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Sample records for loop homology modeling

  1. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

    Science.gov (United States)

    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

  2. Conformal boundary loop models

    International Nuclear Information System (INIS)

    Jacobsen, Jesper Lykke; Saleur, Hubert

    2008-01-01

    We study a model of densely packed self-avoiding loops on the annulus, related to the Temperley-Lieb algebra with an extra idempotent boundary generator. Four different weights are given to the loops, depending on their homotopy class and whether they touch the outer rim of the annulus. When the weight of a contractible bulk loop x≡q+q -1 element of (-2,2], this model is conformally invariant for any real weight of the remaining three parameters. We classify the conformal boundary conditions and give exact expressions for the corresponding boundary scaling dimensions. The amplitudes with which the sectors with any prescribed number and types of non-contractible loops appear in the full partition function Z are computed rigorously. Based on this, we write a number of identities involving Z which hold true for any finite size. When the weight of a contractible boundary loop y takes certain discrete values, y r ≡([r+1] q )/([r] q ) with r integer, other identities involving the standard characters K r,s of the Virasoro algebra are established. The connection with Dirichlet and Neumann boundary conditions in the O(n) model is discussed in detail, and new scaling dimensions are derived. When q is a root of unity and y=y r , exact connections with the A m type RSOS model are made. These involve precise relations between the spectra of the loop and RSOS model transfer matrices, valid in finite size. Finally, the results where y=y r are related to the theory of Temperley-Lieb cabling

  3. Modeling of compact loop antennas

    International Nuclear Information System (INIS)

    Baity, F.W.

    1987-01-01

    A general compact loop antenna model which treats all elements of the antenna as lossy transmission lines has been developed. In addition to capacitively-tuned resonant double loop (RDL) antennas the model treats stub-tuned resonant double loop antennas. Calculations using the model have been compared with measurements on full-scale mockups of resonant double loop antennas for ATF and TFTR in order to refine the transmission line parameters. Results from the model are presented for RDL antenna designs for ATF, TFTR, Tore Supra, and for the Compact Ignition Tokamak

  4. Modeling Non-homologous End Joining

    Science.gov (United States)

    Li, Yongfeng

    2013-01-01

    Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

  5. HOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDY OF MYCOBACTERIUM TUBERCULOSIS UREASE

    Directory of Open Access Journals (Sweden)

    Lisnyak Yu. V.

    2017-10-01

    Full Text Available Introduction. M. tuberculosis urease (MTU is an attractive target for chemotherapeutic intervention in tuberculosis by designing new safe and efficient enzyme inhibitors. A prerequisite for designing such inhibitors is an understanding of urease's three-dimensional (3D structure organization. 3D structure of M. tuberculosis urease is unknown. When experimental three-dimensional structure of a protein is not known, homology modeling, the most commonly used computational structure prediction method, is the technique of choice. This paper aimed to build a 3D-structure of M. tuberculosis urease by homology modeling and to study its stability by molecular dynamics simulations. Materials and methods. To build MTU model, five high-resolution X-ray structures of bacterial ureases with three-subunit composition (2KAU, 5G4H, 4UBP, 4СEU, and 4EPB have been selected as templates. For each template five stochastic alignments were created and for each alignment, a three-dimensional model was built. Then, each model was energy minimized and the models were ranked by quality Z-score. The MTU model with highest quality estimation amongst 25 potential models was selected. To further improve structure quality the model was refined by short molecular dynamics simulation that resulted in 20 snapshots which were rated according to their energy and the quality Z-score. The best scoring model having minimum energy was chosen as a final homology model of 3D structure for M. tuberculosis. The final model of MTU was also validated by using PDBsum and QMEAN servers. These checks confirmed good quality of MTU homology model. Results and discussion. Homology model of MTU is a nonamer (homotrimer of heterotrimers, (αβγ3 consisting of 2349 residues. In MTU heterotrimer, sub-units α, β, and γ tightly interact with each other at a surface of approximately 3000 Å2. Sub-unit α contains the enzyme active site with two Ni atoms coordinated by amino acid residues His347, His

  6. A geometric model for Hochschild homology of Soergel bimodules

    DEFF Research Database (Denmark)

    Webster, Ben; Williamson, Geordie

    2008-01-01

    An important step in the calculation of the triply graded link homology of Khovanov and Rozansky is the determination of the Hochschild homology of Soergel bimodules for SL(n). We present a geometric model for this Hochschild homology for any simple group G, as B–equivariant intersection cohomology...... on generators whose degree is explicitly determined by the geometry of the orbit closure, and to describe its Hilbert series, proving a conjecture of Jacob Rasmussen....

  7. Mathematical Modeling of Loop Heat Pipes

    Science.gov (United States)

    Kaya, Tarik; Ku, Jentung; Hoang, Triem T.; Cheung, Mark L.

    1998-01-01

    The primary focus of this study is to model steady-state performance of a Loop Heat Pipe (LHP). The mathematical model is based on the steady-state energy balance equations at each component of the LHP. The heat exchange between each LHP component and the surrounding is taken into account. Both convection and radiation environments are modeled. The loop operating temperature is calculated as a function of the applied power at a given loop condition. Experimental validation of the model is attempted by using two different LHP designs. The mathematical model is tested at different sink temperatures and at different elevations of the loop. Tbc comparison of the calculations and experimental results showed very good agreement (within 3%). This method proved to be a useful tool in studying steady-state LHP performance characteristics.

  8. Sigma models and renormalization of string loops

    International Nuclear Information System (INIS)

    Tseytlin, A.A.

    1989-05-01

    An extension of the ''σ-model β-functions - string equations of motion'' correspondence to the string loop level is discussed. Special emphasis is made on how the renormalization group acts in string loops and, in particular, on the renormalizability property of the generating functional Z-circumflex for string amplitudes (related to the σ model partition function integrated over moduli). Renormalization of Z-circumflex at one and two loop order is analyzed in some detail. We also discuss an approach to renormalization based on operators of insertion of topological fixtures. (author). 70 refs

  9. Mechanism of Transport Modulation by an Extracellular Loop in an Archaeal Excitatory Amino Acid Transporter (EAAT) Homolog*

    Science.gov (United States)

    Mulligan, Christopher; Mindell, Joseph A.

    2013-01-01

    Secondary transporters in the excitatory amino acid transporter family terminate glutamatergic synaptic transmission by catalyzing Na+-dependent removal of glutamate from the synaptic cleft. Recent structural studies of the aspartate-specific archaeal homolog, GltPh, suggest that transport is achieved by a rigid body, piston-like movement of the transport domain, which houses the substrate-binding site, between the extracellular and cytoplasmic sides of the membrane. This transport domain is connected to an immobile scaffold by three loops, one of which, the 3–4 loop (3L4), undergoes substrate-sensitive conformational change. Proteolytic cleavage of the 3L4 was found to abolish transport activity indicating an essential function for this loop in the transport mechanism. Here, we demonstrate that despite the presence of fully cleaved 3L4, GltPh is still able to sample conformations relevant for transport. Optimized reconstitution conditions reveal that fully cleaved GltPh retains some transport activity. Analysis of the kinetics and temperature dependence of transport accompanied by direct measurements of substrate binding reveal that this decreased transport activity is not due to alteration of the substrate binding characteristics but is caused by the significantly reduced turnover rate. By measuring solute counterflow activity and cross-link formation rates, we demonstrate that cleaving 3L4 severely and specifically compromises one or more steps contributing to the movement of the substrate-loaded transport domain between the outward- and inward-facing conformational states, sparing the equivalent step(s) during the movement of the empty transport domain. These results reveal a hitherto unknown role for the 3L4 in modulating an essential step in the transport process. PMID:24155238

  10. Prefiltering Model for Homology Detection Algorithms on GPU.

    Science.gov (United States)

    Retamosa, Germán; de Pedro, Luis; González, Ivan; Tamames, Javier

    2016-01-01

    Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA's graphics processing units (GPUs) and multicore processors. Depending on the sensitivity settings, this makes it possible to quickly reduce the sequence database by factors between 50% and 95%, while rejecting no significant sequences. Furthermore, this prefiltering application can be used together with multiple homology detection algorithms as a part of a next-generation sequencing system. Extensive performance and accuracy tests have been carried out in the Spanish National Centre for Biotechnology (NCB). The results show that GPU hardware can accelerate the execution times of former homology detection applications, such as National Centre for Biotechnology Information (NCBI), Basic Local Alignment Search Tool for Proteins (BLASTP), up to a factor of 4.

  11. Protein homology model refinement by large-scale energy optimization.

    Science.gov (United States)

    Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E; DiMaio, Frank; Baker, David

    2018-03-20

    Proteins fold to their lowest free-energy structures, and hence the most straightforward way to increase the accuracy of a partially incorrect protein structure model is to search for the lowest-energy nearby structure. This direct approach has met with little success for two reasons: first, energy function inaccuracies can lead to false energy minima, resulting in model degradation rather than improvement; and second, even with an accurate energy function, the search problem is formidable because the energy only drops considerably in the immediate vicinity of the global minimum, and there are a very large number of degrees of freedom. Here we describe a large-scale energy optimization-based refinement method that incorporates advances in both search and energy function accuracy that can substantially improve the accuracy of low-resolution homology models. The method refined low-resolution homology models into correct folds for 50 of 84 diverse protein families and generated improved models in recent blind structure prediction experiments. Analyses of the basis for these improvements reveal contributions from both the improvements in conformational sampling techniques and the energy function.

  12. Rapid Simulation of Flat Knitting Loops Based On the Yarn Texture and Loop Geometrical Model

    Directory of Open Access Journals (Sweden)

    Lu Zhiwen

    2017-06-01

    Full Text Available In order to create realistic loop primitives suitable for the fast computer-aided design (CAD of the flat knitted fabric, we have a research on the geometric model of the loop as well as the variation of the loop surface. Establish the texture variation model based on the changing process from the normal yarn to loop that provides the realistic texture of the simulative loop. Then optimize the simulative loop based on illumination variation. This paper develops the computer program with the optimization algorithm and achieves the loop simulation of different yarns to verify the feasibility of the proposed algorithm. Our work provides a fast CAD of the flat knitted fabric with loop simulation, and it is not only more realistic but also material adjustable. Meanwhile it also provides theoretical value for the flat knitted fabric computer simulation.

  13. MollDE: a homology modeling framework you can click with.

    Science.gov (United States)

    Canutescu, Adrian A; Dunbrack, Roland L

    2005-06-15

    Molecular Integrated Development Environment (MolIDE) is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and streamlined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE. http://dunbrack.fccc.edu/molide/molide.php rl_dunbrack@fccc.edu.

  14. Flat Knitting Loop Deformation Simulation Based on Interlacing Point Model

    Directory of Open Access Journals (Sweden)

    Jiang Gaoming

    2017-12-01

    Full Text Available In order to create realistic loop primitives suitable for the faster CAD of the flat-knitted fabric, we have performed research on the model of the loop as well as the variation of the loop surface. This paper proposes an interlacing point-based model for the loop center curve, and uses the cubic Bezier curve to fit the central curve of the regular loop, elongated loop, transfer loop, and irregular deformed loop. In this way, a general model for the central curve of the deformed loop is obtained. The obtained model is then utilized to perform texture mapping, texture interpolation, and brightness processing, simulating a clearly structured and lifelike deformed loop. The computer program LOOP is developed by using the algorithm. The deformed loop is simulated with different yarns, and the deformed loop is applied to design of a cable stitch, demonstrating feasibility of the proposed algorithm. This paper provides a loop primitive simulation method characterized by lifelikeness, yarn material variability, and deformation flexibility, and facilitates the loop-based fast computer-aided design (CAD of the knitted fabric.

  15. Diverse binding site structures revealed in homology models of polyreactive immunoglobulins

    Science.gov (United States)

    Ramsland, Paul A.; Guddat, Luke W.; Edmundson, Allen B.; Raison, Robert L.

    1997-09-01

    We describe here computer-assisted homology models of the combiningsite structure of three polyreactive immunoglobulins. Template-based modelsof Fv (VL-VH) fragments were derived forthe surface IgM expressed by the malignant CD5 positive B cells from threepatients with chronic lymphocytic leukaemia (CLL). The conserved frameworkregions were constructed using crystal coordinates taken from highlyhomologous human variable domain structures (Pot and Hil). Complementaritydetermining regions (CDRs) were predicted by grafting loops, taken fromknown immunoglobulin structures, onto the Fv framework models. The CDRtemplates were chosen, where possible, to be of the same length and of highresidue identity or similarity. LCDR1, 2 and 3 as well as HCDR1 and 2 forthe Fv were constructed using this strategy. For HCDR3 prediction, adatabase containing the Cartesian coordinates of 30 of these loops wascompiled from unliganded antibody X-ray crystallographic structures and anHCDR3 of the same length as that of the B CLL Fv was selected as a template.In one case (Yar), the resulting HCDR3 model gave unfavourable interactionswhen incorporated into the Fv model. This HCDR3 was therefore modelled usingan alternative strategy of construction of the loop stems, using apreviously described HCDR3 conformation (Pot), followed by chain closurewith a β-turn. The template models were subjected to positionalrefinement using energy minimisation and molecular dynamics simulations(X-PLOR). An electrostatic surface description (GRASP) did not reveal acommon structural feature within the binding sites of the three polyreactiveFv. Thus, polyreactive immunoglobulins may recognise similar and multipleantigens through a diverse array of binding site structures.

  16. Homologous Basal Ganglia Network Models in Physiological and Parkinsonian Conditions

    Directory of Open Access Journals (Sweden)

    Jyotika Bahuguna

    2017-08-01

    Full Text Available The classical model of basal ganglia has been refined in recent years with discoveries of subpopulations within a nucleus and previously unknown projections. One such discovery is the presence of subpopulations of arkypallidal and prototypical neurons in external globus pallidus, which was previously considered to be a primarily homogeneous nucleus. Developing a computational model of these multiple interconnected nuclei is challenging, because the strengths of the connections are largely unknown. We therefore use a genetic algorithm to search for the unknown connectivity parameters in a firing rate model. We apply a binary cost function derived from empirical firing rate and phase relationship data for the physiological and Parkinsonian conditions. Our approach generates ensembles of over 1,000 configurations, or homologies, for each condition, with broad distributions for many of the parameter values and overlap between the two conditions. However, the resulting effective weights of connections from or to prototypical and arkypallidal neurons are consistent with the experimental data. We investigate the significance of the weight variability by manipulating the parameters individually and cumulatively, and conclude that the correlation observed between the parameters is necessary for generating the dynamics of the two conditions. We then investigate the response of the networks to a transient cortical stimulus, and demonstrate that networks classified as physiological effectively suppress activity in the internal globus pallidus, and are not susceptible to oscillations, whereas parkinsonian networks show the opposite tendency. Thus, we conclude that the rates and phase relationships observed in the globus pallidus are predictive of experimentally observed higher level dynamical features of the physiological and parkinsonian basal ganglia, and that the multiplicity of solutions generated by our method may well be indicative of a natural

  17. Jordan cells of periodic loop models

    International Nuclear Information System (INIS)

    Morin-Duchesne, Alexi; Saint-Aubin, Yvan

    2013-01-01

    Jordan cells in transfer matrices of finite lattice models are a signature of the logarithmic character of the conformal field theories that appear in their thermodynamical limit. The transfer matrix of periodic loop models, T N , is an element of the periodic Temperley–Lieb algebra EPTL N (β,α), where N is the number of sites on a section of the cylinder, and β = −q − q −1 = 2cos λ and α the weights of contractible and non-contractible loops. The thermodynamic limit of T N is believed to describe a conformal field theory of central charge c = 1 − 6λ 2 /(π(λ − π)). The abstract element T N acts naturally on (a sum of) spaces V-tilde N d , similar to those upon which the standard modules of the (classical) Temperley–Lieb algebra act. These spaces known as sectors are labeled by the numbers of defects d and depend on a twist parameter v that keeps track of the winding of defects around the cylinder. Criteria are given for non-trivial Jordan cells of T N both between sectors with distinct defect numbers and within a given sector. (paper)

  18. Multi-loop PWR modeling and hardware-in-the-loop testing using ACSL

    International Nuclear Information System (INIS)

    Thomas, V.M.; Heibel, M.D.; Catullo, W.J.

    1989-01-01

    Westinghouse has developed an Advanced Digital Feedwater Control System (ADFCS) which is aimed at reducing feedwater related reactor trips through improved control performance for pressurized water reactor (PWR) power plants. To support control system setpoint studies and functional design efforts for the ADFCS, an ACSL based model of the nuclear steam supply system (NSSS) of a Westinghouse (PWR) was generated. Use of this plant model has been extended from system design to system testing through integration of the model into a Hardware-in-Loop test environment for the ADFCS. This integration includes appropriate interfacing between a Gould SEL 32/87 computer, upon which the plant model executes in real time, and the Westinghouse Distributed Processing family (WDPF) test hardware. A development program has been undertaken to expand the existing ACSL model to include capability to explicitly model multiple plant loops, steam generators, and corresponding feedwater systems. Furthermore, the program expands the ADFCS Hardware-in-Loop testing to include the multi-loop plant model. This paper provides an overview of the testing approach utilized for the ADFCS with focus on the role of Hardware-in-Loop testing. Background on the plant model, methodology and test environment is also provided. Finally, an overview is presented of the program to expand the model and associated Hardware-in-Loop test environment to handle multiple loops

  19. A model for a stable coronal loop

    International Nuclear Information System (INIS)

    Hoven, G.V.; Chiuderi, C.; Giachetti, R.

    1977-01-01

    We present here a new plasma-physics model of a stable active-region arch which corresponds to the structure observed in the EUV. Pressure gradients are seen, so that the equilibrium magnetic field must depart from the force-free form valid in the surrounding corona. We take advantage of the data and of the approximate cylindrical symmetry to develop a modified form of the commonly assumed sheared-spiral structure. The dynamic MHD behavior of this new pressure/field model is then evaluated by the Newcomb criterion, taken from controlled-fusion physics, and the results show short-wavelength stability in a specific parameter range. Thus we demonstrate the possibility, for pressure profiles with widths of the order of the magnetic-field scale, that such arches can persist for reasonable periods. Finally, the spatial proportions and magnetic fields of a characteristic stable coronal loop are described

  20. Fast loop modeling for protein structures

    Science.gov (United States)

    Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

    2015-03-01

    X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

  1. Binding Mode Prediction of 5-Hydroxytryptamine 2C Receptor Ligands by Homology Modeling and Molecular Docking Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Asif; Nagarajan, Shanthi; Doddareddy, Munikumar Reddy; Cho, Yong Seo; Pae, Ae Nim [Korea Institute of Science and Technology, Seoul (Korea, Republic of)

    2011-06-15

    Serotonin or 5-hydroxytryptamine subtype 2C (5-HT{sub 2C}) receptor belongs to class A amine subfamily of Gprotein- coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (β2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.

  2. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2010-01-01

    CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.......0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models.......3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is...

  3. Modeling Human Serum Albumin Tertiary Structure to Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics

    Science.gov (United States)

    Petrovic, Dus?an; Zlatovic´, Mario

    2015-01-01

    A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL…

  4. A detailed BWR recirculation loop model for RELAP

    Energy Technology Data Exchange (ETDEWEB)

    Araiza-Martínez, Enrique, E-mail: enrique.araiza@inin.gob.mx; Ortiz-Villafuerte, Javier, E-mail: javier.ortiz@inin.gob.mx; Castillo-Durán, Rogelio, E-mail: rogelio.castillo@inin.gob.mx

    2017-01-15

    Highlights: • A new detailed BWR recirculation loop model was developed for RELAP. • All jet pumps, risers, manifold, suction and control valves, and recirculation pump are modeled. • Model is tested against data from partial blockage of two jet pumps. • For practical applications, simulation results showed good agreement with available data. - Abstract: A new detailed geometric model of the whole recirculation loop of a BWR has been developed for the code RELAP. This detailed model includes the 10 jet pumps, 5 risers, manifold, suction and control valves, and the recirculation pump, per recirculation loop. The model is tested against data from an event of partial blockage at the entrance nozzle of one jet pump in both recirculation loops. For practical applications, simulation results showed good agreement with data. Then, values of parameters considered as figure of merit (reactor power, dome pressure, core flow, among others) for this event are compared against those from the common 1 jet pump per loop model. The results show that new detailed model led to a closer prediction of the reported power change. The detailed recirculation loop model can provide more reliable boundary condition data to a CFD models for studies of, for example, flow induced vibration, wear, and crack initiation.

  5. A Culture-Behavior-Brain Loop Model of Human Development.

    Science.gov (United States)

    Han, Shihui; Ma, Yina

    2015-11-01

    Increasing evidence suggests that cultural influences on brain activity are associated with multiple cognitive and affective processes. These findings prompt an integrative framework to account for dynamic interactions between culture, behavior, and the brain. We put forward a culture-behavior-brain (CBB) loop model of human development that proposes that culture shapes the brain by contextualizing behavior, and the brain fits and modifies culture via behavioral influences. Genes provide a fundamental basis for, and interact with, the CBB loop at both individual and population levels. The CBB loop model advances our understanding of the dynamic relationships between culture, behavior, and the brain, which are crucial for human phylogeny and ontogeny. Future brain changes due to cultural influences are discussed based on the CBB loop model. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Nonlinear model predictive control for chemical looping process

    Science.gov (United States)

    Joshi, Abhinaya; Lei, Hao; Lou, Xinsheng

    2017-08-22

    A control system for optimizing a chemical looping ("CL") plant includes a reduced order mathematical model ("ROM") that is designed by eliminating mathematical terms that have minimal effect on the outcome. A non-linear optimizer provides various inputs to the ROM and monitors the outputs to determine the optimum inputs that are then provided to the CL plant. An estimator estimates the values of various internal state variables of the CL plant. The system has one structure adapted to control a CL plant that only provides pressure measurements in the CL loops A and B, a second structure adapted to a CL plant that provides pressure measurements and solid levels in both loops A, and B, and a third structure adapted to control a CL plant that provides full information on internal state variables. A final structure provides a neural network NMPC controller to control operation of loops A and B.

  7. Homology modeling of the serotonin transporter: Insights into the primary escitalopram-binding Site

    DEFF Research Database (Denmark)

    Jørgensen, Anne Marie; Tagmose, L.; Jørgensen, A.M.M.

    2007-01-01

    -ray structure of the closely related amino acid transporter, Aquifex aeolicus leucine transporter (LeuT), provides an opportunity to develop a three-dimensional model of the structure of SERT. We present herein a homology model of SERT using LeuT as the template and containing escitalopram as a bound ligand...

  8. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles.

    Science.gov (United States)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl

    2010-07-01

    CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is web server is available at http://www.cbs.dtu.dk/services/CPHmodels/.

  9. Dilaton gravity, Poisson sigma models and loop quantum gravity

    International Nuclear Information System (INIS)

    Bojowald, Martin; Reyes, Juan D

    2009-01-01

    Spherically symmetric gravity in Ashtekar variables coupled to Yang-Mills theory in two dimensions and its relation to dilaton gravity and Poisson sigma models are discussed. After introducing its loop quantization, quantum corrections for inverse triad components are shown to provide a consistent deformation without anomalies. The relation to Poisson sigma models provides a covariant action principle of the quantum-corrected theory with effective couplings. Results are also used to provide loop quantizations of spherically symmetric models in arbitrary D spacetime dimensions.

  10. Loop equations for multi-cut matrix models

    International Nuclear Information System (INIS)

    Akemann, G.

    1995-03-01

    The loop equation for the complex one-matrix model with a multi-cut structure is derived and solved in the planar limit. An iterative scheme for higher genus contributions to the free energy and the multi-loop correlators is presented for the two-cut model, where explicit results are given up to and including genus two. The double-scaling limit is analyzed and the relation to the one-cut solution of the hermitian and complex one-matrix model is discussed. (orig.)

  11. Loop groups, the Luttinger model, anyons, and Sutherland systems

    International Nuclear Information System (INIS)

    Langmann, E.; Carey, A.L.

    1998-01-01

    We discuss the representation theory of loop groups and examples of how it is used in physics. These examples include the construction and solution of the Luttinger model and other 1 + 1-dimensional interacting quantum field theories, the construction of anyon field operators on the circle, and the '2 nd quantization' of the Sutherland model using anyons

  12. Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model.

    Directory of Open Access Journals (Sweden)

    Thomas Stockner

    Full Text Available The high-resolution crystal structure of the leucine transporter (LeuT is frequently used as a template for homology models of the dopamine transporter (DAT. Although similar in structure, DAT differs considerably from LeuT in a number of ways: (i when compared to LeuT, DAT has very long intracellular amino and carboxyl termini; (ii LeuT and DAT share a rather low overall sequence identity (22% and (iii the extracellular loop 2 (EL2 of DAT is substantially longer than that of LeuT. Extracellular zinc binds to DAT and restricts the transporter's movement through the conformational cycle, thereby resulting in a decrease in substrate uptake. Residue H293 in EL2 praticipates in zinc binding and must be modelled correctly to allow for a full understanding of its effects. We exploited the high-affinity zinc binding site endogenously present in DAT to create a model of the complete transmemberane domain of DAT. The zinc binding site provided a DAT-specific molecular ruler for calibration of the model. Our DAT model places EL2 at the transporter lipid interface in the vicinity of the zinc binding site. Based on the model, D206 was predicted to represent a fourth co-ordinating residue, in addition to the three previously described zinc binding residues H193, H375 and E396. This prediction was confirmed by mutagenesis: substitution of D206 by lysine and cysteine affected the inhibitory potency of zinc and the maximum inhibition exerted by zinc, respectively. Conversely, the structural changes observed in the model allowed for rationalizing the zinc-dependent regulation of DAT: upon binding, zinc stabilizes the outward-facing state, because its first coordination shell can only be completed in this conformation. Thus, the model provides a validated solution to the long extracellular loop and may be useful to address other aspects of the transport cycle.

  13. Cellulase enzyme: Homology modeling, binding site identification and molecular docking

    Science.gov (United States)

    Selvam, K.; Senbagam, D.; Selvankumar, T.; Sudhakar, C.; Kamala-Kannan, S.; Senthilkumar, B.; Govarthanan, M.

    2017-12-01

    Cellulase is an enzyme that degrades the linear polysaccharide like cellulose into glucose by breaking the β-1,4- glycosidic bonds. These enzymes are the third largest enzymes with a great potential towards the ethanol production and play a vital role in degrading the biomass. The production of ethanol depends upon the ability of the cellulose to utilize the wide range of substrates. In this study, the 3D structure of cellulase from Acinetobacter sp. was modeled by using Modeler 9v9 and validated by Ramachandran plot. The accuracy of the predicted 3D structure was checked using Ramachandran plot analysis showed that 81.1% in the favored region, compatibility of an atomic model (3D) with amino acid sequence (1D) for the model was observed as 78.21% and 49.395% for Verify 3D and ERRAT at SAVES server. As the binding efficacy with the substrate might suggests the choice of the substrate as carbon and nitrogen sources, the cellobiose, cellotetraose, cellotetriose and laminaribiose were employed in the docking studies. The docking of cellobiose, cellotetraose, cellotetriose and laminaribiose with cellulase exhibited the binding energy of -6.1523 kJ/mol, -7.8759 kJ/mol,-6.1590 kJ/mol and -6.7185 kJ/mol, respectively. These docking studies revealed that cellulase has the greater potential towards the cellotetraose as a substrate for the high yield of ethanol.

  14. Loop Corrections to Standard Model fields in inflation

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xingang [Institute for Theory and Computation, Harvard-Smithsonian Center for Astrophysics,60 Garden Street, Cambridge, MA 02138 (United States); Department of Physics, The University of Texas at Dallas,800 W Campbell Rd, Richardson, TX 75080 (United States); Wang, Yi [Department of Physics, The Hong Kong University of Science and Technology,Clear Water Bay, Kowloon, Hong Kong (China); Xianyu, Zhong-Zhi [Center of Mathematical Sciences and Applications, Harvard University,20 Garden Street, Cambridge, MA 02138 (United States)

    2016-08-08

    We calculate 1-loop corrections to the Schwinger-Keldysh propagators of Standard-Model-like fields of spin-0, 1/2, and 1, with all renormalizable interactions during inflation. We pay special attention to the late-time divergences of loop corrections, and show that the divergences can be resummed into finite results in the late-time limit using dynamical renormalization group method. This is our first step toward studying both the Standard Model and new physics in the primordial universe.

  15. Comparison between two models of energy balance in coronal loops

    Science.gov (United States)

    Mac Cormack, C.; López Fuentes, M.; Vásquez, A. M.; Nuevo, F. A.; Frazin, R. A.; Landi, E.

    2017-10-01

    In this work we compare two models to analyze the energy balance along coronal magnetic loops. For the first stationary model we deduce an expression of the energy balance along the loops expressed in terms of quantities provided by the combination of differential emission measure tomography (DEMT) applied to EUV images time series and potential extrapolations of the coronal magnetic field. The second applied model is a 0D hydrodynamic model that provides the evolution of the average properties of the coronal plasma along the loops, using as input parameters the loop length and the heating rate obtained with the first model. We compare the models for two Carrington rotations (CR) corresponding to different periods of activity: CR 2081, corresponding to a period of minimum activity observed with the Extreme Ultraviolet Imager (EUVI) on board of the Solar Terrestrial Relations Observatory (STEREO), and CR 2099, corresponding to a period of activity increase observed with the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO). The results of the models are consistent for both rotations.

  16. Illustrating and homology modeling the proteins of the Zika virus [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2016-09-01

    Full Text Available The Zika virus (ZIKV is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.

  17. Challenges in LCA modelling of multiple loops for aluminium cans

    DEFF Research Database (Denmark)

    Niero, Monia; Olsen, Stig Irving

    considered the case of closed-loop recycling for aluminium cans, where body and lid are different alloys, and discussed the abovementioned challenge. The Life Cycle Inventory (LCI) modelling of aluminium processes is traditionally based on a pure aluminium flow, therefore neglecting the presence of alloying...... elements. We included the effect of alloying elements on the LCA modelling of aluminium can recycling. First, we performed a mass balance of the main alloying elements (Mn, Fe, Si, Cu) in aluminium can recycling at increasing levels of recycling rate. The analysis distinguished between different aluminium...... packaging scrap sources (i.e. used beverage can and mixed aluminium packaging) to understand the limiting factors for multiple loop aluminium can recycling. Secondly, we performed a comparative LCA of aluminium can production and recycling in multiple loops considering the two aluminium packaging scrap...

  18. MHD modeling of coronal loops: the transition region throat

    Science.gov (United States)

    Guarrasi, M.; Reale, F.; Orlando, S.; Mignone, A.; Klimchuk, J. A.

    2014-04-01

    Context. The expansion of coronal loops in the transition region may considerably influence the diagnostics of the plasma emission measure. The cross-sectional area of the loops is expected to depend on the temperature and pressure, and might be sensitive to the heating rate. Aims: The approach here is to study the area response to slow changes in the coronal heating rate, and check the current interpretation in terms of steady heating models. Methods: We study the area response with a time-dependent 2D magnetohydrodynamic (MHD) loop model, including the description of the expanding magnetic field, coronal heating and losses by thermal conduction, and radiation from optically thin plasma. We run a simulation for a loop 50 Mm long and quasi-statically heated to about 4 MK. Results: We find that the area can change substantially with the quasi-steady heating rate, e.g., by ~40% at 0.5 MK as the loop temperature varies between 1 MK and 4 MK, and, therefore, affects the interpretation of the differential emission measure vs. temperature (DEM(T)) curves. The movie associated to Fig. 4 is available in electronic form at http://www.aanda.org

  19. [Preparation of monoclonal antibody against 4-amylphenol and homology modeling of its Fv fragment].

    Science.gov (United States)

    Cheng, Lei; Wu, Haizhen; Fei, Jing; Zhang, Lujia; Ye, Jiang; Zhang, Huizhan

    2017-03-01

    Objective To prepare and characterize a monoclonal antibody (mAb) against 4-amylphenol (4-AP), clone its cDNA sequence and make homology modeling for its Fv fragment. Methods A high-affinity anti-4-AP mAb was generated from a hybridoma cell line F10 using electrofusion between splenocytes from APA-BSA-immunized mouse and Sp2/0 myeloma cells. Then we extracted the mRNA of F10 cells and cloned the cDNA of mAb. The homology modeling and molecular docking of its Fv fragment was conducted with biological software. Results Under the optimum conditions, the ic-ELISA equation was y=A 2 +(A 1 -A 2 )/(1+(x/x 0 ) p ) (A 1 =1.28; A 2 =-0.066; x 0 =12560.75; p=0.74) with a correlation coefficient (R 2 ) of 0.997. The lowest detectable limit was 0.65 μg/mL. The heavy and light chains of mAb respectively belonged to IgG1 and Kappa. The homology modeling and molecular docking studies revealed that the binding of 4-Ap and mAb was attributed to the hydrogen bond and hydrophobic interactions. Conclusion The study successfully established a stable 4-AP mAb-secreting hybridoma cell line. The study on spatial structure of Fv fragment using homology modeling provided a reference for the development and design of single chain variable fragments.

  20. One-loop Yukawa Couplings in Local Models

    CERN Document Server

    Conlon, Joseph P; Palti, Eran; 10.1007

    2010-01-01

    We calculate the one-loop Yukawa couplings and threshold corrections for supersymmetric local models of branes at singularities in type IIB string theory. We compute the corrections coming both from wavefunction and vertex renormalisation. The former comes in the IR from conventional field theory running and in the UV from threshold corrections that cause it to run from the winding scale associated to the full Calabi-Yau volume. The vertex correction is naively absent as it appears to correspond to superpotential renormalisation. However, we find that while the Wilsonian superpotential is not renormalised there is a physical vertex correction in the 1PI action associated to light particle loops.

  1. One-loop Yukawa couplings in local models

    Energy Technology Data Exchange (ETDEWEB)

    Conlon, Joseph P. [Rudolf Peierls Center for Theoretical Physics, Oxford (United Kingdom); Balliol College, Oxford (United Kingdom); Goodsell, Mark [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Palti, Eran [Centre de Physique Theorique, Ecole Polytechnique, CNRS, Palaiseau (France)

    2010-07-15

    We calculate the one-loop Yukawa couplings and threshold corrections for supersymmetric local models of branes at singularities in type IIB string theory. We compute the corrections coming both from wavefunction and vertex renormalisation. The former comes in the IR from conventional field theory running and in the UV from threshold corrections that cause it to run from the winding scale associated to the full Calabi-Yau volume. The vertex correction is naively absent as it appears to correspond to superpotential renormalisation. However, we find that while the Wilsonian superpotential is not renormalised there is a physical vertex correction in the 1PI action associated to light particle loops. (orig.)

  2. One-loop Yukawa couplings in local models

    International Nuclear Information System (INIS)

    Conlon, Joseph P.; Goodsell, Mark; Palti, Eran

    2010-07-01

    We calculate the one-loop Yukawa couplings and threshold corrections for supersymmetric local models of branes at singularities in type IIB string theory. We compute the corrections coming both from wavefunction and vertex renormalisation. The former comes in the IR from conventional field theory running and in the UV from threshold corrections that cause it to run from the winding scale associated to the full Calabi-Yau volume. The vertex correction is naively absent as it appears to correspond to superpotential renormalisation. However, we find that while the Wilsonian superpotential is not renormalised there is a physical vertex correction in the 1PI action associated to light particle loops. (orig.)

  3. Nonplanar loops leave the Veneziano model photon massless

    NARCIS (Netherlands)

    Foda, O.

    1987-01-01

    The absence of a pole at p2=0 in the orientable nonplanar one-loop photon self-energy in the Veneziano model is verified. Thus the photon remains massless, and spontaneous symmetry breaking - at least as reported in this context in the literature - is not found.

  4. Nonplanar loops leave the Veneziano model photon massless

    International Nuclear Information System (INIS)

    Foda, O.

    1987-01-01

    The absence of a pole at p 2 =0 in the orientable nonplanar one-loop photon self-energy in the Veneziano model is verified. Thus the photon remains massless, and spontaneous symmetry breaking - at least as reported in this context in the literature - is not found. (orig.)

  5. Nonplanar loops leave the Veneziano model photon massless

    Energy Technology Data Exchange (ETDEWEB)

    Foda, O.

    1987-04-16

    The absence of a pole at p/sup 2/=0 in the orientable nonplanar one-loop photon self-energy in the Veneziano model is verified. Thus the photon remains massless, and spontaneous symmetry breaking - at least as reported in this context in the literature - is not found.

  6. Two-loop neutrino model with exotic leptons

    Science.gov (United States)

    Okada, Hiroshi; Orikasa, Yuta

    2016-01-01

    We propose a two-loop induced neutrino mass model, in which we show some bench mark points to satisfy the observed neutrino oscillation, the constraints of lepton flavor violations, and the relic density in the coannihilation system satisfying the current upper bound on the spin independent scattering cross section with nuclei. We also discuss new sources of muon anomalous magnetic moments.

  7. Binding modes of dihydroquinoxalinones in a homology model of bradykinin receptor 1.

    Science.gov (United States)

    Ha, Sookhee N; Hey, Pat J; Ransom, Rick W; Harrell, C Meacham; Murphy, Kathryn L; Chang, Ray; Chen, Tsing-Bau; Su, Dai-Shi; Markowitz, M Kristine; Bock, Mark G; Freidinger, Roger M; Hess, Fred J

    2005-05-27

    We report the first homology model of human bradykinin receptor B1 generated from the crystal structure of bovine rhodopsin as a template. Using an automated docking procedure, two B1 receptor antagonists of the dihydroquinoxalinone structural class were docked into the receptor model. Site-directed mutagenesis data of the amino acid residues in TM1, TM3, TM6, and TM7 were incorporated to place the compounds in the binding site of the homology model of the human B1 bradykinin receptor. The best pose in agreement with the mutation data was selected for detailed study of the receptor-antagonist interaction. To test the model, the calculated antagonist-receptor binding energy was correlated with the experimentally measured binding affinity (K(i)) for nine dihydroquinoxalinone analogs. The model was used to gain insight into the molecular mechanism for receptor function and to optimize the dihydroquinoxalinone analogs.

  8. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel

    2015-08-06

    Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.

  9. A Looping-Based Model for Quenching Repression.

    Directory of Open Access Journals (Sweden)

    Yaroslav Pollak

    2017-01-01

    Full Text Available We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. The reduced probability of looping can be explained via an eclipse-like model, which provides a novel inhibitory mechanism. We test the eclipse model on two possible transcription-factor occupancy states of the D. melanogaster eve 3/7 enhancer, and show that it provides a possible explanation for the experimentally-observed eve stripe 3 and 7 expression patterns.

  10. Accurate protein structure modeling using sparse NMR data and homologous structure information.

    Science.gov (United States)

    Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

    2012-06-19

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

  11. A Statistical Model of Current Loops and Magnetic Monopoles

    International Nuclear Information System (INIS)

    Ayyer, Arvind

    2015-01-01

    We formulate a natural model of loops and isolated vertices for arbitrary planar graphs, which we call the monopole-dimer model. We show that the partition function of this model can be expressed as a determinant. We then extend the method of Kasteleyn and Temperley-Fisher to calculate the partition function exactly in the case of rectangular grids. This partition function turns out to be a square of a polynomial with positive integer coefficients when the grid lengths are even. Finally, we analyse this formula in the infinite volume limit and show that the local monopole density, free energy and entropy can be expressed in terms of well-known elliptic functions. Our technique is a novel determinantal formula for the partition function of a model of isolated vertices and loops for arbitrary graphs

  12. Loop algorithms for quantum simulations of fermion models on lattices

    International Nuclear Information System (INIS)

    Kawashima, N.; Gubernatis, J.E.; Evertz, H.G.

    1994-01-01

    Two cluster algorithms, based on constructing and flipping loops, are presented for world-line quantum Monte Carlo simulations of fermions and are tested on the one-dimensional repulsive Hubbard model. We call these algorithms the loop-flip and loop-exchange algorithms. For these two algorithms and the standard world-line algorithm, we calculated the autocorrelation times for various physical quantities and found that the ordinary world-line algorithm, which uses only local moves, suffers from very long correlation times that makes not only the estimate of the error difficult but also the estimate of the average values themselves difficult. These difficulties are especially severe in the low-temperature, large-U regime. In contrast, we find that new algorithms, when used alone or in combinations with themselves and the standard algorithm, can have significantly smaller autocorrelation times, in some cases being smaller by three orders of magnitude. The new algorithms, which use nonlocal moves, are discussed from the point of view of a general prescription for developing cluster algorithms. The loop-flip algorithm is also shown to be ergodic and to belong to the grand canonical ensemble. Extensions to other models and higher dimensions are briefly discussed

  13. One-loop dimensional reduction of the linear σ model

    International Nuclear Information System (INIS)

    Malbouisson, A.P.C.; Silva-Neto, M.B.; Svaiter, N.F.

    1997-05-01

    We perform the dimensional reduction of the linear σ model at one-loop level. The effective of the reduced theory obtained from the integration over the nonzero Matsubara frequencies is exhibited. Thermal mass and coupling constant renormalization constants are given, as well as the thermal renormalization group which controls the dependence of the counterterms on the temperature. We also recover, for the reduced theory, the vacuum instability of the model for large N. (author)

  14. Conformational sampling in template-free protein loop structure modeling: an overview.

    Science.gov (United States)

    Li, Yaohang

    2013-01-01

    Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

  15. CONFORMATIONAL SAMPLING IN TEMPLATE-FREE PROTEIN LOOP STRUCTURE MODELING: AN OVERVIEW

    Directory of Open Access Journals (Sweden)

    Yaohang Li

    2013-02-01

    Full Text Available Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

  16. Driver steering model for closed-loop steering function analysis

    Science.gov (United States)

    Bolia, Pratiksh; Weiskircher, Thomas; Müller, Steffen

    2014-05-01

    In this paper, a two level preview driver steering control model for the use in numerical vehicle dynamics simulation is introduced. The proposed model is composed of cascaded control loops: The outer loop is the path following layer based on potential field framework. The inner loop tries to capture the driver's physical behaviour. The proposed driver model allows easy implementation of different driving situations to simulate a wide range of different driver types, moods and vehicle types. The expediency of the proposed driver model is shown with the help of developed driver steering assist (DSA) function integrated with a conventional series production (Electric Power steering System with rack assist servo unit) system. With the help of the DSA assist function, the driver is prevented from over saturating the front tyre forces and loss of stability and controllability during cornering. The simulation results show different driver reactions caused by the change in the parameters or properties of the proposed driver model if the DSA assist function is activated. Thus, the proposed driver model is useful for the advanced driver steering and vehicle stability assist function evaluation in the early stage of vehicle dynamics handling and stability evaluation.

  17. Transient modelling of a natural circulation loop under variable pressure

    International Nuclear Information System (INIS)

    Vianna, Andre L.B.; Faccini, Jose L.H.; Su, Jian; Instituto de Engenharia Nuclear

    2017-01-01

    The objective of the present work is to model the transient operation of a natural circulation loop, which is one-tenth scale in height to a typical Passive Residual Heat Removal system (PRHR) of an Advanced Pressurized Water Nuclear Reactor and was designed to meet the single and two-phase flow similarity criteria to it. The loop consists of a core barrel with electrically heated rods, upper and lower plena interconnected by hot and cold pipe legs to a seven-tube shell heat exchanger of countercurrent design, and an expansion tank with a descending tube. A long transient characterized the loop operation, during which a phenomenon of self-pressurization, without self-regulation of the pressure, was experimentally observed. This represented a unique situation, named natural circulation under variable pressure (NCVP). The self-pressurization was originated in the air trapped in the expansion tank and compressed by the loop water dilatation, as it heated up during each experiment. The mathematical model, initially oriented to the single-phase flow, included the heat capacity of the structure and employed a cubic polynomial approximation for the density, in the buoyancy term calculation. The heater was modelled taking into account the different heat capacities of the heating elements and the heater walls. The heat exchanger was modelled considering the coolant heating, during the heat exchanging process. The self-pressurization was modelled as an isentropic compression of a perfect gas. The whole model was computationally implemented via a set of finite difference equations. The corresponding computational algorithm of solution was of the explicit, marching type, as for the time discretization, in an upwind scheme, regarding the space discretization. The computational program was implemented in MATLAB. Several experiments were carried out in the natural circulation loop, having the coolant flow rate and the heating power as control parameters. The variables used in the

  18. Transient modelling of a natural circulation loop under variable pressure

    Energy Technology Data Exchange (ETDEWEB)

    Vianna, Andre L.B.; Faccini, Jose L.H.; Su, Jian, E-mail: avianna@nuclear.ufrj.br, E-mail: sujian@nuclear.ufrj.br, E-mail: faccini@ien.gov.br [Coordenacao de Pos-Graduacao e Pesquisa de Engenharia (COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Programa de Engenharia Nuclear; Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil). Lab. de Termo-Hidraulica Experimental

    2017-07-01

    The objective of the present work is to model the transient operation of a natural circulation loop, which is one-tenth scale in height to a typical Passive Residual Heat Removal system (PRHR) of an Advanced Pressurized Water Nuclear Reactor and was designed to meet the single and two-phase flow similarity criteria to it. The loop consists of a core barrel with electrically heated rods, upper and lower plena interconnected by hot and cold pipe legs to a seven-tube shell heat exchanger of countercurrent design, and an expansion tank with a descending tube. A long transient characterized the loop operation, during which a phenomenon of self-pressurization, without self-regulation of the pressure, was experimentally observed. This represented a unique situation, named natural circulation under variable pressure (NCVP). The self-pressurization was originated in the air trapped in the expansion tank and compressed by the loop water dilatation, as it heated up during each experiment. The mathematical model, initially oriented to the single-phase flow, included the heat capacity of the structure and employed a cubic polynomial approximation for the density, in the buoyancy term calculation. The heater was modelled taking into account the different heat capacities of the heating elements and the heater walls. The heat exchanger was modelled considering the coolant heating, during the heat exchanging process. The self-pressurization was modelled as an isentropic compression of a perfect gas. The whole model was computationally implemented via a set of finite difference equations. The corresponding computational algorithm of solution was of the explicit, marching type, as for the time discretization, in an upwind scheme, regarding the space discretization. The computational program was implemented in MATLAB. Several experiments were carried out in the natural circulation loop, having the coolant flow rate and the heating power as control parameters. The variables used in the

  19. Homology modelling of Drosophila cytochrome P450 enzymes associated with insecticide resistance.

    Science.gov (United States)

    Jones, Robert T; Bakker, Saskia E; Stone, Deborah; Shuttleworth, Sally N; Boundy, Sam; McCart, Caroline; Daborn, Phillip J; ffrench-Constant, Richard H; van den Elsen, Jean M H

    2010-10-01

    Overexpression of the cytochrome P450 gene Cyp6g1 confers resistance against DDT and a broad range of other insecticides in Drosophila melanogaster Meig. In the absence of crystal structures of CYP6G1 or complexes with its substrates, structural studies rely on homology modelling and ligand docking to understand P450-substrate interactions. Homology models are presented for CYP6G1, a P450 associated with resistance to DDT and neonicotinoids, and two other enzymes associated with insecticide resistance in D. melanogaster, CYP12D1 and CYP6A2. The models are based on a template of the X-ray structure of the phylogenetically related human CYP3A4, which is known for its broad substrate specificity. The model of CYP6G1 has a much smaller active site cavity than the template. The cavity is also 'V'-shaped and is lined with hydrophobic residues, showing high shape and chemical complementarity with the molecular characteristics of DDT. Comparison of the DDT-CYP6G1 complex and a non-resistant CYP6A2 homology model implies that tight-fit recognition of this insecticide is important in CYP6G1. The active site can accommodate differently shaped substrates ranging from imidacloprid to malathion but not the pyrethroids permethrin and cyfluthrin. The CYP6G1, CYP12D1 and CYP6A2 homology models can provide a structural insight into insecticide resistance in flies overexpressing P450 enzymes with broad substrate specificities.

  20. GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models.

    Science.gov (United States)

    Miszta, Przemyslaw; Pasznik, Pawel; Jakowiecki, Jakub; Sztyler, Agnieszka; Latek, Dorota; Filipek, Slawomir

    2018-05-21

    Due to the involvement of G protein-coupled receptors (GPCRs) in most of the physiological and pathological processes in humans they have been attracting a lot of attention from pharmaceutical industry as well as from scientific community. Therefore, the need for new, high quality structures of GPCRs is enormous. The updated homology modeling service GPCRM (http://gpcrm.biomodellab.eu/) meets those expectations by greatly reducing the execution time of submissions (from days to hours/minutes) with nearly the same average quality of obtained models. Additionally, due to three different scoring functions (Rosetta, Rosetta-MP, BCL::Score) it is possible to select accurate models for the required purposes: the structure of the binding site, the transmembrane domain or the overall shape of the receptor. Currently, no other web service for GPCR modeling provides this possibility. GPCRM is continually upgraded in a semi-automatic way and the number of template structures has increased from 20 in 2013 to over 90 including structures the same receptor with different ligands which can influence the structure not only in the on/off manner. Two types of protein viewers can be used for visual inspection of obtained models. The extended sortable tables with available templates provide links to external databases and display ligand-receptor interactions in visual form.

  1. 3D MHD MODELING OF TWISTED CORONAL LOOPS

    Energy Technology Data Exchange (ETDEWEB)

    Reale, F.; Peres, G. [Dipartimento di Fisica and Chimica, Università di Palermo, Piazza del Parlamento 1, I-90134 Palermo (Italy); Orlando, S. [INAF-Osservatorio Astronomico di Palermo, Piazza del Parlamento 1, I-90134 Palermo (Italy); Guarrasi, M. [CINECA—Interuniversity consortium, via Magnanelli 6/3, I-40033, Casalecchio di Reno, Bologna (Italy); Mignone, A. [Dipartimento di Fisica Generale, Università di Torino, via Pietro Giuria 1, I-10125, Torino (Italy); Hood, A. W.; Priest, E. R., E-mail: fabio.reale@unipa.it [School of Mathematics and Statistics, University of St. Andrews, St. Andrews, KY16 9SS (United Kingdom)

    2016-10-10

    We perform MHD modeling of a single bright coronal loop to include the interaction with a non-uniform magnetic field. The field is stressed by random footpoint rotation in the central region and its energy is dissipated into heating by growing currents through anomalous magnetic diffusivity that switches on in the corona above a current density threshold. We model an entire single magnetic flux tube in the solar atmosphere extending from the high- β chromosphere to the low- β corona through the steep transition region. The magnetic field expands from the chromosphere to the corona. The maximum resolution is ∼30 km. We obtain an overall evolution typical of loop models and realistic loop emission in the EUV and X-ray bands. The plasma confined in the flux tube is heated to active region temperatures (∼3 MK) after ∼2/3 hr. Upflows from the chromosphere up to ∼100 km s{sup −1} fill the core of the flux tube to densities above 10{sup 9} cm{sup −3}. More heating is released in the low corona than the high corona and is finely structured both in space and time.

  2. Homology modelling and docking analysis of L-lactate dehydrogenase from Streptococcus thermopilus

    Directory of Open Access Journals (Sweden)

    Vukić Vladimir R.

    2016-01-01

    Full Text Available The aim of this research was to create a three-dimensional model of L-lactate dehydrogenase from the main yoghurt starter culture - Streptococcus thermopilus, to analyse its structural features and investigate substrate binding in the active site. NCBI BlastP was used against the Protein Data Bank database in order to identify the template for construction of homology models. Multiple sequence alignment was performed using the program MUSCULE within the UGENE 1.11.3 program. Homology models were constructed using the program Modeller v. 9.17. The obtained 3D model was verified by Ramachandran plots. Molecular docking simulations were performed using the program Surflex-Dock. The highest sequence similarity was observed with L-lactate dehydrogenase from Lactobacillus casei subsp. casei, with 69% identity. Therefore, its structure (PDB ID: 2ZQY:A was selected as a modelling template for homology modelling. Active residues are by sequence similarity predicted: S. thermophilus - HIS181 and S. aureus - HIS179. Binding energy of pyruvate to L-lactate dehydrogenase of S. thermopilus was - 7.874 kcal/mol. Pyruvate in L-lactate dehydrogenase of S. thermopilus makes H bonds with catalytic HIS181 (1.9 Å, as well as with THR235 (3.6 Å. Although our results indicate similar position of substrates between L-lactate dehydrogenase of S. thermopilus and S. aureus, differences in substrate distances and binding energy values could influence the reaction rate. Based on these results, the L-lactate dehydrogenase model proposed here could be used as a guide for further research, such as transition states of the reaction through molecular dynamics. [Projekat Ministarstva nauke Republike Srbije, br. III 46009

  3. A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.

    Science.gov (United States)

    Cole, R T; Lucas, C L; Cascio, W E; Johnson, T A

    2005-11-01

    While numerous computer models exist for the circulatory system, many are limited in scope, contain unwanted features or incorporate complex components specific to unique experimental situations. Our purpose was to develop a basic, yet multifaceted, computer model of the left heart and systemic circulation in LabVIEW having universal appeal without sacrificing crucial physiologic features. The program we developed employs Windkessel-type impedance models in several open-loop configurations and a closed-loop model coupling a lumped impedance and ventricular pressure source. The open-loop impedance models demonstrate afterload effects on arbitrary aortic pressure/flow inputs. The closed-loop model catalogs the major circulatory waveforms with changes in afterload, preload, and left heart properties. Our model provides an avenue for expanding the use of the ventricular equations through closed-loop coupling that includes a basic coronary circuit. Tested values used for the afterload components and the effects of afterload parameter changes on various waveforms are consistent with published data. We conclude that this model offers the ability to alter several circulatory factors and digitally catalog the most salient features of the pressure/flow waveforms employing a user-friendly platform. These features make the model a useful instructional tool for students as well as a simple experimental tool for cardiovascular research.

  4. 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

  5. Phenomenological aspects of heterotic orbifold models at one loop

    International Nuclear Information System (INIS)

    Birkedal-Hansen, A.; Binetruy, P.; Mambrini, Y.; Nelson, B.

    2003-01-01

    We provide a detailed study of the phenomenology of orbifold compactifications of the heterotic string within the context of supergravity effective theories. Our investigation focuses on those models where the soft Lagrangian is dominated by loop contributions to the various soft supersymmetry breaking parameters. Such models typically predict non-universal soft masses and are thus significantly different from minimal supergravity and other universal models. We consider the pattern of masses that are governed by these soft terms and investigate the implications of certain indirect constraints on supersymmetric models, such as flavor-changing neutral currents, the anomalous magnetic moment of the muon and the density of thermal relic neutralinos. These string-motivated models show novel behavior that interpolates between the phenomenology of unified supergravity models and models dominated by the superconformal anomaly

  6. The Bianchi IX model in loop quantum cosmology

    International Nuclear Information System (INIS)

    Bojowald, Martin; Date, Ghanashyam; Hossain, Golam Mortuza

    2004-01-01

    The Bianchi IX model has been used often to investigate the structure close to singularities of general relativity. Its classical chaos is expected to have, via the BKL scenario, implications even for the approach to general inhomogeneous singularities. Thus, it is a popular model to test consequences of modifications to general relativity suggested by quantum theories of gravity. This paper presents a detailed proof that modifications coming from loop quantum gravity lead to a non-chaotic effective behaviour. The way this is realized, independently of quantization ambiguities, suggests a new look at initial and final singularities

  7. Polyglutamine Disease Modeling: Epitope Based Screen for Homologous Recombination using CRISPR/Cas9 System.

    Science.gov (United States)

    An, Mahru C; O'Brien, Robert N; Zhang, Ningzhe; Patra, Biranchi N; De La Cruz, Michael; Ray, Animesh; Ellerby, Lisa M

    2014-04-15

    We have previously reported the genetic correction of Huntington's disease (HD) patient-derived induced pluripotent stem cells using traditional homologous recombination (HR) approaches. To extend this work, we have adopted a CRISPR-based genome editing approach to improve the efficiency of recombination in order to generate allelic isogenic HD models in human cells. Incorporation of a rapid antibody-based screening approach to measure recombination provides a powerful method to determine relative efficiency of genome editing for modeling polyglutamine diseases or understanding factors that modulate CRISPR/Cas9 HR.

  8. Twist operator correlation functions in O(n) loop models

    International Nuclear Information System (INIS)

    Simmons, Jacob J H; Cardy, John

    2009-01-01

    Using conformal field theoretic methods we calculate correlation functions of geometric observables in the loop representation of the O(n) model at the critical point. We focus on correlation functions containing twist operators, combining these with anchored loops, boundaries with SLE processes and with double SLE processes. We focus further upon n = 0, representing self-avoiding loops, which corresponds to a logarithmic conformal field theory (LCFT) with c = 0. In this limit the twist operator plays the role of a 0-weight indicator operator, which we verify by comparison with known examples. Using the additional conditions imposed by the twist operator null states, we derive a new explicit result for the probabilities that an SLE 8/3 winds in various ways about two points in the upper half-plane, e.g. that the SLE passes to the left of both points. The collection of c = 0 logarithmic CFT operators that we use deriving the winding probabilities is novel, highlighting a potential incompatibility caused by the presence of two distinct logarithmic partners to the stress tensor within the theory. We argue that both partners do appear in the theory, one in the bulk and one on the boundary and that the incompatibility is resolved by restrictive bulk-boundary fusion rules

  9. DockoMatic 2.0: high throughput inverse virtual screening and homology modeling.

    Science.gov (United States)

    Bullock, Casey; Cornia, Nic; Jacob, Reed; Remm, Andrew; Peavey, Thomas; Weekes, Ken; Mallory, Chris; Oxford, Julia T; McDougal, Owen M; Andersen, Timothy L

    2013-08-26

    DockoMatic is a free and open source application that unifies a suite of software programs within a user-friendly graphical user interface (GUI) to facilitate molecular docking experiments. Here we describe the release of DockoMatic 2.0; significant software advances include the ability to (1) conduct high throughput inverse virtual screening (IVS); (2) construct 3D homology models; and (3) customize the user interface. Users can now efficiently setup, start, and manage IVS experiments through the DockoMatic GUI by specifying receptor(s), ligand(s), grid parameter file(s), and docking engine (either AutoDock or AutoDock Vina). DockoMatic automatically generates the needed experiment input files and output directories and allows the user to manage and monitor job progress. Upon job completion, a summary of results is generated by Dockomatic to facilitate interpretation by the user. DockoMatic functionality has also been expanded to facilitate the construction of 3D protein homology models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides an interface that accesses the basic local alignment search tool (BLAST) and MODELER programs and guides the user through the necessary steps to easily and efficiently create 3D homology models for biomacromolecular structures. The DockoMatic GUI can be customized by the user, and the software design makes it relatively easy to integrate additional docking engines, scoring functions, or third party programs. DockoMatic is a free comprehensive molecular docking software program for all levels of scientists in both research and education.

  10. Closed Loop Brain Model of Neocortical Information Based Exchange

    Directory of Open Access Journals (Sweden)

    James eKozloski

    2016-01-01

    Full Text Available Here we describe an information based exchange' model of brain function that ascribes to neocortex, basal ganglia, and thalamus distinct network functions. The model allows us to analyze whole brain system set point measures, such as the rate and heterogeneity of transitions in striatum and neocortex, in the context of neuromodulation and other perturbations. Our closed-loop model is grounded in neuroanatomical observations, proposing a novel Grand Loop through neocortex, and invokes different forms of plasticity at specific tissue interfaces and their principle cell synapses to achieve these transitions. By implementing a system for maximum information based exchange of action potentials between modeled neocortical areas, we observe changes to these measures in simulation. We hypothesize that similar dynamic set points and modulations exist in the brain's resting state activity, and that different modifications to information based exchange may shift the risk profile of different component tissues, resulting in different neurodegenerative diseases. This model is targeted for further development using IBM's Neural Tissue Simulator, which allows scalable elaboration of networks, tissues, and their neural and synaptic components towards ever greater complexity and biological realism.

  11. Loop quantum cosmology of the Bianchi I model: complete quantization

    International Nuclear Information System (INIS)

    Martín-Benito, M; Garay, L J; Mena Marugán, G A; Wilson-Ewing, E

    2012-01-01

    We complete the canonical quantization of the vacuum Bianchi I model within the improved dynamics scheme of loop quantum cosmology, characterizing the Hilbert structure of the physical states and providing a complete set of observables acting on them. In order to achieve this task, it has been essential to determine the structure of the separable superselection sectors that arise owing to the polymeric quantization, and to prove that the initial value problem obtained when regarding the Hamiltonian constraint as an evolution equation, interpreting the volume as the evolution parameter, is well-posed.

  12. Structural insights into a high affinity nanobody:antigen complex by homology modelling

    DEFF Research Database (Denmark)

    Skottrup, Peter Durand

    2017-01-01

    Porphyromonas gingivalis is a major periodontitis-causing pathogens. P. gingivalis secrete a cysteine protease termed RgpB, which is specific for Arg-Xaa bonds in substrates. Recently, a nanobody-based assay was used to demonstrate that RgpB could represent a novel diagnostic target, thereby...... simplifying. P. gingivalis detection. The nanobody, VHH7, had a high binding affinity and was specific for RgpB, when tested towards the highly identical RgpA. In this study a homology model of VHH7 was build. The complementarity determining regions (CDR) comprising the paratope residues responsible for Rgp...

  13. Cumulative growth of minor hysteresis loops in the Kolmogorov model

    International Nuclear Information System (INIS)

    Meilikhov, E. Z.; Farzetdinova, R. M.

    2013-01-01

    The phenomenon of nonrepeatability of successive remagnetization cycles in Co/M (M = Pt, Pd, Au) multilayer film structures is explained in the framework of the Kolmogorov crystallization model. It is shown that this model of phase transitions can be adapted so as to adequately describe the process of magnetic relaxation in the indicated systems with “memory.” For this purpose, it is necessary to introduce some additional elements into the model, in particular, (i) to take into account the fact that every cycle starts from a state “inherited” from the preceding cycle and (ii) to assume that the rate of growth of a new magnetic phase depends on the cycle number. This modified model provides a quite satisfactory qualitative and quantitative description of all features of successive magnetic relaxation cycles in the system under consideration, including the surprising phenomenon of cumulative growth of minor hysteresis loops.

  14. Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.

