points and shorter than the category spacing. The observation that the mean transmissivity of the gently-dipping deformation zones is c. one to two orders of magnitude greater than the mean transmissivities of all

  18. Comparison of Cole-Cole and Constant Phase Angle modeling in time-domain induced polarization

    DEFF Research Database (Denmark)

    Lajaunie, Myriam; Maurya, Pradip Kumar; Fiandaca, Gianluca

    The Cole-Cole model and the constant phase angle (CPA) model are two prevailing phenomenological descriptions of the induced polarization (IP), used for both frequency domain (FD) and time domain (TD) modeling. The former one is a 4-parameter description, while the latest one involves only two......, forward modeling of quadrupolar sequences on 1D and 2D heterogeneous CPA models shows that the CPA decays differ among each other only by a multiplication factor. Consequently, the inspection of field data in log-log plots gives insight on the modeling needed for fitting them: the CPA inversion cannot...... is reflected in TDIP data, and therefore, at identifying (1) if and when it is possible to distinguish, in time domain, between a Cole-Cole description and a CPA one, and (2) if features of time domain data exist in order to know, from a simple data inspection, which model will be the most adapted to the data...

  19. Ferroelastic domain walls in barium titanate - quantitative phenomenological model

    Czech Academy of Sciences Publication Activity Database

    Hlinka, Jiří; Márton, Pavel

    2009-01-01

    Roč. 101, č. 1 (2009), s. 50-62 ISSN 1058-4587 R&D Projects: GA ČR GA202/06/0411; GA ČR(CZ) GD202/05/H003; GA AV ČR 1ET300100401 Institutional research plan: CEZ:AV0Z10100520 Keywords : ferroelectric and ferroelastic domains * BaTiO 3 * Ginzburg-Landau theory Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.329, year: 2009

  20. A modeling approach to support safety assurance in the automotive domain

    NARCIS (Netherlands)

    Luo, Y.; Brand, van den M.G.J.; Engelen, L.J.P.; Klabbers, M.D.; Selvaraj, H.; Zydek, D.; Chmaj, G.

    2015-01-01

    As safety standards are widely used in safety-critical domains, such as ISO 26262 in the automotive domain, the use of safety cases to demonstrate product safety is stimulated. It is crucial to ensure that a safety case is both correct and clear. To support this, we proposed to make use of modeling

  1. Design of potentially active ligands for SH2 domains by molecular modeling methods

    Directory of Open Access Journals (Sweden)

    Hurmach V. V.

    2014-07-01

    Full Text Available Search for new chemical structures possessing specific biological activity is a complex problem that needs the use of the latest achievements of molecular modeling technologies. It is well known that SH2 domains play a major role in ontogenesis as intermediaries of specific protein-protein interactions. Aim. Developing an algorithm to investigate the properties of SH2 domain binding, search for new potential active compounds for the whole SH2 domains class. Methods. In this paper, we utilize a complex of computer modeling methods to create a generic set of potentially active compounds targeting universally at the whole class of SH2 domains. A cluster analysis of all available three-dimensional structures of SH2 domains was performed and general pharmacophore models were formulated. The models were used for virtual screening of collection of drug-like compounds provided by Enamine Ltd. Results. The design technique for library of potentially active compounds for SH2 domains class was proposed. Conclusions. The original algorithm of SH2 domains research with molecular docking method was developed. Using our algorithm, the active compounds for SH2 domains were found.

  2. Distribution of macular xanthophylls between domains in a model of photoreceptor outer segment membranes.

    Science.gov (United States)

    Wisniewska, Anna; Subczynski, Witold K

    2006-10-15

    A model of photoreceptor outer segment (POS) membranes has been proposed, consisting of an equimolar ternary mixture of 1-palmitoyl-2-docosahexaenoylphosphatidylcholine/distearoylphosphatidylcholine/cholesterol. It was shown that, as in membranes made from the raft-forming mixture, in the model of POS membranes, two domains are formed: the raft domain (detergent resistant membranes, DRM), and the bulk domain (detergent soluble membranes, DSM). Saturation-recovery EPR discrimination by oxygen transport method also demonstrated the presence of two domains in this model system in situ at a wide range of temperatures (10-55 degrees C), showing additionally that neither lutein nor zeaxanthin at 1 mol% affect the formation of these domains. These membrane domains have been separated using cold Triton X-100 extraction from a model of POS membranes containing 1 mol% of either lutein or zeaxanthin. The results indicated that the macular xanthophylls lutein and zeaxanthin are substantially excluded from DRM and remain concentrated in DSM, a domain enriched in highly unsaturated docosahexaenoyl acid which is abundant in retina membranes. The concentration of xanthophylls in DRM and DSM calculated as the mol ratio of either xanthophyll to total lipid (phospholipid+cholesterol) was 0.0028 and 0.0391, respectively. Thus, xanthophylls are about 14 times more concentrated in DSM than in DRM. No significant difference in the distribution of lutein and zeaxanthin was found. The obtained results suggest that in POS membranes macular xanthophylls should also be concentrated in domains enriched in polyunsaturated chains.

  3. Asymmetric cross-domain interference between two working memory tasks : Implications for models of working memory

    NARCIS (Netherlands)

    Morey, Candice C.; Morey, Richard D.; van der Reijden, Madeleine; Holweg, Margot

    2013-01-01

    Observations of higher dual-task costs for within-domain than cross-domain task combinations constitute classic evidence for multi-component models of working memory (e.g., Baddeley, 1986; Logie, 2011). However, we report an asymmetric pattern of interference between verbal and visual-spatial tasks,

  4. Organization Domain Modeling. Volume 1. Conceptual Foundations, Process and Workproduct Description

    Science.gov (United States)

    1993-07-31

    Analysis Companies must often analyze their software products or services relative to those of competitors in the marketplace to determine issues such as...J.A. Hess, W.E. Novak, and A.S. Peterson. Feature-Oriented Domain Analysis ( FODA ) Feasibility Study. Technical Report CMU/SEI-90-TR-21, Software...domain analysis (DA) and modeling, including a structured set of workproducts, a tailorable process model and a set of modeling techniques and guidelines

  5. A multi-domain trust management model for supporting RFID applications of IoT.

    Directory of Open Access Journals (Sweden)

    Xu Wu

    Full Text Available The use of RFID technology in complex and distributed environments often leads to a multi-domain RFID system, in which trust establishment among entities from heterogeneous domains without past interaction or prior agreed policy, is a challenge. The current trust management mechanisms in the literature do not meet the specific requirements in multi-domain RFID systems. Therefore, this paper analyzes the special challenges on trust management in multi-domain RFID systems, and identifies the implications and the requirements of the challenges on the solutions to the trust management of multi-domain RFID systems. A multi-domain trust management model is proposed, which provides a hierarchical trust management framework include a diversity of trust evaluation and establishment approaches. The simulation results and analysis show that the proposed method has excellent ability to deal with the trust relationships, better security, and higher accuracy rate.

  6. Hydrological model performance and parameter estimation in the wavelet-domain

    Directory of Open Access Journals (Sweden)

    B. Schaefli

    2009-10-01

    Full Text Available This paper proposes a method for rainfall-runoff model calibration and performance analysis in the wavelet-domain by fitting the estimated wavelet-power spectrum (a representation of the time-varying frequency content of a time series of a simulated discharge series to the one of the corresponding observed time series. As discussed in this paper, calibrating hydrological models so as to reproduce the time-varying frequency content of the observed signal can lead to different results than parameter estimation in the time-domain. Therefore, wavelet-domain parameter estimation has the potential to give new insights into model performance and to reveal model structural deficiencies. We apply the proposed method to synthetic case studies and a real-world discharge modeling case study and discuss how model diagnosis can benefit from an analysis in the wavelet-domain. The results show that for the real-world case study of precipitation – runoff modeling for a high alpine catchment, the calibrated discharge simulation captures the dynamics of the observed time series better than the results obtained through calibration in the time-domain. In addition, the wavelet-domain performance assessment of this case study highlights the frequencies that are not well reproduced by the model, which gives specific indications about how to improve the model structure.

  7. Dynamical scaling, domain-growth kinetics, and domain-wall shapes of quenched two-dimensional anisotropic XY models

    DEFF Research Database (Denmark)

    Mouritsen, Ole G.; Praestgaard, Eigil

    1988-01-01

    obeys dynamical scaling and the shape of the dynamical scaling function pertaining to the structure factor is found to depend on P. Specifically, this function is described by a Porod-law behavior, q-ω, where ω increases with the wall softness. The kinetic exponent, which describes how the linear domain...... infinite to zero temperature as well as to nonzero temperatures below the ordering transition. The continuous nature of the spin variables causes the domain walls to be ‘‘soft’’ and characterized by a finite thickness. The steady-state thickness of the walls can be varied by a model parameter, P. At zero...... size varies with time, R(t)∼tn, is for both models at zero temperature determined to be n≃0.25, independent of P. At finite temperatures, the growth kinetics is found to cross over to the Lifshitz-Allen-Cahn law characterized by n≃0.50. The results support the idea of two separate zero...

  8. Using the domain identification model to study major and career decision-making processes

    Science.gov (United States)

    Tendhar, Chosang; Singh, Kusum; Jones, Brett D.

    2018-03-01

    The purpose of this study was to examine the extent to which (1) a domain identification model could be used to predict students' engineering major and career intentions and (2) the MUSIC Model of Motivation components could be used to predict domain identification. The data for this study were collected from first-year engineering students. We used a structural equation model to test the hypothesised relationship between variables in the partial domain identification model. The findings suggested that engineering identification significantly predicted engineering major intentions and career intentions and had the highest effect on those two variables compared to other motivational constructs. Furthermore, results suggested that success, interest, and caring are plausible contributors to students' engineering identification. Overall, there is strong evidence that the domain identification model can be used as a lens to study career decision-making processes in engineering, and potentially, in other fields as well.

  9. A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies.

    Science.gov (United States)

    Zahn, Raphael; Osmanović, Dino; Ehret, Severin; Araya Callis, Carolina; Frey, Steffen; Stewart, Murray; You, Changjiang; Görlich, Dirk; Hoogenboom, Bart W; Richter, Ralf P

    2016-04-08

    The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior - a key element for the transport selectivity of the NPC - was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface.

  10. Evapotranspiration Within the Groundwater Model Domain of the Tuba City, Arizona, Disposal Site Interim Report

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2015-03-01

    The revised groundwater model includes estimates of evapotranspiration (ET). The types of vegetation and the influences of ET on groundwater hydrology vary within the model domain. Some plant species within the model domain, classified as phreatophytes, survive by extracting groundwater. ET within these plant communities can result in a net discharge of groundwater if ET exceeds precipitation. Other upland desert plants within the model domain survive on meteoric water, potentially limiting groundwater recharge if ET is equivalent to precipitation. For all plant communities within the model domain, excessive livestock grazing or other disturbances can tip the balance to a net groundwater recharge. This task characterized and mapped vegetation within the groundwater model domain at the Tuba City, Arizona, Site, and then applied a remote sensing algorithm to estimate ET for each vegetation type. The task was designed to address five objectives: 1. Characterize and delineate different vegetation or ET zones within the groundwater model domain, focusing on the separation of plant communities with phreatophytes that survive by tapping groundwater and upland plant communities that are dependent on precipitation. 2. Refine a remote sensing method, developed to estimate ET at the Monument Valley site, for application at the Tuba City site. 3. Estimate recent seasonal and annual ET for all vegetation zones, separating phreatophytic and upland plant communities within the Tuba City groundwater model domain. 4. For selected vegetation zones, estimate ET that might be achieved given a scenario of limited livestock grazing. 5. Analyze uncertainty of ET estimates for each vegetation zone and for the entire groundwater model domain.

  11. Reduced order for nuclear reactor model in frequency and time domain

    International Nuclear Information System (INIS)

    Nugroho, D.H.

    1997-01-01

    In control system theory, a model can be represented by frequency or time domain. In frequency domain, the model was represented by transfer function. in time domain, the model was represented by state space. for the sake of simplification in computation, it is necessary to reduce the model order. the main aim of this research is to find the best in nuclear reactor model. Model order reduction in frequency domain can be done utilizing pole-zero cancellation method; while in time domain utilizing balanced aggregation method the balanced aggregation method was developed by moore (1981). In this paper, the two kinds of method were applied to reduce a nuclear reactor model which was constructed by neutron dynamics and heat transfer equations. to validate that the model characteristics were not change when model order reduction applied, the response was utilized for full and reduced order. it was shown that the nuclear reactor order model can be reduced from order 8 to 2 order 2 is the best order for nuclear reactor model

  12. A Systematic Review of Agent-Based Modelling and Simulation Applications in the Higher Education Domain

    Science.gov (United States)

    Gu, X.; Blackmore, K. L.

    2015-01-01

    This paper presents the results of a systematic review of agent-based modelling and simulation (ABMS) applications in the higher education (HE) domain. Agent-based modelling is a "bottom-up" modelling paradigm in which system-level behaviour (macro) is modelled through the behaviour of individual local-level agent interactions (micro).…

  13. Accuracy and Multi Domain Piezoelectric Power Harvesting Model using VHDL-AMS and SPICE

    NARCIS (Netherlands)

    Da Silva Souza, Flavilene; Oki, N.; Filho, J.V.; Loendersloot, Richard; Berkhoff, Arthur P.

    2016-01-01

    This paper presents a piezoelectric power harvesting model including both the mechanical and electrical domain. It includes a mechanical system, electrical interface, storage capacitor and load. Bridge rectifier, Parallel Synchronized Switch Harvesting on Inductor (P-SSHI) and Synchronous Electric

  14. A Model of Inter and Multi Disciplinary Domains, and their Mutual Interactions

    Directory of Open Access Journals (Sweden)

    Ophir Dan

    2014-02-01

    Full Text Available The Melvil Dewey Decimal Classification system maps the human knowledge domains into a library classification decimal system, which means that the knowledge is discretized. The domains are countable similarly to how Cantor proved the countability of the fractions' domain. The debate about the "inter-" and "multi-" disciplinary domains may also be extended into "sub-domains" or from another point of view – into "super-domains". However, Science and Technology has rapidly developed after it was classified. If at the beginning, two decimal digits were enough to classify the world's knowledge into a knowledge domain, today we need more digits – about five. This means we are able to display about a million domains of knowledge. The decimal point indicates the sub-division in the zooming-in; the number of such decimal points is unlimited. Thus, the number of hierarchical levels in the knowledge-tree is unlimited. The maximal level is unreachable since it propagates in time. This intriguing issue raises doubts whether the tree is the most appropriate structure in the current state of the knowledge classification. However, I believe that the knowledge tree is a convenient way of expressing various connections between the knowledge domains. There are other models such as multi-level graph-networks that approximate closer to reality. These models can be further visualized by graph diagrams. The knowledge diagram is more complicated, considering the interaction between science and industry relative to each domain. The model of reality might be compared to the object-oriented programming languages approximating reality in order to construct more naturally computer programs that can model the world. The mutual correspondence of the knowledge domains is dynamic. Some examples of relatively new domains are as follows: biotechnology, bioinformatics, nanotechnology, integro-differential equations, data warehouse, data mining, requirements engineering, micro

  15. Modeling ferrite electromagnetic response in the time domain

    International Nuclear Information System (INIS)

    Johnson, J.; DeFord, J.F.; Craig, G.D.

    1989-01-01

    The behavior of ferrite loads commonly found in induction accelertors has important consequences for the performance of these accelerators. Previous work by the authors on modeling the electromagnetic fields in induction cavities has focussed upon use of a simple, phenomenological model for the process of magnetization reversal in these ferrite loads. In this paper we consider a model for magnetization reversal which is more deeply rooted in theory, and present a simulation of the reversal process based upon this model for an idealized set of boundary conditions. 7 refs., 3 figs

  16. Contrasting two models of academic self-efficacy--domain-specific versus cross-domain--in children receiving and not receiving special instruction in mathematics.

    Science.gov (United States)

    Jungert, Tomas; Hesser, Hugo; Träff, Ulf

    2014-10-01

    In social cognitive theory, self-efficacy is domain-specific. An alternative model, the cross-domain influence model, would predict that self-efficacy beliefs in one domain might influence performance in other domains. Research has also found that children who receive special instruction are not good at estimating their performance. The aim was to test two models of how self-efficacy beliefs influence achievement, and to contrast children receiving special instruction in mathematics with normally-achieving children. The participants were 73 fifth-grade children who receive special instruction and 70 children who do not receive any special instruction. In year four and five, the children's skills in mathematics and reading were assessed by national curriculum tests, and in their fifth year, self-efficacy in mathematics and reading were measured. Structural equation modeling showed that in domains where children do not receive special instruction in mathematics, self-efficacy is a mediating variable between earlier and later achievement in the same domain. Achievement in mathematics was not mediated by self-efficacy in mathematics for children who receive special instruction. For normal achieving children, earlier achievement in the language domain had an influence on later self-efficacy in the mathematics domain, and self-efficacy beliefs in different domains were correlated. Self-efficacy is mostly domain specific, but may play a different role in academic performance depending on whether children receive special instruction. The results of the present study provided some support of the Cross-Domain Influence Model for normal achieving children. © 2014 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

  17. Infrared images target detection based on background modeling in the discrete cosine domain

    Science.gov (United States)

    Ye, Han; Pei, Jihong

    2018-02-01

    Background modeling is the critical technology to detect the moving target for video surveillance. Most background modeling techniques are aimed at land monitoring and operated in the spatial domain. A background establishment becomes difficult when the scene is a complex fluctuating sea surface. In this paper, the background stability and separability between target are analyzed deeply in the discrete cosine transform (DCT) domain, on this basis, we propose a background modeling method. The proposed method models each frequency point as a single Gaussian model to represent background, and the target is extracted by suppressing the background coefficients. Experimental results show that our approach can establish an accurate background model for seawater, and the detection results outperform other background modeling methods in the spatial domain.

  18. Conceptual language models for domain-specific retrieval

    NARCIS (Netherlands)

    Meij, E.; Trieschnigg, D.; de Rijke, M.; Kraaij, W.

    2010-01-01

    Over the years, various meta-languages have been used to manually enrich documents with conceptual knowledge of some kind. Examples include keyword assignment to citations or, more recently, tags to websites. In this paper we propose generative concept models as an extension to query modeling within

  19. Quark model calculations of current correlators in the nonperturbative domain

    International Nuclear Information System (INIS)

    Celenza, L.S.; Shakin, C.M.; Sun, W.D.

    1995-01-01

    The authors study the vector-isovector current correlator in this work, making use of a generalized Nambu-Jona-Lasinio (NJL) model. In their work, the original NJL model is extended to describe the coupling of the quark-antiquark states to the two-pion continuum. Further, a model for confinement is introduced that is seen to remove the nonphysical cuts that appear in various amplitudes when the quark and antiquark go on mass shell. Quite satisfactory results are obtained for the correlator. The authors also use the correlator to define a T-matrix for confined quarks and discuss a rho-dominance model for that T-matrix. It is also seen that the Bethe-Salpeter equation that determines the rho mass (in the absence of the coupling to the two-pion continuum) has more satisfactory behavior in the generalized model than in the model without confinement. That improved behavior is here related to the absence of the q bar q cut in the basic quark-loop integral of the generalized model. In this model, it is seen how one may work with both quark and hadron degrees of freedom, with only the hadrons appearing as physical particles. 12 refs., 16 figs., 1 tab

  20. Transmembrane helices can induce domain formation in crowded model membranes

    NARCIS (Netherlands)

    Domanski, Jan; Marrink, Siewert J.; Schäfer, Lars V.

    We studied compositionally heterogeneous multi-component model membranes comprised of saturated lipids, unsaturated lipids, cholesterol, and a-helical TM protein models using coarse-grained molecular dynamics simulations. Reducing the mismatch between the length of the saturated and unsaturated

  1. Integrative Approach with Electrophysiological and Theoretical Methods Reveals a New Role of S4 Positively Charged Residues in PKD2L1 Channel Voltage-Sensing.

    Science.gov (United States)

    Numata, Tomohiro; Tsumoto, Kunichika; Yamada, Kazunori; Kurokawa, Tatsuki; Hirose, Shinichi; Nomura, Hideki; Kawano, Mitsuhiro; Kurachi, Yoshihisa; Inoue, Ryuji; Mori, Yasuo

    2017-08-29

    Numerical model-based simulations provide important insights into ion channel gating when experimental limitations exist. Here, a novel strategy combining numerical simulations with patch clamp experiments was used to investigate the net positive charges in the putative transmembrane segment 4 (S4) of the atypical, positively-shifted voltage-dependence of polycystic kidney disease 2-like 1 (PKD2L1) channel. Charge-neutralising mutations (K452Q, K455Q and K461Q) in S4 reduced gating charges, positively shifted the Boltzmann-type activation curve [i.e., open probability (P open )-V curve] and altered the time-courses of activation/deactivation of PKD2L1, indicating that this region constitutes part of a voltage sensor. Numerical reconstruction of wild-type (WT) and mutant PKD2L1-mediated currents necessitated, besides their voltage-dependent gating parameters, a scaling factor that describes the voltage-dependence of maximal conductance, G max . Subsequent single-channel conductance (γ) measurements revealed that voltage-dependence of G max in WT can be explained by the inward-rectifying property of γ, which is greatly changed in PKD2L1 mutants. Homology modelling based on PKD2 and Na V Ab structures suggest that such voltage dependence of P open and γ in PKD2L1 could both reflect the charged state of the S4 domain. The present conjunctive experimental and theoretical approaches provide a framework to explore the undetermined mechanism(s) regulating TRP channels that possess non-classical voltage-dependent properties.

  2. Modeling of Melting and Resolidification in Domain of Metal Film Subjected to a Laser Pulse

    Directory of Open Access Journals (Sweden)

    Majchrzak E.

    2016-03-01

    Full Text Available Thermal processes in domain of thin metal film subjected to a strong laser pulse are discussed. The heating of domain considered causes the melting and next (after the end of beam impact the resolidification of metal superficial layer. The laser action (a time dependent bell-type function is taken into account by the introduction of internal heat source in the energy equation describing the heat transfer in domain of metal film. Taking into account the extremely short duration, extreme temperature gradients and very small geometrical dimensions of the domain considered, the mathematical model of the process is based on the dual phase lag equation supplemented by the suitable boundary-initial conditions. To model the phase transitions the artificial mushy zone is introduced. At the stage of numerical modeling the Control Volume Method is used. The examples of computations are also presented.

  3. Comparison of learning models based on mathematics logical intelligence in affective domain

    Science.gov (United States)

    Widayanto, Arif; Pratiwi, Hasih; Mardiyana

    2018-04-01

    The purpose of this study was to examine the presence or absence of different effects of multiple treatments (used learning models and logical-mathematical intelligence) on the dependent variable (affective domain of mathematics). This research was quasi experimental using 3x3 of factorial design. The population of this research was VIII grade students of junior high school in Karanganyar under the academic year 2017/2018. Data collected in this research was analyzed by two ways analysis of variance with unequal cells using 5% of significance level. The result of the research were as follows: (1) Teaching and learning with model TS lead to better achievement in affective domain than QSH, teaching and learning with model QSH lead to better achievement in affective domain than using DI; (2) Students with high mathematics logical intelligence have better achievement in affective domain than students with low mathematics logical intelligence have; (3) In teaching and learning mathematics using learning model TS, students with moderate mathematics logical intelligence have better achievement in affective domain than using DI; and (4) In teaching and learning mathematics using learning model TS, students with low mathematics logical intelligence have better achievement in affective domain than using QSH and DI.

  4. A Domain-Specific Language for Generic Interlocking Models and Their Properties

    DEFF Research Database (Denmark)

    Vu, Linh Hong; Haxthausen, Anne Elisabeth; Peleska, Jan

    2017-01-01

    of this work is to provide a domain-specific language for generic models and an instantiator tool taking not only configuration data but also a generic model as input instead of using a hard-coded generator for instantiating only one fixed generic model and its properties with configuration data....

  5. Disentangling the Role of Domain-Specific Knowledge in Student Modeling

    Science.gov (United States)

    Ruppert, John; Duncan, Ravit Golan; Chinn, Clark A.

    2017-08-01

    This study explores the role of domain-specific knowledge in students' modeling practice and how this knowledge interacts with two domain-general modeling strategies: use of evidence and developing a causal mechanism. We analyzed models made by middle school students who had a year of intensive model-based instruction. These models were made to explain a familiar but unstudied biological phenomenon: late onset muscle pain. Students were provided with three pieces of evidence related to this phenomenon and asked to construct a model to account for this evidence. Findings indicate that domain-specific resources play a significant role in the extent to which the models accounted for provided evidence. On the other hand, familiarity with the situation appeared to contribute to the mechanistic character of models. Our results indicate that modeling strategies alone are insufficient for the development of a mechanistic model that accounts for provided evidence and that, while learners can develop a tentative model with a basic familiarity of the situation, scaffolding certain domain-specific knowledge is necessary to assist students with incorporating evidence in modeling tasks.

  6. Modeling of earthquake ground motion in the frequency domain

    Science.gov (United States)

    Thrainsson, Hjortur

    In recent years, the utilization of time histories of earthquake ground motion has grown considerably in the design and analysis of civil structures. It is very unlikely, however, that recordings of earthquake ground motion will be available for all sites and conditions of interest. Hence, there is a need for efficient methods for the simulation and spatial interpolation of earthquake ground motion. In addition to providing estimates of the ground motion at a site using data from adjacent recording stations, spatially interpolated ground motions can also be used in design and analysis of long-span structures, such as bridges and pipelines, where differential movement is important. The objective of this research is to develop a methodology for rapid generation of horizontal earthquake ground motion at any site for a given region, based on readily available source, path and site characteristics, or (sparse) recordings. The research includes two main topics: (i) the simulation of earthquake ground motion at a given site, and (ii) the spatial interpolation of earthquake ground motion. In topic (i), models are developed to simulate acceleration time histories using the inverse discrete Fourier transform. The Fourier phase differences, defined as the difference in phase angle between adjacent frequency components, are simulated conditional on the Fourier amplitude. Uniformly processed recordings from recent California earthquakes are used to validate the simulation models, as well as to develop prediction formulas for the model parameters. The models developed in this research provide rapid simulation of earthquake ground motion over a wide range of magnitudes and distances, but they are not intended to replace more robust geophysical models. In topic (ii), a model is developed in which Fourier amplitudes and Fourier phase angles are interpolated separately. A simple dispersion relationship is included in the phase angle interpolation. The accuracy of the interpolation

  7. Sequence Domain Harmonic Modeling of Type-IV Wind Turbines

    DEFF Research Database (Denmark)

    Guest, Emerson; Jensen, Kim Høj; Rasmussen, Tonny Wederberg

    2017-01-01

    -sampled pulsewidth modulation and an analysis of converter generated voltage harmonics due to compensated dead-time. The decoupling capabilities of the proposed the SD harmonic model are verified through a power quality (PQ) assessment of a 3MW Type-IV wind turbine. The assessment shows that the magnitude and phase...... of low-order odd converter generated voltage harmonics are dependent on the converter operating point and the phase of the fundamental component of converter current respectively. The SD harmonic model can be used to make PQ assessments of Type-IV wind turbines or incorporated into harmonic load flows...... for computation of PQ in wind power plants....

  8. Possibilities of Land Administration Domain Model (LADM) implementation in Nigeria

    NARCIS (Netherlands)

    Babalola, S.O.; Rahman, A.A.; Choon, L.T.; Van Oosterom, P.J.M.

    2015-01-01

    LADM covers essential information associated components of land administration and management including those over water and elements above and below the surface of the earth. LADM standard provides an abstract conceptual model with three packages and one sub-package. LADM defined terminology for a

  9. Land administration domain model is an ISO standard now

    NARCIS (Netherlands)

    Lemmen, Christiaan; van Oosterom, Peter; Uitermark, Harry; de Zeeuw, Kees

    2013-01-01

    A group of land administration professionals initiated the development of a data model that facilitates the quick and efficient set-up of land registrations. Just like social issues benefit from proper land administration, land administration systems themselves benefit from proper data standards. In

  10. 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...

  11. Development and application of dispersive soft ferrite models for time-domain simulation

    International Nuclear Information System (INIS)

    DeFord, J.F.; Kamin, G.; Craig, G.D.; Walling, L.

    1992-01-01

    Ferrite has a variety of applications in accelerator components, and the capability to model this magnetic material in the time domain is an important adjunct to currently available accelerator modeling tool. We describe in this report a material model we have developed for the magnetic characteristics of PE11BL, the ferrite found in the ETA-II (Experimental Test Accelerator-II) induction module. This model, which includes the important magnetic dispersion effects found in most soft ferrites, has been implemented in 1-D and 2-D finite-difference time-domain (FDTD) electromagnetic simulators, and comparisons with analytic and experimental results are presented

  12. Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

    Directory of Open Access Journals (Sweden)

    Sofie Van Holle

    2017-05-01

    Full Text Available Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica. The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST, hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.

  13. Boundary regularity of Nevanlinna domains and univalent functions in model subspaces

    International Nuclear Information System (INIS)

    Baranov, Anton D; Fedorovskiy, Konstantin Yu

    2011-01-01

    In the paper we study boundary regularity of Nevanlinna domains, which have appeared in problems of uniform approximation by polyanalytic polynomials. A new method for constructing Nevanlinna domains with essentially irregular nonanalytic boundaries is suggested; this method is based on finding appropriate univalent functions in model subspaces, that is, in subspaces of the form K Θ =H 2 ominus ΘH 2 , where Θ is an inner function. To describe the irregularity of the boundaries of the domains obtained, recent results by Dolzhenko about boundary regularity of conformal mappings are used. Bibliography: 18 titles.

  14. A model for the magnetic domain structure of Gd at 77K

    International Nuclear Information System (INIS)

    Corner, W.D.; Saad, F.M.; Jones, D.W.; Jordan, R.G.

    1978-01-01

    Magnetic domain structures have been observed on planes perpendicular to the c and b axes of Gd crystals at 77K. Various types of domain boundary which might be found in an easy-cone ferromagnet are discussed. A model is presented which is consistent with observations. In this the easy-cone structure is maintained, but it is assumed that owing to the lower basal-plane anisotropy the magnetization component in the basal plane may change in direction within a single domain. (author)

  15. Modeling Operator Performance in Low Task Load Supervisory Domains

    Science.gov (United States)

    2011-06-01

    important to model the best and 65 worst performers separately. It is easy to see that the best performers were better multitaskers and more directed...the expected population this research will influence is expected to contain men and women between the ages of 18 and 50 with an interest in using...for your patience and great sense of humor. I could not ask for a better thesis reader. Thank you, Amy D’Agostino, for taking the time to read my

  16. . Redundancy and blocking in the spatial domain: A connectionist model

    Directory of Open Access Journals (Sweden)

    I. P. L. Mc Laren

    2002-01-01

    Full Text Available How can the observations of spatial blocking (Rodrigo, Chamizo, McLaren & Mackintosh, 1997 and cue redundancy (O’Keefe and Conway, 1978 be reconciled within the framework provided by an error-correcting, connectionist account of spatial navigation? I show that an implementation of McLaren’s (1995 better beta model can serve this purpose, and examine some of the implications for spatial learning and memory.

  17. Finite Difference Time Domain Modeling at USA Instruments, Inc.

    Science.gov (United States)

    Curtis, Richard

    2003-10-01

    Due to the competitive nature of the commercial MRI industry, it is essential for the financial health of a participating company to innovate new coil designs and bring product to market rapidly in response to ever-changing market conditions. However, the technology of MRI coil design is still early in its stage of development and its principles are yet evolving. As a result, it is not always possible to know the relevant electromagnetic effects of a given design since the interaction of coil elements is complex and often counter-intuitive. Even if the effects are known qualitatively, the quantitative results are difficult to obtain. At USA Instruments, Inc., the acquisition of the XFDTDâ electromagnetic simulation tool from REMCOM, Inc., has been helpful in determining the electromagnetic performance characteristics of existing coil designs in the prototype stage before the coils are released for production. In the ideal case, a coil design would be modeled earlier at the conceptual stage, so that only good designs will make it to the prototyping stage and the electromagnetic characteristics better understood very early in the design process and before the testing stage has begun. This paper is a brief overview of using FDTD modeling for MRI coil design at USA Instruments, Inc., and shows some of the highlights of recent FDTD modeling efforts on Birdcage coils, a staple of the MRI coil design portfolio.

  18. Constitutive Modelling of Resins in the Compliance Domain

    Science.gov (United States)

    Klasztorny, M.

    2004-07-01

    A rheological HWKK/H model for resins is developed taking into consideration the up-to-date analyses of experimental results. Constitutive compliance equations of linear are formulated for this model in the shear/bulk form, which describes, among other things, the first-rank reversible isothermal creep. The shear (distorsional) deformations are simulated with three independent stress history functions of fractional and normal exponential types. The volume deformations are simulated as perfectly elastic. The model is described by two elastic and six viscoelastic constants, namely three long-term creep coefficients and three retardation times. The constitutive compliance equations of viscoealsticity for resins are also formulated in the coupled form. Formulae for converting the constants of shear/bulk (uncoupled) viscoelasticity into the constants of coupled viscoelasticity are given too. An algorithm for identifying the material constants, based on the creep of uniaxially tensioned bar samples, is formulated in a way that gives unique results. The material constants are fiund for Epidian 53 epoxy and Polimal 109 polyester resins. The creep processes, simulated based on the experimental data, are presented graphically for both the resins examined.

  19. A simplified approach to control system specification and design using domain modelling and mapping

    International Nuclear Information System (INIS)

    Ludgate, G.A.

    1992-01-01

    Recent developments in the field of accelerator-domain and computer-domain modelling have led to a better understanding of the 'art' of control system specification and design. It now appears possible to 'compile' a control system specification to produce the architectural design. The information required by the 'compiler' is discussed and one hardware optimization algorithm presented. The desired characteristics of the hardware and software components of a distributed control system architecture are discussed and the shortcomings of some commercial products. (author)

  20. Possibilities of Land Administration Domain Model (ladm) Implementation in Nigeria

    Science.gov (United States)

    Babalola, S. O.; Rahman, A. Abdul; Choon, L. T.; Van Oosterom, P. J. M.

    2015-10-01

    LADM covers essential information associated components of land administration and management including those over water and elements above and below the surface of the earth. LADM standard provides an abstract conceptual model with three packages and one sub-package. LADM defined terminology for a land administration system that allows a shared explanation of different formal customary or informal tenures. The standard provides the basis for national and regional profiles and enables the combination of land management information from different sources in a coherent manner. Given this, this paper started with the description of land and land administration in Nigeria. The pre-colonial, colonial and post-colonial era with organization structure was discussed. This discussion is important to present an understanding of the background of any improvement needed for the LADM implementation in Nigeria. The LADM, ISO 19152 and the packages of LADM was discussed, and the comparison of the different aspects of each package and classes were made with Nigerian land administration and the cadastral system. In the comparison made, it was discovered that the concept is similar to LADM packages in Nigerian land administration. Although, the terminology may not be the same in all cases. Having studied conceptualization and the application of LADM, as a model that has essential information associated with components of the land administration. Including those on the land, over water as well as elements above and below the surface of the earth and discovered that the standard is suitable for the country. The model can, therefore, be adopted into Nigerian land administration system by mapping in some of the concepts of LADM.

  1. Quantitative Structure-Use Relationship Model thresholds for Model Validation, Domain of Applicability, and Candidate Alternative Selection

    Data.gov (United States)

    U.S. Environmental Protection Agency — This file contains value of the model training set confusion matrix, domain of applicability evaluation based on training set to predicted chemicals structural...

  2. Infrared maritime target detection using a probabilistic single Gaussian model of sea clutter in Fourier domain

    Science.gov (United States)

    Zhou, Anran; Xie, Weixin; Pei, Jihong; Chen, Yapei

    2018-02-01

    For ship targets detection in cluttered infrared image sequences, a robust detection method, based on the probabilistic single Gaussian model of sea background in Fourier domain, is put forward. The amplitude spectrum sequences at each frequency point of the pure seawater images in Fourier domain, being more stable than the gray value sequences of each background pixel in the spatial domain, are regarded as a Gaussian model. Next, a probability weighted matrix is built based on the stability of the pure seawater's total energy spectrum in the row direction, to make the Gaussian model more accurate. Then, the foreground frequency points are separated from the background frequency points by the model. Finally, the false-alarm points are removed utilizing ships' shape features. The performance of the proposed method is tested by visual and quantitative comparisons with others.

  3. On domain modelling of the service system with its application to enterprise information systems

    Science.gov (United States)

    Wang, J. W.; Wang, H. F.; Ding, J. L.; Furuta, K.; Kanno, T.; Ip, W. H.; Zhang, W. J.

    2016-01-01

    Information systems are a kind of service systems and they are throughout every element of a modern industrial and business system, much like blood in our body. Types of information systems are heterogeneous because of extreme uncertainty in changes in modern industrial and business systems. To effectively manage information systems, modelling of the work domain (or domain) of information systems is necessary. In this paper, a domain modelling framework for the service system is proposed and its application to the enterprise information system is outlined. The framework is defined based on application of a general domain modelling tool called function-context-behaviour-principle-state-structure (FCBPSS). The FCBPSS is based on a set of core concepts, namely: function, context, behaviour, principle, state and structure and system decomposition. Different from many other applications of FCBPSS in systems engineering, the FCBPSS is applied to both infrastructure and substance systems, which is novel and effective to modelling of service systems including enterprise information systems. It is to be noted that domain modelling of systems (e.g. enterprise information systems) is a key to integration of heterogeneous systems and to coping with unanticipated situations facing to systems.

  4. Spatial and frequency domain ring source models for the single muscle fiber action potential

    DEFF Research Database (Denmark)

    Henneberg, Kaj-åge; R., Plonsey

    1994-01-01

    In the paper, single-fibre models for the extracellular action potential are developed that will allow the potential to the evaluated at an arbitrary field point in the extracellular space. Fourier-domain models are restricted in that they evaluate potentials at equidistant points along a line...... parallel to the fibre axis. Consequently, they cannot easily evaluate the potential at the boundary nodes of a boundary-element electrode model. The Fourier-domain models employ axial-symmetric ring source models, and thereby provide higher accuracy that the line source model, where the source is lumped...... including anisotropy show that the spatial models require extreme care in the integration procedure owing to the singularity in the weighting functions. With adequate sampling, the spatial models can evaluate extracellular potentials with high accuracy....

  5. The Role of Domain Knowledge in Cognitive Modeling of Information Search

    NARCIS (Netherlands)

    Karanam, S.; Jorge-Botana, Guillermo; Olmos, Ricardo; van Oostendorp, H.

    2017-01-01

    Computational cognitive models developed so far do not incorporate individual differences in domain knowledge in predicting user clicks on search result pages. We address this problem using a cognitive model of information search which enables us to use two semantic spaces having a low (non-expert

  6. A time-domain binaural detection model and its predictions temporal-resolution data

    NARCIS (Netherlands)

    Breebaart, D.J.; Par, van de S.L.J.D.E.; Kohlrausch, A.G.

    2002-01-01

    This paper discusses the application of a time-domain binaural signal-detection model in the context of estimates of the temporal resolution of the binaural auditory system. It is demonstrated that the optimal detector which is present in the model is crucial to account for specific temporal

  7. A stepwise approach for defining the applicability domain of SAR and QSAR models

    DEFF Research Database (Denmark)

    Dimitrov, Sabcho; Dimitrova, Gergana; Pavlov, Todor

    2005-01-01

    A stepwise approach for determining the model applicability domain is proposed. Four stages are applied to account for the diversity and complexity of the current SAR/QSAR models, reflecting their mechanistic rationality (including metabolic activation of chemicals) and transparency. General para...

  8. A solvable model for coarsening soap froths and other domain boundary networks in two dimensions

    International Nuclear Information System (INIS)

    Flyvbjerg, H.; Jeppesen, C.

    1990-09-01

    The dynamical processes leading to coarsening of soap froths and other domain boundary networks in two dimensions are described statistically by a 'random neighbour model'. The model is solved using the principle of maximum entropy. The solution describes normal growth with realistic probability distribution for area and topology. (orig.)

  9. WESSELÉNYI DOMAIN OF JIBOU, A MODEL OF MULTISECULAR ARRANGEMENT

    Directory of Open Access Journals (Sweden)

    ROZALIA BENEDEK

    2015-10-01

    Full Text Available Wesselényi Domain of Jibou, a Model of Multisecular Arrangement. Nowadays the nobiliary domains arouse the interest of specialists from various field and tourists. The typical nobility constructions are attractive both by their residential function –including curias, castles and palaces in Transylvania – and by the economic function of annexes composed of: mills, barns, stables, riding houses etc. These domains functioned as command centres of territorial arrangements from Medieval Age, premodern and modern ages with implications on the economic and social progress of ages and administrative structures, but also subsequent development. Our study aims to make a presentation of the nobiliary domain Wesselényi in Jibou, aiming to the identification of functions and strategic arrangements for valorisation of the domain as irradiation models of welfare and multiple values, which became a multisecular standard by: emblematic characters, decisive actions carried out by these characters, in Transylvania, Hungary and the Habsburg Empire, to which the Principality of Transylvania belonged until the Great Union of 1918. The management of Jibou domain of Wesselényi family was carried out by various state institutions after the nationalization of 1945, stipulated by Law 187/1945, occasion of new arrangement and valorisation strategies which will also be presented.

  10. Magnetotransport in (Ga,Mn)As on the verge of the single domain model

    Energy Technology Data Exchange (ETDEWEB)

    Rapp, Christoph; Dreher, Lukas; Daeubler, Joachim; Donhauser, Daniela; Glunk, Michael; Schoch, Wladimir; Schwaiger, Stephan; Sauer, Rolf; Limmer, Wolfgang [Institut fuer Halbleiterphysik, Universitaet Ulm (Germany)

    2009-07-01

    We investigate the limits of the single-domain model in (Ga,Mn)As by performing detailed angle- and field-dependent magnetotransport measurements in samples with differing magnetic anisotropies. For this purpose, a series of (Ga,Mn)As layers with Mn concentrations of {proportional_to}5% was grown by low-temperature molecular-beam epitaxy on relaxed (In,Ga)As/GaAs templates with different In-concentrations, realizing different strain conditions from compressive to tensile. In past investigations we have elucidated the strain dependence of the magnetic anisotropy and of the anisotropic magnetoresistance employing a single-domain model. In order to analyze the break-down of the single-domain model, we now study in detail magnetization reversal processes by sweeping an external magnetic field along selected axes. The magnetic-field sweeps are compared with a series of angle-dependent magnetotransport measurements, carried out at weak external magnetic fields.

  11. Birth and death of protein domains: A simple model of evolution explains power law behavior

    Directory of Open Access Journals (Sweden)

    Berezovskaya Faina S

    2002-10-01

    Full Text Available Abstract Background Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connections of enzymes and metabolites in metabolic networks, the number of interactions partners of a given protein, the number of members in paralogous families, and other quantities. In network analysis, power laws imply evolution of the network with preferential attachment, i.e. a greater likelihood of nodes being added to pre-existing hubs. Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution. Results A simple model of evolution of the domain composition of proteomes was developed, with the following elementary processes: i domain birth (duplication with divergence, ii death (inactivation and/or deletion, and iii innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer. This formalism can be described as a birth, death and innovation model (BDIM. The formulas for equilibrium frequencies of domain families of different size and the total number of families at equilibrium are derived for a general BDIM. All asymptotics of equilibrium frequencies of domain families possible for the given type of models are found and their appearance depending on model parameters is investigated. It is proved that the power law asymptotics appears if, and only if, the model is balanced, i.e. domain duplication and deletion rates are asymptotically equal up to the second order. It is further proved that any power asymptotic with the degree not equal to -1 can appear only if the hypothesis of independence of the duplication/deletion rates on the size of a domain family is rejected. Specific cases of BDIMs, namely simple, linear, polynomial and rational

  12. The Arctic Marine Pulses Model: Linking Contiguous Domains in the Pacific Arctic Region

    Science.gov (United States)

    Moore, S. E.; Stabeno, P. J.