    Directory of Open Access Journals (Sweden)

    2005-08-01

    Full Text Available The bias in protein structure and function space resulting from experimental limitations and targeting of particular functional classes of proteins by structural biologists has long been recognized, but never continuously quantified. Using the Enzyme Commission and the Gene Ontology classifications as a reference frame, and integrating structure data from the Protein Data Bank (PDB, target sequences from the structural genomics projects, structure homology derived from the SUPERFAMILY database, and genome annotations from Ensembl and NCBI, we provide a quantified view, both at the domain and whole-protein levels, of the current and projected coverage of protein structure and function space relative to the human genome. Protein structures currently provide at least one domain that covers 37% of the functional classes identified in the genome; whole structure coverage exists for 25% of the genome. If all the structural genomics targets were solved (twice the current number of structures in the PDB, it is estimated that structures of one domain would cover 69% of the functional classes identified and complete structure coverage would be 44%. Homology models from existing experimental structures extend the 37% coverage to 56% of the genome as single domains and 25% to 31% for complete structures. Coverage from homology models is not evenly distributed by protein family, reflecting differing degrees of sequence and structure divergence within families. While these data provide coverage, conversely, they also systematically highlight functional classes of proteins for which structures should be determined. Current key functional families without structure representation are highlighted here; updated information on the "most wanted list" that should be solved is available on a weekly basis from http://function.rcsb.org:8080/pdb/function_distribution/index.html.

  15. Structural insights into a high affinity nanobody:antigen complex by homology modelling.

    Science.gov (United States)

    Skottrup, Peter Durand

    2017-09-01

    Porphyromonas gingivalis is a major periodontitis-causing pathogens. P. gingivalis secrete a cysteine protease termed RgpB, which is specific for Arg-Xaa bonds in substrates. Recently, a nanobody-based assay was used to demonstrate that RgpB could represent a novel diagnostic target, thereby simplifying. P. gingivalis detection. The nanobody, VHH7, had a high binding affinity and was specific for RgpB, when tested towards the highly identical RgpA. In this study a homology model of VHH7 was build. The complementarity determining regions (CDR) comprising the paratope residues responsible for RgpB binding were identified and used as input to the docking. Furthermore, residues likely involved in the RgpB epitope was identified based upon RgpB:RgpA alignment and analysis of residue surface accessibility. CDR residues and putitative RgpB epitope residues were used as input to an information-driven flexible docking approach using the HADDOCK server. Analysis of the VHH7:RgpB model demonstrated that the epitope was found in the immunoglobulin-like domain and residue pairs located at the molecular paratope:epitope interface important for complex stability was identified. Collectively, the VHH7 homology model and VHH7:RgpB docking supplies knowledge of the residues involved in the high affinity interaction. This information could prove valuable in the design of an antibody-drug conjugate for specific RgpB targeting. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Variable selection in near infrared spectroscopy for quantitative models of homologous analogs of cephalosporins

    Directory of Open Access Journals (Sweden)

    Yan-Chun Feng

    2014-07-01

    Full Text Available Two universal spectral ranges (4550–4100 cm-1 and 6190–5510 cm-1 for construction of quantitative models of homologous analogs of cephalosporins were proposed by evaluating the performance of five spectral ranges and their combinations, using three data sets of cephalosporins for injection, i.e., cefuroxime sodium, ceftriaxone sodium and cefoperazone sodium. Subsequently, the proposed ranges were validated by using eight calibration sets of other homologous analogs of cephalosporins for injection, namely cefmenoxime hydrochloride, ceftezole sodium, cefmetazole, cefoxitin sodium, cefotaxime sodium, cefradine, cephazolin sodium and ceftizoxime sodium. All the constructed quantitative models for the eight kinds of cephalosporins using these universal ranges could fulfill the requirements for quick quantification. After that, competitive adaptive reweighted sampling (CARS algorithm and infrared (IR–near infrared (NIR two-dimensional (2D correlation spectral analysis were used to determine the scientific basis of these two spectral ranges as the universal regions for the construction of quantitative models of cephalosporins. The CARS algorithm demonstrated that the ranges of 4550–4100 cm-1 and 6190–5510 cm-1 included some key wavenumbers which could be attributed to content changes of cephalosporins. The IR–NIR 2D spectral analysis showed that certain wavenumbers in these two regions have strong correlations to the structures of those cephalosporins that were easy to degrade.

  17. Two-point boundary correlation functions of dense loop models

    Directory of Open Access Journals (Sweden)

    Alexi Morin-Duchesne, Jesper Lykke Jacobsen

    2018-06-01

    Full Text Available We investigate six types of two-point boundary correlation functions in the dense loop model. These are defined as ratios $Z/Z^0$ of partition functions on the $m\\times n$ square lattice, with the boundary condition for $Z$ depending on two points $x$ and $y$. We consider: the insertion of an isolated defect (a and a pair of defects (b in a Dirichlet boundary condition, the transition (c between Dirichlet and Neumann boundary conditions, and the connectivity of clusters (d, loops (e and boundary segments (f in a Neumann boundary condition. For the model of critical dense polymers, corresponding to a vanishing loop weight ($\\beta = 0$, we find determinant and pfaffian expressions for these correlators. We extract the conformal weights of the underlying conformal fields and find $\\Delta = -\\frac18$, $0$, $-\\frac3{32}$, $\\frac38$, $1$, $\\tfrac \\theta \\pi (1+\\tfrac{2\\theta}\\pi$, where $\\theta$ encodes the weight of one class of loops for the correlator of type f. These results are obtained by analysing the asymptotics of the exact expressions, and by using the Cardy-Peschel formula in the case where $x$ and $y$ are set to the corners. For type b, we find a $\\log|x-y|$ dependence from the asymptotics, and a $\\ln (\\ln n$ term in the corner free energy. This is consistent with the interpretation of the boundary condition of type b as the insertion of a logarithmic field belonging to a rank two Jordan cell. For the other values of $\\beta = 2 \\cos \\lambda$, we use the hypothesis of conformal invariance to predict the conformal weights and find $\\Delta = \\Delta_{1,2}$, $\\Delta_{1,3}$, $\\Delta_{0,\\frac12}$, $\\Delta_{1,0}$, $\\Delta_{1,-1}$ and $\\Delta_{\\frac{2\\theta}\\lambda+1,\\frac{2\\theta}\\lambda+1}$, extending the results of critical dense polymers. With the results for type f, we reproduce a Coulomb gas prediction for the valence bond entanglement entropy of Jacobsen and Saleur.

  18. Finding Positive Feedback Loops in Environmental Models: A Mathematical Investigation

    Science.gov (United States)

    Sheikholeslami, R.; Razavi, S.

    2016-12-01

    Dynamics of most earth and environmental systems are generally governed by interactions between several hydrological (e.g., soil moisture and precipitation), geological (e.g., and erosion), geochemical (e.g., nutrient loading), and atmospheric (e.g., temperature) processes which operate on a range of spatio-temporal scales. These interactions create numerous feedback mechanisms with complex behaviours, and their understanding and representation can vary depending on the scale in space and/or time at which the system is analyzed. One of the most crucial characteristics of such complex systems is the existence of positive feedback loops. The presence of positive feedbacks may increase complexity, accelerate change, or trigger multiple stable states in the underlying dynamical system. Furthermore, because of the inherent non-linearity, it is often very difficult to obtain a general idea of their complex dynamics. Feedback loops in environmental systems have been well recognized and qualitatively discussed. With a quantitative/mathematical view, in this presentation, we address the question of how the positive feedback loops can be identified/implemented in environmental models. We investigate the nature of different feedback mechanisms and dynamics of simple example case studies that underlie fundamental processes such as vegetation, precipitation and soil moisture. To do this, we apply the concept of "interaction graph" from mathematics which is built from the Jacobian matrix of the dynamical system. The Jacobian matrix contains information on how variations of one state variable depends on variations of other variables, and thus can be used to understand the dynamical possibilities of feedback mechanisms in the underlying system. Moreover, this study highlights that there are some situations where the existence of positive feedback loops can cause multiple stable states, and thereby regime shifts in environmental systems. Systems with multiple stable states are

  19. Modeling Loop Reorganization Free Energies of Acetylcholinesterase: A Comparison of Explicit and Implicit Solvent Models

    National Research Council Canada - National Science Library

    Olson, Mark

    2004-01-01

    ... screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy difference between two loop conformations in acetylcholinesterase...

  20. Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode.

    Science.gov (United States)

    Krishnamoorthy, Ezhilarasi; Hassan, Sameer; Hanna, Luke Elizabeth; Padmalayam, Indira; Rajaram, Rama; Viswanathan, Vijay

    2017-05-07

    Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role. A homology model for LIAS protein was generated using X-ray crystallographic structure of Thermosynechococcus elongatus BP-1 (PDB ID: 4U0P). The predicted structure has 93% of the residues in the most favour region of Ramachandran plot. The active site of LIAS protein was mapped and docked with S-Adenosyl Methionine (SAM) using GOLD software. The LIAS-SAM complex was further refined using molecular dynamics simulation within the subsite 1 and subsite 3 of the active site. To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will facilitate a better understanding mode of action of the enzyme-substrate complex for future studies in designing drugs that can target LIAS protein. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Equipment for fully homologous bulb turbine model testing in Laval University

    International Nuclear Information System (INIS)

    Fraser R; Vallée D; Jean Y; Deschênes C

    2014-01-01

    Within the context of liberalisation of the energy market, hydroelectricity remains a first class source of clean and renewable energy. Combining the growing demand of energy, its increasing value and the appreciation associated to the sustainable development, low head sites formerly considered as non-profitable are now exploitable. Bulb turbines likely to equip such sites are traditionally developed on model using right angle transmission leading to piers enlargement for power take off shaft passage, thus restricting possibilities to have fully homologous hydraulic passages. Aiming to sustain good quality development on fully homologous scale model of bulb turbines, the Hydraulic Machines Laboratory (LAMH) of Laval University has developed a brake with an enhanced power to weight ratio. This powerful brake is small enough to be located in the bulb shell while dissipating power without mandatory test head reduction. This paper first presents the basic technology of this brake and its application. Then both its main performance capabilities and dimensional characteristics will be detailed. The instrumentation used to perform accurate measurements will be finally presented

  2. Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening

    Energy Technology Data Exchange (ETDEWEB)

    Kalyanaraman, C.; Imker, H; Fedorov, A; Fedorov, E; Glasner, M; Babbitt, P; Almo, S; Gerlt, J; Jacobson, M

    2008-01-01

    We have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity.

  3. A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

    Directory of Open Access Journals (Sweden)

    Maurer Till

    2005-04-01

    Full Text Available Abstract Background We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Döker et al. (1999, BBRC, 257, 348–350. The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS. Results To test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor γ (Ppar γ. The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar γ was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms. Conclusion In summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

  4. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach...... to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions...... in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural...

  5. Efficient dynamic modeling of manipulators containing closed kinematic loops

    Science.gov (United States)

    Ferretti, Gianni; Rocco, Paolo

    An approach to efficiently solve the forward dynamics problem for manipulators containing closed chains is proposed. The two main distinctive features of this approach are: the dynamics of the equivalent open loop tree structures (any closed loop can be in general modeled by imposing some additional kinematic constraints to a suitable tree structure) is computed through an efficient Newton Euler formulation; the constraint equations relative to the most commonly adopted closed chains in industrial manipulators are explicitly solved, thus, overcoming the redundancy of Lagrange's multipliers method while avoiding the inefficiency due to a numerical solution of the implicit constraint equations. The constraint equations considered for an explicit solution are those imposed by articulated gear mechanisms and planar closed chains (pantograph type structures). Articulated gear mechanisms are actually used in all industrial robots to transmit motion from actuators to links, while planar closed chains are usefully employed to increase the stiffness of the manipulators and their load capacity, as well to reduce the kinematic coupling of joint axes. The accuracy and the efficiency of the proposed approach are shown through a simulation test.

  6. Improving model construction of profile HMMs for remote homology detection through structural alignment

    Directory of Open Access Journals (Sweden)

    Zaverucha Gerson

    2007-11-01

    Full Text Available Abstract Background Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. Results We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. Conclusion We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

  7. Improving model construction of profile HMMs for remote homology detection through structural alignment.

    Science.gov (United States)

    Bernardes, Juliana S; Dávila, Alberto M R; Costa, Vítor S; Zaverucha, Gerson

    2007-11-09

    Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

  8. Homology modeling of parasite histone deacetylases to guide the structure-based design of selective inhibitors.

    Science.gov (United States)

    Melesina, Jelena; Robaa, Dina; Pierce, Raymond J; Romier, Christophe; Sippl, Wolfgang

    2015-11-01

    Histone deacetylases (HDACs) are promising epigenetic targets for the treatment of various diseases, including cancer and neurodegenerative disorders. There is evidence that they can also be addressed to treat parasitic infections. Recently, the first X-ray structure of a parasite HDAC was published, Schistosoma mansoni HDAC8, giving structural insights into its inhibition. However, most of the targets from parasites of interest still lack this structural information. Therefore, we prepared homology models of relevant parasitic HDACs and compared them to human and S. mansoni HDACs. The information about known S. mansoni HDAC8 inhibitors and compounds that affect the growth of Trypanosoma, Leishmania and Plasmodium species was used to validate the models by docking and molecular dynamics studies. Our results provide analysis of structural features of parasitic HDACs and should be helpful for selecting promising candidates for biological testing and for structure-based optimisation of parasite-specific inhibitors. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Rectangular amplitudes, conformal blocks, and applications to loop models

    Energy Technology Data Exchange (ETDEWEB)

    Bondesan, Roberto, E-mail: roberto.bondesan@cea.fr [LPTENS, Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris (France); Institute de Physique Theorique, CEA Saclay, F-91191 Gif-sur-Yvette (France); Jacobsen, Jesper L. [LPTENS, Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris (France); Universite Pierre et Marie Curie, 4 place Jussieu, 75252 Paris (France); Saleur, Hubert [Institute de Physique Theorique, CEA Saclay, F-91191 Gif-sur-Yvette (France); Physics Department, USC, Los Angeles, CA 90089-0484 (United States)

    2013-02-21

    In this paper we continue the investigation of partition functions of critical systems on a rectangle initiated in [R. Bondesan, et al., Nucl. Phys. B 862 (2012) 553-575]. Here we develop a general formalism of rectangle boundary states using conformal field theory, adapted to describe geometries supporting different boundary conditions. We discuss the computation of rectangular amplitudes and their modular properties, presenting explicit results for the case of free theories. In a second part of the paper we focus on applications to loop models, discussing in details lattice discretizations using both numerical and analytical calculations. These results allow to interpret geometrically conformal blocks, and as an application we derive new probability formulas for self-avoiding walks.

  10. Polyakov loop and the hadron resonance gas model.

    Science.gov (United States)

    Megías, E; Arriola, E Ruiz; Salcedo, L L

    2012-10-12

    The Polyakov loop has been used repeatedly as an order parameter in the deconfinement phase transition in QCD. We argue that, in the confined phase, its expectation value can be represented in terms of hadronic states, similarly to the hadron resonance gas model for the pressure. Specifically, L(T)≈1/2[∑(α)g(α)e(-Δ(α)/T), where g(α) are the degeneracies and Δ(α) are the masses of hadrons with exactly one heavy quark (the mass of the heavy quark itself being subtracted). We show that this approximate sum rule gives a fair description of available lattice data with N(f)=2+1 for temperatures in the range 150 MeVmodels. For temperatures below 150 MeV different lattice results disagree. One set of data can be described if exotic hadrons are present in the QCD spectrum while other sets do not require such states.

  11. Electromagnetic Modeling of the Passive Stabilization Loop at EAST

    International Nuclear Information System (INIS)

    Ji Xiang; Song Yuntao; Wu Songtao; Wang Zhibin; Shen Guang; Liu Xufeng; Cao Lei; Zhou Zibo; Peng Xuebing; Wang Chenghao

    2012-01-01

    A passive stabilization loop (PSL) has been designed and manufactured in order to enhance the control of vertical instability and accommodate the new stage for high-performance plasma at EAST. Eddy currents are induced by vertical displacement events (VDEs) and disruption, which can produce a magnetic field to control the vertical instability of the plasma in a short timescale. A finite element model is created and meshed using ANSYS software. Based on the simulation of plasma VDEs and disruption, the distribution and decay curve of the eddy currents on the PSL are obtained. The largest eddy current is 200 kA and the stress is 68 MPa at the outer current bridge, which is the weakest point of the PSL because of the eddy currents and the magnetic fields. The analysis results provide the supporting data for the structural design.

  12. Electromagnetic Modeling of the Passive Stabilization Loop at EAST

    Science.gov (United States)

    Ji, Xiang; Song, Yuntao; Wu, Songtao; Wang, Zhibin; Shen, Guang; Liu, Xufeng; Cao, Lei; Zhou, Zibo; Peng, Xuebing; Wang, Chenghao

    2012-09-01

    A passive stabilization loop (PSL) has been designed and manufactured in order to enhance the control of vertical instability and accommodate the new stage for high-performance plasma at EAST. Eddy currents are induced by vertical displacement events (VDEs) and disruption, which can produce a magnetic field to control the vertical instability of the plasma in a short timescale. A finite element model is created and meshed using ANSYS software. Based on the simulation of plasma VDEs and disruption, the distribution and decay curve of the eddy currents on the PSL are obtained. The largest eddy current is 200 kA and the stress is 68 MPa at the outer current bridge, which is the weakest point of the PSL because of the eddy currents and the magnetic fields. The analysis results provide the supporting data for the structural design.

  13. In silico predictive studies of mAHR congener binding using homology modelling and molecular docking.

    Science.gov (United States)

    Panda, Roshni; Cleave, A Suneetha Susan; Suresh, P K

    2014-09-01

    The aryl hydrocarbon receptor (AHR) is one of the principal xenobiotic, nuclear receptor that is responsible for the early events involved in the transcription of a complex set of genes comprising the CYP450 gene family. In the present computational study, homology modelling and molecular docking were carried out with the objective of predicting the relationship between the binding efficiency and the lipophilicity of different polychlorinated biphenyl (PCB) congeners and the AHR in silico. Homology model of the murine AHR was constructed by several automated servers and assessed by PROCHECK, ERRAT, VERIFY3D and WHAT IF. The resulting model of the AHR by MODWEB was used to carry out molecular docking of 36 PCB congeners using PatchDock server. The lipophilicity of the congeners was predicted using the XLOGP3 tool. The results suggest that the lipophilicity influences binding energy scores and is positively correlated with the same. Score and Log P were correlated with r = +0.506 at p = 0.01 level. In addition, the number of chlorine (Cl) atoms and Log P were highly correlated with r = +0.900 at p = 0.01 level. The number of Cl atoms and scores also showed a moderate positive correlation of r = +0.481 at p = 0.01 level. To the best of our knowledge, this is the first study employing PatchDock in the docking of AHR to the environmentally deleterious congeners and attempting to correlate structural features of the AHR with its biochemical properties with regards to PCBs. The result of this study are consistent with those of other computational studies reported in the previous literature that suggests that a combination of docking, scoring and ranking organic pollutants could be a possible predictive tool for investigating ligand-mediated toxicity, for their subsequent validation using wet lab-based studies. © The Author(s) 2012.

  14. Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview

    OpenAIRE

    Li, Yaohang

    2013-01-01

    Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increas...

  15. Description of the two-loop RELAP5 model of the L-Reactor at the Savannah River Site

    International Nuclear Information System (INIS)

    Cozzuol, J.M.; Davis, C.B.

    1989-12-01

    A two-loop RELAP5 input model of the L-Reactor at the Savannah River Site (SRS) was developed to support thermal-hydraulic analysis of SRS reactors. The model was developed to economically evaluate potential design changes. The primary simplifications in the model were in the number of loops and the detail in the moderator tank. The six loops in the reactor were modeled with two loops, one representing a single loop and the other representing five combined loops. The model has undergone a quality assurance review. This report describes the two-loop model, its limitations, and quality assurance. 29 refs., 18 figs., 10 tabs

  16. Loop Corrections in Very Special Relativity Standard Model

    Science.gov (United States)

    Alfaro, Jorge

    2018-01-01

    In this talk we want to study one-loop corrections in VSRSM. In particular, we use the new Sim(2)-invariant dimensional regularization to compute one-loop corrections to the Effective Action in the subsector of the VSRSM that describe the interaction of photons with charged leptons. New stringent bounds for the masses of ve and vµ are obtained.

  17. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

    KAUST Repository

    Najibi, Seyed Morteza

    2017-02-08

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  18. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

    KAUST Repository

    Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z.; Gao, Xin

    2017-01-01

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  19. Loop quantum cosmology of k=1 FRW models

    International Nuclear Information System (INIS)

    Ashtekar, Abhay; Pawlowski, Tomasz; Singh, Parampreet; Vandersloot, Kevin

    2007-01-01

    The closed, k=1, FRW model coupled to a massless scalar field is investigated in the framework of loop quantum cosmology using analytical and numerical methods. As in the k=0 case, the scalar field can be again used as emergent time to construct the physical Hilbert space and introduce Dirac observables. The resulting framework is then used to address a major challenge of quantum cosmology: resolving the big-bang singularity while retaining agreement with general relativity at large scales. It is shown that the framework fulfills this task. In particular, for states which are semiclassical at some late time, the big bang is replaced by a quantum bounce and a recollapse occurs at the value of the scale factor predicted by classical general relativity. Thus, the ''difficulties'' pointed out by Green and Unruh in the k=1 case do not arise in a more systematic treatment. As in k=0 models, quantum dynamics is deterministic across the deep Planck regime. However, because it also retains the classical recollapse, in contrast to the k=0 case one is now led to a cyclic model. Finally, we clarify some issues raised by Laguna's recent work addressed to computational physicists

  20. Divergent Roles of RPA Homologs of the Model Archaeon Halobacterium salinarum in Survival of DNA Damage.

    Science.gov (United States)

    Evans, Jessica J; Gygli, Patrick E; McCaskill, Julienne; DeVeaux, Linda C

    2018-04-20

    The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the minichromosomes, and one is uniquely euryarchaeal. Radiation-resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes. Here, we have created deletions in the five RPA operons. These deletion mutants were exposed to DNA-damaging conditions: ionizing radiation, UV radiation, and mitomycin C. Deletion of the euryarchaeal homolog, although not lethal as in Haloferax volcanii , causes severe sensitivity to all of these agents. Deletion of the other RPA/SSB homologs imparts a variable sensitivity to these DNA-damaging agents, suggesting that the different RPA homologs have specialized roles depending on the type of genomic insult encountered.

  1. Closed-Loop Supply Chain Planning Model of Rare Metals

    Directory of Open Access Journals (Sweden)

    Dongmin Son

    2018-04-01

    Full Text Available Rare metals (RMs are becoming increasingly important in high-tech industries associated with the Fourth Industrial Revolution, such as the electric vehicle (EV and 3D printer industries. As the growth of these industries accelerates in the near future, manufacturers will also face greater RM supply risks. For this reason, many countries are putting considerable effort into securing the RM supply. For example, countries including Japan, Korea, and the USA have adopted two major policies: the stockpile system and Extended Producer Responsibility (EPR. Therefore, it is necessary for the manufacturers with RMs to establish a suitable supply chain plan that reflects this situation. In this study, the RM classification matrix is created based on the stockpile and recycling level in Korea. Accordingly, three different types of supply chain are designed in order to develop the closed-loop supply chain (CLSC planning model of RM, and the CLSC planning models of RM are validated through experimental analysis. The results show that the stockpiling and the EPR recycling obligation increase the amount of recycled flow and reduce the total cost of the part manufacturing, which means that these two factors are significant for obtaining sustainability of the RMs’ CLSC. In addition, the government needs to set an appropriate sharing cost for promoting the manufacturer’s recycling. Also, from the manufacturer’s perspective, it is better to increase the return rate by making a contract with the collectors to guarantee the collection of used products.

  2. Extending two Higgs doublet models for two-loop neutrino mass generation and one-loop neutrinoless double beta decay

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhen, E-mail: liu-zhen@sjtu.edu.cn; Gu, Pei-Hong, E-mail: peihong.gu@sjtu.edu.cn

    2017-02-15

    We extend some two Higgs doublet models, where the Yukawa couplings for the charged fermion mass generation only involve one Higgs doublet, by two singlet scalars respectively carrying a singly electric charge and a doubly electric charge. The doublet and singlet scalars together can mediate a two-loop diagram to generate a tiny Majorana mass matrix of the standard model neutrinos. Remarkably, the structure of the neutrino mass matrix is fully determined by the symmetric Yukawa couplings of the doubly charged scalar to the right-handed leptons. Meanwhile, a one-loop induced neutrinoless double beta decay can arrive at a testable level even if the electron neutrino has an extremely small Majorana mass. We also study other experimental constraints and implications including some rare processes and Higgs phenomenology.

  3. Extending two Higgs doublet models for two-loop neutrino mass generation and one-loop neutrinoless double beta decay

    Directory of Open Access Journals (Sweden)

    Zhen Liu

    2017-02-01

    Full Text Available We extend some two Higgs doublet models, where the Yukawa couplings for the charged fermion mass generation only involve one Higgs doublet, by two singlet scalars respectively carrying a singly electric charge and a doubly electric charge. The doublet and singlet scalars together can mediate a two-loop diagram to generate a tiny Majorana mass matrix of the standard model neutrinos. Remarkably, the structure of the neutrino mass matrix is fully determined by the symmetric Yukawa couplings of the doubly charged scalar to the right-handed leptons. Meanwhile, a one-loop induced neutrinoless double beta decay can arrive at a testable level even if the electron neutrino has an extremely small Majorana mass. We also study other experimental constraints and implications including some rare processes and Higgs phenomenology.

  4. An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA.

    Science.gov (United States)

    Robledo, Marta; Schlüter, Jan-Philip; Loehr, Lars O; Linne, Uwe; Albaum, Stefan P; Jiménez-Zurdo, José I; Becker, Anke

    2018-01-01

    Adjustment of cell cycle progression is crucial for bacterial survival and adaptation under adverse conditions. However, the understanding of modulation of cell cycle control in response to environmental changes is rather incomplete. In α-proteobacteria, the broadly conserved cell cycle master regulator CtrA underlies multiple levels of control, including coupling of cell cycle and cell differentiation. CtrA levels are known to be tightly controlled through diverse transcriptional and post-translational mechanisms. Here, small RNA (sRNA)-mediated post-transcriptional regulation is uncovered as an additional level of CtrA fine-tuning. Computational predictions as well as transcriptome and proteome studies consistently suggested targeting of ctrA and the putative cold shock chaperone cspA5 mRNAs by the trans- encoded sRNA ( trans- sRNA) GspR (formerly SmelC775) in several Sinorhizobium species. GspR strongly accumulated in the stationary growth phase, especially in minimal medium (MM) cultures. Lack of the gspR locus confers a fitness disadvantage in competition with the wild type, while its overproduction hampers cell growth, suggesting that this riboregulator interferes with cell cycle progression. An eGFP-based reporter in vivo assay, involving wild-type and mutant sRNA and mRNA pairs, experimentally confirmed GspR-dependent post-transcriptional down-regulation of ctrA and cspA5 expression, which most likely occurs through base-pairing to the respective mRNA. The energetically favored secondary structure of GspR is predicted to comprise three stem-loop domains, with stem-loop 1 and stem-loop 3 targeting ctrA and cspA5 mRNA, respectively. Moreover, this work reports evidence for post-transcriptional control of ctrA by CspA5. Thus, this regulation and GspR-mediated post-transcriptional repression of ctrA and cspA5 expression constitute a coherent feed-forward loop, which may enhance the negative effect of GspR on CtrA levels. This novel regulatory circuit involving

  5. HOMOLOGY MODELING AND FUNCTIONAL CHARACTERIZATION OF THREE-DIMENSIONAL STRUCTURE OF DAHP SYNTHASE FROM BRACHYPODIUM DISTACHYON

    Directory of Open Access Journals (Sweden)

    Aditya Dev

    2013-06-01

    Full Text Available The Shikimate pathway is an attractive target for herbicides and antimicrobial agents because it is essential in microbes and plants but absent in animals. The 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS is the first enzyme of this pathway, which is involved in the condensation of phosphoenolpyruvate (PEP and D-erythrose 4-phosphate (E4P to produce 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP. DAHPS enzymes have been divided into two types, class I and class II, based on their primary amino acid sequence and three dimensional structures. The plant DAHPS belongs to class II and is regulated differently than DAHPS from microorganisms. To understand the structural basis of such differences in DAHPS from plants and its catalytic mechanism, we have used sequence analysis, homology modeling and docking approach to generate the three dimensional models of DAHP synthase from Brachypodium distachyon (Bd-DAHPS complexed with substrate PEP for the first time. The three dimensional models of Bd-DAHPS provides a detailed knowledge of the active site and the important secondary structural regions that play significant roles in the regulatory mechanism and further may be helpful for design of specific inhibitors towards herbicide development.

  6. On equivalent radius of curvature for PWL geometrical modeling a loop antenna

    CSIR Research Space (South Africa)

    Lysko, AA

    2012-11-01

    Full Text Available A circular loop antenna is often numerically modeled using a regular polygon. This approach is simple and robust, yet it alters the circumference of the loop and may thus shift the resonance frequency in the numerical model. This letter introduces a...

  7. Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling, flexible docking, and mutational studies.

    Science.gov (United States)

    Lee, Jin Hee; Lee, Yoonji; Ryu, HyungChul; Kang, Dong Wook; Lee, Jeewoo; Lazar, Jozsef; Pearce, Larry V; Pavlyukovets, Vladimir A; Blumberg, Peter M; Choi, Sun

    2011-04-01

    The transient receptor potential vanilloid subtype 1 (TRPV1) is a non-selective cation channel composed of four monomers with six transmembrane helices (TM1-TM6). TRPV1 is found in the central and peripheral nervous system, and it is an important therapeutic target for pain relief. We describe here the construction of a tetrameric homology model of rat TRPV1 (rTRPV1). We experimentally evaluated by mutational analysis the contribution of residues of rTRPV1 contributing to ligand binding by the prototypical TRPV1 agonists, capsaicin and resiniferatoxin (RTX). We then performed docking analysis using our homology model. The docking results with capsaicin and RTX showed that our homology model was reliable, affording good agreement with our mutation data. Additionally, the binding mode of a simplified RTX (sRTX) ligand as predicted by the modeling agreed well with those of capsaicin and RTX, accounting for the high binding affinity of the sRTX ligand for TRPV1. Through the homology modeling, docking and mutational studies, we obtained important insights into the ligand-receptor interactions at the molecular level which should prove of value in the design of novel TRPV1 ligands.

  8. GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models

    Directory of Open Access Journals (Sweden)

    Kreuchwig Annika

    2011-05-01

    Full Text Available Abstract Background G protein-coupled receptors (GPCRs transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. Description Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. Conclusions The data provided by GPCR-SSFE are useful for investigating

  9. GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.

    Science.gov (United States)

    Worth, Catherine L; Kreuchwig, Annika; Kleinau, Gunnar; Krause, Gerd

    2011-05-23

    G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships

  10. New class of two-loop neutrino mass models with distinguishable phenomenology

    Science.gov (United States)

    Cao, Qing-Hong; Chen, Shao-Long; Ma, Ernest; Yan, Bin; Zhang, Dong-Ming

    2018-04-01

    We discuss a new class of neutrino mass models generated in two loops, and explore specifically three new physics scenarios: (A) doubly charged scalar, (B) dark matter, and (C) leptoquark and diquark, which are verifiable at the 14 TeV LHC Run-II. We point out how the different Higgs insertions will distinguish our two-loop topology with others if the new particles in the loop are in the simplest representations of the SM gauge group.

  11. A theoretical model of the tridimensional structure of Bacillus thuringiensis subsp. medellin Cry 11Bb toxin deduced by homology modelling

    Directory of Open Access Journals (Sweden)

    Gutierrez Pablo

    2001-01-01

    Full Text Available Cry11Bb is an insecticidal crystal protein produced by Bacillus thuringiensis subsp. medellin during its stationary phase; this ¶-endotoxin is active against dipteran insects and has great potential for mosquito borne disease control. Here, we report the first theoretical model of the tridimensional structure of a Cry11 toxin. The tridimensional structure of the Cry11Bb toxin was obtained by homology modelling on the structures of the Cry1Aa and Cry3Aa toxins. In this work we give a brief description of our model and hypothesize the residues of the Cry11Bb toxin that could be important in receptor recognition and pore formation. This model will serve as a starting point for the design of mutagenesis experiments aimed to the improvement of toxicity, and to provide a new tool for the elucidation of the mechanism of action of these mosquitocidal proteins.

  12. The Activity of Escherichia coli Dihydroorotate Dehydrogenase Is Dependent on a Conserved Loop Identified by Sequence Homology, Mutagenesis, and Limited Proteolysis

    DEFF Research Database (Denmark)

    Björnberg, Olof; Grüner, Anne Charlotte; Roepstorff, Peter

    1999-01-01

    of dihydroorotate dehydrogenases, but sedimentation in sucrose gradients suggests a dimeric structure also of the E. coli enzyme. Product inhibition showed that the E. coli enzyme, in contrast to the L. lactis enzyme, has separate binding sites for dihydroorotate and the electron acceptor. Trypsin readily cleaved...... the E. coli enzyme into two fragments of 182 and 154 residues, respectively. Cleavage reduced the activity more than 100-fold but left other molecular properties, including the heat stability, intact. The trypsin cleavage site, at R182, is positioned in a conserved region that, in the L. lactis enzyme......, forms a loop where a cysteine residue is very critical for activity. In the corresponding position, the enzyme from E. coli has a serine residue. Mutagenesis of this residue (S175) to alanine or cysteine reduced the activities 10000- and 500-fold, respectively. The S175C mutant was also defective...

  13. Dynamic simulation of perturbation responses in a closed-loop virtual arm model.

    Science.gov (United States)

    Du, Yu-Fan; He, Xin; Lan, Ning

    2010-01-01

    A closed-loop virtual arm (VA) model has been developed in SIMULINK environment by adding spinal reflex circuits and propriospinal neural networks to the open-loop VA model developed in early study [1]. An improved virtual muscle model (VM4.0) is used to speed up simulation and to generate more precise recruitment of muscle force at low levels of muscle activation. Time delays in the reflex loops are determined by their synaptic connections and afferent transmission back to the spinal cord. Reflex gains are properly selected so that closed-loop responses are stable. With the closed-loop VA model, we are developing an approach to evaluate system behaviors by dynamic simulation of perturbation responses. Joint stiffness is calculated based on simulated perturbation responses by a least-squares algorithm in MATLAB. This method of dynamic simulation will be essential for further evaluation of feedforward and reflex control of arm movement and position.

  14. Dynameomics: Data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction

    Science.gov (United States)

    Rysavy, Steven J; Beck, David AC; Daggett, Valerie

    2014-01-01

    Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼25–75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. PMID:25142412

  15. Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

    Science.gov (United States)

    Rysavy, Steven J; Beck, David A C; Daggett, Valerie

    2014-11-01

    Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼ 25-75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. © 2014 The Protein Society.

  16. Two-loop corrections for nuclear matter in the Walecka model

    International Nuclear Information System (INIS)

    Furnstahl, R.J.; Perry, R.J.; Serot, B.D.; Department of Physics, The Ohio State University, Columbus, Ohio 43210; Physics Department and Nuclear Theory Center, Indiana University, Bloomington, Indiana 47405)

    1989-01-01

    Two-loop corrections for nuclear matter, including vacuum polarization, are calculated in the Walecka model to study the loop expansion as an approximation scheme for quantum hadrodynamics. Criteria for useful approximation schemes are discussed, and the concepts of strong and weak convergence are introduced. The two-loop corrections are evaluated first with one-loop parameters and mean fields and then by minimizing the total energy density with respect to the scalar field and refitting parameters to empirical nuclear matter saturation properties. The size and nature of the corrections indicate that the loop expansion is not convergent at two-loop order in either the strong or weak sense. Prospects for alternative approximation schemes are discussed

  17. Reaction mechanism of sterol hydroxylation by steroid C25 dehydrogenase - Homology model, reactivity and isoenzymatic diversity.

    Science.gov (United States)

    Rugor, Agnieszka; Wójcik-Augustyn, Anna; Niedzialkowska, Ewa; Mordalski, Stefan; Staroń, Jakub; Bojarski, Andrzej; Szaleniec, Maciej

    2017-08-01

    Steroid C25 dehydrogenase (S25DH) is a molybdenum-containing oxidoreductase isolated from the anaerobic Sterolibacterium denitrificans Chol-1S. S25DH is classified as 'EBDH-like' enzyme (EBDH, ethylbenzene dehydrogenase) and catalyzes the introduction of an OH group to the C25 atom of a sterol aliphatic side-chain. Due to its regioselectivity, S25DH is proposed as a catalyst in production of pharmaceuticals: calcifediol or 25-hydroxycholesterol. The aim of presented research was to obtain structural model of catalytic subunit α and investigate the reaction mechanism of the O 2 -independent tertiary carbon atom activation. Based on homology modeling and theoretical calculations, a S25DH α subunit model was for the first time characterized and compared to other S25DH-like isoforms. The molecular dynamics simulations of the enzyme-substrate complexes revealed two stable binding modes of a substrate, which are stabilized predominantly by van der Waals forces in the hydrophobic substrate channel. However, H-bond interactions involving polar residues with C3=O/C3-OH in the steroid ring appear to be responsible for positioning the substrate. These results may explain the experimental kinetic results which showed that 3-ketosterols are hydroxylated 5-10-fold faster than 3-hydroxysterols. The reaction mechanism was studied using QM:MM and QM-only cluster models. The postulated mechanism involves homolytic CH cleavage by the MoO ligand, giving rise to a radical intermediate with product obtained in an OH rebound process. The hypothesis was supported by kinetic isotopic effect (KIE) experiments involving 25,26,26,26-[ 2 H]-cholesterol (4.5) and the theoretically predicted intrinsic KIE (7.0-7.2). Finally, we have demonstrated that the recombinant S25DH-like isoform catalyzes the same reaction as S25DH. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

    Science.gov (United States)

    Lukk, Tiit; Sakai, Ayano; Kalyanaraman, Chakrapani; Brown, Shoshana D.; Imker, Heidi J.; Song, Ling; Fedorov, Alexander A.; Fedorov, Elena V.; Toro, Rafael; Hillerich, Brandan; Seidel, Ronald; Patskovsky, Yury; Vetting, Matthew W.; Nair, Satish K.; Babbitt, Patricia C.; Almo, Steven C.; Gerlt, John A.; Jacobson, Matthew P.

    2012-01-01

    The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion. PMID:22392983

  19. Homology modeling, molecular dynamics and inhibitor binding study on MurD ligase of Mycobacterium tuberculosis.

    Science.gov (United States)

    Arvind, Akanksha; Kumar, Vivek; Saravanan, Parameswaran; Mohan, C Gopi

    2012-09-01

    The cell wall of mycobacterium offers well validated targets which can be exploited for discovery of new lead compounds. MurC-MurF ligases catalyze a series of irreversible steps in the biosynthesis of peptidoglycan precursor, i.e. MurD catalyzes the ligation of D-glutamate to the nucleotide precursor UMA. The three dimensional structure of Mtb-MurD is not known and was predicted by us for the first time using comparative homology modeling technique. The accuracy and stability of the predicted Mtb-MurD structure was validated using Procheck and molecular dynamics simulation. Key interactions in Mtb-MurD were studied using docking analysis of available transition state inhibitors of E.coli-MurD. The docking analysis revealed that analogues of both L and D forms of glutamic acid have similar interaction profiles with Mtb-MurD. Further, residues His192, Arg382, Ser463, and Tyr470 are proposed to be important for inhibitor-(Mtb-MurD) interactions. We also identified few pharmacophoric features essential for Mtb-MurD ligase inhibitory activity and which can further been utilized for the discovery of putative antitubercular chemotherapy.

  20. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    KAUST Repository

    Wong, Aloysius Tze; Gehring, Christoph A; Irving, Helen R.

    2015-01-01

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  1. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    KAUST Repository

    Wong, Aloysius Tze

    2015-06-09

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  2. Experimental investigations and modeling of a loop thermosyphon for cooling with zero electrical consumption

    International Nuclear Information System (INIS)

    Chehade, Ali; Louahlia-Gualous, Hasna; Le Masson, Stéphane; Lépinasse, Eric

    2015-01-01

    This paper presents an analytical model for a thermosyphon loop developed for cooling air inside a telecommunication cabinet. The proposed model is based on the combination of thermal and hydraulic management of two-phase flow in the loop. Experimental tests on a closed thermosyphon loop are conducted with different working fluids that could be used for electronic cooling. Correlations for condensation and evaporation heat transfer in the thermosyphon loop are proposed. They are used in the model to calculate condenser and evaporator thermal resistances in order to predict the cabinet operating temperature, the loop's mass flow rate and pressure drops. Furthermore, various figures of merit proposed in the previous works are evaluated in order to be used for selection of the best loop's working fluid. The comparative studies show that the present model well predicts the experimental data. The mean deviation between the predictions of the theoretical model with the measurements for operating temperature is about 6%. Besides, the model is used to define an optimal liquid and vapor lines diameters and the effect of the ambient temperature on the fluid's mass flow rate and pressure drop. - Highlights: • Modeling of thermosyphon loop for cooling telecommunication cabinet. • The cooling system operates with zero electrical consumption. • The new correlations are proposed for condensation and evaporation heat transfer. • FOM equation is defined for selecting the best working fluid. • The proposed model well predicts the experimental data and operating temperature

  3. Computational Model of a Positive BDNF Feedback Loop in Hippocampal Neurons Following Inhibitory Avoidance Training

    Science.gov (United States)

    Zhang, Yili; Smolen, Paul; Alberini, Cristina M.; Baxter, Douglas A.; Byrne, John H.

    2016-01-01

    Inhibitory avoidance (IA) training in rodents initiates a molecular cascade within hippocampal neurons. This cascade contributes to the transition of short- to long-term memory (i.e., consolidation). Here, a differential equation-based model was developed to describe a positive feedback loop within this molecular cascade. The feedback loop begins…

  4. 3D DD modelling of the prismatic loops and dislocations interaction in pure iron

    International Nuclear Information System (INIS)

    Novokshanov, R.; Roberts, S.

    2007-01-01

    Full text of publication follows: Neutron irradiation can increase the yield stress and reduce the ductility of metals. These effects are mainly caused by the interaction of dislocations with damage produced during irradiation. In iron irradiated with fast neutrons the damage takes the form of 1/2 and 1/2 prismatic dislocation loops (the size of the loops varies from 2 nm to 20 nm depending on the dose of irradiation). The interaction between such loops and dislocations is the subject of this research. 3D dislocation dynamics simulations have been carried out to model the interaction between prismatic loops and dis- locations in pure iron subject to uniaxial loading conditions. The primary goal was to understand the mechanism of interaction of a a/2 loop and a mobile dislocation. The simulations have shown a complicated 3D interaction resulting in either bowing around an obstacle (prismatic loop, Orowan mechanism) or cutting it through, carrying part of the loop away and leaving the other part behind. Cross-slip can be important, in a manner depending on the type of mobile dislocation, size, type and orientation of prismatic loop. The secondary goal was to investigate the dependence of the critical stress needed for dislocations to overcome the obstacles as a function of: size of loops, initial separation between loops, the direction of motion of the mobile dislocation and its type (pure edge or screw), and type of a loop (interstitial or vacancy). Many different configurations have been simulated. The size of the loops was varied from 10 nm to 100 nm; the separation between the loops in a row was varied from one to four loop diameters; the distance between the glide plane and the loop plane was varied from 0 to 20 nm. The glide plane of the mobile dislocation was either perpendicular to and or inclined to the loop plane. The results show a strong dependence of the critical stress on the size of the loops and the initial configuration. (authors)

  5. Homology modeling and protein engineering of alkane monooxygenase in Burkholderia thailandensis MSMB121: in silico insights.

    Science.gov (United States)

    Jain, Chakresh Kumar; Gupta, Money; Prasad, Yamuna; Wadhwa, Gulshan; Sharma, Sanjeev Kumar

    2014-07-01

    The degradation of hydrocarbons plays an important role in the eco-balancing of petroleum products, pesticides and other toxic products in the environment. The degradation of hydrocarbons by microbes such as Geobacillus thermodenitrificans, Burkhulderia, Gordonia sp. and Acinetobacter sp. has been studied intensively in the literature. The present study focused on the in silico protein engineering of alkane monooxygenase (ladA)-a protein involved in the alkane degradation pathway. We demonstrated the improvement in substrate binding energy with engineered ladA in Burkholderia thailandensis MSMB121. We identified an ortholog of ladA monooxygenase found in B. thailandensis MSMB121, and showed it to be an enzyme involved in an alkane degradation pathway studied extensively in Geobacillus thermodenitrificans. Homology modeling of the three-dimensional structure of ladA was performed with a crystal structure (protein databank ID: 3B9N) as a template in MODELLER 9v11, and further validated using PROCHECK, VERIFY-3D and WHATIF tools. Specific amino acids were substituted in the region corresponding to amino acids 305-370 of ladA protein, resulting in an enhancement of binding energy in different alkane chain molecules as compared to wild protein structures in the docking experiments. The substrate binding energy with the protein was calculated using Vina (Implemented in VEGAZZ). Molecular dynamics simulations were performed to study the dynamics of different alkane chain molecules inside the binding pockets of wild and mutated ladA. Here, we hypothesize an improvement in binding energies and accessibility of substrates towards engineered ladA enzyme, which could be further facilitated for wet laboratory-based experiments for validation of the alkane degradation pathway in this organism.

  6. Cloning, Expression, Sequence Analysis and Homology Modeling of the Prolyl Endoprotease from Eurygaster integriceps Puton

    Directory of Open Access Journals (Sweden)

    Ravi Chandra Yandamuri

    2014-10-01

    Full Text Available eurygaster integriceps Puton, commonly known as sunn pest, is a major pest of wheat in Northern Africa, the Middle East and Eastern Europe. This insect injects a prolyl endoprotease into the wheat, destroying the gluten. The purpose of this study was to clone the full length cDNA of the sunn pest prolyl endoprotease (spPEP for expression in E. coli and to compare the amino acid sequence of the enzyme to other known PEPs in both phylogeny and potential tertiary structure. Sequence analysis shows that the 5ꞌ UTR contains several putative transcription factor binding sites for transcription factors known to be expressed in Drosophila that might be useful targets for inhibition of the enzyme. The spPEP was first identified as a prolyl endoprotease by Darkoh et al., 2010. The enzyme is a unique serine protease of the S9A family by way of its substrate recognition of the gluten proteins, which are greater than 30 kD in size. At 51% maximum identity to known PEPs, homology modeling using SWISS-MODEL, the porcine brain PEP (PDB: 2XWD was selected in the database of known PEP structures, resulting in a predicted tertiary structure 99% identical to the porcine brain PEP structure. A Km for the recombinant spPEP was determined to be 210 ± 53 µM for the zGly-Pro-pNA substrate in 0.025 M ethanolamine, pH 8.5, containing 0.1 M NaCl at 37 °C with a turnover rate of 172 ± 47 µM Gly-Pro-pNA/s/µM of enzyme.

  7. Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

    Directory of Open Access Journals (Sweden)

    Hahnbeom Park

    Full Text Available Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

  8. Modelling and characterization of an airlift-loop bioreactor

    NARCIS (Netherlands)

    Verlaan, P.

    1987-01-01

    An airlift-loop reactor is a bioreactor for aerobic biotechnological processes. The special feature of the ALR is the recirculation of the liquid through a downcomer connecting the top and the bottom of the main bubbling section. Due to the high circulation-flow rate, efficient mixing and

  9. Estimation of Model Uncertainties in Closed-loop Systems

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Poulsen, Niels Kjølstad

    2008-01-01

    This paper describe a method for estimation of parameters or uncertainties in closed-loop systems. The method is based on an application of the dual YJBK (after Youla, Jabr, Bongiorno and Kucera) parameterization of all systems stabilized by a given controller. The dual YJBK transfer function...

  10. On-line leak detection method for OWL-1 loop by ARX modeling using dewpoint signals

    International Nuclear Information System (INIS)

    Oguma, Ritsuo; Hayashi, Koji; Kitajima, Toshio.

    1981-01-01

    Model identification technique based on ARX (autoregressive model with exogenous variable) process was applied to dewpoint data recorded at OWL-1 (Oarai Water Loop No. 1) loop cubicle in JMTR (Japan Materials Testing Reactor) and the dynamical interrelationship between the supply and exhaust dewpoints in the ventilation system of the cubicle was empirically determined. It was shown that the information so derived on the dewpoint dynamics can assist to enhance the sensitivity of leak detection, if it was incorporated into a leak monitoring system for the OWL-1 loop. A simple digital filter incorporating the dewpoint dynamics was designed in an attempt to develop an efficient leak monitor for the OWL-1 loop. This filter was applied to the dewpoint data recordings during an abnormal leak that had occurred at the OWL-1 loop in the 43 rd cycle of JMTR operation, which demonstrated the effectiveness of the present method for leak detection at its early stage. (author)

  11. A mathematical model for the simulation of thermal transients in the water loop of IPEN

    International Nuclear Information System (INIS)

    Pontedeiro, A.C.

    1980-01-01

    A mathematical model for simulation of thermal transients in the water loop at the Instituto de Pesquisas Energeticas e Nucleares, Sao Paulo, Brasil, is developed. The model is based on energy equations applied to the components of the experimental water loop. The non-linear system of first order diferencial equations and of non-linear algebraic equations obtained through the utilization of the IBM 'System/360-Continous System Modeling Program' (CSMP) is resolved. An optimization of the running time of the computer is made and a typical simulation of the water loop is executed. (Author) [pt

  12. A self-organizing algorithm for modeling protein loops.

    Directory of Open Access Journals (Sweden)

    Pu Liu

    2009-08-01

    Full Text Available Protein loops, the flexible short segments connecting two stable secondary structural units in proteins, play a critical role in protein structure and function. Constructing chemically sensible conformations of protein loops that seamlessly bridge the gap between the anchor points without introducing any steric collisions remains an open challenge. A variety of algorithms have been developed to tackle the loop closure problem, ranging from inverse kinematics to knowledge-based approaches that utilize pre-existing fragments extracted from known protein structures. However, many of these approaches focus on the generation of conformations that mainly satisfy the fixed end point condition, leaving the steric constraints to be resolved in subsequent post-processing steps. In the present work, we describe a simple solution that simultaneously satisfies not only the end point and steric conditions, but also chirality and planarity constraints. Starting from random initial atomic coordinates, each individual conformation is generated independently by using a simple alternating scheme of pairwise distance adjustments of randomly chosen atoms, followed by fast geometric matching of the conformationally rigid components of the constituent amino acids. The method is conceptually simple, numerically stable and computationally efficient. Very importantly, additional constraints, such as those derived from NMR experiments, hydrogen bonds or salt bridges, can be incorporated into the algorithm in a straightforward and inexpensive way, making the method ideal for solving more complex multi-loop problems. The remarkable performance and robustness of the algorithm are demonstrated on a set of protein loops of length 4, 8, and 12 that have been used in previous studies.

  13. Discovery of a Manduca sexta Allatotropin Antagonist from a Manduca sexta Allatotropin Receptor Homology Model.

    Science.gov (United States)

    Kai, Zhen-Peng; Zhu, Jing-Jing; Deng, Xi-Le; Yang, Xin-Ling; Chen, Shan-Shan

    2018-04-03

    Insect G protein coupled receptors (GPCRs) have important roles in modulating biology, physiology and behavior. They have been identified as candidate targets for next-generation insecticides, yet these targets have been relatively poorly exploited for insect control. In this study, we present a pipeline of novel Manduca sexta allatotropin (Manse-AT) antagonist discovery with homology modeling, docking, molecular dynamics simulation and structure-activity relationship. A series of truncated and alanine-replacement analogs of Manse-AT were assayed for the stimulation of juvenile hormone biosynthesis. The minimum sequence required to retain potent biological activity is the C -terminal amidated octapeptide Manse-AT (6-13). We identified three residues essential for bioactivity (Thr⁴, Arg6 and Phe⁸) by assaying alanine-replacement analogs of Manse-AT (6-13). Alanine replacement of other residues resulted in reduced potency but bioactivity was retained. The 3D structure of the receptor (Manse-ATR) was built and the binding pocket was identified. The binding affinities of all the analogs were estimated by calculating the free energy of binding. The calculated binding affinities corresponded to the biological activities of the analogs, which supporting our localization of the binding pocket. Then, based on the docking and molecular dynamics studies of Manse-AT (10-13), we described it can act as a potent Manse-AT antagonist. The antagonistic effect on JH biosynthesis of Manse-AT (10-13) validated our hypothesis. The IC 50 value of antagonist Manse-AT (10-13) is 0.9 nM. The structure-activity relationship of antagonist Manse-AT (10-13) was also studied for the further purpose of investigating theoretically the structure factors influencing activity. These data will be useful for the design of new Manse-AT agonist and antagonist as potential pest control agents.

  14. Discovery of a Manduca sexta Allatotropin Antagonist from a Manduca sexta Allatotropin Receptor Homology Model

    Directory of Open Access Journals (Sweden)

    Zhen-Peng Kai

    2018-04-01

    Full Text Available Insect G protein coupled receptors (GPCRs have important roles in modulating biology, physiology and behavior. They have been identified as candidate targets for next-generation insecticides, yet these targets have been relatively poorly exploited for insect control. In this study, we present a pipeline of novel Manduca sexta allatotropin (Manse-AT antagonist discovery with homology modeling, docking, molecular dynamics simulation and structure-activity relationship. A series of truncated and alanine-replacement analogs of Manse-AT were assayed for the stimulation of juvenile hormone biosynthesis. The minimum sequence required to retain potent biological activity is the C-terminal amidated octapeptide Manse-AT (6–13. We identified three residues essential for bioactivity (Thr4, Arg6 and Phe8 by assaying alanine-replacement analogs of Manse-AT (6–13. Alanine replacement of other residues resulted in reduced potency but bioactivity was retained. The 3D structure of the receptor (Manse-ATR was built and the binding pocket was identified. The binding affinities of all the analogs were estimated by calculating the free energy of binding. The calculated binding affinities corresponded to the biological activities of the analogs, which supporting our localization of the binding pocket. Then, based on the docking and molecular dynamics studies of Manse-AT (10–13, we described it can act as a potent Manse-AT antagonist. The antagonistic effect on JH biosynthesis of Manse-AT (10–13 validated our hypothesis. The IC50 value of antagonist Manse-AT (10–13 is 0.9 nM. The structure-activity relationship of antagonist Manse-AT (10–13 was also studied for the further purpose of investigating theoretically the structure factors influencing activity. These data will be useful for the design of new Manse-AT agonist and antagonist as potential pest control agents.

  15. Homology modeling and in silico prediction of Ulcerative colitis associated polymorphisms of NOD1.

    Science.gov (United States)

    Majumdar, Ishani; Nagpal, Isha; Paul, Jaishree

    2017-10-01

    Cytosolic pattern recognition receptors play key roles in innate immune response. Nucleotide binding and oligomerisation domain containing protein 1 (NOD1) belonging to the Nod-like receptor C (NLRC) sub-family of Nod-like receptors (NLRs) is important for detection and clearance of intra-cellular Gram negative bacteria. NOD1 is involved in activation of pro-inflammatory pathways. Limited structural data is available for NOD1. Using different templates for each domain of NOD1, we determined the full-length homology model of NOD1. ADP binding amino acids within the nucleotide binding domain (NBD) of NOD1 were also predicted. Key residues in inter-domain interaction were identified by sequence comparison with Oryctolagus cuniculus NOD2, a related protein. Interactions between NBD and winged helix domain (WHD) were found to be conserved in NOD1. Functional and structural effect of single nucleotide polymorphisms within the NOD1 NBD domain associated with susceptibility risk to Ulcerative colitis (UC), an inflammatory disorder of the colon was evaluated by in silico studies. Mutations W219R and L349P were predicted to be damaging and disease associated by prediction programs SIFT, PolyPhen2, PANTHER, SNP&GO, PhD SNP and SNAP2. We further validated the effect of W219R and L349P mutation on NOD1 function in vitro. Elevated mRNA expression of pro-inflammatory cytokines IL8 and IL-1β was seen as compared to the wild type NOD1 in intestinal epithelial cell line HT29 when stimulated with NOD1 ligand. Thus, these mutations may indeed have a bearing on pathogenesis of inflammation during UC. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Four-loop beta function in the Wess-Zumino model

    International Nuclear Information System (INIS)

    Avdeev, L.V.; Gorishny, S.G.

    1982-01-01

    A method for calculating momentum integrals, proposed by Chetyrkin and Tkachov, is applied to the foUr-loop calculations of the ν-function in the Wess-Zumino model. The main advantage of the used method is the existence of a relatively simple calculational algorithm that allows one to write an effective computer program on the system of analytical evaluations SCHOONSCHIP. Any three-loop integral with one external momentum can be computed by this program. The four-loop calculation in the WZ model is one of the first and simplest applications of the program

  17. Relative orientation of collagen molecules within a fibril: a homology model for homo sapiens type I collagen.

    Science.gov (United States)

    Collier, Thomas A; Nash, Anthony; Birch, Helen L; de Leeuw, Nora H

    2018-02-15

    Type I collagen is an essential extracellular protein that plays an important structural role in tissues that require high tensile strength. However, owing to the molecule's size, to date no experimental structural data are available for the Homo sapiens species. Therefore, there is a real need to develop a reliable homology model and a method to study the packing of the collagen molecules within the fibril. Through the use of the homology model and implementation of a novel simulation technique, we have ascertained the orientations of the collagen molecules within a fibril, which is currently below the resolution limit of experimental techniques. The longitudinal orientation of collagen molecules within a fibril has a significant effect on the mechanical and biological properties of the fibril, owing to the different amino acid side chains available at the interface between the molecules.

  18. Homology modelling and docking studies on Neuraminidase enzyme as a natural product target for combating influenza

    Directory of Open Access Journals (Sweden)

    Nisha Singh

    2017-10-01

    Full Text Available Influenza remains to be dreadful with yearly epidemics and sudden pandemic outbreaks causing significant mortality, even in nations with the most advanced health care systems. Thus, there has been a long-standing interest to develop effective and safe antiviral agents to treat infected individuals. Attempt to identify suitable molecular targets as antiviral compounds have focused recently on the influenza virus neuraminidase (NA, a key enzyme in viral replication [1]. In this research, virtual screening was done on a total of 600 natural compounds from 22 ethno medicinal Indian herbs for activity against neuraminidase enzyme exploiting representative protein conformations selected from molecular dynamics simulations. Neuraminidase enzyme sequences from different existing strains available on National Center of Biotechnology Information [2] (NCBI protein database were aligned using Clustal W [3] and CLC workbench 10 [4] to find the conserved residues. Neuraminidase protein sequence from H1N1 strain available on NCBI was used to structure 3D target model predicted against dataset from Protein data bank using modeller [5]. The target model was validated on different parameter at SAVES Server [6]. Using this target model a pharmacophore model was developed using ligand based strategy exploiting the three known inhibitors. The docking parameters were validated by redocking Zanamivir to its co-complex 2009 H1N1 NA crystal structure (PDB ID: 3TI5 generating best pose with a RMSD value of 0.7543 A°. This model was then used for in silico analysis of a library of natural compounds from 22 ethno medicinal Indian herbs known to have antiviral activity taken downloaded from PubChem database and selected on the basis of drug likeliness. All the compounds were docked in the binding pocket of neuraminidase. Top compounds having binding affinity better than or comparable to the control drug Zanamivir were selected and analyzed for their ADME and toxicity

  19. Improved Application of Local Models to Steel Corrosion in Lead-Bismuth Loops

    International Nuclear Information System (INIS)

    Zhang Jinsuo; Li Ning

    2003-01-01

    The corrosion of steels exposed to flowing liquid metals is influenced by local and global conditions of flow systems. The present study improves the previous local models when applied to closed loops by incorporating some global condition effects. In particular the bulk corrosion product concentration is calculated based on balancing the dissolution and precipitation in the entire closed loop. Mass transfer expressions developed in aqueous medium and an analytical expression are tested in the liquid-metal environments. The improved model is applied to a pure lead loop and produces results closer to the experimental data than the previous local models do. The model is also applied to a lead-bismuth eutectic (LBE) test loop. Systematic studies illustrate the effects of the flow rate, the oxygen concentration in LBE, and the temperature profile on the corrosion rate

  20. A reduced fidelity model for the rotary chemical looping combustion reactor

    KAUST Repository

    Iloeje, Chukwunwike O.; Zhao, Zhenlong; Ghoniem, Ahmed F.

    2017-01-01

    The rotary chemical looping combustion reactor has great potential for efficient integration with CO capture-enabled energy conversion systems. In earlier studies, we described a one-dimensional rotary reactor model, and used it to demonstrate

  1. An open-loop, physiologic model-based decision support system can provide appropriate ventilator settings

    DEFF Research Database (Denmark)

    Karbing, Dan Stieper; Spadaro, Savino; Dey, Nilanjan

    2018-01-01

    OBJECTIVES: To evaluate the physiologic effects of applying advice on mechanical ventilation by an open-loop, physiologic model-based clinical decision support system. DESIGN: Prospective, observational study. SETTING: University and Regional Hospitals' ICUs. PATIENTS: Varied adult ICU population...

  2. Investigation of reflood models by coupling REFLA-1D and multi-loop system model

    International Nuclear Information System (INIS)

    Sugimoto, Jun; Murao, Yoshio

    1983-09-01

    A system analysis code REFLA-1DS was developed by coupling reflood analysis code REFLA-1D and a multi-loop primary system model. The reflood models in the code were investigated for the development of the integral system analysis code. The REFLA-1D, which was developed with the small scale reflood experiment at JAERI, consists of one-dimensional core model and a primary system model with a constant loop resistance. The multi-loop primary system model was developed with the Cylindrical Core Test Facility of JAERI's large scale reflood tests. The components modeled in the code are the upper plenum, the steam generator, the coolant pump, the ECC injection port, the downcomer and the broken cold leg nozzle. The coupling between the two models in REFLA-1DS is accomplished by applying the equivalent flow resistance calculated with the multiloop model to the REFLA-1D. The characteristics of the code is its simplicity of the system model and the solution method which enables the fast running and the easy reflood analysis for the further model development. A fairly good agreement was obtained with the results of the Cylindrical Core Test Facility for the calculated water levels in the downcomer, the core and the upper plenum. A qualitatively good agreement was obtained concerning the parametric effects of the system pressure, the ECC flow rate and the initial clad temperature. Needs for further code improvements of the models, however, were pointed out. These include the problem concerning the generation rate of the steam and water droplets in the core in an early period, the effect of the flow oscillation on the core cooling, the heat release from the downcomer wall, and the stable system calculation. (author)

  3. Molecular cloning, sequence analysis and homology modeling of the first caudata amphibian antifreeze-like protein in axolotl (Ambystoma mexicanum).