    2016-02-01

    The Pacific Arctic marine ecosystem extends from the northern Bering Sea, across the Chukchi and into the East Siberian and Beaufort seas. Food webs in this domain are short, a simplicity that belies the biophysical complexity underlying trophic linkages from primary production to humans. Existing biophysical models, such as pelagic-benthic coupling and advective processes, provide frameworks for connecting certain aspects of the marine food web, but do not offer a full accounting of events that occur seasonally across the Pacific Arctic. In the course of the Synthesis of Arctic Research (SOAR) project, a holistic Arctic Marine Pulses (AMP) model was developed that depicts seasonal biophysical `pulses' across a latitudinal gradient, and linking four previously-described contiguous domains, including the: (i) Pacific-Arctic domain = the focal region; (ii) seasonal ice zone domain; (iii) Pacific marginal domain; and (iv) riverine coastal domain. The AMP model provides a spatial-temporal framework to guide research on dynamic ecosystem processes during this period of rapid biophysical changes in the Pacific Arctic. Some of the processes included in the model, such as pelagic-benthic coupling in the Northern Bering and Chukchi seas, and advection and upwelling along the Beaufort shelf, are already the focus of sampling via the Distributed Biological Observatory (DBO) and other research programs. Other aspects such as biological processes associated with the seasonal ice zone and trophic responses to riverine outflow have received less attention. The AMP model could be enhanced by the application of visualization tools to provide a means to watch a season unfold in space and time. The capability to track sea ice dynamics and water masses and to move nutrients, prey and upper-trophic predators in space and time would provide a strong foundation for the development of predictive human-inclusive ecosystem models for the Pacific Arctic.

  13. Nonlinear System Identification via Basis Functions Based Time Domain Volterra Model

    Directory of Open Access Journals (Sweden)

    Yazid Edwar

    2014-07-01

    Full Text Available This paper proposes basis functions based time domain Volterra model for nonlinear system identification. The Volterra kernels are expanded by using complex exponential basis functions and estimated via genetic algorithm (GA. The accuracy and practicability of the proposed method are then assessed experimentally from a scaled 1:100 model of a prototype truss spar platform. Identification results in time and frequency domain are presented and coherent functions are performed to check the quality of the identification results. It is shown that results between experimental data and proposed method are in good agreement.

  14. Goal-Based Domain Modeling as a Basis for Cross-Disciplinary Systems Engineering

    Science.gov (United States)

    Jarke, Matthias; Nissen, Hans W.; Rose, Thomas; Schmitz, Dominik

    Small and medium-sized enterprises (SMEs) are important drivers for innovation. In particular, project-driven SMEs that closely cooperate with their customers have specific needs in regard to information engineering of their development process. They need a fast requirements capture since this is most often included in the (unpaid) offer development phase. At the same time, they need to maintain and reuse the knowledge and experiences they have gathered in previous projects extensively as it is their core asset. The situation is complicated further if the application field crosses disciplinary boundaries. To bridge the gaps and perspectives, we focus on shared goals and dependencies captured in models at a conceptual level. Such a model-based approach also offers a smarter connection to subsequent development stages, including a high share of automated code generation. In the approach presented here, the agent- and goal-oriented formalism i * is therefore extended by domain models to facilitate information organization. This extension permits a domain model-based similarity search, and a model-based transformation towards subsequent development stages. Our approach also addresses the evolution of domain models reflecting the experiences from completed projects. The approach is illustrated with a case study on software-intensive control systems in an SME of the automotive domain.

  15. A note on domains of discourse. Logical know-how for integrated environmental modelling

    Energy Technology Data Exchange (ETDEWEB)

    Gerstengarbe, F.W. (ed.); Jaeger, C.C.

    2003-10-01

    Building computer models means implementing a mathematical structure on a piece of hardware in such a way that insights about some other phenomenon can be gained, remembered and communicated. For meaningful computer modelling, the phenomenon to be modelled must be described in a logically coherent way. This can be quite difficult, especially when a combination of highly heterogeneous scientific disciplines is needed, as is often the case in environmental research. The paper shows how the notion of a domain of discourse as developed by logicians can be used to map out the cognitive landscape of integrated modelling. This landscape is not a fixed universe, but a multiverse resonating with an evolving pluralism of domains of discourse. Integrated modelling involves a never-ending activity of translation between such domains, an activity that often goes hand in hand with major efforts to overcome conceptual confusions within given domains. For these purposes, a careful use of mathematics, including tools of formal logic presented in the paper, can be helpful. The concept of vulnerability as currently used in global change research is discussed as an example of the challenges to be met in integrated environmental modelling. (orig.)

  16. Super-Grid Modeling of the Elastic Wave Equation in Semi-Bounded Domains

    Energy Technology Data Exchange (ETDEWEB)

    Petersson, N. Anders; Sjögreen, Björn

    2014-10-01

    Abstract

    We develop a super-grid modeling technique for solving the elastic wave equation in semi-bounded two- and three-dimensional spatial domains. In this method, waves are slowed down and dissipated in sponge layers near the far-field boundaries. Mathematically, this is equivalent to a coordinate mapping that transforms a very large physical domain to a significantly smaller computational domain, where the elastic wave equation is solved numerically on a regular grid. To damp out waves that become poorly resolved because of the coordinate mapping, a high order artificial dissipation operator is added in layers near the boundaries of the computational domain. We prove by energy estimates that the super-grid modeling leads to a stable numerical method with decreasing energy, which is valid for heterogeneous material properties and a free surface boundary condition on one side of the domain. Our spatial discretization is based on a fourth order accurate finite difference method, which satisfies the principle of summation by parts. We show that the discrete energy estimate holds also when a centered finite difference stencil is combined with homogeneous Dirichlet conditions at several ghost points outside of the far-field boundaries. Therefore, the coefficients in the finite difference stencils need only be boundary modified near the free surface. This allows for improved computational efficiency and significant simplifications of the implementation of the proposed method in multi-dimensional domains. Numerical experiments in three space dimensions show that the modeling error from truncating the domain can be made very small by choosing a sufficiently wide super-grid damping layer. The numerical accuracy is first evaluated against analytical solutions of Lamb’s problem, where fourth order accuracy is observed with a sixth order artificial dissipation. We then use successive grid refinements to study the numerical accuracy in the more

  17. Estimation of the applicability domain of kernel-based machine learning models for virtual screening

    Directory of Open Access Journals (Sweden)

    Fechner Nikolas

    2010-03-01

    Full Text Available Abstract Background The virtual screening of large compound databases is an important application of structural-activity relationship models. Due to the high structural diversity of these data sets, it is impossible for machine learning based QSAR models, which rely on a specific training set, to give reliable results for all compounds. Thus, it is important to consider the subset of the chemical space in which the model is applicable. The approaches to this problem that have been published so far mostly use vectorial descriptor representations to define this domain of applicability of the model. Unfortunately, these cannot be extended easily to structured kernel-based machine learning models. For this reason, we propose three approaches to estimate the domain of applicability of a kernel-based QSAR model. Results We evaluated three kernel-based applicability domain estimations using three different structured kernels on three virtual screening tasks. Each experiment consisted of the training of a kernel-based QSAR model using support vector regression and the ranking of a disjoint screening data set according to the predicted activity. For each prediction, the applicability of the model for the respective compound is quantitatively described using a score obtained by an applicability domain formulation. The suitability of the applicability domain estimation is evaluated by comparing the model performance on the subsets of the screening data sets obtained by different thresholds for the applicability scores. This comparison indicates that it is possible to separate the part of the chemspace, in which the model gives reliable predictions, from the part consisting of structures too dissimilar to the training set to apply the model successfully. A closer inspection reveals that the virtual screening performance of the model is considerably improved if half of the molecules, those with the lowest applicability scores, are omitted from the screening

  18. Estimation of the applicability domain of kernel-based machine learning models for virtual screening.

    Science.gov (United States)

    Fechner, Nikolas; Jahn, Andreas; Hinselmann, Georg; Zell, Andreas

    2010-03-11

    The virtual screening of large compound databases is an important application of structural-activity relationship models. Due to the high structural diversity of these data sets, it is impossible for machine learning based QSAR models, which rely on a specific training set, to give reliable results for all compounds. Thus, it is important to consider the subset of the chemical space in which the model is applicable. The approaches to this problem that have been published so far mostly use vectorial descriptor representations to define this domain of applicability of the model. Unfortunately, these cannot be extended easily to structured kernel-based machine learning models. For this reason, we propose three approaches to estimate the domain of applicability of a kernel-based QSAR model. We evaluated three kernel-based applicability domain estimations using three different structured kernels on three virtual screening tasks. Each experiment consisted of the training of a kernel-based QSAR model using support vector regression and the ranking of a disjoint screening data set according to the predicted activity. For each prediction, the applicability of the model for the respective compound is quantitatively described using a score obtained by an applicability domain formulation. The suitability of the applicability domain estimation is evaluated by comparing the model performance on the subsets of the screening data sets obtained by different thresholds for the applicability scores. This comparison indicates that it is possible to separate the part of the chemspace, in which the model gives reliable predictions, from the part consisting of structures too dissimilar to the training set to apply the model successfully. A closer inspection reveals that the virtual screening performance of the model is considerably improved if half of the molecules, those with the lowest applicability scores, are omitted from the screening. The proposed applicability domain formulations

  19. Spectral nudging to eliminate the effects of domain position and geometry in regional climate model simulations

    Science.gov (United States)

    Miguez-Macho, Gonzalo; Stenchikov, Georgiy L.; Robock, Alan

    2004-07-01

    It is well known that regional climate simulations are sensitive to the size and position of the domain chosen for calculations. Here we study the physical mechanisms of this sensitivity. We conducted simulations with the Regional Atmospheric Modeling System (RAMS) for June 2000 over North America at 50 km horizontal resolution using a 7500 km × 5400 km grid and NCEP/NCAR reanalysis as boundary conditions. The position of the domain was displaced in several directions, always maintaining the U.S. in the interior, out of the buffer zone along the lateral boundaries. Circulation biases developed a large scale structure, organized by the Rocky Mountains, resulting from a systematic shifting of the synoptic wave trains that crossed the domain. The distortion of the large-scale circulation was produced by interaction of the modeled flow with the lateral boundaries of the nested domain and varied when the position of the grid was altered. This changed the large-scale environment among the different simulations and translated into diverse conditions for the development of the mesoscale processes that produce most of precipitation for the Great Plains in the summer season. As a consequence, precipitation results varied, sometimes greatly, among the experiments with the different grid positions. To eliminate the dependence of results on the position of the domain, we used spectral nudging of waves longer than 2500 km above the boundary layer. Moisture was not nudged at any level. This constrained the synoptic scales to follow reanalysis while allowing the model to develop the small-scale dynamics responsible for the rainfall. Nudging of the large scales successfully eliminated the variation of precipitation results when the grid was moved. We suggest that this technique is necessary for all downscaling studies with regional models with domain sizes of a few thousand kilometers and larger embedded in global models.

  20. The Four Domains Model: Connecting Spirituality, Health and Well-Being

    Directory of Open Access Journals (Sweden)

    John Fisher

    2011-01-01

    Full Text Available At our core, or coeur, we humans are spiritual beings. Spirituality can be viewed in a variety of ways from a traditional understanding of spirituality as an expression of religiosity, in search of the sacred, through to a humanistic view of spirituality devoid of religion. Health is also multi-faceted, with increasing evidence reporting the relationship of spirituality with physical, mental, emotional, social and vocational well-being. This paper presents spiritual health as a, if not THE, fundamental dimension of people’s overall health and well-being, permeating and integrating all the other dimensions of health. Spiritual health is a dynamic state of being, reflected in the quality of relationships that people have in up to four domains of spiritual well-being: Personal domain where a person intra-relates with self; Communal domain, with in-depth inter-personal relationships; Environmental domain, connecting with nature; Transcendental domain, relating to some-thing or some‑One beyond the human level. The Four Domains Model of Spiritual Health and Well‑Being embraces all extant world-views from the ardently religious to the atheistic rationalist.

  1. Finite difference time domain (FDTD) modeling of implanted deep brain stimulation electrodes and brain tissue.

    Science.gov (United States)

    Gabran, S R I; Saad, J H; Salama, M M A; Mansour, R R

    2009-01-01

    This paper demonstrates the electromagnetic modeling and simulation of an implanted Medtronic deep brain stimulation (DBS) electrode using finite difference time domain (FDTD). The model is developed using Empire XCcel and represents the electrode surrounded with brain tissue assuming homogenous and isotropic medium. The model is created to study the parameters influencing the electric field distribution within the tissue in order to provide reference and benchmarking data for DBS and intra-cortical electrode development.

  2. 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)

  3. Educational Objectives and the Learning Domains: A New Formulation [And] Summary: Pierce-Gray Classification Model for the Cognitive, Affective and Psychomotor Domains.

    Science.gov (United States)

    Gray, Charles E.; Pierce, Walter D.

    This paper examines and summarizes the "Pierce-Gray Classification Model for the Cognitive, Affective, and Psychomotor Domains," a model developed for the classification of educational objectives. The classification system was developed to provide a framework that teachers could use as a guide when developing specific instructional objectives for…

  4. Modelling man-made ground to link the above- and below- ground urban domains

    NARCIS (Netherlands)

    Schokker, J.

    2017-01-01

    This report describes the results of STSM TU1206-36204. During a visit to GEUS (DK) between 23 and 27 January 2017, Jeroen Schokker (TNO-GSN, NL) has focussed on the modelling of man-made ground as a linking pin between the above- and below-ground urban domains. Key results include: • Man-made

  5. Strain localization at the margins of strong lithospheric domains: insights from analogue models

    NARCIS (Netherlands)

    Calignano, Elisa; Sokoutis, Dimitrios; Willingshofer, Ernst; Gueydan, Frederic; Cloetingh, Sierd

    The lateral variation of the mechanical properties of continental lithosphere is an important factor controlling the localization of deformation and thus the deformation history and geometry of intra-plate mountain belts. A series of three-layer lithospheric-scale analog models, with a strong domain

  6. The road to a standard land administration domain model, and beyond ...

    NARCIS (Netherlands)

    Lemmen, C.H.J.; Uitermark, H.T.; Van Oosterom, P.J.M.; Zevenbergen, J.A.; Greenway, I.

    2011-01-01

    The Land Administration Domain Model (LADM) is a Draft International Standard (ISO DIS 19152) and in January 2011 was distributed by the ISO central secretariat for a five month voting and commenting time interval. If everything goes as planned, ISO 19152 will be an International Standard (IS) by

  7. Lifshitz-Allen-Cahn domain-growth kinetics of Ising models with conserved density

    DEFF Research Database (Denmark)

    Fogedby, Hans C.; Mouritsen, Ole G.

    1988-01-01

    The domain-growth kinetics of p=fourfold degenerate (2×1) ordering in two-dimensional Ising models with conserved density is studied as a function of temperature and range of Kawasaki spin exchange. It is found by computer simulations that the zero-temperature freezing-in behavior for nearest-nei...

  8. (Br-SCMM) Brazilian Smart City Maturity Model: A Perspective from the Health Domain.

    Science.gov (United States)

    Afonso, Ricardo Alexandre; dos Santos Brito, Kellyton; Holanda do Nascimento, Clóvis; Campos da Costa, Luciana; Álvaro, Alexandre; Cardoso Garcia, Vinicius

    2015-01-01

    The term definition "Smart City" still allows various interpretations, and this causes some difficulty in establishing parameters to measure how smart the cities can be. This paper presents a Maturity Model that uses a set of minimum domains and indicators that aim to encourage cities of different sizes to identify their potential and improve processes and public policies.

  9. Frequency-Domain Hydrodynamic Modelling of Dense and Sparse Arrays of Wave Energy Converters

    NARCIS (Netherlands)

    Wei, Yanji; Barradas Berglind, Jose de Jesus; Yu, Zhiheng; van Rooij, Marijn; Prins, Wouter; Jayawardhana, Bayu; Vakis, Antonis I.

    2018-01-01

    In this work, we develop a frequency-domain model to study the hydrodynamic behaviour of a floater blanket (FB), i.e., an array of floater elements individually connected to power take-off (PTO) systems, which constitutes the core technology of the novel Ocean Grazer (OG) wave energy converter

  10. A Frequency-Domain Model for a Novel Wave Energy Converter

    NARCIS (Netherlands)

    Wei, Yanji; Yu, Zhiheng; Barradas Berglind, Jose de Jesus; van Rooij, Marijn; Prins, Wouter; Jayawardhana, Bayu; Vakis, Antonis I.

    In this work, we develop a frequency-domain model for the novel Ocean Grazer (OG) wave energy converter (WEC), with the intention to study the hydrodynamic behavior of its array of floater elements individually connected to power take-off (PTO) systems. To investigate these hydrodynamic

  11. Dynamic factor analysis in the frequency domain: causal modeling of multivariate psychophysiological time series

    NARCIS (Netherlands)

    Molenaar, P.C.M.

    1987-01-01

    Outlines a frequency domain analysis of the dynamic factor model and proposes a solution to the problem of constructing a causal filter of lagged factor loadings. The method is illustrated with applications to simulated and real multivariate time series. The latter applications involve topographic

  12. Preconditioned finite-difference frequency-domain for modelling periodic dielectric structures - comparisons with FDTD

    NARCIS (Netherlands)

    Chabory, A.; Hon, de B.P.; Schilders, W.H.A.; Tijhuis, A.G.

    2008-01-01

    Finite-difference techniques are very popular and versatile numerical tools in computational electromagnetics. In this paper, we propose a preconditioned finite-difference frequency-domain method (FDFD) to model periodic structures in 2D and 3D. The preconditioner follows from a modal decoupling

  13. Preconditioned finite-difference frequency-domain for modelling periodic dielectric structures : comparisons with FDTD

    NARCIS (Netherlands)

    Chabory, A.; Hon, de B.P.; Schilders, W.H.A.; Tijhuis, A.G.

    2008-01-01

    Finite-difference techniques are very popular and versatile numerical tools in computational electromagnetics. In this paper, we propose a preconditioned finite-difference frequency-domain method (FDFD) to model periodic structures in 2D and 3D. The preconditioner follows from a modal decoupling

  14. Modeling of Nanophotonic Resonators with the Finite-Difference Frequency-Domain Method

    DEFF Research Database (Denmark)

    Ivinskaya, Aliaksandra; Lavrinenko, Andrei; Shyroki, Dzmitry

    2011-01-01

    Finite-difference frequency-domain method with perfectly matched layers and free-space squeezing is applied to model open photonic resonators of arbitrary morphology in three dimensions. Treating each spatial dimension independently, nonuniform mesh of continuously varying density can be built ea...

  15. Studies in astronomical time series analysis. I - Modeling random processes in the time domain

    Science.gov (United States)

    Scargle, J. D.

    1981-01-01

    Several random process models in the time domain are defined and discussed. Attention is given to the moving average model, the autoregressive model, and relationships between and combinations of these models. Consideration is then given to methods for investigating pulse structure, procedures of model construction, computational methods, and numerical experiments. A FORTRAN algorithm of time series analysis has been developed which is relatively stable numerically. Results of test cases are given to study the effect of adding noise and of different distributions for the pulse amplitudes. A preliminary analysis of the light curve of the quasar 3C 272 is considered as an example.

  16. Flavor connections and neutrino mass hierarchy in variant invisible axion models without domain wall problem

    International Nuclear Information System (INIS)

    Geng, C.Q.; Ng, J.N.

    1988-08-01

    New types of invisible axion model based on the recent variant axion models are presented. They belong to the N=1 type model and hence are free of domain wall problems. The Peccei-Quinn symmetry transformations are not totally generation and flavor blind, which may help in understanding the small values of electron and u-quark and large t-quark masses. The light neutrino mass pattern in the two Higgs singlet models can have a very different hierarchy that differs from the other type invisible axion model. (Author) (25 refs.)

  17. Accelerated pharmacokinetic map determination for dynamic contrast enhanced MRI using frequency-domain based Tofts model.

    Science.gov (United States)

    Vajuvalli, Nithin N; Nayak, Krupa N; Geethanath, Sairam

    2014-01-01

    Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI) is widely used in the diagnosis of cancer and is also a promising tool for monitoring tumor response to treatment. The Tofts model has become a standard for the analysis of DCE-MRI. The process of curve fitting employed in the Tofts equation to obtain the pharmacokinetic (PK) parameters is time-consuming for high resolution scans. Current work demonstrates a frequency-domain approach applied to the standard Tofts equation to speed-up the process of curve-fitting in order to obtain the pharmacokinetic parameters. The results obtained show that using the frequency domain approach, the process of curve fitting is computationally more efficient compared to the time-domain approach.

  18. Efficient expression of SRK intracellular domain by a modeling-based protein engineering.

    Science.gov (United States)

    Murase, Kohji; Hirano, Yoshinori; Takayama, Seiji; Hakoshima, Toshio

    2017-03-01

    S-locus protein kinase (SRK) is a receptor kinase that plays a critical role in self-recognition in the Brassicaceae self-incompatibility (SI) response. SRK is activated by binding of its ligand S-locus protein 11 (SP11) and subsequently induced phosphorylation of the intracellular kinase domain. However, a detailed activation mechanism of SRK is still largely unknown because of the difficulty in stably expressing SRK recombinant proteins. Here, we performed modeling-based protein engineering of the SRK kinase domain for stable expression in Escherichia coli. The engineered SRK intracellular domain was expressed about 54-fold higher production than wild type SRK, without loss of the kinase activity, suggesting it could be useful for further biochemical and structural studies. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Self-organization of domain growth in the Ising model with impurities

    DEFF Research Database (Denmark)

    Andersen, Jørgen Vitting; Mouritsen, Ole G.

    1992-01-01

    We have studied avalanchelike rearrangements of domain patterns in the two-dimensional Ising model with static impurities, which is quenched to low temperatures. When breaking the up-down symmetry of the spins by a small applied field, the mere fluctuation of a single spin eventually results...... in a cascade of spin flips at the domain boundaries. We have analyzed the lifetime and size distribution functions for the avalanches and related the results to the general phenomena of self-organized criticality and to recent experiments on cellular magnetic domain patterns in magnetic garnet films. Our...... results suggest that the self-organized state in this system appears to be subcritical, in agreement with a recent theory....

  20. Stability equation and two-component Eigenmode for domain walls in scalar potential model

    International Nuclear Information System (INIS)

    Dias, G.S.; Graca, E.L.; Rodrigues, R. de Lima

    2002-08-01

    Supersymmetric quantum mechanics involving a two-component representation and two-component eigenfunctions is applied to obtain the stability equation associated to a potential model formulated in terms of two coupled real scalar fields. We investigate the question of stability by introducing an operator technique for the Bogomol'nyi-Prasad-Sommerfield (BPS) and non-BPS states on two domain walls in a scalar potential model with minimal N 1-supersymmetry. (author)

  1. Business Process Modeling for Domain Outbound Logistics System: Analytic Perspective with BPMN 2.0

    OpenAIRE

    Khabbazi, Mahmood Reza; Hasan, M.K; Sulaiman, R; Shapi’i, A

    2013-01-01

    This paper proposes a generic"to-be" business processes model for domain highest-level outbound logistics system representing the possible alternative structure and behaviour of the system in respect to x-party logistics services applicable in Small-to-medium sized enterprises. The generic framework of outbound logistics model consists of one main modular system named as the Shipping System including five internal sub-systems of the shipping core, shipping requirement, First Party Logistics (...

  2. Integral formula for elliptic SOS models with domain walls and a reflecting end

    Energy Technology Data Exchange (ETDEWEB)

    Lamers, Jules, E-mail: j.lamers@uu.nl

    2015-12-15

    In this paper we extend previous work of Galleas and the author to elliptic SOS models. We demonstrate that the dynamical reflection algebra can be exploited to obtain a functional equation characterizing the partition function of an elliptic SOS model with domain-wall boundaries and one reflecting end. Special attention is paid to the structure of the functional equation. Through this approach we find a novel multiple-integral formula for that partition function.

  3. 2.5-D frequency-domain viscoelastic wave modelling using finite-element method

    Science.gov (United States)

    Zhao, Jian-guo; Huang, Xing-xing; Liu, Wei-fang; Zhao, Wei-jun; Song, Jian-yong; Xiong, Bin; Wang, Shang-xu

    2017-10-01

    2-D seismic modelling has notable dynamic information discrepancies with field data because of the implicit line-source assumption, whereas 3-D modelling suffers from a huge computational burden. The 2.5-D approach is able to overcome both of the aforementioned limitations. In general, the earth model is treated as an elastic material, but the real media is viscous. In this study, we develop an accurate and efficient frequency-domain finite-element method (FEM) for modelling 2.5-D viscoelastic wave propagation. To perform the 2.5-D approach, we assume that the 2-D viscoelastic media are based on the Kelvin-Voigt rheological model and a 3-D point source. The viscoelastic wave equation is temporally and spatially Fourier transformed into the frequency-wavenumber domain. Then, we systematically derive the weak form and its spatial discretization of 2.5-D viscoelastic wave equations in the frequency-wavenumber domain through the Galerkin weighted residual method for FEM. Fixing a frequency, the 2-D problem for each wavenumber is solved by FEM. Subsequently, a composite Simpson formula is adopted to estimate the inverse Fourier integration to obtain the 3-D wavefield. We implement the stiffness reduction method (SRM) to suppress artificial boundary reflections. The results show that this absorbing boundary condition is valid and efficient in the frequency-wavenumber domain. Finally, three numerical models, an unbounded homogeneous medium, a half-space layered medium and an undulating topography medium, are established. Numerical results validate the accuracy and stability of 2.5-D solutions and present the adaptability of finite-element method to complicated geographic conditions. The proposed 2.5-D modelling strategy has the potential to address modelling studies on wave propagation in real earth media in an accurate and efficient way.

  4. Calculus domains modelled using an original bool algebra based on polygons

    Science.gov (United States)

    Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.

    2016-08-01

    Analytical and numerical computer based models require analytical definitions of the calculus domains. The paper presents a method to model a calculus domain based on a bool algebra which uses solid and hollow polygons. The general calculus relations of the geometrical characteristics that are widely used in mechanical engineering are tested using several shapes of the calculus domain in order to draw conclusions regarding the most effective methods to discretize the domain. The paper also tests the results of several CAD commercial software applications which are able to compute the geometrical characteristics, being drawn interesting conclusions. The tests were also targeting the accuracy of the results vs. the number of nodes on the curved boundary of the cross section. The study required the development of an original software consisting of more than 1700 computer code lines. In comparison with other calculus methods, the discretization using convex polygons is a simpler approach. Moreover, this method doesn't lead to large numbers as the spline approximation did, in that case being required special software packages in order to offer multiple, arbitrary precision. The knowledge resulted from this study may be used to develop complex computer based models in engineering.

  5. A domain-decomposed multi-model plasma simulation of collisionless magnetic reconnection

    Science.gov (United States)

    Datta, I. A. M.; Shumlak, U.; Ho, A.; Miller, S. T.

    2017-10-01

    Collisionless magnetic reconnection is a process relevant to many areas of plasma physics in which energy stored in magnetic fields within highly conductive plasmas is rapidly converted into kinetic and thermal energy. Both in natural phenomena such as solar flares and terrestrial aurora as well as in magnetic confinement fusion experiments, the reconnection process is observed on timescales much shorter than those predicted by a resistive MHD model. As a result, this topic is an active area of research in which plasma models with varying fidelity have been tested in order to understand the proper physics explaining the reconnection process. In this research, a hybrid multi-model simulation employing the Hall-MHD and two-fluid plasma models on a decomposed domain is used to study this problem. The simulation is set up using the WARPXM code developed at the University of Washington, which uses a discontinuous Galerkin Runge-Kutta finite element algorithm and implements boundary conditions between models in the domain to couple their variable sets. The goal of the current work is to determine the parameter regimes most appropriate for each model to maintain sufficient physical fidelity over the whole domain while minimizing computational expense. This work is supported by a Grant from US AFOSR.

  6. Growth of solid domains in model membranes: quantitative image analysis reveals a strong correlation between domain shape and spatial position

    DEFF Research Database (Denmark)

    Bernchou, Uffe; Ipsen, John Hjort; Simonsen, Adam Cohen

    2009-01-01

    . To analyze this effect, the nucleation points were used as generators in a Voronoi construction. Associated with each generator is a Voronoi polygon that contains all points closer to this generator than to any other. Through a detailed quantitative analysis of the Voronoi cells and the domains, we have...

  7. A Third-Order Item Response Theory Model for Modeling the Effects of Domains and Subdomains in Large-Scale Educational Assessment Surveys

    Science.gov (United States)

    Rijmen, Frank; Jeon, Minjeong; von Davier, Matthias; Rabe-Hesketh, Sophia

    2014-01-01

    Second-order item response theory models have been used for assessments consisting of several domains, such as content areas. We extend the second-order model to a third-order model for assessments that include subdomains nested in domains. Using a graphical model framework, it is shown how the model does not suffer from the curse of…

  8. Domain Modeling for Adaptive Training and Education in Support of the US Army Learning Model-Research Outline

    Science.gov (United States)

    2015-06-01

    Definitions are provided for this section to distinguish between adaptive training and education elements and also to highlight their relationships ...illustrate this point Franke (2011) asserts that through the use of case study examples, instruction can provide the pedagogical foundation for decision...a prime example of an adaptive training and education system: a learner or trainee model, an instructional or pedagogical model, a domain model

  9. Discontinuous Galerkin Time-Domain Modeling of Graphene Nano-Ribbon Incorporating the Spatial Dispersion Effects

    KAUST Repository

    Li, Ping; Jiang, Li Jun; Bagci, Hakan

    2018-01-01

    It is well known that graphene demonstrates spatial dispersion properties, i.e., its conductivity is nonlocal and a function of spectral wave number (momentum operator) q. In this paper, to account for effects of spatial dispersion on transmission of high speed signals along graphene nano-ribbon (GNR) interconnects, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed. The atomically-thick GNR is modeled using a nonlocal transparent surface impedance boundary condition (SIBC) incorporated into the DGTD scheme. Since the conductivity is a complicated function of q (and one cannot find an analytical Fourier transform pair between q and spatial differential operators), an exact time domain SIBC model cannot be derived. To overcome this problem, the conductivity is approximated by its Taylor series in spectral domain under low-q assumption. This approach permits expressing the time domain SIBC in the form of a second-order partial differential equation (PDE) in current density and electric field intensity. To permit easy incorporation of this PDE with the DGTD algorithm, three auxiliary variables, which degenerate the second-order (temporal and spatial) differential operators to first-order ones, are introduced. Regarding to the temporal dispersion effects, the auxiliary differential equation (ADE) method is utilized to eliminates the expensive temporal convolutions. To demonstrate the applicability of the proposed scheme, numerical results, which involve characterization of spatial dispersion effects on the transfer impedance matrix of GNR interconnects, are presented.

  10. Discontinuous Galerkin Time-Domain Modeling of Graphene Nano-Ribbon Incorporating the Spatial Dispersion Effects

    KAUST Repository

    Li, Ping

    2018-04-13

    It is well known that graphene demonstrates spatial dispersion properties, i.e., its conductivity is nonlocal and a function of spectral wave number (momentum operator) q. In this paper, to account for effects of spatial dispersion on transmission of high speed signals along graphene nano-ribbon (GNR) interconnects, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed. The atomically-thick GNR is modeled using a nonlocal transparent surface impedance boundary condition (SIBC) incorporated into the DGTD scheme. Since the conductivity is a complicated function of q (and one cannot find an analytical Fourier transform pair between q and spatial differential operators), an exact time domain SIBC model cannot be derived. To overcome this problem, the conductivity is approximated by its Taylor series in spectral domain under low-q assumption. This approach permits expressing the time domain SIBC in the form of a second-order partial differential equation (PDE) in current density and electric field intensity. To permit easy incorporation of this PDE with the DGTD algorithm, three auxiliary variables, which degenerate the second-order (temporal and spatial) differential operators to first-order ones, are introduced. Regarding to the temporal dispersion effects, the auxiliary differential equation (ADE) method is utilized to eliminates the expensive temporal convolutions. To demonstrate the applicability of the proposed scheme, numerical results, which involve characterization of spatial dispersion effects on the transfer impedance matrix of GNR interconnects, are presented.

  11. Taxonomic analysis of perceived risk: modeling individual and group perceptions within homogeneous hazard domains

    International Nuclear Information System (INIS)

    Kraus, N.N.; Slovic, P.

    1988-01-01

    Previous studies of risk perception have typically focused on the mean judgments of a group of people regarding the riskiness (or safety) of a diverse set of hazardous activities, substances, and technologies. This paper reports the results of two studies that take a different path. Study 1 investigated whether models within a single technological domain were similar to previous models based on group means and diverse hazards. Study 2 created a group taxonomy of perceived risk for only one technological domain, railroads, and examined whether the structure of that taxonomy corresponded with taxonomies derived from prior studies of diverse hazards. Results from Study 1 indicated that the importance of various risk characteristics in determining perceived risk differed across individuals and across hazards, but not so much as to invalidate the results of earlier studies based on group means and diverse hazards. In Study 2, the detailed analysis of railroad hazards produced a structure that had both important similarities to, and dissimilarities from, the structure obtained in prior research with diverse hazard domains. The data also indicated that railroad hazards are really quite diverse, with some approaching nuclear reactors in their perceived seriousness. These results suggest that information about the diversity of perceptions within a single domain of hazards could provide valuable input to risk-management decisions

  12. Domain IV voltage-sensor movement is both sufficient and rate limiting for fast inactivation in sodium channels.

    Science.gov (United States)

    Capes, Deborah L; Goldschen-Ohm, Marcel P; Arcisio-Miranda, Manoel; Bezanilla, Francisco; Chanda, Baron

    2013-08-01

    Voltage-gated sodium channels are critical for the generation and propagation of electrical signals in most excitable cells. Activation of Na(+) channels initiates an action potential, and fast inactivation facilitates repolarization of the membrane by the outward K(+) current. Fast inactivation is also the main determinant of the refractory period between successive electrical impulses. Although the voltage sensor of domain IV (DIV) has been implicated in fast inactivation, it remains unclear whether the activation of DIV alone is sufficient for fast inactivation to occur. Here, we functionally neutralize each specific voltage sensor by mutating several critical arginines in the S4 segment to glutamines. We assess the individual role of each voltage-sensing domain in the voltage dependence and kinetics of fast inactivation upon its specific inhibition. We show that movement of the DIV voltage sensor is the rate-limiting step for both development and recovery from fast inactivation. Our data suggest that activation of the DIV voltage sensor alone is sufficient for fast inactivation to occur, and that activation of DIV before channel opening is the molecular mechanism for closed-state inactivation. We propose a kinetic model of sodium channel gating that can account for our major findings over a wide voltage range by postulating that DIV movement is both necessary and sufficient for fast inactivation.

  13. Nonlinear time-domain cochlear model for transient stimulation and human otoacoustic emission

    DEFF Research Database (Denmark)

    Verhulst, Sarah; Dau, Torsten; Shera, Christopher A.

    2012-01-01

    This paper describes the implementation and performance of a nonlinear time-domain model of the cochlea for transient stimulation and human otoacoustic emission generation. The nonlinearity simulates compressive growth of measured basilar-membrane impulse responses. The model accounts...... for reflection and distortion-source otoacoustic emissions (OAEs) and simulates spontaneous OAEs through manipulation of the middle-ear reflectance. The model was calibrated using human psychoacoustical and otoacoustic tuning parameters. It can be used to investigate time-dependent properties of cochlear...

  14. Sensitivity of simulated regional Arctic climate to the choice of coupled model domain

    Directory of Open Access Journals (Sweden)

    Dmitry V. Sein

    2014-07-01

    Full Text Available The climate over the Arctic has undergone changes in recent decades. In order to evaluate the coupled response of the Arctic system to external and internal forcing, our study focuses on the estimation of regional climate variability and its dependence on large-scale atmospheric and regional ocean circulations. A global ocean–sea ice model with regionally high horizontal resolution is coupled to an atmospheric regional model and global terrestrial hydrology model. This way of coupling divides the global ocean model setup into two different domains: one coupled, where the ocean and the atmosphere are interacting, and one uncoupled, where the ocean model is driven by prescribed atmospheric forcing and runs in a so-called stand-alone mode. Therefore, selecting a specific area for the regional atmosphere implies that the ocean–atmosphere system can develop ‘freely’ in that area, whereas for the rest of the global ocean, the circulation is driven by prescribed atmospheric forcing without any feedbacks. Five different coupled setups are chosen for ensemble simulations. The choice of the coupled domains was done to estimate the influences of the Subtropical Atlantic, Eurasian and North Pacific regions on northern North Atlantic and Arctic climate. Our simulations show that the regional coupled ocean–atmosphere model is sensitive to the choice of the modelled area. The different model configurations reproduce differently both the mean climate and its variability. Only two out of five model setups were able to reproduce the Arctic climate as observed under recent climate conditions (ERA-40 Reanalysis. Evidence is found that the main source of uncertainty for Arctic climate variability and its predictability is the North Pacific. The prescription of North Pacific conditions in the regional model leads to significant correlation with observations, even if the whole North Atlantic is within the coupled model domain. However, the inclusion of the

  15. Adapting and applying a multiple domain model of condom use to Chinese college students.

    Science.gov (United States)

    Xiao, Zhiwen; Palmgreen, Philip; Zimmerman, Rick; Noar, Seth

    2010-03-01

    This study adapts a multiple domain model (MDM) to explain condom use among a sample of sexually active Chinese college students. A cross-sectional survey was conducted and structural equation modeling was used to test the proposed model. Preparatory behaviors, theory of reasoned action (TRA)/theory of planned behavior variables, impulsivity, length of relationship, and alcohol use were significant direct predictors of condom use. The results suggest that MDM can provide a better understanding of heterosexual condom use among Chinese youth, and help in the design of HIV-preventive and safer sex interventions in China.

  16. Numerical modeling of wind turbine aerodynamic noise in the time domain.

    Science.gov (United States)

    Lee, Seunghoon; Lee, Seungmin; Lee, Soogab

    2013-02-01

    Aerodynamic noise from a wind turbine is numerically modeled in the time domain. An analytic trailing edge noise model is used to determine the unsteady pressure on the blade surface. The far-field noise due to the unsteady pressure is calculated using the acoustic analogy theory. By using a strip theory approach, the two-dimensional noise model is applied to rotating wind turbine blades. The numerical results indicate that, although the operating and atmospheric conditions are identical, the acoustical characteristics of wind turbine noise can be quite different with respect to the distance and direction from the wind turbine.

  17. Frequency-Domain Maximum-Likelihood Estimation of High-Voltage Pulse Transformer Model Parameters

    CERN Document Server

    Aguglia, D; Martins, C.D.A.

    2014-01-01

    This paper presents an offline frequency-domain nonlinear and stochastic identification method for equivalent model parameter estimation of high-voltage pulse transformers. Such kinds of transformers are widely used in the pulsed-power domain, and the difficulty in deriving pulsed-power converter optimal control strategies is directly linked to the accuracy of the equivalent circuit parameters. These components require models which take into account electric fields energies represented by stray capacitance in the equivalent circuit. These capacitive elements must be accurately identified, since they greatly influence the general converter performances. A nonlinear frequency-based identification method, based on maximum-likelihood estimation, is presented, and a sensitivity analysis of the best experimental test to be considered is carried out. The procedure takes into account magnetic saturation and skin effects occurring in the windings during the frequency tests. The presented method is validated by experim...

  18. Accurate calibration of the velocity-dependent one-scale model for domain walls

    Energy Technology Data Exchange (ETDEWEB)

    Leite, A.M.M., E-mail: up080322016@alunos.fc.up.pt [Centro de Astrofisica, Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Ecole Polytechnique, 91128 Palaiseau Cedex (France); Martins, C.J.A.P., E-mail: Carlos.Martins@astro.up.pt [Centro de Astrofisica, Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Shellard, E.P.S., E-mail: E.P.S.Shellard@damtp.cam.ac.uk [Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom)

    2013-01-08

    We study the asymptotic scaling properties of standard domain wall networks in several cosmological epochs. We carry out the largest field theory simulations achieved to date, with simulation boxes of size 2048{sup 3}, and confirm that a scale-invariant evolution of the network is indeed the attractor solution. The simulations are also used to obtain an accurate calibration for the velocity-dependent one-scale model for domain walls: we numerically determine the two free model parameters to have the values c{sub w}=0.34{+-}0.16 and k{sub w}=0.98{+-}0.07, which are of higher precision than (but in agreement with) earlier estimates.

  19. Time-domain modeling for shielding effectiveness of materials against electromagnetic pulse based on system identification

    International Nuclear Information System (INIS)

    Chen, Xiang; Chen, Yong Guang; Wei, Ming; Hu, Xiao Feng

    2013-01-01

    Shielding effectiveness (SE) of materials against electromagnetic pulse (EMP) cannot be well estimated by traditional test method of SE of materials which only consider the amplitude-frequency characteristic of materials, but ignore the phase-frequency ones. In order to solve this problem, the model of SE of materials against EMP was established based on system identification (SI) method with time-domain linear cosine frequency sweep signal. The feasibility of the method in this paper was examined depending on infinite planar material and the simulation research of coaxial test method and windowed semi-anechoic box of materials. The results show that the amplitude-frequency and phase-frequency information of each frequency can be fully extracted with this method. SE of materials against strong EMP can be evaluated with time-domain low field strength (voltage) of cosine frequency sweep signal. And SE of materials against a variety EMP will be predicted by the model.

  20. Accurate calibration of the velocity-dependent one-scale model for domain walls

    International Nuclear Information System (INIS)

    Leite, A.M.M.; Martins, C.J.A.P.; Shellard, E.P.S.

    2013-01-01

    We study the asymptotic scaling properties of standard domain wall networks in several cosmological epochs. We carry out the largest field theory simulations achieved to date, with simulation boxes of size 2048 3 , and confirm that a scale-invariant evolution of the network is indeed the attractor solution. The simulations are also used to obtain an accurate calibration for the velocity-dependent one-scale model for domain walls: we numerically determine the two free model parameters to have the values c w =0.34±0.16 and k w =0.98±0.07, which are of higher precision than (but in agreement with) earlier estimates.

  1. Frequency domain modeling and dynamic characteristics evaluation of existing wind turbine systems

    Science.gov (United States)

    Chiang, Chih-Hung; Yu, Chih-Peng

    2016-04-01

    It is quite well accepted that frequency domain procedures are suitable for the design and dynamic analysis of wind turbine structures, especially for floating offshore wind turbines, since random wind loads and wave induced motions are most likely simulated in the frequency domain. This paper presents specific applications of an effective frequency domain scheme to the linear analysis of wind turbine structures in which a 1-D spectral element was developed based on the axially-loaded member. The solution schemes are summarized for the spectral analyses of the tower, the blades, and the combined system with selected frequency-dependent coupling effect from foundation-structure interactions. Numerical examples demonstrate that the modal frequencies obtained using spectral-element models are in good agreement with those found in the literature. A 5-element mono-pile model results in less than 0.3% deviation from an existing 160-element model. It is preliminarily concluded that the proposed scheme is relatively efficient in performing quick verification for test data obtained from the on-site vibration measurement using the microwave interferometer.