    Science.gov (United States)

    Zhang, Songyan; Gao, Jiuxiang; Lu, Yiling; Cai, Shasha; Qiao, Xue; Wang, Yipeng; Yu, Haining

    2013-08-01

    Antifreeze proteins (AFPs) refer to a class of polypeptides that are produced by certain vertebrates, plants, fungi, and bacteria and which permit their survival in subzero environments. In this study, we report the molecular cloning, sequence analysis and three-dimensional structure of the axolotl antifreeze-like protein (AFLP) by homology modeling of the first caudate amphibian AFLP. We constructed a full-length spleen cDNA library of axolotl (Ambystoma mexicanum). An EST having highest similarity (∼42%) with freeze-responsive liver protein Li16 from Rana sylvatica was identified, and the full-length cDNA was subsequently obtained by RACE-PCR. The axolotl antifreeze-like protein sequence represents an open reading frame for a putative signal peptide and the mature protein composed of 93 amino acids. The calculated molecular mass and the theoretical isoelectric point (pl) of this mature protein were 10128.6 Da and 8.97, respectively. The molecular characterization of this gene and its deduced protein were further performed by detailed bioinformatics analysis. The three-dimensional structure of current AFLP was predicted by homology modeling, and the conserved residues required for functionality were identified. The homology model constructed could be of use for effective drug design. This is the first report of an antifreeze-like protein identified from a caudate amphibian.

  4. ANALYSIS AND MODELING OF TWO FLARE LOOPS OBSERVED BY AIA AND EIS

    Energy Technology Data Exchange (ETDEWEB)

    Li, Y.; Ding, M. D. [School of Astronomy and Space Science, Nanjing University, Nanjing 210093 (China); Qiu, J. [Department of Physics, Montana State University, Bozeman, MT 59717 (United States)

    2012-10-10

    We analyze and model an M1.0 flare observed by SDO/AIA and Hinode/EIS to investigate how flare loops are heated and evolve subsequently. The flare is composed of two distinctive loop systems observed in extreme ultraviolet (EUV) images. The UV 1600 A emission at the feet of these loops exhibits a rapid rise, followed by enhanced emission in different EUV channels observed by the Atmospheric Imaging Assembly (AIA) and the EUV Imaging Spectrometer (EIS). Such behavior is indicative of impulsive energy deposit and the subsequent response in overlying coronal loops that evolve through different temperatures. Using the method we recently developed, we infer empirical heating functions from the rapid rise of the UV light curves for the two loop systems, respectively, treating them as two big loops with cross-sectional area of 5'' by 5'', and compute the plasma evolution in the loops using the EBTEL model. We compute the synthetic EUV light curves, which, with the limitation of the model, reasonably agree with observed light curves obtained in multiple AIA channels and EIS lines: they show the same evolution trend and their magnitudes are comparable by within a factor of two. Furthermore, we also compare the computed mean enthalpy flow velocity with the Doppler shift measurements by EIS during the decay phase of the two loops. Our results suggest that the two different loops with different heating functions as inferred from their footpoint UV emission, combined with their different lengths as measured from imaging observations, give rise to different coronal plasma evolution patterns captured both in the model and in observations.

  5. A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models.

    Science.gov (United States)

    Bernardes, Juliana S; Carbone, Alessandra; Zaverucha, Gerson

    2011-03-23

    Remote homology detection is a hard computational problem. Most approaches have trained computational models by using either full protein sequences or multiple sequence alignments (MSA), including all positions. However, when we deal with proteins in the "twilight zone" we can observe that only some segments of sequences (motifs) are conserved. We introduce a novel logical representation that allows us to represent physico-chemical properties of sequences, conserved amino acid positions and conserved physico-chemical positions in the MSA. From this, Inductive Logic Programming (ILP) finds the most frequent patterns (motifs) and uses them to train propositional models, such as decision trees and support vector machines (SVM). We use the SCOP database to perform our experiments by evaluating protein recognition within the same superfamily. Our results show that our methodology when using SVM performs significantly better than some of the state of the art methods, and comparable to other. However, our method provides a comprehensible set of logical rules that can help to understand what determines a protein function. The strategy of selecting only the most frequent patterns is effective for the remote homology detection. This is possible through a suitable first-order logical representation of homologous properties, and through a set of frequent patterns, found by an ILP system, that summarizes essential features of protein functions.

  6. Interacting loop-current model of superconducting networks

    International Nuclear Information System (INIS)

    Chi, C.C.; Santhanam, P.; Bloechl, P.E.

    1992-01-01

    The authors review their recent approximation scheme to calculate the normal-superconducting phase boundary, T c (H), of a superconducting wire network in a magnetic field in terms of interacting loop currents. The theory is based on the London approximation of the linearized Ginzburg-Landau equation. An approximate general formula is derived for any two-dimensional space-filling lattice comprising tiles of two shapes. Many examples are provided illustrating the use of this method, with a particular emphasis on the fluxoid distribution. In addition to periodic lattices, quasiperiodic lattices and fractal Sierpinski gaskets are also discussed

  7. Heteronuclear multidimensional NMR and homology modelling studies of the C-terminal nucleotide-binding domain of the human mitochondrial ABC transporter ABCB6

    Energy Technology Data Exchange (ETDEWEB)

    Kurashima-Ito, Kaori [RIKEN, Cellular and Molecular Biology Laboratory (Japan); Ikeya, Teppei [National Institute of Advanced Industrial Science and Technology (AIST), (Japan); Senbongi, Hiroshi [Mitochondrial Diseases Group, MRC Dunn Human NutritionUnit (United Kingdom); Tochio, Hidehito [International Graduate School of Arts and Sciences, Supramolecular Biology, Yokohama City University, Molecular Biophysics Laboratory (Japan); Mikawa, Tsutomu [RIKEN, Cellular and Molecular Biology Laboratory (Japan); Shibata, Takehiko [RIKEN, Shibata Distinguished Senior Scientist Laboratory (Japan); Ito, Yutaka [RIKEN, Cellular and Molecular Biology Laboratory (Japan)], E-mail: ito-yutaka@center.tmu.ac.jp

    2006-05-15

    Human ATP-binding cassette, sub-family B, member 6 (ABCB6) is a mitochondrial ABC transporter, and presumably contributes to iron homeostasis. Aimed at understanding the structural basis for the conformational changes accompanying the substrate-transportation cycle, we have studied the C-terminal nucleotide-binding domain of ABCB6 (ABCB6-C) in both the nucleotide-free and ADP-bound states by heteronuclear multidimensional NMR and homology modelling. A non-linear sampling scheme was utilised for indirectly acquired {sup 13}C and {sup 15}N dimensions of all 3D triple-resonance NMR experiments, in order to overcome the instability and the low solubility of ABCB6-C. The backbone resonances for approximately 25% of non-proline residues, which are mostly distributed around the functionally important loops and in the Helical domain, were not observed for nucleotide-free form of ABCB6-C. From the pH, temperature and magnetic field strength dependencies of the resonance intensities, we concluded that this incompleteness in the assignments is mainly due to the exchange between multiple conformations at an intermediate rate on the NMR timescale. These localised conformational dynamics remained in ADP-bound ABCB6-C except for the loops responsible for adenine base and {alpha}/{beta}-phosphate binding. These results revealed that the localised dynamic cooperativity, which was recently proposed for a prokaryotic ABC MJ1267, also exists in a higher eukaryotic ABC, and is presumably shared by all members of the ABC family. Since the Helical domain is the putative interface to the transmembrane domain, this cooperativity may explain the coupled functions between domains in the substrate-transportation cycle.

  8. Exchange bias and asymmetric hysteresis loops from a microscopic model of core/shell nanoparticles

    International Nuclear Information System (INIS)

    Iglesias, Oscar; Batlle, Xavier; Labarta, Amilcar

    2007-01-01

    We present Monte Carlo simulations of hysteresis loops of a model of a magnetic nanoparticle with a ferromagnetic core and an antiferromagnetic shell with varying values of the core/shell interface exchange coupling which aim to clarify the microscopic origin of exchange bias observed experimentally. We have found loop shifts in the field direction as well as displacements along the magnetization axis that increase in magnitude when increasing the interfacial exchange coupling. Overlap functions computed from the spin configurations along the loops have been obtained to explain the origin and magnitude of these features microscopically

  9. Modelling of dielectric hysteresis loops in ferroelectric semiconductors with charged defects

    International Nuclear Information System (INIS)

    Morozovska, Anna N; Eliseev, Eugene A

    2004-01-01

    We have proposed the phenomenological description of dielectric hysteresis loops in ferroelectric semiconductors with charged defects and prevailing extrinsic conductivity. We have modified the Landau-Ginsburg approach and shown that the macroscopic state of the aforementioned inhomogeneous system can be described by three coupled equations for three order parameters. Both the experimentally observed coercive field values well below the thermodynamic values and the various hysteresis-loop deformations (constricted and double loops) have been obtained in the framework of our model. The obtained results quantitatively explain the ferroelectric switching in such ferroelectric materials as thick PZT films

  10. Thermohaline loops, Stommel box models, and the Sandström theorem

    OpenAIRE

    Wunsch, Carl

    2005-01-01

    The Stommel two-box, two flow-regime box model is kinematically and dynamically equivalent to the flow in a onedimensional fluid loop, although one having awkward and extreme mixing coefficients. More generally, such a loop, when heated and cooled at the same geopotential, provides a simple example of the working of the Sandström theorem, with flow intensity capable of increasing or decreasing with growing diffusion. Stress dominates real oceanic flows, and its introduction into the purely th...

  11. Two-loop effective potential for Wess-Zumino model using superfields

    International Nuclear Information System (INIS)

    Santos, R.P. dos; Srivastava, P.P.

    1989-01-01

    For the case of several interacting chiral superfields the propagators for the unconstrained superfield potentials in the 'shifted' theory, where the supersymmetry is explicity broken, are derived in a compact form. They are used to compute the one-loop effective potential in the general case, while a superfield calculation of the renormalized effective potential to two loops for the Wess-Zumino models is performed. (authors) [pt

  12. Combined HQSAR, topomer CoMFA, homology modeling and docking studies on triazole derivatives as SGLT2 inhibitors.

    Science.gov (United States)

    Yu, Shuling; Yuan, Jintao; Zhang, Yi; Gao, Shufang; Gan, Ying; Han, Meng; Chen, Yuewen; Zhou, Qiaoqiao; Shi, Jiahua

    2017-06-01

    Sodium-glucose cotransporter 2 (SGLT2) is a promising target for diabetes therapy. We aimed to develop computational approaches to identify structural features for more potential SGLT2 inhibitors. In this work, 46 triazole derivatives as SGLT2 inhibitors were studied using a combination of several approaches, including hologram quantitative structure-activity relationships (HQSAR), topomer comparative molecular field analysis (CoMFA), homology modeling, and molecular docking. HQSAR and topomer CoMFA were used to construct models. Molecular docking was conducted to investigate the interaction of triazole derivatives and homology modeling of SGLT2, as well as to validate the results of the HQSAR and topomer CoMFA models. The most effective HQSAR and topomer CoMFA models exhibited noncross-validated correlation coefficients of 0.928 and 0.891 for the training set, respectively. External predictions were made successfully on a test set and then compared with previously reported models. The graphical results of HQSAR and topomer CoMFA were proven to be consistent with the binding mode of the inhibitors and SGLT2 from molecular docking. The models and docking provided important insights into the design of potent inhibitors for SGLT2.

  13. Molecular modeling used to evaluate CYP2C9-dependent metabolism: homology modeling, molecular dynamics and docking simulations.

    Science.gov (United States)

    Mendieta-Wejebe, Jessica E; Correa-Basurto, José; García-Segovia, Erika M; Ceballos-Cancino, Gisela; Rosales-Hernández, Martha C

    2011-07-01

    Cytochrome P450 (CYP) 2C9 is the principal isoform of the CYP2C subfamily in the human liver and is involved in the oxidation of several endogenous and xenobiotic compounds, including many therapeutic drugs. The metabolism of drugs by CYP2C9 can yield either safe or toxic products, which may be related to the recognition and binding modes of the substrates to this isoform. These interactions can be studied using in silico methods such as quantum chemistry, molecular dynamics and docking simulations, which can also be useful for predicting the structure of metabolites. In these types of studies, the ligand and the protein must be tridimensional models; thus, the protein can be built by homology modeling or retrieved from the Protein Data Bank. Therefore, the current review emphasizes the importance of using in silico methods to predict the metabolism of CYP2C9 because these computational tools have allowed the description of the principal characteristics of the active site of this isoform at the molecular level and the chemical properties of its ligands.

  14. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms.

    Science.gov (United States)

    Vergara-Jaque, Ariela; Fenollar-Ferrer, Cristina; Kaufmann, Desirée; Forrest, Lucy R

    2015-01-01

    Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called "repeat-swap modeling" to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also

  15. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms

    Directory of Open Access Journals (Sweden)

    Cristina eFenollar Ferrer

    2015-09-01

    Full Text Available Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to either the outside or inside of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (asymmetry of these systems has been successfully used as a bioinformatic tool, called repeat-swap modeling to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that

  16. Construction and validation of a homology model of the human voltage-gated proton channel hHV1.

    Science.gov (United States)

    Kulleperuma, Kethika; Smith, Susan M E; Morgan, Deri; Musset, Boris; Holyoake, John; Chakrabarti, Nilmadhab; Cherny, Vladimir V; DeCoursey, Thomas E; Pomès, Régis

    2013-04-01

    The topological similarity of voltage-gated proton channels (H(V)1s) to the voltage-sensing domain (VSD) of other voltage-gated ion channels raises the central question of whether H(V)1s have a similar structure. We present the construction and validation of a homology model of the human H(V)1 (hH(V)1). Multiple structural alignment was used to construct structural models of the open (proton-conducting) state of hH(V)1 by exploiting the homology of hH(V)1 with VSDs of K(+) and Na(+) channels of known three-dimensional structure. The comparative assessment of structural stability of the homology models and their VSD templates was performed using massively repeated molecular dynamics simulations in which the proteins were allowed to relax from their initial conformation in an explicit membrane mimetic. The analysis of structural deviations from the initial conformation based on up to 125 repeats of 100-ns simulations for each system reveals structural features consistently retained in the homology models and leads to a consensus structural model for hH(V)1 in which well-defined external and internal salt-bridge networks stabilize the open state. The structural and electrostatic properties of this open-state model are compatible with proton translocation and offer an explanation for the reversal of charge selectivity in neutral mutants of Asp(112). Furthermore, these structural properties are consistent with experimental accessibility data, providing a valuable basis for further structural and functional studies of hH(V)1. Each Arg residue in the S4 helix of hH(V)1 was replaced by His to test accessibility using Zn(2+) as a probe. The two outermost Arg residues in S4 were accessible to external solution, whereas the innermost one was accessible only to the internal solution. Both modeling and experimental data indicate that in the open state, Arg(211), the third Arg residue in the S4 helix in hH(V)1, remains accessible to the internal solution and is located near the

  17. Enthalpy-Based Thermal Evolution of Loops: II. Improvements to the Model

    Science.gov (United States)

    Cargill, P. J.; Bradshaw, S. J.; Klimchuk, J. A.

    2011-01-01

    This paper further develops the zero-dimensional (0D) hydrodynamic coronal loop model "Enthalpy-based Thermal Evolution of Loops" (EBTEL) originally proposed by Klimchuk et al (2008), which studies the plasma response to evolving coronal heating. It has typically been applied to impulsive heating events. The basis of EBTEL is the modelling of mass exchange between the corona and transition region and chromosphere in response to heating variations, with the key parameter being the ratio of transition region to coronal radiation. We develop new models for this parameter that now include gravitational stratification and a physically motivated approach to radiative cooling. A number of examples are presented, including nanoflares in short and long loops, and a small flare. It is found that while the evolution of the loop temperature is rather insensitive to the details of the model, accurate tracking of the density requires the inclusion of our new features. In particular, we are able to now obtain highly over-dense loops in the late cooling phase and decreases to the coronal density arising due to stratification. The 0D results are compared to a 1D hydro code (Hydrad). The agreement is acceptable, with the exception of the flare case where some versions of Hydrad can give significantly lower densities. This is attributed to the method used to model the chromosphere in a flare. EBTEL is suitable for general use as a tool for (a) quick-look results of loop evolution in response to a given heating function and (b) situations where the modelling of hundreds or thousands of elemental loops is needed. A single run takes a few seconds on a contemporary laptop.

  18. Closed-loop model identification of cooperative manipulators holding deformable objects

    Science.gov (United States)

    Alkathiri, A. A.; Akmeliawati, R.; Azlan, N. Z.

    2017-11-01

    This paper presents system identification to obtain the closed-loop models of a couple of cooperative manipulators in a system, which function to hold deformable objects. The system works using the master-slave principle. In other words, one of the manipulators is position-controlled through encoder feedback, while a force sensor gives feedback to the other force-controlled manipulator. Using the closed-loop input and output data, the closed-loop models, which are useful for model-based control design, are estimated. The criteria for model validation are a 95% fit between the measured and simulated output of the estimated models and residual analysis. The results show that for both position and force control respectively, the fits are 95.73% and 95.88%.

  19. Polar representation of centrifugal pump homologous curves

    International Nuclear Information System (INIS)

    Veloso, Marcelo Antonio; Mattos, Joao Roberto Loureiro de

    2008-01-01

    Essential for any mathematical model designed to simulate flow transient events caused by pump operations is the pump performance data. The performance of a centrifugal pump is characterized by four basic parameters: the rotational speed, the volumetric flow rate, the dynamic head, and the hydraulic torque. Any one of these quantities can be expressed as a function of any two others. The curves showing the relationships between these four variables are called the pump characteristic curves, also referred to as four-quadrant curves. The characteristic curves are empirically developed by the pump manufacturer and uniquely describe head and torque as functions of volumetric flow rate and rotation speed. Because of comprising a large amount of points, the four-quadrant configuration is not suitable for computational purposes. However, it can be converted to a simpler form by the development of the homologous curves, in which dynamic head and hydraulic torque ratios are expressed as functions of volumetric flow and rotation speed ratios. The numerical use of the complete set of homologous curves requires specification of sixteen partial curves, being eight for the dynamic head and eight for the hydraulic torque. As a consequence, the handling of homologous curves is still somewhat complicated. In solving flow transient problems that require the pump characteristic data for all the operation zones, the polar form appears as the simplest way to represent the homologous curves. In the polar method, the complete characteristics of a pump can be described by only two closed curves, one for the dynamic head and other for the hydraulic torque, both in function of a single angular coordinate defined adequately in terms of the quotient between volumetric flow ratio and rotation speed ratio. The usefulness and advantages of this alternative method are demonstrated through a practical example in which the homologous curves for a pump of the type used in the main coolant loops of a

  20. Parametric representation of centrifugal pump homologous curves

    International Nuclear Information System (INIS)

    Veloso, Marcelo A.; Mattos, Joao R.L. de

    2015-01-01

    Essential for any mathematical model designed to simulate flow transient events caused by pump operations is the pump performance data. The performance of a centrifugal pump is characterized by four basic quantities: the rotational speed, the volumetric flow rate, the dynamic head, and the hydraulic torque. The curves showing the relationships between these four variables are called the pump characteristic curves. The characteristic curves are empirically developed by the pump manufacturer and uniquely describe head and torque as functions of volumetric flow rate and rotation speed. Because of comprising a large amount of points, this configuration is not suitable for computational purposes. However, it can be converted to a simpler form by the development of the homologous curves, in which dynamic head and hydraulic torque ratios are expressed as functions of volumetric flow and rotation speed ratios. The numerical use of the complete set of homologous curves requires specification of sixteen partial curves, being eight for the dynamic head and eight for the hydraulic torque. As a consequence, the handling of homologous curves is still somewhat complicated. In solving flow transient problems that require the pump characteristic data for all the operation zones, the parametric form appears as the simplest way to deal with the homologous curves. In this approach, the complete characteristics of a pump can be described by only two closed curves, one for the dynamic head and other for the hydraulic torque, both in function of a single angular coordinate defined adequately in terms of the quotient between volumetric flow ratio and rotation speed ratio. The usefulness and advantages of this alternative method are demonstrated through a practical example in which the homologous curves for a pump of the type used in the main coolant loops of a pressurized water reactor (PWR) are transformed to the parametric form. (author)

  1. Non centered minor hysteresis loops evaluation based on exponential parameters transforms of the modified inverse Jiles–Atherton model

    International Nuclear Information System (INIS)

    Hamimid, M.; Mimoune, S.M.; Feliachi, M.; Atallah, K.

    2014-01-01

    In this present work, a non centered minor hysteresis loops evaluation is performed using the exponential transforms (ET) of the modified inverse Jiles–Atherton model parameters. This model improves the non centered minor hysteresis loops representation. The parameters of the non centered minor hysteresis loops are obtained from exponential expressions related to the major ones. The parameters of minor loops are obtained by identification using the stochastic optimization method “simulated annealing”. The four parameters of JA model (a,α, k and c) obtained by this transformation are applied only in both ascending and descending branches of the non centered minor hysteresis loops while the major ones are applied to the rest of the cycle. This proposal greatly improves both branches and consequently the minor loops. To validate this model, calculated non-centered minor hysteresis loops are compared with measured ones and good agreements are obtained

  2. Comments on the Updated Tetrapartite Pallium Model in the Mouse and Chick, Featuring a Homologous Claustro-Insular Complex.

    Science.gov (United States)

    Puelles, Luis

    2017-01-01

    This essay reviews step by step the conceptual changes of the updated tetrapartite pallium model from its tripartite and early tetrapartite antecedents. The crucial observations in mouse material are explained first in the context of assumptions, tentative interpretations, and literature data. Errors and the solutions offered to resolve them are made explicit. Next, attention is centered on the lateral pallium sector of the updated model, whose definition is novel in incorporating a claustro-insular complex distinct from both olfactory centers (ventral pallium) and the isocortex (dorsal pallium). The general validity of the model is postulated at least for tetrapods. Genoarchitectonic studies performed to check the presence of a claustro-insular field homolog in the avian brain are reviewed next. These studies have indeed revealed the existence of such a complex in the avian mesopallium (though stratified outside-in rather than inside-out as in mammals), and there are indications that the same pattern may be found in reptiles as well. Peculiar pallio-pallial tangential migratory phenomena are apparently shared as well between mice and chicks. The issue of whether the avian mesopallium has connections that are similar to the known connections of the mammalian claustro-insular complex is considered next. Accrued data are consistent with similar connections for the avian insula homolog, but they are judged to be insufficient to reach definitive conclusions about the avian claustrum. An aside discusses that conserved connections are not a necessary feature of field-homologous neural centers. Finally, the present scenario on the evolution of the pallium of sauropsids and mammals is briefly visited, as highlighted by the updated tetrapartite model and present results. © 2017 S. Karger AG, Basel.

  3. Wind turbine model and loop shaping controller design

    Science.gov (United States)

    Gilev, Bogdan

    2017-12-01

    A model of a wind turbine is evaluated, consisting of: wind speed model, mechanical and electrical model of generator and tower oscillation model. Model of the whole system is linearized around of a nominal point. By using the linear model with uncertainties is synthesized a uncertain model. By using the uncertain model is developed a H∞ controller, which provide mode of stabilizing the rotor frequency and damping the tower oscillations. Finally is simulated work of nonlinear system and H∞ controller.

  4. Detection of no-model input-output pairs in closed-loop systems.

    Science.gov (United States)

    Potts, Alain Segundo; Alvarado, Christiam Segundo Morales; Garcia, Claudio

    2017-11-01

    The detection of no-model input-output (IO) pairs is important because it can speed up the multivariable system identification process, since all the pairs with null transfer functions are previously discarded and it can also improve the identified model quality, thus improving the performance of model based controllers. In the available literature, the methods focus just on the open-loop case, since in this case there is not the effect of the controller forcing the main diagonal in the transfer matrix to one and all the other terms to zero. In this paper, a modification of a previous method able to detect no-model IO pairs in open-loop systems is presented, but adapted to perform this duty in closed-loop systems. Tests are performed by using the traditional methods and the proposed one to show its effectiveness. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  5. Homology modeling, molecular docking and DNA binding studies of nucleotide excision repair UvrC protein from M. tuberculosis.

    Science.gov (United States)

    Parulekar, Rishikesh S; Barage, Sagar H; Jalkute, Chidambar B; Dhanavade, Maruti J; Fandilolu, Prayagraj M; Sonawane, Kailas D

    2013-08-01

    Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacterium, is the leading causative agent of most cases of tuberculosis. The pathogenicity of the bacteria is enhanced by its developed DNA repair mechanism which consists of machineries such as nucleotide excision repair. Nucleotide excision repair consists of excinuclease protein UvrABC endonuclease, multi-enzymatic complex which carries out repair of damaged DNA in sequential manner. UvrC protein is a part of this complex and thus helps to repair the damaged DNA of M. tuberculosis. Hence, structural bioinformatics study of UvrC protein from M. tuberculosis was carried out using homology modeling and molecular docking techniques. Assessment of the reliability of the homology model was carried out by predicting its secondary structure along with its model validation. The predicted structure was docked with the ATP and the interacting amino acid residues of UvrC protein with the ATP were found to be TRP539, PHE89, GLU536, ILE402 and ARG575. The binding of UvrC protein with the DNA showed two different domains. The residues from domain I of the protein VAL526, THR524 and LEU521 interact with the DNA whereas, amino acids interacting from the domain II of the UvrC protein included ARG597, GLU595, GLY594 and GLY592 residues. This predicted model could be useful to design new inhibitors of UvrC enzyme to prevent pathogenesis of Mycobacterium and so the tuberculosis.

  6. Empirical potential and elasticity theory modelling of interstitial dislocation loops in UO2 for cluster dynamics application

    International Nuclear Information System (INIS)

    Le-Prioux, Arno

    2017-01-01

    During irradiation in reactor, the microstructure of UO 2 changes and deteriorates, causing modifications of its physical and mechanical properties. The kinetic models used to describe these changes such as cluster dynamics (CRESCENDO calculation code) consider the main microstructural elements that are cavities and interstitial dislocation loops, and provide a rather rough description of the loop thermodynamics. In order to tackle this issue, this work has led to the development of a thermodynamic model of interstitial dislocation loops based on empirical potential calculations. The model considers two types of interstitial dislocation loops on two different size domains: Type 1: Dislocation loops similar to Frank partials in F.C.C. materials which are stable in the smaller size domain. Type 2: Perfect dislocation loops of Burgers vector (a/2)(110) stable in the larger size domain. The analytical formula used to compute the interstitial dislocation loop formation energies is the one for circular loops which has been modified in order to take into account the effects of the dislocation core, which are significant at smaller sizes. The parameters have been determined by empirical potential calculations of the formation energies of prismatic pure edge dislocation loops. The effect of the habit plane reorientation on the formation energies of perfect dislocation loops has been taken into account by a simple interpolation method. All the different types of loops seen during TEM observations are thus accounted for by the model. (author) [fr

  7. How to Choose the Suitable Template for Homology Modelling of GPCRs: 5-HT7 Receptor as a Test Case.

    Science.gov (United States)

    Shahaf, Nir; Pappalardo, Matteo; Basile, Livia; Guccione, Salvatore; Rayan, Anwar

    2016-09-01

    G protein-coupled receptors (GPCRs) are a super-family of membrane proteins that attract great pharmaceutical interest due to their involvement in almost every physiological activity, including extracellular stimuli, neurotransmission, and hormone regulation. Currently, structural information on many GPCRs is mainly obtained by the techniques of computer modelling in general and by homology modelling in particular. Based on a quantitative analysis of eighteen antagonist-bound, resolved structures of rhodopsin family "A" receptors - also used as templates to build 153 homology models - it was concluded that a higher sequence identity between two receptors does not guarantee a lower RMSD between their structures, especially when their pair-wise sequence identity (within trans-membrane domain and/or in binding pocket) lies between 25 % and 40 %. This study suggests that we should consider all template receptors having a sequence identity ≤50 % with the query receptor. In fact, most of the GPCRs, compared to the currently available resolved structures of GPCRs, fall within this range and lack a correlation between structure and sequence. When testing suitability for structure-based drug design, it was found that choosing as a template the most similar resolved protein, based on sequence resemblance only, led to unsound results in many cases. Molecular docking analyses were carried out, and enrichment factors as well as attrition rates were utilized as criteria for assessing suitability for structure-based drug design. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Matrix Solution of Coupled Differential Equations and Looped Car Following Models

    Science.gov (United States)

    McCartney, Mark

    2008-01-01

    A simple mathematical model for the behaviour of how vehicles follow each other along a looped stretch of road is described. The resulting coupled first order differential equations are solved using appropriate matrix techniques and the physical significance of the model is discussed. A number possible classroom exercises are suggested to help…

  9. Modelling and simulation of a U-loop Reactor for Single Cell Protein Production

    DEFF Research Database (Denmark)

    Wu, Mengzhe; Huusom, Jakob Kjøbsted; Gernaey, Krist

    2016-01-01

    In this work, two approaches of modelling a one phase U-loop reactor are presented. A simple CSTR model consisting of first-principles dynamic process equations was implemented in Matlab. The results give a good indication of the basic understanding of the effect of changing operation conditions...

  10. Using Video Modeling with Substitutable Loops to Teach Varied Play to Children with Autism

    Science.gov (United States)

    Dupere, Sally; MacDonald, Rebecca P. F.; Ahearn, William H.

    2013-01-01

    Children with autism often engage in repetitive play with little variation in the actions performed or items used. This study examined the use of video modeling with scripted substitutable loops on children's pretend play with trained and untrained characters. Three young children with autism were shown a video model of scripted toy play that…

  11. Simplified Models for Analysis and Design of the Control System Main Loops of CAREM Reactor

    International Nuclear Information System (INIS)

    Etchepareborda, Andres; Flury, Celso

    2000-01-01

    The target of this work is to show a few models developed for control analysis and design of the reactor CAREM's main control loops within a broad range of power (between 40 % and 100%).By one side, it is shown the main features of a analytic model programed in MATLAB.This model is based on fitting steady state points at different power levels of the CAREM's RETRAN model.By the other side, it is shown linear models of black-box type denoting the perturbed behavior of the system for each level power point.These models are identified from temporal responses of CAREM's RETRAN model to perturbed input signals over the different steady power level points.Then the dynamics of these models are verified contrasting the temporal responses of the RETRAN model versus the responses of the MATLAB model and the identified models, in each steady power level point.Also are contrasting the frequency response of the linearization of MATLAB model versus the frequency response of the identified models, in each steady power level point.Either the MATLAB model as the identified models are good enough for the control analysis and design of the three main control loops.The MATLAB model has a few differences against the RETRAN model in the primary pressure output variable, that it must be taken into account in the design of this control loop if this model is used.The aim of these models is to represent in a satisfactory way the dynamics of the plant for a later control analysis and design of the control loops in a frequency range between 0.01 rad/seg and 0.3 rad/seg, and a power range between 40 % and 100 %

  12. Droop Control with an Adjustable Complex Virtual Impedance Loop based on Cloud Model Theory

    DEFF Research Database (Denmark)

    Li, Yan; Shuai, Zhikang; Xu, Qinming

    2016-01-01

    Droop control framework with an adjustable virtual impedance loop is proposed in this paper, which is based on the cloud model theory. The proposed virtual impedance loop includes two terms: a negative virtual resistor and an adjustable virtual inductance. The negative virtual resistor term...... sometimes. The cloud model theory is applied to get online the changing line impedance value, which relies on the relevance of the reactive power responding the changing line impedance. The verification of the proposed control strategy is done according to the simulation in a low voltage microgrid in Matlab....

  13. Two loop effective Kahler potential of (non)-renormalizable supersymmetric models

    International Nuclear Information System (INIS)

    Groot Nibbelink, S.; Nyawelo, T.S.

    2005-10-01

    We perform a supergraph computation of the effective Kahler potential at one and two loops for general four dimensional N=1 supersymmetric theories described by arbitrary Kahler potential, superpotential and gauge kinetic function. We only insist on gauge invariance of the Kahler potential and the superpotential as we heavily rely on its consequences in the quantum theory. However, we do not require gauge invariance for the gauge kinetic functions, so that our results can also be applied to anomalous theories that involve the Green-Schwarz mechanism. We illustrate our two loop results by considering a few simple models: the (non-)renormalizable Wess-Zumino model and Super Quantum Electrodynamics. (author)

  14. Closing the loop: modelling of heart failure progression from health to end-stage using a meta-analysis of left ventricular pressure-volume loops.

    Science.gov (United States)

    Warriner, David R; Brown, Alistair G; Varma, Susheel; Sheridan, Paul J; Lawford, Patricia; Hose, David R; Al-Mohammad, Abdallah; Shi, Yubing

    2014-01-01

    The American Heart Association (AHA)/American College of Cardiology (ACC) guidelines for the classification of heart failure (HF) are descriptive but lack precise and objective measures which would assist in categorising such patients. Our aim was two fold, firstly to demonstrate quantitatively the progression of HF through each stage using a meta-analysis of existing left ventricular (LV) pressure-volume (PV) loop data and secondly use the LV PV loop data to create stage specific HF models. A literature search yielded 31 papers with PV data, representing over 200 patients in different stages of HF. The raw pressure and volume data were extracted from the papers using a digitising software package and the means were calculated. The data demonstrated that, as HF progressed, stroke volume (SV), ejection fraction (EF%) decreased while LV volumes increased. A 2-element lumped parameter model was employed to model the mean loops and the error was calculated between the loops, demonstrating close fit between the loops. The only parameter that was consistently and statistically different across all the stages was the elastance (Emax). For the first time, the authors have created a visual and quantitative representation of the AHA/ACC stages of LVSD-HF, from normal to end-stage. The study demonstrates that robust, load-independent and reproducible parameters, such as elastance, can be used to categorise and model HF, complementing the existing classification. The modelled PV loops establish previously unknown physiological parameters for each AHA/ACC stage of LVSD-HF, such as LV elastance and highlight that it this parameter alone, in lumped parameter models, that determines the severity of HF. Such information will enable cardiovascular modellers with an interest in HF, to create more accurate models of the heart as it fails.

  15. Closing the loop: modelling of heart failure progression from health to end-stage using a meta-analysis of left ventricular pressure-volume loops.

    Directory of Open Access Journals (Sweden)

    David R Warriner

    Full Text Available INTRODUCTION: The American Heart Association (AHA/American College of Cardiology (ACC guidelines for the classification of heart failure (HF are descriptive but lack precise and objective measures which would assist in categorising such patients. Our aim was two fold, firstly to demonstrate quantitatively the progression of HF through each stage using a meta-analysis of existing left ventricular (LV pressure-volume (PV loop data and secondly use the LV PV loop data to create stage specific HF models. METHODS AND RESULTS: A literature search yielded 31 papers with PV data, representing over 200 patients in different stages of HF. The raw pressure and volume data were extracted from the papers using a digitising software package and the means were calculated. The data demonstrated that, as HF progressed, stroke volume (SV, ejection fraction (EF% decreased while LV volumes increased. A 2-element lumped parameter model was employed to model the mean loops and the error was calculated between the loops, demonstrating close fit between the loops. The only parameter that was consistently and statistically different across all the stages was the elastance (Emax. CONCLUSIONS: For the first time, the authors have created a visual and quantitative representation of the AHA/ACC stages of LVSD-HF, from normal to end-stage. The study demonstrates that robust, load-independent and reproducible parameters, such as elastance, can be used to categorise and model HF, complementing the existing classification. The modelled PV loops establish previously unknown physiological parameters for each AHA/ACC stage of LVSD-HF, such as LV elastance and highlight that it this parameter alone, in lumped parameter models, that determines the severity of HF. Such information will enable cardiovascular modellers with an interest in HF, to create more accurate models of the heart as it fails.

  16. Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom.

    Science.gov (United States)

    Reyes-Velasco, Jacobo; Card, Daren C; Andrew, Audra L; Shaney, Kyle J; Adams, Richard H; Schield, Drew R; Casewell, Nicholas R; Mackessy, Stephen P; Castoe, Todd A

    2015-01-01

    Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete genome of the Burmese python, including information from tissue-specific patterns of gene expression. We identified the orthologs of snake venom genes in the python genome, and conducted detailed analysis of gene expression of these venom homologs to identify patterns that differ between snake venom gene families and all other genes. We found that venom gene homologs in the python are expressed in many different tissues outside of oral glands, which illustrates the pitfalls of using transcriptomic data alone to define "venom toxins." We hypothesize that the python may represent an ancestral state prior to major venom development, which is supported by our finding that the expansion of venom gene families is largely restricted to highly venomous caenophidian snakes. Therefore, the python provides insight into biases in which genes were recruited for snake venom systems. Python venom homologs are generally expressed at lower levels, have higher variance among tissues, and are expressed in fewer organs compared with all other python genes. We propose a model for the evolution of snake venoms in which venom genes are recruited preferentially from genes with particular expression profile characteristics, which facilitate a nearly neutral transition toward specialized venom system expression. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. All-loop anomalous dimensions in integrable λ-deformed σ-models

    Directory of Open Access Journals (Sweden)

    George Georgiou

    2015-12-01

    Full Text Available We calculate the all-loop anomalous dimensions of current operators in λ-deformed σ-models. For the isotropic integrable deformation and for a semi-simple group G we compute the anomalous dimensions using two different methods. In the first we use the all-loop effective action and in the second we employ perturbation theory along with the Callan–Symanzik equation and in conjunction with a duality-type symmetry shared by these models. Furthermore, using CFT techniques we compute the all-loop anomalous dimension of bilinear currents for the isotropic deformation case and a general G. Finally we work out the anomalous dimension matrix for the cases of anisotropic SU(2 and the two couplings, corresponding to the symmetric coset G/H and a subgroup H, splitting of a group G.

  18. String states, loops and effective actions in noncommutative field theory and matrix models

    Directory of Open Access Journals (Sweden)

    Harold C. Steinacker

    2016-09-01

    Full Text Available Refining previous work by Iso, Kawai and Kitazawa, we discuss bi-local string states as a tool for loop computations in noncommutative field theory and matrix models. Defined in terms of coherent states, they exhibit the stringy features of noncommutative field theory. This leads to a closed form for the 1-loop effective action in position space, capturing the long-range non-local UV/IR mixing for scalar fields. The formalism applies to generic fuzzy spaces. The non-locality is tamed in the maximally supersymmetric IKKT or IIB model, where it gives rise to supergravity. The linearized supergravity interactions are obtained directly in position space at one loop using string states on generic noncommutative branes.

  19. String states, loops and effective actions in noncommutative field theory and matrix models

    Energy Technology Data Exchange (ETDEWEB)

    Steinacker, Harold C., E-mail: harold.steinacker@univie.ac.at

    2016-09-15

    Refining previous work by Iso, Kawai and Kitazawa, we discuss bi-local string states as a tool for loop computations in noncommutative field theory and matrix models. Defined in terms of coherent states, they exhibit the stringy features of noncommutative field theory. This leads to a closed form for the 1-loop effective action in position space, capturing the long-range non-local UV/IR mixing for scalar fields. The formalism applies to generic fuzzy spaces. The non-locality is tamed in the maximally supersymmetric IKKT or IIB model, where it gives rise to supergravity. The linearized supergravity interactions are obtained directly in position space at one loop using string states on generic noncommutative branes.

  20. Modeling a forced to natural convection boiling test with the program LOOP-W

    International Nuclear Information System (INIS)

    Carbajo, J.J.

    1984-01-01

    Extensive testing has been conducted in the Simulant Boiling Flow Visualization (SBFV) loop in which water is boiled in a vertical transparent tube by circulating hot glycerine in an annulus surrounding the tube. Tests ranged from nonboiling forced convection to oscillatory boiling natural convection. The program LOOP-W has been developed to analyze these tests. This program is a multi-leg, one-dimensional, two-phase equilibrium model with slip between the phases. In this study, a specific test, performed at low power where non-boiling forced convection was changed to boiling natural convection and then to non-boiling again, has been modeled with the program LOOP-W

  1. Hippocampal closed-loop modeling and implications for seizure stimulation design

    Science.gov (United States)

    Sandler, Roman A.; Song, Dong; Hampson, Robert E.; Deadwyler, Sam A.; Berger, Theodore W.; Marmarelis, Vasilis Z.

    2015-10-01

    Objective. Traditional hippocampal modeling has focused on the series of feedforward synapses known as the trisynaptic pathway. However, feedback connections from CA1 back to the hippocampus through the entorhinal cortex (EC) actually make the hippocampus a closed-loop system. By constructing a functional closed-loop model of the hippocampus, one may learn how both physiological and epileptic oscillations emerge and design efficient neurostimulation patterns to abate such oscillations. Approach. Point process input-output models where estimated from recorded rodent hippocampal data to describe the nonlinear dynamical transformation from CA3 → CA1, via the schaffer-collateral synapse, and CA1 → CA3 via the EC. Each Volterra-like subsystem was composed of linear dynamics (principal dynamic modes) followed by static nonlinearities. The two subsystems were then wired together to produce the full closed-loop model of the hippocampus. Main results. Closed-loop connectivity was found to be necessary for the emergence of theta resonances as seen in recorded data, thus validating the model. The model was then used to identify frequency parameters for the design of neurostimulation patterns to abate seizures. Significance. Deep-brain stimulation (DBS) is a new and promising therapy for intractable seizures. Currently, there is no efficient way to determine optimal frequency parameters for DBS, or even whether periodic or broadband stimuli are optimal. Data-based computational models have the potential to be used as a testbed for designing optimal DBS patterns for individual patients. However, in order for these models to be successful they must incorporate the complex closed-loop structure of the seizure focus. This study serves as a proof-of-concept of using such models to design efficient personalized DBS patterns for epilepsy.

  2. Reactor design, cold-model experiment and CFD modeling for chemical looping combustion

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shaohua; Ma, Jinchen; Hu, Xintao; Zhao, Haibo; Wang, Baowen; Zheng, Chuguang [Huazhong Univ. of Science and Technology, Wuhan (China). State Key Lab. of Coal Combustion

    2013-07-01

    Chemical looping combustion (CLC) is an efficient, clean and cheap technology for CO{sub 2} capture, and an interconnected fluidized bed is more appropriate solution for CLC. This paper aims to design a reactor system for CLC, carry out cold-model experiment of the system, and model fuel reactor using commercial CFD software. As for the CLC system, the air reactor (AR) is designed as a fast fluidized bed while the fuel reactor (FR) is a bubbling bed; a cyclone is used for solid separation of the AR exit flow. The AR and FR are separated by two U-type loop seals to remain gas sealed. Considered the chemical kinetics of oxygen carrier, fluid dynamics, pressure balance and mass balance of the system simultaneously, some key design parameters of a CH{sub 4}-fueled and Fe{sub 2}O{sub 3}/Al{sub 2}O{sub 3}-based CLC reactor (thermal power of 50 kWth) are determined, including key geometric parameters (reactor cross-sectional area and reactor height) and operation parameters (bed material quantity, solid circulation rate, apparent gas velocity of each reactor). A cold-model bench having same geometric parameters with its prototype is built up to study the effects of various operation conditions (including gas velocity in the reactors and loop seals, and bed material height, etc.) on the solids circulation rate, gas leakage, and pressure balance. It is witnessed the cold-model system is able to meet special requirements for CLC system such as gas sealing between AR and FR, the circulation rate and particles residence time. Furthermore, the thermal FR reactor with oxygen carrier of Fe{sub 2}O{sub 3}/Al{sub 2}O{sub 3} and fuel of CH{sub 4} is simulated by commercial CFD solver FLUENT. It is found that for the design case the combustion efficiency of CH{sub 4} reaches 88.2%. A few part of methane is unburned due to fast, large bubbles rising through the reactor.

  3. Toward the virtual screening of potential drugs in the homology modeled NAD+ dependent DNA ligase from Mycobacterium tuberculosis.

    Science.gov (United States)

    Singh, Vijai; Somvanshi, Pallavi

    2010-02-01

    DNA ligase is an important enzyme and it plays vital role in the replication and repair; also catalyzes nick joining between adjacent bases of DNA. The NAD(+) dependent DNA ligase is selectively present in eubacteria and few viruses; but missing in humans. Homology modeling was used to generate 3-D structure of NAD(+) dependent DNA ligase (LigA) of Mycobacterium tuberculosis using the known template (PDB: 2OWO). Furthermore, the stereochemical quality and torsion angle of 3-D structure was validated. Numerous effective drugs were selected and the active amino acid residue in LigA was targeted and virtual screening through molecular docking was done. In this analysis, four drugs Chloroquine, Hydroxychloroquine, Putrienscine and Adriamycin were found more potent in inhibition of M. tuberculosis through the robust binding affinity between protein-drug interactions in comparison with the other studied drugs. A phylogenetic tree was constructed and it was observed that homology of LigA in M. tuberculosis resembled with other Mycobacterium species. The conserved active amino acids of LigA may be useful to target these drugs. These findings could be used as the starting point of a rational design of novel antibacterial drugs and its analogs.

  4. The Life Cycle Evaluation Model of External Diseconomy of Open-loop Supply Chain

    Science.gov (United States)

    Liu, Qian; Hu, Tianjun

    2017-08-01

    In recent years, with the continuous deterioration of pollution, resource space is gradually narrowed, the number of waste items increased, people began to use the method of recycling on waste products to ease the pressure on the environment. This paper adopted the external diseconomy of open-loop supply chain as the research object and constructed the model by the life cycle evaluation method, comparative analysis through the case. This paper also concludes that the key to solving the problem is to realize the closed-loop supply chain and building reverse logistics system is of great significance.

  5. Anderson localization through Polyakov loops: Lattice evidence and random matrix model

    International Nuclear Information System (INIS)

    Bruckmann, Falk; Schierenberg, Sebastian; Kovacs, Tamas G.

    2011-01-01

    We investigate low-lying fermion modes in SU(2) gauge theory at temperatures above the phase transition. Both staggered and overlap spectra reveal transitions from chaotic (random matrix) to integrable (Poissonian) behavior accompanied by an increasing localization of the eigenmodes. We show that the latter are trapped by local Polyakov loop fluctuations. Islands of such ''wrong'' Polyakov loops can therefore be viewed as defects leading to Anderson localization in gauge theories. We find strong similarities in the spatial profile of these localized staggered and overlap eigenmodes. We discuss possible interpretations of this finding and present a sparse random matrix model that reproduces these features.

  6. Binding site analysis of full-length α1a adrenergic receptor using homology modeling and molecular docking

    International Nuclear Information System (INIS)

    Pedretti, Alessandro; Elena Silva, Maria; Villa, Luigi; Vistoli, Giulio

    2004-01-01

    The recent availability of crystal structure of bovine rhodopsin offers new opportunities in order to approach the construction of G protein coupled receptors. This study focuses the attention on the modeling of full-length α 1a adrenergic receptor (α 1a -AR) due to its biological role and significant implications in pharmacological treatment of benign prostate hyperplasia. This work could be considered made up by two main steps: (a) the construction of full structure of α 1a -AR, through homology modeling methods; (b) the automated docking of an endogenous agonist, norepinephrine, and of an antagonist, WB-4101, using BioDock program. The obtained results highlight the key residues involved in binding sites of both agonists and antagonists, confirming the mutagenesis data and giving new suggestions for the rational design of selective ligands

  7. Scalar loops and the Higgs mass in the Salam-Weinberg-Glashow model

    International Nuclear Information System (INIS)

    Ghose, P.

    1982-08-01

    It is shown that spontaneous symmetry breaking is predominantly driven by scalar loops in the standard Salam-Weinberg-Glashow model if lambda approx.=0(e 2 ). The Higgs mass is predicted to be 0(64 GeV), which is considerably higher than the Coleman Weinberg prediction. (author)

  8. The one loop calculation of the strong coupling β function in the Toy Model

    International Nuclear Information System (INIS)

    Bai Zhiming; Jiang Yuanfang

    1991-01-01

    The background field quantization is used to calculate the one-loop β function in the Toy Model which has the strong coupling and the SU(3) symmetry. The function obtained is consistent with the Appalquist-Carrazone theorem in the low energy condition

  9. Two-loop calculation of the effective potential for the Wess-Zumino model

    International Nuclear Information System (INIS)

    Fogleman, G.; Starkmann, G.D.; Viswanathan, K.S.; Simon Fraser Univ., Burnaby, British Columbia

    1983-01-01

    The effective potential for the supersymmetric Wess-Zumino model is computed off-shell to two loops. A renormalization procedure which preserves positivity of the kinetic terms in the effective action is implemented. Supersymmetry is not broken to this order. (orig.)

  10. Optimal closed-loop identification test design for internal model control

    NARCIS (Netherlands)

    Zhu, Y.; Bosch, van den P.P.J.

    2000-01-01

    In this work, optimal closed-loop test design for control is studied. Simple design formulas are derived based on the asymptotic theory of Ljung. The control scheme used is internal model control (IMC) and the design constraint is the power of the process output or that of the reference signal. The

  11. Scalar loops and the Higgs mass in the Salam-Weinberg-Glashow model

    International Nuclear Information System (INIS)

    Ghose, P.

    1983-01-01

    It is shown that spontaneous symmetry breaking is predominantly driven by scalar loops in the standard Salam-Weinberg-Glashow model if lambdaapproximately equal to O(e 2 ). The Higgs mass is predicted to be O(64 GeV), which is considerably higher than the Coleman-Weinberg prediction (1973 Phys. Rev. D 7 1888). (author)

  12. Model Optimization Identification Method Based on Closed-loop Operation Data and Process Characteristics Parameters

    Directory of Open Access Journals (Sweden)

    Zhiqiang GENG

    2014-01-01

    Full Text Available Output noise is strongly related to input in closed-loop control system, which makes model identification of closed-loop difficult, even unidentified in practice. The forward channel model is chosen to isolate disturbance from the output noise to input, and identified by optimization the dynamic characteristics of the process based on closed-loop operation data. The characteristics parameters of the process, such as dead time and time constant, are calculated and estimated based on the PI/PID controller parameters and closed-loop process input/output data. And those characteristics parameters are adopted to define the search space of the optimization identification algorithm. PSO-SQP optimization algorithm is applied to integrate the global search ability of PSO with the local search ability of SQP to identify the model parameters of forward channel. The validity of proposed method has been verified by the simulation. The practicability is checked with the PI/PID controller parameter turning based on identified forward channel model.

  13. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C.; Nesbitt, Anna E.; Hallock, Michael J. [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Rupasinghe, Sanjeewa G. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Tang Ming [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Harris, Jason; Baudry, Jerome [University of Tennessee, Department of Biochemistry, Cellular and Molecular Biology (United States); Schuler, Mary A. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Rienstra, Chad M., E-mail: rienstra@illinois.edu [University of Illinois at Urbana-Champaign, Department of Chemistry (United States)

    2012-01-15

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., {sup 13}C-{sup 13}C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  14. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C [University of Illinois, Urbana-Champaign; Nesbitt, Anna E [University of Illinois, Urbana-Champaign; Hallock, Michael J [University of Illinois, Urbana-Champaign; Rupasinghe, Sanjeewa [University of Illinois, Urbana-Champaign; Tang, Ming [University of Illinois, Urbana-Champaign; Harris, Jason B [ORNL; Baudry, Jerome Y [ORNL; Schuler, Mary A [University of Illinois, Urbana-Champaign; Rienstra, Chad M [University of Illinois, Urbana-Champaign

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  15. One-loop contributions to neutral minima in the inert doublet model

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, P.M. [Instituto Superior de Engenharia de Lisboa - ISEL,1959-007 Lisboa (Portugal); Centro de Física Teórica e Computacional - FCUL,Universidade de Lisboa, R. Ernesto de Vasconcelos, 1749-016 Lisboa (Portugal); Świeżewska, Bogumiła [Faculty of Physics, University of Warsaw,Pasteura 5, 02-093 Warsaw (Poland)

    2016-04-15

    The vacuum structure of the inert doublet model is analysed at the one-loop level using the effective potential formalism, to verify the validity of tree-level predictions for the properties of the global minimum. An inert minimum (with massive fermions) and an inert-like minimum (with massless fermions) can coexist at tree level. But the one-loop analysis reveals that the allowed parameter space for the coexistence of more than one minimum is larger than the tree-level expected one. It is also shown that for some choices of parameters, the global minimum found at the one-loop level may be inert (or inert-like), contrary to what the tree-level analysis indicates.

  16. Two-loop renormalization in the standard model, part I. Prolegomena

    Energy Technology Data Exchange (ETDEWEB)

    Actis, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Ferroglia, A. [Albert-Ludwigs-Univ., Freiburg (Germany). Fakultat fur Phys.]|[Zuerich Univ. (Switzerland). Inst. fuer Theoretische Physik; Passera, M. [Padua Univ. (Italy). Dipt. di Fisica]|[INFN, Sezione di Padova (Italy); Passarino, G. [Torino Univ. (Italy). Dipt. di Fisica Teorica]|[INFN, Sezione di Torino (Italy)

    2006-12-15

    In this paper the building blocks for the two-loop renormalization of the Standard Model are introduced with a comprehensive discussion of the special vertices induced in the Lagrangian by a particular diagonalization of the neutral sector and by two alternative treatments of the Higgs tadpoles. Dyson resummed propagators for the gauge bosons are derived, and two-loop Ward-Slavnov-Taylor identities are discussed. In part II, the complete set of counterterms needed for the two-loop renormalization will be derived. In part III, a renormalization scheme will be introduced, connecting the renormalized quantities to an input parameter set of (pseudo-)experimental data, critically discussing renormalization of a gauge theory with unstable particles. (orig.)

  17. High-Temperature Structural Analysis Model of the Process Heat Exchanger for Helium Gas Loop (II)

    International Nuclear Information System (INIS)

    Song, Kee Nam; Lee, Heong Yeon; Kim, Chan Soo; Hong, Seong Duk; Park, Hong Yoon

    2010-01-01

    PHE (Process Heat Exchanger) is a key component required to transfer heat energy of 950 .deg. C generated in a VHTR (Very High Temperature Reactor) to the chemical reaction that yields a large quantity of hydrogen. Korea Atomic Energy Research Institute established the helium gas loop for the performance test of components, which are used in the VHTR, and they manufactured a PHE prototype to be tested in the loop. In this study, as part of the high temperature structural-integrity evaluation of the PHE prototype, which is scheduled to be tested in the helium gas loop, we carried out high-temperature structural-analysis modeling, thermal analysis, and thermal expansion analysis of the PHE prototype. The results obtained in this study will be used to design the performance test setup for the PHE prototype

  18. The 1-loop effective potential for the Standard Model in curved spacetime

    Science.gov (United States)

    Markkanen, Tommi; Nurmi, Sami; Rajantie, Arttu; Stopyra, Stephen

    2018-06-01

    The renormalisation group improved Standard Model effective potential in an arbitrary curved spacetime is computed to one loop order in perturbation theory. The loop corrections are computed in the ultraviolet limit, which makes them independent of the choice of the vacuum state and allows the derivation of the complete set of β-functions. The potential depends on the spacetime curvature through the direct non-minimal Higgs-curvature coupling, curvature contributions to the loop diagrams, and through the curvature dependence of the renormalisation scale. Together, these lead to significant curvature dependence, which needs to be taken into account in cosmological applications, which is demonstrated with the example of vacuum stability in de Sitter space.

  19. A bag model calculation of the electroweak s → dγ loop

    International Nuclear Information System (INIS)

    Eeg, J.O.; Ruud, J.Aa.

    1990-10-01

    The CP-conservering electroweak transitions s → dγ have been considered. In order to include confinement effects below the charm scale, the loop calculations within the bag model were performed. According to the calculations, confinement effects are rather important and give amplitudes three orders of magnitude larger than those obtained from the free quark loop, which is ∼eG F m c 2 /M W 2 . Moreover, the amplitude is of the same order of magnitude as the perturbative two-loop amplitude ∼eG F α s ln(m c /μ). For the decay mode Ω - → γΞ - , a branching ratio 4.4 x 10 -5 was obtained. Other radiative decays of strange baryons are known to be dominated by pole diagrams. 14 refs., 1 fig

  20. Fault detection in IRIS reactor secondary loop using inferential models

    International Nuclear Information System (INIS)

    Perillo, Sergio R.P.; Upadhyaya, Belle R.; Hines, J. Wesley

    2013-01-01

    The development of fault detection algorithms is well-suited for remote deployment of small and medium reactors, such as the IRIS, and the development of new small modular reactors (SMR). However, an extensive number of tests are still to be performed for new engineering aspects and components that are not yet proven technology in the current PWRs, and present some technological challenges for its deployment since many of its features cannot be proven until a prototype plant is built. In this work, an IRIS plant simulation platform was developed using a Simulink® model. The dynamic simulation was utilized in obtaining inferential models that were used to detect faults artificially added to the secondary system simulations. The implementation of data-driven models and the results are discussed. (author)

  1. Robust Model-based Control of Open-loop Unstable Processes

    International Nuclear Information System (INIS)

    Emad, Ali

    1999-01-01

    This paper addresses the development of new formulations for estimating modeling errors or unmeasured disturbances to be used in Model Predictive Control (MPC) algorithms during open-loop prediction. Two different formulations were developed in this paper. One is used in MPC that directly utilizes linear models and the other in MPC that utilizes non-linear models. These estimation techniques were utilized to provide robust performance for MPC algorithms when the plant is open-loop unstable and under the influence of modeling error and/or unmeasured disturbances. For MPC that utilizes a non-linear model, the estimation technique is formulated as a fixed small size on-line optimization problem, while for linear MPC, the unmeasured disturbances are estimated via a proposed linear disturbance model. The disturbance model coefficients are identified on-line from historical estimates of plant-model mismatch. The effectiveness of incorporating these proposed estimation techniques into MPC is tested through simulated implementation on non-linear unstable exothermic fluidized bed reactor. Closed-loop simulations proved the capability of the proposed estimation methods to stabilize and, thereby, improve the MPC performance in such cases. (Author)

  2. In-the-loop simulation of electronic automatic temperature control systems: HVAC modeling

    Energy Technology Data Exchange (ETDEWEB)

    Domschke, R.; Matthes, M. [Visteon Deutschland GmbH, Kerpen (Germany)

    2006-07-01

    The Electronic Automatic Temperature Control (EATC) ensures the occupant comfort and provides safety features like rapid defrost and demist protection. Doing this, the EATC controller provides a direct interface to the end consumer and has a considerable impact on customer satisfaction. The In-the-loop (IL) simulation process is an integral part of Visteons model-based development process. It helps to design and calibrate the EATC controller. It consists of several IL simulation techniques like Model-in-the-loop (MIL), Software-in-the-loop (SIL) and Hardware-in-the-loop (HIL). In this article, we will focus on MIL/SIL Simulations. MIL/SIL allows simulation of the EATC controller in a virtual vehicle environment from the early states of and throughout the development process. This ensures a rapid, high quality and robust development process. The MIL/SIL model contains a thermal vehicle model, a heating, ventilation and air conditioning (HVAC) unit model and a model of the EATC controller itself. The thermal vehicle model simulates transient temperature and humidity conditions in the passenger compartment of a vehicle, settings from the controller, heat fluxes through the vehicle shell and windows, solar load and several further boundary conditions. Whereas the thermal vehicle model of a specific vehicle can be adapted from a default data base, one has to pay special attention to the HVAC unit model. Visteon has developed a special, physically based HVAC unit model to be adapted and implemented into the MIL/SIL simulation. This HVAC model enables a straightforward implementation of different HVAC architectures into the MIL/SIL simulation. Moreover, changes in the HVAC settings (i.e. different blower/scroll assemblies) can be assessed and the influence on passenger comfort can be quantified. Examples of the MIL/SIL simulation demonstrate the benefits of this approach. Results are discussed and a further outlook provided. (orig.)

  3. Generalized one-loop neutrino mass model with charged particles

    Science.gov (United States)

    Cheung, Kingman; Okada, Hiroshi

    2018-04-01

    We propose a radiative neutrino-mass model by introducing 3 generations of fermion pairs E-(N +1 )/2E+(N +1 )/2 and a couple of multicharged bosonic doublet fields ΦN /2,ΦN /2 +1, where N =1 , 3, 5, 7, 9. We show that the models can satisfy the neutrino masses and oscillation data, and are consistent with lepton-flavor violations, the muon anomalous magnetic moment, the oblique parameters, and the beta function of the U (1 )Y hypercharge gauge coupling. We also discuss the collider signals for various N , namely, multicharged leptons in the final state from the Drell-Yan production of E-(N +1 )/2E+(N +1 )/2. In general, the larger the N the more charged leptons will appear in the final state.

  4. Kinks, chains, and loop groups in the CPn sigma models

    International Nuclear Information System (INIS)

    Harland, Derek

    2009-01-01

    We consider topological solitons in the CP n sigma models in two space dimensions. In particular, we study 'kinks', which are independent of one coordinate up to a rotation of the target space, and 'chains', which are periodic in one coordinate up to a rotation of the target space. Kinks and chains both exhibit constituents, similar to monopoles and calorons in SU(n) Yang-Mills-Higgs and Yang-Mills theories. We examine the constituent structure using Lie algebras.

  5. Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA

    Directory of Open Access Journals (Sweden)

    Eric R. Gamache

    2017-04-01

    Full Text Available The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5′ terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT. To identify RNA motifs involved in dimerization and packaging, a structural model of the TIPIRT domain in vitro was developed from single-nucleotide resolution RNA structural data. In general agreement with previous models, the first 326 nucleotides of Ty1 RNA form a pseudoknot with a 7-bp stem (S1, a 1-nucleotide interhelical loop and an 8-bp stem (S2 that delineate two long, structured loops. Nucleotide substitutions that disrupt either pseudoknot stem greatly reduced helper-Ty1-mediated retrotransposition of a mini-Ty1, but only mutations in S2 destabilized mini-Ty1 RNA in cis and helper-Ty1 RNA in trans. Nested in different loops of the pseudoknot are two hairpins with complementary 7-nucleotide motifs at their apices. Nucleotide substitutions in either motif also reduced retrotransposition and destabilized mini- and helper-Ty1 RNA. Compensatory mutations that restore base-pairing in the S2 stem or between the hairpins rescued retrotransposition and RNA stability in cis and trans. These data inform a model whereby a Ty1 RNA kissing complex with two intermolecular kissing-loop interactions initiates dimerization and packaging.