  2. Critical Domain Problem for the Reaction–Telegraph Equation Model of Population Dynamics

    Directory of Open Access Journals (Sweden)

    Weam Alharbi

    2018-04-01

    Full Text Available A telegraph equation is believed to be an appropriate model of population dynamics as it accounts for the directional persistence of individual animal movement. Being motivated by the problem of habitat fragmentation, which is known to be a major threat to biodiversity that causes species extinction worldwide, we consider the reaction–telegraph equation (i.e., telegraph equation combined with the population growth on a bounded domain with the goal to establish the conditions of species survival. We first show analytically that, in the case of linear growth, the expression for the domain’s critical size coincides with the critical size of the corresponding reaction–diffusion model. We then consider two biologically relevant cases of nonlinear growth, i.e., the logistic growth and the growth with a strong Allee effect. Using extensive numerical simulations, we show that in both cases the critical domain size of the reaction–telegraph equation is larger than the critical domain size of the reaction–diffusion equation. Finally, we discuss possible modifications of the model in order to enhance the positivity of its solutions.

  3. Comparison of the landslide susceptibility models in Taipei Water Source Domain, Taiwan

    Science.gov (United States)

    WU, C. Y.; Yeh, Y. C.; Chou, T. H.

    2017-12-01

    Taipei Water Source Domain, locating at the southeast of Taipei Metropolis, is the main source of water resource in this region. Recently, the downstream turbidity often soared significantly during the typhoon period because of the upstream landslides. The landslide susceptibilities should be analysed to assess the influence zones caused by different rainfall events, and to ensure the abilities of this domain to serve enough and quality water resource. Generally, the landslide susceptibility models can be established based on either a long-term landslide inventory or a specified landslide event. Sometimes, there is no long-term landslide inventory in some areas. Thus, the event-based landslide susceptibility models are established widely. However, the inventory-based and event-based landslide susceptibility models may result in dissimilar susceptibility maps in the same area. So the purposes of this study were to compare the landslide susceptibility maps derived from the inventory-based and event-based models, and to interpret how to select a representative event to be included in the susceptibility model. The landslide inventory from Typhoon Tim in July, 1994 and Typhoon Soudelor in August, 2015 was collected, and used to establish the inventory-based landslide susceptibility model. The landslides caused by Typhoon Nari and rainfall data were used to establish the event-based model. The results indicated the high susceptibility slope-units were located at middle upstream Nan-Shih Stream basin.

  4. Adaptive Noise Model for Transform Domain Wyner-Ziv Video using Clustering of DCT Blocks

    DEFF Research Database (Denmark)

    Luong, Huynh Van; Huang, Xin; Forchhammer, Søren

    2011-01-01

    The noise model is one of the most important aspects influencing the coding performance of Distributed Video Coding. This paper proposes a novel noise model for Transform Domain Wyner-Ziv (TDWZ) video coding by using clustering of DCT blocks. The clustering algorithm takes advantage of the residual...... modelling. Furthermore, the proposed cluster level noise model is adaptively combined with a coefficient level noise model in this paper to robustly improve coding performance of TDWZ video codec up to 1.24 dB (by Bjøntegaard metric) compared to the DISCOVER TDWZ video codec....... information of all frequency bands, iteratively classifies blocks into different categories and estimates the noise parameter in each category. The experimental results show that the coding performance of the proposed cluster level noise model is competitive with state-ofthe- art coefficient level noise...

  5. Voltage dependence of a stochastic model of activation of an alpha helical S4 sensor in a K channel membrane

    Science.gov (United States)

    Vaccaro, S. R.

    2011-09-01

    The voltage dependence of the ionic and gating currents of a K channel is dependent on the activation barriers of a voltage sensor with a potential function which may be derived from the principal electrostatic forces on an S4 segment in an inhomogeneous dielectric medium. By variation of the parameters of a voltage-sensing domain model, consistent with x-ray structures and biophysical data, the lowest frequency of the survival probability of each stationary state derived from a solution of the Smoluchowski equation provides a good fit to the voltage dependence of the slowest time constant of the ionic current in a depolarized membrane, and the gating current exhibits a rising phase that precedes an exponential relaxation. For each depolarizing potential, the calculated time dependence of the survival probabilities of the closed states of an alpha helical S4 sensor are in accord with an empirical model of the ionic and gating currents recorded during the activation process.

  6. Computational models of music perception and cognition II: Domain-specific music processing

    Science.gov (United States)

    Purwins, Hendrik; Grachten, Maarten; Herrera, Perfecto; Hazan, Amaury; Marxer, Ricard; Serra, Xavier

    2008-09-01

    In Part I [Purwins H, Herrera P, Grachten M, Hazan A, Marxer R, Serra X. Computational models of music perception and cognition I: The perceptual and cognitive processing chain. Physics of Life Reviews 2008, in press, doi:10.1016/j.plrev.2008.03.004], we addressed the study of cognitive processes that underlie auditory perception of music, and their neural correlates. The aim of the present paper is to summarize empirical findings from music cognition research that are relevant to three prominent music theoretic domains: rhythm, melody, and tonality. Attention is paid to how cognitive processes like category formation, stimulus grouping, and expectation can account for the music theoretic key concepts in these domains, such as beat, meter, voice, consonance. We give an overview of computational models that have been proposed in the literature for a variety of music processing tasks related to rhythm, melody, and tonality. Although the present state-of-the-art in computational modeling of music cognition definitely provides valuable resources for testing specific hypotheses and theories, we observe the need for models that integrate the various aspects of music perception and cognition into a single framework. Such models should be able to account for aspects that until now have only rarely been addressed in computational models of music cognition, like the active nature of perception and the development of cognitive capacities from infancy to adulthood.

  7. Translating hydrologically-relevant variables from the ice sheet model SICOPOLIS to the Greenland Analog Project hydrologic modeling domain

    Science.gov (United States)

    Vallot, Dorothée; Applegate, Patrick; Pettersson, Rickard

    2013-04-01

    Projecting future climate and ice sheet development requires sophisticated models and extensive field observations. Given the present state of our knowledge, it is very difficult to say what will happen with certainty. Despite the ongoing increase in atmospheric greenhouse gas concentrations, the possibility that a new ice sheet might form over Scandinavia in the far distant future cannot be excluded. The growth of a new Scandinavian Ice Sheet would have important consequences for buried nuclear waste repositories. The Greenland Analogue Project, initiated by the Swedish Nuclear Fuel and Waste Management Company (SKB), is working to assess the effects of a possible future ice sheet on groundwater flow by studying a constrained domain in Western Greenland by field measurements (including deep bedrock drilling in front of the ice sheet) combined with numerical modeling. To address the needs of the GAP project, we interpolated results from an ensemble of ice sheet model runs to the smaller and more finely resolved modeling domain used in the GAP project's hydrologic modeling. Three runs have been chosen with three fairly different positive degree-day factors among those that reproduced the modern ice margin at the borehole position. The interpolated results describe changes in hydrologically-relevant variables over two time periods, 115 ka to 80 ka, and 20 ka to 1 ka. In the first of these time periods, the ice margin advances over the model domain; in the second time period, the ice margin retreats over the model domain. The spatially-and temporally dependent variables that we treated include the ice thickness, basal melting rate, surface mass balance, basal temperature, basal thermal regime (frozen or thawed), surface temperature, and basal water pressure. The melt flux is also calculated.

  8. The use of typed lambda calculus for comprehension and construction of simulation models in the domain of ecology

    Science.gov (United States)

    Uschold, Michael

    1992-01-01

    We are concerned with two important issues in simulation modelling: model comprehension and model construction. Model comprehension is limited because many important choices taken during the modelling process are not documented. This makes it difficult for models to be modified or used by others. A key factor hindering model construction is the vast modelling search space which must be navigated. This is exacerbated by the fact that many modellers are unfamiliar with the terms and concepts catered to by current tools. The root of both problems is the lack of facilities for representing or reasoning about domain concepts in current simulation technology. The basis for our achievements in both of these areas is the development of a language with two distinct levels; one for representing domain information, and the other for representing the simulation model. Of equal importance, is the fact that we make formal connections between these two levels. The domain we are concerned with is ecological modelling. This language, called Elklogic, is based on the typed lambda calculus. Important features include a rich type structure, the use of various higher order functions, and semantics. This enables complex expressions to be constructed from relatively few primitives. The meaning of each expression can be determined in terms of the domain, the simulation model, or the relationship between the two. We describe a novel representation for sets and substructure, and a variety of other general concepts that are especially useful in the ecological domain. We use the type structure in a novel way: for controlling the modelling search space, rather than a proof search space. We facilitate model comprehension by representing modelling decisions that are embodied in the simulation model. We represent the simulation model separately from, but in terms of a domain mode. The explicit links between the two models constitute the modelling decisions. The semantics of Elklogic enables

  9. Interface model conditions for a non-equilibrium heat transfer model for conjugate fluid/porous/solid domains

    International Nuclear Information System (INIS)

    Betchen, L.J.; Straatman, A.G.

    2005-01-01

    A mathematical and numerical model for the treatment of conjugate fluid flow and heat transfer problems in domains containing pure fluid, porous, and pure solid regions has been developed. The model is general and physically reasoned, and allows for local thermal non-equilibrium in the porous region. The model is developed for implementation on a simple collocated finite volume grid. Of particular novelty are the conditions implemented at the interfaces between porous regions, and those containing a pure solid or pure fluid. The model is validated by simulation of a three-dimensional porous plug problem for which experimental results are available. (author)

  10. Impact of time-domain IP pulse length on measured data and inverted models

    DEFF Research Database (Denmark)

    Olsson, P. I.; Fiandaca, G.; Dahlin, T.

    2015-01-01

    The duration of time domain (TD) induced polarization (IP) current injections has significant impact on the acquired IP data as well as on the inversion models, if the standard evaluation procedure is followed. However, it is still possible to retrieve similar inversion models if the waveform...... of the injected current and the IP response waveform are included in the inversion. The on-time also generally affects the signal-tonoise ratio (SNR) where an increased on-time gives higher SNR for the IP data....

  11. Parallel computing of a climate model on the dawn 1000 by domain decomposition method

    Science.gov (United States)

    Bi, Xunqiang

    1997-12-01

    In this paper the parallel computing of a grid-point nine-level atmospheric general circulation model on the Dawn 1000 is introduced. The model was developed by the Institute of Atmospheric Physics (IAP), Chinese Academy of Sciences (CAS). The Dawn 1000 is a MIMD massive parallel computer made by National Research Center for Intelligent Computer (NCIC), CAS. A two-dimensional domain decomposition method is adopted to perform the parallel computing. The potential ways to increase the speed-up ratio and exploit more resources of future massively parallel supercomputation are also discussed.

  12. Dynamic magnetization models for soft ferromagnetic materials with coarse and fine domain structures

    Energy Technology Data Exchange (ETDEWEB)

    Zirka, S.E., E-mail: zirka@email.dp.ua [Department of Physics and Technology, Dnepropetrovsk National University, Gagarin 72, 49050 Dnepropetrovsk (Ukraine); Moroz, Y.I. [Department of Physics and Technology, Dnepropetrovsk National University, Gagarin 72, 49050 Dnepropetrovsk (Ukraine); Steentjes, S.; Hameyer, K. [Institute of Electrical Machines, RWTH Aachen University, Schinkelstr. 4, 52056 Aachen (Germany); Chwastek, K. [Faculty of Electrical Engineering, Czestochowa University of Technology, al. AK 17, 42-201 Czestochowa (Poland); Zurek, S. [Megger Instruments Ltd., Archcliffe Road, Dover, Kent, CT17 9EN (United Kingdom); Harrison, R.G. [Department of Electronics, Carleton University, Ottawa, Canada K1S 5B6 (Canada)

    2015-11-15

    We consider dynamic models, both numerical and analytical, that reproduce the magnetization field H(B) and the energy loss in ferromagnetic sheet materials with different domain structures. Conventional non-oriented (NO) and grain-oriented (GO) electrical steels are chosen as typical representatives of fine-domain and coarse-domain materials. The commonly-accepted loss separation procedures in these materials are critically analyzed. The use of a well-known simplified (“classical”) expression for the eddy-current loss is identified as the primary source of mistaken evaluations of excess loss in NO steel, in which the loss components can only be evaluated using the Maxwell (penetration) equation. The situation is quite different in GO steel, in which the loss separation is uncertain, but the total dynamic loss is several times higher than that explained by any version (numerical or analytical) of the classical approach. To illustrate the uncertainty of the loss separation in GO steel, we show that the magnetization field, and thus the total loss, in this material can be represented with equal accuracy using either the existing three-component approach or our proposed two-component technique, which makes no distinction between classical eddy-current and excess fields and losses. - Highlights: • Critical analysis of a ferromagnetic-material loss-separation principle. • This is to warn materials-science engineers about the inaccuracies resulting from this principle. • A transient model having a single dynamic component is proposed.

  13. Calibrating a Salt Water Intrusion Model with Time-Domain Electromagnetic Data

    DEFF Research Database (Denmark)

    Herckenrath, Daan; Odlum, Nick; Nenna, Vanessa

    2013-01-01

    Salt water intrusion models are commonly used to support groundwater resource management in coastal aquifers. Concentration data used for model calibration are often sparse and limited in spatial extent. With airborne and ground-based electromagnetic surveys, electrical resistivity models can......, we perform a coupled hydrogeophysical inversion (CHI) in which we use a salt water intrusion model to interpret the geophysical data and guide the geophysical inversion. We refer to this methodology as a Coupled Hydrogeophysical Inversion-State (CHI-S), in which simulated salt concentrations...... are transformed to an electrical resistivity model, after which a geophysical forward response is calculated and compared with the measured geophysical data. This approach was applied for a field site in Santa Cruz County, California, where a time-domain electromagnetic (TDEM) dataset was collected...

  14. Detection of Subtle Context-Dependent Model Inaccuracies in High-Dimensional Robot Domains.

    Science.gov (United States)

    Mendoza, Juan Pablo; Simmons, Reid; Veloso, Manuela

    2016-12-01

    Autonomous robots often rely on models of their sensing and actions for intelligent decision making. However, when operating in unconstrained environments, the complexity of the world makes it infeasible to create models that are accurate in every situation. This article addresses the problem of using potentially large and high-dimensional sets of robot execution data to detect situations in which a robot model is inaccurate-that is, detecting context-dependent model inaccuracies in a high-dimensional context space. To find inaccuracies tractably, the robot conducts an informed search through low-dimensional projections of execution data to find parametric Regions of Inaccurate Modeling (RIMs). Empirical evidence from two robot domains shows that this approach significantly enhances the detection power of existing RIM-detection algorithms in high-dimensional spaces.

  15. Time domain system identification of longitudinal dynamics of single rotor model helicopter using sidpac

    International Nuclear Information System (INIS)

    Khaizer, A.N.; Hussain, I.

    2015-01-01

    This paper presents a time-domain approach for identification of longitudinal dynamics of single rotor model helicopter. A frequency sweep excitation input signal is applied for hover flying mode widely used for space state linearized model. A fully automated programmed flight test method provides high quality flight data for system identification using the computer controlled flight simulator X-plane. The flight test data were recorded, analyzed and reduced using the SIDPAC (System Identification Programs for Air Craft) toolbox for MATLAB, resulting in an aerodynamic model of single rotor helicopter. Finally, the identified model of single rotor helicopter is validated on Raptor 30-class model helicopter at hover showing the reliability of proposed approach. (author)

  16. Numerical modeling of time domain 3-D problems in accelerator physics

    International Nuclear Information System (INIS)

    Harfoush, F.A.; Jurgens, T.G.

    1990-06-01

    Time domain analysis is relevant in particle accelerators to study the electromagnetic field interaction of a moving source particle on a lagging test particle as the particles pass an accelerating cavity or some other structure. These fields are called wake fields. The travelling beam inside a beam pipe may undergo more complicated interactions with its environment due to the presence of other irregularities like wires, thin slots, joints and other types of obstacles. Analytical solutions of such problems is impossible and one has to resort to a numerical method. In this paper we present results of our first attempt to model these problems in 3-D using our finite difference time domain (FDTD) code. 10 refs., 9 figs

  17. Distributed HUC-based modeling with SUMMA for ensemble streamflow forecasting over large regional domains.

    Science.gov (United States)

    Saharia, M.; Wood, A.; Clark, M. P.; Bennett, A.; Nijssen, B.; Clark, E.; Newman, A. J.

    2017-12-01

    Most operational streamflow forecasting systems rely on a forecaster-in-the-loop approach in which some parts of the forecast workflow require an experienced human forecaster. But this approach faces challenges surrounding process reproducibility, hindcasting capability, and extension to large domains. The operational hydrologic community is increasingly moving towards `over-the-loop' (completely automated) large-domain simulations yet recent developments indicate a widespread lack of community knowledge about the strengths and weaknesses of such systems for forecasting. A realistic representation of land surface hydrologic processes is a critical element for improving forecasts, but often comes at the substantial cost of forecast system agility and efficiency. While popular grid-based models support the distributed representation of land surface processes, intermediate-scale Hydrologic Unit Code (HUC)-based modeling could provide a more efficient and process-aligned spatial discretization, reducing the need for tradeoffs between model complexity and critical forecasting requirements such as ensemble methods and comprehensive model calibration. The National Center for Atmospheric Research is collaborating with the University of Washington, the Bureau of Reclamation and the USACE to implement, assess, and demonstrate real-time, over-the-loop distributed streamflow forecasting for several large western US river basins and regions. In this presentation, we present early results from short to medium range hydrologic and streamflow forecasts for the Pacific Northwest (PNW). We employ a real-time 1/16th degree daily ensemble model forcings as well as downscaled Global Ensemble Forecasting System (GEFS) meteorological forecasts. These datasets drive an intermediate-scale configuration of the Structure for Unifying Multiple Modeling Alternatives (SUMMA) model, which represents the PNW using over 11,700 HUCs. The system produces not only streamflow forecasts (using the Mizu

  18. Spreading Speed, Traveling Waves, and Minimal Domain Size in Impulsive Reaction–Diffusion Models

    KAUST Repository

    Lewis, Mark A.

    2012-08-15

    How growth, mortality, and dispersal in a species affect the species\\' spread and persistence constitutes a central problem in spatial ecology. We propose impulsive reaction-diffusion equation models for species with distinct reproductive and dispersal stages. These models can describe a seasonal birth pulse plus nonlinear mortality and dispersal throughout the year. Alternatively, they can describe seasonal harvesting, plus nonlinear birth and mortality as well as dispersal throughout the year. The population dynamics in the seasonal pulse is described by a discrete map that gives the density of the population at the end of a pulse as a possibly nonmonotone function of the density of the population at the beginning of the pulse. The dynamics in the dispersal stage is governed by a nonlinear reaction-diffusion equation in a bounded or unbounded domain. We develop a spatially explicit theoretical framework that links species vital rates (mortality or fecundity) and dispersal characteristics with species\\' spreading speeds, traveling wave speeds, as well as minimal domain size for species persistence. We provide an explicit formula for the spreading speed in terms of model parameters, and show that the spreading speed can be characterized as the slowest speed of a class of traveling wave solutions. We also give an explicit formula for the minimal domain size using model parameters. Our results show how the diffusion coefficient, and the combination of discrete- and continuous-time growth and mortality determine the spread and persistence dynamics of the population in a wide variety of ecological scenarios. Numerical simulations are presented to demonstrate the theoretical results. © 2012 Society for Mathematical Biology.

  19. Closed-form estimates of the domain of attraction for nonlinear systems via fuzzy-polynomial models.

    Science.gov (United States)

    Pitarch, José Luis; Sala, Antonio; Ariño, Carlos Vicente

    2014-04-01

    In this paper, the domain of attraction of the origin of a nonlinear system is estimated in closed form via level sets with polynomial boundaries, iteratively computed. In particular, the domain of attraction is expanded from a previous estimate, such as a classical Lyapunov level set. With the use of fuzzy-polynomial models, the domain of attraction analysis can be carried out via sum of squares optimization and an iterative algorithm. The result is a function that bounds the domain of attraction, free from the usual restriction of being positive and decrescent in all the interior of its level sets.

  20. Characterization of non-linear household loads for frequency domain modeling

    Directory of Open Access Journals (Sweden)

    Miguel Fernando Romero

    2015-06-01

    Full Text Available Component-based harmonic studies in public Low Voltage grids require realistic models of individual loads as well as their typical penetration ratios. As fundamental basis for the development of comprehensive models for residential users, this paper identifies the most commonly used household loads in Colombia. The loads are classified according to their Power Factor Correction (PFC circuit topology in no-PFC, passive-PFC and active-PFC devices, and a comprehensive set of loads is selected. Their behavior in terms of harmonic emission is characterized by intensive lab measurements with systematically varied supply voltage distortion. Based on several indices, the suitability of different frequency-domain modeling approaches (e.g. constant current source, decoupled and coupled Norton models is assessed.

  1. Studies in astronomical time series analysis: Modeling random processes in the time domain

    Science.gov (United States)

    Scargle, J. D.

    1979-01-01

    Random process models phased in the time domain are used to analyze astrophysical time series data produced by random processes. A moving average (MA) model represents the data as a sequence of pulses occurring randomly in time, with random amplitudes. An autoregressive (AR) model represents the correlations in the process in terms of a linear function of past values. The best AR model is determined from sampled data and transformed to an MA for interpretation. The randomness of the pulse amplitudes is maximized by a FORTRAN algorithm which is relatively stable numerically. Results of test cases are given to study the effects of adding noise and of different distributions for the pulse amplitudes. A preliminary analysis of the optical light curve of the quasar 3C 273 is given.

  2. Improved virtual channel noise model for transform domain Wyner-Ziv video coding

    DEFF Research Database (Denmark)

    Huang, Xin; Forchhammer, Søren

    2009-01-01

    Distributed video coding (DVC) has been proposed as a new video coding paradigm to deal with lossy source coding using side information to exploit the statistics at the decoder to reduce computational demands at the encoder. A virtual channel noise model is utilized at the decoder to estimate...... the noise distribution between the side information frame and the original frame. This is one of the most important aspects influencing the coding performance of DVC. Noise models with different granularity have been proposed. In this paper, an improved noise model for transform domain Wyner-Ziv video...... coding is proposed, which utilizes cross-band correlation to estimate the Laplacian parameters more accurately. Experimental results show that the proposed noise model can improve the rate-distortion (RD) performance....

  3. Finite element time domain modeling of controlled-Source electromagnetic data with a hybrid boundary condition

    DEFF Research Database (Denmark)

    Cai, Hongzhu; Hu, Xiangyun; Xiong, Bin

    2017-01-01

    method which is unconditionally stable. We solve the diffusion equation for the electric field with a total field formulation. The finite element system of equation is solved using the direct method. The solutions of electric field, at different time, can be obtained using the effective time stepping...... method with trivial computation cost once the matrix is factorized. We try to keep the same time step size for a fixed number of steps using an adaptive time step doubling (ATSD) method. The finite element modeling domain is also truncated using a semi-adaptive method. We proposed a new boundary...... condition based on approximating the total field on the modeling boundary using the primary field corresponding to a layered background model. We validate our algorithm using several synthetic model studies....

  4. Care episode retrieval: distributional semantic models for information retrieval in the clinical domain.

    Science.gov (United States)

    Moen, Hans; Ginter, Filip; Marsi, Erwin; Peltonen, Laura-Maria; Salakoski, Tapio; Salanterä, Sanna

    2015-01-01

    Patients' health related information is stored in electronic health records (EHRs) by health service providers. These records include sequential documentation of care episodes in the form of clinical notes. EHRs are used throughout the health care sector by professionals, administrators and patients, primarily for clinical purposes, but also for secondary purposes such as decision support and research. The vast amounts of information in EHR systems complicate information management and increase the risk of information overload. Therefore, clinicians and researchers need new tools to manage the information stored in the EHRs. A common use case is, given a--possibly unfinished--care episode, to retrieve the most similar care episodes among the records. This paper presents several methods for information retrieval, focusing on care episode retrieval, based on textual similarity, where similarity is measured through domain-specific modelling of the distributional semantics of words. Models include variants of random indexing and the semantic neural network model word2vec. Two novel methods are introduced that utilize the ICD-10 codes attached to care episodes to better induce domain-specificity in the semantic model. We report on experimental evaluation of care episode retrieval that circumvents the lack of human judgements regarding episode relevance. Results suggest that several of the methods proposed outperform a state-of-the art search engine (Lucene) on the retrieval task.

  5. Time-Domain Modeling of RF Antennas and Plasma-Surface Interactions

    Directory of Open Access Journals (Sweden)

    Jenkins Thomas G.

    2017-01-01

    Full Text Available Recent advances in finite-difference time-domain (FDTD modeling techniques allow plasma-surface interactions such as sheath formation and sputtering to be modeled concurrently with the physics of antenna near- and far-field behavior and ICRF power flow. Although typical sheath length scales (micrometers are much smaller than the wavelengths of fast (tens of cm and slow (millimeter waves excited by the antenna, sheath behavior near plasma-facing antenna components can be represented by a sub-grid kinetic sheath boundary condition, from which RF-rectified sheath potential variation over the surface is computed as a function of current flow and local plasma parameters near the wall. These local time-varying sheath potentials can then be used, in tandem with particle-in-cell (PIC models of the edge plasma, to study sputtering effects. Particle strike energies at the wall can be computed more accurately, consistent with their passage through the known potential of the sheath, such that correspondingly increased accuracy of sputtering yields and heat/particle fluxes to antenna surfaces is obtained. The new simulation capabilities enable time-domain modeling of plasma-surface interactions and ICRF physics in realistic experimental configurations at unprecedented spatial resolution. We will present results/animations from high-performance (10k-100k core FDTD/PIC simulations of Alcator C-Mod antenna operation.

  6. Effect of levels of inquiry model of science teaching on scientific literacy domain attitudes

    Science.gov (United States)

    Achmad, Maulana; Suhandi, Andi

    2017-05-01

    The aim of this research was to obtain an overview of the increase scientific literacy attitudes domain in high school students as the effects of the Levels of Inquiry (LOI) model of science teaching. This research using a quasi-experimental methods and randomizedpretest-posttest control group design. The subject of this research was students of grade X in a senior high school in Purwakarta and it consists of two classes who were divided into experimental class (30 students) and control class (30 students). While experimental class was taught LOIand control class was taught Interactive Lecture Demonstration (ILD). Data were collected using an attitude scale scientific literacy test which is based on the Likert scale. Data were analyzed using normality test, homogeneity test, and t-test to the value of N-gain attitude of scientific literacy scale test. The result of percentage average N-gain experimental class and control are 49 and 31 that classified into medium improvement category. Based on the results of hypothesis testing on the N-gain value obtained by the Sig.(One-tailed) 0.000 < 0.050, it means that H1 was accepted. The results showed that scientific literacy domain attitude of students who got learning by LOI is higher than students who got learning by ILD. It can be concluded that the effect of LOI is better to improve scientific literacy domain attitudes significantly.

  7. Characterization and modeling of magnetic domain wall dynamics using reconstituted hysteresis loops from Barkhausen noise

    Energy Technology Data Exchange (ETDEWEB)

    Ducharne, B., E-mail: Benjamin.ducharne@insa-lyon.fr; Le, M.Q.; Sebald, G.; Cottinet, P.J.; Guyomar, D.; Hebrard, Y.

    2017-06-15

    Highlights: • Barkhausen noise energy versus excitation field hysteresis cycles MBN{sub energy}(H). • Difference in the dynamics of the induction field B and of the MBN{sub energy}. • Dynamic behavior of MBN{sub energy}(H) cycles is first-order. • Dynamic behavior of B(H) cycles is non-entire order. - Abstract: By means of a post-processing technique, we succeeded in plotting magnetic Barkhausen noise energy hysteresis cycles MBN{sub energy}(H). These cycles were compared to the usual hysteresis cycles, displaying the evolution of the magnetic induction field B versus the magnetic excitation H. The divergence between these comparisons as the excitation frequency was increased gave rise to the conclusion that there was a difference in the dynamics of the induction field and of the MBN{sub energy} related to the domain wall movements. Indeed, for the MBN{sub energy} hysteresis cycle, merely the domain wall movements were involved. On the other hand, for the usual B(H) cycle, two dynamic contributions were observed: domain wall movements and diffusion of the magnetic field excitation. From a simulation point of view, it was demonstrated that over a large frequency bandwidth a correct dynamic behavior of the domain wall movement MBN{sub energy}(H) cycle could be taken into account using first-order derivation whereas fractional orders were required for the B(H) cycles. The present article also gives a detailed description of how to use the developed process to obtain the MBN{sub energy}(H) hysteresis cycle as well as its evolution as the frequency increases. Moreover, this article provides an interesting explanation of the separation of magnetic loss contributions through a magnetic sample: a wall movement contribution varying according to first-order dynamics and a diffusion contribution which in a lump model can be taken into account using fractional order dynamics.

  8. Domain Independent Vocabulary Generation and Its Use in Category-based Small Footprint Language Model

    Directory of Open Access Journals (Sweden)

    KIM, K.-H.

    2011-02-01

    Full Text Available The work in this paper pertains to domain independent vocabulary generation and its use in category-based small footprint Language Model (LM. Two major constraints of the conventional LMs in the embedded environment are memory capacity limitation and data sparsity for the domain-specific application. This data sparsity adversely affects vocabulary coverage and LM performance. To overcome these constraints, we define a set of domain independent categories using a Part-Of-Speech (POS tagged corpus. Also, we generate a domain independent vocabulary based on this set using the corpus and knowledge base. Then, we propose a mathematical framework for a category-based LM using this set. In this LM, one word can be assigned assign multiple categories. In order to reduce its memory requirements, we propose a tree-based data structure. In addition, we determine the history length of a category n-gram, and the independent assumption applying to a category history generation. The proposed vocabulary generation method illustrates at least 13.68% relative improvement in coverage for a SMS text corpus, where data are sparse due to the difficulties in data collection. The proposed category-based LM requires only 215KB which is 55% and 13% compared to the conventional category-based LM and the word-based LM, respectively. It successively improves the performance, achieving 54.9% and 60.6% perplexity reduction compared to the conventional category-based LM and the word-based LM in terms of normalized perplexity.

  9. Changes in the Welfare of an Injured Working Farm Dog Assessed Using the Five Domains Model

    Directory of Open Access Journals (Sweden)

    Katherine E. Littlewood

    2016-09-01

    Full Text Available The present structured, systematic and comprehensive welfare evaluation of an injured working farm dog using the Five Domains Model is of interest in its own right. It is also an example for others wanting to apply the Model to welfare evaluations in different species and contexts. Six stages of a fictitious scenario involving the dog are considered: (1 its on-farm circumstances before one hind leg is injured; (2 its entanglement in barbed wire, cutting it free and transporting it to a veterinary clinic; (3 the initial veterinary examination and overnight stay; (4 amputation of the limb and immediate post-operative recovery; (5 its first four weeks after rehoming to a lifestyle block; and (6 its subsequent life as an amputee and pet. Not all features of the scenario represent average-to-good practice; indeed, some have been selected to indicate poor practice. It is shown how the Model can draw attention to areas of animal welfare concern and, importantly, to how welfare enhancement may be impeded or facilitated. Also illustrated is how the welfare implications of a sequence of events can be traced and evaluated, and, in relation to specific situations, how the degrees of welfare compromise and enhancement may be graded. In addition, the choice of a companion animal, contrasting its welfare status as a working dog and pet, and considering its treatment in a veterinary clinical setting, help to highlight various welfare impacts of some practices. By focussing attention on welfare problems, the Model can guide the implementation of remedies, including ways of promoting positive welfare states. Finally, wider applications of the Five Domains Model are noted: by enabling both negative and positive welfare-relevant experiences to be graded, the Model can be applied to quality of life assessments and end-of-life decisions and, with particular regard to negative experiences, the Model can also help to strengthen expert witness testimony during

  10. 3D airborne EM modeling based on the spectral-element time-domain (SETD) method

    Science.gov (United States)

    Cao, X.; Yin, C.; Huang, X.; Liu, Y.; Zhang, B., Sr.; Cai, J.; Liu, L.

    2017-12-01

    In the field of 3D airborne electromagnetic (AEM) modeling, both finite-difference time-domain (FDTD) method and finite-element time-domain (FETD) method have limitations that FDTD method depends too much on the grids and time steps, while FETD requires large number of grids for complex structures. We propose a time-domain spectral-element (SETD) method based on GLL interpolation basis functions for spatial discretization and Backward Euler (BE) technique for time discretization. The spectral-element method is based on a weighted residual technique with polynomials as vector basis functions. It can contribute to an accurate result by increasing the order of polynomials and suppressing spurious solution. BE method is a stable tine discretization technique that has no limitation on time steps and can guarantee a higher accuracy during the iteration process. To minimize the non-zero number of sparse matrix and obtain a diagonal mass matrix, we apply the reduced order integral technique. A direct solver with its speed independent of the condition number is adopted for quickly solving the large-scale sparse linear equations system. To check the accuracy of our SETD algorithm, we compare our results with semi-analytical solutions for a three-layered earth model within the time lapse 10-6-10-2s for different physical meshes and SE orders. The results show that the relative errors for magnetic field B and magnetic induction are both around 3-5%. Further we calculate AEM responses for an AEM system over a 3D earth model in Figure 1. From numerical experiments for both 1D and 3D model, we draw the conclusions that: 1) SETD can deliver an accurate results for both dB/dt and B; 2) increasing SE order improves the modeling accuracy for early to middle time channels when the EM field diffuses fast so the high-order SE can model the detailed variation; 3) at very late time channels, increasing SE order has little improvement on modeling accuracy, but the time interval plays

  11. RG domain wall for the general (su)-hat (2) coset models

    Energy Technology Data Exchange (ETDEWEB)

    Stanishkov, Marian [Institute for Nuclear Research and Nuclear Energy,Bulgarian Academy of Sciences, 1784 Sofia (Bulgaria)

    2016-08-16

    We consider a RG flow in a general (su)-hat (2) coset model induced by the least relevant field. This is done using two different approaches. We first compute the mixing coefficients of certain fields in the UV and IR theories using a conformal perturbation theory. The necessary structure constants are computed. The same coefficients can be calculated using the RG domain wall construction of Gaiotto. We compute the corresponding one-point functions and show that the two approaches give the same result in the leading order.

  12. Comparison of Models Needed for Conceptual Design of Man-Machine Systems in Different Application Domains

    DEFF Research Database (Denmark)

    Rasmussen, Jens

    1986-01-01

    and subjective preferences. For design of man-machine systems in process control, a framework has been developed in terms of separate representation of the problem domain, the decision task, and the information processing strategies required. The author analyzes the application of this framework to a number......For systematic and computer-aided design of man-machine systems, a consistent framework is needed, i. e. , a set of models which allows the selection of system characteristics which serve the individual user not only to satisfy his goal, but also to select mental processes that match his resources...

  13. Domain analyses of Usher syndrome causing Clarin-1 and GPR98 protein models.

    Science.gov (United States)

    Khan, Sehrish Haider; Javed, Muhammad Rizwan; Qasim, Muhammad; Shahzadi, Samar; Jalil, Asma; Rehman, Shahid Ur

    2014-01-01

    Usher syndrome is an autosomal recessive disorder that causes hearing loss, Retinitis Pigmentosa (RP) and vestibular dysfunction. It is clinically and genetically heterogeneous disorder which is clinically divided into three types i.e. type I, type II and type III. To date, there are about twelve loci and ten identified genes which are associated with Usher syndrome. A mutation in any of these genes e.g. CDH23, CLRN1, GPR98, MYO7A, PCDH15, USH1C, USH1G, USH2A and DFNB31 can result in Usher syndrome or non-syndromic deafness. These genes provide instructions for making proteins that play important roles in normal hearing, balance and vision. Studies have shown that protein structures of only seven genes have been determined experimentally and there are still three genes whose structures are unavailable. These genes are Clarin-1, GPR98 and Usherin. In the absence of an experimentally determined structure, homology modeling and threading often provide a useful 3D model of a protein. Therefore in the current study Clarin-1 and GPR98 proteins have been analyzed for signal peptide, domains and motifs. Clarin-1 protein was found to be without any signal peptide and consists of prokar lipoprotein domain. Clarin-1 is classified within claudin 2 super family and consists of twelve motifs. Whereas, GPR98 has a 29 amino acids long signal peptide and classified within GPCR family 2 having Concanavalin A-like lectin/glucanase superfamily. It was found to be consists of GPS and G protein receptor F2 domains and twenty nine motifs. Their 3D structures have been predicted using I-TASSER server. The model of Clarin-1 showed only α-helix but no beta sheets while model of GPR98 showed both α-helix and β sheets. The predicted structures were then evaluated and validated by MolProbity and Ramachandran plot. The evaluation of the predicted structures showed 78.9% residues of Clarin-1 and 78.9% residues of GPR98 within favored regions. The findings of present study has resulted in the

  14. Discrete-Time Domain Modelling of Voltage Source Inverters in Standalone Applications

    DEFF Research Database (Denmark)

    Federico, de Bosio; de Sousa Ribeiro, Luiz Antonio; Freijedo Fernandez, Francisco Daniel

    2017-01-01

    modelling of the LC plant with consideration of delay and sample-and-hold effects on the state feedback cross-coupling decoupling is derived. From this plant formulation, current controllers with wide bandwidth and good relative stability properties are developed. Two controllers based on lead compensation......The decoupling of the capacitor voltage and inductor current has been shown to improve significantly the dynamic performance of voltage source inverters in standalone applications. However, the computation and PWM delays still limit the achievable bandwidth. In this paper a discrete-time domain...

  15. Normal Inverse Gaussian Model-Based Image Denoising in the NSCT Domain

    Directory of Open Access Journals (Sweden)

    Jian Jia

    2015-01-01

    Full Text Available The objective of image denoising is to retain useful details while removing as much noise as possible to recover an original image from its noisy version. This paper proposes a novel normal inverse Gaussian (NIG model-based method that uses a Bayesian estimator to carry out image denoising in the nonsubsampled contourlet transform (NSCT domain. In the proposed method, the NIG model is first used to describe the distributions of the image transform coefficients of each subband in the NSCT domain. Then, the corresponding threshold function is derived from the model using Bayesian maximum a posteriori probability estimation theory. Finally, optimal linear interpolation thresholding algorithm (OLI-Shrink is employed to guarantee a gentler thresholding effect. The results of comparative experiments conducted indicate that the denoising performance of our proposed method in terms of peak signal-to-noise ratio is superior to that of several state-of-the-art methods, including BLS-GSM, K-SVD, BivShrink, and BM3D. Further, the proposed method achieves structural similarity (SSIM index values that are comparable to those of the block-matching 3D transformation (BM3D method.

  16. Target Control in Logical Models Using the Domain of Influence of Nodes.

    Science.gov (United States)

    Yang, Gang; Gómez Tejeda Zañudo, Jorge; Albert, Réka

    2018-01-01

    Dynamical models of biomolecular networks are successfully used to understand the mechanisms underlying complex diseases and to design therapeutic strategies. Network control and its special case of target control, is a promising avenue toward developing disease therapies. In target control it is assumed that a small subset of nodes is most relevant to the system's state and the goal is to drive the target nodes into their desired states. An example of target control would be driving a cell to commit to apoptosis (programmed cell death). From the experimental perspective, gene knockout, pharmacological inhibition of proteins, and providing sustained external signals are among practical intervention techniques. We identify methodologies to use the stabilizing effect of sustained interventions for target control in Boolean network models of biomolecular networks. Specifically, we define the domain of influence (DOI) of a node (in a certain state) to be the nodes (and their corresponding states) that will be ultimately stabilized by the sustained state of this node regardless of the initial state of the system. We also define the related concept of the logical domain of influence (LDOI) of a node, and develop an algorithm for its identification using an auxiliary network that incorporates the regulatory logic. This way a solution to the target control problem is a set of nodes whose DOI can cover the desired target node states. We perform greedy randomized adaptive search in node state space to find such solutions. We apply our strategy to in silico biological network models of real systems to demonstrate its effectiveness.

  17. Interoperability challenges in river discharge modelling: A cross domain application scenario

    Science.gov (United States)

    Santoro, Mattia; Andres, Volker; Jirka, Simon; Koike, Toshio; Looser, Ulrich; Nativi, Stefano; Pappenberger, Florian; Schlummer, Manuela; Strauch, Adrian; Utech, Michael; Zsoter, Ervin

    2018-06-01

    River discharge is a critical water cycle variable, as it integrates all the processes (e.g. runoff and evapotranspiration) occurring within a river basin and provides a hydrological output variable that can be readily measured. Its prediction is of invaluable help for many water-related tasks including water resources assessment and management, flood protection, and disaster mitigation. Observations of river discharge are important to calibrate and validate hydrological or coupled land, atmosphere and ocean models. This requires using datasets from different scientific domains (Water, Weather, etc.). Typically, such datasets are provided using different technological solutions. This complicates the integration of new hydrological data sources into application systems. Therefore, a considerable effort is often spent on data access issues instead of the actual scientific question. This paper describes the work performed to address multidisciplinary interoperability challenges related to river discharge modeling and validation. This includes definition and standardization of domain specific interoperability standards for hydrological data sharing and their support in global frameworks such as the Global Earth Observation System of Systems (GEOSS). The research was developed in the context of the EU FP7-funded project GEOWOW (GEOSS Interoperability for Weather, Ocean and Water), which implemented a "River Discharge" application scenario. This scenario demonstrates the combination of river discharge observations data from the Global Runoff Data Centre (GRDC) database and model outputs produced by the European Centre for Medium-Range Weather Forecasts (ECMWF) predicting river discharge based on weather forecast information in the context of the GEOSS.

  18. Identifying Mechanical Properties of Viscoelastic Materials in Time Domain Using the Fractional Zener Model

    Directory of Open Access Journals (Sweden)

    Ana Paula Delowski Ciniello

    Full Text Available Abstract The present paper aims at presenting a methodology for characterizing viscoelastic materials in time domain, taking into account the fractional Zener constitutive model and the influence of temperature through Williams, Landel, and Ferry’s model. To that effect, a set of points obtained experimentally through uniaxial tensile tests with different constant strain rates is considered. The approach is based on the minimization of the quadratic relative distance between the experimental stress-strain curves and the corresponding ones given by the theoretical model. In order to avoid the local minima in the process of optimization, a hybrid technique based on genetic algorithms and non-linear programming techniques is used. The methodology is applied in the characterization of two different commercial viscoelastic materials. The results indicate that the proposed methodology is effective in identifying thermorheologically simple viscoelastic materials.

  19. Peaks, plateaus, canyons, and craters: The complex geometry of simple mid-domain effect models

    DEFF Research Database (Denmark)

    Colwell, Robert K.; Gotelli, Nicholas J.; Rahbek, Carsten

    2009-01-01

    dye algorithm to place assemblages of species of uniform We used a spreading dye algorithm to place assemblages of species of uniform range size in one-dimensional or two-dimensional bounded domains. In some models, we allowed dispersal to introduce range discontinuity. Results: As uniform range size...... increases from small to medium, a flat pattern of species As uniform range size increases from small to medium, a flat pattern of species richness is replaced by a pair of peripheral peaks, separated by a valley (one-dimensional models), or by a cratered ring (two-dimensional models) of species richness...... of a uniform size generate more complex patterns, including peaks, plateaus, canyons, and craters of species richness....