  6. Color superconductivity in the Nambu-Jona-Lasinio model complemented by a Polyakov loop

    Energy Technology Data Exchange (ETDEWEB)

    Blanquier, Eric

    2017-06-15

    The color superconductivity is studied with the Nambu and Jona-Lasinio (NJL) model. This one is coupled to a Polyakov loop, to form the PNJL model. A μ-dependent Polyakov loop potential is also considered (μPNJL model). An objective is to detail the analytical calculations that lead to the equations to be solved, in all of the treated cases. They are the normal quark (NQ), 2-flavor color-superconducting (2SC) and color-flavor-locked (CFL) phases, in an SU(3){sub f} x SU(3){sub c} description. The calculations are performed according to the temperature T, the chemical potentials μ{sub f} or the densities ρ{sub f}, with or without the isospin symmetry. The relation between the μ{sub f} and ρ{sub f} results is studied. The influence of the color superconductivity and the Polyakov loop on the found data is analyzed. A triple coincidence is observed at low T between the chiral restoration, the deconfinement transition described by the Polyakov loop and the NQ/2SC phase transition. Furthermore, an sSC phase is identified in the ρ{sub q}, ρ{sub s} plane. Possible links between certain of the obtained results and physical systems are pointed out. (orig.)

  7. Numerical modeling of supercritical CO{sub 2} natural circulation loop

    Energy Technology Data Exchange (ETDEWEB)

    Archana, V., E-mail: archanav@barc.gov.in [Homi Bhabha National Institute, Mumbai, Maharashtra 400 094 (India); Vaidya, A.M., E-mail: avaidya@barc.gov.in [Bhabha Atomic Research Centre, Mumbai, Maharashtra 400 085 (India); Vijayan, P.K., E-mail: vijayanp@barc.gov.in [Bhabha Atomic Research Centre, Mumbai, Maharashtra 400 085 (India)

    2015-11-15

    Highlights: • Supercritical CO{sub 2} natural circulation loop is modeled by in-house developed 1D and 2D axi-symmetric CFD codes. • Steady state characteristics of VHVC configuration of supercritical CO{sub 2} natural circulation loop are studied over a range of power. • Improved accuracy of predictions by 2D axi-symmetric formulation over 1D formulation is demonstrated. • The validity of correlations used in 1D model such as friction factor and heat transfer correlations is analyzed. • Simulation results shows normal, enhanced and deteriorated heat transfer regimes in supercritical CO{sub 2} natural circulation loop. - Abstract: The objective of this research project is to estimate steady state characteristics of supercritical natural circulation loop (SCNCL) using computational methodology and to compliment on-going experimental investigation of the same at the authors’ organization. For computational investigation, a couple of in-house codes are developed. At first, formulation and a corresponding computer program for the SCNCL based on conservation equations written in 1D framework is developed. Comparison of 1D code results with experimental data showed that, under some operating conditions, there is deviation between computed results and experimental data. To improve predictive capability, it was thought to model the SCNCL using conservation equations in 2D axi-symmetric framework. An existing 2D axi-symmetric code (named NAFA), which was developed and validated for supercritical fluid flow in pipes, is modified for natural circulation loop (NCL) geometry. The modified code, named NAFA-Loop, is subsequently used to compute the steady state characteristics of the SCNCL. These results are compared with experimental data. The steady state characteristics such as the variation of mass flow rate with power, velocity and temperature profiles in heater and cooler are studied using NAFA-Loop. The computed velocity and temperature fields show that the

  8. Four loop wave function renormalization in the non-abelian Thirring model

    International Nuclear Information System (INIS)

    Ali, D.B.; Gracey, J.A.

    2001-01-01

    We compute the anomalous dimension of the fermion field with N f flavours in the fundamental representation of a general Lie colour group in the non-abelian Thirring model at four loops. The implications on the renormalization of the two point Green's function through the loss of multiplicative renormalizability of the model in dimensional regularization due to the appearance of evanescent four fermi operators are considered at length. We observe the appearance of one new colour group Casimir, d F abcd d F abcd , in the final four loop result and discuss its consequences for the relation of the Knizhnik-Zamolodchikov critical exponents in the Wess-Zumino-Witten-Novikov model to the non-abelian Thirring model. Renormalization scheme changes are also considered to ensure that the underlying Fierz symmetry broken by dimensional regularization is restored

  9. Markov chain sampling of the O(n) loop models on the infinite plane

    Science.gov (United States)

    Herdeiro, Victor

    2017-07-01

    A numerical method was recently proposed in Herdeiro and Doyon [Phys. Rev. E 94, 043322 (2016), 10.1103/PhysRevE.94.043322] showing a precise sampling of the infinite plane two-dimensional critical Ising model for finite lattice subsections. The present note extends the method to a larger class of models, namely the O(n) loop gas models for n ∈(1 ,2 ] . We argue that even though the Gibbs measure is nonlocal, it is factorizable on finite subsections when sufficient information on the loops touching the boundaries is stored. Our results attempt to show that provided an efficient Markov chain mixing algorithm and an improved discrete lattice dilation procedure the planar limit of the O(n) models can be numerically studied with efficiency similar to the Ising case. This confirms that scale invariance is the only requirement for the present numerical method to work.

  10. Development of a transient calculation model for a closed sodium natural circulation loop

    International Nuclear Information System (INIS)

    Chang, Won Pyo; Ha, Kwi Seok; Jeong, Hae Yong; Heo, Sun; Lee, Yong Bum

    2003-09-01

    A natural circulation loop has usually adopted for a Liquid Metal Reactor (LMR) because of its high reliability. Up-rating of the current KALIMER capacity requires an additional PDRC to the existing PVCS to remove its decay heat under an accident. As the system analysis code currently used for LMR in Korea does not feature a stand alone capability to simulate a closed natural circulation loop, it is not eligible to be applied to PDRC. To supplement its limitation, a steady state calculation model had been developed during the first phase, and development of the transient model has successively carried out to close the present study. The developed model will then be coupled with the system analysis code, SSC-K to assess a long term cooling for the new conceptual design. The incompressibility assumption of sodium which allows the circuit to be modeled with a single loop flow, makes the model greatly simplified comparing with LWR. Some thermal-hydraulic models developed during this study can be effectively applied to other system analysis codes which require such component models, and the present development will also contribute to establishment of a code system for the LMR analysis

  11. Model-based minimization algorithm of a supercritical helium loop consumption subject to operational constraints

    Science.gov (United States)

    Bonne, F.; Bonnay, P.; Girard, A.; Hoa, C.; Lacroix, B.; Le Coz, Q.; Nicollet, S.; Poncet, J.-M.; Zani, L.

    2017-12-01

    Supercritical helium loops at 4.2 K are the baseline cooling strategy of tokamaks superconducting magnets (JT-60SA, ITER, DEMO, etc.). This loops work with cryogenic circulators that force a supercritical helium flow through the superconducting magnets in order that the temperature stay below the working range all along their length. This paper shows that a supercritical helium loop associated with a saturated liquid helium bath can satisfy temperature constraints in different ways (playing on bath temperature and on the supercritical flow), but that only one is optimal from an energy point of view (every Watt consumed at 4.2 K consumes at least 220 W of electrical power). To find the optimal operational conditions, an algorithm capable of minimizing an objective function (energy consumption at 5 bar, 5 K) subject to constraints has been written. This algorithm works with a supercritical loop model realized with the Simcryogenics [2] library. This article describes the model used and the results of constrained optimization. It will be possible to see that the changes in operating point on the temperature of the magnet (e.g. in case of a change in the plasma configuration) involves large changes on the cryodistribution optimal operating point. Recommendations will be made to ensure that the energetic consumption is kept as low as possible despite the changing operating point. This work is partially supported by EUROfusion Consortium through the Euratom Research and Training Program 20142018 under Grant 633053.

  12. A self-adaptive genetic algorithm to estimate JA model parameters considering minor loops

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Hai-liang; Wen, Xi-shan; Lan, Lei; An, Yun-zhu; Li, Xiao-ping

    2015-01-15

    A self-adaptive genetic algorithm for estimating Jiles–Atherton (JA) magnetic hysteresis model parameters is presented. The fitness function is established based on the distances between equidistant key points of normalized hysteresis loops. Linearity function and logarithm function are both adopted to code the five parameters of JA model. Roulette wheel selection is used and the selection pressure is adjusted adaptively by deducting a proportional which depends on current generation common value. The Crossover operator is established by combining arithmetic crossover and multipoint crossover. Nonuniform mutation is improved by adjusting the mutation ratio adaptively. The algorithm is used to estimate the parameters of one kind of silicon-steel sheet’s hysteresis loops, and the results are in good agreement with published data. - Highlights: • We present a method to find JA parameters for both major and minor loops. • Fitness function is based on distances between key points of normalized loops. • The selection pressure is adjusted adaptively based on generations.

  13. Two-loop renormalization in the standard model, part II. Renormalization procedures and computational techniques

    Energy Technology Data Exchange (ETDEWEB)

    Actis, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Passarino, G. [Torino Univ. (Italy). Dipt. di Fisica Teorica; INFN, Sezione di Torino (Italy)

    2006-12-15

    In part I general aspects of the renormalization of a spontaneously broken gauge theory have been introduced. Here, in part II, two-loop renormalization is introduced and discussed within the context of the minimal Standard Model. Therefore, this paper deals with the transition between bare parameters and fields to renormalized ones. The full list of one- and two-loop counterterms is shown and it is proven that, by a suitable extension of the formalism already introduced at the one-loop level, two-point functions suffice in renormalizing the model. The problem of overlapping ultraviolet divergencies is analyzed and it is shown that all counterterms are local and of polynomial nature. The original program of 't Hooft and Veltman is at work. Finite parts are written in a way that allows for a fast and reliable numerical integration with all collinear logarithms extracted analytically. Finite renormalization, the transition between renormalized parameters and physical (pseudo-)observables, are discussed in part III where numerical results, e.g. for the complex poles of the unstable gauge bosons, are shown. An attempt is made to define the running of the electromagnetic coupling constant at the two-loop level. (orig.)

  14. Modeling and Analysis of a Closed-Loop System for High-Q MEMS Accelerometer Sensor

    Directory of Open Access Journals (Sweden)

    Wang Yalin

    2018-01-01

    Full Text Available High-Q sensing element is desirable for high performance while makes the loop control a great challenge. This paper presents a closed-loop system for high-Q capacitive MEMS accelerometer which has achieved loop control effectively. The proportional-derivative(PDcontrol is developed in the system to improve the system stability. In addition, pulse width modulation (PWM electrostatic force feedback is designed in the loop to overcome the nonlinearity. Furthermore, a sigma-delta (ΣΔ modulator with noise shaping is built to realize digital output. System model is built in Matlab/Simulink. The simulation results indicate that equivalent Q value is reduced to 1.5 to ensure stability and responsiveness of the system. The effective number of bits of system output is 14.7 bits. The system nonlinearity is less than 5‰. The equivalent linear model including main noise factors is built, and then a complete theory of noise and linearity analysis is established to contribute to common MEMS accelerometer research.

  15. A self-adaptive genetic algorithm to estimate JA model parameters considering minor loops

    International Nuclear Information System (INIS)

    Lu, Hai-liang; Wen, Xi-shan; Lan, Lei; An, Yun-zhu; Li, Xiao-ping

    2015-01-01

    A self-adaptive genetic algorithm for estimating Jiles–Atherton (JA) magnetic hysteresis model parameters is presented. The fitness function is established based on the distances between equidistant key points of normalized hysteresis loops. Linearity function and logarithm function are both adopted to code the five parameters of JA model. Roulette wheel selection is used and the selection pressure is adjusted adaptively by deducting a proportional which depends on current generation common value. The Crossover operator is established by combining arithmetic crossover and multipoint crossover. Nonuniform mutation is improved by adjusting the mutation ratio adaptively. The algorithm is used to estimate the parameters of one kind of silicon-steel sheet’s hysteresis loops, and the results are in good agreement with published data. - Highlights: • We present a method to find JA parameters for both major and minor loops. • Fitness function is based on distances between key points of normalized loops. • The selection pressure is adjusted adaptively based on generations

  16. One-loop beta functions for the orientable non-commutative Gross Neveu model TH1"-->

    Science.gov (United States)

    Lakhoua, A.; Vignes-Tourneret, F.; Wallet, J.-C.

    2007-11-01

    We compute at the one-loop order the β-functions for a renormalisable non-commutative analog of the Gross Neveu model defined on the Moyal plane. The calculation is performed within the so called x-space formalism. We find that this non-commutative field theory exhibits asymptotic freedom for any number of colors. The β-function for the non-commutative counterpart of the Thirring model is found to be non vanishing.

  17. Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

    Science.gov (United States)

    Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

    2018-03-01

    The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

  18. Biochemical Kinetics Model of DSB Repair and GammaH2AX FOCI by Non-homologous End Joining

    Science.gov (United States)

    Cucinotta, Francis, A.; Pluth, Janice M.; Anderson, Jennifer A.; Harper, Jane V.; O'Neill, Peter

    2007-01-01

    We developed a biochemical kinetics approach to describe the repair of double strand breaks (DSB) produced by low LET radiation by modeling molecular events associated with the mechanisms of non-homologous end-joining (NHEJ). A system of coupled non-linear ordinary differential equations describes the induction of DSB and activation pathways for major NHEJ components including Ku(sub 70/80), DNA-PK(sub cs), and the Ligase IV-XRCC4 hetero-dimer. The autophosphorylation of DNA-PK(sub cs and subsequent induction of gamma-H2AX foci observed after ionizing radiation exposure were modeled. A two-step model of DNA-PK(sub cs) regulation of repair was developed with the initial step allowing access of other NHEJ components to breaks, and a second step limiting access to Ligase IV-XRCC4. Our model assumes that the transition from the first to second-step depends on DSB complexity, with a much slower-rate for complex DSB. The model faithfully reproduced several experimental data sets, including DSB rejoining as measured by pulsed-field electrophoresis (PFGE), quantification of the induction of gamma-H2AX foci, and live cell imaging of the induction of Ku(sub 70/80). Predictions are made for the behaviors of NHEJ components at low doses and dose-rates, where a steady-state is found at dose-rates of 0.1 Gy/hr or lower.

  19. Discovery of Novel Inhibitors for Nek6 Protein through Homology Model Assisted Structure Based Virtual Screening and Molecular Docking Approaches

    Directory of Open Access Journals (Sweden)

    P. Srinivasan

    2014-01-01

    Full Text Available Nek6 is a member of the NIMA (never in mitosis, gene A-related serine/threonine kinase family that plays an important role in the initiation of mitotic cell cycle progression. This work is an attempt to emphasize the structural and functional relationship of Nek6 protein based on homology modeling and binding pocket analysis. The three-dimensional structure of Nek6 was constructed by molecular modeling studies and the best model was further assessed by PROCHECK, ProSA, and ERRAT plot in order to analyze the quality and consistency of generated model. The overall quality of computed model showed 87.4% amino acid residues under the favored region. A 3 ns molecular dynamics simulation confirmed that the structure was reliable and stable. Two lead compounds (Binding database ID: 15666, 18602 were retrieved through structure-based virtual screening and induced fit docking approaches as novel Nek6 inhibitors. Hence, we concluded that the potential compounds may act as new leads for Nek6 inhibitors designing.

  20. Dose rates modeling of pressurized water reactor primary loop components with SCALE6.0

    International Nuclear Information System (INIS)

    Matijević, Mario; Pevec, Dubravko; Trontl, Krešimir

    2015-01-01

    Highlights: • Shielding analysis of the typical PWR primary loop components was performed. • FW-CADIS methodology was thoroughly investigated using SCALE6.0 code package. • Versatile ability of SCALE6.0/FW-CADIS for deep penetration models was proved. • The adjoint source with focus on specific material can improve MC modeling. - Abstract: The SCALE6.0 simulation model of a typical PWR primary loop components for effective dose rates calculation based on hybrid deterministic–stochastic methodology was created. The criticality sequence CSAS6/KENO-VI of the SCALE6.0 code package, which includes KENO-VI Monte Carlo code, was used for criticality calculations, while neutron and gamma dose rates distributions were determined by MAVRIC/Monaco shielding sequence. A detailed model of a combinatorial geometry, materials and characteristics of a generic two loop PWR facility is based on best available input data. The sources of ionizing radiation in PWR primary loop components included neutrons and photons originating from critical core and photons from activated coolant in two primary loops. Detailed calculations of the reactor pressure vessel and the upper reactor head have been performed. The efficiency of particle transport for obtaining global Monte Carlo dose rates was further examined and quantified with a flexible adjoint source positioning in phase-space. It was demonstrated that generation of an accurate importance map (VR parameters) is a paramount step which enabled obtaining Monaco dose rates with fairly uniform uncertainties. Computer memory consumption by the S N part of hybrid methodology represents main obstacle when using meshes with large number of cells together with high S N /P N parameters. Detailed voxelization (homogenization) process in Denovo together with high S N /P N parameters is essential for precise VR parameters generation which will result in optimized MC distributions. Shielding calculations were also performed for the reduced PWR

  1. The Sustainability Cycle and Loop: models for a more unified understanding of sustainability.

    Science.gov (United States)

    Hay, Laura; Duffy, Alex; Whitfield, R I

    2014-01-15

    In spite of the considerable research on sustainability, reports suggest that we are barely any closer to a more sustainable society. As such, there is an urgent need to improve the effectiveness of human efforts towards sustainability. A clearer and more unified understanding of sustainability among different people and sectors could help to facilitate this. This paper presents the results of an inductive literature investigation, aiming to develop models to explain the nature of sustainability in the Earth system, and how humans can effectively strive for it. The major contributions are two general and complementary models, that may be applied in any context to provide a common basis for understanding sustainability: the Sustainability Cycle (S-Cycle), and the Sustainability Loop (S-Loop). Literature spanning multiple sectors is examined from the perspective of three concepts, emerging as significant in relation to our aim. Systems are shown to provide the context for human action towards sustainability, and the nature of the Earth system and its sub-systems is explored. Activities are outlined as a fundamental target that humans need to sustain, since they produce the entities both needed and desired by society. The basic behaviour of activities operating in the Earth system is outlined. Finally, knowledge is positioned as the driver of human action towards sustainability, and the key components of knowledge involved are examined. The S-Cycle and S-Loop models are developed via a process of induction from the reviewed literature. The S-Cycle describes the operation of activities in a system from the perspective of sustainability. The sustainability of activities in a system depends upon the availability of resources, and the availability of resources depends upon the rate that activities consume and produce them. Humans may intervene in these dynamics via an iterative process of interpretation and action, described in the S-Loop model. The models are briefly

  2. Exploration of freely available web-interfaces for comparative homology modelling of microbial proteins.

    Science.gov (United States)

    Nema, Vijay; Pal, Sudhir Kumar

    2013-01-01

    This study was conducted to find the best suited freely available software for modelling of proteins by taking a few sample proteins. The proteins used were small to big in size with available crystal structures for the purpose of benchmarking. Key players like Phyre2, Swiss-Model, CPHmodels-3.0, Homer, (PS)2, (PS)(2)-V(2), Modweb were used for the comparison and model generation. Benchmarking process was done for four proteins, Icl, InhA, and KatG of Mycobacterium tuberculosis and RpoB of Thermus Thermophilus to get the most suited software. Parameters compared during analysis gave relatively better values for Phyre2 and Swiss-Model. This comparative study gave the information that Phyre2 and Swiss-Model make good models of small and large proteins as compared to other screened software. Other software was also good but is often not very efficient in providing full-length and properly folded structure.

  3. The implementation of a mid-loop model for Doel 1/2 training simulator

    International Nuclear Information System (INIS)

    Houte, U. Van; Damme, M. Van

    1999-01-01

    To cope with upgrade requirements of the Full Scope training simulator of Doel 1/2 (Belgium), a 5-equation model has been implemented for mid-loop operation training. This model will permit to simulate the following conditions: (a) Normal operating conditions; Draining of the primary circuit at vacuum conditions; Venting of the primary loop with the help of a vacuum pump; Filling-up of the primely circuit, (2) Incident and Accident conditions; Loss of RHR (Cavitation of RHR pumps); Reactor heat-up and boiling. In order to simulate the pressurizer water hold-up and loss of steam generator reflux cooling, flooding correlations are used predicting steam generator U-tube and pressurizer surgeline flooding. Loss of horizontal stratification in the hot leg has been taken into account. A steam generator piston model for heat transfer has been implemented. This paper describes the mid-loop model specifications, its implementation and testing in the simulator environment. Special attention is given on how the model has been integrated within the existing simulator. (author)

  4. FORWARD MODELING OF STANDING KINK MODES IN CORONAL LOOPS. II. APPLICATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Ding; Doorsselaere, Tom Van, E-mail: DYuan2@uclan.ac.uk [Centre for Mathematical Plasma Astrophysics, Department of Mathematics, KU Leuven, Celestijnenlaan 200B bus 2400, B-3001 Leuven (Belgium)

    2016-04-15

    Magnetohydrodynamic waves are believed to play a significant role in coronal heating, and could be used for remote diagnostics of solar plasma. Both the heating and diagnostic applications rely on a correct inversion (or backward modeling) of the observables into the thermal and magnetic structures of the plasma. However, due to the limited availability of observables, this is an ill-posed issue. Forward modeling is designed to establish a plausible mapping of plasma structuring into observables. In this study, we set up forward models of standing kink modes in coronal loops and simulate optically thin emissions in the extreme ultraviolet bandpasses, and then adjust plasma parameters and viewing angles to match three events of transverse loop oscillations observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly. We demonstrate that forward models could be effectively used to identify the oscillation overtone and polarization, to reproduce the general profile of oscillation amplitude and phase, and to predict multiple harmonic periodicities in the associated emission intensity and loop width variation.

  5. Dynamic modelling and PID loop control of an oil-injected screw compressor package

    Science.gov (United States)

    Poli, G. W.; Milligan, W. J.; McKenna, P.

    2017-08-01

    A significant amount of time is spent tuning the PID (Proportional, Integral and Derivative) control loops of a screw compressor package due to the unique characteristics of the system. Common mistakes incurred during the tuning of a PID control loop include improper PID algorithm selection and unsuitable tuning parameters of the system resulting in erratic and inefficient operation. This paper details the design and development of software that aims to dynamically model the operation of a single stage oil injected screw compressor package deployed in upstream oil and gas applications. The developed software will be used to assess and accurately tune PID control loops present on the screw compressor package employed in controlling the oil pressures, temperatures and gas pressures, in a bid to improve control of the operation of the screw compressor package. Other applications of the modelling software will include its use as an evaluation tool that can estimate compressor package performance during start up, shutdown and emergency shutdown processes. The paper first details the study into the fundamental operational characteristics of each of the components present on the API 619 screw compressor package and then discusses the creation of a dynamic screw compressor model within the MATLAB/Simulink software suite. The paper concludes by verifying and assessing the accuracy of the created compressor model using data collected from physical screw compressor packages.

  6. Dynamic control of modeled tonic-clonic seizure states with closed-loop stimulation

    Directory of Open Access Journals (Sweden)

    Bryce eBeverlin II

    2013-02-01

    Full Text Available Seizure control using deep brain stimulation (DBS provides an alternative therapy to patients with intractable and drug resistant epilepsy. This paper presents novel DBS stimulus protocols to disrupt seizures. Two protocols are presented: open-loop stimulation and a closed-loop feedback system utilizing measured firing rates to adjust stimulus frequency. Stimulation suppression is demonstrated in a computational model using 3000 excitatory Morris-Lecar model neurons connected with depressing synapses. Cells are connected using second order network topology to simulate network topologies measured in cortical networks. The network spontaneously switches from tonic to clonic as synaptic strengths and tonic input to the neurons decreases. To this model we add periodic stimulation pulses to simulate DBS. Periodic forcing can synchronize or desynchronize an oscillating population of neurons, depending on the stimulus frequency and amplitude. Therefore, it is possible to either extend or truncate the tonic or clonic phases of the seizure. Stimuli applied at the firing rate of the neuron generally synchronize the population while stimuli slightly slower than the firing rate prevent synchronization. We present an adaptive stimulation algorithm that measures the firing rate of a neuron and adjusts the stimulus to maintain a relative stimulus frequency to firing frequency and demonstrate it in a computational model of a tonic-clonic seizure. This adaptive algorithm can affect the duration of the tonic phase using much smaller stimulus amplitudes than the open-loop control.

  7. One-loop corrections for e+e- annihilation into μ+μ- in the Weinberg model

    NARCIS (Netherlands)

    Veltman, M.J.G.; Passarino, G.

    1979-01-01

    Analytical expressions for the cross section including all the one-loop radiative corrections in the context of the Weinberg model are presented. The systematic calculation of one-loop diagrams has been carried out using a recently proposed scheme. Numerical results are shown in a region from

  8. Hardware-in-the-loop vehicle system including dynamic fuel cell model

    Energy Technology Data Exchange (ETDEWEB)

    Lemes, Z.; Lenhart, T.; Braun, M.; Maencher, H. [MAGNUM Automatisierungstechnik GmbH, Darmstadt (Germany)

    2005-07-01

    In order to reduce costs and accelerate the development of fuel cells and systems the usage of hardware-in-the-loop (HIL) testing and dynamic modelling opens new possibilities. The dynamic model of a proton exchange membrane fuel cell (PEMFC) together with a vehicle model is used to carry out a comprehensive system investigation, which allows designing and optimising the behaviour of the components and the entire fuel cell system. The set-up of a HIL system enables real time interaction between the selected hardware and the model. (orig.)

  9. One loop beta functions and fixed points in higher derivative sigma models

    International Nuclear Information System (INIS)

    Percacci, Roberto; Zanusso, Omar

    2010-01-01

    We calculate the one loop beta functions of nonlinear sigma models in four dimensions containing general two- and four-derivative terms. In the O(N) model there are four such terms and nontrivial fixed points exist for all N≥4. In the chiral SU(N) models there are in general six couplings, but only five for N=3 and four for N=2; we find fixed points only for N=2, 3. In the approximation considered, the four-derivative couplings are asymptotically free but the coupling in the two-derivative term has a nonzero limit. These results support the hypothesis that certain sigma models may be asymptotically safe.

  10. Feedback versus open-loop leader/fringe models of the oil supply market

    International Nuclear Information System (INIS)

    Pelot, R.P.; Fuller, J.D.

    1991-01-01

    A multiperiod feedback Stackelberg model of exhaustible resources is presented. The results of the feedback model are compared with those from a corresponding open-loop formulation to determine whether the solution to the latter, and much simpler, model produces the same or similar outcomes. An analysis of the world oil market with OPEC as leader dictating the price to a competitive fringe comprised of the remaining oil suppliers demonstrates the features of the model. It permits variable length periods and cumulative extraction cost functions

  11. A time-dependent stop operator for modeling a class of singular hysteresis loops in a piezoceramic actuator

    Energy Technology Data Exchange (ETDEWEB)

    Al Janaideh, Mohammad, E-mail: aljanaideh@gmail.com [Department of Mechatronics Engineering, The University of Jordan, 11942 Amman (Jordan)

    2013-03-15

    We present a time-dependent stop operator-based Prandtl–Ishlinskii model to characterize singular hysteresis loops in a piezoceramic actuator. The model is constructed based on the time-dependent threshold. The inverse time-dependent stop operator-based Prandtl–Ishlinskii model is obtained analytically and it can be applied as a feedforward compensator to compensate for singular hysteresis loops in a class of smart-material-based actuators. The objective of this study is to present an invertible Prandtl–Ishlinskii model that can be applied as a feedforward compensator to compensate for singular hysteresis loops without inserting a feedback control system.

  12. A time-dependent stop operator for modeling a class of singular hysteresis loops in a piezoceramic actuator

    International Nuclear Information System (INIS)

    Al Janaideh, Mohammad

    2013-01-01

    We present a time-dependent stop operator-based Prandtl–Ishlinskii model to characterize singular hysteresis loops in a piezoceramic actuator. The model is constructed based on the time-dependent threshold. The inverse time-dependent stop operator-based Prandtl–Ishlinskii model is obtained analytically and it can be applied as a feedforward compensator to compensate for singular hysteresis loops in a class of smart-material-based actuators. The objective of this study is to present an invertible Prandtl–Ishlinskii model that can be applied as a feedforward compensator to compensate for singular hysteresis loops without inserting a feedback control system

  13. Gravity loop corrections to the standard model Higgs in Einstein gravity

    International Nuclear Information System (INIS)

    Yugo Abe; Masaatsu Horikoshi; Takeo Inami

    2016-01-01

    We study one-loop quantum gravity corrections to the standard model Higgs potential V(φ) à la Coleman-Weinberg and examine the stability question of V(φ) in the energy region of Planck mass scale, μ ≃ M_P_l (M_P_l = 1.22x10"1"9 GeV). We calculate the gravity one-loop corrections to V(φ) in Einstein gravity by using the momentum cut-off Λ. We have found that even small gravity corrections compete with the standard model term of V(φ) and affect the stability argument of the latter part alone. This is because the latter part is nearly zero in the energy region of M_P_l. (author)

  14. Four-loop critical exponents for the Gross-Neveu-Yukawa models

    International Nuclear Information System (INIS)

    Zerf, Nikolai; Mihaila, Luminita N.; Herbut, Igor F.; Scherer, Michael M.

    2017-09-01

    We study the chiral Ising, the chiral XY and the chiral Heisenberg models at four-loop order with the perturbative renormalization group in 4-ε dimensions and compute critical exponents for the Gross-Neveu-Yukawa fixed points to order O(ε 4 ). Further, we provide Pade estimates for the correlation length exponent, the boson and fermion anomalous dimension as well as the leading correction to scaling exponent in 2+1 dimensions. We also confirm the emergence of supersymmetric field theories at four loops for the chiral Ising and the chiral XY models with N=1/4 and N=1/2 fermions, respectively. Furthermore, applications of our results relevant to various quantum transitions in the context of Dirac and Weyl semimetals are discussed, including interaction-induced transitions in graphene and surface states of topological insulators.

  15. Four-loop critical exponents for the Gross-Neveu-Yukawa models

    Energy Technology Data Exchange (ETDEWEB)

    Zerf, Nikolai; Mihaila, Luminita N. [Heidelberg Univ. (Germany). Inst. fuer Theoretische Physik; Marquard, Peter [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Herbut, Igor F. [Simon Fraser Univ., Burnaby, BC (Canada). Dept. of Physics; Scherer, Michael M. [Koeln Univ. (Germany). Inst. for Theoretical Physics

    2017-09-15

    We study the chiral Ising, the chiral XY and the chiral Heisenberg models at four-loop order with the perturbative renormalization group in 4-ε dimensions and compute critical exponents for the Gross-Neveu-Yukawa fixed points to order O(ε{sup 4}). Further, we provide Pade estimates for the correlation length exponent, the boson and fermion anomalous dimension as well as the leading correction to scaling exponent in 2+1 dimensions. We also confirm the emergence of supersymmetric field theories at four loops for the chiral Ising and the chiral XY models with N=1/4 and N=1/2 fermions, respectively. Furthermore, applications of our results relevant to various quantum transitions in the context of Dirac and Weyl semimetals are discussed, including interaction-induced transitions in graphene and surface states of topological insulators.

  16. In silico sequence analysis and homology modeling of predicted beta-amylase 7-like protein in Brachypodium distachyon L.

    Directory of Open Access Journals (Sweden)

    ERTUĞRUL FILIZ

    2014-04-01

    Full Text Available Beta-amylase (β-amylase, EC 3.2.1.2 is an enzyme that catalyses hydrolysis of glucosidic bonds in polysaccharides. In this study, we analyzed protein sequence of predicted beta-amylase 7-like protein in Brachypodium distachyon. pI (isoelectric point value was found as 5.23 in acidic character, while the instability index (II was found as 50.28 with accepted unstable protein. The prediction of subcellular localization was revealed that the protein may reside in chloroplast by using CELLO v.2.5. The 3D structure of protein was performed using comparative homology modeling with SWISS-MODEL. The accuracy of the predicted 3D structure was checked using Ramachandran plot analysis showed that 95.4% in favored region. The results of our study contribute to understanding of β-amylase protein structure in grass species and will be scientific base for 3D modeling of beta-amylase proteins in further studies.

  17. Modelling of Wheat-Flour Dough Mixing as an Open-Loop Hysteretic Process

    Czech Academy of Sciences Publication Activity Database

    Anderssen, R.; Kružík, Martin

    2013-01-01

    Roč. 18, č. 2 (2013), s. 283-293 ISSN 1531-3492 R&D Projects: GA AV ČR IAA100750802 Keywords : Dissipation * Dough mixing * Rate-independent systems Subject RIV: BA - General Mathematics Impact factor: 0.628, year: 2013 http://library.utia.cas.cz/separaty/2013/MTR/kruzik-modelling of wheat-flour dough mixing as an open-loop hysteretic process.pdf

  18. QSAR models for prediction of chromatographic behavior of homologous Fab variants.

    Science.gov (United States)

    Robinson, Julie R; Karkov, Hanne S; Woo, James A; Krogh, Berit O; Cramer, Steven M

    2017-06-01

    While quantitative structure activity relationship (QSAR) models have been employed successfully for the prediction of small model protein chromatographic behavior, there have been few reports to date on the use of this methodology for larger, more complex proteins. Recently our group generated focused libraries of antibody Fab fragment variants with different combinations of surface hydrophobicities and electrostatic potentials, and demonstrated that the unique selectivities of multimodal resins can be exploited to separate these Fab variants. In this work, results from linear salt gradient experiments with these Fabs were employed to develop QSAR models for six chromatographic systems, including multimodal (Capto MMC, Nuvia cPrime, and two novel ligand prototypes), hydrophobic interaction chromatography (HIC; Capto Phenyl), and cation exchange (CEX; CM Sepharose FF) resins. The models utilized newly developed "local descriptors" to quantify changes around point mutations in the Fab libraries as well as novel cluster descriptors recently introduced by our group. Subsequent rounds of feature selection and linearized machine learning algorithms were used to generate robust, well-validated models with high training set correlations (R 2  > 0.70) that were well suited for predicting elution salt concentrations in the various systems. The developed models then were used to predict the retention of a deamidated Fab and isotype variants, with varying success. The results represent the first successful utilization of QSAR for the prediction of chromatographic behavior of complex proteins such as Fab fragments in multimodal chromatographic systems. The framework presented here can be employed to facilitate process development for the purification of biological products from product-related impurities by in silico screening of resin alternatives. Biotechnol. Bioeng. 2017;114: 1231-1240. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  19. Homology modeling of Leishmania donovani enolase and its molecular interaction with novel inhibitors

    Directory of Open Access Journals (Sweden)

    Jay Prakash Mahato

    2017-01-01

    Full Text Available Introduction: The treatment of Indian tropical disease such as kala-azar is likely to be troublesome to the clinicians as AmpB- and miltefosine-resistant Leishmania donovani has been reported. The rationale behind designed a novel inhibitors of model of L. donovani enolase and performing a binding study with its inhibitors to gain details of the interaction between protein residues and ligand molecules. Methods and Materials: The L. donovani enolase model consists of two typical domains. The N-terminal one contains three-stranded antiparallel β-sheets, followed by six α-helices. The C-terminal domain composes of eleven-stranded mixed α/β-barrel with connectivity. The first α-helix within the C-terminal domain, H7, and the second β-strand, S7, of the barrel domain was arranged in an antiparallel fashion compared to all other α-helices and β-strands. The root-mean-square deviation between predicted model and template is 0.4 Å. The overall conformation of L. donovani enolase model is similar to those of Trypanosoma cruzi enolase and Streptococcus pneumoniae enolase crystal structures. Result: The key amino acid residues within the docking complex model involved in the interaction between model enolase structure and ligand molecule are Lys70, Asn165, Ala168, Asp17, and Asn213. Conclusion: Our theoretical prediction may lead to the establishment of prophylactic and therapeutic approaches for the treatment of kala-azar. This biomedical informatics analysis will help us to combat future kala-azar.

  20. Defining the limits of homology modeling in information-driven protein docking

    NARCIS (Netherlands)

    Garcia Lopes Maia Rodrigues, João; Melquiond, A S J; Karaca, E; Trellet, M; van Dijk, M; van Zundert, G C P; Schmitz, C; de Vries, S J; Bordogna, A; Bonati, L; Kastritis, P L; Bonvin, Alexandre M J J; Garcia Lopes Maia Rodrigues, João

    2013-01-01

    Information-driven docking is currently one of the most successful approaches to obtain structural models of protein interactions as demonstrated in the latest round of CAPRI. While various experimental and computational techniques can be used to retrieve information about the binding mode, the

  1. Loop kinematics

    International Nuclear Information System (INIS)

    Migdal, A.A.

    1982-01-01

    Basic operators acting in the loop space are introduced. The topology of this space and properties of the Stokes type loop functionals are discussed. The parametrically invariant loop calculus developed here is used in the loop dynamics

  2. Mathematical modelling for magnetite (crude removal from primary heat transfer loop by ion-exchange resins

    Directory of Open Access Journals (Sweden)

    Zeeshan Nawaz

    2009-04-01

    Full Text Available The present research focuses to develop mathematical model for the removal of iron (magnetite by ion-exchange resin from primary heat transfer loop of process industries. This mathematical model is based on operating capacities (that’s provide more effective design as compared to loading capacity from static laboratory tests. Results showed non-steady state distribution of external Fe2+ and limitations imposed on operating conditions, these conditions includes; loading and elution cycle time, flow rate, concentration of both loading and removal, volume of resin required. Number of generalized assumptions was made under shortcut modeling techniques to overcome the gap of theoretical and actual process design.

  3. Model-based closed-loop glucose control in type 1 diabetes

    DEFF Research Database (Denmark)

    Schmidt, Signe; Boiroux, Dimitri; Duun-Henriksen, Anne Katrine

    2013-01-01

    To improve type 1 diabetes mellitus (T1DM) management, we developed a model predictive control (MPC) algorithm for closed-loop (CL) glucose control based on a linear second-order deterministic-stochastic model. The deterministic part of the model is specified by three patient-specific parameters......: insulin sensitivity factor, insulin action time, and basal insulin infusion rate. The stochastic part is identical for all patients but identified from data from a single patient. Results of the first clinical feasibility test of the algorithm are presented....

  4. Homology modeling and virtual screening to discover potent inhibitors targeting the imidazole glycerophosphate dehydratase protein in Staphylococcus xylosus

    Science.gov (United States)

    Chen, Xing-Ru; Wang, Xiao-Ting; Hao, Mei-Qi; Zhou, Yong-Hui; Cui, Wen-Qiang; Xing, Xiao-Xu; Xu, Chang-Geng; Bai, Jing-Wen; Li, Yan-Hua

    2017-11-01

    The imidazole glycerophosphate dehydratase (IGPD) protein is a therapeutic target for herbicide discovery. It is also regarded as a possible target in Staphylococcus xylosus (S. xylosus) for solving mastitis in the dairy cow. The 3D structure of IGPD protein is essential for discovering novel inhibitors during high-throughput virtual screening. However, to date, the 3D structure of IGPD protein of S. xylosus has not been solved. In this study, a series of computational techniques including homology modeling, Ramachandran Plots, and Verify 3D were performed in order to construct an appropriate 3D model of IGPD protein of S. xylosus. Nine hits were identified from 2500 compounds by docking studies. Then, these 9 compounds were first tested in vitro in S. xylosus biofilm formation using crystal violet staining. One of the potential compounds, baicalin was shown to significantly inhibit S. xylosus biofilm formation. Finally, the baicalin was further evaluated, which showed better inhibition of biofilm formation capability in S. xylosus by scanning electron microscopy. Hence, we have predicted the structure of IGPD protein of S. xylosus using computational techniques. We further discovered the IGPD protein was targeted by baicalin compound which inhibited the biofilm formation in S. xylosus. Our findings here would provide implications for the further development of novel IGPD inhibitors for the treatment of dairy mastitis.

  5. Dynamic modelling and hardware-in-the-loop testing of PEMFC

    Energy Technology Data Exchange (ETDEWEB)

    Vath, Andreas; Soehn, Matthias; Nicoloso, Norbert; Hartkopf, Thomas [Technische Universitaet Darmstadt/Institut fuer Elektrische Energie wand lung, Landgraf-Georg-Str. 4, D-64283 Darmstadt (Germany); Lemes, Zijad; Maencher, Hubert [MAGNUM Automatisierungstechnik GmbH, Bunsenstr. 22, D-64293 Darmstadt (Germany)

    2006-07-03

    Modelling and hardware-in-the-loop (HIL) testing of fuel cell components and entire systems open new ways for the design and advance development of FCs. In this work proton exchange membrane fuel cells (PEMFC) are dynamically modelled within MATLAB-Simulink at various operation conditions in order to establish a comprehensive description of their dynamic behaviour as well as to explore the modelling facility as a diagnostic tool. Set-up of a hardware-in-the-loop (HIL) system enables real time interaction between the selected hardware and the model. The transport of hydrogen, nitrogen, oxygen, water vapour and liquid water in the gas diffusion and catalyst layers of the stack are incorporated into the model according to their physical and electrochemical characteristics. Other processes investigated include, e.g., the membrane resistance as a function of the water content during fast load changes. Cells are modelled three-dimensionally and dynamically. In case of system simulations a one-dimensional model is preferred to reduce computation time. The model has been verified by experiments with a water-cooled stack. (author)

  6. Two-loop corrections to the ρ parameter in Two-Higgs-Doublet models

    Energy Technology Data Exchange (ETDEWEB)

    Hessenberger, Stephan; Hollik, Wolfgang [Max-Planck-Institut fuer Physik (Werner-Heisenberg-Institut), Muenchen (Germany)

    2017-03-15

    Models with two scalar doublets are among the simplest extensions of the Standard Model which fulfill the relation ρ = 1 at lowest order for the ρ parameter as favored by experimental data for electroweak observables allowing only small deviations from unity. Such small deviations Δρ originate exclusively from quantum effects with special sensitivity to mass splittings between different isospin components of fermions and scalars. In this paper the dominant two-loop electroweak corrections to Δρ are calculated in the CP-conserving THDM, resulting from the top-Yukawa coupling and the self-couplings of the Higgs bosons in the gauge-less limit. The on-shell renormalization scheme is applied. With the assumption that one of the CP-even neutral scalars represents the scalar boson observed by the LHC experiments, with standard properties, the two-loop non-standard contributions in Δρ can be separated from the standard ones. These contributions are of particular interest since they increase with mass splittings between non-standard Higgs bosons and can be additionally enhanced by tanβ and λ{sub 5}, an additional free coefficient of the Higgs potential, and can thus modify the one-loop result substantially. Numerical results are given for the dependence on the various non-standard parameters, and the influence on the calculation of electroweak precision observables is discussed. (orig.)

  7. Generalized nucleation and looping model for epigenetic memory of histone modifications

    Science.gov (United States)

    Erdel, Fabian; Greene, Eric C.

    2016-01-01

    Histone modifications can redistribute along the genome in a sequence-independent manner, giving rise to chromatin position effects and epigenetic memory. The underlying mechanisms shape the endogenous chromatin landscape and determine its response to ectopically targeted histone modifiers. Here, we simulate linear and looping-driven spreading of histone modifications and compare both models to recent experiments on histone methylation in fission yeast. We find that a generalized nucleation-and-looping mechanism describes key observations on engineered and endogenous methylation domains including intrinsic spatial confinement, independent regulation of domain size and memory, variegation in the absence of antagonists, and coexistence of short- and long-term memory at loci with weak and strong constitutive nucleation. These findings support a straightforward relationship between the biochemical properties of chromatin modifiers and the spatiotemporal modification pattern. The proposed mechanism gives rise to a phase diagram for cellular memory that may be generally applicable to explain epigenetic phenomena across different species. PMID:27382173

  8. New Constraints on Dark Matter Effective Theories from Standard Model Loops

    CERN Document Server

    Crivellin, Andreas; Procura, Massimiliano

    2014-01-01

    We consider an effective field theory for a gauge singlet Dirac dark matter (DM) particle interacting with the Standard Model (SM) fields via effective operators suppressed by the scale $\\Lambda \\gtrsim 1$ TeV. We perform a systematic analysis of the leading loop contributions to spin-independent (SI) DM--nucleon scattering using renormalization group evolution between $\\Lambda$ and the low-energy scale probed by direct detection experiments. We find that electroweak interactions induce operator mixings such that operators that are naively velocity-suppressed and spin-dependent can actually contribute to SI scattering. This allows us to put novel constraints on Wilson coefficients that were so far poorly bounded by direct detection. Constraints from current searches are comparable to LHC bounds, and will significantly improve in the near future. Interestingly, the loop contribution we find is maximally isospin violating even if the underlying theory is isospin conserving.

  9. Quark Loop Effects on Dressed Gluon Propagator in Framework of Global Color Symmetry Model

    Institute of Scientific and Technical Information of China (English)

    ZONG Hong-Shi; SUN Wei-Min

    2006-01-01

    Based on the global color symmetry model (GCM), a method for obtaining the quark loop effects on the dressed gluon propagator in GCM is developed. In the chiral limit, it is found that the dressed gluon propagator containing the quark loop effects in the Nambu-Goldstone and Wigner phases are quite different. In solving the quark self-energy functions in the two different phases and subsequent study of bag constant one should use the above dressed gluon propagator as input. The above approach for obtaining the current quark mass effects on the dressed gluon propagator is quite general and can also be used to calculate the chemical potential dependence of the dressed gluon propagator.

  10. Two-loop renormalization in the standard model, part III. Renormalization equations and their solutions

    International Nuclear Information System (INIS)

    Actis, S.; Passarino, G.

    2006-12-01

    In part I and II of this series of papers all elements have been introduced to extend, to two loops, the set of renormalization procedures which are needed in describing the properties of a spontaneously broken gauge theory. In this paper, the final step is undertaken and finite renormalization is discussed. Two-loop renormalization equations are introduced and their solutions discussed within the context of the minimal standard model of fundamental interactions. These equations relate renormalized Lagrangian parameters (couplings and masses) to some input parameter set containing physical (pseudo-)observables. Complex poles for unstable gauge and Higgs bosons are used and a consistent setup is constructed for extending the predictivity of the theory from the Lep1 Z-boson scale (or the Lep2 WW scale) to regions of interest for LHC and ILC physics. (orig.)

  11. Two-loop renormalization in the standard model, part III. Renormalization equations and their solutions

    Energy Technology Data Exchange (ETDEWEB)

    Actis, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Passarino, G. [Torino Univ. (Italy). Dipt. di Fisica Teorica; INFN, Sezione di Torino (Italy)

    2006-12-15

    In part I and II of this series of papers all elements have been introduced to extend, to two loops, the set of renormalization procedures which are needed in describing the properties of a spontaneously broken gauge theory. In this paper, the final step is undertaken and finite renormalization is discussed. Two-loop renormalization equations are introduced and their solutions discussed within the context of the minimal standard model of fundamental interactions. These equations relate renormalized Lagrangian parameters (couplings and masses) to some input parameter set containing physical (pseudo-)observables. Complex poles for unstable gauge and Higgs bosons are used and a consistent setup is constructed for extending the predictivity of the theory from the Lep1 Z-boson scale (or the Lep2 WW scale) to regions of interest for LHC and ILC physics. (orig.)

  12. The model of the thermal and hydraulic behaviour of a out-of-pile test loop; Model thermohidraulickog ponasanja vanreaktorskog exksperimentalnog cirkulacionog kola

    Energy Technology Data Exchange (ETDEWEB)

    Vehauc, A; Stosic, Z [Institut za nuklearne nauke Boris Kidric, Voinca, Belgrade (Yugoslavia)

    1988-07-01

    A complex circulation loop was modeled and a simulation program developed for the determination of the pressure, temperature, velocity and flow rate distribution in legs of the loop. The model was used to study the thermal and hydraulic behaviour of an out-of-pile test loop at IBK-ITE. For a given set of conditions in the test section, the model yields data on all the operating modes possible with the existing control system and in consequence on the optimum operating conditions for the loop as a whole. (author)

  13. Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling

    Directory of Open Access Journals (Sweden)

    Tran Ngoc Tuan

    2016-10-01

    Full Text Available Tumor necrosis factor alpha (TNF- is known to be crucial in many biological activities of organisms. In this study, physicochemical properties and modeling of TNF- protein of fish was analyzed using in silico approach. TNF- proteins selected from fish species, including grass carp (Ctenopharyngodon idella, zebra fish (Danio rerio, Nile tilapia (Oreochromis niloticus, goldfish (Carassius auratus, and rainbow trout (Oncorhynchus mykiss were used in this study. Physicochemical characteristics with molecular weight, theoretical isoelectric point, extinction coefficient, aliphatic index, instability index, total number of negatively charged residues and positively charged residues, and grand average of hydropathicity were computed. All proteins were classified as transmembrane proteins. The “transmembrane region” and “TNF” domain were identified from protein sequences. The function prediction of proteins was also performed. Alpha helices and random coils were dominating in the secondary structure of the proteins. Three-dimensional structures were predicted and verified as good structures for the investigation of TNF- of fish by online server validation.

  14. Solution structure of tRNA{sup Val} from refinement of homology model against residual dipolar coupling and SAXS data

    Energy Technology Data Exchange (ETDEWEB)

    Grishaev, Alexander, E-mail: AlexanderG@intra.niddk.nih.gov; Ying, Jinfa [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Canny, Marella D.; Pardi, Arthur [University of Colorado, Boulder, Department of Chemistry and Biochemistry, 215 UCB (United States)], E-mail: Arthur.Pardi@Colorado.edu; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2008-10-15

    A procedure is presented for refinement of a homology model of E. coli tRNA{sup Val}, originally based on the X-ray structure of yeast tRNA{sup Phe}, using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N-H{sup N} RDCs measured with Pf1 phage alignment, and 20 imino N-H{sup N} RDCs obtained from magnetic field dependent alignment of tRNA{sup Val}. The refinement strategy aims to largely retain the local geometry of the 58% identical tRNA{sup Phe} by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Q{sub free} = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNA{sup Phe}, in agreement with previous NMR-based tRNA{sup Val} models.

  15. A closed-loop model of the respiratory system: focus on hypercapnia and active expiration.

    Directory of Open Access Journals (Sweden)

    Yaroslav I Molkov

    Full Text Available Breathing is a vital process providing the exchange of gases between the lungs and atmosphere. During quiet breathing, pumping air from the lungs is mostly performed by contraction of the diaphragm during inspiration, and muscle contraction during expiration does not play a significant role in ventilation. In contrast, during intense exercise or severe hypercapnia forced or active expiration occurs in which the abdominal "expiratory" muscles become actively involved in breathing. The mechanisms of this transition remain unknown. To study these mechanisms, we developed a computational model of the closed-loop respiratory system that describes the brainstem respiratory network controlling the pulmonary subsystem representing lung biomechanics and gas (O2 and CO2 exchange and transport. The lung subsystem provides two types of feedback to the neural subsystem: a mechanical one from pulmonary stretch receptors and a chemical one from central chemoreceptors. The neural component of the model simulates the respiratory network that includes several interacting respiratory neuron types within the Bötzinger and pre-Bötzinger complexes, as well as the retrotrapezoid nucleus/parafacial respiratory group (RTN/pFRG representing the central chemoreception module targeted by chemical feedback. The RTN/pFRG compartment contains an independent neural generator that is activated at an increased CO2 level and controls the abdominal motor output. The lung volume is controlled by two pumps, a major one driven by the diaphragm and an additional one activated by abdominal muscles and involved in active expiration. The model represents the first attempt to model the transition from quiet breathing to breathing with active expiration. The model suggests that the closed-loop respiratory control system switches to active expiration via a quantal acceleration of expiratory activity, when increases in breathing rate and phrenic amplitude no longer provide sufficient

  16. Loop calculations for the non-commutative U*(1) gauge field model with oscillator term

    International Nuclear Information System (INIS)

    Blaschke, Daniel N.; Grosse, Harald; Kronberger, Erwin; Schweda, Manfred; Wohlgenannt, Michael

    2010-01-01

    Motivated by the success of the non-commutative scalar Grosse-Wulkenhaar model, a non-commutative U * (1) gauge field theory including an oscillator-like term in the action has been put forward in (Blaschke et al. in Europhys. Lett. 79:61002, 2007). The aim of the current work is to analyze whether that action can lead to a fully renormalizable gauge model on non-commutative Euclidean space. In a first step, explicit one-loop graph computations are hence presented, and their results as well as necessary modifications of the action are successively discussed. (orig.)

  17. Reduced Moment-Based Models for Oxygen Precipitates and Dislocation Loops in Silicon

    Science.gov (United States)

    Trzynadlowski, Bart

    The demand for ever smaller, higher-performance integrated circuits and more efficient, cost-effective solar cells continues to push the frontiers of process technology. Fabrication of silicon devices requires extremely precise control of impurities and crystallographic defects. Failure to do so not only reduces performance, efficiency, and yield, it threatens the very survival of commercial enterprises in today's fiercely competitive and price-sensitive global market. The presence of oxygen in silicon is an unavoidable consequence of the Czochralski process, which remains the most popular method for large-scale production of single-crystal silicon. Oxygen precipitates that form during thermal processing cause distortion of the surrounding silicon lattice and can lead to the formation of dislocation loops. Localized deformation caused by both of these defects introduces potential wells that trap diffusing impurities such as metal atoms, which is highly desirable if done far away from sensitive device regions. Unfortunately, dislocations also reduce the mechanical strength of silicon, which can cause wafer warpage and breakage. Engineers must negotiate this and other complex tradeoffs when designing fabrication processes. Accomplishing this in a complex, modern process involving a large number of thermal steps is impossible without the aid of computational models. In this dissertation, new models for oxygen precipitation and dislocation loop evolution are described. An oxygen model using kinetic rate equations to evolve the complete precipitate size distribution was developed first. This was then used to create a reduced model tracking only the moments of the size distribution. The moment-based model was found to run significantly faster than its full counterpart while accurately capturing the evolution of oxygen precipitates. The reduced model was fitted to experimental data and a sensitivity analysis was performed to assess the robustness of the results. Source

  18. MODELING OF REFLECTIVE PROPAGATING SLOW-MODE WAVE IN A FLARING LOOP

    Energy Technology Data Exchange (ETDEWEB)

    Fang, X.; Yuan, D.; Van Doorsselaere, T.; Keppens, R.; Xia, C. [Centre for mathematical Plasma Astrophysics, Department of Mathematics, KU Leuven, Celestijnenlaan 200B, B-3001 Leuven (Belgium)

    2015-11-01

    Quasi-periodic propagating intensity disturbances have been observed in large coronal loops in extreme ultraviolet images over a decade, and are widely accepted to be slow magnetosonic waves. However, spectroscopic observations from Hinode/EIS revealed their association with persistent coronal upflows, making this interpretation debatable. We perform a 2.5D magnetohydrodynamic simulation to imitate the chromospheric evaporation and the following reflected patterns in a flare loop. Our model encompasses the corona, transition region, and chromosphere. We demonstrate that the quasi periodic propagating intensity variations captured by the synthesized Solar Dynamics Observatory/Atmospheric Imaging Assembly 131, 94 Å emission images match the previous observations well. With particle tracers in the simulation, we confirm that these quasi periodic propagating intensity variations consist of reflected slow mode waves and mass flows with an average speed of 310 km s{sup −1} in an 80 Mm length loop with an average temperature of 9 MK. With the synthesized Doppler shift velocity and intensity maps of the Solar and Heliospheric Observatory/Solar Ultraviolet Measurement of Emitted Radiation Fe xix line emission, we confirm that these reflected slow mode waves are propagating waves.

  19. Generation of a homology model of the human histamine H3 receptor for ligand docking and pharmacophore-based screening

    Science.gov (United States)

    Schlegel, Birgit; Laggner, Christian; Meier, Rene; Langer, Thierry; Schnell, David; Seifert, Roland; Stark, Holger; Höltje, Hans-Dieter; Sippl, Wolfgang

    2007-08-01

    The human histamine H3 receptor (hH3R) is a G-protein coupled receptor (GPCR), which modulates the release of various neurotransmitters in the central and peripheral nervous system and therefore is a potential target in the therapy of numerous diseases. Although ligands addressing this receptor are already known, the discovery of alternative lead structures represents an important goal in drug design. The goal of this work was to study the hH3R and its antagonists by means of molecular modelling tools. For this purpose, a strategy was pursued in which a homology model of the hH3R based on the crystal structure of bovine rhodopsin was generated and refined by molecular dynamics simulations in a dipalmitoylphosphatidylcholine (DPPC)/water membrane mimic before the resulting binding pocket was used for high-throughput docking using the program GOLD. Alternatively, a pharmacophore-based procedure was carried out where the alleged bioactive conformations of three different potent hH3R antagonists were used as templates for the generation of pharmacophore models. A pharmacophore-based screening was then carried out using the program Catalyst. Based upon a database of 418 validated hH3R antagonists both strategies could be validated in respect of their performance. Seven hits obtained during this screening procedure were commercially purchased, and experimentally tested in a [3H]Nα-methylhistamine binding assay. The compounds tested showed affinities at hH3R with K i values ranging from 0.079 to 6.3 μM.

  20. Dynamic fuel cell models and their application in hardware in the loop simulation

    Energy Technology Data Exchange (ETDEWEB)

    Lemes, Zijad; Maencher, H. [MAGNUM Automatisierungstechnik GmbH, Bunsenstr. 22, D-64293 Darmstadt (Germany); Vath, Andreas; Hartkopf, Th. [Technische Universitaet Darmstadt/Institut fuer Elektrische Energiewandlung, Landgraf-Georg-Str. 4, D-64283 Darmstadt (Germany)

    2006-03-21

    Currently, fuel cell technology plays an important role in the development of alternative energy converters for mobile, portable and stationary applications. With the help of physical based models of fuel cell systems and appropriate test benches it is possible to design different applications and investigate their stationary and dynamic behaviour. The polymer electrolyte membrane (PEM) fuel cell system model includes gas humidifier, air and hydrogen supply, current converter and a detailed stack model incorporating the physical characteristics of the different layers. In particular, the use of these models together with hardware in the loop (HIL) capable test stands helps to decrease the costs and accelerate the development of fuel cell systems. The interface program provides fast data exchange between the test bench and the physical model of the fuel cell or any other systems in real time. So the flexibility and efficiency of the test bench increase fundamentally, because it is possible to replace real components with their mathematical models. (author)

  1. Modeling active region transient brightenings observed with X-ray telescope as multi-stranded loops

    Energy Technology Data Exchange (ETDEWEB)

    Kobelski, Adam R.; McKenzie, David E. [Department of Physics, P.O. Box 173840, Montana State University, Bozeman, MT 59717-3840 (United States); Donachie, Martin, E-mail: kobelski@solar.physics.montana.edu [University of Glasgow, Glasgow, G128QQ, Scotland (United Kingdom)

    2014-05-10

    Strong evidence exists that coronal loops as observed in extreme ultraviolet and soft X-rays may not be monolithic isotropic structures, but can often be more accurately modeled as bundles of independent strands. Modeling the observed active region transient brightenings (ARTBs) within this framework allows for the exploration of the energetic ramifications and characteristics of these stratified structures. Here we present a simple method of detecting and modeling ARTBs observed with the Hinode X-Ray Telescope (XRT) as groups of zero-dimensional strands, which allows us to probe parameter space to better understand the spatial and temporal dependence of strand heating in impulsively heated loops. This partially automated method can be used to analyze a large number of observations to gain a statistical insight into the parameters of coronal structures, including the number of heating events required in a given model to fit the observations. In this article, we present the methodology and demonstrate its use in detecting and modeling ARTBs in a sample data set from Hinode/XRT. These initial results show that, in general, multiple heating events are necessary to reproduce observed ARTBs, but the spatial dependence of these heating events cannot yet be established.

  2. Modeling active region transient brightenings observed with X-ray telescope as multi-stranded loops

    International Nuclear Information System (INIS)

    Kobelski, Adam R.; McKenzie, David E.; Donachie, Martin

    2014-01-01

    Strong evidence exists that coronal loops as observed in extreme ultraviolet and soft X-rays may not be monolithic isotropic structures, but can often be more accurately modeled as bundles of independent strands. Modeling the observed active region transient brightenings (ARTBs) within this framework allows for the exploration of the energetic ramifications and characteristics of these stratified structures. Here we present a simple method of detecting and modeling ARTBs observed with the Hinode X-Ray Telescope (XRT) as groups of zero-dimensional strands, which allows us to probe parameter space to better understand the spatial and temporal dependence of strand heating in impulsively heated loops. This partially automated method can be used to analyze a large number of observations to gain a statistical insight into the parameters of coronal structures, including the number of heating events required in a given model to fit the observations. In this article, we present the methodology and demonstrate its use in detecting and modeling ARTBs in a sample data set from Hinode/XRT. These initial results show that, in general, multiple heating events are necessary to reproduce observed ARTBs, but the spatial dependence of these heating events cannot yet be established.

  3. Prefabrication of axial vascularized tissue engineering coral bone by an arteriovenous loop: A better model

    International Nuclear Information System (INIS)

    Dong Qingshan; Shang Hongtao; Wu Wei; Chen Fulin; Zhang Junrui; Guo Jiaping; Mao Tianqiu

    2012-01-01

    The most important problem for the survival of thick 3-dimensional tissues is the lack of vascularization in the context of bone tissue engineering. In this study, a modified arteriovenous loop (AVL) was developed to prefabricate an axial vascularized tissue engineering coral bone in rabbit, with comparison of the arteriovenous bundle (AVB) model. An arteriovenous fistula between rabbit femoral artery and vein was anastomosed to form an AVL. It was placed in a circular side groove of the coral block. The complex was wrapped with an expanded-polytetrafluoroethylene membrane and implanted beneath inguinal skin. After 2, 4, 6 and 8 weeks, the degree of vascularization was evaluated by India ink perfusion, histological examination, vascular casts, and scanning electron microscopy images of vascular endangium. Newly formed fibrous tissues and vasculature extended over the surfaces and invaded the interspaces of entire coral block. The new blood vessels robustly sprouted from the AVL. Those invaginated cavities in the vascular endangium from scanning electron microscopy indicated vessel's sprouted pores. Above indexes in AVL model are all superior to that in AVB model, indicating that the modified AVL model could more effectively develop vascularization in larger tissue engineering bone. - Highlights: ► A modified arteriovenous loop (AVL) model in rabbit was developed in this study. ► Axial prevascularization was induced in a larger coral block by using the AVL. ► The prefabrication of axial vascularized coral bone is superior as vascular carrier.

  4. Second and third stages of project for the implementation of two asymmetric cooling loops modeled by the ALMOD3 code

    International Nuclear Information System (INIS)

    Dominguez, L.; Camargo, C.T.M.

    1985-04-01

    The second and third steps of the project for implementation of two non-symmetric cooling loops modeled by the ALMOD3 computer code are presented. These steps consists in activate the option for 2 loops already present in ALMOD3 original version and to introduce the GEVAP model for one of the two steam generators. In ALMOD3 original version the simulation of two non-symmetric loops was only possible using external functions, which provide the removed heat for each time step for one of the steam generators. With the introduction of GEVAP model, it is possible to obtain more accurate results. Due to its simplicity, the computer time required for execution is short. The results obtained in Angra 1 simulations are presented, analysed and compared with results obtained using one loop for simulating symmetric transients. (Author) [pt

  5. A photovoltaic source I/U model suitable for hardware in the loop application

    Directory of Open Access Journals (Sweden)

    Stala Robert

    2017-12-01

    Full Text Available This paper presents a novel, low-complexity method of simulating PV source characteristics suitable for real-time modeling and hardware implementation. The application of the suitable model of the PV source as well as the model of all the PV system components in a real-time hardware gives a safe, fast and low cost method of testing PV systems. The paper demonstrates the concept of the PV array model and the hardware implementation in FPGAs of the system which combines two PV arrays. The obtained results confirm that the proposed model is of low complexity and can be suitable for hardware in the loop (HIL tests of the complex PV system control, with various arrays operating under different conditions.

  6. On the significance of the noise model for the performance of a linear MPC in closed-loop operation

    DEFF Research Database (Denmark)

    Hagdrup, Morten; Boiroux, Dimitri; Mahmoudi, Zeinab

    2016-01-01

    This paper discusses the significance of the noise model for the performance of a Model Predictive Controller when operating in closed-loop. The process model is parametrized as a continuous-time (CT) model and the relevant sampled-data filtering and control algorithms are developed. Using CT...... models typically means less parameters to identify. Systematic tuning of such controllers is discussed. Simulation studies are conducted for linear time-invariant systems showing that choosing a noise model of low order is beneficial for closed-loop performance. (C) 2016, IFAC (International Federation...

  7. Three-loop Standard Model effective potential at leading order in strong and top Yukawa couplings

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Stephen P. [Santa Barbara, KITP

    2014-01-08

    I find the three-loop contribution to the effective potential for the Standard Model Higgs field, in the approximation that the strong and top Yukawa couplings are large compared to all other couplings, using dimensional regularization with modified minimal subtraction. Checks follow from gauge invariance and renormalization group invariance. I also briefly comment on the special problems posed by Goldstone boson contributions to the effective potential, and on the numerical impact of the result on the relations between the Higgs vacuum expectation value, mass, and self-interaction coupling.

  8. Loop equations and topological recursion for the arbitrary-$\\beta$ two-matrix model

    CERN Document Server

    Bergère, Michel; Marchal, Olivier; Prats-Ferrer, Aleix

    2012-01-01

    We write the loop equations for the $\\beta$ two-matrix model, and we propose a topological recursion algorithm to solve them, order by order in a small parameter. We find that to leading order, the spectral curve is a "quantum" spectral curve, i.e. it is given by a differential operator (instead of an algebraic equation for the hermitian case). Here, we study the case where that quantum spectral curve is completely degenerate, it satisfies a Bethe ansatz, and the spectral curve is the Baxter TQ relation.

  9. Little strings, quasi-topological sigma model on loop group, and toroidal Lie algebras

    Science.gov (United States)

    Ashwinkumar, Meer; Cao, Jingnan; Luo, Yuan; Tan, Meng-Chwan; Zhao, Qin

    2018-03-01

    We study the ground states and left-excited states of the Ak-1 N = (2 , 0) little string theory. Via a theorem by Atiyah [1], these sectors can be captured by a supersymmetric nonlinear sigma model on CP1 with target space the based loop group of SU (k). The ground states, described by L2-cohomology classes, form modules over an affine Lie algebra, while the left-excited states, described by chiral differential operators, form modules over a toroidal Lie algebra. We also apply our results to analyze the 1/2 and 1/4 BPS sectors of the M5-brane worldvolume theory.

  10. GoSam 2.0. Automated one loop calculations within and beyond the standard model

    International Nuclear Information System (INIS)

    Greiner, Nicolas; Deutsches Elektronen-Synchrotron

    2014-10-01

    We present GoSam 2.0, a fully automated framework for the generation and evaluation of one loop amplitudes in multi leg processes. The new version offers numerous improvements both on generational aspects as well as on the reduction side. This leads to a faster and more stable code for calculations within and beyond the Standard Model. Furthermore it contains the extended version of the standardized interface to Monte Carlo programs which allows for an easy combination with other existing tools. We briefly describe the conceptual innovations and present some phenomenological results.

  11. Little strings, quasi-topological sigma model on loop group, and toroidal Lie algebras

    Directory of Open Access Journals (Sweden)

    Meer Ashwinkumar

    2018-03-01

    Full Text Available We study the ground states and left-excited states of the Ak−1 N=(2,0 little string theory. Via a theorem by Atiyah [1], these sectors can be captured by a supersymmetric nonlinear sigma model on CP1 with target space the based loop group of SU(k. The ground states, described by L2-cohomology classes, form modules over an affine Lie algebra, while the left-excited states, described by chiral differential operators, form modules over a toroidal Lie algebra. We also apply our results to analyze the 1/2 and 1/4 BPS sectors of the M5-brane worldvolume theory.

  12. Mobile application MDDCS for modeling the expansion dynamics of a dislocation loop in FCC metals

    Science.gov (United States)

    Kirilyuk, Vasiliy; Petelin, Alexander; Eliseev, Andrey

    2017-11-01

    A mobile version of the software package Dynamic Dislocation of Crystallographic Slip (MDDCS) designed for modeling the expansion dynamics of dislocation loops and formation of a crystallographic slip zone in FCC-metals is examined. The paper describes the possibilities for using MDDCS, the application interface, and the database scheme. The software has a simple and intuitive interface and does not require special training. The user can set the initial parameters of the experiment, carry out computational experiments, export parameters and results of the experiment into separate text files, and display the experiment results on the device screen.

  13. Model-Based, Closed-Loop Control of PZT Creep for Cavity Ring-Down Spectroscopy.

    Science.gov (United States)

    McCartt, A D; Ognibene, T J; Bench, G; Turteltaub, K W

    2014-09-01

    Cavity ring-down spectrometers typically employ a PZT stack to modulate the cavity transmission spectrum. While PZTs ease instrument complexity and aid measurement sensitivity, PZT hysteresis hinders the implementation of cavity-length-stabilized, data-acquisition routines. Once the cavity length is stabilized, the cavity's free spectral range imparts extreme linearity and precision to the measured spectrum's wavelength axis. Methods such as frequency-stabilized cavity ring-down spectroscopy have successfully mitigated PZT hysteresis, but their complexity limits commercial applications. Described herein is a single-laser, model-based, closed-loop method for cavity length control.

  14. Homology modeling of dissimilatory APS reductases (AprBA of sulfur-oxidizing and sulfate-reducing prokaryotes.

    Directory of Open Access Journals (Sweden)

    Birte Meyer

    Full Text Available BACKGROUND: The dissimilatory adenosine-5'-phosphosulfate (APS reductase (cofactors flavin adenine dinucleotide, FAD, and two [4Fe-4S] centers catalyzes the transformation of APS to sulfite and AMP in sulfate-reducing prokaryotes (SRP; in sulfur-oxidizing bacteria (SOB it has been suggested to operate in the reverse direction. Recently, the three-dimensional structure of the Archaeoglobus fulgidus enzyme has been determined in different catalytically relevant states providing insights into its reaction cycle. METHODOLOGY/PRINCIPAL FINDINGS: Full-length AprBA sequences from 20 phylogenetically distinct SRP and SOB species were used for homology modeling. In general, the average accuracy of the calculated models was sufficiently good to allow a structural and functional comparison between the beta- and alpha-subunit structures (78.8-99.3% and 89.5-96.8% of the AprB and AprA main chain atoms, respectively, had root mean square deviations below 1 A with respect to the template structures. Besides their overall conformity, the SRP- and SOB-derived models revealed the existence of individual adaptations at the electron-transferring AprB protein surface presumably resulting from docking to different electron donor/acceptor proteins. These structural alterations correlated with the protein phylogeny (three major phylogenetic lineages: (1 SRP including LGT-affected Archaeoglobi and SOB of Apr lineage II, (2 crenarchaeal SRP Caldivirga and Pyrobaculum, and (3 SOB of the distinct Apr lineage I and the presence of potential APS reductase-interacting redox complexes. The almost identical protein matrices surrounding both [4Fe-4S] clusters, the FAD cofactor, the active site channel and center within the AprB/A models of SRP and SOB point to a highly similar catalytic process of APS reduction/sulfite oxidation independent of the metabolism type the APS reductase is involved in and the species it has been originated from. CONCLUSIONS: Based on the comparative

  15. Feedback loops and temporal misalignment in component-based hydrologic modeling

    Science.gov (United States)

    Elag, Mostafa M.; Goodall, Jonathan L.; Castronova, Anthony M.

    2011-12-01

    In component-based modeling, a complex system is represented as a series of loosely integrated components with defined interfaces and data exchanges that allow the components to be coupled together through shared boundary conditions. Although the component-based paradigm is commonly used in software engineering, it has only recently been applied for modeling hydrologic and earth systems. As a result, research is needed to test and verify the applicability of the approach for modeling hydrologic systems. The objective of this work was therefore to investigate two aspects of using component-based software architecture for hydrologic modeling: (1) simulation of feedback loops between components that share a boundary condition and (2) data transfers between temporally misaligned model components. We investigated these topics using a simple case study where diffusion of mass is modeled across a water-sediment interface. We simulated the multimedia system using two model components, one for the water and one for the sediment, coupled using the Open Modeling Interface (OpenMI) standard. The results were compared with a more conventional numerical approach for solving the system where the domain is represented by a single multidimensional array. Results showed that the component-based approach was able to produce the same results obtained with the more conventional numerical approach. When the two components were temporally misaligned, we explored the use of different interpolation schemes to minimize mass balance error within the coupled system. The outcome of this work provides evidence that component-based modeling can be used to simulate complicated feedback loops between systems and guidance as to how different interpolation schemes minimize mass balance error introduced when components are temporally misaligned.

  16. Comparison of Two Coronal Magnetic Field Models to Reconstruct a Sigmoidal Solar Active Region with Coronal Loops

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Aiying; Zhang, Huai [Key Laboratory of Computational Geodynamics, University of Chinese Academy of Sciences, Beijing 100049 (China); Jiang, Chaowei [Institute of Space Science and Applied Technology, Harbin Institute of Technology, Shenzhen, 518055 (China); Hu, Qiang; Gary, G. Allen; Wu, S. T. [Center for Space Plasma and Aeronomic Research, The University of Alabama in Huntsville, Huntsville, AL 35899 (United States); Cao, Jinbin, E-mail: duanaiying@ucas.ac.cn, E-mail: hzhang@ucas.ac.cn, E-mail: chaowei@hit.edu.cn [School of Space and Environment, Beihang University, Beijing 100191 (China)

    2017-06-20

    Magnetic field extrapolation is an important tool to study the three-dimensional (3D) solar coronal magnetic field, which is difficult to directly measure. Various analytic models and numerical codes exist, but their results often drastically differ. Thus, a critical comparison of the modeled magnetic field lines with the observed coronal loops is strongly required to establish the credibility of the model. Here we compare two different non-potential extrapolation codes, a nonlinear force-free field code (CESE–MHD–NLFFF) and a non-force-free field (NFFF) code, in modeling a solar active region (AR) that has a sigmoidal configuration just before a major flare erupted from the region. A 2D coronal-loop tracing and fitting method is employed to study the 3D misalignment angles between the extrapolated magnetic field lines and the EUV loops as imaged by SDO /AIA. It is found that the CESE–MHD–NLFFF code with preprocessed magnetogram performs the best, outputting a field that matches the coronal loops in the AR core imaged in AIA 94 Å with a misalignment angle of ∼10°. This suggests that the CESE–MHD–NLFFF code, even without using the information of the coronal loops in constraining the magnetic field, performs as good as some coronal-loop forward-fitting models. For the loops as imaged by AIA 171 Å in the outskirts of the AR, all the codes including the potential field give comparable results of the mean misalignment angle (∼30°). Thus, further improvement of the codes is needed for a better reconstruction of the long loops enveloping the core region.

  17. Profit Analysis and Supply Chain Planning Model for Closed-Loop Supply Chain in Fashion Industry

    Directory of Open Access Journals (Sweden)

    Jisoo Oh

    2014-12-01

    Full Text Available In recent decades, due to market growth and use of synthetic fiber, the fashion industry faces a rapid increase of CO2 emission throughout the production cycle and raises environmental issues in recovery processing. This study proposes a closed-loop supply chain (CLSC structure in fashion industry and develops its planning model as multi-objective mixed integer linear programming to find an optimal trade-off between CLSC profit and CO2 emission. The planning model is associated with the profit analysis of each member in CLSC to find the optimal price of products on CLSC network. The model determines optimal production, transportation, and inventory quantities on CLSC network. The proposed models are validated using numerical experiments and sensitivity analyses, and from the results some managerial insights are addressed.

  18. A Unified Impedance Model of Voltage-Source Converters with Phase-Locked Loop Effect

    DEFF Research Database (Denmark)

    Wang, Xiongfei; Harnefors, Lennart; Blaabjerg, Frede

    2016-01-01

    This paper proposes a unified impedance model for analyzing the effect of Phase-Locked Loop (PLL) on the stability of grid-connected voltage-source converters. In the approach, the dq-frame impedance model is transformed into the stationary αβ-frame by means of complex transfer functions...... and complex space vectors, which not only predicts the stability impact of the PLL, but reveals also its frequency coupling effect in the phase domain. Thus, the impedance models previously developed in the different domains can be unified. Moreover, the impedance shaping effects of PLL are structurally...... characterized for the current control in the rotating dq-frame and the stationary αβ-frame. Case studies based on the unified impedance model are presented, which are then verified in the time-domain simulations and experiments. The results closely correlate with the impedance-based analysis....

  19. Causal Loop-based Modeling on System Dynamics for Risk Communication

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chang Ju [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of); Kang, Kyung Min [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2009-10-15

    It is true that a national policy should be based on public confidence, analyzing their recognition and attitude on life safety, since they have very special risk perception characteristics. For achieving effective public consensus regarding a national policy such as nuclear power, we have to utilize a risk communication (hereafter, calls RiCom) process. However, domestic research models on RiCom process do not provide a practical guideline, because most of them are still superficial and stick on an administrative aspect. Also, most of current models have no experience in terms of verification and validation for effective applications to diverse stake holders. This study focuses on public's dynamic mechanism through the modeling on system dynamics, basically utilizing casual loop diagram (CLD) and stock flow diagram (SFD), which regards as a critical technique for decision making in many industrial RiCom models.

  20. Causal Loop-based Modeling on System Dynamics for Risk Communication

    International Nuclear Information System (INIS)

    Lee, Chang Ju; Kang, Kyung Min

    2009-01-01

    It is true that a national policy should be based on public confidence, analyzing their recognition and attitude on life safety, since they have very special risk perception characteristics. For achieving effective public consensus regarding a national policy such as nuclear power, we have to utilize a risk communication (hereafter, calls RiCom) process. However, domestic research models on RiCom process do not provide a practical guideline, because most of them are still superficial and stick on an administrative aspect. Also, most of current models have no experience in terms of verification and validation for effective applications to diverse stake holders. This study focuses on public's dynamic mechanism through the modeling on system dynamics, basically utilizing casual loop diagram (CLD) and stock flow diagram (SFD), which regards as a critical technique for decision making in many industrial RiCom models

  1. Simplicity constraints: A 3D toy model for loop quantum gravity

    Science.gov (United States)

    Charles, Christoph

    2018-05-01

    In loop quantum gravity, tremendous progress has been made using the Ashtekar-Barbero variables. These variables, defined in a gauge fixing of the theory, correspond to a parametrization of the solutions of the so-called simplicity constraints. Their geometrical interpretation is however unsatisfactory as they do not constitute a space-time connection. It would be possible to resolve this point by using a full Lorentz connection or, equivalently, by using the self-dual Ashtekar variables. This leads however to simplicity constraints or reality conditions which are notoriously difficult to implement in the quantum theory. We explore in this paper the possibility of using completely degenerate actions to impose such constraints at the quantum level in the context of canonical quantization. To do so, we define a simpler model, in 3D, with similar constraints by extending the phase space to include an independent vielbein. We define the classical model and show that a precise quantum theory by gauge unfixing can be defined out of it, completely equivalent to the standard 3D Euclidean quantum gravity. We discuss possible future explorations around this model as it could help as a stepping stone to define full-fledged covariant loop quantum gravity.

  2. Home-Based Risk of Falling Assessment Test Using a Closed-Loop Balance Model.

    Science.gov (United States)

    Ayena, Johannes C; Zaibi, Helmi; Otis, Martin J-D; Menelas, Bob-Antoine J

    2016-12-01

    The aim of this study is to improve and facilitate the methods used to assess risk of falling at home among older people through the computation of a risk of falling in real time in daily activities. In order to increase a real time computation of the risk of falling, a closed-loop balance model is proposed and compared with One-Leg Standing Test (OLST). This balance model allows studying the postural response of a person having an unpredictable perturbation. Twenty-nine volunteers participated in this study for evaluating the effectiveness of the proposed system which includes seventeen elder participants: ten healthy elderly ( 68.4 ±5.5 years), seven Parkinson's disease (PD) subjects ( 66.28 ±8.9 years), and twelve healthy young adults ( 28.27 ±3.74 years). Our work suggests that there is a relationship between OLST score and the risk of falling based on center of pressure measurement with four low cost force sensors located inside an instrumented insole, which could be predicted using our suggested closed-loop balance model. For long term monitoring at home, this system could be included in a medical electronic record and could be useful as a diagnostic aid tool.

  3. Benchmarking Model Variants in Development of a Hardware-in-the-Loop Simulation System

    Science.gov (United States)

    Aretskin-Hariton, Eliot D.; Zinnecker, Alicia M.; Kratz, Jonathan L.; Culley, Dennis E.; Thomas, George L.

    2016-01-01

    Distributed engine control architecture presents a significant increase in complexity over traditional implementations when viewed from the perspective of system simulation and hardware design and test. Even if the overall function of the control scheme remains the same, the hardware implementation can have a significant effect on the overall system performance due to differences in the creation and flow of data between control elements. A Hardware-in-the-Loop (HIL) simulation system is under development at NASA Glenn Research Center that enables the exploration of these hardware dependent issues. The system is based on, but not limited to, the Commercial Modular Aero-Propulsion System Simulation 40k (C-MAPSS40k). This paper describes the step-by-step conversion from the self-contained baseline model to the hardware in the loop model, and the validation of each step. As the control model hardware fidelity was improved during HIL system development, benchmarking simulations were performed to verify that engine system performance characteristics remained the same. The results demonstrate the goal of the effort; the new HIL configurations have similar functionality and performance compared to the baseline C-MAPSS40k system.

  4. Two aspects of one loop structure: Unitarity delay in the Standard Model and modular invariance in string theory

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, C.

    1989-08-01

    We study two aspects of one loop structures in quantum field theories which describe two different areas of particle physics: the one loop unitarity behavior of the Standard Model of electroweak interactions and modular invariance of string model theory. Loop expansion has its importance in that it contains quantum fluctuations due to all physical states in the theory. Therefore, by studying the various models to one loop, we can understand how the contents of the theory can contribute to physically measurable quantities and how the consistency at quantum level restricts the physical states of the theory, as well. In the first half of the thesis, we study one loop corrections to the process {ital e}{sup +}{ital e}{sup {minus}} {yields} {ital W}{sup +}{ital W}{sup {minus}}. In this process, there is a delicate unitarity-saving cancellation between s-channel and t-channel tree level Feynman diagrams. If the one loop contribution due to heavy particles corrects the channels asymmetrically, the cancellation, hence unitarity, will be delayed up to the mass scale of these heavy particles. We refer to this phenomena as the unitarity delay effect. Due to this effect, cross section below these mass scales can have significant radiative corrections which may provide an appropriate window through which we can see the high energy structure of the Standard Model from relatively low energy experiments. In the second half, we will show how quantum consistency can restrict the physical states in string theory. 53 refs., 13 figs.

  5. Predictive models of circulating fluidized bed combustors: SO[sub 2] sorption in the CFB loop

    Energy Technology Data Exchange (ETDEWEB)

    Gidaspow, D.; Therdthianwong, A. (Illinois Inst. of Tech., Chicago, IL (United States). Dept. of Chemical Engineering)

    1993-02-01

    The overall objective of this investigation is to develop experimentally verified models for circulating fluidized bed (CFB) combustors. Sorption of S0[sub 2] with calcined limestone was studied in a PYROFLOW type CFB loop at conditions approximating those found in a CFB combustor. Initially the CFB loop contained 150 micron CaO particles of a density of 3.3 g/cm[sup 3] and air at 1143[degrees]K and 3.25 atm. Atzero time, air containing 600 ppm SO[sub 2], was introduced into the riser bottom at 1143[degrees]K. The effect of gas velocity, sorbent inventory and inlet pressure on the sorption of SO[sub 2], were studied isothermally by running our hydrodynamic code with the S0[sub 2] sorption conservation of species equation. At a velocity of 5m/sec., reported to be a typical velocity by PYROPOWER, there is reasonably good S0[sub 2] removal. At 10 m/sec the S0[sub 2] removal is poor. The best SO[sub 2], removal is for a velocity of 5 m/s and a high bed inventory, initial bed height, H = 9m. Most of the S0[sub 2] is removed in the first two meters of the reactor. However, the S0[sub 2] removal is not complete at the bed outlet. This is due to mixing. At the left wall of the reactor (wall opposite the solids inlet) the S0[sub 2] removal was poor due to gas bypassing caused by the asymmetrical solids inlet. Simulation of the PYROPOWER loop with a symmetrical inlet gave us an order of magnitude improvement over the conventional PYROPOWER system. These results demonstrate the practical utility of the predictive model that we have developed over the last three years.

  6. Approximate Models for Closed-Loop Trajectory Tracking in Underactuated Systems

    Data.gov (United States)

    National Aeronautics and Space Administration — Control of robotic systems, as a field, spans both traditional closed-loop feedback techniques and modern machine learning strategies, which are primarily open-loop....

  7. Model-Based Closed-Loop Glucose Control in Type 1 Diabetes: The DiaCon Experience

    DEFF Research Database (Denmark)

    Schmidt, Signe; Boiroux, Dimitri; Duun-Henriksen, Anne Katrine

    2013-01-01

    Background: To improve type 1 diabetes mellitus (T1DM) management, we developed a model predictive control (MPC) algorithm for closed-loop (CL) glucose control based on a linear second-order deterministic-stochastic model. The deterministic part of the model is specified by three patient-specific......Background: To improve type 1 diabetes mellitus (T1DM) management, we developed a model predictive control (MPC) algorithm for closed-loop (CL) glucose control based on a linear second-order deterministic-stochastic model. The deterministic part of the model is specified by three patient...... crossover studies. Study 1 compared CL with open-loop (OL) control. Study 2 compared glucose control after CL initiation in the euglycemic (CL-Eu) and hyperglycemic (CL-Hyper) ranges, respectively. Patients were studied from 22:00–07:00 on two separate nights. Results: Each study included six T1DM patients...

  8. Studies on 16α-Hydroxylation of Steroid Molecules and Regioselective Binding Mode in Homology-Modeled Cytochrome P450-2C11

    Directory of Open Access Journals (Sweden)

    Hamed I. Ali

    2011-01-01

    Full Text Available We investigated the 16α-hydroxylation of steroid molecules and regioselective binding mode in homology-modeled cytochrome P450-2C11 to correlate the biological study with the computational molecular modeling. It revealed that there was a positive relationship between the observed inhibitory potencies and the binding free energies. Docking of steroid molecules into this homology-modeled CYP2C11 indicated that 16α-hydroxylation is favored with steroidal molecules possessing the following components, (1 a bent A-B ring configuration (5β-reduced, (2 C-3 α-hydroxyl group, (3 C-17β-acetyl group, and (4 methyl group at both the C-18 and C-19. These respective steroid components requirements were defined as the inhibitory contribution factor. Overall studies of the male rat CYP2C11 metabolism revealed that the above-mentioned steroid components requirements were essential to induce an effective inhibition of [3H]progesterone 16α-hydroxylation. As far as docking of homology-modeled CYP2C11 against investigated steroids is concerned, they are docked at the active site superimposed with flurbiprofen. It was also found that the distance between heme iron and C16α-H was between 4 to 6 Å and that the related angle was in the range of 180±45∘.

  9. SCRINING IN SILICO ACTIVE COMPOUND OF Pachyrrhizus erosus AS ANTITIROSINASE ON Aspergillus oryzae (COMPUTATTIONAL STUDY WITH HOMOLOGY MODELING AND MOLECULAR DOCKING

    Directory of Open Access Journals (Sweden)

    Endang Lukitaningsih

    2015-11-01

    Full Text Available Bengkoang telah banyak digunakan dalam industri kosmetika sebagai whitening agent. Berdasarkan penelitian Lukitaningsih (2009, bengkoang mengandung 6 senyawa aktif yang mampu berperan sebagai whitening agent dengan menghambat aktivitas enzim tirosinase dari jamur Aspergillus oryzae (TyrAo. Namun interaksi senyawa aktif bengkoang dalam menghambat enzim tirosinase belum dapat diketahui. Interaksi senyawa-senyawa aktif bengkoang dengan enzim TyrAo dapat diketahui dengan studi komputasional (in silico. Pemodelan interaksi senyawa aktif bengkoang dengan enzim TyrAo dilakukan dengan metode homology modeling dan molecular docking. Homology modeling dilakukan untuk memodelkan struktur tiga dimensi (3D enzim tirosinase Aspergillus oryzae (TyrAo melalui template berupa protein homolog yang sudah diketahui struktur 3D-nya yaitu enzim TyrAb (PDBID: 2Y9X. Model TyrAo digunakan sebagai target makromolekul dalam metode molecular docking. Metode molecular docking merupakan metode untuk menggambarkan posisi ligan (senyawa-senyawa aktif bengkoang pada sisi aktif reseptor (model TyrAo. Berdasarkan docking yang dilakukan diketahui bahwa residu-residu yang banyak berpengaruh pada interaksi ligan pada sisi aktif adalah residu Thr275 yang berinteraksi secara ikatan hidrogen dengan ligan dan residu His294 yang berinteraksi secara hidrofobik pada cincin aromatik ligan. Penelitian in silico dan in vitro yang telah dilakukan memiliki korelasi (R2 sebesar -0,8366. Korelasi ini menandakan bahwa aktivitas senyawa-senyawa aktif pada bengkoang dalam menghambat enzim TyrAo memiliki hasil yang serupa pada penelitian yang  dilakukan secara in silico dan in vitro.

  10. Pure homology of algebraic varieties

    OpenAIRE

    Weber, Andrzej

    2003-01-01

    We show that for a complete complex algebraic variety the pure component of homology coincides with the image of intersection homology. Therefore pure homology is topologically invariant. To obtain slightly more general results we introduce "image homology" for noncomplete varieties.

  11. Spatiotemporal Analysis of Coronal Loops Using Seismology of Damped Kink Oscillations and Forward Modeling of EUV Intensity Profiles

    Science.gov (United States)

    Pascoe, D. J.; Anfinogentov, S. A.; Goddard, C. R.; Nakariakov, V. M.

    2018-06-01

    The shape of the damping profile of kink oscillations in coronal loops has recently allowed the transverse density profile of the loop to be estimated. This requires accurate measurement of the damping profile that can distinguish the Gaussian and exponential damping regimes, otherwise there are more unknowns than observables. Forward modeling of the transverse intensity profile may also be used to estimate the width of the inhomogeneous layer of a loop, providing an independent estimate of one of these unknowns. We analyze an oscillating loop for which the seismological determination of the transverse structure is inconclusive except when supplemented by additional spatial information from the transverse intensity profile. Our temporal analysis describes the motion of a coronal loop as a kink oscillation damped by resonant absorption, and our spatial analysis is based on forward modeling the transverse EUV intensity profile of the loop under the isothermal and optically thin approximations. We use Bayesian analysis and Markov chain Monte Carlo sampling to apply our spatial and temporal models both individually and simultaneously to our data and compare the results with numerical simulations. Combining the two methods allows both the inhomogeneous layer width and density contrast to be calculated, which is not possible for the same data when each method is applied individually. We demonstrate that the assumption of an exponential damping profile leads to a significantly larger error in the inferred density contrast ratio compared with a Gaussian damping profile.

  12. Modeling and Closed Loop Flight Testing of a Fixed Wing Micro Air Vehicle

    Directory of Open Access Journals (Sweden)

    Harikumar Kandath

    2018-03-01

    Full Text Available This paper presents the nonlinear six degrees of freedom dynamic modeling of a fixed wing micro air vehicle. The static derivatives of the micro air vehicle are obtained through the wind tunnel testing. The propeller effects on the lift, drag, pitching moment and side force are quantified through wind tunnel testing. The dynamic derivatives are obtained through empirical relations available in the literature. The trim conditions are computed for a straight and constant altitude flight condition. The linearized longitudinal and lateral state space models are obtained about trim conditions. The variations in short period mode, phugoid mode, Dutch roll mode, roll subsidence mode and spiral mode with respect to different trim operating conditions is presented. A stabilizing static output feedback controller is designed using the obtained model. Successful closed loop flight trials are conducted with the static output feedback controller.

  13. One-loop potential in the new string model with negative stiffness

    International Nuclear Information System (INIS)

    Kleinert, H.; Chervyakov, A.M.; Nesterenko, V.V.

    1996-01-01

    The color-electric flux tube between quarks has a finite thickness therefore also a finite curvature stiffness. Contrary to earlier rigid-string proposal by Polyakov and Kleinert and motivated by the properties of a magnetic flux tube in a type-II superconductor, we put forward the hypothesis that the stiffness is negative. We set up and study the properties of an idealized string model with such negative stiffness. In contrast to the rigid string, the propagator in the new model has no unphysical pole. One-loop calculations show that the model generates an interquark potential which does not contain the square root singularity even for moderate values of a negative stiffness. At large distances, the potential has usual linearly rising term with the universal Luescher correction

  14. Activity build-up on the circulation loops of boiling water reactors: Basics for modelling of transport and deposition processes

    International Nuclear Information System (INIS)

    Covelli, B.; Alder, H.P.

    1988-03-01

    In the past 20 years the radiation field of nuclear power plant loops outside the core zone was the object of investigations in many countries. In this context test loops were built and basic research done. At our Institute PSI the installation of a LWR-contamination loop is planned for this year. This experimental loop has the purpose to investigate the complex phenomena of activity deposition from the primary fluid of reactor plants and to formulate analytical models. From the literature the following conclusions can be drawn: The principal correlations of the activity build-up outside the core are known. The plant specific single phenomena as corrosion, crud-transport, activation and deposit of cobalt in the oxide layer are complex and only partially understood. The operational experience of particular plants with low contaminated loops (BWR-recirculation loops) show that in principle the problem is manageable. The reduction of the activity build-up in older plants necessitates a combination of measures to modify the crud balance in the primary circuit. In parallel to the experimental work several simulation models in the form of computer programs were developed. These models have the common feature that they are based on mass balances, in which the exchange of materials and the sedimentation processes are described by global empirical transport coefficients. These models yield satisfactory results and allow parameter studies; the application however is restricted to the particular installation. All programs lack models that describe the thermodynamic and hydrodynamic mechanisms on the surface of deposition layers. Analytical investigations on fouling of process equipment led to models that are also applicable to the activity build-up in reactor loops. Therefore it seems appropriate to combine the nuclear simulation models with the fundamental equations for deposition. 10 refs., 18 figs., 3 tabs

  15. A RETRAN-02 model of the Sizewell B PCSR design - the Winfrith one-loop model, version 3.0

    International Nuclear Information System (INIS)

    Kinnersly, S.R.

    1983-11-01

    A one-loop RETRAN-02 model of the Sizewell B Pre Construction Safety Report (PCSR) design, set up at Winfrith, is described and documented. The model is suitable for symmetrical pressurised transients. Comparison with data from the Sizewell B PCSR shows that the model is a good representation of that design. Known errors, limitations and deficiencies are described. The mode of storage and maintenance at Winfrith using PROMUS (Program Maintenance and Update System) is noted. It is recommended that users modify the standard data by adding replacement cards to the end so as to aid in identification, use and maintenance of local versions. (author)

  16. Two-loop renormalization group analysis of supersymmetric SO(10) models with an intermediate scale

    International Nuclear Information System (INIS)

    Bastero-Gil, M.; Brahmachari, B.

    1996-03-01

    Two-loop evolutions of the gauge couplings in a class of intermediate scale supersymmetric SO(10) models including the effect of third generation Yukawa couplings are studied. The unification scale, the intermediate scale and the value of the unification gauge coupling in these models are calculated and the gauge boson mediated proton decay rates are estimated. In some cases the predicted proton lifetime turns out to be in the border-line of experimental limit. The predictions of the top quark mass, the mass ratio m b (m b )/m τ (m τ ) from the two-loop evolution of Yukawa couplings and the mass of the left handed neutrino via see-saw mechanism are summarized. The lower bounds on the ratio of the VEVs of the two low energy doublets (tan β) from the requirement of the perturbative unitarity of the top quark Yukawa coupling up to the grand unification scale are also presented. All the predictions have been compared with those of the one-step unified theory. (author). 33 refs, 5 figs, 1 tab

  17. Closed-loop supply chain models with considering the environmental impact.

    Science.gov (United States)

    Mohajeri, Amir; Fallah, Mohammad

    2014-01-01

    Global warming and climate changes created by large scale emissions of greenhouse gases are a worldwide concern. Due to this, the issue of green supply chain management has received more attention in the last decade. In this study, a closed-loop logistic concept which serves the purposes of recycling, reuse, and recovery required in a green supply chain is applied to integrate the environmental issues into a traditional logistic system. Here, we formulate a comprehensive closed-loop model for the logistics planning considering profitability and ecological goals. In this way, we can achieve the ecological goal reducing the overall amount of CO2 emitted from journeys. Moreover, the profitability criterion can be supported in the cyclic network with the minimum costs and maximum service level. We apply three scenarios and develop problem formulations for each scenario corresponding to the specified regulations and investigate the effect of the regulation on the preferred transport mode and the emissions. To validate the models, some numerical experiments are worked out and a comparative analysis is investigated.

  18. Closed-Loop Supply Chain Models with Considering the Environmental Impact

    Directory of Open Access Journals (Sweden)

    Amir Mohajeri

    2014-01-01

    Full Text Available Global warming and climate changes created by large scale emissions of greenhouse gases are a worldwide concern. Due to this, the issue of green supply chain management has received more attention in the last decade. In this study, a closed-loop logistic concept which serves the purposes of recycling, reuse, and recovery required in a green supply chain is applied to integrate the environmental issues into a traditional logistic system. Here, we formulate a comprehensive closed-loop model for the logistics planning considering profitability and ecological goals. In this way, we can achieve the ecological goal reducing the overall amount of CO2 emitted from journeys. Moreover, the profitability criterion can be supported in the cyclic network with the minimum costs and maximum service level. We apply three scenarios and develop problem formulations for each scenario corresponding to the specified regulations and investigate the effect of the regulation on the preferred transport mode and the emissions. To validate the models, some numerical experiments are worked out and a comparative analysis is investigated.

  19. One-loop correlation functions in the model of noncritical fermionic strings

    International Nuclear Information System (INIS)

    Belokurov, V.V.; Iofa, M.Z.

    1996-01-01

    In the model of noncritical fermionic strings, the David-Distler-Kawai ansatz is used to study one-loop n-point (n≤4) correlation functions for the vertex operators of massless bosonic states. The action functional of the model is the sum of super-Liouville action functional for the conformal mode and the action functional of d scalar supermultiplets. It is assumed that the total cosmological term is equal to zero. The amplitudes are calculated as the residues at the pole of the correlation function that corresponds to the conservation of Liouville momentum in the form Σβi=Q(1-h), where Q=√(9-d)/2 and h is the genus of the work sheet. In the one-loop approximation, the amplitudes can be obtained in the modular-invariant form, provided that the coefficients appearing in the sum over spin structures depend on moduli. In this case, the modular measure is defined up to a modular-invariant factor. This arbitrariness can be used to represent one-point correlation functions in the same functional form as for strings of critical dimension

  20. A model for improving microbial biofuel production using a synthetic feedback loop

    Energy Technology Data Exchange (ETDEWEB)

    Dunlop, Mary; Keasling, Jay; Mukhopadhyay, Aindrila

    2011-07-14

    Cells use feedback to implement a diverse range of regulatory functions. Building synthetic feedback control systems may yield insight into the roles that feedback can play in regulation since it can be introduced independently of native regulation, and alternative control architectures can be compared. We propose a model for microbial biofuel production where a synthetic control system is used to increase cell viability and biofuel yields. Although microbes can be engineered to produce biofuels, the fuels are often toxic to cell growth, creating a negative feedback loop that limits biofuel production. These toxic effects may be mitigated by expressing efflux pumps that export biofuel from the cell. We developed a model for cell growth and biofuel production and used it to compare several genetic control strategies for their ability to improve biofuel yields. We show that controlling efflux pump expression directly with a biofuel-responsive promoter is a straight forward way of improving biofuel production. In addition, a feed forward loop controller is shown to be versatile at dealing with uncertainty in biofuel production rates.

  1. The meson and the baryon in the one-loop dual model of the pomeron

    International Nuclear Information System (INIS)

    Pennington, M.R.; Gula, A.

    1975-01-01

    In the lowest order dual loop perturbation theory the crossing and factorisation properties of the pomeron are considered. It is shown that the baryon loop is the necessary complement of the single crossed meson loop in building the low-energy pomeron. Recent experimental indications that in this energy region the pomeron is different in MM, MB and BB processes are naturally explained. (Auth.)

  2. Hydrodynamical model and experimental results of a calcium looping cycle for CO2 capture

    International Nuclear Information System (INIS)

    Lisbona, Pilar; Martínez, Ana; Romeo, Luis M.

    2013-01-01

    Highlights: ► A scaled experimental cold flow model of a dual fluidized bed facility is presented. ► Two MATLAB models are developed for the single CFB and the dual CFB facility. ► Set of experiments are carried out and used to validate the mathematical model. ► Good agreement between model and experimental tests for sCFB. ► Further work required for validating dual CFB operation. -- Abstract: High temperature looping cycles involving solid circulation, such as carbonation–calcination, play an essential role among the CO 2 capture technologies under development. The low cost and high availability of Ca-based sorbents together with the feasibility of integration between these capture systems and existing power plants lead to very competitive potential costs of avoided CO 2 , below 20 €/tonne. Optimal configurations make use of several interconnected fluidized beds. One promising configuration for Ca-based sorbents looping systems relies on the use of two circulating beds (carbonator and calciner) and two bubbling beds acting as non-mechanical valves. Fluidized beds are well characterized when operating independently since they are extensively used in industrial applications, power and chemical plants. However, the operation when two or more fluidized beds exchange solid material through non-mechanical valves is still uncertain because of the more complex pressure balance of the system. Theoretical studies based on thermo-chemical simulations and experimental studies show that minimum CO 2 capture cost is attained with large solid circulation flow between reactors. The challenge is to reach the required particle circulation in a system with a complex configuration and be able to control it. Solid internal recirculation in any of these fluidized beds would provide flexibility in its control but it will also make harder the characterization of the whole system. The aim of this work is to analyse the hydrodynamics of the system and to generate a

  3. Coronal Heating: Testing Models of Coronal Heating by Forward-Modeling the AIA Emission of the Ansample of Coronal Loops

    Science.gov (United States)

    Malanushenko, A. V.

    2015-12-01

    We present a systemic exploration of the properties of coronal heating, by forward-modeling the emission of the ensemble of 1D quasi-steady loops. This approximations were used in many theoretical models of the coronal heating. The latter is described in many such models in the form of power laws, relating heat flux through the photosphere or volumetric heating to the strength of the magnetic field and length of a given field line. We perform a large search in the parameter space of these power laws, amongst other variables, and compare the resulting emission of the active region to that observed by AIA. We use a recently developed magnetic field model which uses shapes of coronal loops to guide the magnetic model; the result closely resembles observed structures by design. We take advantage of this, by comparing, in individual sub-regions of the active region, the emission of the active region and its synthetic model. This study allows us to rule out many theoretical models and formulate predictions for the heating models to come.

  4. Analysis of Host Range Restriction Determinants in the Rabbit Model: Comparison of Homologous and Heterologous Rotavirus Infections

    Science.gov (United States)

    Ciarlet, Max; Estes, Mary K.; Barone, Christopher; Ramig, Robert F.; Conner, Margaret E.

    1998-01-01

    The main limitation of both the rabbit and mouse models of rotavirus infection is that human rotavirus (HRV) strains do not replicate efficiently in either animal. The identification of individual genes necessary for conferring replication competence in a heterologous host is important to an understanding of the host range restriction of rotavirus infections. We recently reported the identification of the P type of the spike protein VP4 of four lapine rotavirus strains as being P[14]. To determine whether VP4 is involved in host range restriction in rabbits, we evaluated infection in rotavirus antibody-free rabbits inoculated orally with two P[14] HRVs, PA169 (G6) and HAL1166 (G8), and with several other HRV strains and animal rotavirus strains of different P and G types. We also evaluated whether the parental rhesus rotavirus (RRV) (P5B[3], G3) and the derived RRV-HRV reassortant candidate vaccine strains RRV × D (G1), RRV × DS-1 (G2), and RRV × ST3 (G4) would productively infect rabbits. Based on virus shedding, limited replication was observed with the P[14] HRV strains and with the SA11 Cl3 (P[2], G3) and SA11 4F (P6[1], G3) animal rotavirus strains, compared to the homologous ALA strain (P[14], G3). However, even limited infection provided complete protection from rotavirus infection when rabbits were challenged orally 28 days postinoculation (DPI) with 103 50% infective doses of ALA rabbit rotavirus. Other HRVs did not productively infect rabbits and provided no significant protection from challenge, in spite of occasional seroconversion. Simian RRV replicated as efficiently as lapine ALA rotavirus in rabbits and provided complete protection from ALA challenge. Live attenuated RRV reassortant vaccine strains resulted in no, limited, or productive infection of rabbits, but all rabbits were completely protected from heterotypic ALA challenge. The altered replication efficiency of the reassortants in rabbits suggests a role for VP7 in host range restriction

  5. Homology Modeling and Analysis of Structure Predictions of the Bovine Rhinitis B Virus RNA Dependent RNA Polymerase (RdRp

    Directory of Open Access Journals (Sweden)

    Devendra K. Rai

    2012-07-01

    Full Text Available Bovine Rhinitis B Virus (BRBV is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV with a ~43% identical polyprotein sequence and as much as 67% identical sequence for the RNA dependent RNA polymerase (RdRp, which is also known as 3D polymerase (3Dpol. In the present study we carried out phylogenetic analysis, structure based sequence alignment and prediction of three-dimensional structure of BRBV 3Dpol using a combination of different computational tools. Model structures of BRBV 3Dpol were verified for their stereochemical quality and accuracy. The BRBV 3Dpol structure predicted by SWISS-MODEL exhibited highest scores in terms of stereochemical quality and accuracy, which were in the range of 2Å resolution crystal structures. The active site, nucleic acid binding site and overall structure were observed to be in agreement with the crystal structure of unliganded as well as template/primer (T/P, nucleotide tri-phosphate (NTP and pyrophosphate (PPi bound FMDV 3Dpol (PDB, 1U09 and 2E9Z. The closest proximity of BRBV and FMDV 3Dpol as compared to human rhinovirus type 16 (HRV-16 and rabbit hemorrhagic disease virus (RHDV 3Dpols is also substantiated by phylogeny analysis and root-mean square deviation (RMSD between C-α traces of the polymerase structures. The absence of positively charged α-helix at C terminal, significant differences in non-covalent interactions especially salt bridges and CH-pi interactions around T/P channel of BRBV 3Dpol compared to FMDV 3Dpol, indicate that despite a very high homology to FMDV 3Dpol, BRBV 3Dpol may adopt a different mechanism for handling its substrates and adapting to physiological requirements. Our findings will be valuable in the

  6. Homological Order in Three and Four dimensions: Wilson Algebra, Entanglement Entropy and Twist Defects

    Science.gov (United States)

    Roy, Abhishek; Chen, Xiao; Teo, Jeffrey

    2013-03-01

    We investigate homological orders in two, three and four dimensions by studying Zk toric code models on simplicial, cellular or in general differential complexes. The ground state degeneracy is obtained from Wilson loop and surface operators, and the homological intersection form. We compute these for a series of closed 3 and 4 dimensional manifolds and study the projective representations of mapping class groups (modular transformations). Braiding statistics between point and string excitations in (3+1)-dimensions or between dual string excitations in (4+1)-dimensions are topologically determined by the higher dimensional linking number, and can be understood by an effective topological field theory. An algorithm for calculating entanglemnent entropy of any bipartition of closed manifolds is presented, and its topological signature is completely characterized homologically. Extrinsic twist defects (or disclinations) are studied in 2,3 and 4 dimensions and are shown to carry exotic fusion and braiding properties. Simons Fellowship

  7. Homology in Electromagnetic Boundary Value Problems

    Directory of Open Access Journals (Sweden)

    Pellikka Matti

    2010-01-01

    Full Text Available We discuss how homology computation can be exploited in computational electromagnetism. We represent various cellular mesh reduction techniques, which enable the computation of generators of homology spaces in an acceptable time. Furthermore, we show how the generators can be used for setting up and analysis of an electromagnetic boundary value problem. The aim is to provide a rationale for homology computation in electromagnetic modeling software.

  8. Introduction to Loop Heat Pipes

    Science.gov (United States)

    Ku, Jentung

    2015-01-01

    This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

  9. Loop Transfer Matrix and Loop Quantum Mechanics

    International Nuclear Information System (INIS)

    Savvidy, George K.

    2000-01-01

    The gonihedric model of random surfaces on a 3d Euclidean lattice has equivalent representation in terms of transfer matrix K(Q i ,Q f ), which describes the propagation of loops Q. We extend the previous construction of the loop transfer matrix to the case of nonzero self-intersection coupling constant κ. We introduce the loop generalization of Fourier transformation which allows to diagonalize transfer matrices, that depend on symmetric difference of loops only and express all eigenvalues of 3d loop transfer matrix through the correlation functions of the corresponding 2d statistical system. The loop Fourier transformation allows to carry out the analogy with quantum mechanics of point particles, to introduce conjugate loop momentum P and to define loop quantum mechanics. We also consider transfer matrix on 4d lattice which describes propagation of memebranes. This transfer matrix can also be diagonalized by using the generalized Fourier transformation, and all its eigenvalues are equal to the correlation functions of the corresponding 3d statistical system. In particular the free energy of the 4d membrane system is equal to the free energy of 3d gonihedric system of loops and is equal to the free energy of 2d Ising model. (author)

  10. Bending and Twisting the Embryonic Heart: A Computational Model for C-Looping Based on Realistic Geometry

    Directory of Open Access Journals (Sweden)

    Yunfei eShi

    2014-08-01

    Full Text Available The morphogenetic process of cardiac looping transforms the straight heart tube into a curved tube that resembles the shape of the future four-chambered heart. Although great progress has been made in identifying the molecular and genetic factors involved in looping, the physical mechanisms that drive this process have remained poorly understood. Recent work, however, has shed new light on this complicated problem. After briefly reviewing the current state of knowledge, we propose a relatively comprehensive hypothesis for the mechanics of the first phase of looping, termed c-looping, as the straight heart tube deforms into a c-shaped tube. According to this hypothesis, differential hypertrophic growth in the myocardium supplies the main forces that cause the heart tube to bend ventrally, while regional growth and contraction in the omphalomesenteric veins (primitive atria and compressive loads exerted by the splanchnopleuric membrane drive rightward torsion. A computational model based on realistic embryonic heart geometry is used to test this hypothesis. The behavior of the model is in reasonable agreement with available experimental data from control and perturbed embryos, offering support for our hypothesis. The results also suggest, however, that several other mechanisms contribute secondarily to normal looping, and we speculate that these mechanisms play backup roles when looping is perturbed. Finally, some outstanding questions are discussed for future study.

  11. Lectures on functor homology

    CERN Document Server

    Touzé, Antoine

    2015-01-01

    This book features a series of lectures that explores three different fields in which functor homology (short for homological algebra in functor categories) has recently played a significant role. For each of these applications, the functor viewpoint provides both essential insights and new methods for tackling difficult mathematical problems. In the lectures by Aurélien Djament, polynomial functors appear as coefficients in the homology of infinite families of classical groups, e.g. general linear groups or symplectic groups, and their stabilization. Djament’s theorem states that this stable homology can be computed using only the homology with trivial coefficients and the manageable functor homology. The series includes an intriguing development of Scorichenko’s unpublished results. The lectures by Wilberd van der Kallen lead to the solution of the general cohomological finite generation problem, extending Hilbert’s fourteenth problem and its solution to the context of cohomology. The focus here is o...

  12. Surface state decoherence in loop quantum gravity, a first toy model

    International Nuclear Information System (INIS)

    Feller, Alexandre; Livine, Etera R

    2017-01-01

    The quantum-to-classical transition through decoherence is a major facet of the semi-classical analysis of quantum models that are supposed to admit a classical regime, as quantum gravity should be. A particular problem of interest is the decoherence of black hole horizons and holographic screens induced by the bulk-boundary coupling with interior degrees of freedom. Here in this paper we present a first toy-model, in the context of loop quantum gravity, for the dynamics of a surface geometry as an open quantum system. We discuss the resulting decoherence and recoherence and compare the exact density matrix evolution to the commonly used master equation approximation à la Lindblad underlining its merits and limitations. The prospect of this study is to have a clearer understanding of the boundary decoherence of black hole horizons seen by outside observers. (paper)

  13. Quantum Gowdy model within the new loop quantum cosmology improved dynamics

    International Nuclear Information System (INIS)

    Martin-Benito, M; Garay, L J; Mena Marugan, G A

    2011-01-01

    The linearly polarized Gowdy T 3 model can be regarded as compact Bianchi I cosmologies with inhomogeneous modes allowed to travel in one direction. We study a hybrid quantization of this model that combines the loop quantization of the Bianchi I background, adopting the improved dynamics scheme put forward by Ashtekar and Wilson-Ewing, with a Fock quantization for the inhomogeneities. The Hamiltonian constraint operator provides a resolution of the cosmological singularity and superselects separable sectors. We analyze the complicated structure of these sectors. In any of them the Hamiltonian constraint provides an evolution equation with respect to the volume of the associated Bianchi I universe, with a well posed initial value problem. This fact allows us to construct the Hilbert space of physical states and to show that we recover the standard quantum field theory for the inhomogeneities.

  14. Coupling sensing to crop models for closed-loop plant production in advanced life support systems

    Science.gov (United States)

    Cavazzoni, James; Ling, Peter P.

    1999-01-01

    We present a conceptual framework for coupling sensing to crop models for closed-loop analysis of plant production for NASA's program in advanced life support. Crop status may be monitored through non-destructive observations, while models may be independently applied to crop production planning and decision support. To achieve coupling, environmental variables and observations are linked to mode inputs and outputs, and monitoring results compared with model predictions of plant growth and development. The information thus provided may be useful in diagnosing problems with the plant growth system, or as a feedback to the model for evaluation of plant scheduling and potential yield. In this paper, we demonstrate this coupling using machine vision sensing of canopy height and top projected canopy area, and the CROPGRO crop growth model. Model simulations and scenarios are used for illustration. We also compare model predictions of the machine vision variables with data from soybean experiments conducted at New Jersey Agriculture Experiment Station Horticulture Greenhouse Facility, Rutgers University. Model simulations produce reasonable agreement with the available data, supporting our illustration.

  15. Natural Circulation High Pressure Loop Dynamics Around Operating Point, Tests and Modelling With Retran 02

    International Nuclear Information System (INIS)

    Masriera, N.A; Doval, A.S; Mazufri, C.M

    2000-01-01

    The Natural Circulation High Pressure Loop (CAPCN) reproduces in scale all the one-dimensional thermal-hydraulic phenomena occurring in the primary loop of CAREM-25 reactor.It plays an important role in the qualification process of calculating computer codes.This facility demanded to develop several technological solutions in order to achieve the measuring and control quality required by that process.This engineering and experimental development allowed completing the first stage of dynamic tests during 1998.The trends of recorded data were systematically evaluated in terms of the deviations of main variables in response to different perturbations.By this analysis a group of eight transients was selected, providing a Minimum Representative Set (MRS) of dynamic tests, allowing the evaluation of all dynamic phenomena.Each of these transients was simulated with RETRAN-02, using a spreadsheet to facilitate the consistent elaboration and modification of input files.Comparing measured data and computer simulations, it may be concluded that it is possible to reproduce the dynamic response of all the transients with a level of approximation quite homogeneous and generally acceptable.It is possible to identify the detailed physical models that fit better the dynamic phenomena, and which of the limitations of RETRAN code are more relevant

  16. Temporal differential proteomes of Clostridium difficile in the pig ileal-ligated loop model.

    Directory of Open Access Journals (Sweden)

    Tavan Janvilisri

    Full Text Available The impact of Clostridium difficile infection (CDI on healthcare is becoming increasingly recognized as it represents a major cause of nosocomial diarrhea. A rising number of CDI cases and outbreaks have been reported worldwide. Here, we developed the pig ileal-ligated loop model for semi-quantitative analysis comparing temporal differential proteomes in C. difficile following in vivo incubation with in vitro growth using isobaric tags for relative and absolute quantification (iTRAQ. Proteins retrieved from the in vitro cultures and the loop contents after 4, 8, and 12 h in vivo incubation were subjected to in-solution digestion, iTRAQ labeling, two-dimensional liquid chromatography/tandem mass spectrometry and statistical analyses. From a total of 1152 distinct proteins identified in this study, 705 proteins were available for quantitative measures at all time points in both biological and technical replicates; 109 proteins were found to be differentially expressed. With analysis of clusters of orthologous group and protein-protein network interactions, we identified the proteins that might play roles in adaptive responses to the host environment, hence enhancing pathogenicity during CDI. This report represents the quantitative proteomic analysis of C. difficile that demonstrates time-dependent protein expression changes under conditions that mimic in vivo infection and identifies potential candidates for diagnostic or therapeutic measures.

  17. Noise-shaping all-digital phase-locked loops modeling, simulation, analysis and design

    CERN Document Server

    Brandonisio, Francesco

    2014-01-01

    This book presents a novel approach to the analysis and design of all-digital phase-locked loops (ADPLLs), technology widely used in wireless communication devices. The authors provide an overview of ADPLL architectures, time-to-digital converters (TDCs) and noise shaping. Realistic examples illustrate how to analyze and simulate phase noise in the presence of sigma-delta modulation and time-to-digital conversion. Readers will gain a deep understanding of ADPLLs and the central role played by noise-shaping. A range of ADPLL and TDC architectures are presented in unified manner. Analytical and simulation tools are discussed in detail. Matlab code is included that can be reused to design, simulate and analyze the ADPLL architectures that are presented in the book.   • Discusses in detail a wide range of all-digital phase-locked loops architectures; • Presents a unified framework in which to model time-to-digital converters for ADPLLs; • Explains a procedure to predict and simulate phase noise in oscil...

  18. Homology modeling, molecular dynamics, and virtual screening of NorA efflux pump inhibitors of Staphylococcus aureus.

    Science.gov (United States)

    Bhaskar, Baki Vijaya; Babu, Tirumalasetty Muni Chandra; Reddy, Netala Vasudeva; Rajendra, Wudayagiri

    2016-01-01

    Emerging drug resistance in clinical isolates of Staphylococcus aureus might be implicated to the overexpression of NorA efflux pump which is capable of extruding numerous structurally diverse compounds. However, NorA efflux pump is considered as a potential drug target for the development of efflux pump inhibitors. In the present study, NorA model was constructed based on the crystal structure of glycerol-3-phosphate transporter (PDBID: 1PW4). Molecular dynamics (MD) simulation was performed using NAMD2.7 for NorA which is embedded in the hydrated lipid bilayer. Structural design of NorA unveils amino (N)- and carboxyl (C)-terminal domains which are connected by long cytoplasmic loop. N and C domains are composed of six transmembrane α-helices (TM) which exhibits pseudo-twofold symmetry and possess voluminous substrate binding cavity between TM helices. Molecular docking of reserpine, totarol, ferruginol, salvin, thioxanthene, phenothiazine, omeprazole, verapamil, nalidixic acid, ciprofloxacin, levofloxacin, and acridine to NorA found that all the molecules were bound at the large hydrophobic cleft and indicated significant interactions with the key residues. In addition, structure-based virtual screening was employed which indicates that 14 potent novel lead molecules such as CID58685302, CID58685367, CID5799283, CID5578487, CID60028372, ZINC12196383, ZINC72140751, ZINC72137843, ZINC39227983, ZINC43742707, ZINC12196375, ZINC66166948, ZINC39228014, and ZINC14616160 have highest binding affinity for NorA. These lead molecules displayed considerable pharmacological properties as evidenced by Lipinski rule of five and prophecy of toxicity risk assessment. Thus, the present study will be helpful in designing and synthesis of a novel class of NorA efflux pump inhibitors that restore the susceptibilities of drug compounds.

  19. A computational model clarifies the roles of positive and negative feedback loops in the Drosophila circadian clock

    International Nuclear Information System (INIS)

    Wang Junwei; Zhou Tianshou

    2010-01-01

    Previous studies showed that a single negative feedback structure should be sufficient for robust circadian oscillations. It is thus pertinent to ask why current cellular clock models almost universally have interlocked negative feedback loop (NFL) and positive feedback loop (PFL). Here, we propose a molecular model that reflects the essential features of the Drosophila circadian clock to clarify the different roles of negative and positive feedback loops. In agreement with experimental observations, the model can simulate circadian oscillations in constant darkness, entrainment by light-dark cycles, as well as phenotypes of per 01 and clk Jrk mutants. Moreover, sustained oscillations persist when the PFL is removed, implying the crucial role of NFL for rhythm generation. Through parameter sensitivity analysis, it is revealed that incorporation of PFL increases the robustness of the system to regulatory processes in PFL itself. Such reduced models can aid understanding of the design principles of circadian clocks in Drosophila and other organisms with complex transcriptional feedback structures.

  20. A reduced fidelity model for the rotary chemical looping combustion reactor

    KAUST Repository

    Iloeje, Chukwunwike O.

    2017-01-11

    The rotary chemical looping combustion reactor has great potential for efficient integration with CO capture-enabled energy conversion systems. In earlier studies, we described a one-dimensional rotary reactor model, and used it to demonstrate the feasibility of continuous reactor operation. Though this detailed model provides a high resolution representation of the rotary reactor performance, it is too computationally expensive for studies that require multiple model evaluations. Specifically, it is not ideal for system-level studies where the reactor is a single component in an energy conversion system. In this study, we present a reduced fidelity model (RFM) of the rotary reactor that reduces computational cost and determines an optimal combination of variables that satisfy reactor design requirements. Simulation results for copper, nickel and iron-based oxygen carriers show a four-order of magnitude reduction in simulation time, and reasonable prediction accuracy. Deviations from the detailed reference model predictions range from 3% to 20%, depending on oxygen carrier type and operating conditions. This study also demonstrates how the reduced model can be modified to deal with both optimization and design oriented problems. A parametric study using the reduced model is then applied to analyze the sensitivity of the optimal reactor design to changes in selected operating and kinetic parameters. These studies show that temperature and activation energy have a greater impact on optimal geometry than parameters like pressure or feed fuel fraction for the selected oxygen carrier materials.

  1. Identification of putative agouti-related protein(87-132)-melanocortin-4 receptor interactions by homology molecular modeling and validation using chimeric peptide ligands.

    Science.gov (United States)

    Wilczynski, Andrzej; Wang, Xiang S; Joseph, Christine G; Xiang, Zhimin; Bauzo, Rayna M; Scott, Joseph W; Sorensen, Nicholas B; Shaw, Amanda M; Millard, William J; Richards, Nigel G; Haskell-Luevano, Carrie

    2004-04-22

    Agouti-related protein (AGRP) is one of only two naturally known antagonists of G-protein-coupled receptors (GPCRs) identified to date. Specifically, AGRP antagonizes the brain melanocortin-3 and -4 receptors involved in energy homeostasis. Alpha-melanocyte stimulating hormone (alpha-MSH) is one of the known endogenous agonists for these melanocortin receptors. Insight into putative interactions between the antagonist AGRP amino acids with the melanocortin-4 receptor (MC4R) may be important for the design of unique ligands for the treatment of obesity related diseases and is currently lacking in the literature. A three-dimensional homology molecular model of the mouse MC4 receptor complex with the hAGRP(87-132) ligand docked into the receptor has been developed to identify putative antagonist ligand-receptor interactions. Key putative AGRP-MC4R interactions include the Arg111 of hAGRP(87-132) interacting in a negatively charged pocket located in a cavity formed by transmembrane spanning (TM) helices 1, 2, 3, and 7, capped by the acidic first extracellular loop (EL1) and specifically with the conserved melanocortin receptor residues mMC4R Glu92 (TM2), mMC4R Asp114 (TM3), and mMC4R Asp118 (TM3). Additionally, Phe112 and Phe113 of hAGRP(87-132) putatively interact with an aromatic hydrophobic pocket formed by the mMC4 receptor residues Phe176 (TM4), Phe193 (TM5), Phe253 (TM6), and Phe254 (TM6). To validate the AGRP-mMC4R model complex presented herein from a ligand perspective, we generated nine chimeric peptide ligands based on a modified antagonist template of the hAGRP(109-118) (Tyr-c[Asp-Arg-Phe-Phe-Asn-Ala-Phe-Dpr]-Tyr-NH(2)). In these chimeric ligands, the antagonist AGRP Arg-Phe-Phe residues were replaced by the melanocortin agonist His/D-Phe-Arg-Trp amino acids. These peptides resulted in agonist activity at the mouse melanocortin receptors (mMC1R and mMC3-5Rs). The most notable results include the identification of a novel subnanomolar melanocortin peptide

  2. Flare parameters inferred from a 3D loop model data base

    Science.gov (United States)

    Cuambe, Valente A.; Costa, J. E. R.; Simões, P. J. A.

    2018-06-01

    We developed a data base of pre-calculated flare images and spectra exploring a set of parameters which describe the physical characteristics of coronal loops and accelerated electron distribution. Due to the large number of parameters involved in describing the geometry and the flaring atmosphere in the model used, we built a large data base of models (˜250 000) to facilitate the flare analysis. The geometry and characteristics of non-thermal electrons are defined on a discrete grid with spatial resolution greater than 4 arcsec. The data base was constructed based on general properties of known solar flares and convolved with instrumental resolution to replicate the observations from the Nobeyama radio polarimeter spectra and Nobeyama radioheliograph (NoRH) brightness maps. Observed spectra and brightness distribution maps are easily compared with the modelled spectra and images in the data base, indicating a possible range of solutions. The parameter search efficiency in this finite data base is discussed. 8 out of 10 parameters analysed for 1000 simulated flare searches were recovered with a relative error of less than 20 per cent on average. In addition, from the analysis of the observed correlation between NoRH flare sizes and intensities at 17 GHz, some statistical properties were derived. From these statistics, the energy spectral index was found to be δ ˜ 3, with non-thermal electron densities showing a peak distribution ⪅107 cm-3, and Bphotosphere ⪆ 2000 G. Some bias for larger loops with heights as great as ˜2.6 × 109 cm, and looptop events were noted. An excellent match of the spectrum and the brightness distribution at 17 and 34 GHz of the 2002 May 31 flare is presented as well.