  20. BRIDG: a domain information model for translational and clinical protocol-driven research.

    Science.gov (United States)

    Becnel, Lauren B; Hastak, Smita; Ver Hoef, Wendy; Milius, Robert P; Slack, MaryAnn; Wold, Diane; Glickman, Michael L; Brodsky, Boris; Jaffe, Charles; Kush, Rebecca; Helton, Edward

    2017-09-01

    It is critical to integrate and analyze data from biological, translational, and clinical studies with data from health systems; however, electronic artifacts are stored in thousands of disparate systems that are often unable to readily exchange data. To facilitate meaningful data exchange, a model that presents a common understanding of biomedical research concepts and their relationships with health care semantics is required. The Biomedical Research Integrated Domain Group (BRIDG) domain information model fulfills this need. Software systems created from BRIDG have shared meaning "baked in," enabling interoperability among disparate systems. For nearly 10 years, the Clinical Data Standards Interchange Consortium, the National Cancer Institute, the US Food and Drug Administration, and Health Level 7 International have been key stakeholders in developing BRIDG. BRIDG is an open-source Unified Modeling Language-class model developed through use cases and harmonization with other models. With its 4+ releases, BRIDG includes clinical and now translational research concepts in its Common, Protocol Representation, Study Conduct, Adverse Events, Regulatory, Statistical Analysis, Experiment, Biospecimen, and Molecular Biology subdomains. The model is a Clinical Data Standards Interchange Consortium, Health Level 7 International, and International Standards Organization standard that has been utilized in national and international standards-based software development projects. It will continue to mature and evolve in the areas of clinical imaging, pathology, ontology, and vocabulary support. BRIDG 4.1.1 and prior releases are freely available at https://bridgmodel.nci.nih.gov . © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  1. Determination and validation of mTOR kinase-domain 3D structure by homology modeling

    Directory of Open Access Journals (Sweden)

    Lakhlili W

    2015-07-01

    Full Text Available Wiame Lakhlili,1 Gwénaël Chevé,2 Abdelaziz Yasri,2 Azeddine Ibrahimi1 1Laboratoire de Biotechnologie (MedBiotech, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V de Rabat, Rabat, Morroco; 2OriBase Pharma, Cap Gamma, Parc Euromédecine, Montpellier, France Abstract: The AKT/mammalian target of rapamycin (mTOR pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site.Keywords: mTOR, homology modeling, mTOR kinase-domain, docking

  2. Can limited area NWP and/or RCM models improve on large scales inside their domain?

    Science.gov (United States)

    Mesinger, Fedor; Veljovic, Katarina

    2017-04-01

    In a paper in press in Meteorology and Atmospheric Physics at the time this abstract is being written, Mesinger and Veljovic point out four requirements that need to be fulfilled by a limited area model (LAM), be it in NWP or RCM environment, to improve on large scales inside its domain. First, NWP/RCM model needs to be run on a relatively large domain. Note that domain size in quite inexpensive compared to resolution. Second, NWP/RCM model should not use more forcing at its boundaries than required by the mathematics of the problem. That means prescribing lateral boundary conditions only at its outside boundary, with one less prognostic variable prescribed at the outflow than at the inflow parts of the boundary. Next, nudging towards the large scales of the driver model must not be used, as it would obviously be nudging in the wrong direction if the nested model can improve on large scales inside its domain. And finally, the NWP/RCM model must have features that enable development of large scales improved compared to those of the driver model. This would typically include higher resolution, but obviously does not have to. Integrations showing improvements in large scales by LAM ensemble members are summarized in the mentioned paper in press. Ensemble members referred to are run using the Eta model, and are driven by ECMWF 32-day ensemble members, initialized 0000 UTC 4 October 2012. The Eta model used is the so-called "upgraded Eta," or "sloping steps Eta," which is free of the Gallus-Klemp problem of weak flow in the lee of the bell-shaped topography, seemed to many as suggesting the eta coordinate to be ill suited for high resolution models. The "sloping steps" in fact represent a simple version of the cut cell scheme. Accuracy of forecasting the position of jet stream winds, chosen to be those of speeds greater than 45 m/s at 250 hPa, expressed by Equitable Threat (or Gilbert) skill scores adjusted to unit bias (ETSa) was taken to show the skill at large scales

  3. Assessment of Energy Removal Impacts on Physical Systems: Hydrodynamic Model Domain Expansion and Refinement, and Online Dissemination of Model Results

    International Nuclear Information System (INIS)

    Yang, Zhaoqing; Khangaonkar, Tarang; Wang, Taiping

    2010-01-01

    In this report we describe the (1) the expansion of the PNNL hydrodynamic model domain to include the continental shelf along the coasts of Washington, Oregon, and Vancouver Island; and (2) the approach and progress in developing the online/Internet disseminations of model results and outreach efforts in support of the Puget Sound Operational Forecast System (PS-OPF). Submittal of this report completes the work on Task 2.1.2, Effects of Physical Systems, Subtask 2.1.2.1, Hydrodynamics, for fiscal year 2010 of the Environmental Effects of Marine and Hydrokinetic Energy project.

  4. Towards 3D Cadastre in Serbia: Development of Serbian Cadastral Domain Model

    Directory of Open Access Journals (Sweden)

    Aleksandra Radulović

    2017-10-01

    Full Text Available This paper proposes a Serbian cadastral domain model as the country profile for the real estate cadastre, based on the Land Administration Domain Model (LADM, defined within ISO 19152. National laws and other legal acts were analyzed and the incorrect applications of the law are outlined. The national “Strategy of measures and activities for increasing the quality of services in the field of geospatial data and registration of real property rights in the official state records”, which was adopted in 2017, cites the shortcomings of the existing cadastral information system. The proposed profile can solve several problems with the system, such as the lack of interoperability, mismatch of graphic and alphanumeric data, and lack of an integrated cadastral information system. Based on the existing data, the basic concepts of the Serbian cadastre were extracted and the applicability of LADM was tested on an obtained conceptual model. Upon obtaining positive results, a complete country profile was developed according to valid national laws and rulebooks. A table of mappings of LADM classes and country profile classes is presented in this paper, together with an analysis of the conformance level. The proposed Serbian country profile is completely conformant at the medium level and on several high-level classes. LADM also provides support for three-dimensional (3D representations and 3D registration of rights, so the creation of a country profile for Serbia is a starting point toward a 3D cadastre. Given the existence of buildings with overlapping rights and restrictions in 3D, considering expanding the spatial profile with 3D geometries is necessary. Possible solutions to these situations were analyzed. Since the two-dimensional (2D cadastre in Serbia is not fully formed, the proposed solution is to use the 2D model for simple right situations, and the 3D model for more complex situations.

  5. Frequency-domain reduced order models for gravitational waves from aligned-spin compact binaries

    International Nuclear Information System (INIS)

    Pürrer, Michael

    2014-01-01

    Black-hole binary coalescences are one of the most promising sources for the first detection of gravitational waves. Fast and accurate theoretical models of the gravitational radiation emitted from these coalescences are highly important for the detection and extraction of physical parameters. Spinning effective-one-body models for binaries with aligned-spins have been shown to be highly faithful, but are slow to generate and thus have not yet been used for parameter estimation (PE) studies. I provide a frequency-domain singular value decomposition-based surrogate reduced order model that is thousands of times faster for typical system masses and has a faithfulness mismatch of better than ∼0.1% with the original SEOBNRv1 model for advanced LIGO detectors. This model enables PE studies up to signal-to-noise ratios (SNRs) of 20 and even up to 50 for total masses below 50 M ⊙ . This paper discusses various choices for approximations and interpolation over the parameter space that can be made for reduced order models of spinning compact binaries, provides a detailed discussion of errors arising in the construction and assesses the fidelity of such models. (paper)

  6. Feature-opinion pair identification of product reviews in Chinese: a domain ontology modeling method

    Science.gov (United States)

    Yin, Pei; Wang, Hongwei; Guo, Kaiqiang

    2013-03-01

    With the emergence of the new economy based on social media, a great amount of consumer feedback on particular products are conveyed through wide-spreading product online reviews, making opinion mining a growing interest for both academia and industry. According to the characteristic mode of expression in Chinese, this research proposes an ontology-based linguistic model to identify the basic appraisal expression in Chinese product reviews-"feature-opinion pair (FOP)." The product-oriented domain ontology is constructed automatically at first, then algorithms to identify FOP are designed by mapping product features and opinions to the conceptual space of the domain ontology, and finally comparative experiments are conducted to evaluate the model. Experimental results indicate that the performance of the proposed approach in this paper is efficient in obtaining a more accurate result compared to the state-of-art algorithms. Furthermore, through identifying and analyzing FOPs, the unstructured product reviews are converted into structured and machine-sensible expression, which provides valuable information for business application. This paper contributes to the related research in opinion mining by developing a solid foundation for further sentiment analysis at a fine-grained level and proposing a general way for automatic ontology construction.

  7. The development of efficient numerical time-domain modeling methods for geophysical wave propagation

    Science.gov (United States)

    Zhu, Lieyuan

    This Ph.D. dissertation focuses on the numerical simulation of geophysical wave propagation in the time domain including elastic waves in solid media, the acoustic waves in fluid media, and the electromagnetic waves in dielectric media. This thesis shows that a linear system model can describe accurately the physical processes of those geophysical waves' propagation and can be used as a sound basis for modeling geophysical wave propagation phenomena. The generalized stability condition for numerical modeling of wave propagation is therefore discussed in the context of linear system theory. The efficiency of a series of different numerical algorithms in the time-domain for modeling geophysical wave propagation are discussed and compared. These algorithms include the finite-difference time-domain method, pseudospectral time domain method, alternating directional implicit (ADI) finite-difference time domain method. The advantages and disadvantages of these numerical methods are discussed and the specific stability condition for each modeling scheme is carefully derived in the context of the linear system theory. Based on the review and discussion of these existing approaches, the split step, ADI pseudospectral time domain (SS-ADI-PSTD) method is developed and tested for several cases. Moreover, the state-of-the-art stretched-coordinate perfect matched layer (SCPML) has also been implemented in SS-ADI-PSTD algorithm as the absorbing boundary condition for truncating the computational domain and absorbing the artificial reflection from the domain boundaries. After algorithmic development, a few case studies serve as the real-world examples to verify the capacities of the numerical algorithms and understand the capabilities and limitations of geophysical methods for detection of subsurface contamination. The first case is a study using ground penetrating radar (GPR) amplitude variation with offset (AVO) for subsurface non-aqueous-liquid (NAPL) contamination. The

  8. Predictive modeling of nanoscale domain morphology in solution-processed organic thin films

    Science.gov (United States)

    Schaaf, Cyrus; Jenkins, Michael; Morehouse, Robell; Stanfield, Dane; McDowall, Stephen; Johnson, Brad L.; Patrick, David L.

    2017-09-01

    The electronic and optoelectronic properties of molecular semiconductor thin films are directly linked to their extrinsic nanoscale structural characteristics such as domain size and spatial distributions. In films prepared by common solution-phase deposition techniques such as spin casting and solvent-based printing, morphology is governed by a complex interrelated set of thermodynamic and kinetic factors that classical models fail to adequately capture, leaving them unable to provide much insight, let alone predictive design guidance for tailoring films with specific nanostructural characteristics. Here we introduce a comprehensive treatment of solution-based film formation enabling quantitative prediction of domain formation rates, coverage, and spacing statistics based on a small number of experimentally measureable parameters. The model combines a mean-field rate equation treatment of monomer aggregation kinetics with classical nucleation theory and a supersaturation-dependent critical nucleus size to solve for the quasi-two-dimensional temporally and spatially varying monomer concentration, nucleation rate, and other properties. Excellent agreement is observed with measured nucleation densities and interdomain radial distribution functions in polycrystalline tetracene films. Numerical solutions lead to a set of general design rules enabling predictive morphological control in solution-processed molecular crystalline films.

  9. S1 constrains S4 in the voltage sensor domain of Kv7.1 K+ channels.

    Directory of Open Access Journals (Sweden)

    Yoni Haitin

    Full Text Available Voltage-gated K(+ channels comprise a central pore enclosed by four voltage-sensing domains (VSDs. While movement of the S4 helix is known to couple to channel gate opening and closing, the nature of S4 motion is unclear. Here, we substituted S4 residues of Kv7.1 channels by cysteine and recorded whole-cell mutant channel currents in Xenopus oocytes using the two-electrode voltage-clamp technique. In the closed state, disulfide and metal bridges constrain residue S225 (S4 nearby C136 (S1 within the same VSD. In the open state, two neighboring I227 (S4 are constrained at proximity while residue R228 (S4 is confined close to C136 (S1 of an adjacent VSD. Structural modeling predicts that in the closed to open transition, an axial rotation (approximately 190 degrees and outward translation of S4 (approximately 12 A is accompanied by VSD rocking. This large sensor motion changes the intra-VSD S1-S4 interaction to an inter-VSD S1-S4 interaction. These constraints provide a ground for cooperative subunit interactions and suggest a key role of the S1 segment in steering S4 motion during Kv7.1 gating.

  10. A general model and numerical method for multiconductor systems in frequency domain

    Energy Technology Data Exchange (ETDEWEB)

    Jonas, F. [Swedish Transmission Research Inst., Ludvika (Sweden); Varju, G. [Technical Univ. of Budapest (Hungary). Dept. of Electric Power Systems

    1995-12-01

    A general multi-conductor model is described in this article. It is based on the distributed line parameter simulation with acceptance of non-homogeneous line sections, discrete and distributed sources, complex discrete elements of any kind at any point. Every parameter and element can be non-linear. The model and the software implementation has successfully been used for solution of different frequency domain problems, e.g. harmonic penetration in unbalanced power networks, railway circuits with auto- or booster transformers, telecommunication circuits. The results of a number of calculated cases have been verified by field tests. An application example is demonstrated in the article: calculation of telecommunication disturbances caused by a railway line with booster transformers in an armored cable. 10 refs, 10 figs, 2 tabs

  11. Fast simulation approaches for power fluctuation model of wind farm based on frequency domain

    DEFF Research Database (Denmark)

    Lin, Jin; Gao, Wen-zhong; Sun, Yuan-zhang

    2012-01-01

    This paper discusses one model developed by Riso, DTU, which is capable of simulating the power fluctuation of large wind farms in frequency domain. In the original design, the “frequency-time” transformations are time-consuming and might limit the computation speed for a wind farm of large size....... Under this background, this paper proposes four efficient approaches to accelerate the simulation speed. Two of them are based on physical model simplifications, and the other two improve the numerical computation. The case study demonstrates the efficiency of these approaches. The acceleration ratio...... is more than 300 times if all these approaches are adopted, in any low, medium and high wind speed test scenarios....

  12. PSpice modeling of broadband RF cavities for transient and frequency domain simulations

    Energy Technology Data Exchange (ETDEWEB)

    Harzheim, Jens [Institut fuer Theorie Elektromagnetischer Felder, Fachgebiet Beschleunigertechnik, TU Darmstadt (Germany)

    2016-07-01

    In the future accelerator facility FAIR, Barrier-Bucket Systems will play an important role for different longitudinal beam manipulations. As the function of this type of system is to provide single sine gap voltages, the components of the system have to operate in a broad frequency range. To investigate the different effects and to design the different system components, the whole Barrier-Bucket System is to be modeled in PSpice. While for low power signals, the system shows linear behavior, nonlinear effects arise at higher amplitudes. Therefore, simulations in both, frequency and time domain are needed. The highly frequency dependent magnetic alloy ring cores of the future Barrier-Bucket cavity have been mod eled in a first step and based on these models, the whole cavity was analyzed in PSpice. The simulation results show good agreement with former measurements.

  13. A model of the formation of illusory conjunctions in the time domain.

    Science.gov (United States)

    Botella, J; Suero, M; Barriopedro, M I

    2001-12-01

    The authors present a model to account for the miscombination of features when stimuli are presented using the rapid serial visual presentation (RSVP) technique (illusory conjunctions in the time domain). It explains the distributions of responses through a mixture of trial outcomes. In some trials, attention is successfully focused on the target, whereas in others, the responses are based on partial information. Two experiments are presented that manipulated the mean processing time of the target-defining dimension and of the to-be-reported dimension, respectively. As predicted, the average origin of the responses is delayed when lengthening the target-defining dimension, whereas it is earlier when lengthening the to-be-reported dimension; in the first case the number of correct responses is dramatically reduced, whereas in the second it does not change. The results, a review of other research, and simulations carried out with a formal version of the model are all in close accordance with the predictions.

  14. A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils

    Science.gov (United States)

    Louros, Nikolaos N.; Baltoumas, Fotis A.; Hamodrakas, Stavros J.; Iconomidou, Vassiliki A.

    2016-02-01

    Pmel17 is a multidomain protein involved in biosynthesis of melanin. This process is facilitated by the formation of Pmel17 amyloid fibrils that serve as a scaffold, important for pigment deposition in melanosomes. A specific luminal domain of human Pmel17, containing 10 tandem imperfect repeats, designated as repeat domain (RPT), forms amyloid fibrils in a pH-controlled mechanism in vitro and has been proposed to be essential for the formation of the fibrillar matrix. Currently, no three-dimensional structure has been resolved for the RPT domain of Pmel17. Here, we examine the structure of the RPT domain by performing sequence threading. The resulting model was subjected to energy minimization and validated through extensive molecular dynamics simulations. Structural analysis indicated that the RPT model exhibits several distinct properties of β-solenoid structures, which have been proposed to be polymerizing components of amyloid fibrils. The derived model is stabilized by an extensive network of hydrogen bonds generated by stacking of highly conserved polar residues of the RPT domain. Furthermore, the key role of invariant glutamate residues is proposed, supporting a pH-dependent mechanism for RPT domain assembly. Conclusively, our work attempts to provide structural insights into the RPT domain structure and to elucidate its contribution to Pmel17 amyloid fibril formation.

  15. Exact Solution of the Six-Vertex Model with Domain Wall Boundary Conditions. Disordered Phase

    CERN Document Server

    Bleher, P M

    2005-01-01

    The six-vertex model, or the square ice model, with domain wall boundary conditions (DWBC) has been introduced and solved for finite $N$ by Korepin and Izergin. The solution is based on the Yang-Baxter equations and it represents the free energy in terms of an $N\\times N$ Hankel determinant. Paul Zinn-Justin observed that the Izergin-Korepin formula can be re-expressed in terms of the partition function of a random matrix model with a nonpolynomial interaction. We use this observation to obtain the large $N$ asymptotics of the six-vertex model with DWBC in the disordered phase. The solution is based on the Riemann-Hilbert approach and the Deift-Zhou nonlinear steepest descent method. As was noticed by Kuperberg, the problem of enumeration of alternating sign matrices (the ASM problem) is a special case of the the six-vertex model. We compare the obtained exact solution of the six-vertex model with known exact results for the 1, 2, and 3 enumerations of ASMs, and also with the exact solution on the so-called f...

  16. Modeling and Analysis Compute Environments, Utilizing Virtualization Technology in the Climate and Earth Systems Science domain

    Science.gov (United States)

    Michaelis, A.; Nemani, R. R.; Wang, W.; Votava, P.; Hashimoto, H.

    2010-12-01

    Given the increasing complexity of climate modeling and analysis tools, it is often difficult and expensive to build or recreate an exact replica of the software compute environment used in past experiments. With the recent development of new technologies for hardware virtualization, an opportunity exists to create full modeling, analysis and compute environments that are “archiveable”, transferable and may be easily shared amongst a scientific community or presented to a bureaucratic body if the need arises. By encapsulating and entire modeling and analysis environment in a virtual machine image, others may quickly gain access to the fully built system used in past experiments, potentially easing the task and reducing the costs of reproducing and verify past results produced by other researchers. Moreover, these virtual machine images may be used as a pedagogical tool for others that are interested in performing an academic exercise but don't yet possess the broad expertise required. We built two virtual machine images, one with the Community Earth System Model (CESM) and one with Weather Research Forecast Model (WRF), then ran several small experiments to assess the feasibility, performance overheads costs, reusability, and transferability. We present a list of the pros and cons as well as lessoned learned from utilizing virtualization technology in the climate and earth systems modeling domain.

  17. Extending NGOMSL Model for Human-Humanoid Robot Interaction in the Soccer Robotics Domain

    Directory of Open Access Journals (Sweden)

    Rajesh Elara Mohan

    2008-01-01

    Full Text Available In the field of human-computer interaction, the Natural Goals, Operators, Methods, and Selection rules Language (NGOMSL model is one of the most popular methods for modelling knowledge and cognitive processes for rapid usability evaluation. The NGOMSL model is a description of the knowledge that a user must possess to operate the system represented as elementary actions for effective usability evaluations. In the last few years, mobile robots have been exhibiting a stronger presence in commercial markets and very little work has been done with NGOMSL modelling for usability evaluations in the human-robot interaction discipline. This paper focuses on extending the NGOMSL model for usability evaluation of human-humanoid robot interaction in the soccer robotics domain. The NGOMSL modelled human-humanoid interaction design of Robo-Erectus Junior was evaluated and the results of the experiments showed that the interaction design was able to find faults in an average time of 23.84 s. Also, the interaction design was able to detect the fault within the 60 s in 100% of the cases. The Evaluated Interaction design was adopted by our Robo-Erectus Junior version of humanoid robots in the RoboCup 2007 humanoid soccer league.

  18. Improvements in fast-response flood modeling: desktop parallel computing and domain tracking

    Energy Technology Data Exchange (ETDEWEB)

    Judi, David R [Los Alamos National Laboratory; Mcpherson, Timothy N [Los Alamos National Laboratory; Burian, Steven J [UNIV. OF UTAH

    2009-01-01

    It is becoming increasingly important to have the ability to accurately forecast flooding, as flooding accounts for the most losses due to natural disasters in the world and the United States. Flood inundation modeling has been dominated by one-dimensional approaches. These models are computationally efficient and are considered by many engineers to produce reasonably accurate water surface profiles. However, because the profiles estimated in these models must be superimposed on digital elevation data to create a two-dimensional map, the result may be sensitive to the ability of the elevation data to capture relevant features (e.g. dikes/levees, roads, walls, etc...). Moreover, one-dimensional models do not explicitly represent the complex flow processes present in floodplains and urban environments and because two-dimensional models based on the shallow water equations have significantly greater ability to determine flow velocity and direction, the National Research Council (NRC) has recommended that two-dimensional models be used over one-dimensional models for flood inundation studies. This paper has shown that two-dimensional flood modeling computational time can be greatly reduced through the use of Java multithreading on multi-core computers which effectively provides a means for parallel computing on a desktop computer. In addition, this paper has shown that when desktop parallel computing is coupled with a domain tracking algorithm, significant computation time can be eliminated when computations are completed only on inundated cells. The drastic reduction in computational time shown here enhances the ability of two-dimensional flood inundation models to be used as a near-real time flood forecasting tool, engineering, design tool, or planning tool. Perhaps even of greater significance, the reduction in computation time makes the incorporation of risk and uncertainty/ensemble forecasting more feasible for flood inundation modeling (NRC 2000; Sayers et al

  19. Hybrid meshes and domain decomposition for the modeling of oil reservoirs; Maillages hybrides et decomposition de domaine pour la modelisation des reservoirs petroliers

    Energy Technology Data Exchange (ETDEWEB)

    Gaiffe, St

    2000-03-23

    In this thesis, we are interested in the modeling of fluid flow through porous media with 2-D and 3-D unstructured meshes, and in the use of domain decomposition methods. The behavior of flow through porous media is strongly influenced by heterogeneities: either large-scale lithological discontinuities or quite localized phenomena such as fluid flow in the neighbourhood of wells. In these two typical cases, an accurate consideration of the singularities requires the use of adapted meshes. After having shown the limits of classic meshes we present the future prospects offered by hybrid and flexible meshes. Next, we consider the generalization possibilities of the numerical schemes traditionally used in reservoir simulation and we draw two available approaches: mixed finite elements and U-finite volumes. The investigated phenomena being also characterized by different time-scales, special treatments in terms of time discretization on various parts of the domain are required. We think that the combination of domain decomposition methods with operator splitting techniques may provide a promising approach to obtain high flexibility for a local tune-steps management. Consequently, we develop a new numerical scheme for linear parabolic equations which allows to get a higher flexibility in the local space and time steps management. To conclude, a priori estimates and error estimates on the two variables of interest, namely the pressure and the velocity are proposed. (author)

  20. Site descriptive modelling Forsmark, stage 2.2. A fracture domain concept as a basis for the statistical modelling of fractures and minor deformation zones, and interdisciplinary coordination

    Energy Technology Data Exchange (ETDEWEB)

    Olofsson, Isabelle; Simeonov, Assen [Swedish Nuclear Fuel and Waste Manageme nt Co., Stockholm (Sweden); Stephens, Michael [Geological Survey of Sweden (SGU), U ppsala (Sweden); Follin, Sven [SF GeoLogic AB, Taeby (Sweden); Nilsson, Ann-Chatrin [G eosigma AB, Uppsala (Sweden); Roeshoff, Kennert; Lindberg, Ulrika; Lanaro, Flavio [Bergbygg konsult AB, Haesselby (Sweden); Fredriksson, Anders; Persson, Lars [Golder Associat es AB (Sweden)

    2007-04-15

    The Swedish Nuclear Fuel and Waste Management Company (SKB) is undertaking site characterization at two different locations, Forsmark and Simpevarp/Laxemar, with the objective of siting a final waste repository at depth for spent nuclear fuel. The programme is built upon the development of site descriptive models after each data freeze. This report describes the first attempt to define fracture domains for the Forsmark site modelling in stage 2.2. Already during model version 1.2 at Forsmark, significant spatial variability in the fracture pattern was observed. The variability appeared to be so significant that it provoked the need for a subdivision of the model volume for the treatment of geological and hydrogeological data into sub-volumes. Subsequent analyses of data collected up to data freeze 2.1 led to a better understanding of the site and a concept for the definition of fracture domains based on geological characteristics matured. The main objectives of this report are to identify and describe fracture domains at the site on the basis of geological data and to compile hydrogeological, hydrogeochemical and rock mechanics data within each fracture domain and address the implications of this integration activity. On the basis of borehole data, six fracture domains (FFM01-FFM06) have been recognized inside and immediately around the candidate volume. Three of these domains (FFM01, FFM02 and FFM06) lie inside the target volume for a potential repository in the northwestern part of the candidate area, and need to be addressed in the geological DFN modelling work. The hydrogeological data support the subdivision of the bedrock into fracture domains FFM01, FFM02 and FFM03. Few or no data are available for the other three domains. The hydrogeochemical data also support the subdivision into fracture domains FFM01 and FFM02. Since few data are available from the bedrock between deformation zones inside FFM03, there is little information on the hydrogeochemical

  1. Three-dimensional inverse modelling of damped elastic wave propagation in the Fourier domain

    Science.gov (United States)

    Petrov, Petr V.; Newman, Gregory A.

    2014-09-01

    3-D full waveform inversion (FWI) of seismic wavefields is routinely implemented with explicit time-stepping simulators. A clear advantage of explicit time stepping is the avoidance of solving large-scale implicit linear systems that arise with frequency domain formulations. However, FWI using explicit time stepping may require a very fine time step and (as a consequence) significant computational resources and run times. If the computational challenges of wavefield simulation can be effectively handled, an FWI scheme implemented within the frequency domain utilizing only a few frequencies, offers a cost effective alternative to FWI in the time domain. We have therefore implemented a 3-D FWI scheme for elastic wave propagation in the Fourier domain. To overcome the computational bottleneck in wavefield simulation, we have exploited an efficient Krylov iterative solver for the elastic wave equations approximated with second and fourth order finite differences. The solver does not exploit multilevel preconditioning for wavefield simulation, but is coupled efficiently to the inversion iteration workflow to reduce computational cost. The workflow is best described as a series of sequential inversion experiments, where in the case of seismic reflection acquisition geometries, the data has been laddered such that we first image highly damped data, followed by data where damping is systemically reduced. The key to our modelling approach is its ability to take advantage of solver efficiency when the elastic wavefields are damped. As the inversion experiment progresses, damping is significantly reduced, effectively simulating non-damped wavefields in the Fourier domain. While the cost of the forward simulation increases as damping is reduced, this is counterbalanced by the cost of the outer inversion iteration, which is reduced because of a better starting model obtained from the larger damped wavefield used in the previous inversion experiment. For cross-well data, it is

  2. Impedance based time-domain modeling of lithium-ion batteries: Part I

    Science.gov (United States)

    Gantenbein, Sophia; Weiss, Michael; Ivers-Tiffée, Ellen

    2018-03-01

    This paper presents a novel lithium-ion cell model, which simulates the current voltage characteristic as a function of state of charge (0%-100%) and temperature (0-30 °C). It predicts the cell voltage at each operating point by calculating the total overvoltage from the individual contributions of (i) the ohmic loss η0, (ii) the charge transfer loss of the cathode ηCT,C, (iii) the charge transfer loss and the solid electrolyte interface loss of the anode ηSEI/CT,A, and (iv) the solid state and electrolyte diffusion loss ηDiff,A/C/E. This approach is based on a physically meaningful equivalent circuit model, which is parametrized by electrochemical impedance spectroscopy and time domain measurements, covering a wide frequency range from MHz to μHz. The model is exemplarily parametrized to a commercial, high-power 350 mAh graphite/LiNiCoAlO2-LiCoO2 pouch cell and validated by continuous discharge and charge curves at varying temperature. For the first time, the physical background of the model allows the operator to draw conclusions about the performance-limiting factor at various operating conditions. Not only can the model help to choose application-optimized cell characteristics, but it can also support the battery management system when taking corrective actions during operation.

  3. A fuzzy ontology modeling for case base knowledge in diabetes mellitus domain

    Directory of Open Access Journals (Sweden)

    Shaker El-Sappagh

    2017-06-01

    Full Text Available Knowledge-Intensive Case-Based Reasoning Systems (KI-CBR mainly depend on ontologies. Ontology can play the role of case-base knowledge. The combination of ontology and fuzzy logic reasoning is critical in the medical domain. Case-base representation based on fuzzy ontology is expected to enhance the semantic and storage of CBR knowledge-base. This paper provides an advancement to the research of diabetes diagnosis CBR by proposing a novel case-base fuzzy OWL2 ontology (CBRDiabOnto. This ontology can be considered as the first fuzzy case-base ontology in the medical domain. It is based on a case-base fuzzy Extended Entity Relation (EER data model. It contains 63 (fuzzy classes, 54 (fuzzy object properties, 138 (fuzzy datatype properties, and 105 fuzzy datatypes. We populated the ontology with 60 cases and used SPARQL-DL for its query. The evaluation of CBRDiabOnto shows that it is accurate, consistent, and cover terminologies and logic of diabetes mellitus diagnosis.

  4. Formal Analysis of Security Models for Mobile Devices, Virtualization Platforms, and Domain Name Systems

    Directory of Open Access Journals (Sweden)

    Gustavo Betarte

    2015-12-01

    Full Text Available In this work we investigate the security of security-critical applications, i.e. applications in which a failure may produce consequences that are unacceptable. We consider three areas: mobile devices, virtualization platforms, and domain name systems. The Java Micro Edition platform defines the Mobile Information Device Profile (MIDP to facilitate the development of applications for mobile devices, like cell phones and PDAs. We first study and compare formally several variants of the security model specified by MIDP to access sensitive resources of a mobile device. Hypervisors allow multiple guest operating systems to run on shared hardware, and offer a compelling means of improving the security and the flexibility of software systems. In this work we present a formalization of an idealized model of a hypervisor. We establish (formally that the hypervisor ensures strong isolation properties between the different operating systems, and guarantees that requests from guest operating systems are eventually attended. We show also that virtualized platforms are transparent, i.e. a guest operating system cannot distinguish whether it executes alone or together with other guest operating systems on the platform. The Domain Name System Security Extensions (DNSSEC is a suite of specifications that provides origin authentication and integrity assurance services for DNS data. We finally introduce a minimalistic specification of a DNSSEC model which provides the grounds needed to formally state and verify security properties concerning the chain of trust of the DNSSEC tree. We develop all our formalizations in the Calculus of Inductive Constructions --formal language that combines a higher-order logic and a richly-typed functional programming language-- using the Coq proof assistant.

  5. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    politicians and in the media, especially in the discussion whether some languages undergo ‘domain loss’ vis-à-vis powerful international languages like English. An objection that has been raised here is that domains, as originally conceived, are parameters of language choice and not properties of languages...

  6. A time-domain finite element model reduction method for viscoelastic linear and nonlinear systems

    Directory of Open Access Journals (Sweden)

    Antônio Marcos Gonçalves de Lima

    Full Text Available AbstractMany authors have shown that the effective design of viscoelastic systems can be conveniently carried out by using modern mathematical models to represent the frequency- and temperature-dependent behavior of viscoelastic materials. However, in the quest for design procedures of real-word engineering structures, the large number of exact evaluations of the dynamic responses during iterative procedures, combined with the typically high dimensions of large finite element models, makes the numerical analysis very costly, sometimes unfeasible. It is especially true when the viscoelastic materials are used to reduce vibrations of nonlinear systems. As a matter of fact, which the resolution of the resulting nonlinear equations of motion with frequency- and temperature-dependent viscoelastic damping forces is an interesting, but hard-to-solve problem. Those difficulties motivate the present study, in which a time-domain condensation strategy of viscoelastic systems is addressed, where the viscoelastic behavior is modeled by using a four parameter fractional derivative model. After the discussion of various theoretical aspects, the exact and reduced time responses are calculated for a three-layer sandwich plate by considering nonlinear boundary conditions.

  7. Modeling and Simulation of Voids in Composite Tape Winding Process Based on Domain Superposition Technique

    Science.gov (United States)

    Deng, Bo; Shi, Yaoyao

    2017-11-01

    The tape winding technology is an effective way to fabricate rotationally composite materials. Nevertheless, some inevitable defects will seriously influence the performance of winding products. One of the crucial ways to identify the quality of fiber-reinforced composite material products is examining its void content. Significant improvement in products' mechanical properties can be achieved by minimizing the void defect. Two methods were applied in this study, finite element analysis and experimental testing, respectively, to investigate the mechanism of how void forming in composite tape winding processing. Based on the theories of interlayer intimate contact and Domain Superposition Technique (DST), a three-dimensional model of prepreg tape void with SolidWorks has been modeled in this paper. Whereafter, ABAQUS simulation software was used to simulate the void content change with pressure and temperature. Finally, a series of experiments were performed to determine the accuracy of the model-based predictions. The results showed that the model is effective for predicting the void content in the composite tape winding process.

  8. Multipass forging of Inconel 718 in the delta-Supersolvus domain: assessing and modeling microstructure evolution

    Directory of Open Access Journals (Sweden)

    Zouari Meriem

    2014-01-01

    Full Text Available This work is focused on the evolution of the microstructure of Inconel 718 during multi-pass forging processes. During the forming process, the material is subjected to several physical phenomena such as work-hardening, recovery, recrystallization and grain growth. In this work, transformation kinetics are modeled in the δ-Supersolvus domain (T>Tsolvus where the alloy is single-phase, all the alloying elements being dissolved into the FCC matrix. Torsion tests were used to simulate the forging process and recrystallization kinetics was modeled using a discontinuous dynamic recrystallization (DDRX two-site mean field model. The microstructure evolution under hot forging conditions is predicted in both dynamic and post-dynamic regimes based on the initial distribution of grain size and the evolution of dislocation density distribution during each step of the process. The model predicts recrystallization kinetics, recrystallized grain size distribution and stress–strain curve for different thermo-mechanical conditions and makes the connection between dynamic and post-dynamic regimes.

  9. Model checking of safety-critical software in the nuclear engineering domain

    International Nuclear Information System (INIS)

    Lahtinen, J.; Valkonen, J.; Björkman, K.; Frits, J.; Niemelä, I.; Heljanko, K.

    2012-01-01

    Instrumentation and control (I and C) systems play a vital role in the operation of safety-critical processes. Digital programmable logic controllers (PLC) enable sophisticated control tasks which sets high requirements for system validation and verification methods. Testing and simulation have an important role in the overall verification of a system but are not suitable for comprehensive evaluation because only a limited number of system behaviors can be analyzed due to time limitations. Testing is also performed too late in the development lifecycle and thus the correction of design errors is expensive. This paper discusses the role of formal methods in software development in the area of nuclear engineering. It puts forward model checking, a computer-aided formal method for verifying the correctness of a system design model, as a promising approach to system verification. The main contribution of the paper is the development of systematic methodology for modeling safety critical systems in the nuclear domain. Two case studies are reviewed, in which we have found errors that were previously not detected. We also discuss the actions that should be taken in order to increase confidence in the model checking process.

  10. Time Domain Analysis of Graphene Nanoribbon Interconnects Based on Transmission Line ‎Model

    Directory of Open Access Journals (Sweden)

    S. Haji Nasiri

    2012-03-01

    Full Text Available Time domain analysis of multilayer graphene nanoribbon (MLGNR interconnects, based on ‎transmission line modeling (TLM using a six-order linear parametric expression, has been ‎presented for the first time. We have studied the effects of interconnect geometry along with ‎its contact resistance on its step response and Nyquist stability. It is shown that by increasing ‎interconnects dimensions their propagation delays are increased and accordingly the system ‎becomes relatively more stable. In addition, we have compared time responses and Nyquist ‎stabilities of MLGNR and SWCNT bundle interconnects, with the same external dimensions. ‎The results show that under the same conditions, the propagation delays for MLGNR ‎interconnects are smaller than those of SWCNT bundle interconnects are. Hence, SWCNT ‎bundle interconnects are relatively more stable than their MLGNR rivals.‎

  11. Investigation of nucleon-induced reactions in the Fermi energy domain within the microscopic DYWAN model

    Energy Technology Data Exchange (ETDEWEB)

    Sebille, F.; Bonilla, C. [SUBATECH, Universite de Nantes, CNRS/IN2P3, 44 - Nantes (France); Blideanu, V.; Lecolley, J.F. [Laboratoire de Physique Corpusculaire, ENSICAEN, Universite de Caen, IN2P3-CNRS, 14 - Caen (France)

    2004-06-01

    A microscopic investigation of nucleon-induced reactions is addressed within the DYWAN model, which is based on the projection methods of out of equilibrium statistical physics and on the mathematical theory of wavelets. Due to a strongly compressed representation of the fermionic wave-functions, the numerical simulations of the nucleon transport in target are therefore able to preserve the quantum nature of the colliding system, as well as a least biased many-body information needed to keep track of the cluster formation. A special attention is devoted to the fingerprints of the phase space topology induced by the fluctuations of the self-consistent mean-field. Comparisons be ween theoretical results and experimental data point out that ETDHF type approaches are well suited to describe reaction mechanisms in the Fermi energy domain. The observed sensitivity to physical effects shows that the nucleon-induced reactions provide a valuable probe of the nuclear interaction in this range of energy. (authors)

  12. A financial market model with two discontinuities: Bifurcation structures in the chaotic domain

    Science.gov (United States)

    Panchuk, Anastasiia; Sushko, Iryna; Westerhoff, Frank

    2018-05-01

    We continue the investigation of a one-dimensional piecewise linear map with two discontinuity points. Such a map may arise from a simple asset-pricing model with heterogeneous speculators, which can help us to explain the intricate bull and bear behavior of financial markets. Our focus is on bifurcation structures observed in the chaotic domain of the map's parameter space, which is associated with robust multiband chaotic attractors. Such structures, related to the map with two discontinuities, have been not studied before. We show that besides the standard bandcount adding and bandcount incrementing bifurcation structures, associated with two partitions, there exist peculiar bandcount adding and bandcount incrementing structures involving all three partitions. Moreover, the map's three partitions may generate intriguing bistability phenomena.

  13. Computer simulation of temperature-dependent growth of fractal and compact domains in diluted Ising models

    DEFF Research Database (Denmark)

    Sørensen, Erik Schwartz; Fogedby, Hans C.; Mouritsen, Ole G.

    1989-01-01

    temperature are studied as functions of temperature, time, and concentration. At zero temperature and high dilution, the growing solid is found to have a fractal morphology and the effective fractal exponent D varies with concentration and ratio of time scales of the two dynamical processes. The mechanism...... responsible for forming the fractal solid is shown to be a buildup of a locally high vacancy concentration in the active growth zone. The growth-probability measure of the fractals is analyzed in terms of multifractality by calculating the f(α) spectrum. It is shown that the basic ideas of relating...... probability measures of static fractal objects to the growth-probability distribution during formation of the fractal apply to the present model. The f(α) spectrum is found to be in the universality class of diffusion-limited aggregation. At finite temperatures, the fractal solid domains become metastable...

  14. Harmonic Domain Modelling of Transformer Core Nonlinearities Using the DIgSILENT PowerFactory Software

    DEFF Research Database (Denmark)

    Bak, Claus Leth; Bak-Jensen, Birgitte; Wiechowski, Wojciech

    2008-01-01

    This paper demonstrates the results of implementation and verification of an already existing algorithm that allows for calculating saturation characteristics of singlephase power transformers. The algorithm was described for the first time in 1993. Now this algorithm has been implemented using...... the DIgSILENT Programming Language (DPL) as an external script in the harmonic domain calculations of a power system analysis tool PowerFactory [10]. The algorithm is verified by harmonic measurements on a single-phase power transformer. A theoretical analysis of the core nonlinearities phenomena...... in single and three-phase transformers is also presented. This analysis leads to the conclusion that the method can be applied for modelling nonlinearities of three-phase autotransformers....

  15. Automated detection of microcalcification clusters in digital mammograms based on wavelet domain hidden Markov tree modeling

    International Nuclear Information System (INIS)

    Regentova, E.; Zhang, L.; Veni, G.; Zheng, J.

    2007-01-01

    A system is designed for detecting microcalcification clusters (MCC) in digital mammograms. The system is intended for computer-aided diagnostic prompting. Further discrimination of MCC as benign or malignant is assumed to be performed by radiologists. Processing of mammograms is based on the statistical modeling by means of wavelet domain hidden markov trees (WHMT). Segmentation is performed by the weighted likelihood evaluation followed by the classification based on spatial filters for a single microcalcification (MC) and a cluster of MC detection. The analysis is carried out on FROC curves for 40 mammograms from the mini-MIAS database and for 100 mammograms with 50 cancerous and 50 benign cases from DDSM database. The designed system is capable to detect 100% of true positive cases in these sets. The rate of false positives is 2.9 per case for mini-MIAS dataset; and 0.01 for the DDSM images. (orig.)

  16. New business models: the Agents and Inter-Agents in a neuroscientific domain

    Directory of Open Access Journals (Sweden)

    Michela Balconi

    2017-04-01

    Full Text Available Agency has been classically defined as the ability to sense and judge ourselves as the generators of an action and of its effects. In interactions, the ability to sense and consciously recognize that we – me and you – are the ones that are generating an action and causing its effects has been instead defined inter-agency or joint-agency. The implications of having developed good agency-related skills and of being aware of such processes become crucially important when we think at complex situations that characterize the real-life professional domain. Based on the crucial role of relationship with other social agents, cooperation and team-work for business and management activities, novel business models might benefit from an increased awareness of the way we and our co-workers plan, behave, make decisions, and manage action outcomes.

  17. Medication Reconciliation: Work Domain Ontology, prototype development, and a predictive model.

    Science.gov (United States)

    Markowitz, Eliz; Bernstam, Elmer V; Herskovic, Jorge; Zhang, Jiajie; Shneiderman, Ben; Plaisant, Catherine; Johnson, Todd R

    2011-01-01

    Medication errors can result from administration inaccuracies at any point of care and are a major cause for concern. To develop a successful Medication Reconciliation (MR) tool, we believe it necessary to build a Work Domain Ontology (WDO) for the MR process. A WDO defines the explicit, abstract, implementation-independent description of the task by separating the task from work context, application technology, and cognitive architecture. We developed a prototype based upon the WDO and designed to adhere to standard principles of interface design. The prototype was compared to Legacy Health System's and Pre-Admission Medication List Builder MR tools via a Keystroke-Level Model analysis for three MR tasks. The analysis found the prototype requires the fewest mental operations, completes tasks in the fewest steps, and completes tasks in the least amount of time. Accordingly, we believe that developing a MR tool, based upon the WDO and user interface guidelines, improves user efficiency and reduces cognitive load.

  18. Integrating the context-appropriate balanced attention model and reinforcement sensitivity theory: Towards a domain-general personality process model.