  3. A Mixed Integer Linear Programming Model for the Design of Remanufacturing Closed–loop Supply Chain Network

    Directory of Open Access Journals (Sweden)

    Mbarek Elbounjimi

    2015-11-01

    Full Text Available Closed-loop supply chain network design is a critical issue due to its impact on both economic and environmental performances of the supply chain. In this paper, we address the problem of designing a multi-echelon, multi-product and capacitated closed-loop supply chain network. First, a mixed-integer linear programming formulation is developed to maximize the total profit. The main contribution of the proposed model is addressing two economic viability issues of closed-loop supply chain. The first issue is the collection of sufficient quantity of end-of-life products are assured by retailers against an acquisition price. The second issue is exploiting the benefits of colocation of forward facilities and reverse facilities. The presented model is solved by LINGO for some test problems. Computational results and sensitivity analysis are conducted to show the performance of the proposed model.

  4. A closed-loop hybrid physiological model relating to subjects under physical stress.

    Science.gov (United States)

    El-Samahy, Emad; Mahfouf, Mahdi; Linkens, Derek A

    2006-11-01

    The objective of this research study is to derive a comprehensive physiological model relating to subjects under physical stress conditions. The model should describe the behaviour of the cardiovascular system, respiratory system, thermoregulation and brain activity in response to physical workload. An experimental testing rig was built which consists of recumbent high performance bicycle for inducing the physical load and a data acquisition system comprising monitors and PCs. The signals acquired and used within this study are the blood pressure, heart rate, respiration, body temperature, and EEG signals. The proposed model is based on a grey-box based modelling approach which was used because of the sufficient level of details it provides. Cardiovascular and EEG Data relating to 16 healthy subject volunteers (data from 12 subjects were used for training/validation and the data from 4 subjects were used for model testing) were collected using the Finapres and the ProComp+ monitors. For model validation, residual analysis via the computing of the confidence intervals as well as related histograms was performed. Closed-loop simulations for different subjects showed that the model can provide reliable predictions for heart rate, blood pressure, body temperature, respiration, and the EEG signals. These findings were also reinforced by the residual analyses data obtained, which suggested that the residuals were within the 90% confidence bands and that the corresponding histograms were of a normal distribution. A higher intelligent level was added to the model, based on neural networks, to extend the capabilities of the model to predict over a wide range of subjects dynamics. The elicited physiological model describing the effect of physiological stress on several physiological variables can be used to predict performance breakdown of operators in critical environments. Such a model architecture lends itself naturally to exploitation via feedback control in a 'reverse

  5. Modeling Open-Loop MEMS Tunneling Accelerometer Based on Circular Plate

    Directory of Open Access Journals (Sweden)

    Hossein Jodat Kordlar

    2007-04-01

    Full Text Available In this paper open-loop MEMS tunneling accelerometer was modeled based on a clamped micro circular plate with a tip tunneling at its centre. Mechanical behavior of the micro plate was studied deriving governing equation based on classic Kirchhoff thin plate theory and it was discretized using Galerkin method. Dynamic response of the proposed accelerometer due to step and harmonic external excitation was studied and the magnitude of the applied acceleration was identified by measuring of the changing of tunneling current. Obtained results show that the proposed tunneling accelerometer very sensitive and it can be measure acceleration with very high resolution but very small gap of tip tunneling limit the range of measurable acceleration.

  6. Numerical Modeling of an Integrated Vehicle Fluids System Loop for Pressurizing a Cryogenic Tank

    Science.gov (United States)

    LeClair, A. C.; Hedayat, A.; Majumdar, A. K.

    2017-01-01

    This paper presents a numerical model of the pressurization loop of the Integrated Vehicle Fluids (IVF) system using the Generalized Fluid System Simulation Program (GFSSP). The IVF propulsion system, being developed by United Launch Alliance to reduce system weight and enhance reliability, uses boiloff propellants to drive thrusters for the reaction control system as well as to run internal combustion engines to develop power and drive compressors to pressurize propellant tanks. NASA Marshall Space Flight Center (MSFC) conducted tests to verify the functioning of the IVF system using a flight-like tank. GFSSP, a finite volume based flow network analysis software developed at MSFC, has been used to support the test program. This paper presents the simulation of three different test series, comparison of numerical prediction and test data and a novel method of presenting data in a dimensionless form. The paper also presents a methodology of implementing a compressor map in a system level code.

  7. A genetic algorithm approach for solving a closed loop supply chain model

    DEFF Research Database (Denmark)

    Kannan, G.; Sasikumar, P.; Kannan, Devika

    2010-01-01

    in reverse logistics is to take back the used products, either under warranty or at the end of use or at the end of lease, so that the products or its parts are appropriately disposed, recycled, reused or remanufactured. In order to overcome this issue, it is necessary to setup a logistics network...... for arising goods flow from end users to manufacturers. In this study, the optimum usage of secondary lead recovered from the spent lead-acid batteries for producing new battery is presented. The disposal in surface or sewage water or land of liquid content of the lead-acid batteries is strictly restricted....... Because of the need for environmental protection and the lack of considerable lead resources, the spent batteries treatment and lead recovery are becoming crucial now-a-days. The objective of this paper is to develop a multi echelon, multi period, multi product closed loop supply chain network model...

  8. Evolution of the pion wave function in the scalar /phi/63 model: two-loop calculation

    International Nuclear Information System (INIS)

    Mikhailov, S.V.; Radyushkin, A.V.

    1986-01-01

    The authors study the structure of the contributions that violate the multiplicative renormalizability of the conformal operators in the model based on the /phi/ 6 3 theory in space-time of six dimensions. This theory has a number of features in common with QCD in four dimensions. The basic propositions are presented and the key elements of the calculation are demonstrated. The connection between the kernels for exclusive and inclusive processes are discused and the structure of the two-loop evolution kernel V(x,y) and the solution of the evolution equation are discussed. Main conclusions are formulated and the results of the calculations for concrete diagrams are deferred to in Appendix A. Formulas for the transition from the exclusive to the inclusive kernels are presented in Appendix B

  9. Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

    Science.gov (United States)

    Joo, Hyun; Chavan, Archana G; Day, Ryan; Lennox, Kristin P; Sukhanov, Paul; Dahl, David B; Vannucci, Marina; Tsai, Jerry

    2011-10-01

    Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

  10. Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

    Directory of Open Access Journals (Sweden)

    Hyun Joo

    2011-10-01

    Full Text Available Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM. Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å, this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

  11. Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

    Science.gov (United States)

    Day, Ryan; Lennox, Kristin P.; Sukhanov, Paul; Dahl, David B.; Vannucci, Marina; Tsai, Jerry

    2011-01-01

    Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/. PMID:22028638

  12. Homological stabilizer codes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Jonas T., E-mail: jonastyleranderson@gmail.com

    2013-03-15

    In this paper we define homological stabilizer codes on qubits which encompass codes such as Kitaev's toric code and the topological color codes. These codes are defined solely by the graphs they reside on. This feature allows us to use properties of topological graph theory to determine the graphs which are suitable as homological stabilizer codes. We then show that all toric codes are equivalent to homological stabilizer codes on 4-valent graphs. We show that the topological color codes and toric codes correspond to two distinct classes of graphs. We define the notion of label set equivalencies and show that under a small set of constraints the only homological stabilizer codes without local logical operators are equivalent to Kitaev's toric code or to the topological color codes. - Highlights: Black-Right-Pointing-Pointer We show that Kitaev's toric codes are equivalent to homological stabilizer codes on 4-valent graphs. Black-Right-Pointing-Pointer We show that toric codes and color codes correspond to homological stabilizer codes on distinct graphs. Black-Right-Pointing-Pointer We find and classify all 2D homological stabilizer codes. Black-Right-Pointing-Pointer We find optimal codes among the homological stabilizer codes.

  13. Enforced neutrality and color-flavor unlocking in the three-flavor Polyakov-loop Nambu-Jona-Lasinio model

    International Nuclear Information System (INIS)

    Abuki, H.; Ciminale, M.; Nardulli, G.; Ruggieri, M.; Gatto, R.

    2008-01-01

    We study how the charge neutrality affects the phase structure of the three-flavor Polyakov-loop Nambu-Jona-Lasinio (PNJL) model. We point out that, within the conventional PNJL model at finite density, the color neutrality is missing because the Wilson line serves as an external colored field coupled to dynamical quarks. In this paper we heuristically assume that the model may still be applicable. To get color neutrality, one has then to allow nonvanishing color chemical potentials. We study how the quark matter phase diagram in (T,m s 2 /μ)-plane is affected by imposing neutrality and by including the Polyakov-loop dynamics. Although these two effects are correlated in a nonlinear way, the impact of the Polyakov loop turns out to be significant in the T direction, while imposing neutrality brings a remarkable effect in the m s 2 /μ direction. In particular, we find a novel unlocking transition, when the temperature is increased, even in the chiral SU(3) limit. We clarify how and why this is possible once the dynamics of the colored Polyakov loop is taken into account. Also we succeed in giving an analytic expression for T c for the transition from two-flavor pairing (2SC) to unpaired quark matter in the presence of the Polyakov loop.

  14. A reduced fidelity model for the rotary chemical looping combustion reactor

    International Nuclear Information System (INIS)

    Iloeje, Chukwunwike O.; Zhao, Zhenlong; Ghoniem, Ahmed F.

    2017-01-01

    Highlights: • Methodology for developing a reduced fidelity rotary CLC reactor model is presented. • The reduced model determines optimal reactor configuration that meets design and operating requirements. • A 4-order of magnitude reduction in computational cost is achieved with good prediction accuracy. • Sensitivity studies demonstrate importance of accurate kinetic parameters for reactor optimization. - Abstract: The rotary chemical looping combustion reactor has great potential for efficient integration with CO_2 capture-enabled energy conversion systems. In earlier studies, we described a one-dimensional rotary reactor model, and used it to demonstrate the feasibility of continuous reactor operation. Though this detailed model provides a high resolution representation of the rotary reactor performance, it is too computationally expensive for studies that require multiple model evaluations. Specifically, it is not ideal for system-level studies where the reactor is a single component in an energy conversion system. In this study, we present a reduced fidelity model (RFM) of the rotary reactor that reduces computational cost and determines an optimal combination of variables that satisfy reactor design requirements. Simulation results for copper, nickel and iron-based oxygen carriers show a four-order of magnitude reduction in simulation time, and reasonable prediction accuracy. Deviations from the detailed reference model predictions range from 3% to 20%, depending on oxygen carrier type and operating conditions. This study also demonstrates how the reduced model can be modified to deal with both optimization and design oriented problems. A parametric study using the reduced model is then applied to analyze the sensitivity of the optimal reactor design to changes in selected operating and kinetic parameters. These studies show that temperature and activation energy have a greater impact on optimal geometry than parameters like pressure or feed fuel

  15. Enlarged symmetry algebras of spin chains, loop models, and S-matrices

    International Nuclear Information System (INIS)

    Read, N.; Saleur, H.

    2007-01-01

    The symmetry algebras of certain families of quantum spin chains are considered in detail. The simplest examples possess m states per site (m>=2), with nearest-neighbor interactions with U(m) symmetry, under which the sites transform alternately along the chain in the fundamental m and its conjugate representation m-bar. We find that these spin chains, even with arbitrary coefficients of these interactions, have a symmetry algebra A m much larger than U(m), which implies that the energy eigenstates fall into sectors that for open chains (i.e., free boundary conditions) can be labeled by j=0,1,...,L, for the 2L-site chain such that the degeneracies of all eigenvalues in the jth sector are generically the same and increase rapidly with j. For large j, these degeneracies are much larger than those that would be expected from the U(m) symmetry alone. The enlarged symmetry algebra A m (2L) consists of operators that commute in this space of states with the Temperley-Lieb algebra that is generated by the set of nearest-neighbor interaction terms; A m (2L) is not a Yangian. There are similar results for supersymmetric chains with gl(m+n|n) symmetry of nearest-neighbor interactions, and a richer representation structure for closed chains (i.e., periodic boundary conditions). The symmetries also apply to the loop models that can be obtained from the spin chains in a spacetime or transfer matrix picture. In the loop language, the symmetries arise because the loops cannot cross. We further define tensor products of representations (for the open chains) by joining chains end to end. The fusion rules for decomposing the tensor product of representations labeled j 1 and j 2 take the same form as the Clebsch-Gordan series for SU(2). This and other structures turn the symmetry algebra A m into a ribbon Hopf algebra, and we show that this is 'Morita equivalent' to the quantum group U q (sl 2 ) for m=q+q -1 . The open-chain results are extended to the cases vertical bar m vertical

  16. Order α'(two-loop) equivalence of the string equations of motion and the σ-model Weyl invariance conditions

    International Nuclear Information System (INIS)

    Metsaev, R.R.; Tseytlin, A.A.

    1987-01-01

    We prove the on-shell equivalence of the order α' terms in the string effective equations (for the graviton, dilaton and the antisymmetric tensor) to the vanishing of the corresponding (two-loop) terms in the Weyl anomaly coefficients for the general bosonic σ-model. We first determine the α' term in the string effective action starting with the known expression for the 3- and 4-point string amplitudes. Then we compute the two-loop β-function in the general σ-model with the antisymmetric tensor coupling. Special emphasis is made on the renormalization scheme dependence of the β-function. Our result disagrees with the previously known one and cannot be manifestly expressed in terms of the generalized curvature for the connection with torsion. We also prove (to the order α' 2 ) that the parallelizable spaces are solutions of the string equations of motion and establish the complete 3-loop expression for the 'central charge' coefficient. (orig.)

  17. Experimental tests for the Babu-Zee two-loop model of Majorana neutrino masses

    International Nuclear Information System (INIS)

    Sierra, Diego Aristizabal; Hirsch, Martin

    2006-01-01

    The smallness of the observed neutrino masses might have a radiative origin. Here we revisit a specific two-loop model of neutrino mass, independently proposed by Babu and Zee. We point out that current constraints from neutrino data can be used to derive strict lower limits on the branching ratio of flavour changing charged lepton decays, such as μ→eγ. Non-observation of Br(μ→eγ) at the level of 10 -13 would rule out singly charged scalar masses smaller than 590 GeV (5.04 TeV) in case of normal (inverse) neutrino mass hierarchy. Conversely, decay branching ratios of the non-standard scalars of the model can be fixed by the measured neutrino angles (and mass scale). Thus, if the scalars of the model are light enough to be produced at the LHC or ILC, measuring their decay properties would serve as a direct test of the model as the origin of neutrino masses

  18. Experimental tests for the Babu-Zee two-loop model of Majorana neutrino masses

    International Nuclear Information System (INIS)

    Aristizabal, D.

    2006-01-01

    Abstract: The smallness of the observed neutrino masses might have a radiative origin. Here we revisit a specific two-loop model of neutrino mass, independently proposed by Babu and Zee. We point out that current constraints from neutrino data can be used to derive strict lower limits on the branching ratio of flavour changing charged lepton decays, such as μ → e γ. Non-observation of Br(μ → e γ) at the level of 10 -13 would rule out singly charged scalar masses smaller than 590 GeV (5.04 TeV) in case of normal (inverse) neutrino mass hierarchy. Conversely, decay branching ratios of the non-standard scalars of the model can be fixed by the measured neutrino angles (and mass scale). Thus, if the scalars of the model are light enough to be produced at the LHC or ILC, measuring their decay properties would serve as a direct test of the model as the origin of neutrino masses. (author)

  19. Prefabrication of axial vascularized tissue engineering coral bone by an arteriovenous loop: a better model.

    Science.gov (United States)

    Dong, Qing-shan; Shang, Hong-tao; Wu, Wei; Chen, Fu-lin; Zhang, Jun-rui; Guo, Jia-ping; Mao, Tian-qiu

    2012-08-01

    The most important problem for the survival of thick 3-dimensional tissues is the lack of vascularization in the context of bone tissue engineering. In this study, a modified arteriovenous loop (AVL) was developed to prefabricate an axial vascularized tissue engineering coral bone in rabbit, with comparison of the arteriovenous bundle (AVB) model. An arteriovenous fistula between rabbit femoral artery and vein was anastomosed to form an AVL. It was placed in a circular side groove of the coral block. The complex was wrapped with an expanded-polytetrafluoroethylene membrane and implanted beneath inguinal skin. After 2, 4, 6 and 8 weeks, the degree of vascularization was evaluated by India ink perfusion, histological examination, vascular casts, and scanning electron microscopy images of vascular endangium. Newly formed fibrous tissues and vasculature extended over the surfaces and invaded the interspaces of entire coral block. The new blood vessels robustly sprouted from the AVL. Those invaginated cavities in the vascular endangium from scanning electron microscopy indicated vessel's sprouted pores. Above indexes in AVL model are all superior to that in AVB model, indicating that the modified AVL model could more effectively develop vascularization in larger tissue engineering bone. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. 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.

  1. Theoretical Modeling and Simulation of Phase-Locked Loop (PLL for Clock Data Recovery (CDR

    Directory of Open Access Journals (Sweden)

    Zainab Mohamad Ashari

    2012-01-01

    Full Text Available Modern communication and computer systems require rapid (Gbps, efficient  and large bandwidth data transfers. Agressive scaling of digital integrated systems  allow buses and communication controller circuits to be integrated with the microprocessor on the same chip. The  Peripheral Component Interconnect Express (PCIe protocol handles all communcation between the central processing unit (CPU and hardware devices. PCIe buses require efficient clock data recovery circuits (CDR to recover clock signals embedded in data during transmission. This paper describes the theoretical modeling and simulation of a phase-locked loop (PLL used in a CDR circuit. A simple PLL architecture for a 5 GHz CDR circuit is proposed  and elaborated in this work. Simulations were carried out using a Hardware Description Language, Verilog-AMS. The effect of jitter on the proposed design is also simulated and evaluated in this work. It was found that the proposed design is robust against both input and VCO jitter.ABSTRAK: Sistem komunikasi dan komputer moden memerlukan pemindahan data yang cekap (Gbps, dan bandwidth yang besar. Pengecilan agresif menggunakan teknik sistem digital bersepadu membenarkan bas dan litar pengawal komunikasi disatukan dengan  mikroprocessor dalam cip yang sama. Protokol persisian komponen sambung tara ekspres (PCIe mengendalikan semua komunikasi antara unit pemprosesan pusat (CPU dan peranti perkakasan. Bas PCIe memerlukan litar jam pemulihan data (CDR yang cekap untuk mendapatkan kembali isyarat jam yang tertanam dalam data semasa transmisi. Karya ini menerangkan teori pemodelan dan simulasi gelung fasa terkunci (PLL untuk CDR. Rekabentuk 5 GHz PLL yang mudah telah dicadangkan dalm kertas kerja ini. Simulasi telah dijalankan menggunakan perisian verilog-AMS. Simulasi mengunnakan kesan ketar dalam reka bentuk yang dicadangkan telah dinilai. Reka bentuk yang dicadangkan terbukti teguh mengatasi ganguan ketar di input dan VCO.KEY WORDS

  2. A differential equation approach to minor loops in the Jiles-Atherton hysteresis model

    International Nuclear Information System (INIS)

    Carpenter, K.H.

    1991-01-01

    Jiles and Atherton, in a series of papers, present physically based differential equations for magnetization in ferromagnetic materials. however, if one directly solves their differential equations, the minor loops obtained can be negative slopes, which is a nonphysical behavior. Only one of their papers gives a method for obtaining minor loops, and the method does not use a differential equation, but requires a priori knowledge of the loop turning points in order to obtain a scale factor and offset which allow a portion of a major loop to serve as a portion of a minor one. In this paper, the reason for the failure of the differential equations to yield physical minor loops is explained, and a modified solution for minor loops is presented which retains the features of Jiles and Atherton's original minor loops, but only requires knowledge of the initial point on each portion of the loop to obtain the solution. This yields a general differential equation formulation for the Jiles-Atherton theory that can be used with circuit simulations having arbitrary excitations and initial conditions for ferromagnetic components

  3. First step of the project for implementation of two non-symmetric cooling loops modeled by the ALMOD3 code

    International Nuclear Information System (INIS)

    Dominguez, L.; Camargo, C.T.M.

    1984-09-01

    The first step of the project for implementation of two non-symmetric cooling loops modeled by the ALMOD3 computer code is presented. This step consists of the introduction of a simplified model for simulating the steam generator. This model is the GEVAP computer code, integrant part of LOOP code, which simulates the primary coolant circuit of PWR nuclear power plants during transients. The ALMOD3 computer code has a model for the steam generator, called UTSG, which is very detailed. This model has spatial dependence, correlations for 2-phase flow, distinguished correlations for different heat transfer process. The GEVAP model has thermal equilibrium between phases (gaseous and liquid homogeneous mixture), no spatial dependence and uses only one generalized correlation to treat several heat transfer processes. (Author) [pt

  4. REFLECTION OF PROPAGATING SLOW MAGNETO-ACOUSTIC WAVES IN HOT CORONAL LOOPS: MULTI-INSTRUMENT OBSERVATIONS AND NUMERICAL MODELING

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, Sudip; Banerjee, Dipankar; Pant, Vaibhav [Indian Institute of Astrophysics, Koramangala, Bangalore 560034 (India); Yuan, Ding; Fang, Xia; Doorsselaere, Tom Van, E-mail: sudip@iiap.res.in, E-mail: xia.fang@wis.kuleuven.be [Centre for mathematical Plasma Astrophysics, Department of Mathematics, KU Leuven, Celestijnenlaan 200B, bus 2400, 3001, Leuven (Belgium)

    2016-09-10

    Slow MHD waves are important tools for understanding coronal structures and dynamics. In this paper, we report a number of observations from the X-Ray Telescope (XRT) on board HINODE and Solar Dynamic Observatory /Atmospheric Imaging Assembly (AIA) of reflecting longitudinal waves in hot coronal loops. To our knowledge, this is the first report of this kind as seen from the XRT and simultaneously with the AIA. The wave appears after a micro-flare occurs at one of the footpoints. We estimate the density and temperature of the loop plasma by performing differential emission measure (DEM) analysis on the AIA image sequence. The estimated speed of propagation is comparable to or lower than the local sound speed, suggesting it to be a propagating slow wave. The intensity perturbation amplitude, in every case, falls very rapidly as the perturbation moves along the loop and eventually vanishes after one or more reflections. To check the consistency of such reflection signatures with the obtained loop parameters, we perform a 2.5D MHD simulation, which uses the parameters obtained from our observation as inputs, and perform forward modeling to synthesize AIA 94 Å images. Analyzing the synthesized images, we obtain the same properties of the observables as for the real observation. From the analysis we conclude that a footpoint heating can generate a slow wave which then reflects back and forth in the coronal loop before fading. Our analysis of the simulated data shows that the main agent for this damping is anisotropic thermal conduction.

  5. Modeling of the Near Field Coupling Between an External Loop and an Implantable Spiral Chip Antennas in Biosensor Systems

    Science.gov (United States)

    Simons, Rainee N.; Miranda, Felix A.

    2006-01-01

    In this paper, the near field coupling between an external hand-held loop antenna and an implantable miniature (1x1 mm) printed square spiral chip antenna used in bio-MEMS sensors for contact-less powering and RF telemetry is investigated. The loop and the spiral are inductively coupled and effectively form a transformer. The numerical results include the quasi-stationary magnetic field pattern of the implanted antenna, near zone wave impedance as a function of the radial distance and the values of the lumped elements in the equivalent circuit model for the transformer.

  6. Hardware-in-the-Loop Modeling and Simulation Methods for Daylight Systems in Buildings

    Science.gov (United States)

    Mead, Alex Robert

    This dissertation introduces hardware-in-the-loop modeling and simulation techniques to the daylighting community, with specific application to complex fenestration systems. No such application of this class of techniques, optimally combining mathematical-modeling and physical-modeling experimentation, is known to the author previously in the literature. Daylighting systems in buildings have a large impact on both the energy usage of a building as well as the occupant experience within a space. As such, a renewed interest has been placed on designing and constructing buildings with an emphasis on daylighting in recent times as part of the "green movement.''. Within daylighting systems, a specific subclass of building envelope is receiving much attention: complex fenestration systems (CFSs). CFSs are unique as compared to regular fenestration systems (e.g. glazing) in the regard that they allow for non-specular transmission of daylight into a space. This non-specular nature can be leveraged by designers to "optimize'' the times of the day and the days of the year that daylight enters a space. Examples of CFSs include: Venetian blinds, woven fabric shades, and prismatic window coatings. In order to leverage the non-specular transmission properties of CFSs, however, engineering analysis techniques capable of faithfully representing the physics of these systems are needed. Traditionally, the analysis techniques available to the daylighting community fall broadly into three classes: simplified techniques, mathematical-modeling and simulation, and physical-modeling and experimentation. Simplified techniques use "rules-of-thumb'' heuristics to provide insights for simple daylighting systems. Mathematical-modeling and simulation use complex numerical models to provide more detailed insights into system performance. Finally, physical-models can be instrumented and excited using artificial and natural light sources to provide performance insight into a daylighting system

  7. Chapter 5: Modeling and Control of Three-Phase AC/DC Converter Including Phase-Locked Loop

    DEFF Research Database (Denmark)

    Zhou, Dao; Song, Yipeng; Blaabjerg, Frede

    2018-01-01

    In this chapter, a mathematical model of the power circuit of a three-phase AC/DC converter is developed in the stationary and synchronous reference frames. Then, the operation principle of the phasor locked loop is addressed to exact the angle information of the power grid to realize the accurat...

  8. MODELING OF THE HEAT PUMP STATION CONTROLABLE LOOP OF AN INTERMEDIATE HEAT-TRANSFER AGENT (Part II

    Directory of Open Access Journals (Sweden)

    Sit M.L.

    2011-08-01

    Full Text Available It is studied the model of the heat pump station controllable loop of an intermediate heat-transfer agent for the use in wineries. There are demonstrated transients after the disturbing action of the temperature on the input of cooling jacket of the fermentation stirred tank. There are compared different control laws of the object.

  9. Fermion loops in the effective potential of N = 1 supergravity, with application to no-scale models

    International Nuclear Information System (INIS)

    Burton, J.W.

    1990-01-01

    Powerful and quite general arguments suggest that N = 1 supergravity, and in particular the superstring-inspired no-scale models, may describe the physics of the four-dimensional vacuum at energy densities below the Planck scale. These models are not renormalizable, since they arise as effective theories after the large masses have been integrated out of the fundamental theory; thus, they have divergences in their loop amplitudes that must be regulated by imposing a cutoff. Before physics at experimental energies can be extracted from these models, the true vacuum state or states must be identified: at tree level, the ground states of the effective theories are highly degenerate. Radiative corrections at the one-loop level have been shown to break the degeneracy sufficiently to identify the states of vanishing vacuum energy. As the concluding step in a program to calculate these corrections within a self-consistent cutoff prescription, all fermionic one-loop divergent corrections to the scalar effective potential are evaluated. (The corresponding bosonic contributions have been found elsewhere.) The total effective scalar Lagrange density for N = 1 supergravity is written down, and comments are made about cancellations between the fermionic and bosonic loops. Finally, the result is specialized to a toy no-scale model with a single generation of matter fields, and prospects for eventual phenomenological constraints on theories of this type are briefly discussed. 48 refs

  10. Chemical looping reforming in packed-bed reactors : modelling, experimental validation and large-scale reactor design

    NARCIS (Netherlands)

    Spallina, V.; Marinello, B.; Gallucci, F.; Romano, M.C.; van Sint Annaland, M.

    This paper addresses the experimental demonstration and model validation of chemical looping reforming in dynamically operated packed-bed reactors for the production of H2 or CH3OH with integrated CO2 capture. This process is a combination of auto-thermal and steam methane reforming and is carried

  11. Hidden attractors in dynamical models of phase-locked loop circuits: Limitations of simulation in MATLAB and SPICE

    Science.gov (United States)

    Kuznetsov, N. V.; Leonov, G. A.; Yuldashev, M. V.; Yuldashev, R. V.

    2017-10-01

    During recent years it has been shown that hidden oscillations, whose basin of attraction does not overlap with small neighborhoods of equilibria, may significantly complicate simulation of dynamical models, lead to unreliable results and wrong conclusions, and cause serious damage in drilling systems, aircrafts control systems, electromechanical systems, and other applications. This article provides a survey of various phase-locked loop based circuits (used in satellite navigation systems, optical, and digital communication), where such difficulties take place in MATLAB and SPICE. Considered examples can be used for testing other phase-locked loop based circuits and simulation tools, and motivate the development and application of rigorous analytical methods for the global analysis of phase-locked loop based circuits.

  12. SIMULATION MODELLING OF VITÓRIA-MINAS CLOSED-LOOP RAIL NETWORK

    Directory of Open Access Journals (Sweden)

    Carlos Henrique Fernandes de FARIA

    2015-12-01

    Full Text Available This paper presents a closed loop simulation model that represents the mining logistics chain of the Vitória Minas Railway (VMR, Brazil. The simulator includes the loading process, circulation of loaded trains, unloading of ores for external and internal markets and the distribution of empty trains for new loads. General cargo and passengers trains are also included in the model, which, along with the queues formed in the circulation and the preventive and corrective maintenance of rolling stock, tracks and equipment, interfere with the transportation of iron ore. The primary objective of the iron ore transport is to meet the daily loading and unloading schedules and minimize queues by maximizing the operations at the loading and unloading points. The VMR simulator developed uses macro-mesoscopic approach with Monte Carlo simulation. To validate the simulator, we used actual data of the railway and compared with reality. We obtained a very good adhesion to the value of 2.9% for the validation scenario (Scenario 1 and 3.4% for the scenario with reducing the number of lots of wagons (Scenario 2. We concluded with this simulation that it is possible to reduce the number of GDE wagons without reducing the current level of productivity of the rail system.

  13. Reliability Measure Model for Assistive Care Loop Framework Using Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Venki Balasubramanian

    2010-01-01

    Full Text Available Body area wireless sensor networks (BAWSNs are time-critical systems that rely on the collective data of a group of sensor nodes. Reliable data received at the sink is based on the collective data provided by all the source sensor nodes and not on individual data. Unlike conventional reliability, the definition of retransmission is inapplicable in a BAWSN and would only lead to an elapsed data arrival that is not acceptable for time-critical application. Time-driven applications require high data reliability to maintain detection and responses. Hence, the transmission reliability for the BAWSN should be based on the critical time. In this paper, we develop a theoretical model to measure a BAWSN's transmission reliability, based on the critical time. The proposed model is evaluated through simulation and then compared with the experimental results conducted in our existing Active Care Loop Framework (ACLF. We further show the effect of the sink buffer in transmission reliability after a detailed study of various other co-existing parameters.

  14. Geometric homology revisited

    OpenAIRE

    Ruffino, Fabio Ferrari

    2013-01-01

    Given a cohomology theory, there is a well-known abstract way to define the dual homology theory using the theory of spectra. In [4] the author provides a more geometric construction of the homology theory, using a generalization of the bordism groups. Such a generalization involves in its definition the vector bundle modification, which is a particular case of the Gysin map. In this paper we provide a more natural variant of that construction, which replaces the vector bundle modification wi...

  15. Effects of design variables predicted by a steady - state thermal performance analysis model of a loop heat pipe

    International Nuclear Information System (INIS)

    Jung, Eui Guk; Boo, Joon Hong

    2008-01-01

    This study deals with a mathematical modeling for the steady-state temperature characteristics of an entire loop heat pipe. The lumped layer model was applied to each node for temperature analysis. The flat type evaporator and condenser in the model had planar dimensions of 40 mm (W) x 50 mm (L). The wick material was a sintered metal and the working fluid was methanol. The molecular kinetic theory was employed to model the phase change phenomena in the evaporator and the condenser. Liquid-vapor interface configuration was expressed by the thin film theories available in the literature. Effects of design factors of loop heat pipe on the thermal performance were investigated by the modeling proposed in this study

  16. Modeling and performance analysis of a closed-loop supply chain using first-order hybrid Petri nets

    Directory of Open Access Journals (Sweden)

    Imane Outmal

    2016-05-01

    Full Text Available Green or closed-loop supply chain had been the focus of many manufacturers during the last decade. The application of closed-loop supply chain in today’s manufacturing is not only due to growing environmental concerns and the recognition of its benefits in reducing greenhouse gas emissions, energy consumption, and meeting a more strict environmental regulations but it also offers economic competitive advantages if appropriately managed. First-order hybrid Petri nets represent a powerful graphical and mathematical formalism to map and analyze the dynamics of complex systems such as closed-loop supply chain networks. This article aims at illustrating the use of first-order hybrid Petri nets to model a closed-loop supply chain network and evaluate its operational, financial, and environmental performance measures under different management policies. Actual data from auto manufacturer in the United States are used to validate network’s performance under both tactical and strategic decision-making, namely, (1 tactical decision—production policies: increase of recovered versus new components and (2 strategic decision—closed-loop supply chain network structure: manufacturer internal recovery process or recovery process done by a third-party collection and recovery center. The work presented in this article is an extension of the use of first-order hybrid Petri nets as a modeling and performance analysis tool from supply chain to closed-loop supply chain. The modularity property of first-order hybrid Petri nets has been used in the modeling process, and the simulation and analysis of the modeled network are done in MATLAB® environment. The results of the experiments depict that first-order hybrid Petri nets are a powerful modeling and analysis formalism for closed-loop supply chain networks and can be further used as an efficient decision-making tool at both tactical and strategic levels. Unlike other researches on modeling supply chain

  17. Benchmarking of thermalhydraulic loop models for lead-alloy-cooled advanced nuclear energy systems. Phase I: Isothermal forced convection case

    International Nuclear Information System (INIS)

    2012-06-01

    Under the auspices of the NEA Nuclear Science Committee (NSC), the Working Party on Scientific Issues of the Fuel Cycle (WPFC) has been established to co-ordinate scientific activities regarding various existing and advanced nuclear fuel cycles, including advanced reactor systems, associated chemistry and flowsheets, development and performance of fuel and materials and accelerators and spallation targets. The WPFC has different expert groups to cover a wide range of scientific issues in the field of nuclear fuel cycle. The Task Force on Lead-Alloy-Cooled Advanced Nuclear Energy Systems (LACANES) was created in 2006 to study thermal-hydraulic characteristics of heavy liquid metal coolant loop. The objectives of the task force are to (1) validate thermal-hydraulic loop models for application to LACANES design analysis in participating organisations, by benchmarking with a set of well-characterised lead-alloy coolant loop test data, (2) establish guidelines for quantifying thermal-hydraulic modelling parameters related to friction and heat transfer by lead-alloy coolant and (3) identify specific issues, either in modelling and/or in loop testing, which need to be addressed via possible future work. Nine participants from seven different institutes participated in the first phase of the benchmark. This report provides details of the benchmark specifications, method and code characteristics and results of the preliminary study: pressure loss coefficient and Phase-I. A comparison and analysis of the results will be performed together with Phase-II

  18. One-loop radiative correction to the triple Higgs coupling in the Higgs singlet model

    Directory of Open Access Journals (Sweden)

    Shi-Ping He

    2017-01-01

    Full Text Available Though the 125 GeV Higgs boson is consistent with the standard model (SM prediction until now, the triple Higgs coupling can deviate from the SM value in the physics beyond the SM (BSM. In this paper, the radiative correction to the triple Higgs coupling is calculated in the minimal extension of the SM by adding a real gauge singlet scalar. In this model there are two scalars h and H and both of them are mixing states of the doublet and singlet. Provided that the mixing angle is set to be zero, namely the SM limit, h is the pure left-over of the doublet and its behavior is the same as that of the SM at the tree level. However the loop corrections can alter h-related couplings. In this SM limit case, the effect of the singlet H may show up in the h-related couplings, especially the triple h coupling. Our numerical results show that the deviation is sizable. For λΦS=1 (see text for the parameter definition, the deviation δhhh(1 can be 40%. For λΦS=1.5, the δhhh(1 can reach 140%. The sizable radiative correction is mainly caused by three reasons: the magnitude of the coupling λΦS, light mass of the additional scalar and the threshold enhancement. The radiative corrections for the hVV, hff couplings are from the counter-terms, which are the universal correction in this model and always at O(1%. The hZZ coupling, which can be precisely measured, may be a complementarity to the triple h coupling to search for the BSM. In the optimal case, the triple h coupling is very sensitive to the BSM physics, and this model can be tested at future high luminosity hadron colliders and electron–positron colliders.

  19. Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense.

    Science.gov (United States)

    Arya, Preeti; Acharya, Vishal

    2018-02-01

    STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.

  20. A novel heart rate control model provides insights linking LF-HRV behavior to the open-loop gain.

    Science.gov (United States)

    Dvir, Hila; Bobrovsky, Ben Zion; Gabbay, Uri

    2013-09-20

    Low-frequency heart rate variability (LF-HRV) at rest has already been successfully modeled as self-sustained oscillations in a nonlinear control loop, but these models fail to simulate LF-HRV decreases either during aerobic exercise or in heart failure patients. Following control engineering practices, we assume the existence of a biological excitation (dither) within the heart rate control loop that softens the nonlinearity and studied LF-HRV behavior in a dither-embedded model. We adopted the Ottesen model with some revisions and induced a dither of high-frequency stochastic perturbations. We simulated scenarios of a healthy subject at rest and during aerobic exercise (by decreasing peripheral vascular resistance) and a heart failure patient (by decreasing stroke volume). The simulations resembled physiological LF-HRV behavior, i.e., LF-HRV decreased during aerobic exercise and in the heart failure patient. The simulations exhibited LF-HRV dependency on the open-loop gain, which is related to the product of the feedback gain and the feed forward gain. We are the first to demonstrate that LF-HRV may be dependent on the open-loop gain. Accordingly, reduced open-loop gain results in decreased LF-HRV, and vice versa. Our findings explain a well-known but unexplained observed phenomenon of reduced LF-HRV both in heart failure patients and in healthy subjects performing aerobic exercise. These findings have implications on how changes in LF-HRV can be interpreted physiologically, a necessary step towards the clinical utilization of LF-HRV. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  1. Comparison of Two Foreign Body Retrieval Devices with Adjustable Loops in a Swine Model

    International Nuclear Information System (INIS)

    Konya, Andras

    2006-01-01

    The purpose of the study was to compare two similar foreign body retrieval devices, the Texan TM (TX) and the Texan LONGhorn TM (TX-LG), in a swine model. Both devices feature a ≤30-mm adjustable loop. Capture times and total procedure times for retrieving foreign bodies from the infrarenal aorta, inferior vena cava, and stomach were compared. All attempts with both devices (TX, n = 15; TX-LG, n = 14) were successful. Foreign bodies in the vasculature were captured quickly using both devices (mean ± SD, 88 ± 106 sec for TX vs 67 ± 42 sec for TX-LG) with no significant difference between them. The TX-LG, however, allowed significantly better capture times than the TX in the stomach (p = 0.022), Overall, capture times for the TX-LG were significantly better than for the TX (p = 0.029). There was no significant difference between the total procedure times in any anatomic region. TX-LG performed significantly better than the TX in the stomach and therefore overall. The better torque control and maneuverability of TX-LG resulted in better performance in large anatomic spaces

  2. PROPERTIES AND MODELING OF UNRESOLVED FINE STRUCTURE LOOPS OBSERVED IN THE SOLAR TRANSITION REGION BY IRIS

    Energy Technology Data Exchange (ETDEWEB)

    Brooks, David H. [College of Science, George Mason University, 4400 University Drive, Fairfax, VA 22030 (United States); Reep, Jeffrey W.; Warren, Harry P. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States)

    2016-08-01

    Recent observations from the Interface Region Imaging Spectrograph ( IRIS ) have discovered a new class of numerous low-lying dynamic loop structures, and it has been argued that they are the long-postulated unresolved fine structures (UFSs) that dominate the emission of the solar transition region. In this letter, we combine IRIS measurements of the properties of a sample of 108 UFSs (intensities, lengths, widths, lifetimes) with one-dimensional non-equilibrium ionization simulations, using the HYDRAD hydrodynamic model to examine whether the UFSs are now truly spatially resolved in the sense of being individual structures rather than being composed of multiple magnetic threads. We find that a simulation of an impulsively heated single strand can reproduce most of the observed properties, suggesting that the UFSs may be resolved, and the distribution of UFS widths implies that they are structured on a spatial scale of 133 km on average. Spatial scales of a few hundred kilometers appear to be typical for a range of chromospheric and coronal structures, and we conjecture that this could be an important clue for understanding the coronal heating process.

  3. A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loops.

    Directory of Open Access Journals (Sweden)

    Réka Albert

    2017-09-01

    several predictions of the model with regard to reactive oxygen species, cytosolic Ca2+ (Ca2+c, and heterotrimeric G-protein signaling. We analyzed dynamics-determining positive and negative feedback loops, thereby elucidating the attractor (dynamic behavior repertoire of the system and the groups of nodes that determine each attractor. Based on this analysis, we predict the likely presence of a previously unrecognized feedback mechanism dependent on Ca2+c. This mechanism would provide model agreement with 10 additional experimental observations, for a validation rate of 85%. Our research underscores the importance of feedback regulation in generating robust and adaptable biological responses. The high validation rate of our model illustrates the advantages of discrete dynamic modeling for complex, nonlinear systems common in biology.

  4. A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loops.

    Science.gov (United States)

    Albert, Réka; Acharya, Biswa R; Jeon, Byeong Wook; Zañudo, Jorge G T; Zhu, Mengmeng; Osman, Karim; Assmann, Sarah M

    2017-09-01

    of the model with regard to reactive oxygen species, cytosolic Ca2+ (Ca2+c), and heterotrimeric G-protein signaling. We analyzed dynamics-determining positive and negative feedback loops, thereby elucidating the attractor (dynamic behavior) repertoire of the system and the groups of nodes that determine each attractor. Based on this analysis, we predict the likely presence of a previously unrecognized feedback mechanism dependent on Ca2+c. This mechanism would provide model agreement with 10 additional experimental observations, for a validation rate of 85%. Our research underscores the importance of feedback regulation in generating robust and adaptable biological responses. The high validation rate of our model illustrates the advantages of discrete dynamic modeling for complex, nonlinear systems common in biology.

  5. Influence of the CVCS Modelling on Results of the Loss of Offsite Power (LOOP) Safety Analysis for NPP Krsko

    International Nuclear Information System (INIS)

    Bencik, V.; Bajs, T.; Debrecin, N.

    2006-01-01

    A Loss of Offsite Power (LOOP) transient scenario is based on a complete loss of non-emergency AC power that results in the loss of all power to the plant auxiliaries, i.e., the Reactor Coolant Pumps (RCPs), condensate pumps, etc. An actual LOOP event would cause a loss of all feedwater, a loss of forced Reactor Coolant System (RCS) flow and a reactor trip within less than 2 seconds as a result of either loss of power to the rod cluster assembly gripper coils or any RCS flow trips. For safety analysis purposes the LOOP event is conservatively modelled as a Loss of Normal Feedwater (LONF) transient with a subsequent loss of offsite power as a result of a reactor trip. The reactor trip followed by RCP trip are delayed until a low-low Steam Generator (SG) level signal is reached. This is a more conservative scenario than the LOOP event because the least amount of SG secondary side water mass available for heat removal and the increased amount of the stored energy in the primary circuit at the time of the loss of RCS flow result. The standard LOOP safety analysis is aimed to demonstrate the natural circulation capability of the RCS to remove residual and decay heat from the core aided by Auxiliary Feedwater in the secondary system. In addition to this goal the presented work is aimed to resolve the potential safety issue resulting from the influence of the Chemical and Volume Control System (CVCS) operation during LOOP event for NPP Krsko. The potential safety concern for the LOOP analysis is that the loss of instrument air system may occur thus leading to the CVCS charging and letdown flow imbalance. A net RCS inventory addition may result with water solid pressurizer condition. Water discharge through the pressurizer relief and safety valves could lead to overpressurization of the Pressurizer Relief Tank (PRT) and rupture of the PRT rupture disks. Additional concern is that pressurizer relief and safety valves may fail to properly reseat when exposed to water relief

  6. Cloning, expression, and homology modeling of GroEL protein from Leptospira interrogans serovar autumnalis strain N2.

    Science.gov (United States)

    Natarajaseenivasan, Kalimuthusamy; Shanmughapriya, Santhanam; Velineni, Sridhar; Artiushin, Sergey C; Timoney, John F

    2011-10-01

    Leptospirosis is an infectious bacterial disease caused by Leptospira species. In this study, we cloned and sequenced the gene encoding the immunodominant protein GroEL from L. interrogans serovar Autumnalis strain N2, which was isolated from the urine of a patient during an outbreak of leptospirosis in Chennai, India. This groEL gene encodes a protein of 60 kDa with a high degree of homology (99% similarity) to those of other leptospiral serovars. Recombinant GroEL was overexpressed in Escherichia coli. Immunoblot analysis indicated that the sera from confirmed leptospirosis patients showed strong reactivity with the recombinant GroEL while no reactivity was observed with the sera from seronegative control patient. In addition, the 3D structure of GroEL was constructed using chaperonin complex cpn60 from Thermus thermophilus as template and validated. The results indicated a Z-score of -8.35, which is in good agreement with the expected value for a protein. The superposition of the Ca traces of cpn60 structure and predicted structure of leptospiral GroEL indicates good agreement of secondary structure elements with an RMSD value of 1.5 Å. Further study is necessary to evaluate GroEL for serological diagnosis of leptospirosis and for its potential as a vaccine component. Copyright © 2011 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

  7. Modeling and Compensation Design for a Power Hardware-in-the-Loop Simulation of an AC Distribution System: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Prabakar, Kumaraguru [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Ainsworth, Nathan [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Pratt, Annabelle [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Baggu, Murali M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hariri, Ali [Formerly NREL

    2017-10-06

    Power hardware-in-the-loop (PHIL) simulation, where actual hardware under text is coupled with a real-time digital model in closed loop, is a powerful tool for analyzing new methods of control for emerging distributed power systems. However, without careful design and compensation of the interface between the simulated and actual systems, PHIL simulations may exhibit instability and modeling inaccuracies. This paper addresses issues that arise in the PHIL simulation of a hardware battery inverter interfaced with a simulated distribution feeder. Both the stability and accuracy issues are modeled and characterized, and a methodology for design of PHIL interface compensation to ensure stability and accuracy is presented. The stability and accuracy of the resulting compensated PHIL simulation is then shown by experiment.

  8. Model experiments on simulation of the WWER water-chemical conditions at loop facilities of the MIR reactor

    International Nuclear Information System (INIS)

    Benderskaya, O.S.; Zotov, E.A.; Kuprienko, V.A.; Ovchinnikov, V.A.

    1999-01-01

    The experiments on simulation of the WWER type reactors water-chemical conditions have been started at the State Scientific Center RIAR. These experiments are being conducted at the multi-loop research MIR reactor at the PVK-2 loop facility. The dosage stand was created. It allows introduction of boric acid, potassium and lithium hydroxides, ammonia solutions and gaseous hydrogen. Corrosion tests of the Russian E-635 and E-110 alloys are being conducted at the PVK-2 loop under the WWER water-chemical conditions. If necessary, fuel elements are periodically extracted from the reactor to perform visual examination, to measure their length, diameter, to remove the deposits from the claddings, to measure the burnup and to distribute the fission products over the fuel element by gamma-spectrometry. The chemical analytical 'on line' equipment produced by the ORBISPHERE Laboratory (Switzerland) will be commissioned in the nearest future to measure concentration of the dissolved hydrogen and oxygen as well as pH and specific conductivity. The objective of the report is to familiarize the participants of the IAEA Technical Committee with the capabilities of performing the model water-chemical experiments under the MIR reactor loop facility conditions. (author)

  9. Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment.

    Science.gov (United States)

    Capriles, Priscila V S Z; Guimarães, Ana C R; Otto, Thomas D; Miranda, Antonio B; Dardenne, Laurent E; Degrave, Wim M

    2010-10-29

    Trypanosoma cruzi is the etiological agent of Chagas' disease, an endemic infection that causes thousands of deaths every year in Latin America. Therapeutic options remain inefficient, demanding the search for new drugs and/or new molecular targets. Such efforts can focus on proteins that are specific to the parasite, but analogous enzymes and enzymes with a three-dimensional (3D) structure sufficiently different from the corresponding host proteins may represent equally interesting targets. In order to find these targets we used the workflows MHOLline and AnEnΠ obtaining 3D models from homologous, analogous and specific proteins of Trypanosoma cruzi versus Homo sapiens. We applied genome wide comparative modelling techniques to obtain 3D models for 3,286 predicted proteins of T. cruzi. In combination with comparative genome analysis to Homo sapiens, we were able to identify a subset of 397 enzyme sequences, of which 356 are homologous, 3 analogous and 38 specific to the parasite. In this work, we present a set of 397 enzyme models of T. cruzi that can constitute potential structure-based drug targets to be investigated for the development of new strategies to fight Chagas' disease. The strategies presented here support the concept of structural analysis in conjunction with protein functional analysis as an interesting computational methodology to detect potential targets for structure-based rational drug design. For example, 2,4-dienoyl-CoA reductase (EC 1.3.1.34) and triacylglycerol lipase (EC 3.1.1.3), classified as analogous proteins in relation to H. sapiens enzymes, were identified as new potential molecular targets.

  10. Internal and External Reconnection Series Homologous Solar Flares

    Science.gov (United States)

    Sterling, Alphonse C.; Moore, Ronald L.

    2001-01-01

    Using data from the extreme ultraviolet imaging telescope (EIT) on SOHO and the soft X-ray telescope (SXT) on Yohkoh, we examine a series of morphologically homologous solar flares occurring in National Oceanic and Atmospheric Administration (NOAA) active region 8210 over May 1-2, 1998. An emerging flux region (EFR) impacted against a sunspot to the west and next to a coronal hole to the east is the source of the repeated flaring. An SXT sigmoid parallels the EFR's neutral line at the site of the initial flaring in soft X rays. In EIT each flaring episode begins with the formation of a crinkle pattern external to the EFR. These EIT crinkles move out from, and then in toward, the EFR with velocities approx. 20 km/ s. A shrinking and expansion of the width of the coronal hole coincides with the crinkle activity, and generation and evolution of a postflare loop system begins near the time of crinkle formation. Using a schematic based on magnetograms of the region, we suggest that these observations are consistent with the standard reconnection-based model for solar eruptions but are modified by the presence of the additional magnetic fields of the sunspot and coronal hole. In the schematic, internal reconnection begins inside of the EFR-associated fields, unleashing a flare, postflare loops, and a coronal mass ejection (CME). External reconnection, first occurring between the escaping CME and the coronal hole field and second occurring between fields formed as a result of the first external reconnection, results in the EIT crinkles and changes in the coronal hole boundary. By the end of the second external reconnection, the initial setup is reinstated; thus the sequence can repeat, resulting in morphologically homologous eruptions. Our inferred magnetic topology is similar to that suggested in the "breakout model" of eruptions although we cannot determine if our eruptions are released primarily by the breakout mechanism (external reconnection) or, alternatively

  11. A computational model clarifies the roles of positive and negative feedback loops in the Drosophila circadian clock

    Energy Technology Data Exchange (ETDEWEB)

    Wang Junwei, E-mail: wangjunweilj@yahoo.com.c [Cisco School of Informatics, Guangdong University of Foreign Studies, Guangzhou 510006 (China); Zhou Tianshou [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China)

    2010-06-14

    Previous studies showed that a single negative feedback structure should be sufficient for robust circadian oscillations. It is thus pertinent to ask why current cellular clock models almost universally have interlocked negative feedback loop (NFL) and positive feedback loop (PFL). Here, we propose a molecular model that reflects the essential features of the Drosophila circadian clock to clarify the different roles of negative and positive feedback loops. In agreement with experimental observations, the model can simulate circadian oscillations in constant darkness, entrainment by light-dark cycles, as well as phenotypes of per{sup 01} and clk{sup Jrk} mutants. Moreover, sustained oscillations persist when the PFL is removed, implying the crucial role of NFL for rhythm generation. Through parameter sensitivity analysis, it is revealed that incorporation of PFL increases the robustness of the system to regulatory processes in PFL itself. Such reduced models can aid understanding of the design principles of circadian clocks in Drosophila and other organisms with complex transcriptional feedback structures.

  12. Process modelling and techno-economic analysis of natural gas combined cycle integrated with calcium looping

    Directory of Open Access Journals (Sweden)

    Erans María

    2016-01-01

    Full Text Available Calcium looping (CaL is promising for large-scale CO2 capture in the power generation and industrial sectors due to the cheap sorbent used and the relatively low energy penalties achieved with this process. Because of the high operating temperatures the heat utilisation is a major advantage of the process, since a significant amount of power can be generated from it. However, this increases its complexity and capital costs. Therefore, not only the energy efficiency performance is important for these cycles, but also the capital costs must be taken into account, i.e. techno-economic analyses are required in order to determine which parameters and configurations are optimal to enhance technology viability in different integration scenarios. In this study the integration scenarios of CaL cycles and natural gas combined cycles (NGCC are explored. The process models of the NGCC and CaL capture plant are developed to explore the most promising scenarios for NGCC-CaL integration with regards to efficiency penalties. Two scenarios are analysed in detail, and show that the system with heat recovery steam generator (HRSG before and after the capture plant exhibited better performance of 49.1% efficiency compared with that of 45.7% when only one HRSG is located after the capture plant. However, the techno-economic analyses showed that the more energy efficient case, with two HRSGs, implies relatively higher cost of electricity (COE, 44.1€/MWh, when compared to that of the reference plant system (33.1€/MWh. The predicted cost of CO2 avoided for the case with two HRSGS is 29.3 €/ton CO2.

  13. Study on the Operating Characteristics and System Modelling of Loop type Thermosyphon for Using Solar Thermal Energy

    International Nuclear Information System (INIS)

    Kang, Myeong Cheol

    1999-02-01

    Solar energy is one of the promising resources of renewable energy. It is of particular interest due to the energy shortage and environment pollution problems. Water heating by solar energy for domestic use is one of the most successful and feasible applications of solar energy. The thermosyphon SDHWS and the loop type thermosyphon systems are widely used for domestic hot water system. The loop type thermosyphon is a circulation device for transferring the heat produced at the evaporator area to the condenser area in the loop by a working fluid. The system has the advantage of high heat transfer rate. A phase change of the working fluid occurs at the evaporator section and the vapor is transported to the condenser by the density gradient. The loop type thermosyphon collector can be made of smaller area and has higher efficiency than the present thermosyphon SDHWS. In this study, the operating characteristics of various working fluids being used have been identified. The working fluids employed in the study were ethanol, water and a binary mixture of ethanol and water. The volume of working fluid used in this study were 30%, 40%, 50%, 60% and 70% of evaporator volume. An increased heat was applied with the increased volume of working fluid. It is observed that, in the thermosyphon with low volume of working fluid, such as 30% or 40%, the fluid was dried out. The average efficiency of the loop type thermosyphon was 46% with high solar irradiation and 43% with low irradiation. The flow pattern and mechanism of the heat transfer were identified through this study. Flow patterns of the binary mixture working fluid were also investigated, and the patterns were recorded in the camera. The system parameters were calculated using the thermal performance data. Modelling of the system was carried out using PSTAR method and TRNSYS program

  14. Two-loop O(ααs) corrections to the on-shell fermion propagator in the standard model

    International Nuclear Information System (INIS)

    Eiras, Dolors; Steinhauser, Matthias

    2006-01-01

    In this paper we consider mixed two-loop electroweak corrections to the top quark propagator in the Standard Model. In particular, we compute the on-shell renormalization constant for the mass and wave function, which constitute building blocks for many physical processes. The results are expressed in terms of master integrals. For the latter practical approximations are derived. In the case of the mass renormalization constant we find agreement with the results in the literature

  15. Validation of the generalized model of two-phase thermosyphon loop based on experimental measurements of volumetric flow rate

    Science.gov (United States)

    Bieliński, Henryk

    2016-09-01

    The current paper presents the experimental validation of the generalized model of the two-phase thermosyphon loop. The generalized model is based on mass, momentum, and energy balances in the evaporators, rising tube, condensers and the falling tube. The theoretical analysis and the experimental data have been obtained for a new designed variant. The variant refers to a thermosyphon loop with both minichannels and conventional tubes. The thermosyphon loop consists of an evaporator on the lower vertical section and a condenser on the upper vertical section. The one-dimensional homogeneous and separated two-phase flow models were used in calculations. The latest minichannel heat transfer correlations available in literature were applied. A numerical analysis of the volumetric flow rate in the steady-state has been done. The experiment was conducted on a specially designed test apparatus. Ultrapure water was used as a working fluid. The results show that the theoretical predictions are in good agreement with the measured volumetric flow rate at steady-state.

  16. Discovery of novel inhibitors of Mycobacterium tuberculosis MurG: homology modelling, structure based pharmacophore, molecular docking, and molecular dynamics simulations.

    Science.gov (United States)

    Saxena, Shalini; Abdullah, Maaged; Sriram, Dharmarajan; Guruprasad, Lalitha

    2017-10-17

    MurG (Rv2153c) is a key player in the biosynthesis of the peptidoglycan layer in Mycobacterium tuberculosis (Mtb). This work is an attempt to highlight the structural and functional relationship of Mtb MurG, the three-dimensional (3D) structure of protein was constructed by homology modelling using Discovery Studio 3.5 software. The quality and consistency of generated model was assessed by PROCHECK, ProSA and ERRAT. Later, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with substrate Uridine-diphosphate-N-acetylglucosamine (UD1) facilitated us to employ structure-based virtual screening approach to obtain new hits from Asinex database using energy-optimized pharmacophore modelling (e-pharmacophore). The pharmacophore model was validated using enrichment calculations, and finally, validated model was employed for high-throughput virtual screening and molecular docking to identify novel Mtb MurG inhibitors. This study led to the identification of 10 potential compounds with good fitness, docking score, which make important interactions with the protein active site. The 25 ns MD simulations of three potential lead compounds with protein confirmed that the structure was stable and make several non-bonding interactions with amino acids, such as Leu290, Met310 and Asn167. Hence, we concluded that the identified compounds may act as new leads for the design of Mtb MurG inhibitors.

  17. Validation of a homology model of Mycobacterium tuberculosis DXS: rationalization of observed activities of thiamine derivatives as potent inhibitors of two orthologues of DXS.

    Science.gov (United States)

    Masini, T; Lacy, B; Monjas, L; Hawksley, D; de Voogd, A R; Illarionov, B; Iqbal, A; Leeper, F J; Fischer, M; Kontoyianni, M; Hirsch, A K H

    2015-12-14

    The enzyme DXS catalyzes the first, rate-limiting step of the 2-C-methyl-d-erythritol-4-phosphate (MEP, 1) pathway using thiamine diphosphate (ThDP) as cofactor; the DXS-catalyzed reaction constitutes also the first step in vitamin B1 and B6 metabolism in bacteria. DXS is the least studied among the enzymes of this pathway in terms of crystallographic information, with only one complete crystal structure deposited in the Protein Data Bank (Deinococcus radiodurans DXS, PDB: ). We synthesized a series of thiamine and ThDP derivatives and tested them for their biochemical activity against two DXS orthologues, namely D. radiodurans DXS and Mycobacterium tuberculosis DXS. These experimental results, combined with advanced docking studies, led to the development and validation of a homology model of M. tuberculosis DXS, which, in turn, will guide medicinal chemists in rationally designing potential inhibitors for M. tuberculosis DXS.

  18. Multi-loop correlators for rational theories of 2D gravity from the generalized Kontsevich models

    DEFF Research Database (Denmark)

    Kristjansen, C.

    1994-01-01

    functions of the susceptibilities and the eigenvalues of the external field. We furthermore use the moment technique to derive a closed expression for the genus zero multi-loop correlators for $(3,3m-1)$ and $(3,3m-2)$ rational matter fields coupled to gravity. We comment on the relation between the two-matrix...

  19. Observation and Modeling of Chromospheric Evaporation in a Coronal Loop Related to Active Region Transient Brightening

    Science.gov (United States)

    Gupta, G. R.; Sarkar, Aveek; Tripathi, Durgesh

    2018-04-01

    Using the observations recorded by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory and the Interface Region Imaging Spectrograph (IRIS) and the Extreme-ultraviolet Imaging Spectrometer and X-Ray Telescope both on board Hinode, we present evidence of chromospheric evaporation in a coronal loop after the occurrence of two active region transient brightenings (ARTBs) at the two footpoints. The chromospheric evaporation started nearly simultaneously in all of the three hot channels of AIA 131, 94, and 335 Å and was observed to be temperature dependent, being fastest in the highest temperature channel. The whole loop became fully brightened following the ARTBs after ≈25 s in 131 Å, ≈40 s in 94 Å, and ≈6.5 minutes in 335 Å. The differential emission measurements at the two footpoints (i.e., of two ARTBs) and at the loop top suggest that the plasma attained a maximum temperature of ∼10 MK at all these locations. The spectroscopic observations from IRIS revealed the presence of redshifted emission of ∼20 km s‑1 in cooler lines like C II and Si IV during the ARTBs that was cotemporal with the evaporation flow at the footpoint of the loop. During the ARTBs, the line width of C II and Si IV increased nearly by a factor of two during the peak emission. Moreover, enhancement in the line width preceded that in the Doppler shift, which again preceded enhancement in the intensity. The observed results were qualitatively reproduced by 1D hydrodynamic simulations, where energy was deposited at both of the footpoints of a monolithic coronal loop that mimicked the ARTBs identified in the observations.

  20. GoSam-2.0. A tool for automated one-loop calculations within the Standard Model and beyond

    International Nuclear Information System (INIS)

    Cullen, Gavin; Deurzen, Hans van; Greiner, Nicolas

    2014-05-01

    We present the version 2.0 of the program package GoSam for the automated calculation of one-loop amplitudes. GoSam is devised to compute one-loop QCD and/or electroweak corrections to multi-particle processes within and beyond the Standard Model. The new code contains improvements in the generation and in the reduction of the amplitudes, performs better in computing time and numerical accuracy, and has an extended range of applicability. The extended version of the ''Binoth-Les-Houches-Accord'' interface to Monte Carlo programs is also implemented. We give a detailed description of installation and usage of the code, and illustrate the new features in dedicated examples.

  1. A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system.

    Science.gov (United States)

    D'Souza, Alicia D; Belotserkovskii, Boris P; Hanawalt, Philip C

    2018-02-01

    The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Rapid isolation of gene homologs across taxa: Efficient identification and isolation of gene orthologs from non-model organism genomes, a technical report

    Directory of Open Access Journals (Sweden)

    Heffer Alison

    2011-03-01

    Full Text Available Abstract Background Tremendous progress has been made in the field of evo-devo through comparisons of related genes from diverse taxa. While the vast number of species in nature precludes a complete analysis of the molecular evolution of even one single gene family, this would not be necessary to understand fundamental mechanisms underlying gene evolution if experiments could be designed to systematically sample representative points along the path of established phylogenies to trace changes in regulatory and coding gene sequence. This isolation of homologous genes from phylogenetically diverse, representative species can be challenging, especially if the gene is under weak selective pressure and evolving rapidly. Results Here we present an approach - Rapid Isolation of Gene Homologs across Taxa (RIGHT - to efficiently isolate specific members of gene families. RIGHT is based upon modification and a combination of degenerate polymerase chain reaction (PCR and gene-specific amplified fragment length polymorphism (AFLP. It allows targeted isolation of specific gene family members from any organism, only requiring genomic DNA. We describe this approach and how we used it to isolate members of several different gene families from diverse arthropods spanning millions of years of evolution. Conclusions RIGHT facilitates systematic isolation of one gene from large gene families. It allows for efficient gene isolation without whole genome sequencing, RNA extraction, or culturing of non-model organisms. RIGHT will be a generally useful method for isolation of orthologs from both distant and closely related species, increasing sample size and facilitating the tracking of molecular evolution of gene families and regulatory networks across the tree of life.

  3. A new deformation of W-infinity and applications to the two-loop WZNW and conformal affine Toda models

    International Nuclear Information System (INIS)

    Aratyn, H.; Ferreira, L.A.; Gomes, J.F.; Zimerman, A.H.

    1992-01-01

    We constructed a center less W-infinity type of algebra in terms of a generator of a center less Virasoro algebra and an Abelian spin-1 current. This algebra conventionally emerges in the study of pseudo-differential operators on a circle or alternatively within KP hierarchy with Watanabe's bracket. Construction used here is based on a special deformation of the algebra w ∞ of area preserving diffeomorphisms of a 2-manifold. We show that this deformation technique applies to the two-loop WZNW and conformal affine Toda models, establishing henceforth W ∞ invariance of these models. (author)

  4. One loop corrections to the lightest Higgs mass in the minimal η model with a heavy Z'

    International Nuclear Information System (INIS)

    Comelli, D.

    1992-06-01

    We have evaluated the one loop correction to the bound on the lightest Higgs mass valid in the minimal, E 6 based, supersymmetric η model in the presence of a 'heavy' Z', M z' ≥1 TeV. The dominant contribution from the fermion sfermion sector increases the 108 GeV tree level value by an amount that depends on the top mass in a way that is largely reminescent of minimal SUSY models. For M t ≤150 GeV, Msub(t tilde)=1 TeV, the 'light' Higgs mass is always ≤130 GeV. (orig.)

  5. Models for Master-Slave Clock Distribution Networks with Third-Order Phase-Locked Loops

    OpenAIRE

    Piqueira, José Roberto Castilho; de Carvalho Freschi, Marcela

    2007-01-01

    The purpose of this work is to study the processing and transmission of clock signals in networks of geographically distributed nodes, in order to derive conditions for frequency and phase synchronization between the nodes. The focus is on the master-slave architecture, which presents a priority scheme of clock distribution. One-way master-slave (OWMS ) and two-way master-slave (TWMS) chains are studied, considering that the slave nodes are third-order phase-locked loops...

  6. Diagnostics of electron-heated solar flare models. III - Effects of tapered loop geometry and preheating

    Science.gov (United States)

    Emslie, A. G.; Li, Peng; Mariska, John T.

    1992-01-01

    A series of hydrodynamic numerical simulations of nonthermal electron-heated solar flare atmospheres and their corresponding soft X-ray Ca XIX emission-line profiles, under the conditions of tapered flare loop geometry and/or a preheated atmosphere, is presented. The degree of tapering is parameterized by the magnetic mirror ratio, while the preheated atmosphere is parameterized by the initial upper chromospheric pressure. In a tapered flare loop, it is found that the upward motion of evaporated material is faster compared with the case where the flare loop is uniform. This is due to the diverging nozzle seen by the upflowing material. In the case where the flare atmosphere is preheated and the flare geometry is uniform, the response of the atmosphere to the electron collisional heating is slow. The upward velocity of the hydrodynamic gas is reduced due not only to the large coronal column depth, but also to the increased inertia of the overlying material. It is concluded that the only possible electron-heated scenario in which the predicted Ca XIX line profiles agree with the BCS observations is when the impulsive flare starts in a preheated dense corona.

  7. A RECONNECTION-DRIVEN MODEL OF THE HARD X-RAY LOOP-TOP SOURCE FROM FLARE 2004 FEBRUARY 26

    Energy Technology Data Exchange (ETDEWEB)

    Longcope, Dana; Qiu, Jiong; Brewer, Jasmine [Department of Physics, Montana State University, Bozeman, MT 59717 (United States)

    2016-12-20

    A compact X-class flare on 2004 February 26 showed a concentrated source of hard X-rays at the tops of the flare’s loops. This was analyzed in previous work and interpreted as plasma heated and compressed by slow magnetosonic shocks (SMSs) generated during post-reconnection retraction of the flux. That work used analytic expressions from a thin flux tube (TFT) model, which neglected many potentially important factors such as thermal conduction and chromospheric evaporation. Here we use a numerical solution of the TFT equations to produce a more comprehensive and accurate model of the same flare, including those effects previously omitted. These simulations corroborate the prior hypothesis that slow-mode shocks persist well after the retraction has ended, thus producing a compact, loop-top source instead of an elongated jet, as steady reconnection models predict. Thermal conduction leads to densities higher than analytic estimates had predicted, and evaporation enhances the density still higher, but at lower temperatures. X-ray light curves and spectra are synthesized by convolving the results from a single TFT simulation with the rate at which flux is reconnected, as measured through motion of flare ribbons, for example. These agree well with light curves observed by RHESSI and GOES and spectra from RHESSI . An image created from a superposition of TFT model runs resembles one produced from RHESSI observations. This suggests that the HXR loop-top source, at least the one observed in this flare, could be the result of SMSs produced in fast reconnection models like Petschek’s.

  8. One-loop analysis of the electroweak breaking in supersymmetric models and the fine-tuning problem

    CERN Document Server

    De Carlos, B

    1993-01-01

    We examine the electroweak breaking mechanism in the minimal supersymmetric standard model (MSSM) using the {\\em complete} one-loop effective potential $V_1$. First, we study what is the region of the whole MSSM parameter space (i.e. $M_{1/2},m_o,\\mu,...$) that leads to a succesful $SU(2)\\times U(1)$ breaking with an acceptable top quark mass. In doing this it is observed that all the one-loop corrections to $V_1$ (even the apparently small ones) must be taken into account in order to get reliable results. We find that the allowed region of parameters is considerably enhanced with respect to former "improved" tree level results. Next, we study the fine-tuning problem associated with the high sensitivity of $M_Z$ to $h_t$ (the top Yukawa coupling). Again, we find that this fine-tuning is appreciably smaller once the one-loop effects are considered than in previous tree level calculations. Finally, we explore the ambiguities and limitations of the ordinary criterion to estimate the degree of fine-tuning. As a r...

  9. Mouse model for Usher syndrome: linkage mapping suggests homology to Usher type I reported at human chromosome 11p15.

    OpenAIRE

    Heckenlively, J R; Chang, B; Erway, L C; Peng, C; Hawes, N L; Hageman, G S; Roderick, T H

    1995-01-01

    Usher syndrome is a group of diseases with autosomal recessive inheritance, congenital hearing loss, and the development of retinitis pigmentosa, a progressive retinal degeneration characterized by night blindness and visual field loss over several decades. The causes of Usher syndrome are unknown and no animal models have been available for study. Four human gene sites have been reported, suggesting at least four separate forms of Usher syndrome. We report a mouse model of type I Usher syndr...

  10. Four-loop divergences of the two-dimensional (1,1) supersymmetric non-linear sigma model with a Wess-Zumino-Witten term

    International Nuclear Information System (INIS)

    Deriglazov, A.A.; Ketov, S.V.

    1991-01-01

    The four-loop divergences of the (1,1) supersymmetric two-dimensional non-linear σ-model with a Wess-Zumino-Witten term are analyzed. All the four-loop 1/ε-divergences in the general case (and an overall coefficient at the total four-loop contribution to the β-function) are shown to be reducible to only structures proportional to ζ(3). We explicitly calculate non-derivative contributions to the four-loop β-function from logarithmically divergent graphs. As a by-product, we obtain the complete four-loop β-function for the supersymmetric Wess-Zumino-Witten model. We use the partial results for the general four-loop β-function to shed some light on the structure of the (α') 3 -corrections to the superstring effective-action with antisymmetric-tensor field coupling. An inconsistency of the supersymmetrical dimensional regularisation via dimensional reduction in the presence of torsion is discovered at four loops, unless the string interpretation for the σ-model is adopted. (orig.)

  11. Passive immunization with a polyclonal antiserum to the hemoglobin receptor of Haemophilus ducreyi confers protection against a homologous challenge in the experimental swine model of chancroid.

    Science.gov (United States)

    Leduc, Isabelle; Fusco, William G; Choudhary, Neelima; Routh, Patty A; Cholon, Deborah M; Hobbs, Marcia M; Almond, Glen W; Orndorff, Paul E; Elkins, Christopher

    2011-08-01

    Haemophilus ducreyi, the etiologic agent of chancroid, has an obligate requirement for heme. Heme is acquired by H. ducreyi from its human host via TonB-dependent transporters expressed at its bacterial surface. Of 3 TonB-dependent transporters encoded in the genome of H. ducreyi, only the hemoglobin receptor, HgbA, is required to establish infection during the early stages of the experimental human model of chancroid. Active immunization with a native preparation of HgbA (nHgbA) confers complete protection in the experimental swine model of chancroid, using either Freund's or monophosphoryl lipid A as adjuvants. To determine if transfer of anti-nHgbA serum is sufficient to confer protection, a passive immunization experiment using pooled nHgbA antiserum was conducted in the experimental swine model of chancroid. Pigs receiving this pooled nHgbA antiserum were protected from a homologous, but not a heterologous, challenge. Passively transferred polyclonal antibodies elicited to nHgbA bound the surface of H. ducreyi and partially blocked hemoglobin binding by nHgbA, but were not bactericidal. Taken together, these data suggest that the humoral immune response to the HgbA vaccine is protective against an H. ducreyi infection, possibly by preventing acquisition of the essential nutrient heme.

  12. Passive Immunization with a Polyclonal Antiserum to the Hemoglobin Receptor of Haemophilus ducreyi Confers Protection against a Homologous Challenge in the Experimental Swine Model of Chancroid▿

    Science.gov (United States)

    Leduc, Isabelle; Fusco, William G.; Choudhary, Neelima; Routh, Patty A.; Cholon, Deborah M.; Hobbs, Marcia M.; Almond, Glen W.; Orndorff, Paul E.; Elkins, Christopher

    2011-01-01

    Haemophilus ducreyi, the etiologic agent of chancroid, has an obligate requirement for heme. Heme is acquired by H. ducreyi from its human host via TonB-dependent transporters expressed at its bacterial surface. Of 3 TonB-dependent transporters encoded in the genome of H. ducreyi, only the hemoglobin receptor, HgbA, is required to establish infection during the early stages of the experimental human model of chancroid. Active immunization with a native preparation of HgbA (nHgbA) confers complete protection in the experimental swine model of chancroid, using either Freund's or monophosphoryl lipid A as adjuvants. To determine if transfer of anti-nHgbA serum is sufficient to confer protection, a passive immunization experiment using pooled nHgbA antiserum was conducted in the experimental swine model of chancroid. Pigs receiving this pooled nHgbA antiserum were protected from a homologous, but not a heterologous, challenge. Passively transferred polyclonal antibodies elicited to nHgbA bound the surface of H. ducreyi and partially blocked hemoglobin binding by nHgbA, but were not bactericidal. Taken together, these data suggest that the humoral immune response to the HgbA vaccine is protective against an H. ducreyi infection, possibly by preventing acquisition of the essential nutrient heme. PMID:21646451

  13. Neutron transport in irradiation loops (IRENE loop)

    International Nuclear Information System (INIS)

    Sarsam, Maher.

    1980-09-01

    This thesis is composed of two parts with different aspects. Part one is a technical description of the loop and its main ancillary facilities as well as of the safety and operational regulations. The measurement methods on the model of the ISIS reactor and on the loop in the OSIRIS reactor are described. Part two deals with the possibility of calculating the powers dissipated by each rod of the fuel cluster, using appropriate computer codes, not only in the reflector but also in the core and to suggest a method of calculation [fr

  14. Heat transfer modelling in the vertical tubes of a natural circulation passive containment loop with noncondensable gas

    International Nuclear Information System (INIS)

    Herranz, L.E.; Munoz-Cobo, J.L.; Tachenko, I.; Sancho, J.; Escriva, A.; Verdu, G.

    1994-01-01

    One of the key safety systems of the Simplified Boiling Water Reactor (SBWR) of General Electric is the Passive Containment Cooling System (PCCS). This system is designed to behave as a heat sink without need of operator actions in case of a reactor accident. Such a function relies on setting up a natural circulation loop between drywell and wetwell. Along this loop heat is removed by condensing the steam coming from the drywell onto the inner surface of externally cooled vertical tubes. Therefore, a successful design of the condenser requires a good knowledge of the local heat transmission coefficients. In this paper a model of steam condensation into vertical tubes is presented. Based on a modified diffusion boundary layer approach for noncondensables, this model accounts for the effect of shear stress caused by the cocurrent steam-gas mixture on the liquid film thickness. An approximate method to calculate film thickness, avoiding iterative algorithms, has been proposed. At present, this model has been implemented in HTCPIPE code and its results are being checked in terms of local heat transfer coefficients against the experimental data available. A good agreement between measurements and predictions is being observed for tests at atmospheric pressure. Further development and validation of the model is needed to consider aspects such as mist formation, wavy flow and high pressure. (author)

  15. On a family of (1+1)-dimensional scalar field theory models: Kinks, stability, one-loop mass shifts

    Energy Technology Data Exchange (ETDEWEB)

    Alonso-Izquierdo, A., E-mail: alonsoiz@usal.es [Departamento de Matematica Aplicada and IUFFyM, Universidad de Salamanca (Spain); Mateos Guilarte, J. [Departamento de Fisica Fundamental and IUFFyM, Universidad de Salamanca (Spain)

    2012-09-15

    In this paper we construct a one-parametric family of (1+1)-dimensional one-component scalar field theory models supporting kinks. Inspired by the sine-Gordon and {phi}{sup 4} models, we look at all possible extensions such that the kink second-order fluctuation operators are Schroedinger differential operators with Poeschl-Teller potential wells. In this situation, the associated spectral problem is solvable and therefore we shall succeed in analyzing the kink stability completely and in computing the one-loop quantum correction to the kink mass exactly. When the parameter is a natural number, the family becomes the hierarchy for which the potential wells are reflectionless, the two first levels of the hierarchy being the sine-Gordon and {phi}{sup 4} models. - Highlights: Black-Right-Pointing-Pointer We construct a family of scalar field theory models supporting kinks. Black-Right-Pointing-Pointer The second-order kink fluctuation operators involve Poeschl-Teller potential wells. Black-Right-Pointing-Pointer We compute the one-loop quantum correction to the kink mass with different methods.

  16. Reduction of the N-component scalar model at the two-loop level

    International Nuclear Information System (INIS)

    Jakovac, A.

    1996-01-01

    Dimensional reduction of high temperature field theories improves IR features of their perturbative treatment. A crucial question is the following: What three-dimensional theory is representing the full system the most faithful way? A careful investigation of the induced three-dimensional counterterm structure of the finite temperature 4D O(N) symmetric scalar theory at the two-loop level leads to proposing the presence of nonlocal operators in the effective theory. A three-dimensional matching process is applied for the construction of the optimal local, superrenormalizable approximation. copyright 1996 The American Physical Society

  17. Structural characterization of respiratory syncytial virus fusion inhibitor escape mutants: homology model of the F protein and a syncytium formation assay

    International Nuclear Information System (INIS)

    Morton, Craig J.; Cameron, Rachel; Lawrence, Lynne J.; Lin Bo; Lowe, Melinda; Luttick, Angela; Mason, Anthony; McKimm-Breschkin, Jenny; Parker, Michael W.; Ryan, Jane; Smout, Michael; Sullivan, Jayne; Tucker, Simon P.; Young, Paul R.

    2003-01-01

    Respiratory syncytial virus (RSV) is a ubiquitous human pathogen and the leading cause of lower respiratory tract infections in infants. Infection of cells and subsequent formation of syncytia occur through membrane fusion mediated by the RSV fusion protein (RSV-F). A novel in vitro assay of recombinant RSV-F function has been devised and used to characterize a number of escape mutants for three known inhibitors of RSV-F that have been isolated. Homology modeling of the RSV-F structure has been carried out on the basis of a chimera derived from the crystal structures of the RSV-F core and a fragment from the orthologous fusion protein from Newcastle disease virus (NDV). The structure correlates well with the appearance of RSV-F in electron micrographs, and the residues identified as contributing to specific binding sites for several monoclonal antibodies are arranged in appropriate solvent-accessible clusters. The positions of the characterized resistance mutants in the model structure identify two promising regions for the design of fusion inhibitors

  18. Homology modeling and docking analyses of M. leprae Mur ligases reveals the common binding residues for structure based drug designing to eradicate leprosy.

    Science.gov (United States)

    Shanmugam, Anusuya; Natarajan, Jeyakumar

    2012-06-01

    Multi drug resistance capacity for Mycobacterium leprae (MDR-Mle) demands the profound need for developing new anti-leprosy drugs. Since most of the drugs target a single enzyme, mutation in the active site renders the antibiotic ineffective. However, structural and mechanistic information on essential bacterial enzymes in a pathway could lead to the development of antibiotics that targets multiple enzymes. Peptidoglycan is an important component of the cell wall of M. leprae. The biosynthesis of bacterial peptidoglycan represents important targets for the development of new antibacterial drugs. Biosynthesis of peptidoglycan is a multi-step process that involves four key Mur ligase enzymes: MurC (EC:6.3.2.8), MurD (EC:6.3.2.9), MurE (EC:6.3.2.13) and MurF (EC:6.3.2.10). Hence in our work, we modeled the three-dimensional structure of the above Mur ligases using homology modeling method and analyzed its common binding features. The residues playing an important role in the catalytic activity of each of the Mur enzymes were predicted by docking these Mur ligases with their substrates and ATP. The conserved sequence motifs significant for ATP binding were predicted as the probable residues for structure based drug designing. Overall, the study was successful in listing significant and common binding residues of Mur enzymes in peptidoglycan pathway for multi targeted therapy.

  19. Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

    KAUST Repository

    Maadooliat, Mehdi

    2015-10-21

    This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

  20. Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

    KAUST Repository

    Maadooliat, Mehdi; Zhou, Lan; Najibi, Seyed Morteza; Gao, Xin; Huang, Jianhua Z.

    2015-01-01

    This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

  1. SUSY non-Abelian gauge models: exact beta function from one loop of perturbation theory

    International Nuclear Information System (INIS)

    Shifman, M.A.; Vajnshtejn, A.I.; Zakharov, V.I.

    1985-01-01

    The method for calculating the exact β function (to all orders in the coupling constant) proposed earlier in supersymmetric electrodynamics is extended. The starting point is the observation that the low-energy effective action is exhausted by one loop provided that the theory is regularized supersymmetrically both in the ultraviolet and infrared domains in four dimensions. The Pouli-Villars method of the ultraviolet regularization is used. Two methods for the infrared regularization are considered. The first one - quantization in a box with a finite volume L 3 - is universally applicable to anygauge theory. The second method is based on the effective Higgs mechanism for mass generation and requires the presence of certain matter superfields in the lagrangian. Within this method the necessary condition is the existence of flat directions, so called valeys, along which the vacuum energy vanishes. The theory is quantized near epsilon non-vanishing value of the scalar field from the bottom of the valley. After calculating the one-loop effective action one and the same exact expression is obtained for the β function within the both approaches, and it also coincides with our earlier result extracted from instanton calculus. A few remarks on the problem of anomalies in SUSY gauge theories are presented

  2. A Closed-Loop Model of Operator Visual Attention, Situation Awareness, and Performance Across Automation Mode Transitions.

    Science.gov (United States)

    Johnson, Aaron W; Duda, Kevin R; Sheridan, Thomas B; Oman, Charles M

    2017-03-01

    This article describes a closed-loop, integrated human-vehicle model designed to help understand the underlying cognitive processes that influenced changes in subject visual attention, mental workload, and situation awareness across control mode transitions in a simulated human-in-the-loop lunar landing experiment. Control mode transitions from autopilot to manual flight may cause total attentional demands to exceed operator capacity. Attentional resources must be reallocated and reprioritized, which can increase the average uncertainty in the operator's estimates of low-priority system states. We define this increase in uncertainty as a reduction in situation awareness. We present a model built upon the optimal control model for state estimation, the crossover model for manual control, and the SEEV (salience, effort, expectancy, value) model for visual attention. We modify the SEEV attention executive to direct visual attention based, in part, on the uncertainty in the operator's estimates of system states. The model was validated using the simulated lunar landing experimental data, demonstrating an average difference in the percentage of attention ≤3.6% for all simulator instruments. The model's predictions of mental workload and situation awareness, measured by task performance and system state uncertainty, also mimicked the experimental data. Our model supports the hypothesis that visual attention is influenced by the uncertainty in system state estimates. Conceptualizing situation awareness around the metric of system state uncertainty is a valuable way for system designers to understand and predict how reallocations in the operator's visual attention during control mode transitions can produce reallocations in situation awareness of certain states.

  3. Analysis of Mesh Distribution Systems Considering Load Models and Load Growth Impact with Loops on System Performance

    Science.gov (United States)

    Kumar Sharma, A.; Murty, V. V. S. N.

    2014-12-01

    The distribution system is the final link between bulk power system and consumer end. A distinctive load flow solution method is used for analysis of the load flow of radial and weakly meshed network based on Kirchhoff's Current Law (KCL) and KVL. This method has excellent convergence characteristics for both radial as well as weakly meshed structure and is based on bus injection to branch current and branch-current to bus-voltage matrix. The main contribution of the paper is: (i) an analysis has been carried out for a weekly mesh network considering number of loops addition and its impact on the losses, kW and kVAr requirements from a system, and voltage profile, (ii) different load models, realistic ZIP load model and load growth impact on losses, voltage profile, kVA and kVAr requirements, (iii) impact of addition of loops on losses, voltage profile, kVA and kVAr requirements from substation, and (iv) comparison of system performance with radial distribution system. Voltage stability is a major concern in planning and operation of power systems. This paper also includes identifying the closeness critical bus which is the most sensitive to the voltage collapse in radial distribution networks. Node having minimum value of voltage stability index is the most sensitive node. Voltage stability index values are computed for meshed network with number of loops added in the system. The results have been obtained for IEEE 33 and 69 bus test system. The results have also been obtained for radial distribution system for comparison.

  4. Predictive models of circulating fluidized bed combustors: SO{sub 2} sorption in the CFB loop. Fourteenth technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    Gidaspow, D.; Therdthianwong, A. [Illinois Inst. of Tech., Chicago, IL (United States). Dept. of Chemical Engineering

    1993-02-01

    The overall objective of this investigation is to develop experimentally verified models for circulating fluidized bed (CFB) combustors. Sorption of S0{sub 2} with calcined limestone was studied in a PYROFLOW type CFB loop at conditions approximating those found in a CFB combustor. Initially the CFB loop contained 150 micron CaO particles of a density of 3.3 g/cm{sup 3} and air at 1143{degrees}K and 3.25 atm. Atzero time, air containing 600 ppm SO{sub 2}, was introduced into the riser bottom at 1143{degrees}K. The effect of gas velocity, sorbent inventory and inlet pressure on the sorption of SO{sub 2}, were studied isothermally by running our hydrodynamic code with the S0{sub 2} sorption conservation of species equation. At a velocity of 5m/sec., reported to be a typical velocity by PYROPOWER, there is reasonably good S0{sub 2} removal. At 10 m/sec the S0{sub 2} removal is poor. The best SO{sub 2}, removal is for a velocity of 5 m/s and a high bed inventory, initial bed height, H = 9m. Most of the S0{sub 2} is removed in the first two meters of the reactor. However, the S0{sub 2} removal is not complete at the bed outlet. This is due to mixing. At the left wall of the reactor (wall opposite the solids inlet) the S0{sub 2} removal was poor due to gas bypassing caused by the asymmetrical solids inlet. Simulation of the PYROPOWER loop with a symmetrical inlet gave us an order of magnitude improvement over the conventional PYROPOWER system. These results demonstrate the practical utility of the predictive model that we have developed over the last three years.

  5. Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.

    Directory of Open Access Journals (Sweden)

    Zheng-Yu Jiang

    Full Text Available Degradation of certain proteins through the ubiquitin-proteasome pathway is a common strategy taken by the key modulators responsible for stress responses. Kelch-like ECH-associated protein-1(Keap1, a substrate adaptor component of the Cullin3 (Cul3-based ubiquitin E3 ligase complex, mediates the ubiquitination of two key modulators, NF-E2-related factor 2 (Nrf2 and IκB kinase β (IKKβ, which are involved in the redox control of gene transcription. However, compared to the Keap1-Nrf2 protein-protein interaction (PPI, the intermolecular recognition mechanism of Keap1 and IKKβ has been poorly investigated. In order to explore the binding pattern between Keap1 and IKKβ, the PPI model of Keap1 and IKKβ was investigated. The structure of human IKKβ was constructed by means of the homology modeling method and using reported crystal structure of Xenopus laevis IKKβ as the template. A protein-protein docking method was applied to develop the Keap1-IKKβ complex model. After the refinement and visual analysis of docked proteins, the chosen pose was further optimized through molecular dynamics simulations. The resulting structure was utilized to conduct the virtual alanine mutation for the exploration of hot-spots significant for the intermolecular interaction. Overall, our results provided structural insights into the PPI model of Keap1-IKKβ and suggest that the substrate specificity of Keap1 depend on the interaction with the key tyrosines, namely Tyr525, Tyr574 and Tyr334. The study presented in the current project may be useful to design molecules that selectively modulate Keap1. The selective recognition mechanism of Keap1 with IKKβ or Nrf2 will be helpful to further know the crosstalk between NF-κB and Nrf2 signaling.

  6. Persistent homology and string vacua

    Energy Technology Data Exchange (ETDEWEB)

    Cirafici, Michele [Center for Mathematical Analysis, Geometry and Dynamical Systems,Instituto Superior Técnico, Universidade de Lisboa,Av. Rovisco Pais, 1049-001 Lisboa (Portugal); Institut des Hautes Études Scientifiques,Le Bois-Marie, 35 route de Chartres, F-91440 Bures-sur-Yvette (France)

    2016-03-08

    We use methods from topological data analysis to study the topological features of certain distributions of string vacua. Topological data analysis is a multi-scale approach used to analyze the topological features of a dataset by identifying which homological characteristics persist over a long range of scales. We apply these techniques in several contexts. We analyze N=2 vacua by focusing on certain distributions of Calabi-Yau varieties and Landau-Ginzburg models. We then turn to flux compactifications and discuss how we can use topological data analysis to extract physical information. Finally we apply these techniques to certain phenomenologically realistic heterotic models. We discuss the possibility of characterizing string vacua using the topological properties of their distributions.

  7. Structure-function relationship of a plant NCS1 member - Homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from arabidopsis

    KAUST Repository

    Witz, Sandra

    2014-03-12

    Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. 2014 Witz et al.

  8. Analysis of Multi-Loop Control Structures of Dividing-Wall Distillation Columns Using a Fundamental Model

    Directory of Open Access Journals (Sweden)

    Salvador Tututi-Avila

    2014-02-01

    Full Text Available Dividing-wall columns (DWCs have significant potential as energy-efficient processes for the separation of multicomponent mixtures. However, in addition to an efficient steady state design, dynamics and control also play a major part for the success of a technology. This is especially so for complex distillation systems. This paper investigates the dynamics of a dividing wall column used for the separation of ternary mixtures. A detailed dynamic first principles-based model of the column I s developed in gPROMS. The model is used to generate data used for control loop pairing via the Relative Gain Array (RGA, and controller parameters are found by using Internal Model Control (IMC tuning. The best control structures for DWC systems, involving four different ternary mixtures, and two different feed compositions for each mixture, are investigated.

  9. Operating cycle resolved modelling and hardware-in-the-loop-simulation of diesel engines of automobiles with turbocharging; Arbeitsspielaufgeloeste Modellbildung und Hardware-in-the-Loop-Simulation von Pkw-Dieselmotoren mit Abgasturboaufladung

    Energy Technology Data Exchange (ETDEWEB)

    Zahn, Sebastian

    2012-11-01

    Model-based and simulation-based approaches increasingly are used in the process of software development and function development for automobile control devices in order to reduce the development time as well as to save test-stand trials. The author of the contribution under consideration reports on the design of a dynamic model of a diesel engine for the hardware-in-the-loop test environment. The development, the test and pre-application of modern engine control units of automobiles with a cylinder-based combustion control is in the focus of the model application. The developed real-time model of the engine consists of a air pathway model, an exhaust gas pathway model, a VTG turbocharger model, a model of the cylinder group as well as an emission model. The parametrization of the engine model requires a continuous setting method. The model is validated by means of stationary and dynamic measured data of the engine test stand.

  10. The stomatogastric nervous system as a model for studying sensorimotor interactions in real-time closed-loop conditions

    Directory of Open Access Journals (Sweden)

    Nelly eDaur

    2012-03-01

    Full Text Available The perception of proprioceptive signals that report the internal state of the body is one of the essential tasks of the nervous system and helps to continuously adapt body movements to changing circumstances. Despite the impact of proprioceptive feedback on motor activity it has rarely been studied in conditions in which motor output and sensory activity interact as they do in behaving animals, i.e. in closed-loop conditions. The interaction of motor and sensory activities, however, can create emergent properties that may govern the functional characteristics of the system. We here demonstrate the use of a well-characterized model system for central pattern generation, the stomatogastric nervous system, for studying these properties in vitro. We created a real-time computer model of a single-cell muscle tendon organ in the gastric mill of the crab foregut that uses intracellular current injections to control the activity of the biological proprioceptor. The resulting motor output of a gastric mill motor neuron is then recorded intracellularly and fed into a simple muscle model consisting of a series of low-pass filters. The muscle output is used to activate a one-dimensional Hodgkin-Huxley type model of the muscle tendon organ in real-time, allowing closed-loop conditions. Model properties were either hand-tuned to achieve the best match with data from semi-intact muscle preparations, or an exhaustive search was performed to determine the best set of parameters. We report the real-time capabilities of our models, its performance and its interaction with the biological motor system.

  11. Modelling and hardware-in-the-loop simulation of the blowout tract components for passenger compartment air conditioning of motor vehicles; Modellierung und Hardware-in-the-Loop-Simulation der Komponenten des Ausblastraktes zur Kraftfahrzeuginnenraumklimatisierung

    Energy Technology Data Exchange (ETDEWEB)

    Michalek, David

    2009-07-01

    The author investigated the modelling and hardware-in-the-loop simulation of components of the blowout tract of motor car air conditioning systems. The control systems and air conditioning systems are gone into, from the air entering the car to the control systems and sensors for monitoring state variables. The function of the control equipment hardware and software was to be analyzed reproducibly in order to save time and cost. The models were verified using available data. Validation criteria were established for the hardware-in-the-loop simulator. On the basis of selected operating conditions, the performance of the air conditioning control unit inside the vehicle was compared with the simulation results and was evaluated on the basis of the established criteria. (orig.)

  12. Analysis of ultraviolet and X-ray observations of three homologous solar flares from SMM

    Science.gov (United States)

    Cheng, Chung-Chieh; Pallavicini, Roberto

    1987-01-01

    Three homologous flares observed in the UV lines of Fe XXI and O V and in X-rays from the SMM were studied. It was found that: (1) the homology of the flares was most noticeable in Fe XXI and soft X-ray emissions; (2) the three flares shared many of the same loop footprints which were located in O V bright kernals associated with hard X-ray bursts; and (3) in spite of the strong spatial homology, the temporal evolution in UV and X-ray emissions varied from flare to flare. A comparison between the UV observations and photospheric magnetograms revealed that the basic flare configuration was a complex loop system consisting of many loops or bundles of loops.

  13. Thermosyphoning analysis with the CATHENA model of the blanket and first wall cooling loop for the SEAFP reactor design

    International Nuclear Information System (INIS)

    Ross, W.E.

    1994-02-01

    This report documents the thermosyphoning analysis which was performed with the CATHENA network model of one of the blanket and first wall cooling loops of the SEAFP reactor design. This thermosyphoning analysis includes four simulations, each with a slightly different model feature or assumption. These simulations are performed to assess the primary heat transport system behaviour for a complete loss of electrical power event (total loss of flow) and to estimate the rate and extent of heat-up of the incore components. For each event, a description of some of the important aspects of the transient thermalhydraulic behaviour including coolant temperatures, circuit and sector flows, circuit pressure, pressurizer level and outflow, and first wall and blanket temperatures is provided. (author). 4 refs., 2 tabs., 32 figs

  14. Detection of the antiviral activity of epicatechin isolated from Salacia crassifolia (Celastraceae) against Mayaro virus based on protein C homology modelling and virtual screening.

    Science.gov (United States)

    Ferreira, P G; Ferraz, A C; Figueiredo, J E; Lima, C F; Rodrigues, V G; Taranto, A G; Ferreira, J M S; Brandão, G C; Vieira-Filho, S A; Duarte, L P; de Brito Magalhães, C L; de Magalhães, J C

    2018-02-24

    Mayaro fever, caused by Mayaro virus (MAYV) is a sub-lethal disease with symptoms that are easily confused with those of dengue fever, except for polyarthralgia, which may culminate in physical incapacitation. Recently, outbreaks of MAYV have been documented in metropolitan areas, and to date, there is no therapy or vaccine available. Moreover, there is no information regarding the three-dimensional structure of the viral proteins of MAYV, which is important in the search for antivirals. In this work, we constructed a three-dimensional model of protein C of MAYV by homology modelling, and this was employed in a manner similar to that of receptors in virtual screening studies to evaluate 590 molecules as prospective antiviral agents. In vitro bioassays were utilized to confirm the potential antiviral activity of the flavonoid epicatechin isolated from Salacia crassifolia (Celastraceae). The virtual screening showed that six flavonoids were promising ligands for protein C. The bioassays showed potent antiviral action of epicatechin, which protected the cells from almost all of the effects of viral infection. An effective concentration (EC 50 ) of 0.247 μmol/mL was observed with a selectivity index (SI) of 7. The cytotoxicity assay showed that epicatechin has low toxicity, with a 50% cytotoxic concentration (CC 50 ) greater than 1.723 µmol/mL. Epicatechin was found to be twice as potent as the reference antiviral ribavirin. Furthermore, a replication kinetics assay showed a strong inhibitory effect of epicatechin on MAYV growth, with a reduction of at least four logs in virus production. Our results indicate that epicatechin is a promising candidate for further testing as an antiviral agent against Mayaro virus and other alphaviruses.

  15. A Hydrodynamic Model of Alfvénic Wave Heating in a Coronal Loop and Its Chromospheric Footpoints

    Science.gov (United States)

    Reep, Jeffrey W.; Russell, Alexander J. B.; Tarr, Lucas A.; Leake, James E.

    2018-02-01

    Alfvénic waves have been proposed as an important energy transport mechanism in coronal loops, capable of delivering energy to both the corona and chromosphere and giving rise to many observed features of flaring and quiescent regions. In previous work, we established that resistive dissipation of waves (ambipolar diffusion) can drive strong chromospheric heating and evaporation, capable of producing flaring signatures. However, that model was based on a simplified assumption that the waves propagate instantly to the chromosphere, an assumption that the current work removes. Via a ray-tracing method, we have implemented traveling waves in a field-aligned hydrodynamic simulation that dissipate locally as they propagate along the field line. We compare this method to and validate against the magnetohydrodynamics code Lare3D. We then examine the importance of travel times to the dynamics of the loop evolution, finding that (1) the ionization level of the plasma plays a critical role in determining the location and rate at which waves dissipate; (2) long duration waves effectively bore a hole into the chromosphere, allowing subsequent waves to penetrate deeper than previously expected, unlike an electron beam whose energy deposition rises in height as evaporation reduces the mean-free paths of the electrons; and (3) the dissipation of these waves drives a pressure front that propagates to deeper depths, unlike energy deposition by an electron beam.

  16. An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.

    Directory of Open Access Journals (Sweden)

    Art F Y Poon

    2007-11-01

    Full Text Available The third variable loop (V3 of the human immunodeficiency virus type 1 (HIV-1 envelope is a principal determinant of antibody neutralization and progression to AIDS. Although it is undoubtedly an important target for vaccine research, extensive genetic variation in V3 remains an obstacle to the development of an effective vaccine. Comparative methods that exploit the abundance of sequence data can detect interactions between residues of rapidly evolving proteins such as the HIV-1 envelope, revealing biological constraints on their variability. However, previous studies have relied implicitly on two biologically unrealistic assumptions: (1 that founder effects in the evolutionary history of the sequences can be ignored, and; (2 that statistical associations between residues occur exclusively in pairs. We show that comparative methods that neglect the evolutionary history of extant sequences are susceptible to a high rate of false positives (20%-40%. Therefore, we propose a new method to detect interactions that relaxes both of these assumptions. First, we reconstruct the evolutionary history of extant sequences by maximum likelihood, shifting focus from extant sequence variation to the underlying substitution events. Second, we analyze the joint distribution of substitution events among positions in the sequence as a Bayesian graphical model, in which each branch in the phylogeny is a unit of observation. We perform extensive validation of our models using both simulations and a control case of known interactions in HIV-1 protease, and apply this method to detect interactions within V3 from a sample of 1,154 HIV-1 envelope sequences. Our method greatly reduces the number of false positives due to founder effects, while capturing several higher-order interactions among V3 residues. By mapping these interactions to a structural model of the V3 loop, we find that the loop is stratified into distinct evolutionary clusters. We extend our model to

  17. Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8

    Directory of Open Access Journals (Sweden)

    Lawal Garba

    2018-03-01

    Full Text Available Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10 positions of most saturated substrates. As the three-dimensional structures of the bacterial membrane fatty acid desaturases are not available, relevant information about the enzymes are derived from their amino acid sequences, site-directed mutagenesis and domain swapping in similar membrane-bound desaturases. The cold-tolerant Pseudomonas sp. AMS8 was found to produce high amount of monounsaturated fatty acids at low temperature. Subsequently, an active Δ9-fatty acid desaturase was isolated and functionally expressed in Escherichia coli. In this paper we report homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8 for the first time to the best of our knowledge. Three dimensional structure of the enzyme was built using MODELLER version 9.18 using a suitable template. The protein model contained the three conserved-histidine residues typical for all membrane-bound desaturase catalytic activity. The structure was subjected to energy minimization and checked for correctness using Ramachandran plots and ERRAT, which showed a good quality model of 91.6 and 65.0%, respectively. The protein model was used to preform MD simulation and docking of palmitic acid using CHARMM36 force field in GROMACS Version 5 and Autodock tool Version 4.2, respectively. The docking simulation with the lowest binding energy, −6.8 kcal/mol had a number of residues in close contact with the docked palmitic acid namely, Ile26, Tyr95, Val179, Gly180, Pro64, Glu203, His34, His206, His71, Arg182, Thr85, Lys98 and His177. Interestingly, among the binding residues are His34, His71 and His206 from the first, second, and third conserved histidine motif, respectively

  18. Study on the radiative decays of h{sub c} via intermediate meson loops model

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Qi; Li, Gang; Zhang, Yawei [Qufu Normal University, College of Physics and Engineering, Qufu (China)

    2017-05-15

    Recently, the BESIII Collaboration reported two new decay processes: h{sub c}(1P) → γη and γη{sup '}. Inspired by this measurement, we propose to study the radiative decays of h{sub c} via intermediate charmed meson loops in an effective Lagrangian approach. With the acceptable cutoff parameter range, the calculated branching ratios of h{sub c}(1P) → γη and γη{sup '} are of the orders of 10{sup -4} to 10{sup -3} and 10{sup -3} to 10{sup -2}, respectively. The ratio R{sub h{sub c}} = B(h{sub c} → γη)/ B(h{sub c} → γη{sup '}) can reproduce the experimental measurements with the commonly acceptable α range. This ratio provide us with some information on the η-η{sup '} mixing, which may be helpful for us to test the SU(3)-flavor symmetries in QCD. (orig.)

  19. An axial heat transfer analytical model for capillary-pumped loop vapor line temperature distributions

    International Nuclear Information System (INIS)

    Lin, H.-W.; Lin, W.-K.

    2007-01-01

    This paper aims to study the capillary-pumped loop (CPL) vapor line temperature distributions. A simple axial heat transfer method is developed to predict the vapor line temperature from evaporator outlet to condenser inlet. CPL is a high efficiency two-phase heat transfer device. Since it does not need any other mechanical force such as pump, furthermore, it might be used to do the thermal management of high power electronic component such as spacecraft, notebook and computer servers. It is a cyclic circulation pumped by capillary force, and this force is generated from the fine porous structure in evaporator. A novel semi-arc porous evaporator to CPL in 1U server is designed on the ground with a horizontal position and scale down the whole device to the miniature size. From the experimental results, the CPL could remove heat 90 W in steady-state and keep the heat source temperature about 70 deg. C. Finally, a good agreement between the simulation and experimental values has been achieved. Comparing with experiment and simulation results, the deviation values of the distributions of the condenser inlet temperature are less than 8%

  20. Comparative analysis of the simulation of the instantaneous closing of the discharge valve of a recirculation loop of a BWR with a model of recirculation loop with 2 jet pumps and another model with 20 jet pumps using RELAP5/SCDAPSIM Mod. 3.4

    International Nuclear Information System (INIS)

    Araiza M, E.; Ortiz V, J.; Martinez C, E.; Amador G, R.; Castillo D, R.

    2016-09-01

    This work presents the results of the simulation of the instantaneous closing of the water hammer, of a recirculation loop using two different arrangements in the loops. One of these arrangements corresponds to the traditional model that uses only two jet pumps to simulate the twenty pumps of the two recirculation loops of a BWR. The second nodalization models each of the ten jet pumps of each recirculation loop. The results obtained from the execution of both models are compared, using important variables such as pressures and mass costs for the same components of both models. In addition, the maximum pressure value generated on the pipe located upstream of the water hammer, relative to the design pressure of the pipe, is compared for each arrangement. (Author)

  1. Zinc ion coordination as a modulating factor of the ZnuA histidine-rich loop flexibility: A molecular modeling and fluorescence spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Castelli, Silvia [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Stella, Lorenzo [Department of Chemical Sciences and Technologies, University of Roma Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Neuromed, IRCCS, Pozzilli 86077 (Italy); Petrarca, Patrizia [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Battistoni, Andrea [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy); Desideri, Alessandro [Department of Biology, University of Rome Tor Vergata and CIBB, Center of Biostatistics and Bioinformatics, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy); Falconi, Mattia, E-mail: falconi@uniroma2.it [Department of Biology, University of Rome Tor Vergata and CIBB, Center of Biostatistics and Bioinformatics, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy)

    2013-01-11

    Highlights: Black-Right-Pointing-Pointer Fluorescence data indicate that the His-loop of ZnuA interacts with Zn{sup +2} ions. Black-Right-Pointing-Pointer The ZnuA structural model proposed validates these spectroscopic findings. Black-Right-Pointing-Pointer It is proposed that a zinc loaded His-loop may facilitate the ZnuA-ZnuB recognition. -- Abstract: ZnuA is the soluble component of the high-affinity ZnuABC zinc transporter belonging to the ATP-binding cassette-type periplasmic Zn-binding proteins. The zinc transporter ZnuABC is composed by three proteins: ZnuB, the membrane permease, ZnuC, the ATPase component and ZnuA, the soluble periplasmic metal-binding protein which captures Zn and delivers it to ZnuB. The ZnuA protein contains a charged flexible loop, rich in histidines and acidic residues, showing significant species-specific differences. Various studies have established that this loop contributes to the formation of a secondary zinc binding site, which has been proposed to be important in the acquisition of periplasmic Zn for its delivery to ZnuB or for regulation of zinc uptake. Due to its high mobility the structure of the histidine-rich loop has never been solved by X-ray diffraction studies. In this paper, through a combined use of molecular modeling, mutagenesis and fluorescence spectroscopy, we confirm the presence of two zinc binding sites characterized by different affinities for the metal ion and show that the flexibility of the loop is modulated by the binding of the zinc ions to the protein. The data obtained by fluorescence spectroscopy have then be used to validate a 3D model including the unsolved histidine-rich loop.

  2. COMMUNICATION: Toward closed-loop optimization of deep brain stimulation for Parkinson's disease: concepts and lessons from a computational model

    Science.gov (United States)

    Feng, Xiao-jiang; Greenwald, Brian; Rabitz, Herschel; Shea-Brown, Eric; Kosut, Robert

    2007-06-01

    Deep brain stimulation (DBS) of the subthalamic nucleus with periodic, high-frequency pulse trains is an increasingly standard therapy for advanced Parkinson's disease. Here, we propose that a closed-loop global optimization algorithm may identify novel DBS waveforms that could be more effective than their high-frequency counterparts. We use results from a computational model of the Parkinsonian basal ganglia to illustrate general issues relevant to eventual clinical or experimental tests of such an algorithm. Specifically, while the relationship between DBS characteristics and performance is highly complex, global search methods appear able to identify novel and effective waveforms with convergence rates that are acceptably fast to merit further investigation in laboratory or clinical settings.

  3. Chemical shift homology in proteins

    International Nuclear Information System (INIS)

    Potts, Barbara C.M.; Chazin, Walter J.

    1998-01-01

    The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of C α protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins

  4. Higher dimensional loop quantum cosmology

    International Nuclear Information System (INIS)

    Zhang, Xiangdong

    2016-01-01

    Loop quantum cosmology (LQC) is the symmetric sector of loop quantum gravity. In this paper, we generalize the structure of loop quantum cosmology to the theories with arbitrary spacetime dimensions. The isotropic and homogeneous cosmological model in n + 1 dimensions is quantized by the loop quantization method. Interestingly, we find that the underlying quantum theories are divided into two qualitatively different sectors according to spacetime dimensions. The effective Hamiltonian and modified dynamical equations of n + 1 dimensional LQC are obtained. Moreover, our results indicate that the classical big bang singularity is resolved in arbitrary spacetime dimensions by a quantum bounce. We also briefly discuss the similarities and differences between the n + 1 dimensional model and the 3 + 1 dimensional one. Our model serves as a first example of higher dimensional loop quantum cosmology and offers the possibility to investigate quantum gravity effects in higher dimensional cosmology. (orig.)

  5. Immunogenicity and Protective Efficacy of Brugia malayi Heavy Chain Myosin as Homologous DNA, Protein and Heterologous DNA/Protein Prime Boost Vaccine in Rodent Model.

    Directory of Open Access Journals (Sweden)

    Jyoti Gupta

    Full Text Available We earlier demonstrated the immunoprophylactic efficacy of recombinant heavy chain myosin (Bm-Myo of Brugia malayi (B. malayi in rodent models. In the current study, further attempts have been made to improve this efficacy by employing alternate approaches such as homologous DNA (pcD-Myo and heterologous DNA/protein prime boost (pcD-Myo+Bm-Myo in BALB/c mouse model. The gene bm-myo was cloned in a mammalian expression vector pcDNA 3.1(+ and protein expression was confirmed in mammalian Vero cell line. A significant degree of protection (79.2%±2.32 against L3 challenge in pcD-Myo+Bm-Myo immunized group was observed which was much higher than that exerted by Bm-Myo (66.6%±2.23 and pcD-Myo (41.6%±2.45. In the heterologous immunized group, the percentage of peritoneal leukocytes such as macrophages, neutrophils, B cells and T cells marginally increased and their population augmented further significantly following L3 challenge. pcD-Myo+Bm-Myo immunization elicited robust cellular and humoral immune responses as compared to pcD-Myo and Bm-Myo groups as evidenced by an increased accumulation of CD4+, CD8+ T cells and CD19+ B cells in the mouse spleen and activation of peritoneal macrophages. Though immunized animals produced antigen-specific IgG antibodies and isotypes, sera of mice receiving pcD-Myo+Bm-Myo or Bm-Myo developed much higher antibody levels than other groups and there was profound antibody-dependent cellular adhesion and cytotoxicity (ADCC to B. malayi infective larvae (L3. pcD-Myo+Bm-Myo as well as Bm-Myo mice generated a mixed T helper cell phenotype as evidenced by the production of both pro-inflammatory (IL-2, IFN-γ and anti-inflammatory (IL-4, IL-10 cytokines. Mice receiving pcD-Myo on contrary displayed a polarized pro-inflammatory immune response. The findings suggest that the priming of animals with DNA followed by protein booster generates heightened and mixed pro- and anti-inflammatory immune responses that are capable of

  6. Reliable design of a closed loop supply chain network under uncertainty: An interval fuzzy possibilistic chance-constrained model

    Science.gov (United States)

    Vahdani, Behnam; Tavakkoli-Moghaddam, Reza; Jolai, Fariborz; Baboli, Arman

    2013-06-01

    This article seeks to offer a systematic approach to establishing a reliable network of facilities in closed loop supply chains (CLSCs) under uncertainties. Facilities that are located in this article concurrently satisfy both traditional objective functions and reliability considerations in CLSC network designs. To attack this problem, a novel mathematical model is developed that integrates the network design decisions in both forward and reverse supply chain networks. The model also utilizes an effective reliability approach to find a robust network design. In order to make the results of this article more realistic, a CLSC for a case study in the iron and steel industry has been explored. The considered CLSC is multi-echelon, multi-facility, multi-product and multi-supplier. Furthermore, multiple facilities exist in the reverse logistics network leading to high complexities. Since the collection centres play an important role in this network, the reliability concept of these facilities is taken into consideration. To solve the proposed model, a novel interactive hybrid solution methodology is developed by combining a number of efficient solution approaches from the recent literature. The proposed solution methodology is a bi-objective interval fuzzy possibilistic chance-constraint mixed integer linear programming (BOIFPCCMILP). Finally, computational experiments are provided to demonstrate the applicability and suitability of the proposed model in a supply chain environment and to help decision makers facilitate their analyses.

  7. Investigation, modelling and control of the 1.9 K cooling loop for superconducting magnets for the Large Hadron Collider

    CERN Document Server

    Flemsæter, Bjorn

    2000-01-01

    The temperature of the superconducting magnets for the 27 km LHC particle accelerator under construction at CERN is a control parameter with strict operating constraints imposed by (a) the maximum temperature at which the magnets can operate, (b) the cooling capacity of the cryogenic system, (c) the variability of applied heat loads and (d) the accuracy of the instrumentation. A pilot plant for studying aspects beyond single magnet testing has been constructed. This magnet test string is a 35-m full-scale model if the LHC and consists of four superconducting cryogmagnets operating in a static bath of He II at 1.9 K. An experimental investigation of the properties dynamic characteristics of the 1.9 K cooling loop of the magnet test string has been carried out. A first principle model of the system has been created. A series of experiments designed for system identification purposes have been carried out, and black box models of the system have been created on the basis on the recorded data. A Model Predictive ...

  8. Detailed Modeling of Distillation Technologies for Closed-Loop Water Recovery Systems

    Science.gov (United States)

    Allada, Rama Kumar; Lange, Kevin E.; Anderson, Molly S.

    2011-01-01

    Detailed chemical process simulations are a useful tool in designing and optimizing complex systems and architectures for human life support. Dynamic and steady-state models of these systems help contrast the interactions of various operating parameters and hardware designs, which become extremely useful in trade-study analyses. NASA?s Exploration Life Support technology development project recently made use of such models to compliment a series of tests on different waste water distillation systems. This paper presents efforts to develop chemical process simulations for three technologies: the Cascade Distillation System (CDS), the Vapor Compression Distillation (VCD) system and the Wiped-Film Rotating Disk (WFRD) using the Aspen Custom Modeler and Aspen Plus process simulation tools. The paper discusses system design, modeling details, and modeling results for each technology and presents some comparisons between the model results and recent test data. Following these initial comparisons, some general conclusions and forward work are discussed.

  9. Mod two homology and cohomology

    CERN Document Server

    Hausmann, Jean-Claude

    2014-01-01

    Cohomology and homology modulo 2 helps the reader grasp more readily the basics of a major tool in algebraic topology. Compared to a more general approach to (co)homology this refreshing approach has many pedagogical advantages: It leads more quickly to the essentials of the subject, An absence of signs and orientation considerations simplifies the theory, Computations and advanced applications can be presented at an earlier stage, Simple geometrical interpretations of (co)chains. Mod 2 (co)homology was developed in the first quarter of the twentieth century as an alternative to integral homology, before both became particular cases of (co)homology with arbitrary coefficients. The first chapters of this book may serve as a basis for a graduate-level introductory course to (co)homology. Simplicial and singular mod 2 (co)homology are introduced, with their products and Steenrod squares, as well as equivariant cohomology. Classical applications include Brouwer's fixed point theorem, Poincaré duality, Borsuk-Ula...

  10. Dynamic Modeling of Process Technologies for Closed-Loop Water Recovery Systems

    Science.gov (United States)

    Allada, Rama Kumar; Lange, Kevin E.; Anderson, Molly S.

    2012-01-01

    Detailed chemical process simulations are a useful tool in designing and optimizing complex systems and architectures for human life support. Dynamic and steady-state models of these systems help contrast the interactions of various operating parameters and hardware designs, which become extremely useful in trade-study analyses. NASA s Exploration Life Support technology development project recently made use of such models to compliment a series of tests on different waste water distillation systems. This paper presents dynamic simulations of chemical process for primary processor technologies including: the Cascade Distillation System (CDS), the Vapor Compression Distillation (VCD) system, the Wiped-Film Rotating Disk (WFRD), and post-distillation water polishing processes such as the Volatiles Removal Assembly (VRA). These dynamic models were developed using the Aspen Custom Modeler (Registered TradeMark) and Aspen Plus(Registered TradeMark) process simulation tools. The results expand upon previous work for water recovery technology models and emphasize dynamic process modeling and results. The paper discusses system design, modeling details, and model results for each technology and presents some comparisons between the model results and available test data. Following these initial comparisons, some general conclusions and forward work are discussed.

  11. A Multiscale Closed-Loop Cardiovascular Model, with Applications to Heart Pacing and Hemorrhage

    Science.gov (United States)

    Canuto, Daniel; Eldredge, Jeff; Chong, Kwitae; Benharash, Peyman; Dutson, Erik

    2017-11-01

    A computational tool is developed for simulating the dynamic response of the human cardiovascular system to various stressors and injuries. The tool couples zero-dimensional models of the heart, pulmonary vasculature, and peripheral vasculature to one-dimensional models of the major systemic arteries. To simulate autonomic response, this multiscale circulatory model is integrated with a feedback model of the baroreflex, allowing control of heart rate, cardiac contractility, and peripheral impedance. The performance of the tool is demonstrated in two scenarios: increasing heart rate by stimulating the sympathetic nervous system, and an acute 10 percent hemorrhage from the left femoral artery.

  12. Construction and modelling of an inducible positive feedback loop stably integrated in a mammalian cell-line.

    Directory of Open Access Journals (Sweden)

    Velia Siciliano

    2011-06-01

    Full Text Available Understanding the relationship between topology and dynamics of transcriptional regulatory networks in mammalian cells is essential to elucidate the biology of complex regulatory and signaling pathways. Here, we characterised, via a synthetic biology approach, a transcriptional positive feedback loop (PFL by generating a clonal population of mammalian cells (CHO carrying a stable integration of the construct. The PFL network consists of the Tetracycline-controlled transactivator (tTA, whose expression is regulated by a tTA responsive promoter (CMV-TET, thus giving rise to a positive feedback. The same CMV-TET promoter drives also the expression of a destabilised yellow fluorescent protein (d2EYFP, thus the dynamic behaviour can be followed by time-lapse microscopy. The PFL network was compared to an engineered version of the network lacking the positive feedback loop (NOPFL, by expressing the tTA mRNA from a constitutive promoter. Doxycycline was used to repress tTA activation (switch off, and the resulting changes in fluorescence intensity for both the PFL and NOPFL networks were followed for up to 43 h. We observed a striking difference in the dynamics of the PFL and NOPFL networks. Using non-linear dynamical models, able to recapitulate experimental observations, we demonstrated a link between network topology and network dynamics. Namely, transcriptional positive autoregulation can significantly slow down the "switch off" times, as compared to the non-autoregulated system. Doxycycline concentration can modulate the response times of the PFL, whereas the NOPFL always switches off with the same dynamics. Moreover, the PFL can exhibit bistability for a range of Doxycycline concentrations. Since the PFL motif is often found in naturally occurring transcriptional and signaling pathways, we believe our work can be instrumental to characterise their behaviour.

  13. Construction and modelling of an inducible positive feedback loop stably integrated in a mammalian cell-line.

    Science.gov (United States)

    Siciliano, Velia; Menolascina, Filippo; Marucci, Lucia; Fracassi, Chiara; Garzilli, Immacolata; Moretti, Maria Nicoletta; di Bernardo, Diego

    2011-06-01

    Understanding the relationship between topology and dynamics of transcriptional regulatory networks in mammalian cells is essential to elucidate the biology of complex regulatory and signaling pathways. Here, we characterised, via a synthetic biology approach, a transcriptional positive feedback loop (PFL) by generating a clonal population of mammalian cells (CHO) carrying a stable integration of the construct. The PFL network consists of the Tetracycline-controlled transactivator (tTA), whose expression is regulated by a tTA responsive promoter (CMV-TET), thus giving rise to a positive feedback. The same CMV-TET promoter drives also the expression of a destabilised yellow fluorescent protein (d2EYFP), thus the dynamic behaviour can be followed by time-lapse microscopy. The PFL network was compared to an engineered version of the network lacking the positive feedback loop (NOPFL), by expressing the tTA mRNA from a constitutive promoter. Doxycycline was used to repress tTA activation (switch off), and the resulting changes in fluorescence intensity for both the PFL and NOPFL networks were followed for up to 43 h. We observed a striking difference in the dynamics of the PFL and NOPFL networks. Using non-linear dynamical models, able to recapitulate experimental observations, we demonstrated a link between network topology and network dynamics. Namely, transcriptional positive autoregulation can significantly slow down the "switch off" times, as compared to the non-autoregulated system. Doxycycline concentration can modulate the response times of the PFL, whereas the NOPFL always switches off with the same dynamics. Moreover, the PFL can exhibit bistability for a range of Doxycycline concentrations. Since the PFL motif is often found in naturally occurring transcriptional and signaling pathways, we believe our work can be instrumental to characterise their behaviour.

  14. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel; Lepore, Rosalba; Tramontano, Anna

    2015-01-01

    ) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has

  15. Closing the loop: integrating human impacts on water resources to advanced land surface models

    Science.gov (United States)

    Zaitchik, B. F.; Nie, W.; Rodell, M.; Kumar, S.; Li, B.

    2016-12-01

    Advanced Land Surface Models (LSMs), including those used in the North American Land Data Assimilation System (NLDAS), offer a physically consistent and spatially and temporally complete analysis of the distributed water balance. These models are constrained both by physically-based process representation and by observations ingested as meteorological forcing or as data assimilation updates. As such, they have become important tools for hydrological monitoring and long-term climate analysis. The representation of water management, however, is extremely limited in these models. Recent advances have brought prognostic irrigation routines into models used in NLDAS, while assimilation of Gravity Recovery and Climate Experiment (GRACE) derived estimates of terrestrial water storage anomaly has made it possible to nudge models towards observed states in water storage below the root zone. But with few exceptions these LSMs do not account for the source of irrigation water, leading to a disconnect between the simulated water balance and the observed human impact on water resources. This inconsistency is unacceptable for long-term studies of climate change and human impact on water resources in North America. Here we define the modeling challenge, review instances of models that have begun to account for water withdrawals (e.g., CLM), and present ongoing efforts to improve representation of human impacts on water storage across models through integration of irrigation routines, water withdrawal information, and GRACE Data Assimilation in NLDAS LSMs.

  16. Getting the Client Into the Loop in Information Systems Modelling Courses

    NARCIS (Netherlands)

    Sikkel, Nicolaas; Daneva, Maia

    2011-01-01

    Information system modelling is more than a translation of requirements from one notation into another, it is part of the requirements analysis process. Adding explicitness and making design choices should provide critical feedback to the requirements document being modelled. We want our students to

  17. Dynamic Modeling of Process Technologies for Closed-Loop Water Recovery Systems

    Science.gov (United States)

    Allada, Rama Kumar; Lange, Kevin; Anderson, Molly

    2011-01-01

    Detailed chemical process simulations are a useful tool in designing and optimizing complex systems and architectures for human life support. Dynamic and steady-state models of these systems help contrast the interactions of various operating parameters and hardware designs, which become extremely useful in trade-study analyses. NASA s Exploration Life Support technology development project recently made use of such models to compliment a series of tests on different waste water distillation systems. This paper presents dynamic simulations of chemical process for primary processor technologies including: the Cascade Distillation System (CDS), the Vapor Compression Distillation (VCD) system, the Wiped-Film Rotating Disk (WFRD), and post-distillation water polishing processes such as the Volatiles Removal Assembly (VRA) that were developed using the Aspen Custom Modeler and Aspen Plus process simulation tools. The results expand upon previous work for water recovery technology models and emphasize dynamic process modeling and results. The paper discusses system design, modeling details, and model results for each technology and presents some comparisons between the model results and available test data. Following these initial comparisons, some general conclusions and forward work are discussed.

  18. Structural Characterization of the Loop at the Alpha-Subunit C-Terminus of the Mixed Lineage Leukemia Protein Activating Protease Taspase1.