    Science.gov (United States)

    Collins, Michael D; Jackson, Chris J; Walker, Benjamin R; O'Connor, Peter J; Gardiner, Elliroma

    2017-01-01

    Over the last 40 years or more the personality literature has been dominated by trait models based on the Big Five (B5). Trait-based models describe personality at the between-person level but cannot explain the within-person mental mechanisms responsible for personality. Nor can they adequately account for variations in emotion and behavior experienced by individuals across different situations and over time. An alternative, yet understated, approach to personality architecture can be found in neurobiological theories of personality, most notably reinforcement sensitivity theory (RST). In contrast to static trait-based personality models like the B5, RST provides a more plausible basis for a personality process model, namely, one that explains how emotions and behavior arise from the dynamic interaction between contextual factors and within-person mental mechanisms. In this article, the authors review the evolution of a neurobiologically based personality process model based on RST, the response modulation model and the context-appropriate balanced attention model. They argue that by integrating this complex literature, and by incorporating evidence from personality neuroscience, one can meaningfully explain personality at both the within- and between-person levels. This approach achieves a domain-general architecture based on RST and self-regulation that can be used to align within-person mental mechanisms, neurobiological systems and between-person measurement models. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  19. Psychopathology and friendship in children and adolescents: disentangling the role of co-occurring symptom domains with serial mediation models.

    Science.gov (United States)

    Manfro, Arthur Gus; Pan, Pedro M; Gadelha, Ary; Fleck, Marcelo; do Rosário, Maria C; Cogo-Moreira, Hugo; Affonseca-Bressan, Rodrigo; Mari, Jair; Miguel, Euripedes C; Rohde, Luis A; Salum, Giovanni A

    2017-11-01

    The consolidation of social friendship groups is a vital part of human development. The objective of this study is to understand the direct and indirect influences of three major symptomatic domains-emotional, hyperkinetic, and conduct-on friendship. Specifically, we aim to study if the associations of one domain with friendship may be mediated by co-occurring symptoms from another domain. A total of 2512 subjects aged 6-14 years participated in this study. Friendship was evaluated by the Development and Well-Being Assessment's friendship section. We evaluated two main constructs as outcomes: (1) social isolation and (2) friendship latent construct. Emotional, hyperkinetic, and conduct symptomatic domains were evaluated with the Strengths and Difficulties Questionnaire (SDQ). All SDQ domains were positively associated with social isolation and negatively associated with friendship latent construct in univariate analysis. However, serial mediation models showed that the association between conduct domains with social isolation was mediated by emotion and hyperkinetic domains. Moreover, the associations between emotional and hyperkinetic domains with friendship latent construct in non-isolated children were mediated by the conduct domain. Emotion and hyperkinetic domains were directly and indirectly associated with social isolation, whereas conduct was directly and indirectly associated with overall friendship in non-isolated children. Results suggest that interventions aimed to improve social life in childhood and adolescence may have stronger effects if directed towards the treatment of emotion and hyperkinetic symptoms in socially isolated children and directed towards the treatment of conduct symptoms in children with fragile social connections.

  20. GPS, BDS and Galileo ionospheric correction models: An evaluation in range delay and position domain

    Science.gov (United States)

    Wang, Ningbo; Li, Zishen; Li, Min; Yuan, Yunbin; Huo, Xingliang

    2018-05-01

    The performance of GPS Klobuchar (GPSKlob), BDS Klobuchar (BDSKlob) and NeQuick Galileo (NeQuickG) ionospheric correction models are evaluated in the range delay and position domains over China. The post-processed Klobuchar-style (CODKlob) coefficients provided by the Center for Orbit Determination in Europe (CODE) and our own fitted NeQuick coefficients (NeQuickC) are also included for comparison. In the range delay domain, BDS total electrons contents (TEC) derived from 20 international GNSS Monitoring and Assessment System (iGMAS) stations and GPS TEC obtained from 35 Crust Movement Observation Network of China (CMONC) stations are used as references. Compared to BDS TEC during the short period (doy 010-020, 2015), GPSKlob, BDSKlob and NeQuickG can correct 58.4, 66.7 and 54.7% of the ionospheric delay. Compared to GPS TEC for the long period (doy 001-180, 2015), the three ionospheric models can mitigate the ionospheric delay by 64.8, 65.4 and 68.1%, respectively. For the two comparison cases, CODKlob shows the worst performance, which only reduces 57.9% of the ionospheric range errors. NeQuickC exhibits the best performance, which outperforms GPSKlob, BDSKlob and NeQuickG by 6.7, 2.1 and 6.9%, respectively. In the position domain, single-frequency stand point positioning (SPP) was conducted at the selected 35 CMONC sites using GPS C/A pseudorange with and without ionospheric corrections. The vertical position error of the uncorrected case drops significantly from 10.3 m to 4.8, 4.6, 4.4 and 4.2 m for GPSKlob, CODKlob, BDSKlob and NeQuickG, however, the horizontal position error (3.2) merely decreases to 3.1, 2.7, 2.4 and 2.3 m, respectively. NeQuickG outperforms GPSKlob and BDSKlob by 5.8 and 1.9% in vertical component, and by 25.0 and 3.2% in horizontal component.

  1. A Multi-Level Model of Information Seeking in the Clinical Domain

    Science.gov (United States)

    Hung, Peter W.; Johnson, Stephen B.; Kaufman, David R.; Mendonça, Eneida A.

    2008-01-01

    Objective: Clinicians often have difficulty translating information needs into effective search strategies to find appropriate answers. Information retrieval systems employing an intelligent search agent that generates adaptive search strategies based on human search expertise could be helpful in meeting clinician information needs. A prerequisite for creating such systems is an information seeking model that facilitates the representation of human search expertise. The purpose of developing such a model is to provide guidance to information seeking system development and to shape an empirical research program. Design: The information seeking process was modeled as a complex problem-solving activity. After considering how similarly complex activities had been modeled in other domains, we determined that modeling context-initiated information seeking across multiple problem spaces allows the abstraction of search knowledge into functionally consistent layers. The knowledge layers were identified in the information science literature and validated through our observations of searches performed by health science librarians. Results: A hierarchical multi-level model of context-initiated information seeking is proposed. Each level represents (1) a problem space that is traversed during the online search process, and (2) a distinct layer of knowledge that is required to execute a successful search. Grand strategy determines what information resources will be searched, for what purpose, and in what order. The strategy level represents an overall approach for searching a single resource. Tactics are individual moves made to further a strategy. Operations are mappings of abstract intentions to information resource-specific concrete input. Assessment is the basis of interaction within the strategic hierarchy, influencing the direction of the search. Conclusion: The described multi-level model provides a framework for future research and the foundation for development of an

  2. Model Checking and Model-based Testing in the Railway Domain

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth; Peleska, Jan

    2015-01-01

    This chapter describes some approaches and emerging trends for verification and model-based testing of railway control systems. We describe state-of-the-art methods and associated tools for verifying interlocking systems and their configuration data, using bounded model checking and k...... with good test strength are explained. Interlocking systems represent just one class of many others, where concrete system instances are created from generic representations, using configuration data for determining the behaviour of the instances. We explain how the systematic transition from generic...... to concrete instances in the development path is complemented by associated transitions in the verification and testing paths....

  3. 多域环境下的分布式RBAC模型%A distributed role-based access control model for multi-domain environments

    Institute of Scientific and Technical Information of China (English)

    洪帆; 朱贤; 邢光林

    2006-01-01

    Access control in multi-domain environments is an important question in building coalition between domains. Based on the RBAC access control model and the concepts of secure domain,the role delegation and role mapping are proposed, which support the third-party authorization. A distributed RBAC model is then presented. Finally implementation issues are discussed.

  4. Modeling the Development of Vocational Competence: A Psychometric Model for Economic Domains

    Science.gov (United States)

    Klotz, Viola Katharina; Winther, Esther; Festner, Dagmar

    2015-01-01

    This article discusses the development of vocational competence through economic vocational educational training (VET) from a theoretical and psychometric perspective. Most assessment and competence models tend to adopt a state perspective toward assessments of competence and carve out different structures of competence for diverse vocational…

  5. Forsmark site investigation. Assessment of the validity of the rock domain model, version 1.2, based on the modelling of gravity and petrophysical data

    International Nuclear Information System (INIS)

    Isaksson, Hans; Stephens, Michael B.

    2007-11-01

    This document reports the results gained by the geophysical modelling of rock domains based on gravity and petrophysical data, which is one of the activities performed within the site investigation work at Forsmark. The main objective with this activity is to assess the validity of the geological rock domain model version 1.2, and to identify discrepancies in the model that may indicate a need for revision of the model or a need for additional investigations. The verification is carried out by comparing the calculated gravity model response, which takes account of the geological model, with a local gravity anomaly that represents the measured data. The model response is obtained from the three-dimensional geometry and the petrophysical data provided for each rock domain in the geological model. Due to model boundary conditions, the study is carried out in a smaller area within the regional model area. Gravity model responses are calculated in three stages; an initial model, a base model and a refined base model. The refined base model is preferred and is used for comparison purposes. In general, there is a good agreement between the refined base model that makes use of the rock domain model, version 1.2 and the measured gravity data, not least where it concerns the depth extension of the critical rock domain RFM029. The most significant discrepancy occurs in the area extending from the SFR office to the SFR underground facility and further to the northwest. It is speculated that this discrepancy is caused by a combination of an overestimation of the volume of gabbro (RFM016) that plunges towards the southeast in the rock domain model, and an underestimation of the volume of occurrence of pegmatite and pegmatitic granite that are known to be present and occur as larger bodies around SFR. Other discrepancies are noted in rock domain RFM022, which is considered to be overestimated in the rock domain model, version 1.2, and in rock domain RFM017, where the gravity

  6. Frequency domain reflectometry modeling for nondestructive evaluation of nuclear power plant cables

    Science.gov (United States)

    Glass, S. W.; Fifield, L. S.; Jones, A. M.; Hartman, T. S.

    2018-04-01

    Cable insulation polymers are among the more susceptible materials to age-related degradation within a nuclear power plant. This is recognized by both regulators and utilities, so all plants have developed cable aging management programs to detect damage before critical component failure in compliance with regulatory guidelines. Although a wide range of tools are available to evaluate cables and cable systems, cable aging management programs vary in how condition monitoring and nondestructive examinations are conducted as utilities search for the most reliable and cost-effective ways to assess cable system condition. Frequency domain reflectometry (FDR) is emerging as one valuable tool to locate and assess damaged portions of a cable system with minimal cost and only requires access in most cases to one of the cable terminal ends. Since laboratory studies to evaluate the use of FDR for inspection of aged cables can be expensive and data interpretation may be confounded by multiple factors which influence results, a model-based approach is desired to parametrically investigate the effect of insulation material damage in a controlled manner. This work describes development of a physics-based FDR model which uses finite element simulations of cable segments in conjunction with cascaded circuit element simulations to efficiently study a cable system. One or more segments of the cable system model have altered physical or electrical properties which represent the degree of damage and the location of the damage in the system. This circuit model is then subjected to a simulated FDR examination. The modeling approach is verified using several experimental cases and by comparing it to a commercial simulator suitable for simulation of some cable configurations. The model is used to examine a broad range of parameters including defect length, defect profile, degree of degradation, number and location of defects, FDR bandwidth, and addition of impedance-matched extensions to

  7. Frequency domain finite-element and spectral-element acoustic wave modeling using absorbing boundaries and perfectly matched layer

    Science.gov (United States)

    Rahimi Dalkhani, Amin; Javaherian, Abdolrahim; Mahdavi Basir, Hadi

    2018-04-01

    Wave propagation modeling as a vital tool in seismology can be done via several different numerical methods among them are finite-difference, finite-element, and spectral-element methods (FDM, FEM and SEM). Some advanced applications in seismic exploration benefit the frequency domain modeling. Regarding flexibility in complex geological models and dealing with the free surface boundary condition, we studied the frequency domain acoustic wave equation using FEM and SEM. The results demonstrated that the frequency domain FEM and SEM have a good accuracy and numerical efficiency with the second order interpolation polynomials. Furthermore, we developed the second order Clayton and Engquist absorbing boundary condition (CE-ABC2) and compared it with the perfectly matched layer (PML) for the frequency domain FEM and SEM. In spite of PML method, CE-ABC2 does not add any additional computational cost to the modeling except assembling boundary matrices. As a result, considering CE-ABC2 is more efficient than PML for the frequency domain acoustic wave propagation modeling especially when computational cost is high and high-level absorbing performance is unnecessary.

  8. A Proposal for the Time Domain Modeling of Split Air Conditioners for Consumer Reimbursement Studies

    Science.gov (United States)

    Rezende, Paulo Henrique Oliveira; Almeida Junior, Afonso Bernardino; Gondim, Isaque Nogueira; Oliveira, José Carlos

    2015-04-01

    This paper deals with computer application procedures for the evaluation of the causal consistency between anomalous phenomena manifested in electrical networks, along with the physical damage associated with electrical equipment and possible reimbursement requests. The focus is on the development of an air conditioner appliance model of the type known as split founded upon a representation, in the time domain, in accordance with the Alternative Transients Program (ATP) simulator requirements. This approach permits investigations concerning the performance of the product when submitted to ideal and non-ideal supply conditions. Once the equipment model is implemented in the program, a set of investigative studies are carried out to show the device performance under specific energy quality disturbance conditions. In addition, there are still the results for the validation of the process established through the correlation between computational performance of the air conditioner with corresponding studies carried out experimentally, which are presented herein. Moreover, once the effectiveness of the developed model is verified, it is implemented into the Requests for Reimbursement Software. Investigations related to the correlation between disturbances and the levels of thermal and dielectric tolerance are then performed aiming at illustrating the use of the research results for the reimbursement analyzes purposes.

  9. An Inverse Neural Controller Based on the Applicability Domain of RBF Network Models

    Directory of Open Access Journals (Sweden)

    Alex Alexandridis

    2018-01-01

    Full Text Available This paper presents a novel methodology of generic nature for controlling nonlinear systems, using inverse radial basis function neural network models, which may combine diverse data originating from various sources. The algorithm starts by applying the particle swarm optimization-based non-symmetric variant of the fuzzy means (PSO-NSFM algorithm so that an approximation of the inverse system dynamics is obtained. PSO-NSFM offers models of high accuracy combined with small network structures. Next, the applicability domain concept is suitably tailored and embedded into the proposed control structure in order to ensure that extrapolation is avoided in the controller predictions. Finally, an error correction term, estimating the error produced by the unmodeled dynamics and/or unmeasured external disturbances, is included to the control scheme to increase robustness. The resulting controller guarantees bounded input-bounded state (BIBS stability for the closed loop system when the open loop system is BIBS stable. The proposed methodology is evaluated on two different control problems, namely, the control of an experimental armature-controlled direct current (DC motor and the stabilization of a highly nonlinear simulated inverted pendulum. For each one of these problems, appropriate case studies are tested, in which a conventional neural controller employing inverse models and a PID controller are also applied. The results reveal the ability of the proposed control scheme to handle and manipulate diverse data through a data fusion approach and illustrate the superiority of the method in terms of faster and less oscillatory responses.

  10. PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain.

    Science.gov (United States)

    Younesi, Erfan; Malhotra, Ashutosh; Gündel, Michaela; Scordis, Phil; Kodamullil, Alpha Tom; Page, Matt; Müller, Bernd; Springstubbe, Stephan; Wüllner, Ullrich; Scheller, Dieter; Hofmann-Apitius, Martin

    2015-09-22

    Despite the unprecedented and increasing amount of data, relatively little progress has been made in molecular characterization of mechanisms underlying Parkinson's disease. In the area of Parkinson's research, there is a pressing need to integrate various pieces of information into a meaningful context of presumed disease mechanism(s). Disease ontologies provide a novel means for organizing, integrating, and standardizing the knowledge domains specific to disease in a compact, formalized and computer-readable form and serve as a reference for knowledge exchange or systems modeling of disease mechanism. The Parkinson's disease ontology was built according to the life cycle of ontology building. Structural, functional, and expert evaluation of the ontology was performed to ensure the quality and usability of the ontology. A novelty metric has been introduced to measure the gain of new knowledge using the ontology. Finally, a cause-and-effect model was built around PINK1 and two gene expression studies from the Gene Expression Omnibus database were re-annotated to demonstrate the usability of the ontology. The Parkinson's disease ontology with a subclass-based taxonomic hierarchy covers the broad spectrum of major biomedical concepts from molecular to clinical features of the disease, and also reflects different views on disease features held by molecular biologists, clinicians and drug developers. The current version of the ontology contains 632 concepts, which are organized under nine views. The structural evaluation showed the balanced dispersion of concept classes throughout the ontology. The functional evaluation demonstrated that the ontology-driven literature search could gain novel knowledge not present in the reference Parkinson's knowledge map. The ontology was able to answer specific questions related to Parkinson's when evaluated by experts. Finally, the added value of the Parkinson's disease ontology is demonstrated by ontology-driven modeling of PINK1

  11. Comparing Cognitive Models of Domain Mastery and Task Performance in Algebra: Validity Evidence for a State Assessment

    Science.gov (United States)

    Warner, Zachary B.

    2013-01-01

    This study compared an expert-based cognitive model of domain mastery with student-based cognitive models of task performance for Integrated Algebra. Interpretations of student test results are limited by experts' hypotheses of how students interact with the items. In reality, the cognitive processes that students use to solve each item may be…

  12. Moving domain computational fluid dynamics to interface with an embryonic model of cardiac morphogenesis.

    Directory of Open Access Journals (Sweden)

    Juhyun Lee

    Full Text Available Peristaltic contraction of the embryonic heart tube produces time- and spatial-varying wall shear stress (WSS and pressure gradients (∇P across the atrioventricular (AV canal. Zebrafish (Danio rerio are a genetically tractable system to investigate cardiac morphogenesis. The use of Tg(fli1a:EGFP (y1 transgenic embryos allowed for delineation and two-dimensional reconstruction of the endocardium. This time-varying wall motion was then prescribed in a two-dimensional moving domain computational fluid dynamics (CFD model, providing new insights into spatial and temporal variations in WSS and ∇P during cardiac development. The CFD simulations were validated with particle image velocimetry (PIV across the atrioventricular (AV canal, revealing an increase in both velocities and heart rates, but a decrease in the duration of atrial systole from early to later stages. At 20-30 hours post fertilization (hpf, simulation results revealed bidirectional WSS across the AV canal in the heart tube in response to peristaltic motion of the wall. At 40-50 hpf, the tube structure undergoes cardiac looping, accompanied by a nearly 3-fold increase in WSS magnitude. At 110-120 hpf, distinct AV valve, atrium, ventricle, and bulbus arteriosus form, accompanied by incremental increases in both WSS magnitude and ∇P, but a decrease in bi-directional flow. Laminar flow develops across the AV canal at 20-30 hpf, and persists at 110-120 hpf. Reynolds numbers at the AV canal increase from 0.07±0.03 at 20-30 hpf to 0.23±0.07 at 110-120 hpf (p< 0.05, n=6, whereas Womersley numbers remain relatively unchanged from 0.11 to 0.13. Our moving domain simulations highlights hemodynamic changes in relation to cardiac morphogenesis; thereby, providing a 2-D quantitative approach to complement imaging analysis.

  13. NovelFam3000 – Uncharacterized human protein domains conserved across model organisms

    Science.gov (United States)

    Kemmer, Danielle; Podowski, Raf M; Arenillas, David; Lim, Jonathan; Hodges, Emily; Roth, Peggy; Sonnhammer, Erik LL; Höög, Christer; Wasserman, Wyeth W

    2006-01-01

    Background Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. Description From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. Conclusion Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families. PMID:16533400

  14. NovelFam3000 – Uncharacterized human protein domains conserved across model organisms

    Directory of Open Access Journals (Sweden)

    Sonnhammer Erik LL

    2006-03-01

    Full Text Available Abstract Background Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. Description From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. Conclusion Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families.

  15. Advantages of frequency-domain modeling in dynamic-susceptibility contrast magnetic resonance cerebral blood flow quantification.

    Science.gov (United States)

    Chen, Jean J; Smith, Michael R; Frayne, Richard

    2005-03-01

    In dynamic-susceptibility contrast magnetic resonance perfusion imaging, the cerebral blood flow (CBF) is estimated from the tissue residue function obtained through deconvolution of the contrast concentration functions. However, the reliability of CBF estimates obtained by deconvolution is sensitive to various distortions including high-frequency noise amplification. The frequency-domain Fourier transform-based and the time-domain singular-value decomposition-based (SVD) algorithms both have biases introduced into their CBF estimates when noise stability criteria are applied or when contrast recirculation is present. The recovery of the desired signal components from amid these distortions by modeling the residue function in the frequency domain is demonstrated. The basic advantages and applicability of the frequency-domain modeling concept are explored through a simple frequency-domain Lorentzian model (FDLM); with results compared to standard SVD-based approaches. The performance of the FDLM method is model dependent, well representing residue functions in the exponential family while less accurately representing other functions. (c) 2005 Wiley-Liss, Inc.

  16. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.

    Directory of Open Access Journals (Sweden)

    Raffi Tonikian

    2009-10-01

    Full Text Available SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast, Saccharomyces cerevisiae. Although most of the SH3 domains fall into the canonical classes I and II, each domain utilizes distinct features of its cognate ligands to achieve binding selectivity. Furthermore, we uncovered several SH3 domains with specificity profiles that clearly deviate from the two canonical classes. In conjunction with phage display, we used yeast two-hybrid and peptide array screening to independently identify SH3 domain binding partners. The results from the three complementary techniques were integrated using a Bayesian algorithm to generate a high-confidence yeast SH3 domain interaction map. The interaction map was enriched for proteins involved in endocytosis, revealing a set of SH3-mediated interactions that underlie formation of protein complexes essential to this biological pathway. We used the SH3 domain interaction network to predict the dynamic localization of several previously uncharacterized endocytic proteins, and our analysis suggests a novel role for the SH3 domains of Lsb3p and Lsb4p as hubs that recruit and assemble several endocytic complexes.

  17. Random-field Potts model for the polar domains of lead magnesium niobate and lead scandium tantalate

    Energy Technology Data Exchange (ETDEWEB)

    Qian, H.; Bursill, L.A

    1997-06-01

    A random filed Potts model is used to establish the spatial relationship between the nanoscale distribution of charges chemical defects and nanoscale polar domains for the perovskite-based relaxor materials lead magnesium niobate (PMN) and lead scandium tantalate (PST). The random fields are not set stochastically but are determined initially by the distribution of B-site cations (Mg, Nb) or (Sc, Ta) generated by Monte Carlo NNNI-model simulations for the chemical defects. An appropriate random field Potts model is derived and algorithms developed for a 2D lattice. It is shown that the local fields are strongly correlated with the chemical domain walls and that polar domains as a function of decreasing temperature is simulated for the two cases of PMN and PST. The dynamics of the polar clusters is also discussed. 33 refs., 9 figs.

  18. 3D SEMANTIC LABELING OF ALS DATA BASED ON DOMAIN ADAPTION BY TRANSFERRING AND FUSING RANDOM FOREST MODELS

    Directory of Open Access Journals (Sweden)

    J. Wu

    2018-04-01

    Full Text Available Labeling 3D point cloud data with traditional supervised learning methods requires considerable labelled samples, the collection of which is cost and time expensive. This work focuses on adopting domain adaption concept to transfer existing trained random forest classifiers (based on source domain to new data scenes (target domain, which aims at reducing the dependence of accurate 3D semantic labeling in point clouds on training samples from the new data scene. Firstly, two random forest classifiers were firstly trained with existing samples previously collected for other data. They were different from each other by using two different decision tree construction algorithms: C4.5 with information gain ratio and CART with Gini index. Secondly, four random forest classifiers adapted to the target domain are derived through transferring each tree in the source random forest models with two types of operations: structure expansion and reduction-SER and structure transfer-STRUT. Finally, points in target domain are labelled by fusing the four newly derived random forest classifiers using weights of evidence based fusion model. To validate our method, experimental analysis was conducted using 3 datasets: one is used as the source domain data (Vaihingen data for 3D Semantic Labelling; another two are used as the target domain data from two cities in China (Jinmen city and Dunhuang city. Overall accuracies of 85.5 % and 83.3 % for 3D labelling were achieved for Jinmen city and Dunhuang city data respectively, with only 1/3 newly labelled samples compared to the cases without domain adaption.

  19. D Semantic Labeling of ALS Data Based on Domain Adaption by Transferring and Fusing Random Forest Models

    Science.gov (United States)

    Wu, J.; Yao, W.; Zhang, J.; Li, Y.

    2018-04-01

    Labeling 3D point cloud data with traditional supervised learning methods requires considerable labelled samples, the collection of which is cost and time expensive. This work focuses on adopting domain adaption concept to transfer existing trained random forest classifiers (based on source domain) to new data scenes (target domain), which aims at reducing the dependence of accurate 3D semantic labeling in point clouds on training samples from the new data scene. Firstly, two random forest classifiers were firstly trained with existing samples previously collected for other data. They were different from each other by using two different decision tree construction algorithms: C4.5 with information gain ratio and CART with Gini index. Secondly, four random forest classifiers adapted to the target domain are derived through transferring each tree in the source random forest models with two types of operations: structure expansion and reduction-SER and structure transfer-STRUT. Finally, points in target domain are labelled by fusing the four newly derived random forest classifiers using weights of evidence based fusion model. To validate our method, experimental analysis was conducted using 3 datasets: one is used as the source domain data (Vaihingen data for 3D Semantic Labelling); another two are used as the target domain data from two cities in China (Jinmen city and Dunhuang city). Overall accuracies of 85.5 % and 83.3 % for 3D labelling were achieved for Jinmen city and Dunhuang city data respectively, with only 1/3 newly labelled samples compared to the cases without domain adaption.

  20. Exploratory analysis regarding the domain definitions for computer based analytical models

    Science.gov (United States)

    Raicu, A.; Oanta, E.; Barhalescu, M.

    2017-08-01

    Our previous computer based studies dedicated to structural problems using analytical methods defined the composite cross section of a beam as a result of Boolean operations with so-called ‘simple’ shapes. Using generalisations, in the class of the ‘simple’ shapes were included areas bounded by curves approximated using spline functions and areas approximated as polygons. However, particular definitions lead to particular solutions. In order to ascend above the actual limitations, we conceived a general definition of the cross sections that are considered now calculus domains consisting of several subdomains. The according set of input data use complex parameterizations. This new vision allows us to naturally assign a general number of attributes to the subdomains. In this way there may be modelled new phenomena that use map-wise information, such as the metal alloys equilibrium diagrams. The hierarchy of the input data text files that use the comma-separated-value format and their structure are also presented and discussed in the paper. This new approach allows us to reuse the concepts and part of the data processing software instruments already developed. The according software to be subsequently developed will be modularised and generalised in order to be used in the upcoming projects that require rapid development of computer based models.

  1. A Model to Support Decision Making in the Idea Management Domain

    Directory of Open Access Journals (Sweden)

    Marina Carradore Sérgio

    2015-12-01

    Full Text Available Taking into account the global competitiveness, innovation has become a challenge for organizations. Idea management is an integral part of the innovation process and it is presented as an essential factor for achieving success. Due to the volume and sudden peaks in submissions of ideas, the appropriate analysis and the allocation of resources for investment are important issues to be addressed. The objective of this paper is to present a model for the management of ideas based on ontology and cluster analysis in order to maximize resources for investment in ideas. So as to demonstrate the model feasibility it was prepared a dataset comprised of fifty-five ideas collected from the Starbucks® site. These ideas were then stored in the domain ontology and were used as subsidies for the cluster analysis and for the building of a knowledge base. As a result, it was identified groups with similar ideas that, when analyzed, foster a greater potential for observation and may indicate patterns and trends that can assist in decision making.

  2. Distributed electrical time domain reflectometry (ETDR) structural sensors: design models and proof-of-concept experiments

    Science.gov (United States)

    Stastny, Jeffrey A.; Rogers, Craig A.; Liang, Chen

    1993-07-01

    A parametric design model has been created to optimize the sensitivity of the sensing cable in a distributed sensing system. The system consists of electrical time domain reflectometry (ETDR) signal processing equipment and specially designed sensing cables. The ETDR equipment sends a high-frequency electric pulse (in the giga hertz range) along the sensing cable. Some portion of the electric pulse will be reflected back to the ETDR equipment as a result of the variation of the cable impedance. The electric impedance variation in the sensing cable can be related to its mechanical deformation, such as cable elongation (change in the resistance), shear deformation (change in the capacitance), corrosion of the cable or the materials around the cable (change in inductance and capacitance), etc. The time delay, amplitude, and shape of the reflected pulse provides the means to locate, determine the magnitude, and indicate the nature of the change in the electrical impedance, which is then related to the distributed structural deformation. The sensing cables are an essential part of the health-monitoring system. By using the parametric design model, the optimum cable parameters can be determined for specific deformation. Proof-of-concept experiments also are presented in the paper to demonstrate the utility of an electrical TDR system in distributed sensing applications.

  3. Respiratory system dynamical mechanical properties: modeling in time and frequency domain.

    Science.gov (United States)

    Carvalho, Alysson Roncally; Zin, Walter Araujo

    2011-06-01

    The mechanical properties of the respiratory system are important determinants of its function and can be severely compromised in disease. The assessment of respiratory system mechanical properties is thus essential in the management of some disorders as well as in the evaluation of respiratory system adaptations in response to an acute or chronic process. Most often, lungs and chest wall are treated as a linear dynamic system that can be expressed with differential equations, allowing determination of the system's parameters, which will reflect the mechanical properties. However, different models that encompass nonlinear characteristics and also multicompartments have been used in several approaches and most specifically in mechanically ventilated patients with acute lung injury. Additionally, the input impedance over a range of frequencies can be assessed with a convenient excitation method allowing the identification of the mechanical characteristics of the central and peripheral airways as well as lung periphery impedance. With the evolution of computational power, the airway pressure and flow can be recorded and stored for hours, and hence continuous monitoring of the respiratory system mechanical properties is already available in some mechanical ventilators. This review aims to describe some of the most frequently used models for the assessment of the respiratory system mechanical properties in both time and frequency domain.

  4. Sensitivity analysis with the regional climate model COSMO-CLM over the CORDEX-MENA domain

    Science.gov (United States)

    Bucchignani, E.; Cattaneo, L.; Panitz, H.-J.; Mercogliano, P.

    2016-02-01

    The results of a sensitivity work based on ERA-Interim driven COSMO-CLM simulations over the Middle East-North Africa (CORDEX-MENA) domain are presented. All simulations were performed at 0.44° spatial resolution. The purpose of this study was to ascertain model performances with respect to changes in physical and tuning parameters which are mainly related to surface, convection, radiation and cloud parameterizations. Evaluation was performed for the whole CORDEX-MENA region and six sub-regions, comparing a set of 26 COSMO-CLM runs against a combination of available ground observations, satellite products and reanalysis data to assess temperature, precipitation, cloud cover and mean sea level pressure. The model proved to be very sensitive to changes in physical parameters. The optimized configuration allows COSMO-CLM to improve the simulated main climate features of this area. Its main characteristics consist in the new parameterization of albedo, based on Moderate Resolution Imaging Spectroradiometer data, and the new parameterization of aerosol, based on NASA-GISS AOD distributions. When applying this configuration, Mean Absolute Error values for the considered variables are as follows: about 1.2 °C for temperature, about 15 mm/month for precipitation, about 9 % for total cloud cover, and about 0.6 hPa for mean sea level pressure.

  5. Event-based aquifer-to-atmosphere modeling over the European CORDEX domain

    Science.gov (United States)

    Keune, J.; Goergen, K.; Sulis, M.; Shrestha, P.; Springer, A.; Kusche, J.; Ohlwein, C.; Kollet, S. J.

    2014-12-01

    Despite the fact that recent studies focus on the impact of soil moisture on climate and especially land-energy feedbacks, groundwater dynamics are often neglected or conceptual groundwater flow models are used. In particular, in the context of climate change and the occurrence of droughts and floods, a better understanding and an improved simulation of the physical processes involving groundwater on continental scales is necessary. This requires the implementation of a physically consistent terrestrial modeling system, which explicitly incorporates groundwater dynamics and the connection with shallow soil moisture. Such a physics-based system enables simulations and monitoring of groundwater storage and enhanced representations of the terrestrial energy and hydrologic cycles over long time periods. On shorter timescales, the prediction of groundwater-related extremes, such as floods and droughts, are expected to improve, because of the improved simulation of components of the hydrological cycle. In this study, we present a fully coupled aquifer-to-atmosphere modeling system over the European CORDEX domain. The integrated Terrestrial Systems Modeling Platform, TerrSysMP, consisting of the three-dimensional subsurface model ParFlow, the Community Land Model CLM3.5 and the numerical weather prediction model COSMO of the German Weather Service, is used. The system is set up with a spatial resolution of 0.11° (12.5km) and closes the terrestrial water and energy cycles from aquifers into the atmosphere. Here, simulations of the fully coupled system are performed over events, such as the 2013 flood in Central Europe and the 2003 European heat wave, and over extended time periods on the order of 10 years. State and flux variables of the terrestrial hydrologic and energy cycle are analyzed and compared to both in situ (e.g. stream and water level gauge networks, FLUXNET) and remotely sensed observations (e.g. GRACE, ESA ICC ECV soil moisture and SMOS). Additionally, the

  6. Blue light-excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis.

    Science.gov (United States)

    Oide, Mao; Okajima, Koji; Nakagami, Hirofumi; Kato, Takayuki; Sekiguchi, Yuki; Oroguchi, Tomotaka; Hikima, Takaaki; Yamamoto, Masaki; Nakasako, Masayoshi

    2018-01-19

    Phototropin2 (phot2) is a blue-light (BL) receptor that regulates BL-dependent activities for efficient photosynthesis in plants. phot2 comprises two BL-receiving light-oxygen-voltage-sensing domains (LOV1 and LOV2) and a kinase domain. BL-excited LOV2 is thought to be primarily responsible for the BL-dependent activation of the kinase. However, the molecular mechanisms by which small BL-induced conformational changes in the LOV2 domain are transmitted to the kinase remain unclear. Here, we used full-length wild-type and mutant phot2 proteins from Arabidopsis to study their molecular properties in the dark and under BL irradiation. Phosphorylation assays and absorption measurements indicated that the LOV1 domain assists the thermal relaxation of BL-excited LOV2 and vice versa. Using small-angle X-ray scattering and electron microscopy, we observed that phot2 forms a dimer and has a rod shape with a maximum length of 188 Å and a radius of gyration of 44 Å. Under BL, phot2 displayed large conformational changes that bent the rod shape. By superimposing the crystal structures of the LOV1 dimer, LOV2, and a homology model of the kinase to the observed changes, we inferred that the BL-dependent change consisted of positional shifts of both LOV2 and the kinase relative to LOV1. Furthermore, phot2 mutants lacking the photocycle in LOV1 or LOV2 still exhibited conformational changes under BL, suggesting that LOV1 and LOV2 cooperatively contribute to the conformational changes that activate the kinase. These results suggest that BL-activated LOV1 contributes to the kinase activity of phot2. We discuss the possible intramolecular interactions and signaling mechanisms in phot2. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Couplings in Phase Domain Impedance Modelling of Grid-Connected Converters

    DEFF Research Database (Denmark)

    Dowlatabadi, Mohammadkazem Bakhshizadeh; Wang, Xiongfei; Blaabjerg, Frede

    2016-01-01

    The output impedance of a power converter plays an important role in the stability assessment of the converter. The impedance can be expressed in different frames such as the stationary frame (phase domain) or in the synchronous frame (dq domain). To treat the three-phase system like a single...

  8. Domain Walls and Textured Vortices in a Two-Component Ginzburg-Landau Model

    DEFF Research Database (Denmark)

    Madsen, Søren Peder; Gaididei, Yu. B.; Christiansen, Peter Leth

    2005-01-01

    coupling between the two order parameters a ''textured vortex'' is found by analytical and numerical solution of the Ginzburg-Landau equations. With a Josephson type coupling between the two order parameters we find the system to split up in two domains separated by a domain wall, where the order parameter...... is depressed to zero....

  9. Reference architecture and interoperability model for data mining and fusion in scientific cross-domain infrastructures

    Science.gov (United States)

    Haener, Rainer; Waechter, Joachim; Grellet, Sylvain; Robida, Francois

    2017-04-01

    , business logic and processes on the basis of a minimal set of well-known, established standards. It implements the representation of knowledge with the application of domain-controlled vocabularies to statements about resources, information, facts, and complex matters (ontologies). Seismic experts for example, would be interested in geological models or borehole measurements at a certain depth, based on which it is possible to correlate and verify seismic profiles. The entire model is built upon standards from the Open Geospatial Consortium (Dictionaries, Service Layer), the International Organisation for Standardisation (Registries, Metadata), and the World Wide Web Consortium (Resource Description Framework, Spatial Data on the Web Best Practices). It has to be emphasised that this approach is scalable to the greatest possible extent: All information, necessary in the context of cross-domain infrastructures is referenced via vocabularies and knowledge bases containing statements that provide either the information itself or resources (service-endpoints), the information can be retrieved from. The entire infrastructure communication is subject to a broker-based business logic integration platform where the information exchanged between involved participants, is managed on the basis of standardised dictionaries, repositories, and registries. This approach also enables the development of Systems-of-Systems (SoS), which allow the collaboration of autonomous, large scale concurrent, and distributed systems, yet cooperatively interacting as a collective in a common environment.

  10. Time Domain Modeling and Simulation of Nonlinear Slender Viscoelastic Beams Associating Cosserat Theory and a Fractional Derivative Model

    Directory of Open Access Journals (Sweden)

    Adailton S. Borges

    Full Text Available Abstract A broad class of engineering systems can be satisfactory modeled under the assumptions of small deformations and linear material properties. However, many mechanical systems used in modern applications, like structural elements typical of aerospace and petroleum industries, have been characterized by increased slenderness and high static and dynamic loads. In such situations, it becomes indispensable to consider the nonlinear geometric effects and/or material nonlinear behavior. At the same time, in many cases involving dynamic loads, there comes the need for attenuation of vibration levels. In this context, this paper describes the development and validation of numerical models of viscoelastic slender beam-like structures undergoing large displacements. The numerical approach is based on the combination of the nonlinear Cosserat beam theory and a viscoelastic model based on Fractional Derivatives. Such combination enables to derive nonlinear equations of motion that, upon finite element discretization, can be used for predicting the dynamic behavior of the structure in the time domain, accounting for geometric nonlinearity and viscoelastic damping. The modeling methodology is illustrated and validated by numerical simulations, the results of which are compared to others available in the literature.

  11. On the practical modeling of conceptual overlap among multiple facets in ontology domain concepts (Mini-thesis)

    OpenAIRE

    Rodriguez-Castro, Benedicto; Glaser, Hugh; Carr, Leslie

    2007-01-01

    This report presents a study on the practical modelling of the conceptual overlap that might exist among the multiple facets that define a particular ontology domain concept. The notions of conceptual overlap and facet are defined, together with their relation to scenarios of multiple inheritance in ontology models. Starting from the notion of a value partition, a terminology of ontology modelling constructs is introduced that allows the characterization of two types of conceptual overlap wit...

  12. Microvascular anastomosis in rodent model evaluated by Fourier domain Doppler optical coherence tomography

    Science.gov (United States)

    Huang, Yong; Tong, Dedi; Zhu, Shan; Wu, Lehao; Ibrahim, Zuhaib; Lee, WP Andrew; Brandacher, Gerald; Kang, Jin U.

    2014-03-01

    Vascular and microvascular anastomosis are critical components of reconstructive microsurgery, vascular surgery and transplant surgery. Imaging modality that provides immediate, real-time in-depth view and 3D structure and flow information of the surgical site can be a great valuable tool for the surgeon to evaluate surgical outcome following both conventional and innovative anastomosis techniques, thus potentially increase the surgical success rate. Microvascular anastomosis for vessels with outer diameter smaller than 1.0 mm is extremely challenging and effective evaluation of the outcome is very difficult if not impossible using computed tomography (CT) angiograms, magnetic resonance (MR) angiograms and ultrasound Doppler. Optical coherence tomography (OCT) is a non-invasive high-resolution (micron level), high-speed, 3D imaging modality that has been adopted widely in biomedical and clinical applications. Phaseresolved Doppler OCT that explores the phase information of OCT signals has been shown to be capable of characterizing dynamic blood flow clinically. In this work, we explore the capability of Fourier domain Doppler OCT as an evaluation tool to detect commonly encountered post-operative complications that will cause surgical failure and to confirm positive result with surgeon's observation. Both suture and cuff based techniques were evaluated on the femoral artery and vein in the rodent model.

  13. F4 , E6 and G2 exceptional gauge groups in the vacuum domain structure model

    Science.gov (United States)

    Shahlaei, Amir; Rafibakhsh, Shahnoosh

    2018-03-01

    Using a vacuum domain structure model, we calculate trivial static potentials in various representations of F4 , E6, and G2 exceptional groups by means of the unit center element. Due to the absence of the nontrivial center elements, the potential of every representation is screened at far distances. However, the linear part is observed at intermediate quark separations and is investigated by the decomposition of the exceptional group to its maximal subgroups. Comparing the group factor of the supergroup with the corresponding one obtained from the nontrivial center elements of S U (3 ) subgroup shows that S U (3 ) is not the direct cause of temporary confinement in any of the exceptional groups. However, the trivial potential obtained from the group decomposition into the S U (3 ) subgroup is the same as the potential of the supergroup itself. In addition, any regular or singular decomposition into the S U (2 ) subgroup that produces the Cartan generator with the same elements as h1, in any exceptional group, leads to the linear intermediate potential of the exceptional gauge groups. The other S U (2 ) decompositions with the Cartan generator different from h1 are still able to describe the linear potential if the number of S U (2 ) nontrivial center elements that emerge in the decompositions is the same. As a result, it is the center vortices quantized in terms of nontrivial center elements of the S U (2 ) subgroup that give rise to the intermediate confinement in the static potentials.

  14. Feasibility of spatial frequency domain imaging (SFDI) for optically characterizing a preclinical oncology model.

    Science.gov (United States)

    Tabassum, Syeda; Zhao, Yanyu; Istfan, Raeef; Wu, Junjie; Waxman, David J; Roblyer, Darren

    2016-10-01

    Determination of chemotherapy efficacy early during treatment would provide more opportunities for physicians to alter and adapt treatment plans. Diffuse optical technologies may be ideally suited to track early biological events following chemotherapy administration due to low cost and high information content. We evaluated the use of spatial frequency domain imaging (SFDI) to characterize a small animal tumor model in order to move towards the goal of endogenous optical monitoring of cancer therapy in a controlled preclinical setting. The effects of key measurement parameters including the choice of imaging spatial frequency and the repeatability of measurements were evaluated. The precision of SFDI optical property extractions over repeat mouse measurements was determined to be within 3.52% for move and replace experiments. Baseline optical properties and chromophore values as well as intratumor heterogeneity were evaluated over 25 tumors. Additionally, tumor growth and chemotherapy response were monitored over a 45 day longitudinal study in a small number of mice to demonstrate the ability of SFDI to track treatment effects. Optical scattering and oxygen saturation increased as much as 70% and 25% respectively in treated tumors, suggesting SFDI may be useful for preclinical tracking of cancer therapies.

  15. Domain-domain interactions determine the gating, permeation, pharmacology, and subunit modulation of the IKs ion channel.

    Science.gov (United States)

    Zaydman, Mark A; Kasimova, Marina A; McFarland, Kelli; Beller, Zachary; Hou, Panpan; Kinser, Holly E; Liang, Hongwu; Zhang, Guohui; Shi, Jingyi; Tarek, Mounir; Cui, Jianmin

    2014-12-23

    Voltage-gated ion channels generate electrical currents that control muscle contraction, encode neuronal information, and trigger hormonal release. Tissue-specific expression of accessory (β) subunits causes these channels to generate currents with distinct properties. In the heart, KCNQ1 voltage-gated potassium channels coassemble with KCNE1 β-subunits to generate the IKs current (Barhanin et al., 1996; Sanguinetti et al., 1996), an important current for maintenance of stable heart rhythms. KCNE1 significantly modulates the gating, permeation, and pharmacology of KCNQ1 (Wrobel et al., 2012; Sun et al., 2012; Abbott, 2014). These changes are essential for the physiological role of IKs (Silva and Rudy, 2005); however, after 18 years of study, no coherent mechanism explaining how KCNE1 affects KCNQ1 has emerged. Here we provide evidence of such a mechanism, whereby, KCNE1 alters the state-dependent interactions that functionally couple the voltage-sensing domains (VSDs) to the pore.

  16. Operational Details of the Five Domains Model and Its Key Applications to the Assessment and Management of Animal Welfare

    Science.gov (United States)

    Mellor, David J.

    2017-01-01

    Simple Summary The Five Domains Model is a focusing device to facilitate systematic, structured, comprehensive and coherent assessment of animal welfare; it is not a definition of animal welfare, nor is it intended to be an accurate representation of body structure and function. The purpose of each of the five domains is to draw attention to areas that are relevant to both animal welfare assessment and management. This paper begins by briefly describing the major features of the Model and the operational interactions between the five domains, and then it details seven interacting applications of the Model. These underlie its utility and increasing application to welfare assessment and management in diverse animal use sectors. Abstract In accord with contemporary animal welfare science understanding, the Five Domains Model has a significant focus on subjective experiences, known as affects, which collectively contribute to an animal’s overall welfare state. Operationally, the focus of the Model is on the presence or absence of various internal physical/functional states and external circumstances that give rise to welfare-relevant negative and/or positive mental experiences, i.e., affects. The internal states and external circumstances of animals are evaluated systematically by referring to each of the first four domains of the Model, designated “Nutrition”, “Environment”, “Health” and “Behaviour”. Then affects, considered carefully and cautiously to be generated by factors in these domains, are accumulated into the fifth domain, designated “Mental State”. The scientific foundations of this operational procedure, published in detail elsewhere, are described briefly here, and then seven key ways the Model may be applied to the assessment and management of animal welfare are considered. These applications have the following beneficial objectives—they (1) specify key general foci for animal welfare management; (2) highlight the foundations of

  17. Effects of temperature on domain-growth kinetics of fourfold-degenerate (2×1) ordering in Ising models

    DEFF Research Database (Denmark)

    Høst-Madsen, Anders; Shah, Peter Jivan; Hansen, Torben

    1987-01-01

    Computer-simulation techniques are used to study the domain-growth kinetics of (2×1) ordering in a two-dimensional Ising model with nonconserved order parameter and with variable ratio α of next-nearest- and nearest-neighbor interactions. At zero temperature, persistent growth characterized...

  18. Modeling and experimental assessment of a buried Leu–Ile mutation in dengue envelope domain III

    Energy Technology Data Exchange (ETDEWEB)

    Kulkarni, Manjiri R. [Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei-shi, Tokyo, 184-8588 (Japan); Numoto, Nobutaka; Ito, Nobutoshi [Department of Structural Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima Bunkyo-ku, Tokyo, 113-8510 (Japan); Kuroda, Yutaka, E-mail: ykuroda@cc.tuat.ac.jp [Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei-shi, Tokyo, 184-8588 (Japan)

    2016-02-26

    Envelope protein domain III (ED3) of the dengue virus is important for both antibody binding and host cell interaction. Here, we focused on how a L387I mutation in the protein core could take place in DEN4 ED3, but cannot be accommodated in DEN3 ED3 without destabilizing its structure. To this end, we modeled a DEN4-L387I structure using the Penultimate Rotamer Library and taking the DEN4 ED3 main-chain as a fixed template. We found that three out of seven Ile{sup 387} conformers fit in DEN4 ED3 without introducing the severe atomic clashes that are observed when DEN3 serotype’s ED3 is used as a template. A more extensive search using 273 side-chain rotamers of the residues surrounding Ile{sup 387} confirmed this prediction. In order to assess the prediction, we determined the crystal structure of DEN4-L387I at 2 Å resolution. Ile{sup 387} indeed adopted one of the three predicted rotamers. Altogether, this study demonstrates that the effects of single mutations are to a large extent successfully predicted by systematically modeling the side-chain structures of the mutated as well as those of its surrounding residues using fixed main-chain structures and assessing inter-atomic steric clashes. More accurate and reliable predictions require considering sub-angstrom main-chain deformation, which remains a challenging task. - Highlights: • We mutated L387I of DEN4 ED3 and examined its effects on structure and stability. • We modeled the side-chain of Ile{sup 387} using DEN4 ED3's structure as a template. • We determined the crystal structure of DEN4-L387I and confirmed the modeling. • Side-chain repacking occurring around Ile{sup 387} involved >3 inter-connected residues. • These results explained why L387I mutation in DEN4 ED3 conserves thermostability.

  19. Modeling and experimental assessment of a buried Leu–Ile mutation in dengue envelope domain III

    International Nuclear Information System (INIS)

    Kulkarni, Manjiri R.; Numoto, Nobutaka; Ito, Nobutoshi; Kuroda, Yutaka

    2016-01-01

    Envelope protein domain III (ED3) of the dengue virus is important for both antibody binding and host cell interaction. Here, we focused on how a L387I mutation in the protein core could take place in DEN4 ED3, but cannot be accommodated in DEN3 ED3 without destabilizing its structure. To this end, we modeled a DEN4-L387I structure using the Penultimate Rotamer Library and taking the DEN4 ED3 main-chain as a fixed template. We found that three out of seven Ile"3"8"7 conformers fit in DEN4 ED3 without introducing the severe atomic clashes that are observed when DEN3 serotype’s ED3 is used as a template. A more extensive search using 273 side-chain rotamers of the residues surrounding Ile"3"8"7 confirmed this prediction. In order to assess the prediction, we determined the crystal structure of DEN4-L387I at 2 Å resolution. Ile"3"8"7 indeed adopted one of the three predicted rotamers. Altogether, this study demonstrates that the effects of single mutations are to a large extent successfully predicted by systematically modeling the side-chain structures of the mutated as well as those of its surrounding residues using fixed main-chain structures and assessing inter-atomic steric clashes. More accurate and reliable predictions require considering sub-angstrom main-chain deformation, which remains a challenging task. - Highlights: • We mutated L387I of DEN4 ED3 and examined its effects on structure and stability. • We modeled the side-chain of Ile"3"8"7 using DEN4 ED3's structure as a template. • We determined the crystal structure of DEN4-L387I and confirmed the modeling. • Side-chain repacking occurring around Ile"3"8"7 involved >3 inter-connected residues. • These results explained why L387I mutation in DEN4 ED3 conserves thermostability.

  20. Effects of clinically relevant MPL mutations in the transmembrane domain revealed at the atomic level through computational modeling.

    Science.gov (United States)

    Lee, Tai-Sung; Kantarjian, Hagop; Ma, Wanlong; Yeh, Chen-Hsiung; Giles, Francis; Albitar, Maher

    2011-01-01

    Mutations in the thrombopoietin receptor (MPL) may activate relevant pathways and lead to chronic myeloproliferative neoplasms (MPNs). The mechanisms of MPL activation remain elusive because of a lack of experimental structures. Modern computational biology techniques were utilized to explore the mechanisms of MPL protein activation due to various mutations. Transmembrane (TM) domain predictions, homology modeling, ab initio protein structure prediction, and molecular dynamics (MD) simulations were used to build structural dynamic models of wild-type and four clinically observed mutants of MPL. The simulation results suggest that S505 and W515 are important in keeping the TM domain in its correct position within the membrane. Mutations at either of these two positions cause movement of the TM domain, altering the conformation of the nearby intracellular domain in unexpected ways, and may cause the unwanted constitutive activation of MPL's kinase partner, JAK2. Our findings represent the first full-scale molecular dynamics simulations of the wild-type and clinically observed mutants of the MPL protein, a critical element of the MPL-JAK2-STAT signaling pathway. In contrast to usual explanations for the activation mechanism that are based on the relative translational movement between rigid domains of MPL, our results suggest that mutations within the TM region could result in conformational changes including tilt and rotation (azimuthal) angles along the membrane axis. Such changes may significantly alter the conformation of the adjacent and intrinsically flexible intracellular domain. Hence, caution should be exercised when interpreting experimental evidence based on rigid models of cytokine receptors or similar systems.

  1. UPCaD: A Methodology of Integration Between Ontology-Based Context-Awareness Modeling and Relational Domain Data

    Directory of Open Access Journals (Sweden)

    Vinícius Maran

    2018-01-01

    Full Text Available Context-awareness is a key feature for ubiquitous computing scenarios applications. Currently, technologies and methodologies have been proposed for the integration of context-awareness concepts in intelligent information systems to adapt them to the execution of services, user interfaces and data retrieval. Recent research proposed conceptual modeling alternatives to the integration of the domain modeling in RDBMS and context-awareness modeling. The research described using highly expressiveness ontologies. The present work describes the UPCaD (Unified Process for Integration between Context-Awareness and Domain methodology, which is composed of formalisms and processes to guide the data integration considering RDBMS and context modeling. The methodology was evaluated in a virtual learning environment application. The evaluation shows the possibility to use a highly expressive context ontology to filter the relational data query and discusses the main contributions of the methodology compared with recent approaches.

  2. Plasmonic Resonances for Spectroscopy Applications using 3D Finite-Difference Time-Domain Models

    Science.gov (United States)

    Ravi, Aruna

    Tuning plasmonic extinction resonances of sub-wavelength scale structures is essential to achieve maximum sensitivity and accuracy. These resonances can be controlled with careful design of nanoparticle geometries and incident wave attributes. In the first part of this dissertation, plasmonically enhanced effects on hexagonal-arrays of metal nanoparticles, metal-hole arrays (micro-mesh), and linear-arrays of metal nanorings are analyzed using three-dimensional Finite-Difference Time-Domain (3D-FDTD) simulations. The effect of particle size, lattice spacing, and lack of monodispersity of a self-assembled, hexagonal array layer of silver (Ag) nanoparticles on the extinction resonance is investigated to help determine optimal design specifications for efficient organic solar power harvesting. The enhancement of transmission resonances using plasmonic thin metal films with arrays of holes which enable recording of scatter-free infrared (IR) transmission spectra of individual particles is also explored. This method is quantitative, non-destructive and helps in better understanding the interaction of light with sub-wavelength particles. Next, plasmonically enhanced effects on linear arrays of gold (Au) rings are studied. Simulations employing 3D-FDTD can be used to determine the set of geometrical parameters to attain localized surface plasmon resonance (LSPR). The shifts in resonances due to changes in the effective dielectric of the structure are investigated, which is useful in sensing applications. Computational models enrich experimental studies. In the second part of this dissertation, the effect of particle size, shape and orientation on the IR spectra is investigated using 3D-FDTD and Mie-Bruggeman models. This computational analysis is extended to include clusters of particles of mixed composition. The prediction of extinction and absorption spectra of single particles of mixed composition helps in interpreting their physical properties and predict chemical

  3. Magnetic hysteresis at the domain scale of a multi-scale material model for magneto-elastic behaviour

    Energy Technology Data Exchange (ETDEWEB)

    Vanoost, D., E-mail: dries.vanoost@kuleuven-kulak.be [KU Leuven Technology Campus Ostend, ReMI Research Group, Oostende B-8400 (Belgium); KU Leuven Kulak, Wave Propagation and Signal Processing Research Group, Kortrijk B-8500 (Belgium); Steentjes, S. [Institute of Electrical Machines, RWTH Aachen University, Aachen D-52062 (Germany); Peuteman, J. [KU Leuven Technology Campus Ostend, ReMI Research Group, Oostende B-8400 (Belgium); KU Leuven, Department of Electrical Engineering, Electrical Energy and Computer Architecture, Heverlee B-3001 (Belgium); Gielen, G. [KU Leuven, Department of Electrical Engineering, Microelectronics and Sensors, Heverlee B-3001 (Belgium); De Gersem, H. [KU Leuven Kulak, Wave Propagation and Signal Processing Research Group, Kortrijk B-8500 (Belgium); TU Darmstadt, Institut für Theorie Elektromagnetischer Felder, Darmstadt D-64289 (Germany); Pissoort, D. [KU Leuven Technology Campus Ostend, ReMI Research Group, Oostende B-8400 (Belgium); KU Leuven, Department of Electrical Engineering, Microelectronics and Sensors, Heverlee B-3001 (Belgium); Hameyer, K. [Institute of Electrical Machines, RWTH Aachen University, Aachen D-52062 (Germany)

    2016-09-15

    This paper proposes a multi-scale energy-based material model for poly-crystalline materials. Describing the behaviour of poly-crystalline materials at three spatial scales of dominating physical mechanisms allows accounting for the heterogeneity and multi-axiality of the material behaviour. The three spatial scales are the poly-crystalline, grain and domain scale. Together with appropriate scale transitions rules and models for local magnetic behaviour at each scale, the model is able to describe the magneto-elastic behaviour (magnetostriction and hysteresis) at the macroscale, although the data input is merely based on a set of physical constants. Introducing a new energy density function that describes the demagnetisation field, the anhysteretic multi-scale energy-based material model is extended to the hysteretic case. The hysteresis behaviour is included at the domain scale according to the micro-magnetic domain theory while preserving a valid description for the magneto-elastic coupling. The model is verified using existing measurement data for different mechanical stress levels. - Highlights: • A ferromagnetic hysteretic energy-based multi-scale material model is proposed. • The hysteresis is obtained by new proposed hysteresis energy density function. • Avoids tedious parameter identification.

  4. Evaluation of different time domain peak models using extreme learning machine-based peak detection for EEG signal.

    Science.gov (United States)

    Adam, Asrul; Ibrahim, Zuwairie; Mokhtar, Norrima; Shapiai, Mohd Ibrahim; Cumming, Paul; Mubin, Marizan

    2016-01-01

    Various peak models have been introduced to detect and analyze peaks in the time domain analysis of electroencephalogram (EEG) signals. In general, peak model in the time domain analysis consists of a set of signal parameters, such as amplitude, width, and slope. Models including those proposed by Dumpala, Acir, Liu, and Dingle are routinely used to detect peaks in EEG signals acquired in clinical studies of epilepsy or eye blink. The optimal peak model is the most reliable peak detection performance in a particular application. A fair measure of performance of different models requires a common and unbiased platform. In this study, we evaluate the performance of the four different peak models using the extreme learning machine (ELM)-based peak detection algorithm. We found that the Dingle model gave the best performance, with 72 % accuracy in the analysis of real EEG data. Statistical analysis conferred that the Dingle model afforded significantly better mean testing accuracy than did the Acir and Liu models, which were in the range 37-52 %. Meanwhile, the Dingle model has no significant difference compared to Dumpala model.

  5. Application of mixture length turbulence models in the domain of condensation; Application des modeles de turbulence de longueur de melange dans le domaine de la condensation

    Energy Technology Data Exchange (ETDEWEB)

    Louahlia, H.; Panday, P.K. [Institut de Genie Energetique, 90 - Belfort (France)

    1997-12-31

    This paper presents a comparison between turbulence models based on Prandtl theory and applied to the problem of pure fluids condensation. A theoretical model is defined which allows to determine the physical characteristics of condensation between two vertical or horizontal flat plates. The total heat flux exchanged at the wall and the mean Nusselt number are calculated using several closure models in the liquid and vapor phases. Calculation results obtained for the R123 condensation between two vertical plates show that the Pletcher`s model or the Groenwald and Kroeger`s one applied to the vapor flow and the Von Karman`s model used for the liquid film predict thermal fluxes close to the measured ones. It has been noticed also that the condensation heat transfer is underestimated in the laminar model. In the case of the R113 condensation on an horizontal flat plate, the mean Nusselt numbers estimated in the Pletcher`s model applied to both phases are close to the measurements performed by Lu and Suryanarayana. (J.S.) 12 refs.

  6. Semantics-driven modelling of user preferences for information retrieval in the biomedical domain.

    Science.gov (United States)

    Gladun, Anatoly; Rogushina, Julia; Valencia-García, Rafael; Béjar, Rodrigo Martínez

    2013-03-01

    A large amount of biomedical and genomic data are currently available on the Internet. However, data are distributed into heterogeneous biological information sources, with little or even no organization. Semantic technologies provide a consistent and reliable basis with which to confront the challenges involved in the organization, manipulation and visualization of data and knowledge. One of the knowledge representation techniques used in semantic processing is the ontology, which is commonly defined as a formal and explicit specification of a shared conceptualization of a domain of interest. The work presented here introduces a set of interoperable algorithms that can use domain and ontological information to improve information-retrieval processes. This work presents an ontology-based information-retrieval system for the biomedical domain. This system, with which some experiments have been carried out that are described in this paper, is based on the use of domain ontologies for the creation and normalization of lightweight ontologies that represent user preferences in a determined domain in order to improve information-retrieval processes.

  7. Studying behavior of multilayer materials: A 1-D model correlated to magnetic domain walls through complex permeability

    International Nuclear Information System (INIS)

    Ahmadi, B.; Chazal, H.; Waeckerle, T.; Roudet, J.

    2008-01-01

    Multilayer cores are suitable for integrated planar magnetic components. We proposed here to investigate the frequency behavior of multilayer nanocrystalline cores in the frame of a one-dimensional (1-D) electromagnetic propagation model. Electromagnetic wave equations are considered to explain the phenomena from the macroscopic point of view. A domain wall description is considered to take into account non-homogeneity of magnetic media. This mesoscopic model is correlated to macroscopic model through complex permeability. The scope of validity of the model is determined by means of indirect permeability measurement. Finally, the behavior of the multilayer core is predicted by using an equivalent electrical circuit and will interest component designers

  8. Finite-element time-domain modeling of electromagnetic data in general dispersive medium using adaptive Padé series

    Science.gov (United States)

    Cai, Hongzhu; Hu, Xiangyun; Xiong, Bin; Zhdanov, Michael S.

    2017-12-01

    The induced polarization (IP) method has been widely used in geophysical exploration to identify the chargeable targets such as mineral deposits. The inversion of the IP data requires modeling the IP response of 3D dispersive conductive structures. We have developed an edge-based finite-element time-domain (FETD) modeling method to simulate the electromagnetic (EM) fields in 3D dispersive medium. We solve the vector Helmholtz equation for total electric field using the edge-based finite-element method with an unstructured tetrahedral mesh. We adopt the backward propagation Euler method, which is unconditionally stable, with semi-adaptive time stepping for the time domain discretization. We use the direct solver based on a sparse LU decomposition to solve the system of equations. We consider the Cole-Cole model in order to take into account the frequency-dependent conductivity dispersion. The Cole-Cole conductivity model in frequency domain is expanded using a truncated Padé series with adaptive selection of the center frequency of the series for early and late time. This approach can significantly increase the accuracy of FETD modeling.

  9. Dual Phase Lag Model of Melting Process in Domain of Metal Film Subjected to an External Heat Flux

    Directory of Open Access Journals (Sweden)

    Mochnacki B.

    2016-12-01

    Full Text Available Heating process in the domain of thin metal film subjected to a strong laser pulse are discussed. The mathematical model of the process considered is based on the dual-phase-lag equation (DPLE which results from the generalized form of the Fourier law. This approach is, first of all, used in the case of micro-scale heat transfer problems (the extremely short duration, extreme temperature gradients and very small geometrical dimensions of the domain considered. The external heating (a laser action is substituted by the introduction of internal heat source to the DPLE. To model the melting process in domain of pure metal (chromium the approach basing on the artificial mushy zone introduction is used and the main goal of investigation is the verification of influence of the artificial mushy zone ‘width’ on the results of melting modeling. At the stage of numerical modeling the author’s version of the Control Volume Method is used. In the final part of the paper the examples of computations and conclusions are presented.

  10. Aggression and Moral Development: Integrating Social Information Processing and Moral Domain Models

    Science.gov (United States)

    Arsenio, William F.; Lemerise, Elizabeth A.

    2004-01-01

    Social information processing and moral domain theories have developed in relative isolation from each other despite their common focus on intentional harm and victimization, and mutual emphasis on social cognitive processes in explaining aggressive, morally relevant behaviors. This article presents a selective summary of these literatures with…

  11. Mutant Mice Lacking the p53 C-Terminal Domain Model Telomere Syndromes

    NARCIS (Netherlands)

    Simeonova, I.; Jaber, S.; Draskovic, I.; Bardot, B.; Fang, M.; Bouarich-Bourimi, R.; Lejour, V.; Charbonnier, L.; Soudais, C.; Bourdon, J.C.; Huerre, M.; Londono-Vallejo, A.; Toledo, F.

    2013-01-01

    Mutations in p53, although frequent in human cancers, have not been implicated in telomere-related syndromes. Here, we show that homozygous mutant mice expressing p53(Delta31), a p53 lacking the C-terminal domain, exhibit increased p53 activity and suffer from aplastic anemia and pulmonary fibrosis,

  12. Open-geometry Fourier modal method: modeling nanophotonic structures in infinite domains

    DEFF Research Database (Denmark)

    Häyrynen, Teppo; de Lasson, Jakob Rosenkrantz; Gregersen, Niels

    2016-01-01

    We present an open-geometry Fourier modal method based on a new combination of open boundary conditions and an efficient k-space discretization. The open boundary of the computational domain is obtained using basis functions that expand the whole space, and the integrals subsequently appearing due...

  13. The Potato Ontology: Delimitation of the Domain, Modelling Concepts, and Prospects of Performance

    NARCIS (Netherlands)

    Haverkort, A.J.; Top, J.

    2011-01-01

    The ever increasing amount of data gathered by more growers in more years offers possibilities to add value. Therefore—for interested parties and stakeholders—a common and controlled vocabulary of the potato domain that describes concepts, attributes, and the relations between them in a formal way

  14. The Potato Ontology: Delimitation of the Domain, Modelling Concepts, and Prospects of Performance.

    NARCIS (Netherlands)

    Haverkort, A.J.; Top, J.L.

    2011-01-01

    The ever increasing amount of data gathered by more growers in more years offers possibilities to add value. Therefore-for interested parties and stakeholders-a common and controlled vocabulary of the potato domain that describes concepts, attributes, and the relations between them in a formal way

  15. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

    The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studies....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

  16. Domain wall partition function of the eight-vertex model with a non-diagonal reflecting end

    International Nuclear Information System (INIS)

    Yang Wenli; Chen Xi; Feng Jun; Hao Kun; Shi Kangjie; Sun Chengyi; Yang Zhanying; Zhang Yaozhong

    2011-01-01

    With the help of the Drinfeld twist or factorizing F-matrix for the eight-vertex SOS model, we derive the recursion relations of the partition function for the eight-vertex model with a generic non-diagonal reflecting end and domain wall boundary condition. Solving the recursion relations, we obtain the explicit determinant expression of the partition function. Our result shows that, contrary to the eight-vertex model without a reflecting end, the partition function can be expressed as a single determinant.

  17. An extension of the talbot-ogden hydrology model to an affine multi-dimensional moisture content domain

    KAUST Repository

    Yu, Han

    2013-09-01

    The Talbot-Ogden hydrology model provides a fast mass conservative method to compute infiltration in unsaturated soils. As a replacement for a model based on Richards equation, it separates the groundwater movement into infiltration and redistribution for every time step. The typical feature making this method fast is the discretization of the moisture content domain rather than the spatial one. The Talbot-Ogden model rapidly determines how well ground water and aquifers are recharged only. Hence, it differs from models based on advanced reservoir modeling that are uniformly far more expensive computationally since they determine where the water moves in space instead, a completely different and more complex problem.According to the pore-size distribution curve for many soils, this paper extends the one dimensional moisture content domain into a two dimensional one by keeping the vertical spatial axis. The proposed extension can describe any pore-size or porosity distribution as an important soil feature. Based on this extension, infiltration and redistribution are restudied. The unconditional conservation of mass in the Talbot-Ogden model is inherited in this extended model. A numerical example is given for the extended model.

  18. A Model-free Approach to Fault Detection of Continuous-time Systems Based on Time Domain Data

    Institute of Scientific and Technical Information of China (English)

    Ping Zhang; Steven X. Ding

    2007-01-01

    In this paper, a model-free approach is presented to design an observer-based fault detection system of linear continuoustime systems based on input and output data in the time domain. The core of the approach is to directly identify parameters of the observer-based residual generator based on a numerically reliable data equation obtained by filtering and sampling the input and output signals.

  19. The topogenic function of S4 promotes membrane insertion of the voltage-sensor domain in the KvAP channel.

    Science.gov (United States)

    Mishima, Eriko; Sato, Yoko; Nanatani, Kei; Hoshi, Naomi; Lee, Jong-Kook; Schiller, Nina; von Heijne, Gunnar; Sakaguchi, Masao; Uozumi, Nobuyuki

    2016-12-01

    Voltage-dependent K + (K V ) channels control K + permeability in response to shifts in the membrane potential. Voltage sensing in K V channels is mediated by the positively charged transmembrane domain S4. The best-characterized K V channel, KvAP, lacks the distinct hydrophilic region corresponding to the S3-S4 extracellular loop that is found in other K + channels. In the present study, we evaluated the topogenic properties of the transmembrane regions within the voltage-sensing domain in KvAP. S3 had low membrane insertion activity, whereas S4 possessed a unique type-I signal anchor (SA-I) function, which enabled it to insert into the membrane by itself. S4 was also found to function as a stop-transfer signal for retention in the membrane. The length and structural nature of the extracellular S3-S4 loop affected the membrane insertion of S3 and S4, suggesting that S3 membrane insertion was dependent on S4. Replacement of charged residues within the transmembrane regions with residues of opposite charge revealed that Asp 72 in S2 and Glu 93 in S3 contributed to membrane insertion of S3 and S4, and increased the stability of S4 in the membrane. These results indicate that the SA-I function of S4, unique among K + channels studied to date, promotes the insertion of S3 into the membrane, and that the charged residues essential for voltage sensing contribute to the membrane-insertion of the voltage sensor domain in KvAP. © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  20. Time-domain simulation of constitutive relations for nonlinear acoustics including relaxation for frequency power law attenuation media modeling

    Science.gov (United States)

    Jiménez, Noé; Camarena, Francisco; Redondo, Javier; Sánchez-Morcillo, Víctor; Konofagou, Elisa E.

    2015-10-01

    We report a numerical method for solving the constitutive relations of nonlinear acoustics, where multiple relaxation processes are included in a generalized formulation that allows the time-domain numerical solution by an explicit finite differences scheme. Thus, the proposed physical model overcomes the limitations of the one-way Khokhlov-Zabolotskaya-Kuznetsov (KZK) type models and, due to the Lagrangian density is implicitly included in the calculation, the proposed method also overcomes the limitations of Westervelt equation in complex configurations for medical ultrasound. In order to model frequency power law attenuation and dispersion, such as observed in biological media, the relaxation parameters are fitted to both exact frequency power law attenuation/dispersion media and also empirically measured attenuation of a variety of tissues that does not fit an exact power law. Finally, a computational technique based on artificial relaxation is included to correct the non-negligible numerical dispersion of the finite difference scheme, and, on the other hand, improve stability trough artificial attenuation when shock waves are present. This technique avoids the use of high-order finite-differences schemes leading to fast calculations. The present algorithm is especially suited for practical configuration where spatial discontinuities are present in the domain (e.g. axisymmetric domains or zero normal velocity boundary conditions in general). The accuracy of the method is discussed by comparing the proposed simulation solutions to one dimensional analytical and k-space numerical solutions.

  1. Time domain models for damping-controlled fluidelastic instability forces in multi-span tubes with loose supports

    International Nuclear Information System (INIS)

    Hassan, M.A.; Rogers, R.J.; Gerber, A.G.

    2009-01-01

    This paper presents simulations of a loosely supported multi-span tube subjected to turbulence and fluidelastic instability forces. Several time-domain fluid force models simulating the damping controlled fluidelastic instability mechanism in tube arrays have been presented. These models include the negative damping model based on the Connors equation, fluid force coefficient-based models (Chen and Tanaka and Takahara), and two semi-analytical models (Price and Paidoussis; and Lever and Weaver) were implemented in an in-house finite code. Time domain modeling challenges for each of these theories were discussed. The implemented models were validated against available experimental data. The linear simulations showed that the Connors-equation based model exhibits the most conservative prediction of the critical flow velocity when the recommended design values for the Connors equation were used. The models were then utilized to simulate the nonlinear response of a three-span cantilever tube in a square lattice bar support subjected to air crossflow. The tube was subjected to a single-phase flow passing over one of the tube's spans. For each of these models the flow velocity and the support clearance were varied. Special attention was paid to the tube/support interaction parameters that affect wear, such as impact forces, contact ratio, and normal work rate. As the prediction of the linear threshold varies depending on the utilized model, the nonlinear response also differs. The investigated models exhibit similar response characteristics for the impact force, tip lift response, and work rate. Simulation results show that the Connors-based model underestimates the response and the tube/support interaction parameters for the loose support case. (author)

  2. An Enterprise Model for Real-Time Inter-domain Billing of Services

    OpenAIRE

    Le, V.M.; van Beijnum, Bernhard J.F.; Nieuwenhuis, Lambertus Johannes Maria; Huitema, G.B.

    2008-01-01

    The technological developments in networking solutions, information and communication services create the basis for the provisioning of complex, realtime services. This paper addresses the charging and billing of such advanced services. Advanced services will be composed of services provided by various 3rd party providers residing in different domains. Hence, charging and billing of advanced services requires a billing system capable of composing charging and billing information from provider...

  3. Harmonic Domain Modelling of Transformer Core Nonlinearities Using the DIgSILENT PowerFactory Software

    OpenAIRE

    Bak, Claus Leth; Bak-Jensen, Birgitte; Wiechowski, Wojciech

    2008-01-01

    This paper demonstrates the results of implementation and verification of an already existing algorithm that allows for calculating saturation characteristics of singlephase power transformers. The algorithm was described for the first time in 1993. Now this algorithm has been implemented using the DIgSILENT Programming Language (DPL) as an external script in the harmonic domain calculations of a power system analysis tool PowerFactory [10]. The algorithm is verified by harmonic measurements ...

  4. An Ontology-Based Knowledge Modelling for a Sustainability Assessment Domain

    Directory of Open Access Journals (Sweden)

    Agnieszka Konys

    2018-01-01

    Full Text Available Sustainability assessment has received more and more attention from researchers and it offers a large number of opportunities to measure and evaluate the level of its accomplishment. However, proper selection of a particular sustainability assessment approach, reflecting problem properties and the evaluator’s preferences, is a complex and important issue. Due to an existing number of different approaches dedicated to assessing, supporting, or measuring the level of sustainability and their structure oriented on the particular domain usage, problems with accurate matching frequently occur. On the other hand, the efficiency of sustainability assessment depends on the available knowledge of the ongoing capabilities. Additionally, actual research trends confirm that knowledge engineering gives a method to handle domain knowledge practically and effectively. Unfortunately, literature studies confirm that there is a lack of knowledge systematization in the sustainability assessment domain, however. The practical application of knowledge-based mechanisms may cover this gap. In this paper, we provide formal, practical and technological guidance to a knowledge management-based approach to sustainability assessment. We propose ontology as a form of knowledge conceptualization and using knowledge engineering, we make gathered knowledge publicly available and reusable, especially in terms of interoperability of collected knowledge.

  5. Building a patchwork - The yeast plasma membrane as model to study lateral domain formation.

    Science.gov (United States)

    Schuberth, Christian; Wedlich-Söldner, Roland

    2015-04-01

    The plasma membrane (PM) has to fulfill a wide range of biological functions including selective uptake of substances, signal transduction and modulation of cell polarity and cell shape. To allow efficient regulation of these processes many resident proteins and lipids of the PM are laterally segregated into different functional domains. A particularly striking example of lateral segregation has been described for the budding yeast PM, where integral membrane proteins as well as lipids exhibit very slow translational mobility and form a patchwork of many overlapping micron-sized domains. Here we discuss the molecular and physical mechanisms contributing to the formation of a multi-domain membrane and review our current understanding of yeast PM organization. Many of the fundamental principles underlying membrane self-assembly and organization identified in yeast are expected to equally hold true in other organisms, even for the more transient and elusive organization of the PM in mammalian cells. This article is part of a Special Issue entitled: Nanoscale membrane organisation and signalling. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Modeling reactive transport processes in fractured rock using the time domain random walk approach within a dual-porosity framework

    Science.gov (United States)

    Roubinet, D.; Russian, A.; Dentz, M.; Gouze, P.

    2017-12-01

    Characterizing and modeling hydrodynamic reactive transport in fractured rock are critical challenges for various research fields and applications including environmental remediation, geological storage, and energy production. To this end, we consider a recently developed time domain random walk (TDRW) approach, which is adapted to reproduce anomalous transport behaviors and capture heterogeneous structural and physical properties. This method is also very well suited to optimize numerical simulations by memory-shared massive parallelization and provide numerical results at various scales. So far, the TDRW approach has been applied for modeling advective-diffusive transport with mass transfer between mobile and immobile regions and simple (theoretical) reactions in heterogeneous porous media represented as single continuum domains. We extend this approach to dual-continuum representations considering a highly permeable fracture network embedded into a poorly permeable rock matrix with heterogeneous geochemical reactions occurring in both geological structures. The resulting numerical model enables us to extend the range of the modeled heterogeneity scales with an accurate representation of solute transport processes and no assumption on the Fickianity of these processes. The proposed model is compared to existing particle-based methods that are usually used to model reactive transport in fractured rocks assuming a homogeneous surrounding matrix, and is used to evaluate the impact of the matrix heterogeneity on the apparent reaction rates for different 2D and 3D simple-to-complex fracture network configurations.

  7. Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling.

    Science.gov (United States)

    Rizzo, Alessandro A; Suhanovsky, Margaret M; Baker, Matthew L; Fraser, LaTasha C R; Jones, Lisa M; Rempel, Don L; Gross, Michael L; Chiu, Wah; Alexandrescu, Andrei T; Teschke, Carolyn M

    2014-06-10

    Some capsid proteins built on the ubiquitous HK97-fold have accessory domains imparting specific functions. Bacteriophage P22 coat protein has a unique insertion domain (I-domain). Two prior I-domain models from subnanometer cryoelectron microscopy (cryoEM) reconstructions differed substantially. Therefore, the I-domain's nuclear magnetic resonance structure was determined and also used to improve cryoEM models of coat protein. The I-domain has an antiparallel six-stranded β-barrel fold, not previously observed in HK97-fold accessory domains. The D-loop, which is dynamic in the isolated I-domain and intact monomeric coat protein, forms stabilizing salt bridges between adjacent capsomers in procapsids. The S-loop is important for capsid size determination, likely through intrasubunit interactions. Ten of 18 coat protein temperature-sensitive-folding substitutions are in the I-domain, indicating its importance in folding and stability. Several are found on a positively charged face of the β-barrel that anchors the I-domain to a negatively charged surface of the coat protein HK97-core. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Modeling Bidirectional Reflectance Distribution Function of One-dimensional Random Rough Surfaces with the Finite Difference Time Domain Method

    Directory of Open Access Journals (Sweden)

    Min-Jhong Gu

    2014-08-01

    Full Text Available This article describes the development of a suite of programs that is capable of simulating the radiation properties of a random rough surface (RRS. The fundamental approach involves the generation, by fast Fourier transform (FFT built with rigorous finite difference time domain (FDTD, as the theoretical basis for the simulation of a bidirectional reflectance distribution function (BRDF of the RRS. The results are compared with the measurements and modeling of existing work to verify the feasibility of customized programming. It was found that the results of this study were a better match to the measurement data than those achieved in other modeling work.

  9. An efficient realization of frequency dependent boundary conditions in an acoustic finite-difference time-domain model

    DEFF Research Database (Denmark)

    Escolano-Carrasco, José; Jacobsen, Finn; López, J.J.

    2008-01-01

    The finite-difference time-domain (FDTD) method provides a simple and accurate way of solving initial boundary value problems. However, most acoustic problems involve frequency dependent boundary conditions, and it is not easy to include such boundary conditions in an FDTD model. Although solutions...... to this problem exist, most of them have high computational costs, and stability cannot always be ensured. In this work, a solution is proposed based on "mixing modelling strategies"; this involves separating the FDTD mesh and the boundary conditions (a digital filter representation of the impedance...

  10. Development of a Finite-Difference Time Domain (FDTD) Model for Propagation of Transient Sounds in Very Shallow Water.

    Science.gov (United States)

    Sprague, Mark W; Luczkovich, Joseph J

    2016-01-01

    This finite-difference time domain (FDTD) model for sound propagation in very shallow water uses pressure and velocity grids with both 3-dimensional Cartesian and 2-dimensional cylindrical implementations. Parameters, including water and sediment properties, can vary in each dimension. Steady-state and transient signals from discrete and distributed sources, such as the surface of a vibrating pile, can be used. The cylindrical implementation uses less computation but requires axial symmetry. The Cartesian implementation allows asymmetry. FDTD calculations compare well with those of a split-step parabolic equation. Applications include modeling the propagation of individual fish sounds, fish aggregation sounds, and distributed sources.

  11. Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains.

    Science.gov (United States)

    Ron, Gil; Globerson, Yuval; Moran, Dror; Kaplan, Tommy

    2017-12-21

    Proximity-ligation methods such as Hi-C allow us to map physical DNA-DNA interactions along the genome, and reveal its organization into topologically associating domains (TADs). As the Hi-C data accumulate, computational methods were developed for identifying domain borders in multiple cell types and organisms. Here, we present PSYCHIC, a computational approach for analyzing Hi-C data and identifying promoter-enhancer interactions. We use a unified probabilistic model to segment the genome into domains, which we then merge hierarchically and fit using a local background model, allowing us to identify over-represented DNA-DNA interactions across the genome. By analyzing the published Hi-C data sets in human and mouse, we identify hundreds of thousands of putative enhancers and their target genes, and compile an extensive genome-wide catalog of gene regulation in human and mouse. As we show, our predictions are highly enriched for ChIP-seq and DNA accessibility data, evolutionary conservation, eQTLs and other DNA-DNA interaction data.

  12. Co-evolution of intelligent socio-technical systems modelling and applications in large scale emergency and transport domains

    CERN Document Server

    2013-01-01

    As the interconnectivity between humans through technical devices is becoming ubiquitous, the next step is already in the making: ambient intelligence, i.e. smart (technical) environments, which will eventually play the same active role in communication as the human players, leading to a co-evolution in all domains where real-time communication is essential. This topical volume, based on the findings of the Socionical European research project, gives equal attention to two highly relevant domains of applications: transport, specifically traffic, dynamics from the viewpoint of a socio-technical interaction and evacuation scenarios for large-scale emergency situations. Care was taken to investigate as much as possible the limits of scalability and to combine the modeling using complex systems science approaches with relevant data analysis.

  13. The finite element model for the propagation of light in scattering media: a direct method for domains with nonscattering regions.

    Science.gov (United States)

    Arridge, S R; Dehghani, H; Schweiger, M; Okada, E

    2000-01-01

    We present a method for handling nonscattering regions within diffusing domains. The method develops from an iterative radiosity-diffusion approach using Green's functions that was computationally slow. Here we present an improved implementation using a finite element method (FEM) that is direct. The fundamental idea is to introduce extra equations into the standard diffusion FEM to represent nondiffusive light propagation across a nonscattering region. By appropriate mesh node ordering the computational time is not much greater than for diffusion alone. We compare results from this method with those from a discrete ordinate transport code, and with Monte Carlo calculations. The agreement is very good, and, in addition, our scheme allows us to easily model time-dependent and frequency domain problems.

  14. Collective coordinate models of domain wall motion in perpendicularly magnetized systems under the spin hall effect and longitudinal fields

    Energy Technology Data Exchange (ETDEWEB)

    Nasseri, S. Ali, E-mail: ali.nasseri@isi.it [ISI Foundation - Via Alassio 11/c –10126 Torino (Italy); Politecnico di Torino - Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Moretti, Simone; Martinez, Eduardo [University of Salamanca - Cardenal Plá y Deniel, 22, 37008 Salamanca (Spain); Serpico, Claudio [ISI Foundation - Via Alassio 11/c –10126 Torino (Italy); University of Naples Federico II - Via Claudio 21, 80125 Napoli (Italy); Durin, Gianfranco [ISI Foundation - Via Alassio 11/c –10126 Torino (Italy); Istituto Nazionale di Ricerca Metrologica (INRIM) - Strada delle Cacce 91, 10135 Torino (Italy)

    2017-03-15

    Recent studies on heterostructures of ultrathin ferromagnets sandwiched between a heavy metal layer and an oxide have highlighted the importance of spin-orbit coupling (SOC) and broken inversion symmetry in domain wall (DW) motion. Specifically, chiral DWs are stabilized in these systems due to the Dzyaloshinskii-Moriya interaction (DMI). SOC can also lead to enhanced current induced DW motion, with the Spin Hall effect (SHE) suggested as the dominant mechanism for this observation. The efficiency of SHE driven DW motion depends on the internal magnetic structure of the DW, which could be controlled using externally applied longitudinal in-plane fields. In this work, micromagnetic simulations and collective coordinate models are used to study current-driven DW motion under longitudinal in-plane fields in perpendicularly magnetized samples with strong DMI. Several extended collective coordinate models are developed to reproduce the micromagnetic results. While these extended models show improvements over traditional models of this kind, there are still discrepancies between them and micromagnetic simulations which require further work. - Highlights: • Moving DWs in PMA material maintain their structure under longitudinal in-plane fields. • As a result of longitudinal fields, magnetization in the domains becomes canted. • A critical longitudinal field was identified and correlated with the DMI strength. • A canted collective coordinate model was developed for DW motion under in-plane fields.

  15. Modeling growth and dissemination of lymphoma in a co-evolving lymph node: a diffuse-domain approach

    Science.gov (United States)

    Chuang, Yao-Li; Cristini, Vittorio; Chen, Ying; Li, Xiangrong; Frieboes, Hermann; Lowengrub, John

    2013-03-01

    While partial differential equation models of tumor growth have successfully described various spatiotemporal phenomena observed for in-vitro tumor spheroid experiments, one challenge towards taking these models to further study in-vivo tumors is that instead of relatively static tissue culture with regular boundary conditions, in-vivo tumors are often confined in organ tissues that co-evolve with the tumor growth. Here we adopt a recently developed diffuse-domain method to account for the co-evolving domain boundaries, adapting our previous in-vitro tumor model for the development of lymphoma encapsulated in a lymph node, which may swell or shrink due to proliferation and dissemination of lymphoma cells and treatment by chemotherapy. We use the model to study the induced spatial heterogeneity, which may arise as an emerging phenomenon in experimental observations and model analysis. Spatial heterogeneity is believed to lead to tumor infiltration patterns and reduce the efficacy of chemotherapy, leaving residuals that cause cancer relapse after the treatment. Understanding the spatiotemporal evolution of in-vivo tumors can be an essential step towards more effective strategies of curing cancer. Supported by NIH-PSOC grant 1U54CA143907-01.

  16. Concrete domains

    OpenAIRE

    Kahn, G.; Plotkin, G.D.

    1993-01-01

    This paper introduces the theory of a particular kind of computation domains called concrete domains. The purpose of this theory is to find a satisfactory framework for the notions of coroutine computation and sequentiality of evaluation.

  17. Final Technical Report - Integrated Hydrogeophysical and Hydrogeologic Driven Parameter Upscaling for Dual-Domain Transport Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Shafer, John M

    2012-11-05

    The three major components of this research were: 1. Application of minimally invasive, cost effective hydrogeophysical techniques (surface and borehole), to generate fine scale (~1m or less) 3D estimates of subsurface heterogeneity. Heterogeneity is defined as spatial variability in hydraulic conductivity and/or hydrolithologic zones. 2. Integration of the fine scale characterization of hydrogeologic parameters with the hydrogeologic facies to upscale the finer scale assessment of heterogeneity to field scale. 3. Determination of the relationship between dual-domain parameters and practical characterization data.