    Directory of Open Access Journals (Sweden)

    Johannes van den Boom

    Full Text Available Type 2 asparaginases, a subfamily of N-terminal nucleophile (Ntn hydrolases, are activated by limited proteolysis. This activation yields a heterodimer and a loop region at the C-terminus of the α-subunit is released. Since this region is unresolved in all type 2 asparaginase crystal structures but is close to the active site residues, we explored this loop region in six members of the type 2 asparaginase family using homology modeling. As the loop model for the childhood cancer-relevant protease Taspase1 differed from the other members, Taspase1 activation as well as the conformation and dynamics of the 56 amino acids loop were investigated by CD and NMR spectroscopy. We propose a helix-turn-helix motif, which can be exploited as novel anticancer target to inhibit Taspase1 proteolytic activity.

  19. A vector model for off-axis hysteresis loops using anisotropy field

    International Nuclear Information System (INIS)

    Jamali, Ali; Torre, Edward Della; Cardelli, Ermanno; ElBidweihy, Hatem; Bennett, Lawrence H.

    2016-01-01

    A model for the off-axis vector magnetization of a distribution of uniaxial particles is presented. Recent work by the authors decomposed the magnetization into two components and modeled the total vector magnetization as their vector sum. In this paper, to account for anisotropy, the direction of the reversible magnetization component is specified by the vector sum of the applied field and an effective anisotropy field. The formulation of the new anisotropy field (AF) model is derived and its results are discussed considering (i) oscillation and rotational modes, (ii) lag angle, and (iii) unitary magnetization. The advantages of the AF model are outlined by comparing its results to the results of the classical Stoner–Wohlfarth model.

  20. A vector model for off-axis hysteresis loops using anisotropy field

    Energy Technology Data Exchange (ETDEWEB)

    Jamali, Ali, E-mail: alijamal@gwu.edu [Electrical and Computer Engineering Department, The George Washington University, Washington, D.C. 20052 (United States); Torre, Edward Della [Electrical and Computer Engineering Department, The George Washington University, Washington, D.C. 20052 (United States); Cardelli, Ermanno [Department of Engineering, University of Perugia, Perugia (Italy); ElBidweihy, Hatem [Electrical and Computer Engineering Department, United States Naval Academy, Annapolis, MD 21402 (United States); Bennett, Lawrence H. [Electrical and Computer Engineering Department, The George Washington University, Washington, D.C. 20052 (United States)

    2016-11-15

    A model for the off-axis vector magnetization of a distribution of uniaxial particles is presented. Recent work by the authors decomposed the magnetization into two components and modeled the total vector magnetization as their vector sum. In this paper, to account for anisotropy, the direction of the reversible magnetization component is specified by the vector sum of the applied field and an effective anisotropy field. The formulation of the new anisotropy field (AF) model is derived and its results are discussed considering (i) oscillation and rotational modes, (ii) lag angle, and (iii) unitary magnetization. The advantages of the AF model are outlined by comparing its results to the results of the classical Stoner–Wohlfarth model.

  1. A Step Forward to Closing the Loop between Static and Dynamic Reservoir Modeling

    Directory of Open Access Journals (Sweden)

    Cancelliere M.

    2014-12-01

    Full Text Available The current trend for history matching is to find multiple calibrated models instead of a single set of model parameters that match the historical data. The advantage of several current workflows involving assisted history matching techniques, particularly those based on heuristic optimizers or direct search, is that they lead to a number of calibrated models that partially address the problem of the non-uniqueness of the solutions. The importance of achieving multiple solutions is that calibrated models can be used for a true quantification of the uncertainty affecting the production forecasts, which represent the basis for technical and economic risk analysis. In this paper, the importance of incorporating the geological uncertainties in a reservoir study is demonstrated. A workflow, which includes the analysis of the uncertainty associated with the facies distribution for a fluvial depositional environment in the calibration of the numerical dynamic models and, consequently, in the production forecast, is presented. The first step in the workflow was to generate a set of facies realizations starting from different conceptual models. After facies modeling, the petrophysical properties were assigned to the simulation domains. Then, each facies realization was calibrated separately by varying permeability and porosity fields. Data assimilation techniques were used to calibrate the models in a reasonable span of time. Results showed that even the adoption of a conceptual model for facies distribution clearly representative of the reservoir internal geometry might not guarantee reliable results in terms of production forecast. Furthermore, results also showed that realizations which seem fully acceptable after calibration were not representative of the true reservoir internal configuration and provided wrong production forecasts; conversely, realizations which did not show a good fit of the production data could reliably predict the reservoir

  2. An Integrated Loop Model of Corrective Feedback and Oral English Learning: A Case of International Students in the United States

    Science.gov (United States)

    Lee, Eun Jeong

    2017-01-01

    The author in this study introduces an integrated corrective feedback (CF) loop to schematize the interplay between CF and independent practice in L2 oral English learning among advanced-level adult ESL students. The CF loop integrates insights from the Interaction, Output, and Noticing Hypotheses to show how CF can help or harm L2 learners'…

  3. Compositional Homology and Creative Thinking

    Directory of Open Access Journals (Sweden)

    Salvatore Tedesco

    2015-05-01

    Full Text Available The concept of homology is the most solid theoretical basis elaborated by the morphological thinking during its history. The enucleation of some general criteria for the interpretation of homology is today a fundamental tool for life sciences, and for restoring their own opening to the question of qualitative innovation that arose so powerfully in the original Darwinian project. The aim of this paper is to verify the possible uses of the concept of compositional homology in order to provide of an adequate understanding of the dynamics of creative thinking.

  4. Closed-Loop Supply Chain Planning Model for a Photovoltaic System Manufacturer with Internal and External Recycling

    Directory of Open Access Journals (Sweden)

    Songi Kim

    2016-06-01

    Full Text Available The photovoltaic (PV generation system has been widely used since the late 1990s. Considering its lifespan of 20 to 30 years, many end-of-life systems will emerge in the near future. This is why recycling PV systems will be beneficial (and may even be detrimental to both the environment and the economy. Through the recycling process, hazardous by-product substances such as cadmium and lead can be treated properly. Moreover, valuable materials including indium, gallium, and tellurium can be extracted and reused for manufacturing purposes. Even though many studies have dealt with issues related to the PV system and its recycling policy, they lack significant factors regarding the recycling policy. This study analyzes and compares three real cases of manufacturer’s recycling policy, including Deutsche Solar, First Solar, and PV Cycle, from the perspective of a closed-loop supply chain. Two mathematical models are developed to help PV system manufacturers establish supply chain planning and choose suitable recycling policies in consideration of different circumstances. Furthermore, an experimental example of these models will be used to validate and conclude the significance of the models. The results from this study will show that recycling CdTe PV systems is much more efficient than recycling c-Si PV systems and that, in the case of c-Si, it is better to outsource recycling end-of-life systems and dispose of all manufacturing scrap.

  5. Mathematical Modeling of the Pituitary-Thyroid Feedback Loop: Role of a TSH-T3-Shunt and Sensitivity Analysis.

    Science.gov (United States)

    Berberich, Julian; Dietrich, Johannes W; Hoermann, Rudolf; Müller, Matthias A

    2018-01-01

    Despite significant progress in assay technology, diagnosis of functional thyroid disorders may still be a challenge, as illustrated by the vague upper limit of the reference range for serum thyrotropin ( TSH ). Diagnostical problems also apply to subjects affected by syndrome T, i.e., those 10% of hypothyroid patients who continue to suffer from poor quality of life despite normal TSH concentrations under substitution therapy with levothyroxine ( L - T 4 ). In this paper, we extend a mathematical model of the pituitary-thyroid feedback loop in order to improve the understanding of thyroid hormone homeostasis. In particular, we incorporate a TSH - T 3 -shunt inside the thyroid, whose existence has recently been demonstrated in several clinical studies. The resulting extended model shows good accordance with various clinical observations, such as a circadian rhythm in free peripheral triiodothyronine ( FT 3 ). Furthermore, we perform a sensitivity analysis of the derived model, revealing the dependence of TSH and hormone concentrations on different system parameters. The results have implications for clinical interpretation of thyroid tests, e.g., in the differential diagnosis of subclinical hypothyroidism.

  6. Resolution of an uncertain closed-loop logistics model: an application to fuzzy linear programs with risk analysis.

    Science.gov (United States)

    Wang, Hsiao-Fan; Hsu, Hsin-Wei

    2010-11-01

    With the urgency of global warming, green supply chain management, logistics in particular, has drawn the attention of researchers. Although there are closed-loop green logistics models in the literature, most of them do not consider the uncertain environment in general terms. In this study, a generalized model is proposed where the uncertainty is expressed by fuzzy numbers. An interval programming model is proposed by the defined means and mean square imprecision index obtained from the integrated information of all the level cuts of fuzzy numbers. The resolution for interval programming is based on the decision maker (DM)'s preference. The resulting solution provides useful information on the expected solutions under a confidence level containing a degree of risk. The results suggest that the more optimistic the DM is, the better is the resulting solution. However, a higher risk of violation of the resource constraints is also present. By defining this probable risk, a solution procedure was developed with numerical illustrations. This provides a DM trade-off mechanism between logistic cost and the risk. Copyright 2010 Elsevier Ltd. All rights reserved.

  7. Respiratory system model for quasistatic pulmonary pressure-volume (P-V) curve: inflation-deflation loop analyses.

    Science.gov (United States)

    Amini, R; Narusawa, U

    2008-06-01

    A respiratory system model (RSM) is developed for the deflation process of a quasistatic pressure-volume (P-V) curve, following the model for the inflation process reported earlier. In the RSM of both the inflation and the deflation limb, a respiratory system consists of a large population of basic alveolar elements, each consisting of a piston-spring-cylinder subsystem. A normal distribution of the basic elements is derived from Boltzmann statistical model with the alveolar closing (opening) pressure as the distribution parameter for the deflation (inflation) process. An error minimization by the method of least squares applied to existing P-V loop data from two different data sources confirms that a simultaneous inflation-deflation analysis is required for an accurate determination of RSM parameters. Commonly used terms such as lower inflection point, upper inflection point, and compliance are examined based on the P-V equations, on the distribution function, as well as on the geometric and physical properties of the basic alveolar element.

  8. Mathematical Modeling of the Pituitary–Thyroid Feedback Loop: Role of a TSH-T3-Shunt and Sensitivity Analysis

    Directory of Open Access Journals (Sweden)

    Julian Berberich

    2018-03-01

    Full Text Available Despite significant progress in assay technology, diagnosis of functional thyroid disorders may still be a challenge, as illustrated by the vague upper limit of the reference range for serum thyrotropin (TSH. Diagnostical problems also apply to subjects affected by syndrome T, i.e., those 10% of hypothyroid patients who continue to suffer from poor quality of life despite normal TSH concentrations under substitution therapy with levothyroxine (L-T4. In this paper, we extend a mathematical model of the pituitary–thyroid feedback loop in order to improve the understanding of thyroid hormone homeostasis. In particular, we incorporate a TSH-T3-shunt inside the thyroid, whose existence has recently been demonstrated in several clinical studies. The resulting extended model shows good accordance with various clinical observations, such as a circadian rhythm in free peripheral triiodothyronine (FT3. Furthermore, we perform a sensitivity analysis of the derived model, revealing the dependence of TSH and hormone concentrations on different system parameters. The results have implications for clinical interpretation of thyroid tests, e.g., in the differential diagnosis of subclinical hypothyroidism.

  9. Mathematical Modeling of the Pituitary–Thyroid Feedback Loop: Role of a TSH-T3-Shunt and Sensitivity Analysis

    Science.gov (United States)

    Berberich, Julian; Dietrich, Johannes W.; Hoermann, Rudolf; Müller, Matthias A.

    2018-01-01

    Despite significant progress in assay technology, diagnosis of functional thyroid disorders may still be a challenge, as illustrated by the vague upper limit of the reference range for serum thyrotropin (TSH). Diagnostical problems also apply to subjects affected by syndrome T, i.e., those 10% of hypothyroid patients who continue to suffer from poor quality of life despite normal TSH concentrations under substitution therapy with levothyroxine (L-T4). In this paper, we extend a mathematical model of the pituitary–thyroid feedback loop in order to improve the understanding of thyroid hormone homeostasis. In particular, we incorporate a TSH-T3-shunt inside the thyroid, whose existence has recently been demonstrated in several clinical studies. The resulting extended model shows good accordance with various clinical observations, such as a circadian rhythm in free peripheral triiodothyronine (FT3). Furthermore, we perform a sensitivity analysis of the derived model, revealing the dependence of TSH and hormone concentrations on different system parameters. The results have implications for clinical interpretation of thyroid tests, e.g., in the differential diagnosis of subclinical hypothyroidism. PMID:29619006

  10. Mathematical Modeling of Loop Heat Pipes with Multiple Capillary Pumps and Multiple Condensers. Part 1; Stead State Stimulations

    Science.gov (United States)

    Hoang, Triem T.; OConnell, Tamara; Ku, Jentung

    2004-01-01

    Loop Heat Pipes (LHPs) have proven themselves as reliable and robust heat transport devices for spacecraft thermal control systems. So far, the LHPs in earth-orbit satellites perform very well as expected. Conventional LHPs usually consist of a single capillary pump for heat acquisition and a single condenser for heat rejection. Multiple pump/multiple condenser LHPs have shown to function very well in ground testing. Nevertheless, the test results of a dual pump/condenser LHP also revealed that the dual LHP behaved in a complicated manner due to the interaction between the pumps and condensers. Thus it is redundant to say that more research is needed before they are ready for 0-g deployment. One research area that perhaps compels immediate attention is the analytical modeling of LHPs, particularly the transient phenomena. Modeling a single pump/single condenser LHP is difficult enough. Only a handful of computer codes are available for both steady state and transient simulations of conventional LHPs. No previous effort was made to develop an analytical model (or even a complete theory) to predict the operational behavior of the multiple pump/multiple condenser LHP systems. The current research project offered a basic theory of the multiple pump/multiple condenser LHP operation. From it, a computer code was developed to predict the LHP saturation temperature in accordance with the system operating and environmental conditions.

  11. Approximation methods in loop quantum cosmology: from Gowdy cosmologies to inhomogeneous models in Friedmann–Robertson–Walker geometries

    International Nuclear Information System (INIS)

    Martín-Benito, Mercedes; Martín-de Blas, Daniel; Marugán, Guillermo A Mena

    2014-01-01

    We develop approximation methods in the hybrid quantization of the Gowdy model with linear polarization and a massless scalar field, for the case of three-torus spatial topology. The loop quantization of the homogeneous gravitational sector of the Gowdy model (according to the improved dynamics prescription) and the presence of inhomogeneities lead to a very complicated Hamiltonian constraint. Therefore, the extraction of physical results calls for the introduction of well justified approximations. We first show how to approximate the homogeneous part of the Hamiltonian constraint, corresponding to Bianchi I geometries, as if it described a Friedmann–Robertson–Walker (FRW) model corrected with anisotropies. This approximation is valid in the sector of high energies of the FRW geometry (concerning its contribution to the constraint) and for anisotropy profiles that are sufficiently smooth. In addition, for certain families of states related to regimes of physical interest, with negligible quantum effects of the anisotropies and small inhomogeneities, one can approximate the Hamiltonian constraint of the inhomogeneous system by that of an FRW geometry with a relatively simple matter content, and then obtain its solutions. (paper)

  12. A Kind of Urban Road Travel Time Forecasting Model with Loop Detectors

    OpenAIRE

    Zhu, Guangyu; Wang, Li; Zhang, Peng; Song, Kang

    2016-01-01

    Urban road travel time is an important parameter to reflect the traffic flow state. Besides, it is one of the important parameters for the traffic management department to formulate guidance measures, provide traffic information service, and improve the efficiency of the detectors group. Therefore, it is crucial to improve the forecast accuracy of travel time in traffic management practice. Based on the analysis of the change-point and the ARIMA model, this paper constructs a model for the ma...

  13. Closed-loop model: An optimization of integrated thin-film magnetic devices

    Energy Technology Data Exchange (ETDEWEB)

    El-Ghazaly, Amal, E-mail: amale@stanford.edu [Electrical Engineering, Stanford University, Stanford, CA 94305 (United States); Sato, Noriyuki [Electrical Engineering, Stanford University, Stanford, CA 94305 (United States); White, Robert M. [Materials Science and Engineering, Stanford University, Stanford, CA 94305 (United States); Wang, Shan X. [Electrical Engineering, Stanford University, Stanford, CA 94305 (United States); Materials Science and Engineering, Stanford University, Stanford, CA 94305 (United States)

    2017-06-15

    Highlights: • An analytical model for inductance of thin-film magnetic devices was developed. • Different device topologies and magnetic permeabilities were addressed. • Inductance of various topologies were calculated and compared with simulation. • The model predicts simulated values with excellent accuracy. - Abstract: A generic analytical model has been developed to fully describe the flux closure through magnetic inductors. The model was applied to multiple device topologies including solenoidal single return path and dual return path inductors as well as spiral magnetic inductors for a variety of permeabilities and dimensions. The calculated inductance values from the analytical model were compared with simulated results for each of the analyzed device topologies and found to agree within 0.1 nH for the range of typical thin-film magnetic permeabilities (∼10{sup 2} to 10{sup 3}). Furthermore, the model can be used to evaluate behavior in other integrated or discrete magnetic devices with either non-isotropic or isotropic permeability and used to produce more efficient device designs in the future.

  14. Top quark rare decays via loop-induced FCNC interactions in extended mirror fermion model

    Science.gov (United States)

    Hung, P. Q.; Lin, Yu-Xiang; Nugroho, Chrisna Setyo; Yuan, Tzu-Chiang

    2018-02-01

    Flavor changing neutral current (FCNC) interactions for a top quark t decays into Xq with X represents a neutral gauge or Higgs boson, and q a up- or charm-quark are highly suppressed in the Standard Model (SM) due to the Glashow-Iliopoulos-Miami mechanism. Whilst current limits on the branching ratios of these processes have been established at the order of 10-4 from the Large Hadron Collider experiments, SM predictions are at least nine orders of magnitude below. In this work, we study some of these FCNC processes in the context of an extended mirror fermion model, originally proposed to implement the electroweak scale seesaw mechanism for non-sterile right-handed neutrinos. We show that one can probe the process t → Zc for a wide range of parameter space with branching ratios varying from 10-6 to 10-8, comparable with various new physics models including the general two Higgs doublet model with or without flavor violations at tree level, minimal supersymmetric standard model with or without R-parity, and extra dimension model.

  15. A new integration model of the calcium looping technology into coal fired power plants for CO_2 capture

    International Nuclear Information System (INIS)

    Ortiz, C.; Chacartegui, R.; Valverde, J.M.; Becerra, J.A.

    2016-01-01

    Highlights: • A CaL-CFPP (coal fired power plant) integration model is proposed and efficiency penalty is estimated. • Carbonation in the diffusion stage is considered to predict the capture efficiency. • Low efficiency penalty may be achieved by operating with longer particles’ residence time. • Simulation results show that the energy penalty ranges between 4% and 7% points. - Abstract: The Ca-Looping (CaL) process is at the root of a promising 2nd generation technology for post-combustion CO_2 capture at coal fired power plants. The process is based on the reversible and quick carbonation/calcination reaction of CaO/CaCO_​_3 at high temperatures and allows using low cost, widely available and non toxic CaO precursors such as natural limestone. In this work, the efficiency penalty caused by the integration of the Ca-looping technology into a coal fired power plant is analyzed. The results of the simulations based on the proposed integration model show that efficiency penalty varies between 4% and 7% points, which yields lower energy costs than other more mature post-combustion CO_2 capture technologies such as the currently commercial amine scrubbing technology. A principal feature of the CaL process at CO_2 capture conditions is that it produces a large amount of energy and therefore an optimized integration of the systems energy flows is essential for the feasibility of the integration at the commercial level. As a main novel contribution, CO_2 capture efficiency is calculated in our work by considering the important role of the solid-state diffusion controlled carbonation phase, which becomes relevant when CaO regeneration is carried out under high CO_2 partial pressure as is the case with the CaL process for CO_2 capture. The results obtained based on the new model suggest that integration energy efficiency would be significantly improved as the solids residence time in the carbonator reactor is increased.

  16. Preoperative irradiation with 5x5 Gy in a murine isolated colon loop model does not cause anastomotic weakening after colon resection

    NARCIS (Netherlands)

    Karliczek, A.; Zeebregts, C. J.; Benaron, D. A.; Coppes, R. P.; Wiggers, T.; van Dam, G. M.

    2008-01-01

    Introduction There are conflicting studies on the influence of fractionated preoperative 5 days of 5 Gy irradiation on tissue oxygenation and subsequent colonic anastomotic strength. To elucidate the effect of preoperative irradiation on anastomotic strength, an isolated colon loop model was

  17. CALCULATION OF DESORPTION BRANCH OF HYSTERESIS LOOP TOR THE ADSORBENTS OF CORPUSCULAR STRUCTURE ON THE BASIS OF MODEL OF CYLINDRICAL PORES

    Directory of Open Access Journals (Sweden)

    V. V. Kutarov

    2015-02-01

    Full Text Available The method of calculation of desorption branch of hysteresis loop for the adsorbents of corpus­cular structure is offered. The method is based on the model of cylindrical pores. Applicability of equation is tested by a way comparing of calculation results to information, certain on experimental isotherms, on the example of two adsorption systems with different adsorbents and adsorbats

  18. Nutrients and Energy Balance Analysis for a Conceptual Model of a Three Loops off Grid, Aquaponics

    Directory of Open Access Journals (Sweden)

    Uri Yogev

    2016-12-01

    Full Text Available Food security, specifically in water scarce regions, is an increasing local and global challenge. Finding new ways to increase agricultural production in a sustainable manner is required. The current study suggests a conceptual model to integrate established recirculating aquaculture practices into a near-zero discharge aquaponic system that efficiently utilizes water, excreted nutrients and organic matter for energy. The suggested model allows to significantly extend the planted area and recover energy in the form of biogas to operate the system off-grid. A mass balance model of nitrogen, carbon and energy was established and solved, based on data from the literature. Results demonstrate that a fish standing stock of about 700 kg would produce 3.4 tons of fish annually and enough nutrients to grow about 35 tons of tomatoes per year (chosen as a model plant and recover sufficient energy (70 kWh/day to run the system on biogas and use less water. If proven successful, this approach may play a major role in sustainably enhancing food security in rural and water scarce regions.

  19. Analysis, Modelling, and Simulation of Droop Control with Virtual Impedance Loop Applied to Parallel UPS Systems

    DEFF Research Database (Denmark)

    Lima, Francisco Kleber A.; Branco, Carlos Gustavo C.; Guerrero, Josep M.

    2013-01-01

    is difficult due to its physical location. This paper has considered that the UPS systems there were no comunication between their controls. A detailed mathematical model about the explored system is shown in that work and simulation results are presented in order to prove the theory presented....

  20. Numerical modelling of the dehydration of waste concrete fines : An attempt to close the recycling loop

    NARCIS (Netherlands)

    Teklay, Abraham; Vahidi, A.; Lotfi, Somayeh; Di Maio, F.; Rem, P.C.; Di Maio, F.; Lotfi, S.; Bakker, M.; Hu, M.; Vahidi, A.

    2017-01-01

    The ever-increasing interest on sustainable raw materials has urged the quest for recycled materials that can be used as a partial or total replacement of fine fractions in the production of concrete. This paper demonstrates a modelling study of recycled concrete waste fines and the possibility of

  1. Modelling and analysis of an open-loop induction motor drive ...

    Indian Academy of Sciences (India)

    The objective of this paper is to study the influence of inverter dead-time on steady as well as dynamic operation of an .... Modelling of IM drive incorporating dead-time effect. 127 ...... stator resistance in series with the stator reactance). Hence.

  2. Hardware-in-the-Loop Simulation of a Distribution System with Air Conditioners under Model Predictive Control: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Sparn, Bethany F [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Ruth, Mark F [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Krishnamurthy, Dheepak [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Pratt, Annabelle [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Lunacek, Monte S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Jones, Wesley B [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Wu, Hongyu [Kansas State University; Mittal, Saurabh [Mitre Corporation; Marks, Jesse [University of Missouri

    2017-08-01

    Many have proposed that responsive load provided by distributed energy resources (DERs) and demand response (DR) are an option to provide flexibility to the grid and especially to distribution feeders. However, because responsive load involves a complex interplay between tariffs and DER and DR technologies, it is challenging to test and evaluate options without negatively impacting customers. This paper describes a hardware-in-the-loop (HIL) simulation system that has been developed to reduce the cost of evaluating the impact of advanced controllers (e.g., model predictive controllers) and technologies (e.g., responsive appliances). The HIL simulation system combines large-scale software simulation with a small set of representative building equipment hardware. It is used to perform HIL simulation of a distribution feeder and the loads on it under various tariff structures. In the reported HIL simulation, loads include many simulated air conditioners and one physical air conditioner. Independent model predictive controllers manage operations of all air conditioners under a time-of-use tariff. Results from this HIL simulation and a discussion of future development work of the system are presented.

  3. Automated service quality and its behavioural consequences in CRM Environment: A structural equation modeling and causal loop diagramming approach

    Directory of Open Access Journals (Sweden)

    Arup Kumar Baksi

    2012-08-01

    Full Text Available Information technology induced communications (ICTs have revolutionized the operational aspects of service sector and have triggered a perceptual shift in service quality as rapid dis-intermediation has changed the access-mode of services on part of the consumers. ICT-enabled services further stimulated the perception of automated service quality with renewed dimensions and there subsequent significance to influence the behavioural outcomes of the consumers. Customer Relationship Management (CRM has emerged as an offshoot to technological breakthrough as it ensured service-encapsulation by integrating people, process and technology. This paper attempts to explore the relationship between automated service quality and its behavioural consequences in a relatively novel business-philosophy – CRM. The study has been conducted on the largest public sector bank of India - State bank of India (SBI at Kolkata which has successfully completed its decade-long operational automation in the year 2008. The study used structural equation modeling (SEM to justify the proposed model construct and causal loop diagramming (CLD to depict the negative and positive linkages between the variables.

  4. {Delta}r in the Two-Higgs-Doublet Model at full one loop level - and beyond

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Val, David [Universitaet Heidelberg, Institut fuer Theoretische Physik, Heidelberg (Germany); Sola, Joan [Universitat de Barcelona, Dept. Estructura i Constituents de la Materia, Barcelona, Catalonia (Spain); Institut de Ciencies del Cosmos, Barcelona, Catalonia (Spain)

    2013-04-15

    After the recent discovery of a Higgs-like boson particle at the CERN LHC-collider, it becomes more necessary than ever to prepare ourselves for identifying its standard or non-standard nature. The fundamental parameter {Delta}r, relating the values of the electroweak gauge boson masses and the Fermi constant, is the traditional observable encoding high precision information of the quantum effects. In this work we present a complete quantitative study of {Delta}r in the framework of the general Two-Higgs-Doublet Model (2HDM). While the one-loop analysis of {Delta}r in this model was carried out long ago, in the first part of our work we consistently incorporate the higher order effects that have been computed since then for the SM part of {Delta}r. Within the on-shell scheme, we find typical corrections leading to shifts of {proportional_to}20-40 MeV on the W mass, resulting in a better agreement with its experimentally measured value and in a degree no less significant than in the MSSM case. In the second part of our study we devise a set of effective couplings that capture the dominant higher order genuine 2HDM quantum effects on the {delta}{rho} part of {Delta}r in the limit of large Higgs boson self-interactions. This limit constitutes a telltale property of the general 2HDM which is unmatched by e.g. the MSSM. (orig.)

  5. Δr in the Two-Higgs-Doublet Model at full one loop level - and beyond

    International Nuclear Information System (INIS)

    Lopez-Val, David; Sola, Joan

    2013-01-01

    After the recent discovery of a Higgs-like boson particle at the CERN LHC-collider, it becomes more necessary than ever to prepare ourselves for identifying its standard or non-standard nature. The fundamental parameter Δr, relating the values of the electroweak gauge boson masses and the Fermi constant, is the traditional observable encoding high precision information of the quantum effects. In this work we present a complete quantitative study of Δr in the framework of the general Two-Higgs-Doublet Model (2HDM). While the one-loop analysis of Δr in this model was carried out long ago, in the first part of our work we consistently incorporate the higher order effects that have been computed since then for the SM part of Δr. Within the on-shell scheme, we find typical corrections leading to shifts of ∝20-40 MeV on the W mass, resulting in a better agreement with its experimentally measured value and in a degree no less significant than in the MSSM case. In the second part of our study we devise a set of effective couplings that capture the dominant higher order genuine 2HDM quantum effects on the δρ part of Δr in the limit of large Higgs boson self-interactions. This limit constitutes a telltale property of the general 2HDM which is unmatched by e.g. the MSSM. (orig.)

  6. One-loop effects on top pair production in the littlest Higgs model with T-parity at the LHC

    International Nuclear Information System (INIS)

    Yang, Bingfang; Liu, Ning

    2013-01-01

    In this work, we systematically investigate the one-loop corrections to t anti t production in the littlest Higgs model with T-parity (LHT) at the LHC for √(s) = 8,14 TeV. We focus on the effects of LHT particles on t anti t cross section, polarization asymmetries, spin correlation and charge asymmetry at the LHC. We also study the top quark forward-backward asymmetry at Tevatron and its correlations with the LHC observables. We found that: (1) the contributions of the LHT particles to t anti t production can only reach about 1 % at the 14 TeV LHC. Meanwhile, the anomalous top quark forward-backward asymmetry at Tevatron is also hardly to be explained in the LHT model. (2) The parity violating asymmetries in t anti t production, such as left-right asymmetry vertical stroke A LR vertical stroke and the polarization vertical stroke P t vertical stroke can, respectively, reach 1.1 % and 0.5 %, which may have the potential to provide a signal of LHT at the LHC. (orig.)

  7. Statistical Inference for Porous Materials using Persistent Homology.

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Chul [Univ. of Georgia, Athens, GA (United States); Heath, Jason E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mitchell, Scott A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-12-01

    We propose a porous materials analysis pipeline using persistent homology. We rst compute persistent homology of binarized 3D images of sampled material subvolumes. For each image we compute sets of homology intervals, which are represented as summary graphics called persistence diagrams. We convert persistence diagrams into image vectors in order to analyze the similarity of the homology of the material images using the mature tools for image analysis. Each image is treated as a vector and we compute its principal components to extract features. We t a statistical model using the loadings of principal components to estimate material porosity, permeability, anisotropy, and tortuosity. We also propose an adaptive version of the structural similarity index (SSIM), a similarity metric for images, as a measure to determine the statistical representative elementary volumes (sREV) for persistence homology. Thus we provide a capability for making a statistical inference of the uid ow and transport properties of porous materials based on their geometry and connectivity.

  8. A Multiple-Plasticity Spiking Neural Network Embedded in a Closed-Loop Control System to Model Cerebellar Pathologies.

    Science.gov (United States)

    Geminiani, Alice; Casellato, Claudia; Antonietti, Alberto; D'Angelo, Egidio; Pedrocchi, Alessandra

    2018-06-01

    The cerebellum plays a crucial role in sensorimotor control and cerebellar disorders compromise adaptation and learning of motor responses. However, the link between alterations at network level and cerebellar dysfunction is still unclear. In principle, this understanding would benefit of the development of an artificial system embedding the salient neuronal and plastic properties of the cerebellum and operating in closed-loop. To this aim, we have exploited a realistic spiking computational model of the cerebellum to analyze the network correlates of cerebellar impairment. The model was modified to reproduce three different damages of the cerebellar cortex: (i) a loss of the main output neurons (Purkinje Cells), (ii) a lesion to the main cerebellar afferents (Mossy Fibers), and (iii) a damage to a major mechanism of synaptic plasticity (Long Term Depression). The modified network models were challenged with an Eye-Blink Classical Conditioning test, a standard learning paradigm used to evaluate cerebellar impairment, in which the outcome was compared to reference results obtained in human or animal experiments. In all cases, the model reproduced the partial and delayed conditioning typical of the pathologies, indicating that an intact cerebellar cortex functionality is required to accelerate learning by transferring acquired information to the cerebellar nuclei. Interestingly, depending on the type of lesion, the redistribution of synaptic plasticity and response timing varied greatly generating specific adaptation patterns. Thus, not only the present work extends the generalization capabilities of the cerebellar spiking model to pathological cases, but also predicts how changes at the neuronal level are distributed across the network, making it usable to infer cerebellar circuit alterations occurring in cerebellar pathologies.

  9. An empirical approach for quantifying loop-mediated isothermal amplification (LAMP using Escherichia coli as a model system.

    Directory of Open Access Journals (Sweden)

    Sowmya Subramanian

    Full Text Available Loop mediated isothermal amplification (LAMP is a highly efficient, selective and rapid DNA amplification technique for genetic screening of pathogens. However, despite its popularity, there is yet no mathematical model to quantify the outcome and no well-defined metric for comparing results that are available. LAMP is intrinsically complex and involves multiple pathways for gene replication, making fundamental modelling nearly intractable. To circumvent this difficulty, an alternate, empirical model is introduced that will allow one to extract a set of parameters from the concentration versus time curves. A simple recipe to deduce the time to positive, Tp--a parameter analogous to the threshold cycling time in polymerase chain reaction (PCR, is also provided. These parameters can be regarded as objective and unambiguous indicators of LAMP amplification. The model is exemplified on Escherichia coli strains by using the two gene fragments responsible for vero-toxin (VT production and tested against VT-producing (O157 and O45 and non-VT producing (DH5 alpha strains. Selective amplification of appropriate target sequences was made using well established LAMP primers and protocols, and the concentrations of the amplicons were measured using a Qubit 2.0 fluorometer at specific intervals of time. The data is fitted to a generalized logistic function. Apart from providing precise screening indicators, representing the data with a small set of numbers offers significant advantages. It facilitates comparisons of LAMP reactions independently of the sampling technique. It also eliminates subjectivity in interpretation, simplifies data analysis, and allows easy data archival, retrieval and statistical analysis for large sample populations. To our knowledge this work represents a first attempt to quantitatively model LAMP and offer a standard method that could pave the way towards high throughput automated screening.

  10. Are there CP-violating processes in the standard model without loop corrections

    International Nuclear Information System (INIS)

    Nowakowski, M.; Pilaftsis, A.

    1989-01-01

    In an effort to find new CP-violating phenomena in the Standard Model, the authors present a new type of CP asymmetries which have interesting theoretical features. They investigate the possibility of CP nonconservation manifesting itself at Born level. They find that such processes indeed exist provided the reaction under consideration includes two W's coupled to two different flavors and an additional boson (γ, g, Z O , H O ). A second interesting aspect of these phenomena is the property that the CP-violation appears in a scattering process as opposed to that in a decay of a particle. The authors estimate the values of these CP asymmetries within the Standard Model with three and four generations and show that the effect is, in principle, measurable if the masses of the quarks belonging to the fourth generation are large

  11. Linear Model-Based Predictive Control of the LHC 1.8 K Cryogenic Loop

    CERN Document Server

    Blanco-Viñuela, E; De Prada-Moraga, C

    1999-01-01

    The LHC accelerator will employ 1800 superconducting magnets (for guidance and focusing of the particle beams) in a pressurized superfluid helium bath at 1.9 K. This temperature is a severely constrained control parameter in order to avoid the transition from the superconducting to the normal state. Cryogenic processes are difficult to regulate due to their highly non-linear physical parameters (heat capacity, thermal conductance, etc.) and undesirable peculiarities like non self-regulating process, inverse response and variable dead time. To reduce the requirements on either temperature sensor or cryogenic system performance, various control strategies have been investigated on a reduced-scale LHC prototype built at CERN (String Test). Model Based Predictive Control (MBPC) is a regulation algorithm based on the explicit use of a process model to forecast the plant output over a certain prediction horizon. This predicted controlled variable is used in an on-line optimization procedure that minimizes an approp...

  12. Development of a vivo rabbit ligated intestinal Loop Model for HCMV infection

    OpenAIRE

    Tang, Jin; Wu, Qiaoxing; Tang, Xinming; Shi, Ruihan; Suo, Jingxia; Huang, Guangping; An, Junqing; Wang, Jingyuan; Yang, Jinling; Hao, Wenzhuo; She, Ruiping; Suo, Xun

    2016-01-01

    Background Human Cytomegalovirus (HCMV) infections can be found throughout the body, especially in epithelial tissue. Animal model was established by inoculation of HCMV (strain AD-169) or coinoculation with Hepatitis E virus (HEV) into the ligated sacculus rotundus and vermiform appendix in living rabbits. The specimens were collected from animals sacrificed 1 and a half hours after infection. Results The virus was found to be capable of reproducing in these specimens through RT-PCR and West...

  13. Model-based rational feedback controller design for closed-loop deep brain stimulation of Parkinson's disease

    Science.gov (United States)

    Gorzelic, P.; Schiff, S. J.; Sinha, A.

    2013-04-01

    Objective. To explore the use of classical feedback control methods to achieve an improved deep brain stimulation (DBS) algorithm for application to Parkinson's disease (PD). Approach. A computational model of PD dynamics was employed to develop model-based rational feedback controller design. The restoration of thalamocortical relay capabilities to patients suffering from PD is formulated as a feedback control problem with the DBS waveform serving as the control input. Two high-level control strategies are tested: one that is driven by an online estimate of thalamic reliability, and another that acts to eliminate substantial decreases in the inhibition from the globus pallidus interna (GPi) to the thalamus. Control laws inspired by traditional proportional-integral-derivative (PID) methodology are prescribed for each strategy and simulated on this computational model of the basal ganglia network. Main Results. For control based upon thalamic reliability, a strategy of frequency proportional control with proportional bias delivered the optimal control achieved for a given energy expenditure. In comparison, control based upon synaptic inhibitory output from the GPi performed very well in comparison with those of reliability-based control, with considerable further reduction in energy expenditure relative to that of open-loop DBS. The best controller performance was amplitude proportional with derivative control and integral bias, which is full PID control. We demonstrated how optimizing the three components of PID control is feasible in this setting, although the complexity of these optimization functions argues for adaptive methods in implementation. Significance. Our findings point to the potential value of model-based rational design of feedback controllers for Parkinson's disease.

  14. Fluctuations and the Phase Transition in a Chiral Model with Polyakov Loops%引入Polyakov环路的手征模型中的涨落与相变

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    We explore the NJL model with Polyakov loops for a system of three colors and two flavors within the mean-field approximation, where both chiral symmetry and confinement are taken into account. We focus on the phase structure of the model and study the chiral and Polyakov loop susceptibilities.

  15. Decision tree based knowledge acquisition and failure diagnosis using a PWR loop vibration model

    International Nuclear Information System (INIS)

    Bauernfeind, V.; Ding, Y.

    1993-01-01

    An analytical vibration model of the primary system of a 1300 MW PWR was used for simulating mechanical faults. Deviations in the calculated power density spectra and coherence functions are determined and classified. The decision tree technique is then used for a personal computer supported knowledge presentation and for optimizing the logical relationships between the simulated faults and the observed symptoms. The optimized decision tree forms the knowledge base and can be used to diagnose known cases as well as to include new data into the knowledge base if new faults occur. (author)

  16. Simulation Loop between CAD systems, Geant4 and GeoModel: Implementation and Results

    CERN Document Server

    Sharmazanashvili, Alexander; The ATLAS collaboration

    2015-01-01

    Data_vs_MonteCarlo discrepancy is one of the most important field of investigation for ATLAS simulation studies. There are several reasons of above mentioned discrepancies but primary interest is falling on geometry studies and investigation of how geometry descriptions of detector in simulation adequately representing “as-built” descriptions. Shapes consistency and detalization is not important while adequateness of volumes and weights of detector components are essential for tracking. There are 2 main reasons of faults of geometry descriptions in simulation: 1/ Inconsistency to “as-built” geometry descriptions; 2/Internal inaccuracies of transactions added by simulation packages itself. Georgian Engineering team developed hub on the base of CATIA platform and several tools enabling to read in CATIA different descriptions used by simulation packages, like XML/Persint->CATIA; IV/VP1->CATIA; GeoModel->CATIA; Geant4->CATIA. As a result it becomes possible to compare different descriptions with each othe...

  17. Designing Closed-Loop Brain-Machine Interfaces Using Model Predictive Control

    Directory of Open Access Journals (Sweden)

    Gautam Kumar

    2016-06-01

    Full Text Available Brain-machine interfaces (BMIs are broadly defined as systems that establish direct communications between living brain tissue and external devices, such as artificial arms. By sensing and interpreting neuronal activities to actuate an external device, BMI-based neuroprostheses hold great promise in rehabilitating motor disabled subjects, such as amputees. In this paper, we develop a control-theoretic analysis of a BMI-based neuroprosthetic system for voluntary single joint reaching task in the absence of visual feedback. Using synthetic data obtained through the simulation of an experimentally validated psycho-physiological cortical circuit model, both the Wiener filter and the Kalman filter based linear decoders are developed. We analyze the performance of both decoders in the presence and in the absence of natural proprioceptive feedback information. By performing simulations, we show that the performance of both decoders degrades significantly in the absence of the natural proprioception. To recover the performance of these decoders, we propose two problems, namely tracking the desired position trajectory and tracking the firing rate trajectory of neurons which encode the proprioception, in the model predictive control framework to design optimal artificial sensory feedback. Our results indicate that while the position trajectory based design can only recover the position and velocity trajectories, the firing rate trajectory based design can recover the performance of the motor task along with the recovery of firing rates in other cortical regions. Finally, we extend our design by incorporating a network of spiking neurons and designing artificial sensory feedback in the form of a charged balanced biphasic stimulating current.

  18. PEMBELAJARAN MATEMATIKA MODEL DOUBLE LOOP PROBLEM SOLVING DENGAN PENDEKATAN PMRI BERMUATAN KARAKTER UNTUK MENINGKATKAN KEMAMPUAN PEMECAHAN MASALAH

    Directory of Open Access Journals (Sweden)

    Indrati Rahayu

    2014-06-01

    /construction, (4 test, evaluation and revision, and (5 implementation. The result of the study shows: (1 The learning instruments that is developed is valid, (2 the result of  experimental instrument  shows : (a the individual problem solving abilities exceed the KKM value = 70  and 93,75 % of the students can achieve above the standard  of  80%. The conclusions of  this study is the  model of  Double Loop Problem Solving Learning with PMRI to enhance the Problem Solving Abilities is a Learning Model that is valid, practical and effective.

  19. Internal model control for industrial wireless plant using WirelessHART hardware-in-the-loop simulator.

    Science.gov (United States)

    Tran, Chung Duc; Ibrahim, Rosdiazli; Asirvadam, Vijanth Sagayan; Saad, Nordin; Sabo Miya, Hassan

    2018-04-01

    The emergence of wireless technologies such as WirelessHART and ISA100 Wireless for deployment at industrial process plants has urged the need for research and development in wireless control. This is in view of the fact that the recent application is mainly in monitoring domain due to lack of confidence in control aspect. WirelessHART has an edge over its counterpart as it is based on the successful Wired HART protocol with over 30 million devices as of 2009. Recent works on control have primarily focused on maintaining the traditional PID control structure which is proven not adequate for the wireless environment. In contrast, Internal Model Control (IMC), a promising technique for delay compensation, disturbance rejection and setpoint tracking has not been investigated in the context of WirelessHART. Therefore, this paper discusses the control design using IMC approach with a focus on wireless processes. The simulation and experimental results using real-time WirelessHART hardware-in-the-loop simulator (WH-HILS) indicate that the proposed approach is more robust to delay variation of the network than the PID. Copyright © 2017. Published by Elsevier Ltd.

  20. Rotary Bed Reactor for Chemical-Looping Combustion with Carbon Capture. Part 1: Reactor Design and Model Development

    KAUST Repository

    Zhao, Zhenlong

    2013-01-17

    Chemical-looping combustion (CLC) is a novel and promising technology for power generation with inherent CO2 capture. Currently, almost all of the research has been focused on developing CLC-based interconnected fluidized-bed reactors. In this two-part series, a new rotary reactor concept for gas-fueled CLC is proposed and analyzed. In part 1, the detailed configuration of the rotary reactor is described. In the reactor, a solid wheel rotates between the fuel and air streams at the reactor inlet and exit. Two purging sectors are used to avoid the mixing between the fuel stream and the air stream. The rotary wheel consists of a large number of channels with copper oxide coated on the inner surface of the channels. The support material is boron nitride, which has high specific heat and thermal conductivity. Gas flows through the reactor at elevated pressure, and it is heated to a high temperature by fuel combustion. Typical design parameters for a thermal capacity of 1 MW have been proposed, and a simplified model is developed to predict the performances of the reactor. The potential drawbacks of the rotary reactor are also discussed. © 2012 American Chemical Society.

  1. Modeling the interaction of a heavily beam loaded SRF cavity with its low-level RF feedback loops

    Science.gov (United States)

    Liu, Zong-Kai; Wang, Chaoen; Chang, Lung-Hai; Yeh, Meng-Shu; Chang, Fu-Yu; Chang, Mei-Hsia; Chang, Shian-Wen; Chen, Ling-Jhen; Chung, Fu-Tsai; Lin, Ming-Chyuan; Lo, Chih-Hung; Yu, Tsung-Chi

    2018-06-01

    A superconducting radio frequency (SRF) cavity provides superior stability to power high intensity light sources and can suppress coupled-bunch instabilities due to its smaller impedance for higher order modes. Because of these features, SRF cavities are commonly used for modern light sources, such as the TLS, CLS, DLS, SSRF, PLS-II, TPS, and NSLS-II, with an aggressive approach to operate the light sources at high beam currents. However, operating a SRF cavity at high beam currents may result with unacceptable stability problems of the low level RF (LLRF) system, due to drifts of the cavity resonant frequency caused by unexpected perturbations from the environment. As the feedback loop gets out of control, the cavity voltage may start to oscillate with a current-dependent characteristic frequency. Such situations can cause beam abort due to the activation of the interlock protection system, i.e. false alarm of quench detection. This malfunction of the light source reduces the reliability of SRF operation. Understanding this unstable mechanism to prevent its appearance becomes a primary task in the pursuit of highly reliable SRF operation. In this paper, a Pedersen model, including the response of the LLRF system, was used to simulate the beam-cavity interaction of a SRF cavity under heavy beam loading. Causes for the onset of instability at high beam current will be discussed as well as remedies to assure the design of a stable LLRF system.

  2. Homology-based Modeling of Rhodopsin-like Family Members in the Inactive State: Structural Analysis and Deduction of Tips for Modeling and Optimization.

    Science.gov (United States)

    Pappalardo, Matteo; Rayan, Mahmoud; Abu-Lafi, Saleh; Leonardi, Martha E; Milardi, Danilo; Guccione, Salvatore; Rayan, Anwar

    2017-08-01

    Modeling G-Protein Coupled Receptors (GPCRs) is an emergent field of research, since utility of high-quality models in receptor structure-based strategies might facilitate the discovery of interesting drug candidates. The findings from a quantitative analysis of eighteen resolved structures of rhodopsin family "A" receptors crystallized with antagonists and 153 pairs of structures are described. A strategy termed endeca-amino acids fragmentation was used to analyze the structures models aiming to detect the relationship between sequence identity and Root Mean Square Deviation (RMSD) at each trans-membrane-domain. Moreover, we have applied the leave-one-out strategy to study the shiftiness likelihood of the helices. The type of correlation between sequence identity and RMSD was studied using the aforementioned set receptors as representatives of membrane proteins and 98 serine proteases with 4753 pairs of structures as representatives of globular proteins. Data analysis using fragmentation strategy revealed that there is some extent of correlation between sequence identity and global RMSD of 11AA width windows. However, spatial conservation is not always close to the endoplasmic side as was reported before. A comparative study with globular proteins shows that GPCRs have higher standard deviation and higher slope in the graph with correlation between sequence identity and RMSD. The extracted information disclosed in this paper could be incorporated in the modeling protocols while using technique for model optimization and refinement. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Matrix factorizations and homological mirror symmetry on the torus

    International Nuclear Information System (INIS)

    Knapp, Johanna; Omer, Harun

    2007-01-01

    We consider matrix factorizations and homological mirror symmetry on the torus T 2 using a Landau-Ginzburg description. We identify the basic matrix factorizations of the Landau-Ginzburg superpotential and compute the full spectrum taking into account the explicit dependence on bulk and boundary moduli. We verify homological mirror symmetry by comparing three-point functions in the A-model and the B-model

  4. One loop electro-weak radiative corrections in the standard model

    International Nuclear Information System (INIS)

    Kalyniak, P.; Sundaresan, M.K.

    1987-01-01

    This paper reports on the effect of radiative corrections in the standard model. A sensitive test of the three gauge boson vertices is expected to come from the work in LEPII in which the reaction e + e - → W + W - can occur. Two calculations of radiative corrections to the reaction e + e - → W + W - exist at present. The results of the calculations although very similar disagree with one another as to the actual magnitude of the correction. Some of the reasons for the disagreement are understood. However, due to the reasons mentioned below, another look must be taken at these lengthy calculations to resolve the differences between the two previous calculations. This is what is being done in the present work. There are a number of reasons why we must take another look at the calculation of the radiative corrections. The previous calculations were carried out before the UA1, UA2 data on W and Z bosons were obtained. Experimental groups require a computer program which can readily calculate the radiative corrections ab initio for various experimental conditions. The normalization of sin 2 θ w in the previous calculations was done in a way which is not convenient for use in the experimental work. It would be desirable to have the analytical expressions for the corrections available so that the renormalization scheme dependence of the corrections could be studied

  5. Schwinger-Dyson loop equations as the w1+∞-like constraints for hermitian multi-matrix chain model at finite N

    International Nuclear Information System (INIS)

    Cheng, Yi-Xin

    1992-01-01

    The Schwinger-Dyson loop equations for the hermitian multi-matrix chain models at finite N, are derived from the Ward identities of the partition functional under the infinitesimal field transformations. The constraint operators W n (m) satisfy the w 1+∞ -like algebra up to a linear combination of the lower spin operators. We find that the all the higher spin constraints are reducible to the Virasoro-type constraints for all the matrix chain models. (author)

  6. Altered 13C glucose metabolism in the cortico-striato-thalamo-cortical loop in the MK-801 rat model of schizophrenia

    DEFF Research Database (Denmark)

    Eyjolfsson, Elvar M; Nilsen, Linn Hege; Kondziella, Daniel

    2011-01-01

    Using a modified MK-801 (dizocilpine) N-methyl-D-aspartic acid (NMDA) receptor hypofunction model for schizophrenia, we analyzed glycolysis, as well as glutamatergic, GABAergic, and monoaminergic neurotransmitter synthesis and degradation. Rats received an injection of MK-801 daily for 6 days...... in all regions. In conclusion, neurotransmitter metabolism in the cortico-striato-thalamo-cortical loop is severely impaired in the MK-801 (dizocilpine) NMDA receptor hypofunction animal model for schizophrenia....

  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. A PHF8 homolog in C. elegans promotes DNA repair via homologous recombination.

    Directory of Open Access Journals (Sweden)

    Changrim Lee

    Full Text Available PHF8 is a JmjC domain-containing histone demethylase, defects in which are associated with X-linked mental retardation. In this study, we examined the roles of two PHF8 homologs, JMJD-1.1 and JMJD-1.2, in the model organism C. elegans in response to DNA damage. A deletion mutation in either of the genes led to hypersensitivity to interstrand DNA crosslinks (ICLs, while only mutation of jmjd-1.1 resulted in hypersensitivity to double-strand DNA breaks (DSBs. In response to ICLs, JMJD-1.1 did not affect the focus formation of FCD-2, a homolog of FANCD2, a key protein in the Fanconi anemia pathway. However, the dynamic behavior of RPA-1 and RAD-51 was affected by the mutation: the accumulations of both proteins at ICLs appeared normal, but their subsequent disappearance was retarded, suggesting that later steps of homologous recombination were defective. Similar changes in the dynamic behavior of RPA-1 and RAD-51 were seen in response to DSBs, supporting a role of JMJD-1.1 in homologous recombination. Such a role was also supported by our finding that the hypersensitivity of jmjd-1.1 worms to ICLs was rescued by knockdown of lig-4, a homolog of Ligase 4 active in nonhomologous end-joining. The hypersensitivity of jmjd-1.1 worms to ICLs was increased by rad-54 knockdown, suggesting that JMJD-1.1 acts in parallel with RAD-54 in modulating chromatin structure. Indeed, the level of histone H3 Lys9 tri-methylation, a marker of heterochromatin, was higher in jmjd-1.1 cells than in wild-type cells. We conclude that the histone demethylase JMJD-1.1 influences homologous recombination either by relaxing heterochromatin structure or by indirectly regulating the expression of multiple genes affecting DNA repair.

  9. Alternative loop rings

    CERN Document Server

    Goodaire, EG; Polcino Milies, C

    1996-01-01

    For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

  10. Analysis of the production of Higgs boson pairs at the one-loop level in the minimal supersymmetric standard model

    International Nuclear Information System (INIS)

    Philippov, Yu. P.

    2009-01-01

    Within the minimal supersymmetric standard model, the amplitudes and total cross sections for the processes e + e - → hh, e + e - → hH, e + e - → HH, and e + e - → AA are calculated in the first order of perturbation theory with allowance for a complete set of one-loop diagrams in the m e → 0 approximation. Analytic expressions are obtained for the quantities under consideration; numerical results are presented in a graphical form. It is shown that the cross section for the process e + e - → hh is larger than those for the other processes (and is on the same order of magnitude as the cross section for the corresponding processes in the Standard Model). In the case of the collision energy equal to √s = 500 GeV, an integrated luminosity in the region ∫ L ≥ 500 fb -1 , and a longitudinal polarization of the e + e- beams used, 520, 320, and 300 production events are possible in the processes e + e - → hh (at M h = 115 GeV), e + e - → HH, and e + e - → AA (at M H,A = 120 GeV), respectively. Even at M H,A ∼ 500 GeV and √s = 1.5 TeV, not less than 200 events for each of the processes can be accumulated. The cross section for the process e + e - → hH is small (about 10 -2 fb), which complicates the detection of the sought signal significantly.

  11. BMN correlators by loop equations

    International Nuclear Information System (INIS)

    Eynard, Bertrand; Kristjansen, Charlotte

    2002-01-01

    In the BMN approach to N=4 SYM a large class of correlators of interest are expressible in terms of expectation values of traces of words in a zero-dimensional gaussian complex matrix model. We develop a loop-equation based, analytic strategy for evaluating such expectation values to any order in the genus expansion. We reproduce the expectation values which were needed for the calculation of the one-loop, genus one correction to the anomalous dimension of BMN-operators and which were earlier obtained by combinatorial means. Furthermore, we present the expectation values needed for the calculation of the one-loop, genus two correction. (author)

  12. Persistent homology of complex networks

    International Nuclear Information System (INIS)

    Horak, Danijela; Maletić, Slobodan; Rajković, Milan

    2009-01-01

    Long-lived topological features are distinguished from short-lived ones (considered as topological noise) in simplicial complexes constructed from complex networks. A new topological invariant, persistent homology, is determined and presented as a parameterized version of a Betti number. Complex networks with distinct degree distributions exhibit distinct persistent topological features. Persistent topological attributes, shown to be related to the robust quality of networks, also reflect the deficiency in certain connectivity properties of networks. Random networks, networks with exponential connectivity distribution and scale-free networks were considered for homological persistency analysis

  13. Internal and External reconnection in a Series of Homologous Solar Flares

    Science.gov (United States)

    Sterling, Alphonse C.; Moore, Ronald L.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Using data from the Extreme Ultraviolet Telescope (EIT) on SOHO and the Soft X-ray Telescope (SXT) on Yohkoh, we examine a series of morphologically homologous solar flares occurring in NOAA AR 8210 over May 1-2, 1998. An emerging flux region (EFR) impacted against a sunspot to the west and next to a coronal hole to the east is the source of the repeated flaring. An SXT sigmoid parallels the EFR's neutral line at the site of the initial flaring in soft X-rays. In EIT, each flaring episode begins with the formation of a crinkle pattern external to the EFR. These EIT crinkles move out from, and then in toward, the EFR with velocities approximately 20 km/s. A shrinking and expansion of the width of the coronal hole coincides with the crinkle activity, and generation and evolution of a postflare loop system begins near the. time of crinkle formation. Using a schematic based on magnetograms of the region, we suggest that these observations are consistent with the standard reconnection-based model for solar eruptions, but modified by the presence of the additional magnetic fields of the sunspot and coronal hole. In the schematic, internal reconnection begins inside of the EFR-associated fields, unleashing a flare, postflare loops, and a CME. External reconnection, first occurring between the escaping CME and the coronal hole field, and second occurring between fields formed as a result of the first external reconnection, results in the EIT crinkles and changes in the coronal hole boundary. By the end of the second external reconnection, the initial setup is reinstated; thus the sequence can repeat, resulting in morphologically homologous eruptions. Our inferred magnetic topology is similar to that suggested in the "breakout model" of eruptions [Antiochos, 1998], although we cannot determine if our eruptions are released primarily by the breakout mechanism (external reconnection) or, alternatively, are released primarily by the internal reconnection.

  14. Analysis of telomerase target gene expression effects from murine models in patient cohorts by homology translation and random survival forest modeling

    Directory of Open Access Journals (Sweden)

    Frederik Otzen Bagger

    2016-03-01

    Full Text Available Acute myeloid leukemia (AML is an aggressive and rapidly fatal blood cancer that affects patients of any age group. Despite an initial response to standard chemotherapy, most patients relapse and this relapse is mediated by leukemia stem cell (LSC populations. We identified a functional requirement for telomerase in sustaining LSC populations in murine models of AML and validated this requirement using an inhibitor of telomerase in human AML. Here, we describe in detail the contents, quality control and methods of the gene expression analysis used in the published study (Gene Expression Omnibus GSE63242. Additionally, we provide annotated gene lists of telomerase regulated genes in AML and R code snippets to access and analyze the data used in the original manuscript. Keywords: AML, Leukemia, Stem cells, Telomere, Telomerase

  15. A prototype framework for models of socio-hydrology: identification of key feedback loops and parameterisation approach

    Science.gov (United States)

    Elshafei, Y.; Sivapalan, M.; Tonts, M.; Hipsey, M. R.

    2014-06-01

    It is increasingly acknowledged that, in order to sustainably manage global freshwater resources, it is critical that we better understand the nature of human-hydrology interactions at the broader catchment system scale. Yet to date, a generic conceptual framework for building models of catchment systems that include adequate representation of socioeconomic systems - and the dynamic feedbacks between human and natural systems - has remained elusive. In an attempt to work towards such a model, this paper outlines a generic framework for models of socio-hydrology applicable to agricultural catchments, made up of six key components that combine to form the coupled system dynamics: namely, catchment hydrology, population, economics, environment, socioeconomic sensitivity and collective response. The conceptual framework posits two novel constructs: (i) a composite socioeconomic driving variable, termed the Community Sensitivity state variable, which seeks to capture the perceived level of threat to a community's quality of life, and acts as a key link tying together one of the fundamental feedback loops of the coupled system, and (ii) a Behavioural Response variable as the observable feedback mechanism, which reflects land and water management decisions relevant to the hydrological context. The framework makes a further contribution through the introduction of three macro-scale parameters that enable it to normalise for differences in climate, socioeconomic and political gradients across study sites. In this way, the framework provides for both macro-scale contextual parameters, which allow for comparative studies to be undertaken, and catchment-specific conditions, by way of tailored "closure relationships", in order to ensure that site-specific and application-specific contexts of socio-hydrologic problems can be accommodated. To demonstrate how such a framework would be applied, two socio-hydrological case studies, taken from the Australian experience, are presented

  16. A three-dimensional mathematical model to predict air-cooling flow and temperature distribution of wire loops in the Stelmor air-cooling system

    International Nuclear Information System (INIS)

    Hong, Lingxiang; Wang, Bo; Feng, Shuai; Yang, Zhiliang; Yu, Yaowei; Peng, Wangjun; Zhang, Jieyu

    2017-01-01

    Highlights: • A 3-dimentioanl mathematical models for complex wire loops was set up in Stelmor. • The air flow field in the cooling process was simulated. • The convective heat transfer coefficient was simulated coupled with air flow field. • The temperature distribution with distances was predicted. - Abstract: Controlling the forced air cooling conditions in the Stelmor conveyor line is important for improving the microstructure and mechanical properties of steel wire rods. A three-dimensional mathematical model incorporating the turbulent flow of the cooling air and heat transfer of the wire rods was developed to predict the cooling process in the Stelmor air-cooling line of wire rolling mills. The distribution of cooling air from the plenum chamber and the forced convective heat transfer coefficient for the wire loops were simulated at the different locations over the conveyor. The temperature profiles and cooling curves of the wire loops in Stelmor conveyor lines were also calculated by considering the convective heat transfer, radiative heat transfer as well as the latent heat during transformation. The calculated temperature results using this model agreed well with the available measured results in the industrial tests. Thus, it was demonstrated that this model can be useful for studying the air-cooling process and predicting the temperature profile and microstructure evolution of the wire rods.

  17. Non-homologous end joining mediated DNA repair is impaired in the NUP98-HOXD13 mouse model for myelodysplastic syndrome.

    Science.gov (United States)

    Puthiyaveetil, Abdul Gafoor; Reilly, Christopher M; Pardee, Timothy S; Caudell, David L

    2013-01-01

    Chromosomal translocations typically impair cell differentiation and often require secondary mutations for malignant transformation. However, the role of a primary translocation in the development of collaborating mutations is debatable. To delineate the role of leukemic translocation NUP98-HOXD13 (NHD13) in secondary mutagenesis, DNA break and repair mechanisms in stimulated mouse B lymphocytes expressing NHD13 were analyzed. Our results showed significantly reduced expression of non-homologous end joining (NHEJ)-mediated DNA repair genes, DNA Pkcs, DNA ligase4, and Xrcc4 leading to cell cycle arrest at G2/M phase. Our results showed that expression of NHD13 fusion gene resulted in impaired NHEJ-mediated DNA break repair. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. RTEL1 maintains genomic stability by suppressing homologous recombination.

    Science.gov (United States)

    Barber, Louise J; Youds, Jillian L; Ward, Jordan D; McIlwraith, Michael J; O'Neil, Nigel J; Petalcorin, Mark I R; Martin, Julie S; Collis, Spencer J; Cantor, Sharon B; Auclair, Melissa; Tissenbaum, Heidi; West, Stephen C; Rose, Ann M; Boulton, Simon J

    2008-10-17

    Homologous recombination (HR) is an important conserved process for DNA repair and ensures maintenance of genome integrity. Inappropriate HR causes gross chromosomal rearrangements and tumorigenesis in mammals. In yeast, the Srs2 helicase eliminates inappropriate recombination events, but the functional equivalent of Srs2 in higher eukaryotes has been elusive. Here, we identify C. elegans RTEL-1 as a functional analog of Srs2 and describe its vertebrate