  18. Multiscale Modeling using Molecular Dynamics and Dual Domain Material Point Method

    Energy Technology Data Exchange (ETDEWEB)

    Dhakal, Tilak Raj [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division. Fluid Dynamics and Solid Mechanics Group, T-3; Rice Univ., Houston, TX (United States)

    2016-07-07

    For problems involving large material deformation rate, the material deformation time scale can be shorter than the material takes to reach a thermodynamical equilibrium. For such problems, it is difficult to obtain a constitutive relation. History dependency become important because of thermodynamic non-equilibrium. Our goal is to build a multi-scale numerical method which can bypass the need for a constitutive relation. In conclusion, multi-scale simulation method is developed based on the dual domain material point (DDMP). Molecular dynamics (MD) simulation is performed to calculate stress. Since the communication among material points is not necessary, the computation can be done embarrassingly parallel in CPU-GPU platform.

  19. Nonlinear wave equation in frequency domain: accurate modeling of ultrafast interaction in anisotropic nonlinear media

    DEFF Research Database (Denmark)

    Guo, Hairun; Zeng, Xianglong; Zhou, Binbin

    2013-01-01

    We interpret the purely spectral forward Maxwell equation with up to third-order induced polarizations for pulse propagation and interactions in quadratic nonlinear crystals. The interpreted equation, also named the nonlinear wave equation in the frequency domain, includes quadratic and cubic...... nonlinearities, delayed Raman effects, and anisotropic nonlinearities. The full potential of this wave equation is demonstrated by investigating simulations of solitons generated in the process of ultrafast cascaded second-harmonic generation. We show that a balance in the soliton delay can be achieved due...

  20. Domain Engineering

    Science.gov (United States)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  1. Source Reconstruction of Brain Potentials Using Bayesian Model Averaging to Analyze Face Intra-Domain vs. Face-Occupation Cross-Domain Processing.

    Science.gov (United States)

    Olivares, Ela I; Lage-Castellanos, Agustín; Bobes, María A; Iglesias, Jaime

    2018-01-01

    We investigated the neural correlates of the access to and retrieval of face structure information in contrast to those concerning the access to and retrieval of person-related verbal information, triggered by faces. We experimentally induced stimulus familiarity via a systematic learning procedure including faces with and without associated verbal information. Then, we recorded event-related potentials (ERPs) in both intra-domain (face-feature) and cross-domain (face-occupation) matching tasks while N400-like responses were elicited by incorrect eyes-eyebrows completions and occupations, respectively. A novel Bayesian source reconstruction approach plus conjunction analysis of group effects revealed that in both cases the generated N170s were of similar amplitude but had different neural origin. Thus, whereas the N170 of faces was associated predominantly to right fusiform and occipital regions (the so-called "Fusiform Face Area", "FFA" and "Occipital Face Area", "OFA", respectively), the N170 of occupations was associated to a bilateral very posterior activity, suggestive of basic perceptual processes. Importantly, the right-sided perceptual P200 and the face-related N250 were evoked exclusively in the intra-domain task, with sources in OFA and extensively in the fusiform region, respectively. Regarding later latencies, the intra-domain N400 seemed to be generated in right posterior brain regions encompassing mainly OFA and, to some extent, the FFA, likely reflecting neural operations triggered by structural incongruities. In turn, the cross-domain N400 was related to more anterior left-sided fusiform and temporal inferior sources, paralleling those described previously for the classic verbal N400. These results support the existence of differentiated neural streams for face structure and person-related verbal processing triggered by faces, which can be activated differentially according to specific task demands.

  2. Source Reconstruction of Brain Potentials Using Bayesian Model Averaging to Analyze Face Intra-Domain vs. Face-Occupation Cross-Domain Processing

    Directory of Open Access Journals (Sweden)

    Ela I. Olivares

    2018-03-01

    Full Text Available We investigated the neural correlates of the access to and retrieval of face structure information in contrast to those concerning the access to and retrieval of person-related verbal information, triggered by faces. We experimentally induced stimulus familiarity via a systematic learning procedure including faces with and without associated verbal information. Then, we recorded event-related potentials (ERPs in both intra-domain (face-feature and cross-domain (face-occupation matching tasks while N400-like responses were elicited by incorrect eyes-eyebrows completions and occupations, respectively. A novel Bayesian source reconstruction approach plus conjunction analysis of group effects revealed that in both cases the generated N170s were of similar amplitude but had different neural origin. Thus, whereas the N170 of faces was associated predominantly to right fusiform and occipital regions (the so-called “Fusiform Face Area”, “FFA” and “Occipital Face Area”, “OFA”, respectively, the N170 of occupations was associated to a bilateral very posterior activity, suggestive of basic perceptual processes. Importantly, the right-sided perceptual P200 and the face-related N250 were evoked exclusively in the intra-domain task, with sources in OFA and extensively in the fusiform region, respectively. Regarding later latencies, the intra-domain N400 seemed to be generated in right posterior brain regions encompassing mainly OFA and, to some extent, the FFA, likely reflecting neural operations triggered by structural incongruities. In turn, the cross-domain N400 was related to more anterior left-sided fusiform and temporal inferior sources, paralleling those described previously for the classic verbal N400. These results support the existence of differentiated neural streams for face structure and person-related verbal processing triggered by faces, which can be activated differentially according to specific task demands.

  3. Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

    Science.gov (United States)

    Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

    2018-04-17

    Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  4. The full Keller-Segel model is well-posed on nonsmooth domains

    Science.gov (United States)

    Horstmann, D.; Meinlschmidt, H.; Rehberg, J.

    2018-04-01

    In this paper we prove that the full Keller-Segel system, a quasilinear strongly coupled reaction-crossdiffusion system of four parabolic equations, is well-posed in the sense that it always admits an unique local-in-time solution in an adequate function space, provided that the initial values are suitably regular. The proof is done via an abstract solution theorem for nonlocal quasilinear equations by Amann and is carried out for general source terms. It is fundamentally based on recent nontrivial elliptic and parabolic regularity results which hold true even on rather general nonsmooth spatial domains. For space dimensions 2 and 3, this enables us to work in a nonsmooth setting which is not available in classical parabolic systems theory. Apparently, there exists no comparable existence result for the full Keller-Segel system up to now. Due to the large class of possibly nonsmooth domains admitted, we also obtain new results for the ‘standard’ Keller-Segel system consisting of only two equations as a special case. This work is dedicated to Prof Willi Jäger.

  5. NMR derived model of GTPase effector domain (GED self association: relevance to dynamin assembly.

    Directory of Open Access Journals (Sweden)

    Swagata Chakraborty

    Full Text Available Self-association of dynamin to form spiral structures around lipidic vesicles during endocytosis is largely mediated by its 'coiled coil' GTPase Effector Domain (GED, which, in vitro, self-associates into huge helical assemblies. Residue-level structural characterizations of these assemblies and understanding the process of association have remained a challenge. It is also impossible to get folded monomers in the solution phase. In this context, we have developed here a strategy to probe the self-association of GED by first dissociating the assembly using Dimethyl Sulfoxide (DMSO and then systematically monitoring the refolding into helix and concomitant re-association using NMR spectroscopy, as DMSO concentration is progressively reduced. The short segment, Arg109 - Met116, acts as the nucleation site for helix formation and self-association. Hydrophobic and complementary charge interactions on the surfaces drive self-association, as the helices elongate in both the directions resulting in an antiparallel stack. A small N-terminal segment remains floppy in the assembly. Following these and other published results on inter-domain interactions, we have proposed a plausible mode of dynamin self assembly.

  6. Model-free methods of analyzing domain motions in proteins from simulation : A comparison of normal mode analysis and molecular dynamics simulation of lysozyme

    NARCIS (Netherlands)

    Hayward, S.; Kitao, A.; Berendsen, H.J.C.

    Model-free methods are introduced to determine quantities pertaining to protein domain motions from normal mode analyses and molecular dynamics simulations, For the normal mode analysis, the methods are based on the assumption that in low frequency modes, domain motions can be well approximated by

  7. Using the Five Domains Model to Assess the Adverse Impacts of Husbandry, Veterinary, and Equitation Interventions on Horse Welfare

    Science.gov (United States)

    McGreevy, Paul; Berger, Jeannine; de Brauwere, Nic; Doherty, Orla; Harrison, Anna; Fiedler, Julie; Jones, Claudia; McDonnell, Sue; McLean, Andrew; Nakonechny, Lindsay; Preshaw, Liane; Tzioumis, Vicky; Webster, John; Wolfensohn, Sarah; Yeates, James; Jones, Bidda

    2018-01-01

    Simple Summary Using an adaptation of the domain-based welfare assessment model, a panel of horse welfare professionals (with professional expertise in psychology, equitation science, veterinary science, education, welfare, equestrian coaching, advocacy, and community engagement) assessed the perceived harms, if any, resulting from 116 interventions that are commonly applied to horses. Scores for Domain 5 (the integrated mental impact) gathered after extensive discussion during a four-day workshop aligned well with overall impact scores assigned by the same panellists individually before the workshop, although some rankings changed after workshop participation. Domain 4 (Behaviour) had the strongest association with Domain 5, whilst Domain 1 (Nutrition) had the weakest association with Domain 5, implying that the panellists considered commonly applied nutritional interventions to have less of a bearing on subjective mental state than commonly applied behavioural restrictions. The workshop defined each intervention, and stated assumptions around each, resulting in a set of exemplar procedures that could be used in future equine welfare assessments. Abstract The aim of this study was to conduct a series of paper-based exercises in order to assess the negative (adverse) welfare impacts, if any, of common interventions on domestic horses across a broad range of different contexts of equine care and training. An international panel (with professional expertise in psychology, equitation science, veterinary science, education, welfare, equestrian coaching, advocacy, and community engagement; n = 16) met over a four-day period to define and assess these interventions, using an adaptation of the domain-based assessment model. The interventions were considered within 14 contexts: C1 Weaning; C2 Diet; C3 Housing; C4 Foundation training; C5 Ill-health and veterinary interventions (chiefly medical); C6 Ill-health and veterinary interventions (chiefly surgical); C7 Elective

  8. Harmonic Domain Modeling of a Distribution System Using the DIgSILENT PowerFactory Software

    OpenAIRE

    Wasilewski, J.; Wiechowski, Wojciech Tomasz; Bak, Claus Leth

    2005-01-01

    The first part of this paper presents the comparison between two models of distribution system created in computer simulation software PowerFactory (PF). Model A is an exciting simplified equivalent model of the distribution system used by Transmission System Operator (TSO) Eltra for balenced load-flow calculation and stability studies. Model B is accurate model of the distribution system created on the basis of the detailed data of the investigated network and is used as a reference. The har...

  9. Time-domain seismic modeling in viscoelastic media for full waveform inversion on heterogeneous computing platforms with OpenCL

    Science.gov (United States)

    Fabien-Ouellet, Gabriel; Gloaguen, Erwan; Giroux, Bernard

    2017-03-01

    Full Waveform Inversion (FWI) aims at recovering the elastic parameters of the Earth by matching recordings of the ground motion with the direct solution of the wave equation. Modeling the wave propagation for realistic scenarios is computationally intensive, which limits the applicability of FWI. The current hardware evolution brings increasing parallel computing power that can speed up the computations in FWI. However, to take advantage of the diversity of parallel architectures presently available, new programming approaches are required. In this work, we explore the use of OpenCL to develop a portable code that can take advantage of the many parallel processor architectures now available. We present a program called SeisCL for 2D and 3D viscoelastic FWI in the time domain. The code computes the forward and adjoint wavefields using finite-difference and outputs the gradient of the misfit function given by the adjoint state method. To demonstrate the code portability on different architectures, the performance of SeisCL is tested on three different devices: Intel CPUs, NVidia GPUs and Intel Xeon PHI. Results show that the use of GPUs with OpenCL can speed up the computations by nearly two orders of magnitudes over a single threaded application on the CPU. Although OpenCL allows code portability, we show that some device-specific optimization is still required to get the best performance out of a specific architecture. Using OpenCL in conjunction with MPI allows the domain decomposition of large models on several devices located on different nodes of a cluster. For large enough models, the speedup of the domain decomposition varies quasi-linearly with the number of devices. Finally, we investigate two different approaches to compute the gradient by the adjoint state method and show the significant advantages of using OpenCL for FWI.

  10. Differential dynamic and structural behavior of lipid-cholesterol domains in model membranes.

    Directory of Open Access Journals (Sweden)

    Luis F Aguilar

    Full Text Available Changes in the cholesterol (Chol content of biological membranes are known to alter the physicochemical properties of the lipid lamella and consequently the function of membrane-associated enzymes. To characterize these changes, we used steady-state and time resolved fluorescence spectroscopy and two photon-excitation microscopy techniques. The membrane systems were chosen according to the techniques that were used: large unilamellar vesicles (LUVs for cuvette and giant unilamellar vesicles (GUVs for microscopy measurements; they were prepared from dipalmitoyl phosphatidylcholine (DPPC and dioctadecyl phosphatidylcholine (DOPC in mixtures that are well known to form lipid domains. Two fluorescent probes, which insert into different regions of the bilayer, were selected: 1,6-diphenyl-1,3,5-hexatriene (DPH was located at the deep hydrophobic core of the acyl chain regions and 2-dimethylamino-6-lauroylnaphthalene (Laurdan at the hydrophilic-hydrophobic membrane interface. Our spectroscopy results show that (i the changes induced by cholesterol in the deep hydrophobic phospholipid acyl chain domain are different from the ones observed in the superficial region of the hydrophilic-hydrophobic interface, and these changes depend on the state of the lamella and (ii the incorporation of cholesterol into the lamella induces an increase in the orientation dynamics in the deep region of the phospholipid acyl chains with a corresponding decrease in the orientation at the region close to the polar lipid headgroups. The microscopy data from DOPC/DPPC/Chol GUVs using Laurdan generalized polarization (Laurdan GP suggest that a high cholesterol content in the bilayer weakens the stability of the water hydrogen bond network and hence the stability of the liquid-ordered phase (Lo.

  11. Image-Based Modeling Reveals Dynamic Redistribution of DNA Damageinto Nuclear Sub-Domains

    Energy Technology Data Exchange (ETDEWEB)

    Costes Sylvain V., Ponomarev Artem, Chen James L.; Nguyen, David; Cucinotta, Francis A.; Barcellos-Hoff, Mary Helen

    2007-08-03

    Several proteins involved in the response to DNA doublestrand breaks (DSB) f orm microscopically visible nuclear domains, orfoci, after exposure to ionizing radiation. Radiation-induced foci (RIF)are believed to be located where DNA damage occurs. To test thisassumption, we analyzed the spatial distribution of 53BP1, phosphorylatedATM, and gammaH2AX RIF in cells irradiated with high linear energytransfer (LET) radiation and low LET. Since energy is randomly depositedalong high-LET particle paths, RIF along these paths should also berandomly distributed. The probability to induce DSB can be derived fromDNA fragment data measured experimentally by pulsed-field gelelectrophoresis. We used this probability in Monte Carlo simulations topredict DSB locations in synthetic nuclei geometrically described by acomplete set of human chromosomes, taking into account microscope opticsfrom real experiments. As expected, simulations produced DNA-weightedrandom (Poisson) distributions. In contrast, the distributions of RIFobtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) werenon-random. This deviation from the expected DNA-weighted random patterncan be further characterized by "relative DNA image measurements." Thisnovel imaging approach shows that RIF were located preferentially at theinterface between high and low DNA density regions, and were morefrequent than predicted in regions with lower DNA density. The samepreferential nuclear location was also measured for RIF induced by 1 Gyof low-LET radiation. This deviation from random behavior was evidentonly 5 min after irradiation for phosphorylated ATM RIF, while gammaH2AXand 53BP1 RIF showed pronounced deviations up to 30 min after exposure.These data suggest that DNA damage induced foci are restricted to certainregions of the nucleus of human epithelial cells. It is possible that DNAlesions are collected in these nuclear sub-domains for more efficientrepair.

  12. Structural modeling of the N-terminal signal–receiving domain of IκBα

    Directory of Open Access Journals (Sweden)

    Samira eYazdi

    2015-06-01

    Full Text Available The transcription factor nuclear factor-κB (NF-κB exerts essential roles in many biological processes including cell growth, apoptosis and innate and adaptive immunity. The NF-kB inhibitor (IκBα retains NF-κB in the cytoplasm and thus inhibits nuclear localization of NF-κB and its association with DNA. Recent protein crystal structures of the C-terminal part of IκBα in complex with NF-κB provided insights into the protein-protein interactions but could not reveal structural details about the N-terminal signal receiving domain (SRD. The SRD of IκBα contains a degron, formed following phosphorylation by IκB kinases (IKK. In current protein X-ray structures, however, the SRD is not resolved and assumed to be disordered. Here, we combined secondary structure annotation and domain threading followed by long molecular dynamics (MD simulations and showed that the SRD possesses well-defined secondary structure elements. We show that the SRD contains 3 additional stable α-helices supplementing the six ARDs present in crystallized IκBα. The IκBα/NF-κB protein-protein complex remained intact and stable during the entire simulations. Also in solution, free IκBα retains its structural integrity. Differences in structural topology and dynamics were observed by comparing the structures of NF-κB free and NF-κB bound IκBα-complex. This study paves the way for investigating the signaling properties of the SRD in the IκBα degron. A detailed atomic scale understanding of molecular mechanism of NF-κB activation, regulation and the protein-protein interactions may assist to design and develop novel chronic inflammation modulators.

  13. Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models

    Science.gov (United States)

    Candy, Adam S.; Pietrzak, Julie D.

    2018-01-01

    The approaches taken to describe and develop spatial discretisations of the domains required for geophysical simulation models are commonly ad hoc, model- or application-specific, and under-documented. This is particularly acute for simulation models that are flexible in their use of multi-scale, anisotropic, fully unstructured meshes where a relatively large number of heterogeneous parameters are required to constrain their full description. As a consequence, it can be difficult to reproduce simulations, to ensure a provenance in model data handling and initialisation, and a challenge to conduct model intercomparisons rigorously. This paper takes a novel approach to spatial discretisation, considering it much like a numerical simulation model problem of its own. It introduces a generalised, extensible, self-documenting approach to carefully describe, and necessarily fully, the constraints over the heterogeneous parameter space that determine how a domain is spatially discretised. This additionally provides a method to accurately record these constraints, using high-level natural language based abstractions that enable full accounts of provenance, sharing, and distribution. Together with this description, a generalised consistent approach to unstructured mesh generation for geophysical models is developed that is automated, robust and repeatable, quick-to-draft, rigorously verified, and consistent with the source data throughout. This interprets the description above to execute a self-consistent spatial discretisation process, which is automatically validated to expected discrete characteristics and metrics. Library code, verification tests, and examples available in the repository at https://github.com/shingleproject/Shingle. Further details of the project presented at http://shingleproject.org.

  14. Frequency-domain optical tomographic image reconstruction algorithm with the simplified spherical harmonics (SP3) light propagation model.

    Science.gov (United States)

    Kim, Hyun Keol; Montejo, Ludguier D; Jia, Jingfei; Hielscher, Andreas H

    2017-06-01

    We introduce here the finite volume formulation of the frequency-domain simplified spherical harmonics model with n -th order absorption coefficients (FD-SP N ) that approximates the frequency-domain equation of radiative transfer (FD-ERT). We then present the FD-SP N based reconstruction algorithm that recovers absorption and scattering coefficients in biological tissue. The FD-SP N model with 3 rd order absorption coefficient (i.e., FD-SP 3 ) is used as a forward model to solve the inverse problem. The FD-SP 3 is discretized with a node-centered finite volume scheme and solved with a restarted generalized minimum residual (GMRES) algorithm. The absorption and scattering coefficients are retrieved using a limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm. Finally, the forward and inverse algorithms are evaluated using numerical phantoms with optical properties and size that mimic small-volume tissue such as finger joints and small animals. The forward results show that the FD-SP 3 model approximates the FD-ERT (S 12 ) solution within relatively high accuracy; the average error in the phase (<3.7%) and the amplitude (<7.1%) of the partial current at the boundary are reported. From the inverse results we find that the absorption and scattering coefficient maps are more accurately reconstructed with the SP 3 model than those with the SP 1 model. Therefore, this work shows that the FD-SP 3 is an efficient model for optical tomographic imaging of small-volume media with non-diffuse properties both in terms of computational time and accuracy as it requires significantly lower CPU time than the FD-ERT (S 12 ) and also it is more accurate than the FD-SP 1 .

  15. Estimation of the domain containing all compact invariant sets of a system modelling the amplitude of a plasma instability

    International Nuclear Information System (INIS)

    Krishchenko, Alexander; Starkov, Konstantin

    2007-01-01

    In this Letter we describe localization results of all compact invariant sets of a system modelling the amplitude of a plasma instability proposed by Pikovski, Rabinovich and Trakhtengerts. We derive ellipsoidal and polytopic localization sets for a number of domains in the 4-dimensional parametrical space of this system. Other localization sets have been obtained by using paraboloids of a revolution, a circular cylinder and an elliptic paraboloid. Our approach is based on the solution of the first order extremum problem. A comparison of our method with the method of semipermeable surfaces is presented as well

  16. Estimation of the domain containing all compact invariant sets of a system modelling the amplitude of a plasma instability

    Energy Technology Data Exchange (ETDEWEB)

    Krishchenko, Alexander [Bauman Moscow State Technical University, 2nd Baumanskaya str., 5, Moscow 105005 (Russian Federation)]. E-mail: apkri@bmstu.ru; Starkov, Konstantin [CITEDI-IPN, Av. del Parque 1310, Mesa de Otay, Tijuana, BC (Mexico)]. E-mail: konst@citedi.mx

    2007-07-16

    In this Letter we describe localization results of all compact invariant sets of a system modelling the amplitude of a plasma instability proposed by Pikovski, Rabinovich and Trakhtengerts. We derive ellipsoidal and polytopic localization sets for a number of domains in the 4-dimensional parametrical space of this system. Other localization sets have been obtained by using paraboloids of a revolution, a circular cylinder and an elliptic paraboloid. Our approach is based on the solution of the first order extremum problem. A comparison of our method with the method of semipermeable surfaces is presented as well.

  17. The framing of scientific domains

    DEFF Research Database (Denmark)

    Dam Christensen, Hans

    2014-01-01

    domains, and UNISIST helps understanding this navigation. Design/methodology/approach The UNISIST models are tentatively applied to the domain of art history at three stages, respectively two modern, partially overlapping domains, as well as an outline of an art historical domain anno c1820...

  18. Development and evaluation of multi-agent models predicting Twitter trends in multiple domains

    NARCIS (Netherlands)

    Attema, T.; Maanen, P.P. van; Meeuwissen, E.

    2015-01-01

    This paper concerns multi-agent models predicting Twitter trends. We use a step-wise approach to develop a novel agent-based model with the following properties: (1) it uses individual behavior parameters for a set of Twitter users and (2) it uses a retweet graph to model the underlying social

  19. Harmonic Domain Modeling of a Distribution System Using the DIgSILENT PowerFactory Software

    DEFF Research Database (Denmark)

    Wasilewski, J.; Wiechowski, Wojciech Tomasz; Bak, Claus Leth

    The first part of this paper presents the comparison between two models of distribution system created in computer simulation software PowerFactory (PF). Model A is an exciting simplified equivalent model of the distribution system used by Transmission System Operator (TSO) Eltra for balenced load...

  20. Preliminary study on performance of a coupled hydrodynamic and sediment transport model on small domain

    Science.gov (United States)

    Rasyif, Teuku M.; Kato, Shigeru; Syamsidik, Okabe, Takumi

    2017-10-01

    Numerical simulation is one of the useful tools to analyze natural phenomena in the earth such as the tsunami disaster. Several numerical models can simulate the tsunami wave from its generation, propagation, and inundation. However, most tsunami models do not include the sediment transport module. The tsunami wave actually induces a lot of sediment during the propagation in the coastal area. In the case of Indian Ocean Tsunami in 2004, massive morphological changes were caused by the tsunami waves around Sumatra coast. In Aceh, some areas eroded by the tsunami wave were living place for a local community. It is indispensable for the resident in the coastal area to estimate the risk of morphological changes due to a tsunami wave. Therefore, a model that can investigate the morphological changes due tsunami wave is necessary. The result of this model can be used to consider a countermeasure for tsunami wave impact in the coastal area, such as land-use management and planning. The COMCOT-SED model had been developed by several researchers. This model combines the hydrodynamic module and the sediment module. The aim of this study is to get general information about performance of the COMCOT-SED model and to modify the model for more accurate results. Firstly, the model was demonstrated in the ideal condition to confirm the model validity. Then, we evaluated the model performance comparing the model results and the laboratory experiment data which was conducted by other researcher. The authors found that the results of water level and bottom profile by the original model in the ideal condition are not suitable. The model modification will give us more suitable results. The modified model will be applied to simulate the tsunami wave and sediment transport in the small area.

  1. Cross-band noise model refinement for transform domain Wyner–Ziv video coding

    DEFF Research Database (Denmark)

    Huang, Xin; Forchhammer, Søren

    2012-01-01

    TDWZ video coding trails that of conventional video coding solutions, mainly due to the quality of side information, inaccurate noise modeling and loss in the final coding step. The major goal of this paper is to enhance the accuracy of the noise modeling, which is one of the most important aspects...... influencing the coding performance of DVC. A TDWZ video decoder with a novel cross-band based adaptive noise model is proposed, and a noise residue refinement scheme is introduced to successively update the estimated noise residue for noise modeling after each bit-plane. Experimental results show...... that the proposed noise model and noise residue refinement scheme can improve the rate-distortion (RD) performance of TDWZ video coding significantly. The quality of the side information modeling is also evaluated by a measure of the ideal code length....

  2. Business Process Modeling for Domain Inbound Logistics System : Analytical Perspective with BPMN 2.0

    OpenAIRE

    Khabbazi, Mahmood Reza; Hasan, M. K; Sulaiman, R; Shapi’i, A

    2013-01-01

    Among different Business Process Management strategies and methodologies, one common feature is to captureexisting processes and representing the new processes adequately. Business Process Modelling (BPM) plays acrucial role on such an effort. This paper proposes a “to-be” inbound logistics business processes model usingBPMN 2.0 standard specifying the structure and behaviour of the system within the SME environment. Thegeneric framework of inbound logistics model consists of one main high-le...

  3. Solving Problems in Various Domains by Hybrid Models of High Performance Computations

    Directory of Open Access Journals (Sweden)

    Yurii Rogozhin

    2014-03-01

    Full Text Available This work presents a hybrid model of high performance computations. The model is based on membrane system (P~system where some membranes may contain quantum device that is triggered by the data entering the membrane. This model is supposed to take advantages of both biomolecular and quantum paradigms and to overcome some of their inherent limitations. The proposed approach is demonstrated through two selected problems: SAT, and image retrieving.

  4. Modeling of VSC-Based Power Systems in The Extended Harmonic Domain

    DEFF Research Database (Denmark)

    Esparza, Miguel; Segundo-Ramirez, Juan; Kwon, Jun Bum

    2017-01-01

    Averaged modeling is a commonly used approach used to obtain mathematical representations of VSC-based systems. However, essential characteristics mainly related to the modulation process and the harmonic distortion of the signals are not able to be accurately captured and analyzed. The extended ...... on simulations and experimental case studies. The obtained results show that the resulting EHD models are accurate and reliable, while the memory and computation time are improved with the proposed model order reductions....

  5. Spatial frequency domain imaging of burn wounds in a preclinical model of graded burn severity

    Science.gov (United States)

    Nguyen, John Quan; Crouzet, Christian; Mai, Tuan; Riola, Kathleen; Uchitel, Daniel; Liaw, Lih-Huei; Bernal, Nicole; Ponticorvo, Adrien; Choi, Bernard; Durkin, Anthony J.

    2013-06-01

    Frequent monitoring of early-stage burns is necessary for deciding optimal treatment and management. Both superficial and full thickness burns are relatively easy to diagnose based on clinical observation. In between these two extremes are superficial-partial thickness and deep-partial thickness burns. These burns, while visually similar, differ dramatically in terms of clinical treatment and are known to progress in severity over time. The objective of this study was to determine the potential of spatial frequency domain imaging (SFDI) for noninvasively mapping quantitative changes in chromophore and optical properties that may be an indicative of burn wound severity. A controlled protocol of graded burn severity was developed and applied to 17 rats. SFDI data was acquired at multiple near-infrared wavelengths over a course of 3 h. Burn severity was verified using hematoxylin and eosin histology. From this study, we found that changes in water concentration (edema), deoxygenated hemoglobin concentration, and optical scattering (tissue denaturation) to be statistically significant at differentiating superficial partial-thickness burns from deep-partial thickness burns.

  6. Persistent junk solutions in time-domain modeling of extreme mass ratio binaries

    International Nuclear Information System (INIS)

    Field, Scott E.; Hesthaven, Jan S.; Lau, Stephen R.

    2010-01-01

    In the context of metric perturbation theory for nonspinning black holes, extreme mass ratio binary systems are described by distributionally forced master wave equations. Numerical solution of a master wave equation as an initial boundary value problem requires initial data. However, because the correct initial data for generic-orbit systems is unknown, specification of trivial initial data is a common choice, despite being inconsistent and resulting in a solution which is initially discontinuous in time. As is well known, this choice leads to a burst of junk radiation which eventually propagates off the computational domain. We observe another potential consequence of trivial initial data: development of a persistent spurious solution, here referred to as the Jost junk solution, which contaminates the physical solution for long times. This work studies the influence of both types of junk on metric perturbations, waveforms, and self-force measurements, and it demonstrates that smooth modified source terms mollify the Jost solution and reduce junk radiation. Our concluding section discusses the applicability of these observations to other numerical schemes and techniques used to solve distributionally forced master wave equations.

  7. Mutant Mice Lacking the p53 C-Terminal Domain Model Telomere Syndromes

    Directory of Open Access Journals (Sweden)

    Iva Simeonova

    2013-06-01

    Full Text Available Mutations in p53, although frequent in human cancers, have not been implicated in telomere-related syndromes. Here, we show that homozygous mutant mice expressing p53Δ31, a p53 lacking the C-terminal domain, exhibit increased p53 activity and suffer from aplastic anemia and pulmonary fibrosis, hallmarks of syndromes caused by short telomeres. Indeed, p53Δ31/Δ31 mice had short telomeres and other phenotypic traits associated with the telomere disease dyskeratosis congenita and its severe variant the Hoyeraal-Hreidarsson syndrome. Heterozygous p53+/Δ31 mice were only mildly affected, but decreased levels of Mdm4, a negative regulator of p53, led to a dramatic aggravation of their symptoms. Importantly, several genes involved in telomere metabolism were downregulated in p53Δ31/Δ31 cells, including Dyskerin, Rtel1, and Tinf2, which are mutated in dyskeratosis congenita, and Terf1, which is implicated in aplastic anemia. Together, these data reveal that a truncating mutation can activate p53 and that p53 plays a major role in the regulation of telomere metabolism.

  8. The Tofts model in frequency domain: fast and robust determination of pharmacokinetic maps for dynamic contrast enhancement MRI

    Science.gov (United States)

    Vajuvalli, Nithin N.; Chikkemenahally, Dharmendra Kumar K.; Nayak, Krupa N.; Bhosale, Manoj G.; Geethanath, Sairam

    2016-12-01

    Dynamic contrast enhancement magnetic resonance imaging (DCE-MRI) is a well-established method for non-invasive detection and therapeutic monitoring of pathologies through administration of intravenous contrast agent. Quantification of pharmacokinetic (PK) maps can be achieved through application of compartmental models relevant to the pathophysiology of the tissue under interrogation. The determination of PK parameters involves fitting of time-concentration data to these models. In this work, the Tofts model in frequency domain (TM-FD) is applied to a weakly vascularized tissue such as the breast. It is derived as a convolution-free model from the conventional Tofts model in the time domain (TM-TD). This reduces the dimensionality of the curve-fitting problem from two to one. The approaches of TM-FD and TM-TD were applied to two kinds of in silico phantoms and six in vivo breast DCE data sets with and without the addition of noise. The results showed that computational time taken to estimate PK maps using TM-FD was 16-25% less than with TM-TD. Normalized root mean square error (NRMSE) calculation and Pearson correlation analyses were performed to validate robustness and accuracy of the TM-FD and TM-TD approaches. These compared with ground truth values in the case of phantom studies for four different temporal resolutions. Results showed that NRMSE values for TM-FD were significantly lower than those of TM-TD as validated by a paired t-test along with reduced computational time. This approach therefore enables online evaluation of PK maps by radiologists in a clinical setting, aiding in the evaluation of 3D and/or increased coverage of the tissue of interest.

  9. Predicting the multi-domain progression of Parkinson's disease: a Bayesian multivariate generalized linear mixed-effect model.

    Science.gov (United States)

    Wang, Ming; Li, Zheng; Lee, Eun Young; Lewis, Mechelle M; Zhang, Lijun; Sterling, Nicholas W; Wagner, Daymond; Eslinger, Paul; Du, Guangwei; Huang, Xuemei

    2017-09-25

    It is challenging for current statistical models to predict clinical progression of Parkinson's disease (PD) because of the involvement of multi-domains and longitudinal data. Past univariate longitudinal or multivariate analyses from cross-sectional trials have limited power to predict individual outcomes or a single moment. The multivariate generalized linear mixed-effect model (GLMM) under the Bayesian framework was proposed to study multi-domain longitudinal outcomes obtained at baseline, 18-, and 36-month. The outcomes included motor, non-motor, and postural instability scores from the MDS-UPDRS, and demographic and standardized clinical data were utilized as covariates. The dynamic prediction was performed for both internal and external subjects using the samples from the posterior distributions of the parameter estimates and random effects, and also the predictive accuracy was evaluated based on the root of mean square error (RMSE), absolute bias (AB) and the area under the receiver operating characteristic (ROC) curve. First, our prediction model identified clinical data that were differentially associated with motor, non-motor, and postural stability scores. Second, the predictive accuracy of our model for the training data was assessed, and improved prediction was gained in particularly for non-motor (RMSE and AB: 2.89 and 2.20) compared to univariate analysis (RMSE and AB: 3.04 and 2.35). Third, the individual-level predictions of longitudinal trajectories for the testing data were performed, with ~80% observed values falling within the 95% credible intervals. Multivariate general mixed models hold promise to predict clinical progression of individual outcomes in PD. The data was obtained from Dr. Xuemei Huang's NIH grant R01 NS060722 , part of NINDS PD Biomarker Program (PDBP). All data was entered within 24 h of collection to the Data Management Repository (DMR), which is publically available ( https://pdbp.ninds.nih.gov/data-management ).

  10. Using the Five Domains Model to Assess the Adverse Impacts of Husbandry, Veterinary, and Equitation Interventions on Horse Welfare.

    Science.gov (United States)

    McGreevy, Paul; Berger, Jeannine; de Brauwere, Nic; Doherty, Orla; Harrison, Anna; Fiedler, Julie; Jones, Claudia; McDonnell, Sue; McLean, Andrew; Nakonechny, Lindsay; Nicol, Christine; Preshaw, Liane; Thomson, Peter; Tzioumis, Vicky; Webster, John; Wolfensohn, Sarah; Yeates, James; Jones, Bidda

    2018-03-18

    The aim of this study was to conduct a series of paper-based exercises in order to assess the negative (adverse) welfare impacts, if any, of common interventions on domestic horses across a broad range of different contexts of equine care and training. An international panel (with professional expertise in psychology, equitation science, veterinary science, education, welfare, equestrian coaching, advocacy, and community engagement; n = 16) met over a four-day period to define and assess these interventions, using an adaptation of the domain-based assessment model. The interventions were considered within 14 contexts: C1 Weaning; C2 Diet; C3 Housing; C4 Foundation training; C5 Ill-health and veterinary interventions (chiefly medical); C6 Ill-health and veterinary interventions (chiefly surgical); C7 Elective procedures; C8 Care procedures; C9 Restraint for management procedures; C10 Road transport; C11 Activity-competition; C12 Activity-work; C13 Activity-breeding females; and C14 Activity-breeding males. Scores on a 1-10 scale for Domain 5 (the mental domain) gathered during the workshop were compared with overall impact scores on a 1-10 scale assigned by the same panellists individually before the workshop. The most severe (median and interquartile range, IQR) impacts within each context were identified during the workshop as: C1 abrupt, individual weaning (10 IQR 1); C2 feeding 100% low-energy concentrate (8 IQR 2.5); C3 indoor tie stalls with no social contact (9 IQR 1.5); C4 both (i) dropping horse with ropes (9 IQR 0.5) and forced flexion (9 IQR 0.5); C5 long-term curative medical treatments (8 IQR 3); C6 major deep intracavity surgery (8.5 IQR 1); C7 castration without veterinary supervision (10 IQR 1); C8 both (i) tongue ties (8 IQR 2.5) and (ii) restrictive nosebands (8 IQR 2.5); C9 ear twitch (8 IQR 1); C10 both (i) individual transport (7.00 IQR 1.5) and group transport with unfamiliar companions (7 IQR 1.5); C11 both (i) jumps racing (8 IQR 2.5) and

  11. Using the Five Domains Model to Assess the Adverse Impacts of Husbandry, Veterinary, and Equitation Interventions on Horse Welfare

    Directory of Open Access Journals (Sweden)

    Paul McGreevy

    2018-03-01

    Full Text Available The aim of this study was to conduct a series of paper-based exercises in order to assess the negative (adverse welfare impacts, if any, of common interventions on domestic horses across a broad range of different contexts of equine care and training. An international panel (with professional expertise in psychology, equitation science, veterinary science, education, welfare, equestrian coaching, advocacy, and community engagement; n = 16 met over a four-day period to define and assess these interventions, using an adaptation of the domain-based assessment model. The interventions were considered within 14 contexts: C1 Weaning; C2 Diet; C3 Housing; C4 Foundation training; C5 Ill-health and veterinary interventions (chiefly medical; C6 Ill-health and veterinary interventions (chiefly surgical; C7 Elective procedures; C8 Care procedures; C9 Restraint for management procedures; C10 Road transport; C11 Activity—competition; C12 Activity—work; C13 Activity—breeding females; and C14 Activity—breeding males. Scores on a 1–10 scale for Domain 5 (the mental domain gathered during the workshop were compared with overall impact scores on a 1–10 scale assigned by the same panellists individually before the workshop. The most severe (median and interquartile range, IQR impacts within each context were identified during the workshop as: C1 abrupt, individual weaning (10 IQR 1; C2 feeding 100% low-energy concentrate (8 IQR 2.5; C3 indoor tie stalls with no social contact (9 IQR 1.5; C4 both (i dropping horse with ropes (9 IQR 0.5 and forced flexion (9 IQR 0.5; C5 long-term curative medical treatments (8 IQR 3; C6 major deep intracavity surgery (8.5 IQR 1; C7 castration without veterinary supervision (10 IQR 1; C8 both (i tongue ties (8 IQR 2.5 and (ii restrictive nosebands (8 IQR 2.5; C9 ear twitch (8 IQR 1; C10 both (i individual transport (7.00 IQR 1.5 and group transport with unfamiliar companions (7 IQR 1.5; C11 both (i jumps racing (8 IQR 2

  12. Exploring inter-frame correlation analysis and wavelet-domain modeling for real-time caption detection in streaming video

    Science.gov (United States)

    Li, Jia; Tian, Yonghong; Gao, Wen

    2008-01-01

    In recent years, the amount of streaming video has grown rapidly on the Web. Often, retrieving these streaming videos offers the challenge of indexing and analyzing the media in real time because the streams must be treated as effectively infinite in length, thus precluding offline processing. Generally speaking, captions are important semantic clues for video indexing and retrieval. However, existing caption detection methods often have difficulties to make real-time detection for streaming video, and few of them concern on the differentiation of captions from scene texts and scrolling texts. In general, these texts have different roles in streaming video retrieval. To overcome these difficulties, this paper proposes a novel approach which explores the inter-frame correlation analysis and wavelet-domain modeling for real-time caption detection in streaming video. In our approach, the inter-frame correlation information is used to distinguish caption texts from scene texts and scrolling texts. Moreover, wavelet-domain Generalized Gaussian Models (GGMs) are utilized to automatically remove non-text regions from each frame and only keep caption regions for further processing. Experiment results show that our approach is able to offer real-time caption detection with high recall and low false alarm rate, and also can effectively discern caption texts from the other texts even in low resolutions.

  13. Gating transitions in the selectivity filter region of a sodium channel are coupled to the domain IV voltage sensor.

    Science.gov (United States)

    Capes, Deborah L; Arcisio-Miranda, Manoel; Jarecki, Brian W; French, Robert J; Chanda, Baron

    2012-02-14

    Voltage-dependent ion channels are crucial for generation and propagation of electrical activity in biological systems. The primary mechanism for voltage transduction in these proteins involves the movement of a voltage-sensing domain (D), which opens a gate located on the cytoplasmic side. A distinct conformational change in the selectivity filter near the extracellular side has been implicated in slow inactivation gating, which is important for spike frequency adaptation in neural circuits. However, it remains an open question whether gating transitions in the selectivity filter region are also actuated by voltage sensors. Here, we examine conformational coupling between each of the four voltage sensors and the outer pore of a eukaryotic voltage-dependent sodium channel. The voltage sensors of these sodium channels are not structurally symmetric and exhibit functional specialization. To track the conformational rearrangements of individual voltage-sensing domains, we recorded domain-specific gating pore currents. Our data show that, of the four voltage sensors, only the domain IV voltage sensor is coupled to the conformation of the selectivity filter region of the sodium channel. Trapping the outer pore in a particular conformation with a high-affinity toxin or disulphide crossbridge impedes the return of this voltage sensor to its resting conformation. Our findings directly establish that, in addition to the canonical electromechanical coupling between voltage sensor and inner pore gates of a sodium channel, gating transitions in the selectivity filter region are also coupled to the movement of a voltage sensor. Furthermore, our results also imply that the voltage sensor of domain IV is unique in this linkage and in the ability to initiate slow inactivation in sodium channels.

  14. Seismic wavefield modeling based on time-domain symplectic and Fourier finite-difference method

    Science.gov (United States)

    Fang, Gang; Ba, Jing; Liu, Xin-xin; Zhu, Kun; Liu, Guo-Chang

    2017-06-01

    Seismic wavefield modeling is important for improving seismic data processing and interpretation. Calculations of wavefield propagation are sometimes not stable when forward modeling of seismic wave uses large time steps for long times. Based on the Hamiltonian expression of the acoustic wave equation, we propose a structure-preserving method for seismic wavefield modeling by applying the symplectic finite-difference method on time grids and the Fourier finite-difference method on space grids to solve the acoustic wave equation. The proposed method is called the symplectic Fourier finite-difference (symplectic FFD) method, and offers high computational accuracy and improves the computational stability. Using acoustic approximation, we extend the method to anisotropic media. We discuss the calculations in the symplectic FFD method for seismic wavefield modeling of isotropic and anisotropic media, and use the BP salt model and BP TTI model to test the proposed method. The numerical examples suggest that the proposed method can be used in seismic modeling of strongly variable velocities, offering high computational accuracy and low numerical dispersion. The symplectic FFD method overcomes the residual qSV wave of seismic modeling in anisotropic media and maintains the stability of the wavefield propagation for large time steps.

  15. Modeling management information systems’ success: a study in the domain of further education and training

    CSIR Research Space (South Africa)

    Visser, M

    2012-10-01

    Full Text Available was applied in a survey at one public FET college to evaluate the success of the MIS deployed at the college. Findings from the survey lead to the refinement of the model which is also articulated in this paper and reflected as the SAFETMIS model. The paper...

  16. A Comprehensive Web-based Platform For Domain-Specific Biological Models

    Czech Academy of Sciences Publication Activity Database

    Klement, M.; Šafránek, D.; Děd, J.; Pejznoch, A.; Nedbal, Ladislav; Steuer, Ralf; Červený, Jan; Müller, Stefan

    2013-01-01

    Roč. 299, 25 Dec (2013), s. 61-67 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * simulation * database Subject RIV: EH - Ecology, Behaviour

  17. Fractional cable equation models for anomalous electrodiffusion in nerve cells: infinite domain solutions.

    Science.gov (United States)

    Langlands, T A M; Henry, B I; Wearne, S L

    2009-12-01

    We introduce fractional Nernst-Planck equations and derive fractional cable equations as macroscopic models for electrodiffusion of ions in nerve cells when molecular diffusion is anomalous subdiffusion due to binding, crowding or trapping. The anomalous subdiffusion is modelled by replacing diffusion constants with time dependent operators parameterized by fractional order exponents. Solutions are obtained as functions of the scaling parameters for infinite cables and semi-infinite cables with instantaneous current injections. Voltage attenuation along dendrites in response to alpha function synaptic inputs is computed. Action potential firing rates are also derived based on simple integrate and fire versions of the models. Our results show that electrotonic properties and firing rates of nerve cells are altered by anomalous subdiffusion in these models. We have suggested electrophysiological experiments to calibrate and validate the models.

  18. On two-point boundary correlations in the six-vertex model with domain wall boundary conditions

    Science.gov (United States)

    Colomo, F.; Pronko, A. G.

    2005-05-01

    The six-vertex model with domain wall boundary conditions on an N × N square lattice is considered. The two-point correlation function describing the probability of having two vertices in a given state at opposite (top and bottom) boundaries of the lattice is calculated. It is shown that this two-point boundary correlator is expressible in a very simple way in terms of the one-point boundary correlators of the model on N × N and (N - 1) × (N - 1) lattices. In alternating sign matrix (ASM) language this result implies that the doubly refined x-enumerations of ASMs are just appropriate combinations of the singly refined ones.

  19. Staggered-grid finite-difference acoustic modeling with the Time-Domain Atmospheric Acoustic Propagation Suite (TDAAPS).

    Energy Technology Data Exchange (ETDEWEB)

    Aldridge, David Franklin; Collier, Sandra L. (U.S. Army Research Laboratory); Marlin, David H. (U.S. Army Research Laboratory); Ostashev, Vladimir E. (NOAA/Environmental Technology Laboratory); Symons, Neill Phillip; Wilson, D. Keith (U.S. Army Cold Regions Research Engineering Lab.)

    2005-05-01

    This document is intended to serve as a users guide for the time-domain atmospheric acoustic propagation suite (TDAAPS) program developed as part of the Department of Defense High-Performance Modernization Office (HPCMP) Common High-Performance Computing Scalable Software Initiative (CHSSI). TDAAPS performs staggered-grid finite-difference modeling of the acoustic velocity-pressure system with the incorporation of spatially inhomogeneous winds. Wherever practical the control structure of the codes are written in C++ using an object oriented design. Sections of code where a large number of calculations are required are written in C or F77 in order to enable better compiler optimization of these sections. The TDAAPS program conforms to a UNIX style calling interface. Most of the actions of the codes are controlled by adding flags to the invoking command line. This document presents a large number of examples and provides new users with the necessary background to perform acoustic modeling with TDAAPS.

  20. Development of the Real Time Situation Identification Model for Adaptive Service Support in Vehicular Communication Networks Domain

    Directory of Open Access Journals (Sweden)

    Mindaugas Kurmis

    2013-01-01

    Full Text Available The article discusses analyses and assesses the key proposals how to deal with the situation identification for the heterogeneous service support in vehicular cooperation environment. This is one of the most important topics of the pervasive computing. Without the solution it is impossible to adequately respond to the user's needs and to provide needed services in the right place at the right moment and in the right way. In this work we present our developed real time situation identification model for adaptive service support in vehicular communication networks domain. Our solution is different from the others as it uses additional virtual context information source - information from other vehicles which for our knowledge is not addressed in the past. The simulation results show the promising context exchange rate between vehicles. The other vehicles provided additional context source in our developed model helps to increase situations identification level.

  1. Heritage house maintenance using 3D city model application domain extension approach

    DEFF Research Database (Denmark)

    Mohd, Zulaikha Hana; Ujang, Uznir; Choon, Tan Liat

    2017-01-01

    leakage and exfoliation of wall. One of the initiatives for maintaining and documenting this heritage house is through Three-dimensional (3D) of technology. 3D city models are widely used now and much used by researchers for management and analysis. CityGML is a standard tool that usually used...... by researchers to exchange, storing and managing virtual 3D city models either geometric and semantic information. Moreover, it also represent multi-scale of 3D model in five level of details (LoDs) whereby each of level give a distinctive functions. The extension of CityGML was recently introduced and can...

  2. Design of broadband time-domain impedance boundary conditions using the oscillatory-diffusive representation of acoustical models.

    Science.gov (United States)

    Monteghetti, Florian; Matignon, Denis; Piot, Estelle; Pascal, Lucas

    2016-09-01

    A methodology to design broadband time-domain impedance boundary conditions (TDIBCs) from the analysis of acoustical models is presented. The derived TDIBCs are recast exclusively as first-order differential equations, well-suited for high-order numerical simulations. Broadband approximations are yielded from an elementary linear least squares optimization that is, for most models, independent of the absorbing material geometry. This methodology relies on a mathematical technique referred to as the oscillatory-diffusive (or poles and cuts) representation, and is applied to a wide range of acoustical models, drawn from duct acoustics and outdoor sound propagation, which covers perforates, semi-infinite ground layers, as well as cavities filled with a porous medium. It is shown that each of these impedance models leads to a different TDIBC. Comparison with existing numerical models, such as multi-pole or extended Helmholtz resonator, provides insights into their suitability. Additionally, the broadly-applicable fractional polynomial impedance models are analyzed using fractional calculus.

  3. Modeling Malicious Domain Name Take-down Dynamics: Why eCrime Pays

    Science.gov (United States)

    2014-04-01

    of take-down measures per unit of resources devoted. It is estimable by observa- tion, in principle . Block listing has been observed to be reasonably...6). The lack of non-technical aspects would be most important to the model in (6), so here this modeling choice is most acutely felt. In principle ...Wilkins company, 1925. [6] J. Henderson and R. Quandt, Microeconomic the- ory: A mathematical approach. McGraw-Hill New York, third ed., 1980. [7] T

  4. Domain Modeling and Application Development of an Archetype- and XML-based EHRS. Practical Experiences and Lessons Learnt.

    Science.gov (United States)

    Kropf, Stefan; Chalopin, Claire; Lindner, Dirk; Denecke, Kerstin

    2017-06-28

    Access to patient data within the hospital or between hospitals is still problematic since a variety of information systems is in use applying different vendor specific terminologies and underlying knowledge models. Beyond, the development of electronic health record systems (EHRSs) is time and resource consuming. Thus, there is a substantial need for a development strategy of standardized EHRSs. We are applying a reuse-oriented process model and demonstrate its feasibility and realization on a practical medical use case, which is an EHRS holding all relevant data arising in the context of treatment of tumors of the sella region. In this paper, we describe the development process and our practical experiences. Requirements towards the development of the EHRS were collected by interviews with a neurosurgeon and patient data analysis. For modelling of patient data, we selected openEHR as standard and exploited the software tools provided by the openEHR foundation. The patient information model forms the core of the development process, which comprises the EHR generation and the implementation of an EHRS architecture. Moreover, a reuse-oriented process model from the business domain was adapted to the development of the EHRS. The reuse-oriented process model is a model for a suitable abstraction of both, modeling and development of an EHR centralized EHRS. The information modeling process resulted in 18 archetypes that were aggregated in a template and built the boilerplate of the model driven development. The EHRs and the EHRS were developed by openEHR and W3C standards, tightly supported by well-established XML techniques. The GUI of the final EHRS integrates and visualizes information from various examinations, medical reports, findings and laboratory test results. We conclude that the development of a standardized overarching EHR and an EHRS is feasible using openEHR and W3C standards, enabling a high degree of semantic interoperability. The standardized

  5. Evaluation of precipitation extremes over the Asian domain: observation and modelling studies

    Science.gov (United States)

    Kim, In-Won; Oh, Jaiho; Woo, Sumin; Kripalani, R. H.

    2018-04-01

    In this study, a comparison in the precipitation extremes as exhibited by the seven reference datasets is made to ascertain whether the inferences based on these datasets agree or they differ. These seven datasets, roughly grouped in three categories i.e. rain-gauge based (APHRODITE, CPC-UNI), satellite-based (TRMM, GPCP1DD) and reanalysis based (ERA-Interim, MERRA, and JRA55), having a common data period 1998-2007 are considered. Focus is to examine precipitation extremes in the summer monsoon rainfall over South Asia, East Asia and Southeast Asia. Measures of extreme precipitation include the percentile thresholds, frequency of extreme precipitation events and other quantities. Results reveal that the differences in displaying extremes among the datasets are small over South Asia and East Asia but large differences among the datasets are displayed over the Southeast Asian region including the maritime continent. Furthermore, precipitation data appear to be more consistent over East Asia among the seven datasets. Decadal trends in extreme precipitation are consistent with known results over South and East Asia. No trends in extreme precipitation events are exhibited over Southeast Asia. Outputs of the Coupled Model Intercomparison Project Phase 5 (CMIP5) simulation data are categorized as high, medium and low-resolution models. The regions displaying maximum intensity of extreme precipitation appear to be dependent on model resolution. High-resolution models simulate maximum intensity of extreme precipitation over the Indian sub-continent, medium-resolution models over northeast India and South China and the low-resolution models over Bangladesh, Myanmar and Thailand. In summary, there are differences in displaying extreme precipitation statistics among the seven datasets considered here and among the 29 CMIP5 model data outputs.

  6. HIGHLY-ACCURATE MODEL ORDER REDUCTION TECHNIQUE ON A DISCRETE DOMAIN

    Directory of Open Access Journals (Sweden)

    L. D. Ribeiro

    2015-09-01

    Full Text Available AbstractIn this work, we present a highly-accurate technique of model order reduction applied to staged processes. The proposed method reduces the dimension of the original system based on null values of moment-weighted sums of heat and mass balance residuals on real stages. To compute these sums of weighted residuals, a discrete form of Gauss-Lobatto quadrature was developed, allowing a high degree of accuracy in these calculations. The locations where the residuals are cancelled vary with time and operating conditions, characterizing a desirable adaptive nature of this technique. Balances related to upstream and downstream devices (such as condenser, reboiler, and feed tray of a distillation column are considered as boundary conditions of the corresponding difference-differential equations system. The chosen number of moments is the dimension of the reduced model being much lower than the dimension of the complete model and does not depend on the size of the original model. Scaling of the discrete independent variable related with the stages was crucial for the computational implementation of the proposed method, avoiding accumulation of round-off errors present even in low-degree polynomial approximations in the original discrete variable. Dynamical simulations of distillation columns were carried out to check the performance of the proposed model order reduction technique. The obtained results show the superiority of the proposed procedure in comparison with the orthogonal collocation method.

  7. Intercomparison of IPCC AR4 models with ERA-40 and NCEP/NCAR reanalysis within the AFRICA-CORDEX domain

    Science.gov (United States)

    León, M.; González, Y.; Díaz, J. P.; Expósito, F. J.; Pérez, J. C.; González, A.

    2012-04-01

    One of the most useful techniques to obtain regional climate projections along the XXI century is to run a mesoscale model driven by coarse input data (initial and boundaries conditions) obtained from Atmosphere-Ocean coupled Global Circulation Models (AOGCM). This is the dynamical downscaling approach. To correctly configure the dynamical downscaling approach it is necessary to choose the correct input dataset that project the climatic situation in a more accurate way and to establish a boundary to the errors in the results associated to these input data. In this study, we consider that the agreement of models with present observations is a way to assign confidence to the quality of a model. With this aim we intercompare the surface temperature of 21 IPCC AR4 runs models with the results from the reanalysis databases ERA40 and NCEP/NCAR in the CORDEX-AFRICA domain in the period 1961-2000. Thus, we have studied the seasonal cycles of the four decades of this period in addition to the probability density functions (PDFs) of the IPCC models. The statistical study allows us to classify the IPCC AR4 models according to their discrepancies with reanalysis data for the CORDEX domain. In general, the MRI CGCM 2.3.2 IPCC AR4 model presents the best fits compared with the reanalysis databases regarding to the correlation factor, root mean square (rms) and PDF skill score. For the intercomparison with ERA-40, the percentage of points with rms lower than 2°C is over 80%, for the four decades; with 89% of the points showing correlations coefficients larger than 0.80 and a 76 % of the data presents skill-scores values, based on the common areas of the PDFs, above a threshold of 0.7. Acknowledgements The authors acknowledge to the MEC (Ministry of Education and Science, Spain) for the next supports: projects CGL2007-66477-C02-02/CLI, CGL2008-04740/CLI, CGL2010-21366-C04-01 and UNLL08-3E-007.

  8. Informing groundwater model hydrostratigraphy with airborne time-domain electromagnetic data and borehole logs

    DEFF Research Database (Denmark)

    Marker, Pernille Aabye; Bauer-Gottwein, Peter; Mosegaard, Klaus

    lithological information directly into groundwater models is proposed. The approach builds on a clay-fraction inversion which is a spatially variable translation of resistivity values from EM data into clay-fraction values using borehole lithological information. Hydrostratigraphical units are obtained through...... a k-means cluster analysis of the principal components of resistivity and clay-fraction values. Under the assumption that the units have uniform hydrological properties, the units constitute the hydrostratigraphy for a groundwater model. Only aquifer structures are obtained from geophysical...... and lithological data, while the estimation of the hydrological properties of the units is inversely derived from the groundwater model and hydrological data. A synthetic analysis was performed to investigate the principles underlying the clustering approach using three petrophysical relationships between...

  9. Modeling induced polarization effects in helicopter time domain electromagnetic data: Synthetic case studies

    DEFF Research Database (Denmark)

    Viezzoli, Andrea; Kaminskiy, Vladislav; Fiandaca, Gianluca

    2017-01-01

    constrained multiparametric inversion was evaluated, including recovery of chargeability distributions from shallow and deep targets based on analysis of induced polarization (IP) effects, simulated in airborne TDEM data. Different scenarios were studied, including chargeable targets associated...... processing and the effect of constraints, and a priori information. We have used a 1D layered earth model approximation and lateral constraints. Synthetic simulations were performed for several models and the corresponding Cole-Cole parameters. The possibility to recover these models by means of laterally...... the airborne electromagnetic is most sensitive (e.g., approximately 1 ms), it is possible to recover deep chargeable targets (to depths more than 130 m) in association with high electrical conductivity and in resistive environments. Furthermore, it was found that the recovery of a deep conductor, masked...

  10. Wave propagation numerical models in damage detection based on the time domain spectral element method

    International Nuclear Information System (INIS)

    Ostachowicz, W; Kudela, P

    2010-01-01

    A Spectral Element Method is used for wave propagation modelling. A 3D solid spectral element is derived with shape functions based on Lagrange interpolation and Gauss-Lobatto-Legendre points. This approach is applied for displacement approximation suited for fundamental modes of Lamb waves as well as potential distribution in piezoelectric transducers. The novelty is the model geometry extension from flat to curved elements for application in shell-like structures. Exemplary visualisations of waves excited by the piezoelectric transducers in curved shell structure made of aluminium alloy are presented. Simple signal analysis of wave interaction with crack is performed. The crack is modelled by separation of appropriate nodes between elements. An investigation of influence of the crack length on wave propagation signals is performed. Additionally, some aspects of the spectral element method implementation are discussed.

  11. Embedding complex hydrology in the regional climate system – Dynamic coupling across different modelling domains

    DEFF Research Database (Denmark)

    Butts, Michael; Drews, Martin; Larsen, Morten Andreas Dahl

    2014-01-01

    the atmosphere and the groundwater via the land surface and can represent the lateral movement of water in both the surface and subsurface and their interactions, not normally accounted for in climate models. Meso-scale processes are important for climate in general and rainfall in particular. Hydrological......To improve our understanding of the impacts of feedback between the atmosphere and the terrestrial water cycle including groundwater and to improve the integration of water resource management modelling for climate adaption we have developed a dynamically coupled climate–hydrological modelling...... impacts are assessed at the catchment scale, the most important scale for water management. Feedback between groundwater, the land surface and the atmosphere occurs across a range of scales. Recognising this, the coupling was developed to allow dynamic exchange of water and energy at the catchment scale...

  12. Frequency Domain Modeling and Simulation of DC Power Electronic Systems Using Harmonic State Space Method

    DEFF Research Database (Denmark)

    Kwon, Jun Bum; Wang, Xiongfei; Blaabjerg, Frede

    2017-01-01

    For the efficiency and simplicity of electric systems, the dc power electronic systems are widely used in a variety of applications such as electric vehicles, ships, aircraft and also in homes. In these systems, there could be a number of dynamic interactions and frequency coupling between network...... with different switching frequency or harmonics from ac-dc converters makes that harmonics and frequency coupling are both problems of ac system and challenges of dc system. This paper presents a modeling and simulation method for a large dc power electronic system by using Harmonic State Space (HSS) modeling...

  13. A Cross-Domain Survey of Metrics for Modelling and Evaluating Collisions

    Directory of Open Access Journals (Sweden)

    Jeremy A. Marvel

    2014-09-01

    Full Text Available This paper provides a brief survey of the metrics for measuring probability, degree, and severity of collisions as applied to autonomous and intelligent systems. Though not exhaustive, this survey evaluates the state-of-the-art of collision metrics, and assesses which are likely to aid in the establishment and support of autonomous system collision modelling. The survey includes metrics for 1 robot arms; 2 mobile robot platforms; 3 nonholonomic physical systems such as ground vehicles, aircraft, and naval vessels, and; 4 virtual and mathematical models.

  14. A high-order multiscale finite-element method for time-domain acoustic-wave modeling

    Science.gov (United States)

    Gao, Kai; Fu, Shubin; Chung, Eric T.

    2018-05-01

    Accurate and efficient wave equation modeling is vital for many applications in such as acoustics, electromagnetics, and seismology. However, solving the wave equation in large-scale and highly heterogeneous models is usually computationally expensive because the computational cost is directly proportional to the number of grids in the model. We develop a novel high-order multiscale finite-element method to reduce the computational cost of time-domain acoustic-wave equation numerical modeling by solving the wave equation on a coarse mesh based on the multiscale finite-element theory. In contrast to existing multiscale finite-element methods that use only first-order multiscale basis functions, our new method constructs high-order multiscale basis functions from local elliptic problems which are closely related to the Gauss-Lobatto-Legendre quadrature points in a coarse element. Essentially, these basis functions are not only determined by the order of Legendre polynomials, but also by local medium properties, and therefore can effectively convey the fine-scale information to the coarse-scale solution with high-order accuracy. Numerical tests show that our method can significantly reduce the computation time while maintain high accuracy for wave equation modeling in highly heterogeneous media by solving the corresponding discrete system only on the coarse mesh with the new high-order multiscale basis functions.

  15. Poisson-Gaussian Noise Reduction Using the Hidden Markov Model in Contourlet Domain for Fluorescence Microscopy Images

    Science.gov (United States)

    Yang, Sejung; Lee, Byung-Uk

    2015-01-01

    In certain image acquisitions processes, like in fluorescence microscopy or astronomy, only a limited number of photons can be collected due to various physical constraints. The resulting images suffer from signal dependent noise, which can be modeled as a Poisson distribution, and a low signal-to-noise ratio. However, the majority of research on noise reduction algorithms focuses on signal independent Gaussian noise. In this paper, we model noise as a combination of Poisson and Gaussian probability distributions to construct a more accurate model and adopt the contourlet transform which provides a sparse representation of the directional components in images. We also apply hidden Markov models with a framework that neatly describes the spatial and interscale dependencies which are the properties of transformation coefficients of natural images. In this paper, an effective denoising algorithm for Poisson-Gaussian noise is proposed using the contourlet transform, hidden Markov models and noise estimation in the transform domain. We supplement the algorithm by cycle spinning and Wiener filtering for further improvements. We finally show experimental results with simulations and fluorescence microscopy images which demonstrate the improved performance of the proposed approach. PMID:26352138

  16. Genomic, RNAseq, and Molecular Modeling Evidence Suggests That the Major Allergen Domain in Insects Evolved from a Homodimeric Origin

    Science.gov (United States)

    Randall, Thomas A.; Perera, Lalith; London, Robert E.; Mueller, Geoffrey A.

    2013-01-01

    The major allergen domain (MA) is widely distributed in insects. The crystal structure of a single Bla g 1 MA revealed a novel protein fold in which the fundamental structure was a duplex of two subsequences (monomers), which had diverged over time. This suggested that the evolutionary origin of the MA structure may have been a homodimer of this smaller subsequence. Using publicly available genomic data, the distribution of the basic unit of this class of proteins was determined to better understand its evolutionary history. The duplication and divergence is examined at three distinct levels of resolution: 1) within the orders Diptera and Hymenoptera, 2) within one genus Drosophila, and 3) within one species Aedes aegypti. Within the family Culicidae, we have found two separate occurrences of monomers as independent genes. The organization of the gene family in A. aegypti shows a common evolutionary origin for its monomer and several closely related MAs. Molecular modeling of the A. aegypti monomer with the unique Bla g 1 fold confirms the distant evolutionary relationship and supports the feasibility of homodimer formation from a single monomer. RNAseq data for A. aegypti confirms that the monomer is expressed in the mosquito similar to other A. aegypti MAs after a blood meal. Together, these data support the contention that the detected monomer shares similar functional characteristics to related MAs in other insects. An extensive search for this domain outside of Insecta confirms that the MAs are restricted to insects. PMID:24253356

  17. Knowledge, Skills and Competence Modelling in Nuclear Engineering Domain using Singular Value Decomposition (SVD) and Latent Semantic Analysis (LSA)

    International Nuclear Information System (INIS)

    Kuo, V.

    2016-01-01

    Full text: The European Qualifications Framework categorizes learning objectives into three qualifiers “knowledge”, “skills”, and “competences” (KSCs) to help improve the comparability between different fields and disciplines. However, the management of KSCs remains a great challenge given their semantic fuzziness. Similar texts may describe different concepts and different texts may describe similar concepts among different domains. This is difficult for the indexing, searching and matching of semantically similar KSCs within an information system, to facilitate transfer and mobility of KSCs. We present a working example using a semantic inference method known as Latent Semantic Analysis, employing a matrix operation called Singular Value Decomposition, which have been shown to infer semantic associations within unstructured textual data comparable to that of human interpretations. In our example, a few natural language text passages representing KSCs in the nuclear sector are used to demonstrate the capabilities of the system. It can be shown that LSA is able to infer latent semantic associations between texts, and cluster and match separate text passages semantically based on these associations. We propose this methodology for modelling existing natural language KSCs in the nuclear domain so they can be semantically queried, retrieved and filtered upon request. (author

  18. Detailed Equivalent VSC-HVDC Modelling for Time Domain Harmonic Stability Studies in Wind Power Plants

    DEFF Research Database (Denmark)

    Glasdam, Jakob Bærholm; Bak, Claus Leth; Kocewiak, Lukasz Hubert

    2018-01-01

    system with 201 voltage levels, without loss of accuracy compared to conventional modelling of the converter. Harmonic stability is a core concern for both existing and future offshore wind power plants (OWPPs). A harmonic stability study will be undertaken with focus on the number of wind turbine...

  19. Improving the process of process modelling by the use of domain process patterns

    NARCIS (Netherlands)

    Koschmider, A.; Reijers, H.A.

    2015-01-01

    The use of business process models has become prevalent in a wide area of enterprise applications. But while their popularity is expanding, concerns are growing with respect to their proper creation and maintenance. An obvious way to boost the efficiency of creating high-quality business process

  20. Analytic Models of Domain-Averaged Fermi Holes: A New Tool for the

    Czech Academy of Sciences Publication Activity Database

    Ponec, Robert; Cooper, D.L.; Savin, A.

    2008-01-01

    Roč. 14, č. 11 (2008), s. 3338-3345 ISSN 0947-6539 R&D Projects: GA AV ČR(CZ) IAA4072403 Institutional research plan: CEZ:AV0Z40720504 Keywords : bond theory * fermi hole analysis * lewis model Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.454, year: 2008

  1. Domain Models of "The Market" - In Preparation for E-Commerce

    DEFF Research Database (Denmark)

    Bjørner, Dines

    2003-01-01

    An analysis is presented, in the form both of an informal narrative and a formal model of "The Market" of buyers and sellers, agents, brokers and traders - who inquire about products and services, issue quotations, orders, delivers, receives, accepts, invoices, pays, rejects, returns and gets ref...

  2. Towards a time-domain modeling framework for small-signal analysis of unbalanced microgrids

    OpenAIRE

    Ojo, Y; Schiffer, JF

    2017-01-01

    Small-signal analysis is one of the most frequently used techniques to assess the operating conditions of power systems. Typically, this analysis is conducted by employing a phasor-based model of the power network derived under the assumption of balanced operating conditions. However, distribution networks and, amongst these, microgrids are often unbalanced. Hence, their analysis requires the development of tools and methods valid under such conditions. Motivated by this, we propose a modelin...

  3. A Business Intelligence Model to Predict Bankruptcy using Financial Domain Ontology with Association Rule Mining Algorithm

    OpenAIRE

    Martin, A.; Manjula, M.; Venkatesan, Dr. V. Prasanna

    2011-01-01

    Today in every organization financial analysis provides the basis for understanding and evaluating the results of business operations and delivering how well a business is doing. This means that the organizations can control the operational activities primarily related to corporate finance. One way that doing this is by analysis of bankruptcy prediction. This paper develops an ontological model from financial information of an organization by analyzing the Semantics of the financial statement...

  4. Assimilation of Spatially Sparse In Situ Soil Moisture Networks into a Continuous Model Domain

    Science.gov (United States)

    Gruber, A.; Crow, W. T.; Dorigo, W. A.

    2018-02-01

    Growth in the availability of near-real-time soil moisture observations from ground-based networks has spurred interest in the assimilation of these observations into land surface models via a two-dimensional data assimilation system. However, the design of such systems is currently hampered by our ignorance concerning the spatial structure of error afflicting ground and model-based soil moisture estimates. Here we apply newly developed triple collocation techniques to provide the spatial error information required to fully parameterize a two-dimensional (2-D) data assimilation system designed to assimilate spatially sparse observations acquired from existing ground-based soil moisture networks into a spatially continuous Antecedent Precipitation Index (API) model for operational agricultural drought monitoring. Over the contiguous United States (CONUS), the posterior uncertainty of surface soil moisture estimates associated with this 2-D system is compared to that obtained from the 1-D assimilation of remote sensing retrievals to assess the value of ground-based observations to constrain a surface soil moisture analysis. Results demonstrate that a fourfold increase in existing CONUS ground station density is needed for ground network observations to provide a level of skill comparable to that provided by existing satellite-based surface soil moisture retrievals.

  5. HERITAGE HOUSE MAINTENANCE USING 3D CITY MODEL APPLICATION DOMAIN EXTENSION APPROACH

    Directory of Open Access Journals (Sweden)

    Z. H. Mohd

    2017-11-01

    Full Text Available Heritage house is part of the architectural heritage of Malaysia that highly valued. Many efforts by the Department of Heritage to preserve this heritage house such as monitoring the damage problems of heritage house. The damage problems of heritage house might be caused by wooden decay, roof leakage and exfoliation of wall. One of the initiatives for maintaining and documenting this heritage house is through Three-dimensional (3D of technology. 3D city models are widely used now and much used by researchers for management and analysis. CityGML is a standard tool that usually used by researchers to exchange, storing and managing virtual 3D city models either geometric and semantic information. Moreover, it also represent multi-scale of 3D model in five level of details (LoDs whereby each of level give a distinctive functions. The extension of CityGML was recently introduced and can be used for problems monitoring and the number of habitants of a house.

  6. Geospatial Database for Strata Objects Based on Land Administration Domain Model (ladm)

    Science.gov (United States)

    Nasorudin, N. N.; Hassan, M. I.; Zulkifli, N. A.; Rahman, A. Abdul

    2016-09-01

    Recently in our country, the construction of buildings become more complex and it seems that strata objects database becomes more important in registering the real world as people now own and use multilevel of spaces. Furthermore, strata title was increasingly important and need to be well-managed. LADM is a standard model for land administration and it allows integrated 2D and 3D representation of spatial units. LADM also known as ISO 19152. The aim of this paper is to develop a strata objects database using LADM. This paper discusses the current 2D geospatial database and needs for 3D geospatial database in future. This paper also attempts to develop a strata objects database using a standard data model (LADM) and to analyze the developed strata objects database using LADM data model. The current cadastre system in Malaysia includes the strata title is discussed in this paper. The problems in the 2D geospatial database were listed and the needs for 3D geospatial database in future also is discussed. The processes to design a strata objects database are conceptual, logical and physical database design. The strata objects database will allow us to find the information on both non-spatial and spatial strata title information thus shows the location of the strata unit. This development of strata objects database may help to handle the strata title and information.

  7. Conserved Domain Database (CDD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins.

  8. The CPAT 2.0.2 Domain Model - How CPAT 2.0.2 "Thinks" From an Analyst Perspective.

    Energy Technology Data Exchange (ETDEWEB)

    Waddell, Lucas [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Muldoon, Frank [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Melander, Darryl J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Backlund, Peter [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Henry, Stephen Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hoffman, Matthew John [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Zwerneman, April Marie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lawton, Craig R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Rice, Roy Eugene [Teledyne Brown Engineering, Huntsville, AL (United States)

    2017-09-01

    To help effectively plan the management and modernization of their large and diverse fleets of vehicles, the Program Executive Office Ground Combat Systems (PEO GCS) and the Program Executive Office Combat Support and Combat Service Support (PEO CS &CSS) commissioned the development of a large - scale portfolio planning optimization tool. This software, the Capability Portfolio Analysis Tool (CPAT), creates a detailed schedule that optimally prioritizes the modernization or replacement of vehicles within the fleet - respecting numerous business rules associated with fleet structure, budgets, industrial base, research and testing, etc., while maximizing overall fleet performance through time. This report contains a description of the organizational fleet structure and a thorough explanation of the business rules that the CPAT formulation follows involving performance, scheduling, production, and budgets. This report, which is an update to the original CPAT domain model published in 2015 (SAND2015 - 4009), covers important new CPAT features. This page intentionally left blank

  9. Sparkling feather reflections of a bird-of-paradise explained by finite-difference time-domain modeling.

    Science.gov (United States)

    Wilts, Bodo D; Michielsen, Kristel; De Raedt, Hans; Stavenga, Doekele G

    2014-03-25

    Birds-of-paradise are nature's prime examples of the evolution of color by sexual selection. Their brilliant, structurally colored feathers play a principal role in mating displays. The structural coloration of both the occipital and breast feathers of the bird-of-paradise Lawes' parotia is produced by melanin rodlets arranged in layers, together acting as interference reflectors. Light reflection by the silvery colored occipital feathers is unidirectional as in a classical multilayer, but the reflection by the richly colored breast feathers is three-directional and extraordinarily complex. Here we show that the reflection properties of both feather types can be quantitatively explained by finite-difference time-domain modeling using realistic feather anatomies and experimentally determined refractive index dispersion values of keratin and melanin. The results elucidate the interplay between avian coloration and vision and indicate tuning of the mating displays to the spectral properties of the avian visual system.

  10. Model-Based Development and Evaluation of Control for Complex Multi-Domain Systems

    DEFF Research Database (Denmark)

    Grujic, Ivan; Nilsson, Rene

    A Cyber-Physical System (CPS) incorporates sensing, actuating, computing and communicative capabilities, which are often combined to control the system. The development of CPSs poses a challenge, since the complexity of the physical system dynamics must be taken into account when designing...... Unmanned Aerial Vehicle (UAV) has been constructed and used to develop an attitude controller based on Model Predictive Control (MPC). The MPC controller has been compared to an existing open source Proportional Integral Derivative (PID) attitude controller. This thesis contributes to the discipline...

  11. Exponential attractors for a Cahn-Hilliard model in bounded domains with permeable walls

    Directory of Open Access Journals (Sweden)

    Ciprian G. Gal

    2006-11-01

    Full Text Available In a previous article [7], we proposed a model of phase separation in a binary mixture confined to a bounded region which may be contained within porous walls. The boundary conditions were derived from a mass conservation law and variational methods. In the present paper, we study the problem further. Using a Faedo-Galerkin method, we obtain the existence and uniqueness of a global solution to our problem, under more general assumptions than those in [7]. We then study its asymptotic behavior and prove the existence of an exponential attractor (and thus of a global attractor with finite dimension.

  12. Finite difference time domain modeling of light matter interaction in light-propelled microtools

    DEFF Research Database (Denmark)

    Bañas, Andrew Rafael; Palima, Darwin; Aabo, Thomas

    2013-01-01

    save time as it helps optimize the structures prior to fabrication and experiments. In addition to field distributions, optical forces can also be obtained using the Maxwell stress tensor formulation. By calculating the forces on bent waveguides subjected to tailored static light distributions, we...... may trigger highly localized non linear processes in the surface of a cell. Since these functionalities are strongly dependent on design, it is important to use models that can handle complexities and take in little simplifying assumptions about the system. Hence, we use the finite difference time...

  13. Modeling Turkey National 2D Geo-Data Model as a CityGML Application Domain Extension in UML

    Directory of Open Access Journals (Sweden)

    Serpil Ates Aydar

    2016-12-01

    Full Text Available This paper presents the generation of the 3D national geo-data model of Turkey, which is compatible with the international OGC CityGML Encoding Standard. We prepare an ADE named CityGML-TRKBIS that is produced by extending existing thematic modules of CityGML according to TRKBIS needs. All thematic data groups in TRKBIS geo-data model have been remodeled in order to generate the national large scale 3D geodata model for Turkey. Within the concept of reference model-driven framework for modelling CityGML ADEs in UML, the first step is conceptual mapping between CityGML and national information model. To test all stages of the framework for Urban GIS Turkey, Building data theme is mapped with CityGML-Building thematic model. All classes, attributes, code lists and code list values of the TRKBIS is tried to be mapped with related CityGML concept. New classes, attributes and code list values that will be added to CityGML Building model are determined based on this conceptual mapping. Finally the new model for CityGML-TRKBIS.BI is established in UML with subclassing of the related CityGML classes. This study provides new insights into 3D applications in Turkey. The generated 3D geo-data model for building thematic class will be used as a common exchange format that meets 2D, 2.5D and 3D implementation needs at national level.

  14. Modeling distortion of HIT by an Actuator Disk in a periodic domain

    Science.gov (United States)

    Ghate, Aditya; Ghaisas, Niranjan; Lele, Sanjiva

    2017-11-01

    We study the distortion of incompressible, homogeneous isotropic turbulence (HIT) by a dragging actuator disk with a fixed thrust coefficient (under the large Reynolds number limit), using Large Eddy Simulation (LES). The HIT inflow is tailored to ensure that the largest length scales in the flow are smaller than the actuator disk diameter in order to minimize the meandering of the turbulent wake and isolate the length scales that undergo distortion. The numerical scheme (Fourier collocation with dealiasing) and the SGS closure (anisotropic minimum dissipation model) are carefully selected to minimize numerical artifacts expected due to the inviscid assumption. The LES is used to characterize the following 3 properties of the flow a) distortion of HIT due to the expanding streamtube resulting in strong anisotropy, b) turbulent pressure modulation across the actuator disk, and the c) turbulent wake state. Finally, we attempt to model the initial distortion and the pressure modulation using a WKB variant of RDT solved numerically using a set of discrete Gabor modes. Funding provided by Precourt Institute for Energy at Stanford University.

  15. Sensitivity study of heavy precipitation in Limited Area Model climate simulations: influence of the size of the domain and the use of the spectral nudging technique

    Science.gov (United States)

    Colin, Jeanne; Déqué, Michel; Radu, Raluca; Somot, Samuel

    2010-10-01

    We assess the impact of two sources of uncertainties in a limited area model (LAM) on the representation of intense precipitation: the size of the domain of integration and the use of the spectral nudging technique (driving of the large-scale within the domain of integration). We work in a perfect-model approach where the LAM is driven by a general circulation model (GCM) run at the same resolution and sharing the same physics and dynamics as the LAM. A set of three 50 km resolution simulations run over Western Europe with the LAM ALADIN-Climate and the GCM ARPEGE-Climate are performed to address this issue. Results are consistent with previous studies regarding the seasonal-mean fields. Furthermore, they show that neither the use of the spectral nudging nor the choice of a small domain are detrimental to the modelling of heavy precipitation in the present experiment.

  16. Structural models of zebrafish (Danio rerio NOD1 and NOD2 NACHT domains suggest differential ATP binding orientations: insights from computational modeling, docking and molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Jitendra Maharana

    Full Text Available Nucleotide-binding oligomerization domain-containing protein 1 (NOD1 and NOD2 are cytosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively and undergoes conformational alternation and ATP-dependent self-oligomerization of NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT domain confines our understanding about the NOD-mediated signaling mechanism. Here, we predicted the structure of NACHT domain of both NOD1 and NOD2 from model organism zebrafish (Danio rerio using computational methods. Our study highlighted the differential ATP binding modes in NOD1 and NOD2. In NOD1, γ-phosphate of ATP faced toward the central nucleotide binding cavity like NLRC4, whereas in NOD2 the cavity was occupied by adenine moiety. The conserved 'Lysine' at Walker A formed hydrogen bonds (H-bonds and Aspartic acid (Walker B formed electrostatic interaction with ATP. At Sensor 1, Arg328 of NOD1 exhibited an H-bond with ATP, whereas corresponding Arg404 of NOD2 did not. 'Proline' of GxP motif (Pro386 of NOD1 and Pro464 of NOD2 interacted with adenine moiety and His511 at Sensor 2 of NOD1 interacted with γ-phosphate group of ATP. In contrast, His579 of NOD2 interacted with the adenine moiety having a relatively inverted orientation. Our findings are well supplemented with the molecular interaction of ATP with NLRC4, and consistent with mutagenesis data reported for human, which indicates evolutionary shared NOD signaling mechanism. Together, this study provides novel insights into ATP binding mechanism, and highlights the differential ATP binding modes in zebrafish NOD1 and NOD2.

  17. Feature-level domain adaptation

    DEFF Research Database (Denmark)

    Kouw, Wouter M.; Van Der Maaten, Laurens J P; Krijthe, Jesse H.

    2016-01-01

    -level domain adaptation (flda), that models the dependence between the two domains by means of a feature-level transfer model that is trained to describe the transfer from source to target domain. Subsequently, we train a domain-adapted classifier by minimizing the expected loss under the resulting transfer...... modeled via a dropout distribution, which allows the classiffier to adapt to differences in the marginal probability of features in the source and the target domain. Our experiments on several real-world problems show that flda performs on par with state-of-the-art domainadaptation techniques.......Domain adaptation is the supervised learning setting in which the training and test data are sampled from different distributions: training data is sampled from a source domain, whilst test data is sampled from a target domain. This paper proposes and studies an approach, called feature...

  18. Knowledge representation requirements for model sharing between model-based reasoning and simulation in process flow domains

    Science.gov (United States)

    Throop, David R.

    1992-01-01

    The paper examines the requirements for the reuse of computational models employed in model-based reasoning (MBR) to support automated inference about mechanisms. Areas in which the theory of MBR is not yet completely adequate for using the information that simulations can yield are identified, and recent work in these areas is reviewed. It is argued that using MBR along with simulations forces the use of specific fault models. Fault models are used so that a particular fault can be instantiated into the model and run. This in turn implies that the component specification language needs to be capable of encoding any fault that might need to be sensed or diagnosed. It also means that the simulation code must anticipate all these faults at the component level.

  19. Homology-modeled ligand-binding domains of medaka estrogen receptors and androgen receptors: A model system for the study of reproduction

    International Nuclear Information System (INIS)

    Cui Jianzhou; Shen Xueyan; Yan Zuowei; Zhao Haobin; Nagahama, Yoshitaka

    2009-01-01

    Estrogen and androgen and their receptors play critical roles in physiological processes such as sexual differentiation and development. Using the available structural models for the human estrogen receptors alpha and beta and androgen receptor as templates, we designed in silico agonist and antagonist models of medaka estrogen receptor (meER) alpha, beta-1, and beta-2, and androgen receptor (meAR) alpha and beta. Using these models, we studied (1) the structural relationship between the ligand-binding domains (LBDs) of ERs and ARs of human and medaka, and (2) whether medaka ER and AR can be potential models for studying the ligand-binding activities of various agonists and antagonists of these receptors by docking analysis. A high level of conservation was observed between the sequences of the ligand-binding domains of meERα and huERα, meERβ1 and huERβ, meERβ2, and huERβ with 62.8%, 66.4%, and 65.1% identity, respectively. The sequence conservation between meARα and huAR, meARβ, and huAR was found with 70.1% and 61.0% of identity, respectively. Thirty-three selected endocrine disrupting chemicals (EDCs), including both agonists and antagonists, were docked into the LBD of ER and AR, and the corresponding docking score for medaka models and human templates were calculated. In order to confirm the conservation of the overall geometry and the binding pocket, the backbone root mean square deviation (RMSD) for Cα atoms was derived from the structure superposition of all 10 medaka homology models to the six human templates. Our results suggested conformational conservation between the ERs and ARs of medaka and human, Thus, medaka could be highly useful as a model system for studies involving estrogen and androgen interaction with their receptors.

  20. Petrogenesis of incipient charnockite in the Ikalamavony sub-domain, south-central Madagascar: New insights from phase equilibrium modeling

    Science.gov (United States)

    Endo, Takahiro; Tsunogae, Toshiaki; Santosh, M.; Shaji, E.; Rambeloson, Roger A.

    2017-06-01

    Incipient charnockites representing granulite formation on a mesoscopic scale occur in the Ambodin Ifandana area of Ikalamavony sub-domain in south-central Madagascar. Here we report new petrological data from these rocks, and discuss the process of granulite formation on the basis of petrography, mineral equilibrium modeling, and fluid inclusion studies. The incipient charnockites occur as brownish patches, lenses, and layers characterized by an assemblage of biotite + orthopyroxene + K-feldspar + plagioclase + quartz + magnetite + ilmenite within host orthopyroxene-free biotite gneiss with an assemblage of biotite + K-feldspar + plagioclase + quartz + magnetite + ilmenite. Lenses and layers of calc-silicate rock (clinopyroxene + garnet + plagioclase + quartz + titanite + calcite) are typically associated with the charnockite. Coarse-grained charnockite occurs along the contact between the layered charnockite and calc-silicate rock. The application of mineral equilibrium modeling on the mineral assemblages in charnockite and biotite gneiss employing the NCKFMASHTO system as well as fluid inclusion study on coarse-grained charnockite defines a P-T range of 8.5-10.5 kbar and 880-900 °C, which is nearly consistent with the inferred P-T condition of the Ikalamavony sub-domain (8.0-10.5 kbar and 820-880 °C). The result of T versus H2O activity (a(H2O)) modeling demonstrates that orthopyroxene-bearing assemblage in charnockite is stable under relatively low a(H2O) condition of 0.42-0.43, which is consistent with the popular models of incipient-charnockite formation related to the lowering of water activity and stabilization of orthopyroxene through dehydration of biotite. The occurrence of calc-silicate rocks adjacent to the charnockite suggests that the CO2-bearing fluid that caused dehydration and incipient-charnockite formation might have been derived through decarbonation of calc-silicate rocks during the initial stage of decompression slightly after the peak